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  • Evolution  (386)
  • Springer  (386)
  • American Meteorological Society
  • 1995-1999  (207)
  • 1990-1994  (178)
  • 1965-1969  (1)
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  • 1
    Electronic Resource
    Electronic Resource
    Pollen mitosis in the slipper orchid Cypripedium fasciculatum (1994)
    Springer
    Sexual plant reproduction 7 (1994), S. 87-94 
    Details
    ISSN: 1432-2145
    Keywords: Evolution ; Microtubules ; Polarity Pollen ; Mitosis ; Orchids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Pollen mitosis in the slipper orchid Cypripedium fasciculatum was studied using correlated methods of immunofluorescence and transmission electron microscopy. Unlike the more highly evolved orchids, the cypripedioid orchids shed pollen as monosulcate monads. Prior to pollen mitosis, the microspore nucleus migrates to a proximal position opposite the aperture, as is typical of monocotyledons. There is no distinct generative pole microtubule system (GPMS) like that recently reported in development of pollen polarity in the vandoid moth orchid Phalaenopsis. Instead, microtubules in early prophase are concentrated around the nucleus and extend into the cytoplasm toward the future generative pole. Once the nucleus has migrated to the continuous surface opposite the aperture, microtubules surround the nucleus evenly and show no tendency to be more concentrated in the generative domain. The mitotic spindle, which develops from the perinuclear microtubules, is asymmetrically placed in the microspore and is cone-shaped. The generative pole is broad and closely appressed to the continuous spore surface, while the vegetative pole is pointed and located in the interior of the microspore. As the chromosomes move poleward, microtubules proliferate in the interzone and a phragmoplast develops. The phragmoplast expands in a hemispherical path beyond the interzone following an array of microtubules that radiates from the generative nucleus. Data from this study indicate that evolution of pollen in orchids includes a shift in location of the generative cell from proximal to distal and the evolution of a GPMS, in addition in the well-known trend toward increased pollen aggregation and loss of exine.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00230576
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  • 2
    Electronic Resource
    Electronic Resource
    The evolution of self-incompatibility: a molecular voyeur's perspective (1996)
    Springer
    Sexual plant reproduction 9 (1996), S. 357-361 
    Details
    ISSN: 1432-2145
    Keywords: Self-incompatibility ; Evolution ; S-RNases ; Solanaceae ; Rosaceae ; Scrophulariaceae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This review summarises current understanding of the evolution of self-incompatibility inferred from DNA sequence analysis. Self-incompatibility in many plant families is controlled by a single, highly polymorphicS-locus which, in the Solanaceae, encodes an allelic series of stylar ribonucleases known as the S-RNases. PCR approaches are a convenient way to examine the diversity of S-RNase sequences within and between wild populations of a self-incompatible species and provide a unique view into the species' current and historic population structure. Similar molecular appoaches have also been used to show that S-RNases are involved in self-incompatibility in families other than the Solanaceae. A model for the evolution of ribonuclease-based self-incompatibility systems is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02441956
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  • 3
    Electronic Resource
    Electronic Resource
    Technological change and institutional inertia: a game-theoretic approach (1993)
    Springer
    Journal of evolutionary economics 3 (1993), S. 199-224 
    Details
    ISSN: 1432-1386
    Keywords: Technological change ; Institutions ; Evolution ; Games ; C71 ; 017 ; 031
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract In this paper, we study a co-evolutionary model of economic change at two hierarchical levels. At the lower level, “institutions” are given and the focus is on how resources are allocated and innovation produced in response to the pay-off structure induced by prevailing institutions. At the higher level, it is the institutions themselves that change as the outcome of a process of social bargaining. The main objective of the paper is to study the interaction between these two levels of change, attempting to provide some insight on issues like technological/institutional divergence, technological dead-end, institutional inertia, etc.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01200868
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  • 4
    Electronic Resource
    Electronic Resource
    Nonlinear stochastic effects of substitution — an evolutionary approach (1996)
    Springer
    Journal of evolutionary economics 6 (1996), S. 1-30 
    Details
    ISSN: 1432-1386
    Keywords: Innovation ; Technology ; Master equation ; Survival probability ; Evolution ; O3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract Technological innovations have been investigated by means of substitution and diffusion as well as evolution models, each of them dealing with different aspects of the innovation problem. In this paper we follow the well known research traditions on self-organisation models of complex systems. For the first time in the literature we show the existence of a specific niche effect, which may occur in the first stage of establishment of a new technology. Using a stochastic Master equation approach, we obtain analytical expressions for the survival probabilities of a new technology in smaller or larger ensembles. As a main result we demonstrate how a hyperselection situation might be removed in a stochastic picture and thresholds against the prevailing of a new technology in a step-by-step process can be overcome.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01202370
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  • 5
    Electronic Resource
    Electronic Resource
    The economy as an evolving network (1997)
    Springer
    Journal of evolutionary economics 7 (1997), S. 339-353 
    Details
    ISSN: 1432-1386
    Keywords: Key words: Market organisation ; Network ; Communication ; Evolution ; Learning ; JEL-classification: C70; D23; D40; L11
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract. The purpose of this paper is to suggest a view of the economy as a network of links between the individuals involved. One approach is to consider the structure of links as fixed as is the case with spatial models in which agents are situated on a lattice, another is to regard all links as possible but stochastic. If the probability of any of the links existing is uniform we have the situation familiar from the “population games” of evolutionary game theory. The basic idea here is to allow the network to evolve and to make the probability of each of the links dependent on the experience of the agents involved. Such analysis can give rise to interesting behaviour on the aggregate level which is very different from that which might have been predicted by looking at the individuals in isolation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001910050047
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  • 6
    Electronic Resource
    Electronic Resource
    Detecting self-organisational change in economic processes exhibiting logistic growth (1999)
    Springer
    Journal of evolutionary economics 9 (1999), S. 109-133 
    Details
    ISSN: 1432-1386
    Keywords: Key words: Discontinuity ; Evolution ; Logistic diffusion ; Non-linearity ; Non-stationarity ; Self-organisation ; Spectral methods ; JEL-classification: C4; C5; N1; N2
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract. This paper offers an econometric methodology for the detection of self-organisational change (defined in terms of the presence of time irreversibility, structural change and fundamental uncertainty) in economic processes that follow logistic diffusion growth paths in historical time. The approach we adopted is built upon recent developments in `moving window' spectral methods which are applied to the scaled residuals generated by estimated logistic diffusion models. We illustrate the use of such methods by examining the case of a financial instrument, namely, the Australian Building Society Deposit, which experienced logistic growth in its market share until bank deregulation was enacted in the 1980s. We show that there is clear evidence that self-organisational change is present over the historical period considered.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001910050077
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  • 7
    Electronic Resource
    Electronic Resource
    A note on evolutionary stability of Bertrand equilibrium (1999)
    Springer
    Journal of evolutionary economics 9 (1999), S. 367-371 
    Details
    ISSN: 1432-1386
    Keywords: Key words: Bertrand ; Oligopoly ; Evolution ; Evolutionary stability ; JEL-classification: D43 ; L13 ; C72
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract. It is shown that the equilibrium notion of an evolutionary stable strategy (ESS) does have predictive power for standard models of Bertrand competition. This is in contrast to a recent claim by Qin and Stuart (1997). The claim is based on the observation that the solution concept ESS behaves discontinuously when finite (discrete) action games approach an infinite (continuous) action game in the limit. Furthermore, it is argued that from a model-theoretic point of view evolutionary stability in prices (i.e. in the Bertrand model) is quite different from evolutionary stability in quantities (i.e. in the Cournot model).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001910050087
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  • 8
    Electronic Resource
    Electronic Resource
    Comparison of morphology and physiology of two plurisegmental sound-activated interneurones in a bushcricket (1999)
    Springer
    Journal of comparative physiology 185 (1999), S. 199-205 
    Details
    ISSN: 1432-1351
    Keywords: Key words Hearing ; Orthoptera ; Phaneropteridae ; Cercal system ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The unusual morphology of a sound-activated plurisegmental ascending interneurone (AN5-AG7) in an insect (Ancistrura nigrovittata, Ensifera, Phaneropteridae) is described. This neurone's soma is located in the penultimate abdominal ganglion. The most prominent arborisations with smooth endings are found in the prothoracic ganglion. The neurone terminates with numerous beaded endings in the brain (protocerebrum). All abdominal ganglia including the penultimate contain only tiny side branches of beaded appearance. The neurone's morphology is compared to the morphology of a `typical' sound-activated plurisegmental neurone of bushcrickets with its soma in the prothorax. In the prothoracic ganglion and in the brain the arborisations of the two cells are very similar. Graded potentials and action potentials are generated in the prothoracic portion of both neurones. Both receive excitation mainly by ultrasound, and inhibition by soma-ipsilateral stimuli. Neither wind, substrate vibration nor touch of the abdomen evoke responses in AN5-AG7. It is assumed that early in evolution this neurone had its dendrites in the ganglion which houses the cell body (like cercal interneurones of this neuromere). Profound evolutionary changes probably have taken place to bring about this neuron's modern morphology.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003590050378
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  • 9
    Electronic Resource
    Electronic Resource
    Higher selection processes in evolutionary economic change (1992)
    Springer
    Journal of evolutionary economics 2 (1992), S. 1-16 
    Details
    ISSN: 1432-1386
    Keywords: Evolution ; Innovation ; Selection ; Technology ; JEL classification numbers: 036, 112
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract Virtually all models of economic change are based on a Darwinian picture of a world where change is gradual, smooth, and where economic survival depends on being more efficient. This paper, drawing from current controversies in evolutionary biology, presents a broader interpretation of evolutionary change in which competitive selection is only one possible reason for economic survival. Economic change is presented as a hierarchical process. At one level, change takes place through the accumulation of small changes based on competitive selection at the margin, as described by standard economic theory. At higher levels, survival depends on processes over which the agent being selected has no control.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01196458
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  • 10
    Electronic Resource
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    Firm selection and industry evolution: the post-entry performance of new firms (1994)
    Springer
    Journal of evolutionary economics 4 (1994), S. 243-260 
    Details
    ISSN: 1432-1386
    Keywords: Innovation ; Evolution ; Survival and growth ; O ; O3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract A dynamic framework based on the process of firm selection and industry evolution is used to analyse the post-entry performance of new firms. In particular, it is hypothesized that, based on the stylized fact that virtually all new firms start at a very small scale of output, firm growth and survival are shaped by the need to attain an efficient level of output. The post-entry performance of more than 11,000 U.S. manufacturing firms established in 1976 is tracked throughout the subsequent tenyear period. Firm growth is found to be negatively influenced by firm size but positively related to the extent of scale economies, capital intensity, innovative activity, and market growth. By contrast, the likelihood of survival is identified as being positively influenced by firm size, market growth, and capital intensity, but negatively affected by the degree of scale economies in the industry. When viewed through the dynamic framework of firm selection and industry evolution, the empirical results shed considerable light on several paradoxes in the industrial organization literature, such as the continued persistence over time of an asymmetrical firm-size distribution consisting predominantely of suboptimal scale firms, and the failure of capital intensity and scale economies to substantially deter the entry and start-up of new firms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01236371
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  • 11
    Electronic Resource
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    Economic evolution and the science of synergetics (1996)
    Springer
    Journal of evolutionary economics 6 (1996), S. 239-260 
    Details
    ISSN: 1432-1386
    Keywords: Synergetics ; Self-organisation ; Time-irreversibility ; Evolution ; Structural change ; O30 ; O31 ; C60 ; C63
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract This paper deals with synergetic methods, which have developed as a sub-field of the self-organisation approach in the natural sciences. Such methods have been used successfully to model structural transitions in physio-chemical contexts. The synergetic approach is explained in a non-technical way and the main elements of the synergetic methodology are introduced. The extent to which such methods can be applied in the presence of historical time series data, which are subject to underlying processes of evolutionary economic change, is assessed. Proposals, concerning more appropriate synergetic methods for evolutionary economic application, are considered.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01193632
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  • 12
    Electronic Resource
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    A spectrum of equilibration processes in game theory (1998)
    Springer
    Journal of evolutionary economics 8 (1998), S. 67-87 
    Details
    ISSN: 1432-1386
    Keywords: Key words: Bounded rationality ; Cognitive rationality ; Game equilibrium ; Evolution ; Learning ; JEL-classification: B 41; C 73; D 83; D 84
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract. In game theory, four dynamic processes converging towards an equilibrium are distinguished and ordered by way of agents' decreasing cognitive capacities. In the eductive process, each player has enough information to simulate perfectly the others' behavior and gets immediately to the equilibrium. In epistemic learning, each player updates his beliefs about others' future strategies, with regard to their sequentially observed actions. In behavioral learning, each player modifies his own strategies according to the observed payoffs obtained from his past actions. In the evolutionary process, each agent has a fixed strategy and reproduces in proportion to the utilities obtained through stochastic interactions. All along the spectrum, longer term dynamics makes up for weaker rationality, and physical relations substitute for mental interactions. Convergence, if any, is towards an always stronger equilibrium notion and selection of an equilibrium state becomes more sensitive to context and history. The processes can be mixed if associated to different periods, agents or mechanisms and deepened if obtained by formal reasoning principles.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001910050056
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  • 13
    Electronic Resource
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    Evolutionary dynamics of predator–prey systems: an ecological perspective (1996)
    Springer
    Journal of mathematical biology 34 (1996), S. 556-578 
    Details
    ISSN: 1432-1416
    Keywords: Key words: Dynamical systems ; Evolution ; Game theory ; Asymptotic stability ; Population dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract.  Evolution takes place in an ecological setting that typically involves interactions with other organisms. To describe such evolution, a structure is needed which incorporates the simultaneous evolution of interacting species. Here a formal framework for this purpose is suggested, extending from the microscopic interactions between individuals – the immediate cause of natural selection, through the mesoscopic population dynamics responsible for driving the replacement of one mutant phenotype by another, to the macroscopic process of phenotypic evolution arising from many such substitutions. The process of coevolution that results from this is illustrated in the context of predator–prey systems. With no more than qualitative information about the evolutionary dynamics, some basic properties of predator–prey coevolution become evident. More detailed understanding requires specification of an evolutionary dynamic; two models for this purpose are outlined, one from our own research on a stochastic process of mutation and selection and the other from quantitative genetics. Much of the interest in coevolution has been to characterize the properties of fixed points at which there is no further phenotypic evolution. Stability analysis of the fixed points of evolutionary dynamical systems is reviewed and leads to conclusions about the asymptotic states of evolution rather different from those of game-theoretic methods. These differences become especially important when evolution involves more than one species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002850050021
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  • 14
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    Spatial discrimination of pheromones and behavioural antagonists by the tortricid moths Cydia pomonella and Adoxophyes orana (1999)
    Springer
    Journal of comparative physiology 185 (1999), S. 419-425 
    Details
    ISSN: 1432-1351
    Keywords: Key wordsCydia pomonella ; Adoxophyes orana ; Sex pheromone ; Interspecific interruption ; Evolution ; AbbreviationsZ9-14:Ac (Z9)-tetradecenylacetate Z11-14:Ac (Z11)-tetradecenylacetate ; E8, E10-12:OH (E8, E10)-dodecadienol
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Male moths responding to their species-specific sex pheromone, may cease their upwind flight when pheromone components of sympatric species are added to the mixture. The interspecific interaction between the pheromone response of the tortricid moths Cydia pomonella and Adoxophyes orana was investigated in field-trapping and wind-tunnel studies. Addition of the A. orana pheromone [(Z9)-tetradecenylacetate and (Z11)-tetradecenylacetate] to a source containing the C. pomonella pheromone [(E8, E10)-dodecadienol] resulted in a significant inhibition of attraction by male C. pomonella. It is demonstrated that this behavioural antagonist for C. pomonella must be emitted from the same point source to induce this inhibitory effect. A spatial separation of the two interspecific pheromones (at 14 cm, 5 cm and 0.5 cm crosswind) restored the attraction of the conspecific pheromone for male C. pomonella. In contrast to C. pomonella, male A. orana were not inhibited by point sources releasing both the C. pomonella and A. orana pheromone. We suggest that the discrepancy in the interspecific pheromone interaction between these two tortricids can be explained if we consider the evolutionary ecology of interspecific pheromone communication in C. pomonella and A. orana.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003590050402
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  • 15
    Electronic Resource
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    Olfactory receptors in aquatic and terrestrial vertebrates (1998)
    Springer
    Journal of comparative physiology 183 (1998), S. 635-650 
    Details
    ISSN: 1432-1351
    Keywords: Key words Olfactory receptors ; Multigene families ; Pseudogenes ; Vertebrate species ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract In species representing different levels of vertebrate evolution, olfactory receptor genes have been identified by molecular cloning techniques. Comparing the deduced amino-acid sequences revealed that the olfactory receptor gene family of Rana esculenta resembles that of Xenopus laevis, indicating that amphibians in general may comprise two classes of olfactory receptors. Whereas teleost fish, including the goldfish Carassius auratus, possess only class I receptors, the `living fossil' Latimeria chalumnae is endowed with both receptor classes; interestingly, most of the class II genes turned out to be pseudogenes. Exploring receptor genes in aquatic mammals led to the discovery of a large array of only class II receptor genes in the dolphin Stenella Coeruleoalba; however, all of these genes were found to be non-functional pseudogenes. These results support the notion that class I receptors may be specialized for detecting water-soluble odorants and class II receptors for recognizing volatile odorants. Comparing the structural features of both receptor classes from various species revealed that they differ mainly in their extracellular loop 3, which may contribute to ligand specificity. Comparing the number and diversity of olfactory receptor genes in different species provides insight into the origin and the evolution of this unique gene family.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003590050287
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  • 16
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    A nose that looks like a hand and acts like an eye: the unusual mechanosensory system of the star-nosed mole (1999)
    Springer
    Journal of comparative physiology 185 (1999), S. 367-372 
    Details
    ISSN: 1432-1351
    Keywords: Key words Cortical magnification ; Somatosensory cortex ; Development ; Evolution ; Behavior
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The star-nosed mole (Condylura cristata) has a snout surrounded by 22 fleshy and mobile appendages. This unusual structure is not an olfactory organ, as might be assumed from its location, nor is it used to manipulate objects as might be guessed from its appearance. Rather, the star is devoted to the sense of touch, and for this purpose the appendages are covered with thousands of small mechanoreceptive Eimer's organs. Recent behavioral studies find that the star acts much like a tactile eye, having a small behavioral focus, or “fovea” at the center – used for detailed explorations of objects of interest. The peripheral and central nervous systems of the mole reflect these behavioral specializations, such that the small behavioral focus on the nose is more densely innervated in the periphery, and has a greatly enlarged representation in the somatosensory cortex. This somatosensory representation of the tactile fovea is not correlated with anatomical parameters (innervation density) as found in other species, but rather is highly correlated with patterns of behavior. The many surprising parallels between the somatosensory system of the mole, and the visual systems of other mammals, suggest a convergent and perhaps common organization for highly developed sensory systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003590050396
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  • 17
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    Neural control of the pyloric region in the foregut of the shrimp Penaeus (Decapoda: Penaeidae) (1997)
    Springer
    Journal of comparative physiology 181 (1997), S. 367-382 
    Details
    ISSN: 1432-1351
    Keywords: Key words Stomatogastric ganglion ; Penaeus ; Pyloric circuit ; Neurotransmitter ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Pyloric pattern-generating neurons that control the pyloric region of the foregut were identified in the stomatogastric ganglion of the most primitive decapod genus Penaeus. Five types of motor neurons and one interneuron are involved in generation of pyloric motor pattern. One cell type of motor neurons innervates muscles of both the gastric mill and the pylorus like the gastric motor neurons in Cancer, but unlike those in Panulirus. These identified neurons are connected to each other either by electrical or inhibitory chemical synapses to construct the neural circuit. This pyloric circuit is similar to the homologous circuit of other crustacean species though some differences are seen in synaptic connections, supporting the hypothesis that the basic design of the neural circuit has been conserved during evolution of the Malacostraca, and that differences have occurred in the synaptic connectivity as the foregut structure has become complex. The motor neurons use either acetylcholine or glutamate as a neurotransmitter like in reptantians. The foregut structure, the number of the pyloric cells, muscle innervation, neurotransmitters, and circuitry are compared among malacostracan crustaceans to provide insight into how the neural circuits change and evolve to produce the motor patterns mediating behaviour.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003590050122
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  • 18
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    Bat-deafness in day-flying moths (Lepidoptera, Notodontidae, Dioptinae) (1997)
    Springer
    Journal of comparative physiology 181 (1997), S. 477-483 
    Details
    ISSN: 1432-1351
    Keywords: Key words Insects ; Bats ; Ears ; Evolution ; Neotropics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Assuming that bat-detection is the primary function of moth ears, the ears of moths that are no longer exposed to bats should be deaf to echolocation call frequencies. To test this, we compared the auditory threshold curves of 7 species of Venezuelan day-flying moths (Notodontidae: Dioptinae) to those of 12 sympatric species of nocturnal moths (Notodontidae: Dudusinae, Noctuidae and Arctiidae). Whereas 2 dioptines (Josia turgida, Zunacetha annulata) revealed normal ears, 2 (J. radians, J. gopala) had reduced hearing at bat-specific frequencies (20–80 kHz) and the remaining 3 (Thirmida discinota, Polypoetes circumfumata and Xenorma cytheris) revealed pronounced to complete levels of high-frequency deafness. Although the bat-deaf ears of dioptines could function in other purposes (e.g., social communication), the poor sensitivities of these species even at their best frequencies suggest that these moths represent a state of advanced auditory degeneration brought about by their diurnal life history. The phylogeny of the Notodontidae further suggests that this deafness is a derived (apomorphic) condition and not a retention of a primitive (pleisiomorphic), insensitive state.
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    URL: http://dx.doi.org/10.1007/s003590050131
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  • 19
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    Peripheral frequency mis-match in the primitive ensiferan Cyphoderris monstrosa (Orthoptera: Haglidae) (1999)
    Springer
    Journal of comparative physiology 184 (1999), S. 543-551 
    Details
    ISSN: 1432-1351
    Keywords: Key words Auditory physiology ; Insect ; Frequency discrimination ; Evolution ; Song recognition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Peripheral auditory frequency tuning in the ensiferan insect Cyphoderris monstrosa (Orthoptera: Haglidae) was examined by comparing tympanal vibrations and primary auditory receptor responses. In this species there is a mis-match between the frequency of maximal auditory sensitivity and the frequency content of the species' acoustic signals. The mis-match is not a function of the mechanical properties of the tympanum, but is evident at the level of primary receptors. There are two classes of primary receptors: low-tuned and broadly tuned. Differences in the absolute sensitivity of the two receptor types at the male song frequency would allow the auditory system to discriminate intraspecific signals from sounds containing lower frequencies. Comparisons of tympanal and receptor tuning indicated that the sensitivity of the broadly tuned receptors did not differ from that of the tympanum, while low-tuned receptors had significantly narrower frequency tuning. The results suggest that the limited specialization for the encoding of intraspecific signals in the auditory system of C. monstrosa is a primitive rather than a degenerate condition. The limited specialization of C. monstrosa may reflect the evolutionary origin of communication-related hearing from a generalized precursor through the addition of peripheral adaptations (tympana, additional receptors) to enhance frequency sensitivity and discrimination.
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    URL: http://dx.doi.org/10.1007/s003590050354
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  • 20
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    Acoustic communication underground: vocalization characteristics in subterranean social mole-rats (Cryptomys sp., Bathyergidae) (1997)
    Springer
    Journal of comparative physiology 180 (1997), S. 245-255 
    Details
    ISSN: 1432-1351
    Keywords: Key words Mole-rat  ;  Vocalization  ;  Acoustic communication  ;  Subterranean mammal  ; Hearing  ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract In captive adult Zambian mole-rats 14 different sounds (13 true vocalizations) have been recorded during different behavioural contexts. The sound analysis revealed that all sounds occurred in a low and middle frequency range with main energy below 10 kHz. The majority of calls contained components of 1.6–2 kHz, 0.63–0.8 kHz, and/or 5–6.3 kHz. The vocalization range thus matched well the hearing range as established in other studies. The frequency content of courtship calls in two species of Zambian Cryptomys was compared with that in naked mole-rats (Heterocephalus glaber) and blind mole-rats (Spalax ehrenbergi) as described in the literature. The frequency range of maximum sound energy is negatively correlated with the body weight and coincides with the frequencies of best hearing in the respective species. In general, the vocalization range in subterranean mammals is shifted towards low frequencies which are best propagated in underground burrows.
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    URL: http://dx.doi.org/10.1007/s003590050045
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    Evolutionary optimization and neural network models of behavior (1990)
    Springer
    Journal of mathematical biology 28 (1990), S. 237-256 
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    ISSN: 1432-1416
    Keywords: Behavior ; Evolution ; Neural network ; Dynamic optimization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract One of the main challenges to the adaptionist program in general and the use of optimization models in behavioral and evolutionary ecology, in particular, is that organisms are so constrained' by ontogeny and phylogeny that they may not be able to attain optimal solutions, however those are defined. This paper responds to the challenge through the comparison of optimality and neural network models for the behavior of an individual polychaete worm. The evolutionary optimization model is used to compute behaviors (movement in and out of a tube) that maximize a measure of Darwinian fitness based on individual survival and reproduction. The neural network involves motor, sensory, energetic reserve and clock neuronal groups. Ontogeny of the neural network is the change of connections of a single individual in response to its experiences in the environment. Evolution of the neural network is the natural selection of initial values of connections between groups and learning rules for changing connections. Taken together, these can be viewed as “design parameters”. The best neural networks have fitnesses between 85% and 99% of the fitness of the evolutionary optimization model. More complicated models for polychaete worms are discussed. Formulation of a neural network model for host acceptance decisions by tephritid fruit flies leads to predictions about the neurobiology of the flies. The general conclusion is that neural networks appear to be sufficiently rich and plastic that even weak evolution of design parameters may be sufficient for organisms to achieve behaviors that give fitnesses close to the evolutionary optimal fitness, particularly if the behaviors are relatively simple.
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    URL: http://dx.doi.org/10.1007/BF00178775
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    A branching-process model for the evolution of transposable elements incorporating selection (1991)
    Springer
    Journal of mathematical biology 29 (1991), S. 743-761 
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    ISSN: 1432-1416
    Keywords: Transposable element ; Branching-processes ; Population genetics ; Evolution ; Mobile genetic elements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract We have formulated a very general mathematical model to analyze the evolution of transposable genetic elements in prokaryotic populations. Transposable genetic elements are DNA sequences able to replicate and insert copies of themselves at new locations in the genome. This work characterizes the equilibrium distribution of copy number under the influence of copy number-dependent selection, transposition and deletion. Our principal results concern the equilibrium distribution of copy number in response to various selective regimes. For particular transposition patterns (e.g. unregulated transposition or copy number-dependent transposition), equilibrium distributions are calculated numerically for a variety of specific selection patterns. Selection is quantified through specification of the expected number of offspring for individuals of each type, which is generally a non-increasing function of copy number, in accord with the usual evolutionary speculations.
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    URL: http://dx.doi.org/10.1007/BF00160190
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    Evolutionary dynamics of predator-prey systems: an ecological perspective (1996)
    Springer
    Journal of mathematical biology 34 (1996), S. 556-578 
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    ISSN: 1432-1416
    Keywords: Dynamical systems ; Evolution ; Game theory ; Asymptotic stability ; Population dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract Evolution takes place in an ecological setting that typically involves interactions with other organisms. To describe such evolution, a structure is needed which incorporates the simultaneous evolution of interacting species. Here a formal framework for this purpose is suggested, extending from the microscopic interactions between individuals — the immediate cause of natural selection, through the mesoscopic population dynamics responsible for driving the replacement of one mutant phenotype by another, to the macroscopic process of phenotypic evolution arising from many such substitutions. The process of coevolution that results from this is illustrated in the context of predator-prey systems. With no more than qualitative information about the evolutionary dynamics, some basic properties of predator-prey coevolution become evident. More detailed understanding requires specification of an evolutionary dynamics; two models for this purpose are outlined, one from our own research on a stochastic process of mutation and selection and the other from quantitative genetics. Much of the interest in coevolution has been to characterize the properties of fixed points at which there is no further phenotypic evolution. Stability analysis of the fixed points of evolutionary dynamical systems is reviewed and leads to conclusions about the asymptotic states of evolution rather different from those of game-theoretic methods. These differences become especially important when evolution involves more than one species.
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    URL: http://dx.doi.org/10.1007/BF02409750
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    Detection of multiple stimulus features forces a trade-off in the pyramidal cell network of a gymnotiform electric fish's electrosensory lateral line lobe (1997)
    Springer
    Journal of comparative physiology 182 (1997), S. 103-113 
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    ISSN: 1432-1351
    Keywords: Key words Constraint ; Electroreception ; Evolution ; Sensory system ; Neural network
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Modification of an existing neural structure to support a second function will produce a trade-off between the two functions if they are in some way incompatible. The trade-off between two such sensory functions is modeled here in pyramidal neurons of the gymnotiform electric fish's medullar electrosensory lateral line lobe (ELL). These neurons detect two electric stimulus features produced when a nearby object interferes with the fish's autogenous electric field: (1) amplitude modulation across a cell's entire receptive field and (2) amplitude variation within a cell's receptive field produced by an object's edge. A model of sensory integration shows that detection of amplitude modulation and enhancement of spatial contrast involve an inherent mechanistic trade-off and that the severity of the trade-off depends on the particular algorithm of sensory integration. Electrophysiology data indicate that of the two algorithms for sensory integration modeled here for the gymnotiform fish Brachyhypopomus pinnicaudatus, the algorithm with the better trade-off function is used. Further, the intrinsic trade-off within single cells has been surmounted by the replication of ELL into multiple electrosensory map segments, each specialized to emphasize different sensory features.
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    URL: http://dx.doi.org/10.1007/s003590050162
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    Interactive evolution of equations for procedural models (1993)
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    The visual computer 9 (1993), S. 466-476 
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    ISSN: 1432-2315
    Keywords: Evolution ; Genetic algorithms ; Procedural models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract This paper describes how the evolutionary mechanisms of variation and selection can be used to “evolve” complex equations used by procedural models for computer graphics and animation. An interactive process between the user and the computer allows the user to guide evolving equations by observing results and providing aesthetic information at each step of the process. The computer automatically generates random mutations of equations and combinations between equations to create new generations of results. This repeated interaction between user and computer allows the user to search hyperspaces of posible equations without being required to design the equations by hand or even understand them. Three examples of these techniques have been implemented and are described: procedurally generated pictures and textures, three-dimensional shapes represented by parametric equations, and two-dimensional dynamical systems described by sets of differential equations. It is proposed that these methods have potential as powerful tools for exploring procedural models and achieving flexible complexity with a minimum of user input and knowledge of details.
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    URL: http://dx.doi.org/10.1007/BF01888721
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    Evolutionary analysis of Pinus densata Masters, a putative Tertiary hybrid (1990)
    Springer
    Theoretical and applied genetics 80 (1990), S. 635-640 
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    ISSN: 1432-2242
    Keywords: Pinus ; Species hybridization ; Allozymes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Allozyme differentiation at 13 loci was studied in populations of Pinus tabulaeformis, P. densata, and P. yunnanensis from China. It was previously suggested that P. densata represents a Tertiary hybrid between P. tabulaeformis and P. yunnanensis. The observed levels of allozyme variation within and among the investigated species were comparable to those of other conifers. P. tabulaeformis differed markedly from P. yunnanensis with respect to allozyme frequencies, while P. densata was intermediate between the two putative parents. There was evidence of homozygote excess in embryos from all investigated species, as compared to Hardy-Weinberg expectations. The observed allozyme composition of P. densata conformed to earlier morphological and molecular evidence indicating hybrid origin of this taxon. It was proposed that fusion of gene pools from P. tabulaeformis and P. yunnanensis has led to adaptive evolution of a new species, P. densata.
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    URL: http://dx.doi.org/10.1007/BF00224223
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    Chloroplast DNA evolution in potato (Solanum tuberosum L.) (1991)
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    Theoretical and applied genetics 81 (1991), S. 13-20 
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    ISSN: 1432-2242
    Keywords: Potato ; Chloroplast DNA ; Sequence comparison ; Nucleotide substitution rate ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A deletion specific to chloroplast (ct) DNA of potato (Solanum tuberosum ssp. tuberosum) was determined by comparative sequence analysis. The deletion was 241 bp in size, and was not flanked by direct repeats. Five small, open reading frames were found in the corresponding regions of ctDNAs from wild potato (S. tuberosum ssp. andigena) and tomato (Lycopersicon esculentum). Comparison of the sequences of 1.35-kbp HaeIII ctDNA fragments from potato, tomato, and tobacco (Nicotiana tabacum) revealed the following: the locations of the 5′ ends of both rubisco large subunit (rbcL) and ATPase beta subunit (atpβ) mRNAs were probably the same as those of spinach (Spinacia oleracea); the promoter regions of the two genes were highly conserved among the four species; and the 5′ untranslated regions diverged at high rates. A phylogenetic tree for the three potato cultivars, one tomato cultivar, and one tobacco cultivar has been constructed by the maximum parsimony method from DNA sequence data, demonstrating that the rate of nucleotide substitution in potato ctDNA is much slower than that in tomato ctDNA. This fact might be due to the differences in the method of propagation between the two crops.
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    URL: http://dx.doi.org/10.1007/BF00226106
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    Distribution and organization of a tandemly repeated 352-bp sequence in the oryzae family (1991)
    Springer
    Theoretical and applied genetics 82 (1991), S. 57-64 
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    ISSN: 1432-2242
    Keywords: Cultivated rice ; Wild rice ; RFLP ; Satellite DNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A 352-bp EcoRI fragment from rice DNA was cloned and shown to be a member of a tandem repeat. Sequence determination revealed homologies with human alpha satellite DNA and maize knob heterochromatin specific repeat. This 352-bp sequence is highly specific for the AA genome of rice. However, copy number and sequence organization are variable, depending on the accession analyzed. Several examples of amplification were observed in O. rufipogon and O. longistaminata. Use of resolutive polyacrylamide gel electrophoresis and 4-bp cutter enzymes allowed one to distinguish between the Indica and Japonica subtypes of O. sativa. The same method also discriminates between two groups of O. rufipogon, the presumed ancestor of O. sativa, suggesting that the present day Indica and Japonica subtypes originated independently from two O. rufipogon distinct populations.
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    URL: http://dx.doi.org/10.1007/BF00231278
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    Molecular systematics and genetic differentiation of Pinus sylvestris (L.) and P. densiflora (Sieb. et Zucc.) (1993)
    Springer
    Theoretical and applied genetics 86 (1993), S. 159-165 
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    ISSN: 1432-2242
    Keywords: Allozymes ; Chloroplast DNA ; Introgression ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Allozyme variation was examined in 22 populations of Pinus densiflora (Sieb, et Zucc.) and four geographic varieties of P. sylvestris (L.): var ‘lapponica’ (Fries, Hartman), var ‘armena’ (Komarov), var ‘mongolica’ (Litvinov) and var ‘sylvestriformis’ (Takenouchi). In addition, we developed paternal chloroplast (cp) DNA markers that distinguish P. densiflora from var ‘lapponica’, var ‘armena’ and var ‘mongolica’. UPGMA cluster analysis based on Nei's distances between all pairwise combinations of the 22 populations revealed patterns corresponding strictly to geographic origin and taxonomic status. Analysis of allozyme variation in var ‘lapponica’, var ‘armena’ and var ‘mongolica’ demonstrated a high level of intrapopulational variability but a low level of interpopulational differentiation. It appears that the late Pleistocene blending of genetically diverse populations was responsible for the observed variation patterns. The constructed phylogenetic trees also showed late divergence of these three varieties. The var ‘sylvestri formis’ was genetically distinct from the other three P. sylvestris varieties. The genetic distances separating var ‘sylvestriformis’ from P. densiflora and the other taxa lend support to a separate taxonomic status for var ‘sylvestriformis’ and a close relation with P. densiflora. We found that var ‘sylvestriformis’ harbors admixtures of allozymes and cpDNA from both P. sylvestris and P. densiflora, which suggests an introgressive nature of this variety. Levels of intrapopulational variability were similar in P. sylvestris and P. densiflora, but interpopulational differentiation was much higher in P. densiflora. In the constructed phylogenetic trees, populations of this species were characterized by relatively long internode distances and branch lengths. The present results suggest that P. densiflora has a more advanced evolutionary age than P. sylvestris.
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    URL: http://dx.doi.org/10.1007/BF00222074
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    Phylogenetic relationships between cultivated and wild species of the genusBeta revealed by DNA “fingerprinting” (1993)
    Springer
    Theoretical and applied genetics 86 (1993), S. 449-457 
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    ISSN: 1432-2242
    Keywords: Sugar beet ; Beta species ; DNA “finger-printing” ; Cluster analysis ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Forty-one accessions of the genusBeta representing wild and cultivated species of all sections were analyzed by DNA “fingerprinting”. Four sugar beet minisatellite DNA probes revealed characteristic banding patterns with Southern-hybridizedBeta DNA restricted withHindIII. A total of 111 polymorphic RFLP bands were scored across all accessions. Cluster analysis based on genetic similarity estimates for all 820 combinations of accessions revealed the following results. (1) All accessions could unambiguously be identified by a characteristic RFLP banding pattern. (2) The sugar beet cultivars examined displayed a low level of genetic diversity; they showed high similarity toB. Vulgaris ssp.maritima but low genetic similarity to the other wild species of section I. (3) In most cases, the present taxonomic classification of the genusBeta was confirmed. Species of sections II, III, and IV were clearly distinguishable from those of section I except forB. Macrocarpa, which showed high similarity to wild species of section II. In a second experiment, 108 single-copy RFLP probes from sugar beet were Southern hybridized withB. procumbens DNA. A surprisingly low degree of homology (34%) was found. The results are discussed with regard to the taxonomic classification of the genusBeta.
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    URL: http://dx.doi.org/10.1007/BF00838560
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    Chromosome assortment in Saccharum (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 959-963 
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    ISSN: 1432-2242
    Keywords: Sugarcane ; Polyploidy ; Genetics ; Evolution ; Breeding ; DNA markers ; Arbitrarily primed PCR ; RAPD markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Recent work has revealed random chromosome pairing and assortment in Saccharum spontaneum L., the most widely distributed, and morphologically and cytologically variable of the species of Saccharum. This conclusion was based on the analysis of a segregating population from across between S. spontaneum ‘SES 208’ and a spontaneously-doubled haploid of itself, derived from anther culture. To determine whether polysomic inheritance is common in Saccharum and whether it is observed in a typical biparental cross, we studied chromosome pairing and assortment in 44 progeny of a cross between euploid, meiotically regular, 2n=80 forms of Saccharum officinarum ‘LA Purple’ and Saccharum robustum ‘ Mol 5829’. Papuan 2n=80 forms of S. robustum have been suggested as the immediate progenitor species for cultivated sugarcane (S. officinarum). A total of 738 loci in LA Purple and 720 loci in Mol 5829 were amplified and typed in the progeny by arbitrarily primed PCR using 45 primers. Fifty and 33 single-dose polymorphisms were identified in the S. officinarum and S. robustum genomes, respectively (χ 2 at 98%). Linkage analysis of single-dose polymorphisms in both genomes revealed linkages in repulsion and coupling phases. In the S. officinarum genome, a map hypothesis gave 7 linkage groups with 17 linked and 33 unlinked markers. Four of 13 pairwise linkages were in repulsion phase and 9 were in coupling phase. In the S. robustum genome, a map hypothesis gave 5 linkage groups, defined by 12 markers, with 21 markers unlinked, and 2 of 9 pairwise linkages were in repulsion phase. Therefore, complete polysomic inheritance was not observed in either species, suggesting that chromosomal behavior is different from that observed by linkage analysis of over 500 markers in the S. spontaneum map. Implications of this finding for evolution and breeding are discussed.
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    URL: http://dx.doi.org/10.1007/BF00224524
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    Endosperm Balance Number and the polar-nuclei activation hypotheses for endosperm development in interspecific crosses of Solanaceae and Gramineae, respectively (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 848-855 
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    ISSN: 1432-2242
    Keywords: Endosperm development ; Evolution ; Imprinting ; Incompatibility ; Reciprocal crosses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Endosperm Balance Number (EBN) and the polar-nuclei activation (PNA) hypotheses have been developed to interpret, explain and predict interspecific and interploidy crossabilities in the Solanums and the Gramineae, respectively. Although these two hypotheses evolved independently, they share a number of common features. Assignment of EBNs and ‘activation/response values’ (AVs/RVs) depend on plumpness, size, and germinability of hybrid seeds. Also, both hypotheses emphasize the importance of a balanced parental genic contribution for the normal development of endosperm. However, in the EBN hypothesis a 2 maternal∶1 paternal EBN ratio is a prerequisite for successful interspecific crossability, while the PNA hypothesis is based on the stimulative strength of the male nuclei to initiate mitotic divisions in the primary endosperm nucleus and is idependent on a 2∶1 ratio between the RV of the polar nuclei and the AV of the male gamete. Differences and similarities betweeen the EBN and PNA hypotheses are summarized and contrasted. It is proposed that EBN and PNA be considered as the same concept.
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    URL: http://dx.doi.org/10.1007/BF00223891
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    Length variation in the internal transcribed spacers of ribosomal DNA in Picea abies and related species (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 969-974 
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    ISSN: 1432-2242
    Keywords: Evolution ; rDNA ; Internal transcribed spacers ; Picea
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The structure and variation of nuclear ribosomal DNA (rDNA) units of Picea abies, (L.) Karst. was studied by restriction mapping and Southern hybridization. Conspicuous length variation was found in the internal transcribed spacer (ITS) region of P. abies, although the length of this region is highly conserved both within and among most of the plant species. Two types of ITS variants (A and B), displaying a size difference of 0.5 kb in the ITS2 region, were present within individuals of P. abies from Sweden, Central Europe and Siberia. A preliminary survey of 14 additional Eurasian and North American species of Picea suggested that length variation in the ITS region is widespread in this genus. Alltogether three length variants (A, B and C) were identified. Within individuals of eight Picea species, two length variants were present within the genome (combinations of A and B variants in P. glehnii, P. maximowiczii, P. omorika, P. polita and P. sitchensis and variants B and C in P. jezoensis, P. likiangensis and P. spinulosa). Within individuals from five species, however only one rDNA variant was present in their genome (variant A in P. aurantiaca, P. engelmannii, P. glauca, P. koraiensis and P. koyamai; variant B in P. bicolor). The ITS length variation will be useful as a molecular marker in evolutionary studies of the Picea species complex, whose phylogeny is controversial. The presence of intraindividual variation in, and shared polymorphism of the, ITS length variants raises questions about the occurrence of interspecific hybridization during the evolutionary history of Picea.
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    Species-specific evolution of telomeric and rDNA repeats in the tobacco composite genome (1996)
    Springer
    Theoretical and applied genetics 92 (1996), S. 1108-1111 
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    ISSN: 1432-2242
    Keywords: Evolution ; Tobacco ; Telomeres ; Ribosomal genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to investigate possible interactions between parental genomes in the composite genome of Nicotiana tabacum we have analyzed the organization of telomeric (TTTAGGG)n and ribosomal gene (rDNA) repeats in the progenitor genomes Nicotiana sylvestris and Nicotiana tomentosiformis or Nicotiana otophora. Telomeric arrays in the Nicotiana species tested are heterogeneous in length ranging from 20 to 200 kb in N. sylvestris, from 20 to 50 kb in N. tomentosiformis, from 15 to 100kb in N. otophora, and from 40 to 160kb in N. tabacum. The patterns of rDNA repeats (18S, 5.8S, 25S RNA) appeared to be highly homogeneous and speciesspecific; no parental rDNA units corresponding to N. sylvestris, N. tomentosiformis or N. otophora were found in the genome of N. tabacum by Southern hybridization. The results provide evidence for a species-specific evolution of telomeric and ribosomal repeats in the tobacco composite genome.
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    Cloning and analysis of a 6.8-kb rDNA intergenic spacer region of the European ash (Fraxinus excelsior L.) (1996)
    Springer
    Theoretical and applied genetics 92 (1996), S. 1003-1008 
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    ISSN: 1432-2242
    Keywords: Fraxinus ; Evolution ; rDNA ; IGS structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The 6.8-kb rDNA intergenic spacer region of F. excelsior was isolated from a CsCl/actinomycin-D gradient and cloned into pUC18 for further characterization. We observed the presence of subrepeats delimited by HaeIII enzyme sites. These subrepeats were sub-cloned and 11 clones were sequenced. These corresponded to subrepeated elements of either 32 bp or 41 bp that shared a 23-bp common sequence in the 5′ end. Within each family of subrepeats, the percentage of common nucleotides was 84.4% for the 5 32-bp subrepeats and 67.4% for the 640-bp subrepeats. Non-repeated HaeIII fragments of 450 bp and 650 bp were also sub-cloned. To compare homology at the IGS region between the rDNA spacers of F. excelsior and the three related species (F. oxyphylla, F. americana, F. ornus), we conducted Southern hybridization analyses using each member of the 32-bp and 40-bp subrepeat families and the unique 450-bp and 650-bp fragments as probes. These analyses indicated that (1) the American ash is more genetically distant from the other three species that the latter are from each other and (2) F. oxyphylla and F. excelsior are more closely related to each other than to F. ornus.
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    Structural chromosome differentiation between Triticum timopheevii and T. turgidum and T. aestivum (1999)
    Springer
    Theoretical and applied genetics 98 (1999), S. 744-750 
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    ISSN: 1432-2242
    Keywords: Key words Chromosome pairing ; Translocations ; T. timopheevii ; T. turgidum ; T. aestivum ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract.  Chromosome pairing at metaphase-I was analyzed in F1 hybrids among T. turgidum (AABB), T. aestivum (AABBDD), and T. timopheevii (AtAtGG) to study the chromosome structure of T. timopheevii relative to durum (T. turgidum) and bread (T. aestivum) wheats. Individual chromosomes and their arms were identified by means of C-banding. Homologous pairing between the A-genome chromosomes was similar in the three hybrid types AAtBG, AAtBGD, and AABBD. However, associations of B-G were less frequent than B-B. Homoeologous associations were also observed, especially in the AAtBGD hybrids. T. timopheevii chromosomes 1At, 2At, 5At, 7At, 2G, 3G, 5G, and 6G do not differ structurally from their counterpart in the A and B genomes. Thus, these three polyploid species inherited translocation 5AL/4AL from the diploid A-genome donor. Chromosome rearrangements that occurred at the tetraploid level were different in T. turgidum and T. timopheevii. Translocation 4AL/7BS and a pericentric inversion of chromosome 4A originated only in the T. turgidum lineage. The two lines of T. timophevii studied carry four different translocations, 6AtS/1GS, 1GS/4GS, 4GS/4AtL, and 4AtL/3AtL, which most likely arose in that sequence. These structural differences support a diphyletic origin of polyploid wheats.
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    Phylogenetic classification and molecular evolution of knotted1 homeobox genes (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 203-209 
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    ISSN: 1432-2242
    Keywords: Key words Homeobox gene ; KNOTTED1 ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Homeobox genes encode a family of DNA-binding regulatory proteins which are crucial for development. The first plant homeobox gene identified was knotted1 which plays a major role in leaf development. The knotted1 gene has a homeobox which encodes a homeodomain (HD) and HD proteins have been shown to function as transcription factors. A phylogenetic classification of the KNOTTED1 HD is presented. Here, we report six kn1 HDs from the cereals oat, barley, wheat, rye and rice. The KN1 class-I and -II genes can be divided into two distinct clades. Further, we hypothesize that KN1 and BELL1/MEIS HDs, (the closest non-KN1 class HDs) evolved from a common ancestor after divergence from the common precursor of all the homeobox genes. Our analysis clearly shows the presence of an ancestral KN1 HD from which all the known plant kn1 class of genes evolved.
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    Vertebrate protamine gene evolution I. Sequence alignments and gene structure (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 333-346 
    Details
    ISSN: 1432-1432
    Keywords: Protamine ; Evolution ; Nuclear protein ; DNA condensation ; Sperm proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The availability of the amino acid sequence for nine different mammalian P1 family protamines and the revised amino acid sequence of the chicken protamine galline (Oliva and Dixon 1989) reveals a much close relationship between mammalian and avian protamines than was previously thought (Nakano et al. 1976). Dot matrix analysis of all protamine genes for which genomic DNA or cDNA sequence is available reveals both marked sequence similarities in the mammalian protamine gene family and internal repeated sequences in the chicken protamine gene. The detailed alignments of the cis-acting regulatory DNA sequences shows several consensus sequence patterns, particularly the conservation of a cAMP response element (CRE) in all the protamine genes and of the regions flanking the TATA box, CAP site, N-terminal coding region, and polyadenylation signal. In addition we have found a high frequency of the CA dinucleotide immediately adjacent to the CRE element of both the protamine genes and the testis transition proteins, a feature not present in other genes, which suggests the existence of an extended CRE motif involved in the coordinate expression of protamine and transition protein genes during spermatogenesis. Overall these findings suggest the existence of an avian-mammalian P1 protamine gene line and are discussed in the context of different hypotheses for protamine gene evolution and regulation.
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    Phylogeny of the major tetrapod groups: Morphological data and divergence dates (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 409-424 
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    ISSN: 1432-1432
    Keywords: Phylogeny ; Tetrapods ; Morphology ; Cladistics ; Divergence ; Evolution ; Amphibians ; Reptiles ; Birds ; Mammals
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The phylogeny of the major groups of tetrapods (amphibians, reptiles, birds, and mammals) has until recently been poorly understood. Cladistic analyses of morphological data are producing new hypotheses concerning the relationships of the major groups, with a focus on the identification of monophyletic groups. Molecular phylogenies support some of these views and dispute others. Geological dates of the major evolutionary branching points are recalculated on the basis of the cladograms and new fossil finds.
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    Evolutionary origin of aminoglycoside phosphotransferase resistance genes (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 489-492 
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    ISSN: 1432-1432
    Keywords: Actinomyces ; Phosphotransferase ; Aminoglycoside ; Phylogenetic tree ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The protein sequences of seven 3′-aminoglycoside phosphotransferases falling into the six identified types and three 6′-aminoglycoside phosphotransferases were analyzed to give a rooted phylogenetic tree. This tree supports the origin of these groups of enzymes in an ancestor closely related to the actinomycetes, and that horizontal transfer of the resistance genes occurred, possibly via transposons. The implications for genetic engineering of a novel antibiotic are discussed.
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    URL: http://dx.doi.org/10.1007/BF02101103
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    Distribution of the salmonid Hpa 1 family in the salmonid species demonstrated by in vitro runoff transcription assay of total genomic DNA: A procedure to estimate repetitive frequency and sequence divergence of a certain repetitive family with a few known sequences (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 43-52 
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    ISSN: 1432-1432
    Keywords: Retroposon ; Salmonid ; +RNA ; Evolution ; Average sequence divergence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary An in vitro runoff transcription assay of total genomic DNA was developed. As an example of use of this assay, analysis of a highly repetitive sequence in the cherry salmon (Oncorhynchus masou) is described. Total genomic DNA of the cherry salmon was completely digested with Hpa 1, whose site is known to be in the tRNA-unrelated region of the cherry salmon Hpa 1 family. On transcription of the digested DNA in a HeLa cell extract, a discrete-sized RNA of about 100 nucleotides, constituting 70% of the transcripts, was produced, whereas on transcription of the undigested total DNA, only smeared RNA was obtained. In a fingerprint, the oligonucleotides of the discrete transcript from the digested total DNA were very distinct and exactly corresponded to those of a transcript from an Hpa 1 digest of a cloned DNA, but with few extra oligonucleotides. These results showed that the cherry salmon Hpa 1 family constitutes a major repetitive family in the genome of the cherry salmon. For determination of the distribution of the salmonid Hpa 1 family in other salmonid species, the same analysis was applied to DNAs from the chum salmon (Oncorhynchus keta), brown trout (Salmo trutta), Japanese common charr (Salvelinus leucomaenis pluvius), and Japanese huchen (Hucho perryi). The results showed that the salmonid Hpa 1 family is widespread in the genomes of salmonid species. A method and equations are also presented for estimating the relationship between the ratio of a given repetitive family to all the Pol III genes and its average sequence divergence by calculating the molar ratio of the runoff transcript to all the in vitro Pol III transcripts.
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    URL: http://dx.doi.org/10.1007/BF02099928
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    Evolution and sequence analysis of a human Y-chromosomal DNA fragment (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 133-141 
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    ISSN: 1432-1432
    Keywords: Y-chromosome ; DNA ; Human ; Primate ; Evolution ; PUPPY sequence ; Alu element
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A Y-chromosomal DNA fragment has been isolated from a human Y-Charon 21A recombinant library. Evolutionary analysis of 1F5 indicates that the size and sequence of this fragment have been conserved in higher primates. Deletion mapping and in situ hybridization analysis have localized 1F5 to the middle euchromatic portion of the long arm of the human Y chromosome at Yq11.2. Sequence analysis revealed the presence of an atypical Alu element and two regions rich in polypyrimidine-polypurine residues.
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    URL: http://dx.doi.org/10.1007/BF02193627
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    Mitochondrial DNA evolution in lagomorphs: Origin of systematic heteroplasmy and organization of diversity in European rabbits (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 92-102 
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    ISSN: 1432-1432
    Keywords: Lagomorphs ; Rabbit ; Mitochondrial DNA ; Heteroplasmy ; Restriction site polymorphism ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A characterization was conducted on mitochondrial DNA (mtDNA) molecules extracted separately from 107 European rabbits (Oryctolagus cuniculus) both wild and domestic, 13 European hares (Lepus capensis), and 1 eastern cottontail (Sylvilagus floridanus). Experimentally this study took into account restriction site polymorphism, overall length variation of the noncoding region, and numbers of repeated sequences. Nucleotide divergences indicate that the mtDNAs from the three species derived from a common ancestor some 6–8 million years (Myr) ago. Every animal appeared heteroplasmic for a set of molecules with various lengths of the noncoding region and variable numbers of repeated sequences that contribute to them. This systematic heteroplasmy, most probably generated by a rate of localized mtDNA rearrangements high enough to counterbalance the cellular segregation of rearranged molecules, is a shared derived character of leporids. The geographic distribution of mtDNA polymorphism among wild rabbit populations over the western European basin shows that two molecular lineages are represented, one in southern Spain, the second over northern Spain, France, and Tunisia. These two lineages derived from a common ancestor some 2 Myr ago. Their present geographical distribution may be correlated to the separation of rabbits into two stocks at the time of Mindel glaciation. Finally the distribution of mtDNA diversity exhibits a mosaic pattern both at inter- and intrapopulation levels.
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    Structure and evolution of 5S rRNA genes and pseudogenes in the genusAspergillus (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 175-178 
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    ISSN: 1432-1432
    Keywords: Aspergillus ; 5S rRNA genes ; 5S rRNA pseudogenes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned and determined the nucleotide sequence of 18 DNA fragments hybridizing to 5S rRNA from twoAspergillus species-A. wentii andA. awamori. Four of the analyzed sequences were pseudogenes. The gene sequences of these two species were very similar and differed fromAspergillus nidulans at both constant and microheterogeneous sites.
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    Evolutionary relationships among the permease proteins of the bacterial phosphoenolpyruvate: Sugar phosphotransferase system. Construction of phylogenetic trees and possible relatedness to proteins of eukaryotic mitochondria (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 179-193 
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    ISSN: 1432-1432
    Keywords: Bacteria ; Sugars ; Phosphotransferase system ; Transport proteins ; Evolution ; Sequence comparisons ; NADH dehydrogenase ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The amino acid sequences of 15 sugar permeases of the bacterial phosphoenolpyruvatedependent phosphotransferase system (PTS) were divided into four homologous segments, and these segments were analyzed to give phylogenetic trees. The permease segments fell into four clusters: the lactose-cellobiose cluster, the fructose-mannitol cluster, the glucose-N-acetylglucosamine cluster, and the sucrose-β-glucoside cluster. Sequences of the glucitol and mannose permeases (clusters 5 and 6, respectively) were too dissimilar to establish homology with the other permeases, but short regions of statistically significant sequence similarities were noted. The functional and structural relationships of these permease segments are discussed. Some of the homologous PTS permeases were found to exhibit sufficient sequence similarity to subunits 4 and 5 of the eukaryotic mitochondrial NADH dehydrogenase complex to suggest homology. Moreover, subunits 4 and 5 of this complex appeared to be homologous to each other, suggesting that these PTS and mitochondrial proteins comprise a superfamily. The integral membrane subunits of the evolutionarily divergent mannose PTS permease, the P and M subunits, exhibited limited sequence similarity to subunit 6 of the mitochondrial F1F0-ATPase and subunit 5b of cytochrome oxidase, respectively. These results suggest that PTS sugar permeases and mitochondrial proton-translocating proteins may be related, although the possibility of convergent evolution cannot be ruled out.
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    Biogenesis as an evolutionary process (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 207-208 
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    ISSN: 1432-1432
    Keywords: Evolution ; Vesicle ; Biogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The earliest fossil stromatolites present evidence of a complex ecosystem of photosynthetic organisms. Because the origin of present life can be dated within a few hundred million years prior to these fossils, their complexity poses a problem. A heuristic model outlines the first radiation leading to the universal ancestor.
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    Functional elements and domains inferred from sequence comparisons of a heat shock gene in two nematodes (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 3-9 
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    ISSN: 1432-1432
    Keywords: Caenorhabditis elegans ; Caenorhabditis briggsae ; hsp70 ; grp78 ; Gene comparison ; Evolution ; Regulatory elements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Caenorhabditis elegans andCaenorhabditis briggsae are two closely related nematode species that are nearly identical morphologically. Interspecific cross-hybridizing DNA appears to be restricted primarily to coding regions. We compared portions of thehsp-3 homologs two grp 78-like genes, fromC. elegans andC. briggsae and detected regions of DNA identity in the coding region, the 5′ flanking DNAs, and the introns. Thehsp-3 homologs share approximately 98% and 93% identity at the amino acid and nucleotide levels, respectively. Using the nucleotide substitution rate at the silent third position of the codons, we have estimated a lower limit for the date of divergence betweenC. elegans andC. briggsae to be approximately 23–32 million years ago. The 5′ flanking DNAs and one of the introns contain elements that are highly conserved betweenC. elegans andC. briggsae. Some of the regions of nucleotide identity in the 5′ flanking DNAs correspond to previously detected identities including viral enhancer sequences, a heat shock element, and an element present in the regulatory regions of mammalian grp78 and grp94 genes. We propose that a comparison ofC. elegans andC. briggsae sequences will be useful in the detection of potential regulatory and structural elements.
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    Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea starPisaster ochraceus (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 195-204 
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    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Evolution ; Echinoderms ; Sea stars ; DNA sequence ; Mitochondrial proteins ; Mitochondrial tRNA genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned and sequenced over 9 kb of the mitochondrial genome from the sea starPisaster ochraceus. Within a continuous 8.0-kb fragment are located the genes for NADH dehydrogenase subunits 1, 2, 3, and 4L (ND1, ND2, ND3, and ND4L), cytochrome oxidase subunits I, II, and III (COI, COII, and COIII), and adenosine triphosphatase subunits 6 and 8 (ATPase 6 and ATPase 8). This large fragment also contains a cluster of 13 tRNA genes between ND1 and COI as well as the genes for isoleucine tRNA between ND1 and ND2, arginine tRNA between COI and ND4L, lysine tRNA between COII and ATPase 8, and the serine (UCN) tRNA between COIII and ND3. The genes for the other five tRNAs lie outside this fragment. The gene for phenylalanine tRNA is located between cytochrome b and the 12S ribosomal genes. The genes for tRNAglu and tRNAthr are 3′ to the 12S ribosomal gene. The tRNAs for histidine and serine (AGN) are adjacent to each other and lie between ND4 and ND5. These data confirm the novel gene order in mitochondrial DNA (mtDNA) of sea stars and delineate additional distinctions between the sea star and other mtDNA molecules.
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    On the mode of evolution of alpha satellite DNA in human populations (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 42-48 
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    ISSN: 1432-1432
    Keywords: Satellite DNA ; Mouse ; Human chromosomes 13 and 21 ; Evolution ; Saltatory amplification ; Homogenization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The hypothesis that highly reiterated satellite DNAs in present-day populations evolve by molecular mechanisms that create, by saltatory amplification steps, new long arrays of satellite DNA, and that such long arrays are used for homogenization purposes, has been tested both in mouse and in humans. In mouse, the data obtained are consistent with this hypothesis. This was tested in more detail on chromosomes 13 and 21 of the human genome. A Centre d'Etudes du Polymorphisme Humain family, which in some individuals exhibits strong supplementary DNA bands following TaqI restriction endonuclease digestion and conventional gel electrophoresis, was analyzed by pulse field gel electrophoresis following restriction by BamHI. The supplementary bands on chromosome 13 (18 times the basic alpha satellite DNA repeat) and on chromosome 21 (a 9.5-mer) segregated with centromeric alpha satellite DNA blocks of 5 and 5.3 megabases, respectively. These are by far the largest alpha satellite block lengths seen in all chromosome 13 and chromosome 21 centrometric sequences so far analyzed in this manner. The possibility that these supplementary alpha satellite sequences were created in single individuals by saltatory amplification steps is discussed in light of our own data and that published by others. It is proposed that deletion events and unequal cross-overs, which both occur in large satellite DNA arrays, contribute to the homogenization of size and sequence of the alpha satellite DNA on most chromosomes of humans.
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    Compartmentalized isozyme genes and the origin of introns (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 205-210 
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    ISSN: 1432-1432
    Keywords: Isozyme ; Intron ; Phylogenetic tree ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes. The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (=1.3×10−3), suggesting that the conservation of the intron positions has a biological significance. On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes. In the aspartate aminotransferase isozyme genes, five of the introns are at identical places. The origins of the five conserved introns, however, are not obvious at present. It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes.
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    Secondary structural elements exclusive to the sequences flanking ribosomal RNAs lend support to the monophyletic nature of the archaebacteria (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 25-32 
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    ISSN: 1432-1432
    Keywords: Archaebacteria ; rRNA operons ; Secondary structure ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Several sequences flanking the large rRNA genes of several transcripts from extreme thermophiles, extreme halophiles, and methanogens were aligned and analyzed for the presence of common primary and secondary structural features, which would bear on the concept of monphyletic archaebacteria. Few sequences were common to all the archaebacterial transcripts, and these were confined to short regions generally flanking putative double helices. At a secondary structural level, however, in addition to the previously characterized processing stems of the 16S and 23S RNAs, four helices were detected that were common to the archaebacterial transcripts: two in the 16S RNA leader sequence and two in the 16S-23S RNA spacer. Although all of these helices vary in size and form from organism to organism, three of them contain double helical segments that are strongly supported by compensating base changes among the three archaebacterial groups. Three extreme halophiles exhibited two additional helices in their relatively large spacers and a further helix preceding the 5S RNA, which are also supported by compensating base changes. Ribosomal RNA transcripts from eubateria/chloroplasts and eukaryotes were also examined for secondary structural features with locations and forms corresponding to those of the archaebacteria, but none were detected. The analysis provides support for the monophyletic nature of the archaebacteria and reinforces their differences from eubacteria/chloroplasts and eukaryotes.
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    There appear to be conserved constraints on the distribution of nucleotide sequences in cellular genomes (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 24-30 
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    ISSN: 1432-1432
    Keywords: Short sequence distribution ; Sequence constraints ; Averaged sequence ; Sequence structure ; Asymmetric nucleotide sequences ; GC content ; Evolution ; Evolutionary constraints
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The data from a genomic library can be sorted into the frequencies of every possible tetranucleotide in the sequence. This tabulation, a short sequence distribution, contains the frequency of occurrence of the 256 tetranucleotides and thus seems to serve as a vehicle for averaging sequence information. Two such distributions can be readily compared by correlation. Reported here are correlations (Spearmanr s) of the distributions from all of the genomic libraries in GenBank 44.0 with sizes equal to or larger than that ofSalmonella typhimurium, except for the data for mouse and humans. All of the organisms examined showed highly significant correlations between the two DNA strands (not the complementarity expected from base pairing). Of 155 comparisons between libraries, 132 showed significant correlations at the 99% confidence level. Application of the correlation coefficients as a similarity matrix clustered most organisms in a phenogram in a pattern consistent with other hypotheses. This suggests a highly conserved pattern underlying all other genetic information in cellular DNA and affecting both DNA strands, perhaps caused by interaction with conserved factors necessary for DNA packaging.
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    Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 70-78 
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    ISSN: 1432-1432
    Keywords: Phylogenetic tree ; Likelihood method ; RNA polymerase ; Archaebacteria ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogeny, as well as by the neighbor-joining method and the parsimony method, together with bootstrap analyses. It was shown that the best tree topologies predicted by the first two methods are identical, whereas the last one predicts a distinct tree. The maximum likelihood tree revealed that, after the separation from archaebacteria, the three eukaryotic RNA polymerases diverged from an ancestral precursor in the eukaryotic lineage. This result is contrasted with the published result showing multiple origins for the three eukaryotic polymerases. It was shown that eukaryotic RNA polymerase I evolved much more rapidly than RNA polymerases II and III: The N-terminal half of RNA polymerase I shows an extraordinarily high evolutionary rate, possibly due to relaxed functional constraints. In contrast the evolutionary rate of archaebacterial RNA polymerase is remarkably limited. In addition, including the second largest subunit of the RNA polymerase, a detailed analysis for the branching pattern of the three major groups of archaebacteria was carried out by the maximum likelihood method. It was shown that the three major groups of archaebacteria are likely to form a single cluster; that is, archaebacteria are likely to be monophyletic as originally proposed by Woese and his colleagues.
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    Genome variations in the transition from amphibians to reptiles (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 68-75 
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    ISSN: 1432-1432
    Keywords: DNA ; Genome size ; Repetitive DNA ; Amphibians ; Reptiles ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Many characters differentiate amphibian from reptilian genomes. The former have, on the average, larger and more variable genome sizes, a greater repetitive DNA percentage, and a higher interspersion level among DNAs with different degrees of repetitivity. Reptiles have more reduced and uniform genome sizes, a repetitive DNA percentage generally lower than 50%, and a lower interspersion level. Other differences can be observed in the chromosome banding and in the correlations between genome size and other morphometric and functional parameters of the cell. The differences found in amphibians and reptiles seem to indicate that in these two vertebrate classes there is a different tendency toward or tolerance of the accumulation and preservation of genetically dispensable DNA fractions. This might depend either on a different propensity toward genic amplification or on the appearance, in reptiles, of stricter and more efficient constraints regulating genome size.
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    Evolution of proteins of the cystatin superfamily (1990)
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    Journal of molecular evolution 30 (1990), S. 60-71 
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    ISSN: 1432-1432
    Keywords: Cysteine endopeptidase ; Cysteine proteinase ; Inhibitor ; Cystatin ; Kininogen ; Evolution ; Amino acid sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have examined the amino acid sequences of a number of proteins that have been suggested to be related to chicken cystatin, a protein from chicken egg white that inhibits cysteine proteinases. On the basis of statistical analysis, the following proteins were found to be members of the cystatin superfamily: human cystatin A, rat cystatin A(α), human cystatin B, rat cystatin B(β), rice cystatin, human cystatin C, ox colostrum cystatin, human cystatin S, human cystatin SA, human cystatin SN, chicken cystatin, puff adder cystatin, human kininogen, ox kininogen, rat kininogen, rat T-kininogens 1 and 2, human α2HS-glycoprotein, and human histidine-rich glycoprotein. Fibronectin is shown not to be a member of this superfamily, and the c-Ha-ras oncogene protein p21(Val-12) probably is not a member also. It was convenient to divide members of the superfamily into four types on the basis of the presence of one, two, or three copies of cystatin-like segments and the presence or absence of disulfide bonds. Evolutionary dendrograms were calculated by three methods, and from these we have constructed a scheme depicting the sequence of events in the evolution of these proteins. We suggest that about 1000 million years ago a precursor containing disulfide loops appeared, and that all disulfide-containing cystatins are derived from this. We follow the evolution of the proteins of the superfamily along four main lineages, with special attention to the part that duplication of segments has played in the development of the more complex molecules.
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    Evolutionary origin of the class A and class C β-lactamases (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 345-350 
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    ISSN: 1432-1432
    Keywords: Evolution ; β-Lactamase ; Phylogenetic tree ; Horizontal transfer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The protein sequences of 18 class A β-lactamases and 2 class C β-lactamases were analyzed to produce a rooted phylogenetic tree using the DD peptidase of Streptomyces R61 as an outgroup. This tree supports the penicillin-binding proteins as the most likely candidate for the ancestoral origin of the class A and class C β-lactamases, these proteins diverging from a common evolutionary origin close to the DD peptidase. The actinomycetes are clearly shown as the origin of the class A β-lactamases found in other non-actinomycete species. The tree also divides the β-lactamases from the Streptomyces into two subgroups. One subgroup is closer to the DD peptidase root. The other Streptomyces subgroup shares a common branch point with the rest of the class A β-lactamases, showing this subgroup as the origin of the non-actinomycete class A β-lactamases. The non-actinomycete class A β-lactamase phylogenetic tree suggests a spread of these β-lactamases by horizontal transfer from the Streptomyces into the non-actinomycete gram-positive bacteria and thence into the gram-negative bacteria. The phylogenetic tree of the Streptomyces class A β-lactamases supports the possibility that horizontal transfer of class A β-lactamases occurred within the Streptomyces.
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    Organization and evolution of bacterial and bacteriophage primase-helicase systems (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 351-357 
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    ISSN: 1432-1432
    Keywords: Primase-helicase systems ; Evolution ; Bacteria ; Bacteriophage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Amino acid sequences of primases and associated helicases involved in the DNA replication of eubacteria and bacteriophages T7, T3, T4, P4, and P22 were compared by computer-assisted methods. There are two types of such systems, the first one represented by distinct helicase and primase proteins (e.g., DnaB and DnaG proteins of Escherichia coli), and the second one by single polypeptides comprising both activities (gp4 of bacteriophages T7 and T3, and alpha protein of bacteriophage P4). Pronounced sequence similarity was revealed between approximately 250 amino acid residue N-terminal domains of stand-alone primases and the primase-helicase proteins of T7(T3) and P4. All these domains contain, close to their N-termini, a conserved Zn-finger pattern that may be implicated in template DNA recognition by the primases. In addition, they encompass five other conserved motifs some of which may be involved in substrate (NTP) binding. Significant similarity was also observed between the primase-associated helicases (DnaB, gp12 of P22 and gp41 of T4) and the C-terminal domain of T7(T3) gp4. On the other hand the C-terminal domain of P-alpha of P4 is related to another group of DNA and RNA helicases. Tentative phylogenetic trees generated for the primases and the associated helicases showed no grouping of the phage proteins, with the exception of the primase domains of bacteriophages T4 and P4. This may indicate a common origin for one-component primase-helicase systems. Two scenarios for the evolution of primase-helicase systems are discussed. The first one involves fusion of the primase and helicase components (T7 and T3) or fusion of the primase component with a different type of helicase domain (P4). The second possibility is the duplication of an ancestral gene encoding a gp4-like bifunctional protein followed by divergence of the copies, one of which retains the primase and the other the helicase domain.
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    Phenotypic plasticity and nutrition in a phytophagous insect: consequences of colonizing a new host (1994)
    Springer
    Oecologia 100 (1994), S. 379-385 
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    ISSN: 1432-1939
    Keywords: Tephritidae ; Phenotypic plasticity ; Phytophagous insects ; Evolution ; Selection regime
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The European rose-hip fruit fly Rhagoletis alternata (Diptera, Tephritidae) infests hips of Rosa species. This fly includes R. rugosa, an Asian species now cultivated all over Europe, in its host range. Differences in size and biomass of hips between the ancestral host R. canina and the new host translate into better growth, shorter larval development of larvae within hips of R. rugosa and larger body size and fertility of flies which developing in the new host. In turn this causes different interactions with other organisms of the food-web centred on the host plant. The importance of nutrition and phenotypic plasticity is twofold: they generate a considerable part of life-history diversity within a species and reinforce differences in the ecological context of the ancestral and new host.
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    A hypothesis on the evolution of isoprenoid emission by oaks based on the correlation between emission type and Quercus taxonomy (1998)
    Springer
    Oecologia 115 (1998), S. 302-305 
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    ISSN: 1432-1939
    Keywords: Key words Chemo-taxonomy ; Isoprenoid emission ; Evolution ; Quercus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We show that Mediterranean oaks that emit isoprene, monoterpenes or no isoprenoids belong to different subgenera as indicated by morpho-taxonomy and molecular genetics. On the other hand, oaks from North America and Asia that are taxonomically similar to the Mediterranean monoterpene emitter Q. ilex emit isoprene only. We surmise that isoprene emission is a genetic character which evolved ancestrally in the oak genus since this is the prevalent emission type in oaks widespread around the world and adapted to different environments. This ancestral character may have been either lost or modified in more recent clades such as those originating the Mediterranean oaks. If our hypothesis is correct then the taxonomy of European oaks is validated by this independent trait. Isoprenoid emission could serve as a chemo-taxonomical marker and could be used to reconstruct the phylogeny of oaks in association with molecular markers.
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    URL: http://dx.doi.org/10.1007/s004420050520
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    Modelling the nutritional ecology of ungulate herbivores: evolution of body size and competitive interactions (1992)
    Springer
    Oecologia 89 (1992), S. 428-434 
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    ISSN: 1432-1939
    Keywords: Ruminant ; Hindgut fermenter ; Nutritional ecology ; Evolution ; Body size
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A simulation model is used to quantify relationships between diet quality, digestive processes and body weight in ungulate herbivores. Retention time of food in the digestive tract is shown by regression to scale with W0.27, and to be longer in ruminants than in hindgut fermenters. Allometric relationships between whole gut mean retention time (MRT, h) and weight (W) were: MRT=9.4 W0.255 (r 2=0.80) for hindgut fermenters and MRT=15.3 W0.251 (r 2=0.76) in ruminants. Longer retention of ingesta by large-bodied ruminants and hindgut fermenters increases digestive efficiency relative to small animals and permits them to survive on lower-quality foods. Compared with ruminants, hindgut fermenters' faster throughput is an advantage which outweighs their lower digestive efficiency, particularly on poor quality foods, provided that food resources are not limiting. This suggests that the predominance of ruminants in the middle range of body weights results from their more efficient use of scarce resources under conditions of resource depletion. Considering only physical limitations on intake, the model shows that the allometric coefficient which scales energy intake to body mass is 0.88 in ruminants and 0.82 in hindgut fermenters. The advantages of large body size are countered by disadvantages where food quantity is limited, and we suggest that the upper limit to ungulate body size is determined by the ability to extract nutrients from feeding niches during the nadir of the seasonal cycle of resource quality and abundance.
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    Neighbour specificity between Lolium perenne and Trifolium repens from a natural pasture (1992)
    Springer
    Oecologia 91 (1992), S. 404-409 
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    ISSN: 1432-1939
    Keywords: Trifolium repens ; Lolium perenne ; Competition ; Coadaptation ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Five genotypes of Trifolium repens and Lolium perenne were collected as neighbouring pairs along a fertility gradient in a natural pasture. After vegetative multiplication, the 25 possible combinations of Lolium genotype x Trifolium genotype were planted in the greenhouse in order to investigate competition between the genotypes. The comparison of the five combinations whose individual components had been neighbours with the combinations of genotypes that had not coexisted before disclosed no difference in total biomass production over 7 months. However, the yield of Trifolium increased when grown with the Lolium genotype which had been its natural neighbour, while the latter showed a decrease in yield. This neighbour specificity existed even when carryover effects from the sampling site had been eliminated (preconditioning period of 18 months) and when native Rhizobium strains were not present (inoculation with a non-native strain). The complex pattern of neighbour specificity with time indicated the importance of environmental conditions for its outcome. These results are a further confirmation of positive effects on the growth of Trifolium repens when grown together with its natural neighbour. They are discussed in the context of coexistence and coevolution
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    Fisheries as a large-scale experiment on life-history evolution: disentangling phenotypic and genetic effects in changes in maturation and reproduction of North Sea plaice, Pleuronectes platessa L. (1993)
    Springer
    Oecologia 96 (1993), S. 391-401 
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    ISSN: 1432-1939
    Keywords: Plaice ; Life-history ; Evolution ; Maturation ; Reproduction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This paper attempts to interpret the observed changes in reproductive strategy of female North Sea plaice since 1900 in the light of possible genetical selection exerted by the fisheries. Somatic growth of juvenile plaice increased between the 1950s and the 1980s, probably as a response to an increase in food availability. Adult growth rate was constant, except during a period of increased population abundance when somatic growth decreased. Both length (L mat) and age at first sexual maturity decreased since 1990. No firm evidence was obtained for a change in total reproductive investment, although size-specific fecundity was reduced in the period of increased population abundance, suggesting a trade-off between egg numbers and egg size. Analysis of the phenotypic response of maturation to an increase in juvenile growth suggested that only a part of the decrease in L mat could be ascribed to the observed increase in juvenile growth. The unexplained part of the change in L mat corresponded with the predicted change due to genetical selection by the fisheries. This supported the hypothesis that fishing caused a genetical change in L mat, although an unequivocal interpretation is not possible from a descriptive study.
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    The neuroethology of sound production in tiger moths (Lepidoptera, Arctiidae) (1992)
    Springer
    Journal of comparative physiology 170 (1992), S. 575-588 
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    ISSN: 1432-1351
    Keywords: Moth ; Sensorimotor integration ; Neuroethology ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary 1. Certain species of tiger moths emit clicks when stimulated by bat-like sounds. These clicks are generated by modified thoracic episterna (tymbals) (Fig. 1) and constitute a rhythmic behaviour activated by simple sensory input. 2. Tymbal periods are indirectly related to stimulus intensity and periods (Fig. 3). Moths initiate sounds with the tymbal opposite to the stimulated ear and once a sequence commences it continues in an undisrupted fashion. 3. The tymbal is innervated by a pleural branch (IIIN2a) of the metathoracic leg nerve, a similar anatomy to that in the unmodified episterna of silent moths (Fig. 5). Backfills of the IIIN2a in Cycnia tenera reveal sensory fibres and a cluster of 5–9 motor neurons with densely overlying dendritic fields (Fig. 6). 4. Extracellular recordings of the IIIN2a reveal a large impulse preceding each tymbal sound (Fig. 7). I suggest that this impulse results from the synchronous firing of 2–3 motor neurons and is the motor output of the tymbal central pattern generator (CPG). The spikes alternate (Figs. 9, 10) and are bilaterally co-related (Fig. 11) but with an phase asymmetry of 2–3 ms (Fig. 12). 5. Normal motor output continues in the absence of tymbal sounds (Fig. 13) and when all nerve-tymbal connections are severed (Fig. 14, Table 1) therefore this CPG operates independent of sensory feedback. A model is proposed for the tymbal circuitry based upon the present data and the auditory organization of related noctuid moths (Fig. 15). I propose that the tymbal response in modern arctiids evolved from either flight or walking CPGs and that preadaptive circuitry ancestral to tymbal movements still exists in modern silent Lepidoptera.
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    The evolutionary adaptation of flower colours and the insect pollinators' colour vision (1992)
    Springer
    Journal of comparative physiology 171 (1992), S. 171-181 
    Details
    ISSN: 1432-1351
    Keywords: Colour vision ; Flower colours ; Evolution ; Hymenoptera ; Pollination ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The evolutionary tuning between floral colouration and the colour vision of flower-visiting Hymenoptera is quantified by evaluating the informational transfer from the signalling flower to the perceiving pollinator. The analysis of 180 spectral reflection spectra of angiosperm blossoms reveals that sharp steps occur precisely at those wavelengths where the pollinators are most sensitive to spectral differences. Straight-forward model calculations determine the optimal set of 3 spectral photoreceptor types for discrimination of floral colour signals on the basis of perceptual difference values. The results show good agreement with the sets of photoreceptors characterized electrophysiologically in 40 species of Hymenoptera.
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    Did neural pooling for night vision lead to the evolution of neural superposition eyes? (1994)
    Springer
    Journal of comparative physiology 175 (1994), S. 289-302 
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    ISSN: 1432-1351
    Keywords: Compound eye ; Open rhabdom ; Neural superposition ; Visual ecology ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Observations of the infrared deep pseudopupil, optical determinations of the corneal nodal point, and histological methods were used to relate the visual fields of individual rhabdomeres to the array of ommatidial optical axes in four insects with open rhabdoms: the tenebrionid beetle Zophobas morio, the earwig Forficula auricularia, the crane fly Tipula pruinosa, and the backswimmer Notonecta glauca. The open rhabdoms of all four species have a central pair of rhabdomeres surrounded by six peripheral rhabdomeres. At night, a distal pigment aperture is fully open and the rhabdom receives light over an angle approximately six times the interommatidial angle. Different rhabdomeres within the same ommatidium do not share the same visual axis, and the visual fields of the peripheral rhabdomeres overlap the optical axes of several near-by ommatidia. During the day, the pigment aperture is considerably smaller, and all rhabdomeres share the same visual field of about two interommatidial angles, or less, depending on the degree of light adaptation. The pigment aperture serves two functions: (1) it allows the circadian rhythm to switch between the night and day sampling patterns, and (2) it works as a light driven pupil during the day. Theoretical considerations suggest that, in the night eye, the peripheral retinula cells are involved in neural pooling in the lamina, with asymmetric pooling fields matching the visual fields of the rhabdomeres. Such a system provides high sensitivity for nocturnal vision, and the open rhabdom has the potential of feeding information into parallel spatial channels with different tradeoffs between resolution and sensitivity. Modification of this operational principle to suit a strictly diurnal life, makes the contractile pigment aperture superfluous, and decreasing angular sensitivities together with decreasing pooling fields lead to a neural superposition eye.
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    Visual pigment diversity in two genera of mantis shrimps implies rapid evolution (Crustacea; Stomatopoda) (1996)
    Springer
    Journal of comparative physiology 179 (1996), S. 371-384 
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    ISSN: 1432-1351
    Keywords: Visual pigment ; Stomatopoda ; Visual ecology ; Evolution ; Photoreceptor ; Retina
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract 1. Interspecific diversity in the visual pigments of stomatopod crustaceans was characterized using microspectrophotometry. We examined the 10 visual pigments in main rhabdoms in retinas of 3 species of each of two genera of stomatopod crustaceans of the superfamily Gonodactyloidea, Gonodactylus (G. oerstedii, G. aloha, and G. curacaoensis) and Odontodactylus (O. scyllarus, O. brevirostris, and O. “havanensis”). Species were selected to provide a matched diversity of habitats. 2. In each genus, visual pigments varied in λmax in several regions of the retina, as revealed by analysis of variance. The variation within closely related species of the same genus implies that visual pigments can evolve rapidly in stomatopods. 3. In photoreceptors of the peripheral retina, which are devoted to spatial vision, visual pigment λmax decreased as the depth range of the various species increased, a typical pattern for marine animals. In contrast, visual pigment λmax in photoreceptors of retinal regions devoted to polarization vision (midband Rows 5 and 6) is not obviously correlated with the spectral environment, implying that polarization information may be confined to particular spectral ranges. Visual pigments of the tiered rows of the midband, which are committed to spectral analysis, span a larger spectral range in shallow-water than deepwater species.
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    Three unexpected cases of refracting superposition eyes in crustaceans (1990)
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    Journal of comparative physiology 167 (1990), S. 71-78 
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    ISSN: 1432-1351
    Keywords: Compound eye ; Optics ; Crustacea ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Compound eyes of the decapod shrimp Gennadas, the hermit crab Dardanus, and the syncarid crustacean Anaspides are studied histologically and with optical experiments. The results demonstrate that these three crustaceans all have refracting superposition eyes. The conclusion is based on the following observations: 1. There is a wide clear-zone, which allows for a superposition image to be formed. 2. Dark-adapted eyes display a large eye-glow, and the ommatidia are not optically isolated. 3. The crystalline cones have the shape typical for refracting superposition eyes, and they contain the required lens-cylinder gradient of refractive index. Euphausiids and mysids were previously thought to be the only crustaceans with refracting superposition eyes, whereas the species investigated here were assumed to have reflecting superposition eyes (decapod shrimps) or apposition eyes (hermit crabs and syncarids). The present findings increase more than twofold the number of crustacean groups that are known to have developed refracting superposition optics. It also provides insight into the evolutionary mechanisms that may have led to the development of this type of imaging optics.
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    Identification and genetic mapping of Xenopus TAP2 genes (1999)
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    Immunogenetics 49 (1999), S. 171-182 
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    ISSN: 1432-1211
    Keywords: Key words MHC ; Transporter ; Evolution ; PCR cloning ; Allelic lineage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The amphibian Xenopus laevis is one non-mammalian vertebrate in which the major histocompatibility complex (MHC) has been analyzed extensively. Class IIβ, class Ia, LMP2, LMP7, HSP70, C4, Factor B, and Ring3 genes have been identified and mapped to the MHC. Here, we report the isolation of a transporter associated with antigen processing (TAP) gene, TAP2, and demonstrate its linkage to the MHC. While the ATP-binding region of Xenopus TAP2 is highly conserved in evolution, amino acid identity to other vertebrate TAP proteins was not detected in the N-terminal region. Segregation analysis of 34 individuals from two families showed exact restriction fragment length polymorphism matching between the MHC class Ia gene and the one TAP2 gene demonstrating linkage conservation since the mammalian/amphibian divergence ∼350 million years ago. In addition, one non-MHC-linked TAP2–hybridizing fragment was detected in approximately half of the individuals tested. Interestingly, TAP2 allelic lineages appear to match those of LMP7 and classical class I, which previously were categorized into two highly divergent groups that emerged at least 60 million years ago. Similar to LMP7 and class Ia,TAP2 is expressed ubiquitously with highest levels in intestine and spleen.
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    Variation in the number of expressed MHC genes in different cattle class I haplotypes (1999)
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    Immunogenetics 50 (1999), S. 319-328 
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    ISSN: 1432-1211
    Keywords: Key words Cattle ; MHC class I ; Haplotypes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Analysis of cattle major histocompatibility complex (MHC) (BoLA) class I gene expression using serological and biochemical methods has demonstrated a high level of polymorphism. However, analysis of class I cDNA sequences has failed to produce conclusive evidence concerning the number and nature of expressed genes. Such information is essential for detailed studies of cattle immune responses, and to increase our understanding of the mechanisms of MHC evolution. In this study a selective breeding programme has been used to generate a number of MHC homozygous cattle expressing common serologically defined class I specificities. Detailed analysis of five class I haplotypes was carried out, with transcribed class I genes identified and characterized by cDNA cloning, sequence analysis, and transfection/expression studies. Surface expression of the gene products (on lymphocytes) was confirmed using monoclonal antibodies of defined BoLA specificity. Phylogenetic analysis of available transcribed cattle MHC class I sequences revealed complex evolutionary relationships including possible evidence for recombination. The study of individual haplotypes suggests that certain groupings of related sequences may correlate with loci, but overall it was not possible to define the origin of individual alleles using this approach. The most striking finding of this study is that none of the cattle class I genes is consistently expressed, and that in contrast to human, haplotypes differ from one another in both the number and composition of expressed classical class I genes.
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    MHC class I genes in a New World primate, the cotton-top tamarin (Saguinus oedipus), have evolved by an active process of loci turnover (1999)
    Springer
    Immunogenetics 49 (1999), S. 196-205 
    Details
    ISSN: 1432-1211
    Keywords: Key words New world primates ; MHC ; Evolution ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Lymphocytes of a New World primate, the cotton-top tamarin (Saguinus oedipus), express classical G–related major histocompatibility complex (MHC) class I molecules with unusually limited polymorphism and variability. Three G-related loci, an F locus, an E locus, and two pseudogenes (So-N1 and So-N3) have been identified by cDNA library screening and extensive PCR analysis of both cDNA and genomic DNA from the cotton-top tamarin. Furthermore, each genus of the subfamily Callitrichinae (tamarins and marmosets) appears to express its own unique set of MHC class I genes, likely due to a rapid turnover of loci. The rapid emergence of unique MHC class I genes in the Callitrichinae genera, resulting from an active process of duplication and inactivation of loci, may account for the limited diversity of the MHC class I genes in the cotton-top tamarin. To determine the nature of the entire complement of MHC class I genes in the cotton-top tamarin, we synthesized a genomic DNA library and screened it with MHC class I-specific probes. We isolated nine new MHC class I pseudogenes from this library. These newly isolated tamarin G–related MHC class I pseudogenes are not closely related to any of their functional counterparts in the tamarin, suggesting that they do not share a recent common ancestral gene with the tamarin's currently expressed MHC class I loci. In addition, these tamarin sequences display a high rate of nonsynonymous substitutions in their putative peptide binding region. This indicates that the genes from which they have derived were likely subject to positive selection and, therefore, were once functional. Our data support the notion that an extremely high rate of loci turnover is largely responsible for the limited diversity of the MHC class I genes in the cotton-top tamarin.
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    Multiple class I loci expressed by the quail Mhc (1999)
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    Immunogenetics 49 (1999), S. 456-460 
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    ISSN: 1432-1211
    Keywords: Key words Antigen processing ; Evolution ; Cell surface molecules ; Mhc ; Class I antigens
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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    A divergent non-classical class I gene conserved in salmonids (1999)
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    Immunogenetics 49 (1999), S. 479-490 
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    ISSN: 1432-1211
    Keywords: Key words Comparative immunology ; Evolution ; MHC class I ; Molecular biology ; Salmonids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Complementary DNA for two class I genes of the rainbow trout, Oncorhynchus mykiss, were characterized. MhcOnmy-UBA*01 is similar to Onmy-UA-C32 and the classical major histocompatibility complex class I genes of other fish species, whereas Onmy-UAA*01 is divergent from all class I genes so far characterized. Onmy-UAA*01 is expressed at lower levels than Onmy-UBA*01. Although Onmy-UAA*01 exhibits restriction fragment length polymorphism on Southern blotting, the encoded protein is highly conserved. Two allotypes, which differ only by substitution at amino acid position 223 of the α3 domain, have been defined. Onmy-UAA*01 has an exon-intron organization like other class I genes and contains a Tc1-like transposon element in intron III. Orthologues of Onmy-UAA*01 have been characterized in four other species of salmonid. Between four species of Oncorhynchus, UAA*01 proteins differ by only 2–6 amino acids, whereas comparison of Oncorhynchus with Salmo trutta (brown trout) reveals 14–16 amino acid differences. The Onmy-UAA*01 gene has properties indicative of a particularly divergent non-classical class I gene.
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    The isochore patterns of mammalian genomes and their phylogenetic implications (1993)
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    Journal of molecular evolution 37 (1993), S. 93-108 
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    ISSN: 1432-1432
    Keywords: DNA ; Base composition ; Vertebrates ; Eutheria ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The compositional distributions of high molecular weight DNA fragments from 20 species belonging to 9 out of the 17 eutherian orders were investigated by analytical CsCl density gradient centrifugation and by preparative fractionation in Cs2SO4/BAMD density gradients followed by analysis of the fractions in CsCl. These compositional distributions reflect those of the isochores making up the corresponding genomes. A “general distribution” was found in species belonging to eight mammalian orders. A “myomorph distribution” was found in Myomorpha, but not in the other rodent infraorders Sciuromorpha and Histricomorpha, which share the general distribution. Two other distributions were found in a megachiropteran (but not in microchiropteran, which, again, shares the general distribution) and in pangolin (a species from the only genus of the order Pholidota), respectively. The main difference between the general distribution and all other distributions is that the former contains sizable amounts (6–10%) of GC-rich isochores (detected as DNA fragments equal to, or higher than, 1.710 g/cm3 in modal buoyant density), which are scarce, or absent, in the other distributions. This difference is remarkable because gene concentrations in mammalian genomes are paralleled by GC levels, the highest gene concentrations being present in the GC-richest isochores. The compositional distributions of mammalian genomes reported here shed light on mammalian phylogeny. Indeed, all orders investigated, with the exception of Pholidota, seem to share a common ancestor. The compositional patterns of the megachiropteran and of Myomorpha may be derived from the general pattern or have independent origins.
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    Evolution of protamine P1 genes in primates (1993)
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    Journal of molecular evolution 37 (1993), S. 426-434 
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    ISSN: 1432-1432
    Keywords: Primate ; Evolution ; Protamine ; Polymerase chain reaction ; Sperm proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Protamine P1 genes have been sequenced by PCR amplification and direct DNA sequencing from 9 primates representing 5 major families, Cebidae (new world monkeys), Cercopithecidae (old world monkeys), Hylobatidae (gibbons), Pongidae (gorilla, orangutan, and chimpanzee), and Hominidae (human). In this recently diverged group of primates these genes are clearly orthologous but very variable, both at the DNA level and in their expressed amino acid sequences. The rate of variation amongst the protamine Pls indicates that they are amongst the most rapidly diverging polypeptides studied. However, some regions are conserved both in primates and generally in other placental mammals. These are the 13 N-terminal residues (including a region of alternating serine and arginine residues (the motif SRSR, res. 10–13) susceptible to Ser phosphorylation), a tract of six Arg residues (res. 24–29) in the center of the molecule, and a six-residue region (RCCRRR, res. 39–44), consisting of a pair of cysteines flanked by arginines. Detailed consideration of nearest neighbor matrices and trees based on maximum parsimony indicates that PI genes from humans, gorillas, and chimpanzees are very similar. The amino acid and nucleotide differences between humans and gorillas. are fewer than those between humans and chimpanzees. This finding is at variance with data from DNA-DNA hybridization and extensive globin and mitochondrial DNA sequences which place human and chimpanzee as closest relatives in the super family, Hominoidea. This may be related to the fact that protamine Pls are expressed in germ line rather than somatic cells. In contrast to the variability of the exon regions of the protamine P1 genes, the sequence of the single intron is highly conserved.
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    URL: http://dx.doi.org/10.1007/BF00178872
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    Prebiotic chemistry in clouds (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 296-303 
    Details
    ISSN: 1432-1432
    Keywords: Prebiotic chemistry ; Primordial soup ; Oparin hypothesis ; Evolution ; Impact catastrophism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In the traditional concept for the origin of life as proposed by Oparin and Haldane in the 1920s, prebiotic reactants became slowly concentrated in the primordial oceans and life evolved slowly from a series of highly protracted chemical reactions during the first billion years of Earth's history. However, chemical evolution may not have occurred continuously because planetesimals and asterioids impacted the Earth many times during the first billion years, may have sterilized the Earth, and required the process to start over. A rapid process of chemical evolution may have been required in order that life appeared at or before 3.5 billion years ago. Thus, a setting favoring rapid chemical evolution may be required. A chemical evolution hypothesis set forth by Woese in 1979 accomplished prebiotic reactions rapidly in droplets in giant atmospheric reflux columns. However, in 1985 Scherer raised a number of objections to Woese's hypothesis and concluded that it was not valid. We propose a mechanism for prebiotic chemistry in clouds that satisfies Scherer's concerns regarding the Woese hypothesis and includes advantageous droplet chemistry. Prebiotic reactants were supplied to the atmosphere by comets, meteorites, and interplanetary dust or synthesized in the atmosphere from simple compounds using energy sources such as ultraviolet light, corona discharge, or lightning. These prebiotic monomers would have first encountered moisture in cloud drops and precipitation. We propose that rapid prebiotic chemical evolution was facilitated on the primordial Earth by cycles of condensation and evaporation of cloud drops containing clay condensation nuclei and nonvolatile monomers. For example, amino acids supplied by, or synthesized during entry of, meteorites, comets, and interplanetary dust would have been scavenged by cloud drops containing clay condensation nuclei. Polymerization would have occurred within cloud systems during cycles of condensation, freezing, melting, and evaporation of cloud drops. We suggest that polymerization reactions occurred in the atmosphere as in the Woese hypothesis, but life originated in the ocean as in the Oparin-Haldane hypothesis. The rapidity with which chemical evolution could have occurred within clouds accommodates the time constraints suggested by recent astrophysical theories.
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    URL: http://dx.doi.org/10.1007/BF02102187
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    Cloning and characterization of the platypus mitochondrial genome (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 200-205 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Monotreme ; Platypus ; mtDNA ; tRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The vertebrate mitochondrial genome is highly conserved in size and gene content. Among the chordates there appears to be one basic gene arrangement, but rearrangements in the mitochondrial gene order of the avian lineages have indicated that the mitochondrial genome may be more variable than once thought. Different gene orders in marsupials and eutherian mammals leave the ancestral mammalian order in some doubt. We have investigated the mitochondrial gene order in the platypus (Ornithorhynchus anatinus), a representative of the third major group of mammals, to determine which mitochondrial gene arrangement is ancestral in mammals. We have found that the platypus mtDNA conforms to the basic chordate gene arrangement, common to fish, amphibians, and eutherian mammals, indicating that this arrangement was the original mammalian arrangement, and that the unusual rearrangements observed in the avians and marsupials are probably lineage-specific.
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    URL: http://dx.doi.org/10.1007/BF00163808
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    Interspecific comparison of the unusually repetitiveDrosophila locusmastermind (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 415-420 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila melanogaster ; Drosophila virilis ; mastermind ; Gene comparison ; Repetitive sequences ; Homopolymers ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Themastermind gene ofDrosophila melanogaster encodes a novel, highly repetitive nuclear protein required for neural development. To identify functionally important regions we have initiated an interspecific comparison of the gene inDrosophila virilis. Mastermind transcription and genomic organization are similar in both species and sequence analysis reveals significant conservation in a major cluster of charged amino acids. In contrast, extensive variation is noted in homopolymer domains that immediately flank the acidic cluster. Distinct patterns of evolutionary change can be identified: the major difference between unique regions are occasional amino acid substitutions whereas the repetitive areas are characterized by numerous large in-frame insertions/deletions and a nearly threefold higher rate of amino acid replacement. Conservation of the acidic domain suggests that it has an important functional role whereas the hypervariable homopolymer regions appear to be under less selective constraints than adjacent unique areas.
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    URL: http://dx.doi.org/10.1007/BF02101281
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    Characterization of a species-specific satellite DNA family of Dolichopoda schiavazzii (Orthoptera, Rhaphidophoridae) cave crickets (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 274-281 
    Details
    ISSN: 1432-1432
    Keywords: Repetitive DNA ; Tandem repeats ; Sequence analysis ; Recombination ; Isolated populations ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The satellite DNA family pDoP102 is species specific for the cave cricket Dolichopoda schiavazzii, an endemic species of mainland and insular Tuscany. It consists of numerous tandemly arranged repeats, 102 bp in length, and evolved most probably after cladogenesis of D. schiavazzii from the D. baccettii-aegilion group within the last 2.3 ± 0.8 million years. A sequence comparison of 31 clones (53 repetition units) from three isolated populations reveals a very high degree of sequence homogeneity within the species with no evidence for any specific population features. This appears to be in contrast to the results of allozyme analyses which account for a relatively old evolutionary divergence of the Elba island population from the mainland ones. Since the assumption of actual gene flow and recent colonization is rejected, the observed sequence homogeneity is hypothesized to be maintained by recombination processes preventing fixation of newly introduced mutations on pDoP102 sequence clusters.
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    URL: http://dx.doi.org/10.1007/BF00160151
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    Interspecific sequence comparison of the muscle-myosin heavy-chain genes from Drosophila hydei and Drosophila melanogaster (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 357-368 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila ; Muscle-myosin heavy-chain gene ; Alternative exons ; Synonymous substitutions ; Amino acid substitutions ; Evolution ; Testis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The muscle-myosin heavy-chain (mMHC) gene of Drosophila hydei has been sequenced completely (size 23.3 kb). The sequence comparison with the D. melanogaster mMHC gene revealed that the exonintron pattern is identical. The protein coding regions show a high degree of conservation (97%). The alternatively spliced exons (3a-b, 7a-d, 9a-c, 11a-e, and 15a-b) display more variations in the number of nonsynonymous and synonymous substitutions than the common exons (2, 4, 5, 6, 8, 10, 12, 13, 14, 16, 17, and 19). The base composition at synonymous sites of fourfold degenerate codons (third position) is not biased in the alternative exons. In the common exons there exists a bias for C and against A. These findings imply that the alternative exons of the Drosophila mMHC gene evolve at a different, in several cases higher, rate than the common ones. The 5′ splice junctions and 5′ and 3′ untranslated regions show a high level of similarity, indicating a functional constraint on these sequences. The intron regions vary considerably in length within one species, but the corresponding introns are very similar in length between the two species and all contain stretches of sequence similarity. A particular example is the first intron, which contains multiple regions of similarity. In the conserved regions of intron 12 (head-tail border) sequences were found which have the potential to direct another smaller mMHC transcript.
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    URL: http://dx.doi.org/10.1007/BF00160268
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    An analysis of retroposition in plants based on a family of SINEs from Brassica napus (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 378-386 
    Details
    ISSN: 1432-1432
    Keywords: CpG dinucleotides ; Evolution ; Repetitive sequences ; Reverse transcriptase ; S1Bn retroposons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The identification of a family of SINE retroposons dispersed in the genome of oilseed rape Brassica napus has provided the basis for an evolutionary analysis of retroposition in plants. The repetitive elements (called S1Bn) are 170 by long and occupy roughly 500 loci by haploid genome. They present characteristic features of SINE retroposons such as a 3′ terminal A-rich region, two conserved polymerase III motifs (box A and B), flanking direct repeats of variable sizes, and a primary and secondary sequence homology to several tRNA species. A consensus sequence was made from the alignment of 34 members of the family. The retroposon population was divided into five subfamilies based on several correlated sets of mutations from the consensus. These precise separations in subfamilies based on “diagnostic” mutations and the random distribution of mutations observed inside each subfamily are consistent with the master sequence model proposed for the dispersion of mammalian retroposons. An independent analysis of each subfamily provides strong evidence for the coexpression of at least three subfamily master sequences (SMS). In contrast to mammalian retroposition, diagnostic positions are not shared between SMS. We therefore propose that SMS were all derived from a general master sequence (GMS) and independently activated for retroposition after a variable period of random drift. Possible models for plant retroposition are discussed.
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    URL: http://dx.doi.org/10.1007/BF00160270
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    The evolution of the thrombospondin gene family (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 509-516 
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    ISSN: 1432-1432
    Keywords: Thrombospondin ; Evolution ; Adhesive glycoproteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Thrombospondin-1 is an adhesive glycoprotein that is involved in cellular attachment, spreading, migration, and proliferation. To date, four genes have been identified that encode for the members of the thrombospondin gene family. These four genes are homologous to each other in the EGF-like (type 2) repeats, the calcium-binding (type 3) motifs, and the COOH-terminal. The latter has been reported to be a cell-binding domain in thrombospondin-1. Phylogenetic trees have been constructed from the multisequence alignment of thrombospondin sequences from human, mouse, chicken, and frog. Two different algorithms generate comparable results in terms of the topology and the branch lengths. The analysis indicates that an early form of the thrombospondin gene duplicated about 925 million years ago. The gene duplication that produced the thrombospondin-1 and -2 branches of the family is predicted to have occurred 583 million years ago, whereas the gene duplication that produced the thrombospondin-3 and -4 branches of the family is predicted to have occurred 644 million years ago. These results indicate that the members of the thrombospondin gene family have existed throughout the evolution of the animal kingdom and thus probably participate in functions that are common to most of its members.
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    URL: http://dx.doi.org/10.1007/BF00556355
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    The compositional patterns of the avian genomes and their evolutionary implications (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 544-551 
    Details
    ISSN: 1432-1432
    Keywords: Isochores ; DNA ; Coding sequences ; Birds ; Mammals ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The compositional distributions of large (main-band) DNA fragments from eight birds belonging to eight different orders (including both paleognathous and neognathous species) are very broad and extremely close to each other. These findings, which are paralleled by the compositional similarity of homologous coding sequences and their codon positions, support the idea that birds are a monophyletic group. The compositional distribution of third-codon positions of genes from chicken, the only avian species for which a relatively large number of coding sequences is known, is very broad and bimodal, the minor GC-richer peak reaching 100% GC. The very high compositional heterogeneity of avian genomes is accompanied (as in the case of mammalian genomes) by a very high speciation rate compared to cold-blooded vertebrates which are characterized by genomes that are much less heterogeneous. The higher GC levels attained by avian compared to mammalian genomes might be correlated with the higher body temperature (41–43°C) of birds compared to mammals (37°C). A comparison of GC levels of coding sequences and codon positions from man and chicken revealed very close average GC levels and standard deviations. Homologous coding sequences and codon positions from man and chicken showed a surprisingly high degree of compositional similarity which was, however, higher for GC-poor than for GC-rich sequences. This indicates that GC-poor isochores of warm-blooded vertebrates reflect the composition of the isochores of the genome of the common reptilian ancestor of mammals and birds, which underwent only a small compositional change at the transition from cold- to warm-blooded vertebrates. In contrast, the GC-rich isochores of birds and mammals are the result of large compositional changes at the same evolutionary transition, where were in part different in the two classes of warm-blooded vertebrates.
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    URL: http://dx.doi.org/10.1007/BF00160434
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    Evolutionary consequences of nonrandom damage and repair of chromatin domains (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 156-180 
    Details
    ISSN: 1432-1432
    Keywords: DNA damage ; DNA repair ; Chromatin ; Evolution ; Nucleosomes ; Nuclear matrix ; Active genes ; Z-DNA ; Sperm ; Mutation ; Molecular clock
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Some evolutionary consequences of different rates and trends in DNA damage and repair are explained. Different types of DNA damaging agents cause nonrandom lesions along the DNA. The type of DNA sequence motifs to be preferentially attacked depends upon the chemical or physical nature of the assaulting agent and the DNA base composition. Higher-order chromatin structure, the nonrandom nucleosome positioning along the DNA, the absence of nucleosomes from the promoter regions of active genes, curved DNA, the presence of sequence-specific binding proteins, and the torsional strain on the DNA induced by an increased transcriptional activity all are expected to affect rates of damage of individual genes. Furthermore, potential Z-DNA, H-DNA, slippage, and cruciform structures in the regulatory region of some genes or in other genomic loci induced by torsional strain on the DNA are more prone to modification by genotoxic agents. A specific actively transcribed gene may be preferentially damaged over nontranscribed genes only in specific cell types that maintain this gene in active chromatin fractions because of (1) its decondensed chromatin structure, (2) torsional strain in its DNA, (3) absence of nucleosomes from its regulatory region, and (4) altered nucleosome structure in its coding sequence due to the presence of modified histones and HMG proteins. The situation in this regard of germ cell lineages is, of course, the only one to intervene in evolution. Most lesions in DNA such as those caused by UV or DNA alkylating agents tend to diminish the GC content of genomes. Thus, DNA sequences not bound by selective constraints, such as pseudogenes, will show an increase in their AT content during evolution as evidenced by experimental observations. On the other hand, transcriptionally active parts may be repaired at rates higher than inactive parts of the genome, and proliferating cells may display higher repair activities than quiescent cells. This might arise from a tight coupling of the repair process with both transcription and replication, all these processes taking place on the nuclear matrix. Repair activities differ greatly among species, and there is a good correlation between life span and repair among mammals. It is predicted that genes that are transcriptionally active in germ-cell lineages have a lower mutation rate than bulk DNA, a circumstance that is expected to be reflected in evolution. Exception to this rule might be genes containing potential Z-DNA, H-DNA, or cruciform structures in their coding or regulatory regions that appear to be refractory to repair. This study supports the molecular clock hypothesis when applied to one gene within a group of related species and contends that evolutionary rates might vary between genes and gene segments not only as a result of differences in selective constraints but also as a result of differences in the rate of damage minus rate of repair among different segments of chromatin DNA.
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    URL: http://dx.doi.org/10.1007/BF00183227
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    Estimating the fraction of invariable codons with a capture-recapture method (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 253-260 
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    ISSN: 1432-1432
    Keywords: Protein-coding sequences ; DNA sequences ; Evolution ; Evolutionary rates ; Rate heterogeneity ; Maximum likelihood ; Statistical testing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A codon-based approach to estimating the number of variable sites in a protein is presented. When first and second positions of codons are assumed to be replacement positions, a capture-recapture model can be used to estimate the number of variable codons from every pair of homologous and aligned sequences. The capture-recapture estimate is compared to a maximum likelihood estimate of the number of variable codons and to previous approaches that estimate the number of variable sites (not codons) in a sequence. Computer simulations are presented that show under which circumstances the capture-recapture estimate can be used to correct biases in distance matrices. Analysis of published sequences of two genes, calmodulin and serum albumin, shows that distance corrections that employ a capture-recapture estimate of the number of variable sites may be considerably different from corrections that assume that the number of variable sites is equal to the total number of positions in the sequence.
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    URL: http://dx.doi.org/10.1007/BF00178601
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    Investigating hypothetical products from noncoding frames (HyPNoFs) (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 570-577 
    Details
    ISSN: 1432-1432
    Keywords: Alternate reading frames ; Evolution ; Overlapping frames ; Homology search ; Primary sequence analysis ; Polycistronic genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Hypothetical Products from Noncoding Frames (i.e., HyPNoFs) are hypothetical, not-coded proteins, translated from alternate reading frames (i.e., coding+1 and coding+2) of cDNAs. HyPNoFs of CD4, PKC, oncostatin, bcl-2 proto-oncogene, tumor suppressor p53, cystic fibrosis transmembrane regulator (CFTR), and tumor necrosis factors a and β were searched as query sequences vs the SWISS-PROT data bank. Homology searches carried out revealed that hypothetical products (i.e., HyPNoFs) may share high similarity with real protein products actually coded. Sequence similarity of hypothetical products to real proteins is sometimes very high, suggesting common conformational features, according to the Sander and Schneider cutoff value. This finding supports the hypothesis that eukaryotic DNA, currently considered to be monocistronic, might occasionally have polycistronic regions, carrying different protein messages on overlapping frames. As yet, polycistronic genes have been observed in viral genomes only. The presence of polycistronic regions in eukaryotic genes is likely reminiscent of an ancient strategy, rather than a present feature of the genome in eukaryotes. These data suggest that thorough investigation of HyPNoFs is likely to improve our ability to trace genes' evolution and to investigate structure-function relationships of protein and DNA sequences.
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    URL: http://dx.doi.org/10.1007/BF00160503
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    Caenorhabditis elegans contains genes encoding two new members of the Zn-containing alcohol dehydrogenase family (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 46-53 
    Details
    ISSN: 1432-1432
    Keywords: Alcohol dehydrogenase ; Caenorhabditis elegans ; Evolution ; Gene families
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have characterized two cDNA clones from the nematode Caenorhabditis elegans that display similarity to the alcohol dehydrogenase (ADH) gene family. The nucleotide sequences of these cDNAs predict that they encode Zn-containing long-chain ADH enzymes. Phylogenetic analysis suggests that one is most similar to dimeric class III ADHs found in diverse taxa; the other is most similar to the tetrameric forms of ADH previously described only in fungi.
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    URL: http://dx.doi.org/10.1007/BF00174040
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    Phylogeny and physiology of Drosophila opsins (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 250-262 
    Details
    ISSN: 1432-1432
    Keywords: Opsin ; Visual pigments ; Gene family ; Evolution ; Phylogeny ; Spectral sensitivity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic and physiological methods were used to study the evolution of the opsin gene family in Drosophila. A phylogeny based on DNA sequences from 13 opsin genes including representatives from the two major subgenera of Drosophila shows six major, well-supported clades: The “blue opsin” clade includes all of the Rhl and Rh2 genes and is separated into two distinct subclades of Rhl sequences and Rh2 sequences; the ultraviolet opsin clade includes all Rh3 and Rh4 genes and bifurcates into separate Rh3 and Rh4 clades. The duplications that generated this gene family most likely took place before the evolution of the subgenera Drosophila and Sophophora and their component species groups. Numerous changes have occurred in these genes since the duplications, including the loss and/or gain of introns in the different genes and even within the Rhl and Rh4 clades. Despite these changes, the spectral sensitivity of each of the opsins has remained remarkably fixed in a sample of four species representing two species groups in each of the two subgenera. All of the strains that were investigated had R1-6 (Rhl) spectral sensitivity curves that peaked at or near 480 nm, R7 (Rh3 and Rh4) peaks in the ultraviolet range, and ocellar (Rh2) peaks near 420 nm. Each of the four gene clades on the phylogeny exhibits very conservative patterns of amino acid replacement in domains of the protein thought to influence spectral sen sitivity, reflecting strong constraints on the spectrum of light visible to Drosophila.
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    The β-tubulin gene family evolution in theDrosophila montium subgroup of themelanogaster species group (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 293-298 
    Details
    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to theDrosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in themontium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling speciesD. auraria, D. triauraria, andD. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental speciesD. bicomuta, D. serrata, andD. birchii, as well as in the Afrotropical speciesD. diplacantha andD. seguyi. The complete separation of the genes is observed in the Indian speciesD. kikkawai andD. jambulina and in the Afrotropical speciesD. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among themontium species are discussed.
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    URL: http://dx.doi.org/10.1007/BF01215176
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    The β-tubulin gene family evolution in the Drosophila montium subgroup of the melanogaster species group (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 293-298 
    Details
    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to the Drosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in the montium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling species D. auraria, D. triauraria, and D. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental species D. bicomuta, D. serrata, and D. birchii, as well as in the Afrotropical species D. diplacantha and D. seguyi. The complete separation of the genes is observed in the Indian species D. kikkawai and D. jambulina and in the Afrotropical species D. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among the montium species are discussed.
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    URL: http://dx.doi.org/10.1007/BF00186541
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    Convergent evolution of crystallin gene regulation in squid and chicken: The AP-1/ARE connection (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 134-143 
    Details
    ISSN: 1432-1432
    Keywords: Lens ; Crystallin ; Squid ; Chicken ; Gene ; Regulation ; AP-1 ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previous experiments have shown that the minimal promoters required for function of the squid SL20-1 and SL11 crystallin genes in transfected rabbit lens epithelial cells contain an overlapping AP-1/antioxidant responsive element (ARE) upstream of the TATA box. This region resembles the PL-1 and PL-2 elements of the chicken βB 1-cry stallin promoter which are essential for promoter function in transfected primary chicken lens epithelial cells. Here we demonstrate by site-directed mutagenesis that the AP-1/ARE sequence is essential for activity of the squid SL20-1 and SL11 promoters in transfected embryonic chicken lens cells and fibroblasts. Promoter activity was higher in transfected lens cells than in fibroblasts. Electrophoretic mobility shift and DNase protection experiments demonstrated the formation of numerous complexes between nuclear proteins of the embryonic chicken lens and the AP-1/ARE sequences of the squid SL20-1 and SL11 crystallin promoters. One of these complexes comigrated and cross-competed with that formed with the PL-1 element of the chicken βB1-crystallin promoter. This complex formed with nuclear extracts from the lens, heart, brain, and skeletal muscle of embryonic chickens and was eliminated by competition with a consensus AP-1 sequence. The nonfunctional mutant AP-1/ ARE sequences did not compete for complex formation. These data raise the intriguing possibility that entirely different, nonhomologous crystallin genes of the chicken and squid have convergently evolved a similar cis-acting regulatory element (AP-1/ARE) for high expression in the lens.
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    Molecular and phylogenetic analysis of PCR-amplified cyclin-dependent kinase (CDK) family sequences from representatives of the earliest available lineages of eukaryotes (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 407-413 
    Details
    ISSN: 1432-1432
    Keywords: Giardia ; Trichomonas ; CDK ; CDC ; Unicellular ; Metazoa ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cyclin-dependent kinase (CDK) and cell division control (CDC2) sequences are strongly conserved among eukaryotes and may complement the use of other sequence families in eukaryotic phylogenetic inference. We synthesized degenerate PCR primers to amplify the catalytic region of CDK homologs in representatives of the earliest available lineages of eukaryotes. CDK family sequence-based, maximum-likelihood distance measurements with neighbor joining, and Fitch-Margoliash least-squares analyses produced unrooted dendrograms that included protists, yeasts, and higher eukaryotes. Bootstrap confidence estimates supported CDK-based phylogenetic groupings among the protists, fungi, and vertebrates although resolution within these groups was often insignificant. However, Trichomonas vaginalis and Giardia lamblia exhibited two of the most divergent CDK-like sequences consistent with rRNA-phylogenetic inference of early divergence of these eukaryotic lineages. In the evolution from unicellular to multicellular organisms, a constellation of amino acid residues aligning with the human, CDK N-terminal β sheet may have undergone abrupt replacement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160311
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  • 92
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    Molecular evolution of maize catalases and their relationship to other eukaryotic and prokaryotic catalases (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 570-579 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Catalase ; Phylogenetic tree,Zea mays L. ; Isozyme ; Antioxidant genes ; Gene Structure ; Oxidative stress
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have compared the nucleotide and protein sequences of the three maize catalase genes with other plant catalases to reconstruct the evolutionary relationship among these catalases. These sequences were also compared with other eukaryotic and prokaryotic catalases. Phylogenies based on distances and parsimony analysis show that all plant catalases derive from a common ancestral catalase gene and can be divided into three distinct groups. The first, and major, group includes maizeCatl, barleyCat1, riceCatB and most of the dicot catalases. The second group is an apparent dicot-specific catalase group encompassing the tobaccoCat2 and tomatoCat. The third is a monocot-specific catalase class including the maize Cat3, barley Cat2, and riceCatA. The maize Cat2 gene is loosely related to the first group. The distinctive features of monocot-specific catalases are their extreme high codon bias at the third position and low degree of sequence similarity to other plant catalases. Similarities in the intron positions for several plant catalase genes support the conclusion of derivation from a common ancestral gene. The similar intron position between bean catalases and human catalase implies that the animal and plant catalases might have derived from a common progenitor gene sequence.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02352287
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  • 93
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    Evolutionary relationships of the carbamoylphosphate synthetase genes (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 813-832 
    Details
    ISSN: 1432-1432
    Keywords: Phylogeny ; Evolution ; Carbamoylphosphate synthetase ; Dihydroorotase ; Aspartate transcarbamoylase ; Intron ; Exon ; Arginine biosynthesis ; Pyrimidine biosynthesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Carbamoylphosphate is a common intermediate in the metabolic pathways leading to the biosynthesis of arginine and pyrimidines. The amino acid sequences of all available proteins that catalyze the formation of carbamoylphosphate were retrieved from Genbank and aligned to estimate their mutual phylogenetic relations. In gram-negative bacteria carbamoylphosphate is synthesized by a two-subunit enzyme with glutamiriase and carbamoylphosphate synthetase (CPS) activity, respectively. In gram-positive bacteria and lower eukaryotes this two-subunit CPS has become dedicated to arginine biosynthesis, while in higher eukaryotes the two subunits fused and subsequently lost the glutaminase activity. The CPS dedicated to pyrimidine synthesis is part of a multifunctional enzyme (CPS II), encoding in addition dihydroorotase and aspartate transcarbamoylase. Evidence is presented to strengthen the hypothesis that the two “kinas” subdomains of all CPS isozymes arose from a duplication of an ancestral gene in the progenote. A further duplication of the entire CPS gene occurred after the divergence of the plants and before the divergence of the fungi from the eukaryotec root, generating the two isoenzymes involved in either the synthesis of arginine or that of pyrimidines. The mutation rate was found to be five- to tenfold higher after the duplication than before, probably reflecting optimization of the enzymes for their newly acquired specialized function. We hypothesize that this duplication arose from a need for metabolic channeling for pyrimidine biosynthesis as it was accompanied by the tagging of the CPS gene with the genes for dihydroorotase and aspartate transcarbamoylase, and as the duplication occurred independently also in gram-positive bacteria. Analysis of the exon-intron organization of the two “kinase” subdomains in CPS I and II suggests that ancient exons may have comprised approx. 19 amino acids, in accordance with the prediction of the “intron-early” theory.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173161
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  • 94
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    Molecular evolution of genes encoding ribonucleases in ruminant species (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 850-858 
    Details
    ISSN: 1432-1432
    Keywords: Ribonuclease ; Gene duplication ; Evolution ; Ruminants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic analysis, based on the primary structures of mammalian pancreatic-type ribonucleases, indicated that gene duplication events, which occurred during the evolution of ancestral ruminants, gave rise to the three paralogous enzymes present in the bovine species. Herein we report data that demonstrate the existence of the orthologues of the bovine pancreatic, seminal, and cerebral ribonucleases coding sequences in the genomes of giraffe and sheep. The “seminal” sequence is a pseudogene in both species. We also report an analysis of the transcriptional expression of ribonuclease genes in sheep tissues. The data presented support a model for positive selection acting on the molecular evolution of ruminant ribonuclease genes.
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    URL: http://dx.doi.org/10.1007/BF00173164
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  • 95
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    Evolution of disintegrin cysteine-rich and mammalian matrix-degrading metalloproteinases: Gene duplication and divergence of a common ancestor rather than convergent evolution (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 263-269 
    Details
    ISSN: 1432-1432
    Keywords: Metalloproteinase ; Disintegrin ; Evolution ; Venom ; Phylogeny ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolution of the Metalloproteinase Disintegrin Cysteine-rich (MDC) gene family and that of the mammalian Matrix-degrading Metalloproteinases (MMPs) are compared. The alignment of snake venom and mammalian MDC and MMP precursor sequences generated a phylogenetic tree that grouped these proteins mainly according to their function. Based on this observation, a common ancestry is suggested for mammalian and snake venom MDCs; it is also possible that gene duplication of the already-assembled domain structure, followed by divergence of the copies, may have significantly contributed to the evolution of the functionally diverse MDC proteins. The data also suggest that the structural resemblance of the zinc-binding motif of venom MDCs and MMPs may best be explained by common ancestry and conservation of the proteolytic motifs during the divergence of the proteins rather than through convergent evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02338834
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  • 96
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    The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 293-303 
    Details
    ISSN: 1432-1432
    Keywords: Krebs cycle ; Evolution ; Metabolism ; Citric acid cycle ; Chemical design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into asingle-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02338838
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  • 97
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    Prokaryotic and eukaryotic pyridoxal-dependent decarboxylases are homologous (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 325-329 
    Details
    ISSN: 1432-1432
    Keywords: PLP-dependent decarboxylase ; Evolution ; Profile analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A database search has revealed significant and extensive sequence similarities among prokaryotic and eukaryotic pyridoxal phosphate (PLP)-dependent decarboxylases, includingDrosophila glutamic acid decarboxylase (GAD) and bacterial histidine decarboxylase (HDC). Based on these findings, the sequences of seven PLP-dependent decarboxylases from five different organisms have been aligned to derive a consensus sequence for this family of enzymes. In addition, quantitative methods have been employed to calculate the relative evolutionary distances between pairs of the decarboxylases comprising this family. The multiple sequence analysis together with the quantitative results strongly suggest an ancient and common origin for all PLP-dependent decarboxylases. This analysis also indicates that prokaryotic and eukaryotic HDC activities evolved independently. Finally, a sensitive search algorithm (PROFILE) was unable to detect additional members of this decarboxylase family in protein sequence databases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101126
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    Molecular characteristics of the heterochromatic I elements from a reactive strain ofDrosophila melanogaster (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 424-431 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila melanogaster ; Evolution ; Hybrid dysgenesis ; I elements ; Transposons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary There are two categories of strains inDrosophila melanogaster with respect to the I-R system of hybrid dysgenesis. The inducer strains contain particular transposable elements named I factors. They are not present in the strains of the other category called reactive (R) strains. Defective I elements are present in the pericentromeric regions of both categories of strains. This last subfamily of I sequences has not yet been described in detail and little is known about its origin. In this paper, we report that the defective I elements display an average of 94% of sequence identity with each other and with the transposable I factor. The results suggest that they cannot be the progenitors of the present day I factors, but that each of these two subfamilies started to evolve independently several million years ago. Furthermore, the sequence comparison of these I elements with an active I factor fromDrosophila teissieri provides useful information about when the deleted I elements became immobilized.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02106056
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  • 99
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    Regulatory DNA sequence conserved in the course of BK virus evolution (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 485-492 
    Details
    ISSN: 1432-1432
    Keywords: BK virus ; Strains ; Regulatory region ; Late region ; Nucleotide sequence ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Within the genome of human polyomavirus BK (BKV), there exists a noncoding regulatory region toward the late region side of the origin of DNA replication. In most BKV strains isolated by viral culture, this regulatory region contains tandem repeats varying in size. Recently. however, several laboratories isolated new BKV strains (designated as archetypal strains) lacking such repeat sequences. To examine the genetic relationship between archetypal strains, a phylogenetic tree was constructed for seven BKV strains, including three archetypal strains, from DNA sequence data on the late genes, those for leader protein (agnoprotein), and those for structural proteins (VP1, VP2, and VP3). For three strains data previously reported were used, whereas for the others sequences were determined in this study. From total numbers of nucleotide substitutions in each pair of strains, a phylogenetic tree was constructed by the unweighted pair-group method. The phylogenetic tree obtained reveals that BKV strains containing the archetypal regulatory region do not constitute a cluster of closely related strains and that these strains, together with those carrying the major part of the archetypal regulatory region, are widespread in the BKV population. This finding suggests that the basic structure of the archetypal regulatory region has been conserved in the course of BKV evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02102075
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  • 100
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    Molecular evolution of the HSP70 multigene family (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 1-17 
    Details
    ISSN: 1432-1432
    Keywords: HSP70 ; Heat shock ; Evolution ; Phylogeny ; Yeast ; Multigene family ; Subcellular compartmentalization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Eukaryotic genomes encode multiple 70-kDa heat-shock proteins (HSP70s). The Saccharomyces cerevisiae HSP70 family is comprised of eight members. Here we present the nucleotide sequence of the SSA3 and SSB2 genes, completing the nucleotide sequence data for the yeast HSP70 family. We have analyzed these yeast sequences as well as 29 HSP70s from 24 additional eukaryotic and prokaryotic species. Comparison of the sequences demonstrates the extreme conservation of HSP70s; proteins from the most distantly related species share at least 45% identity and more than one-sixth of the amino acids are identical in the aligned region (567 amino acids) among all proteins analyzed. Phylogenetic trees constructed by two independent methods indicate that ancient molecular and cellular events have given rise to at least four monophyletic groups of eukaryotic HSP70 proteins. Each group of evolutionarily similar HSP70s shares a common intracellular localization and is presumed to be comprised of functional homologues; these include heat-shock proteins of the cytoplasm, endoplasmic reticulum, mitochondria, and chloroplasts. HSP70s localized in mitochondria and plastids are most similar to the DnaK HSP70 homologues in purple bacteria and cyanobacteria, respectively, which is consistent with the proposed prokaryotic origin of these organelles. The analyses indicate that the major eukaryotic HSP70 groups arose prior to the divergence of the earliest eukaryotes, roughly 2 billion years ago. In some cases, as exemplified by the SSA genes encoding the cytoplasmic HSP70s of S. cerevisiae, more recent duplication events have given rise to subfamilies within the major groups. The S. cerevisiae SSB proteins comprise a unique subfamily not identified in other species to date. This subfamily appears to have resulted from an ancient gene duplication that occurred at approximately the same time as the origin of the major eukaryotic HSP70 groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00175490
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