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  • Articles  (42)
  • Phylogeny  (42)
  • Springer  (42)
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  • Articles  (42)
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  • 1995-1999  (42)
  • 1990-1994
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  • 1
    Electronic Resource
    Electronic Resource
    The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 1105-1123 
    Details
    ISSN: 1432-1432
    Keywords: RecA ; Small-subunit rRNA ; Bacteria ; Molecular evolution ; Molecular systematics ; Congruence ; Protein ; Phylogeny ; Gram-positive ; Proteobacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolution of the RecA protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete RecA proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The RecA trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the α, β, γ, δ, ε proteobacteria, cyanobacteria, high-GC gram-positives, and the Deinococcus-Thermus group. However, there are interesting differences between the RecA trees and these other trees. For example, in all the RecA trees the proteins from gram-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the RecA analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make RecA useful for molecular systematics and for studies of protein evolution are also discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173192
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  • 2
    Electronic Resource
    Electronic Resource
    Phylogeny of African monkeys based upon mitochondrial 12S rRNA sequences (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 173-180 
    Details
    ISSN: 1432-1432
    Keywords: African monkeys ; mtDNA ; 12S rRNA gene ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The suborder Anthropoidea of the primates has traditionally been divided in three superfamilies: the Hominoidea (apes and humans) and the Cercopithecoidea (Old World monkeys), together comprising the infraorder Catarrhini, and the Ceboidea (New World monkeys) belonging to the infraorder Platyrrhini. We have sequenced an approximately 390-base-pair part of the mitochondrial 12S rRNA gene for 26 species of the major groups of African monkeys and apes and constructed an extensive phylogeny based upon DNA evidence. Not only is this phylogeny of great importance in classification of African guenons, but it also suggests rearrangements in traditional monkey taxonomy and evolution. Baboons and mandrills were found to be not directly related, while we could confirm that the known four superspecies of mangabeys do not form a monophyletic group, but should be separated into two genera, one clustering with baboons and the other with mandrills. Patas monkeys are clearly related to members of the genus Cercopithecus despite their divergence in build and habitat, while the talapoin falls outside the Cercopithecus clade (including the patas monkey).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00167111
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  • 3
    Electronic Resource
    Electronic Resource
    The evolutionary relationships of two families of cottoid fishes of Lake Baikal (East Siberia) as suggested by analysis of mitochondrial DNA (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 392-399 
    Details
    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Sequencing ; Phylogeny ; Cottoid fishes ; Baikal
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Fragments of mtDNA genes Cyt B, ATPase 6, and ATPase 8 of six cottoid fishes species of Lake Baikal (East Siberia) were amplified and sequenced. In addition mtDNAs of the same fish were subjected to restriction analysis. The data obtained were used to construct phylogenetic trees. The topology of the ATPase tree differs from those of the Res (restriction) and Cyt B trees. Clustering of species within the trees confirms the viewpoint of Taliev (1955, Baicalian Sculpins (Cottoidei)) according to which Baikalian cottoids originate from two ancestral forms. The times of branching obtained do not confirm the existing viewpoint according to which the two golomyankas (Comephorus baicalensis and Comephorus dybowskii) are pre-Baikal (Myocene) relicts: these two species may have originated 1.2–1.8 million years ago in Baikal, and they seem to represent an example of rapid morphological evolution which resulted in the formation of a new family.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00164025
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  • 4
    Electronic Resource
    Electronic Resource
    The molecular cloning of a phospholipase A2 from Bothrops jararacussu snake venom: Evolution of venom group II phospholipase A2's may imply gene duplications (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 174-179 
    Details
    ISSN: 1432-1432
    Keywords: Snake venom ; Bothrops ; Phospholipase ; Myotoxin ; Evolution ; cDNA ; Gene duplication ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The sequence coding for a snake venom phospholipase A2 (PLA2), BJUPLA2, has been cloned from a Bothrops jararacussu venom gland cDNA library. The cDNA sequence predicts a precursor containing a 16-residue signal peptide followed by a molecule of 122 amino acid residues with a strong sequence similarity to group II snake venom PLA2's. A striking feature of the cDNA is the high sequence conservation of the 5′ and 3′ untranslated regions in cDNAs coding for PLA2's from a number of viper species. The greatest sequence variation was observed between the regions coding for the mature proteins, with most substitutions occurring in nonsynonymous sites. The phylogenetic tree constructed by alignment of the amino acid sequence of BJUPLA2 with group II PLA2's in general groups them according to current taxonomical divisions and/or functional activity. It also suggests that gene duplications may have occurred at a number of different points during the evolution of snake venom group II PLA2's.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00170670
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  • 5
    Electronic Resource
    Electronic Resource
    Gorilla and orangutan c-myc nucleotide sequences: Inference on hominoid phylogeny (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 262-276 
    Details
    ISSN: 1432-1432
    Keywords: DNA sequencing ; c-myc ; Primates ; Phylogeny ; Gorilla ; Orangutan
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The nucleotide sequences of the gorilla and orangutan mycloci have been determined by the dideoxy nucleotide method. As previously observed in the human and chimpanzee sequences, an open reading frame (ORF) of 188 codons overlapping exon 1 could be deduced from the gorilla sequence. However, no such ORF appeared in the orangutan sequence. The two sequences were aligned with those of human and chimpanzee as hominoids and of gibbon and marmoset as outgroups of hominoids. The branching order in the evolution of primates was inferred from these data by different methods: maximum parsimony and neighborjoining. Our results support the view that the gorilla lineage branched off before the human and chimpanzee diverged and strengthen the hypothesis that chimpanzee and gorilla are more related to human than is orangutan.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01215173
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  • 6
    Electronic Resource
    Electronic Resource
    Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: Phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 803-812 
    Details
    ISSN: 1432-1432
    Keywords: Bacterial rooting ; Hyperthermophily ; Elongation factors ; Phylogeny ; pdxJ gene ; Cyanobacteria-chloroplasts ; Streptomycin operon ; Codon position inequality
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The gene fus (for EF-G) of the hyperthermophilic bacterium Aquifex pyrophilus was cloned and sequenced. Unlike the other bacteria, which display the streptomycin-operon arrangement of EF genes (5′-rps12-rps7 fus-tuf-3′), the Aquifex fus gene (700 codons) is not preceded by the two small ribosomal subunit genes although it is still followed by a tuf gene (for EF-Tu). The opposite strand upstream from the EF-G coding locus revealed an open reading frame (ORF) encoding a polypeptide having 52.5% identity with an E. coli protein (the pdxJ gene product) involved in pyridoxine condensation. The Aquifex EF-G was aligned with available homologs representative of Deinococci, high G + C Gram positives, Proteobacteria, cyanobacteria, and several Archaea. Outgroup-rooted phylogenies were constructed from both the amino acid and the DNA sequences using first and second codon positions in the alignments except sites containing synonymous changes. Both datasets and alternative tree-making methods gave a consistent topology, with Aquifex and Thermotoga maritima (a hyperthermophile) as the first and the second deepest offshoots, respectively. However, the robustness of the inferred phylogenies is not impressive. The branching of Aquifex more deeply than Thennotoga and the branching of Thermotoga more deeply than the other taxa examined are given at bootstrap values between 65 and 70% in the fus-based phylogenies, while the EF-G(2)-based phylogenies do not provide a statistically significant level of support (⩽ 50% bootstrap confirmation) for the emergence of Thermotoga between Aquifex and the successive offshoot (Thermus genus). At present, therefore, the placement of Aquifex at the root of the bacterial tree, albeit reproducible, can be asserted only with reservation, while the emergence of Thermotoga between the Aquificales and the Deinococci remains (statistically) indeterminate.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173160
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  • 7
    Electronic Resource
    Electronic Resource
    The Giardia lamblia actin gene and the phylogeny of eukaryotes (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 841-849 
    Details
    ISSN: 1432-1432
    Keywords: Actin genes ; Giardia lamblia ; GC-content ; Phylogeny ; Slime molds ; Relative rate test
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The single-copy actin gene of Giardia lamblia lacks introns; it has an average of 58% amino acid identity with the actin of other species; and 49 of its amino acids can be aligned with the amino acids of a consensus sequence of heat shock protein 70. Analysis of the potential RNA secondary structure in the transcribed region of the G. lamblia actin gene and of the single-copy actin gene of nine other species did not reveal any conserved structures. The G. lamblia actin sequence was used to root the phylogenetic trees based on 65 actin protein sequences from 43 species. This tree is congruent with small-subunit rRNA trees in that it shows that oomycetes are not related to higher fungi; that kinetoplatid protozoans, green plants, fungi and animals are monophyletic groups; and that the animal and fungal lineages share a more recent common ancestor than either does with the plant lineage. In contrast to smalls-ubunit rRNA trees, this tree shows that slime molds diverged after the plant lineage. The slower rate of evolution of actin genes of slime molds relative to those of plants, fungi, and animals species might be responsible for this incongruent branching.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173163
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  • 8
    Electronic Resource
    Electronic Resource
    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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  • 9
    Electronic Resource
    Electronic Resource
    Molecular evolution of the hepatitis B virus genome (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 587-596 
    Details
    ISSN: 1432-1432
    Keywords: Nucleotide substitution ; Models ; Maximum likelihood ; Rate heterogeneity at sites ; Phylogeny ; Molecular clock ; Hepatitis B virus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The hepatitis B virus (HBV) has a circular DNA genome of about 3,200 base pairs. Economical use of the genome with overlapping reading frames may have led to severe constraints on nucleotide substitutions along the genome and to highly variable rates of substitution among nucleotide sites. Nucleotide sequences from 13 complete HBV genomes were compared to examine such variability of substitution rates among sites and to examine the phylogenetic relationships among the HBV variants. The maximum likelihood method was employed to fit models of DNA sequence evolution that can account for the complexity of the pattern of nucleotide substitution. Comparison of the models suggests that the rates of substitution are different in different genes and codon positions; for example, the third codon position changes at a rate over ten times higher than the second position. Furthermore, substantial variation of substitution rates was detected even after the effects of genes and codon positions were corrected; that is, rates are different at different sites of the same gene or at the same codon position. Such rates after the correction were also found to be positively correlated at adjacent sites, which indicated the existence of conserved and variable domains in the proteins encoded by the viral genome. A multiparameter model validates the earlier finding that the variation in nucleotide conservation is not random around the HBV genome. The test for the existence of a molecular clock suggests that substitution rates are more or less constant among lineages. The phylogenetic relationships among the viral variants were examined. Although the data do not seem to contain sufficient information to resolve the details of the phylogeny, it appears quite certain that the serotypes of the viral variants do not reflect their genetic relatedness.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00175817
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  • 10
    Electronic Resource
    Electronic Resource
    Phylogenetic Analysis of the Aminoacyl-tRNA synthetases (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 487-498 
    Details
    ISSN: 1432-1432
    Keywords: Aminoacyl-tRNA synthetases ; Phylogeny ; Evolution of protein translation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Numerous aminoacyl-tRNA synthetase sequences have been aligned by computer and phylogenetic trees constructed from them for the two classes of these enzymes. Branching orders based on a consensus of these trees have been proposed for the two groups. Although the order of appearance can be rationalized to fit many different scenarios having to do with the genetic code, the invention of a system for translating nucleic acid sequences into polypeptide chains must have predated the existence of these proteins. In the past, a variety of schemes has been proposed for matching amino acids and tRNAs. Most of these have invoked direct recognition of one by the other, whether or not the anticodon was involved. Often ignored is the possibility of a nonprotein (presumably RNA) matchmaker for bringing the two into conjunction. If such had been the case, then the contemporary aminoacyl-tRNA synthetases could have entered the system gradually, each specific type replacing its matchmaking RNA counterpart in turn. A simple displacement scheme of this sort accommodates the existence of two different families of these enzymes, the second being introduced well before the first had undergone sufficient genetic duplications to specify the full gamut of amino acids. Such a scheme is also consistent with similar amino acids often, but not always, being the substrates of enzymes with the most similar amino acid sequences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00166617
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  • 11
    Electronic Resource
    Electronic Resource
    Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 689-697 
    Details
    ISSN: 1432-1432
    Keywords: Phylogeny ; Maximum likelihood ; Least squares ; Consistency ; Sampling error ; Rate variation at sites ; Gamma distribution ; Computer simulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Several maximum likelihood and distance matrix methods for estimating phylogenetic trees from homologous DNA sequences were compared when substitution rates at sites were assumed to follow a gamma distribution. Computer simulations were performed to estimate the probabilities that various tree estimation methods recover the true tree topology. The case of four species was considered, and a few combinations of parameters were examined. Attention was applied to discriminating among different sources of error in tree reconstruction, i.e., the inconsistency of the tree estimation method, the sampling error in the estimated tree due to limited sequence length, and the sampling error in the estimated probability due to the number of simulations being limited. Compared to the least squares method based on pairwise distance estimates, the joint likelihood analysis is found to be more robust when rate variation over sites is present but ignored and an assumption is thus violated. With limited data, the likelihood method has a much higher probability of recovering the true tree and is therefore more efficient than the least squares method. The concept of statistical consistency of a tree estimation method and its implications were explored, and it is suggested that, while the efficiency (or sampling error) of a tree estimation method is a very important property, statistical consistency of the method over a wide range of, if not all, parameter values is prerequisite.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160518
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  • 12
    Electronic Resource
    Electronic Resource
    A method for determining the position and size of optimal sequence regions for phylogenetic analysis (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 1128-1138 
    Details
    ISSN: 1432-1432
    Keywords: Phylogeny ; Neighbor joining method ; Bootstrap ; Optimal size ; Optimal position ; Nonrandom sequence ; Information ; Foot-and-mouth disease virus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173194
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  • 13
    Electronic Resource
    Electronic Resource
    Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: Preliminary report (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 359-365 
    Details
    ISSN: 1432-1432
    Keywords: Gibbons ; Mitochondrial DNA ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We analyzed the 896 base-pair (bp) mitochondrial DNA (mtDNA) sequences for seven gibbons, representative of three out of four subgenera. The result from our molecular analysis is consistent with previous studies as to the monophyly of subgenusHylobates species, yet the relationship among subgenera remains slightly ambiguous. A striking result of the analysis is the phylogenetic location of Kloss's gibbon (H. klossii). Kloss's gibbon has been considered to be an initial off-shoot of the subgenusHylobates because of its morphological primitiveness. However, our molecular data strongly suggest that Kloss's gibbon speciated most recently within the subgenusHylobates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01215183
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  • 14
    Electronic Resource
    Electronic Resource
    Molecular evolution of group II phospholipases A2 (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 867-877 
    Details
    ISSN: 1432-1432
    Keywords: Group II phospholipase A2 ; cDNA ; Phylogeny ; Snake venom ; Accelerated evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The nucleotide sequences of 13 cDNAs encoding group II phospholipases A2 (PLA2 S), which are from viperidae snake venoms and from mammalian sources, were aligned and analyzed by phylogenetic trees constructed using various components of the sequences. The evolutionary trees derived from the combined sequences of the untranslated (5′ and 3′) region and the signal peptide region of cDNAs were in accord with the consequences from taxonomy. In contrast, the evolutionary trees from the mature protein-coding region sequences of cDNAs and from the amino acid sequences showed random patterns. These observations indicated that the mature protein-coding region has evolved through a process differently from the untranslated and signal peptide regions. The trees built from the nucleotide differences at each of three positions of codons in the mature protein-coding region suggested that snakevenom-gland PLA2 genes have evolved via a process different from mammalian PLA2 genes. The occurrence of accelerated evolution has been recently discovered in Trimeresurus flavoviridis venom-gland group II PLA2 isozyme genes (Nakashima et al. 1993, Proc Natl Acad Sci USA 90:5964–5968), so the present phylogenetic analysis together with the estimation of nucleotide divergence of cDNAs provides further evidence that snakevenom-group II PLA2 isozyme genes have evolved by accelerated evolution to gain diverse physiological activities.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173166
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  • 15
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    Revised dinoflagellate phylogeny inferred from molecular analysis of large-subunit ribosomal RNA gene sequences (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 637-645 
    Details
    ISSN: 1432-1432
    Keywords: Dinoflagellate ; Phylogeny ; Large-subunit rRNA ; PCR ; Alexandrium spp ; Prorocentrum spp ; Gymnodinium spp
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The nucleotide sequence analysis of the PCR products corresponding to the variable large-subunit rRNA domains D1, D2, D9, and D10 from ten representative dinoflagellate species is reported. Species were selected among the main laboratory-grown dinoflagellate groups: Prorocentrales, Gymnodiniales, and Peridiniales which comprise a variety of morphological and ecological characteristics. The sequence alignments comprising up to 1,000 nucleotides from all ten species were employed to analyze the phylogenetic relationships among these dinoflagellates. Maximum parsimony and neighbor joining trees were inferred from the data generated and subsequently tested by bootstrapping. Both the D1/D2 and the D9/D10 regions led to coherent trees in which the main class of dinoflagellates, Dinophyceae, is divided in three groups: prorocentroid, gymnodinioid, and peridinioid. An interesting outcome from the molecular phylogeny obtained was the uncertain emergence of Prorocentrum lima. The molecular results reported agreed with morphological classifications within Peridiniales but not with those of Prorocentrales and Gymnodiniales. Additionally, the sequence comparison analysis provided strong evidence to suggest that Alexandrium minutum and Alexandrium lusitanicum were synonymous species given the identical sequence they shared. Moreover, clone Gg1V, which was determined Gymnodinium catenatum based on morphological criteria, would correspond to a new species of the genus Gymnodinium as its sequence clearly differed from that obtained in G. catenatum. The sequence of the amplified fragments was demonstrated to be a valuable tool for phylogenetic and taxonomical analysis among these highly diversified species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00175822
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  • 16
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    Molecular phylogeny of Allomyces macrogynus: Congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 657-665 
    Details
    ISSN: 1432-1432
    Keywords: Ribosomal RNA ; Protein ; Phylogeny ; Mitochondria ; Nuclear ; Lower fungi
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have sequenced the nuclear and mitochondrial small subunit rRNA genes (rns) and the mitochondrial genes coding for subunits 1 and 3 of the cytochrome oxidase (cox1 and cox3, respectively) of the chytridiomycete Allomyces macrogynus. Phylogenetic trees inferred from the derived COX1 and COX3 proteins and the nuclear rns sequences show with good bootstrap support that A. macrogynus is an early diverging fungus. The trees inferred from mitochondrial rns sequences do not yield a topology that is supported by bootstrap analysis. The similarity and the relative robustness of the nuclear rns and the mitochondrial protein-derived phylogenetic trees suggest that protein sequences are of higher value than rRNA sequences for reconstructing mitochondrial evolution. In addition, our trees support a monophyletic origin of mitochondria for the range of analyzed eukaryotes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00175824
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  • 17
    Electronic Resource
    Electronic Resource
    Evolutionary analysis of the picornavirus family (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 362-371 
    Details
    ISSN: 1432-1432
    Keywords: Picornavirus ; Phylogeny ; Neighborjoining method ; Least-squares method ; Bootstrap ; Variance of branch length ; Statistical geometry in distance space ; Split decomposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An exhaustive evolutionary analysis of the picornavirus family has been carried out using the amino acid sequences of several proteins of the viruses including: the capsid proteins (1D, 1B, and 1C) situated at the 5′ end of the genome and responsible for the serotype of the viruses, and the viral polymerase (3D), located at the 3′ end of the genome. The evolutionary relationships found among the viruses studied support the new classification, recently suggested, in contrast to the classical one, and the existence of a new genus for the picornavirus family. In the new taxonomic organization, five genera form the picornavirus family: (1) aphthoviruses, (2) cardioviruses, (3) hepatoviruses (previously classified as enteroviruses), (4) renteroviruses (which mainly constitute a combination of the previous genera rhinovirus and enterovirus), and (5) a new genus, with a new and unique representative: the echovirus 22. Our analysis also allowed us, for the first time, to propose the most probable sequence of speciation events to have given rise to the current picornavirus family. The bootstrap procedure was used to check the reliability of the phylogenetic trees obtained. The application of the method of the statistical geometry in distance space to internal branches of the tree revealed a high degree of evolutionary “noise,” which makes the resolution of some internal branching points difficult.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00164022
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    Evolution of the fibropellin gene family and patterns of fibropellin gene expression in sea urchin phylogeny (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 34-45 
    Details
    ISSN: 1432-1432
    Keywords: Sea urchins ; Phylogeny ; Fibropellins ; Gene evolution ; Evolution of direct development
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This study documents evolutionary modifications in the expression patterns of the sea urchin EGF I and EGF III genes, which encode a family of extracellular matrix proteins, the fibropellins. We show that the sea urchin apical lamina, a macromolecular extracellular matrix that surrounds the sea urchin embryo and is made up of the fibropellins, has been conserved through at least 250 million years of echinoid evolution. The contribution of different fibropellin family members to this structure has, however, changed over the course of sea urchin phylogeny, and between two congeneric species that exhibit different developmental modes. Mapping the evolutionary history of the EGF genes on a cladogram of relationships among sea urchins reveals that EGF I is present in all echinoids examined, while EGF III appears to have arisen by duplication and divergence from EGF I during the radiation of a suborder of the camarodont sea urchins some 35–45 million years ago. Alterations in the temporal expression patterns of these genes as well as the loss of one of the two EGF I transcripts and encoded protein are coincident with the evolution of a direct-developing larval form in Heliocidaris erythrogramma. H. erythrogramma and its congener Heliocidaris tuberculata, which develops via a typical echinopluteus larva, shared a common ancestor about 10 million years ago. The differences in fibropellin representation within the apical lamina of the various taxa indicate that a homologous embryonic structure can undergo substantial changes in composition during its evolutionary history.
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    URL: http://dx.doi.org/10.1007/BF00174039
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    The origin of land plants: Phylogenetic relationships among charophytes, bryophytes, and vascular plants inferred from complete small-subunit ribosomal RNA gene sequences (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 74-84 
    Details
    ISSN: 1432-1432
    Keywords: 18S rRNA ; Sequence analysis ; Phylogeny ; Molecular clock ; Chlorophyceae ; Charophyceae ; Prasinophyceae ; Bryophyta ; Selaginella
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Complete nuclear-encoded small-subunit 18S rRNA (=SSU rRNA) gene sequences were determined for the prasinophyte green alga Mantoniella squamata; the charophycean green algae Chara foetida, Coleochaete scutata, Klebsormidium flaccidum, and Mougeotia scalaris; the bryophytes Marchantia polymorpha, Fossombronia pusilla, and Funaria hygrometrica; and the lycopod Selaginella galleottii to get a better insight into the sequential evolution from green algae to land plants. The sequences were aligned with several previously published SSU rRNA sequences from chlorophytic and charophytic algae as well as from land plants to infer the evolutionary relationships for major evolutionary lineages within the Chlorobionta by distance matrix, maximum parsimony, and maximum likelihood analyses. Phylogenetic trees created by the different methods consistently placed the Charophyceae on the branch leading to the land plants. The Charophyceae were shown to be polyphyletic with the Charales (“charalean” algae) diverging earlier than the Coleochaetales, Klebsormidiales, Chlorokybales, and Zygnematales (“charophycean” algae) which branch from a point closer to the land plants in most analyses. Maximum parsimony and maximum likelihood analyses imply a successive evolution from “charophycean” algae, particularly Coleochaetales, to bryophytes, lycopods, and seed plants. In contrast, distance matrix methods group the bryophytes together with the “charophycean” algae, suggesting a separate evolution of these organisms compared with the club moss and the seed plants.
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    URL: http://dx.doi.org/10.1007/BF00174043
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    Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 203-210 
    Details
    ISSN: 1432-1432
    Keywords: Cyanelles ; Cyanophora paradoxa ; Endosymbiosis ; Evolution ; Glaucocystophyta ; Glaucophyta ; Phylogeny ; Plastid ; 16S ribosomal RNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glaucocystophyte algae (sensu Kies, Berl. Deutsch. Bot. Ges. 92, 1979) contain plastids (cyanelles) that retain the peptidoglycan wall of the putative cyanobacterial endosymbiont; this and other ultrastructural characters (e.g., unstacked thylakoids, phycobilisomes) have suggested that cyanelles are “primitive” plastids that may represent undeveloped associations between heterotrophic “host” cells (i.e., glaucocystophytes) and cyanobacteria. To test the monophyly of glaucocystophyte cyanelles and to determine their evolutionary relationship to other plastids, complete 16S ribosomal RNA sequences were determined for Cyanophora paradoxa, Glaucocystis nostochinearum, Glaucosphaera vacuolata, and Gloeochaete wittrockiana. Plastid rRNAs were analyzed with the maximum-likelihood, maximumparsimony, and neighbor joining methods. The phylogenetic analyses show that the cyanelles of C. paradoxa, G. nostochinearum, and G. wittrockiana form a distinct evolutionary lineage; these cyanelles presumably share a monophyletic origin. The rDNA sequence of G. vacuolata was positioned within the nongreen plastid lineage. This result is consistent with analyses of nuclear-encoded rRNAs that identify G. vacuolata as a rhodophyte and support its removal from the Glaucocystophyta. Results of a global search with the maximumlikelihood method suggest that cyanelles are the first divergence among all plastids; this result is consistent with a single loss of the peptidoglycan wall in plastids after the divergence of the cyanelles. User-defined tree analyses with the maximum-likelihood method indicate, however, that the position of the cyanelles is not stable within the rRNA phylogenies. Both maximumparsimony and neighbor-joining analyses showed a close evolutionary relationship between cyanelles and nongreen plastids; these phylogenetic methods were sensitive to inclusion/exclusion of the G. wittrockiana cyanelle sequence. Base compositional bias within the G. wittrockiana 16S rRNA may explain this result. Taken together the phylogenetic analyses are interpreted as supporting a near-simultaneous radiation of cyanelles and green and nongreen plastids; these organelles are all rooted within the cyanobacteria.
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    URL: http://dx.doi.org/10.1007/BF00170674
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    Gorilla and orangutan c-myc nucleotide sequences: Inference on hominoid phylogeny (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 262-276 
    Details
    ISSN: 1432-1432
    Keywords: DNA sequencing ; c-myc ; Primates ; Phylogeny ; Gorilla ; Orangutan
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The nucleotide sequences of the gorilla and orangutan myc loci have been determined by the dideoxy nucleotide method. As previously observed in the human and chimpanzee sequences, an open reading frame (ORF) of 188 codons overlapping exon 1 could be deduced from the gorilla sequence. However, no such ORF appeared in the orangutan sequence. The two sequences were aligned with those of human and chimpanzee as hominoids and of gibbon and marmoset as outgroups of hominoids. The branching order in the evolution of primates was inferred from these data by different methods: maximum parsimony and neighborjoining. Our results support the view that the gorilla lineage branched off before the human and chimpanzee diverged and strengthen the hypothesis that chimpanzee and gorilla are more related to human than is orangutan.
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    URL: http://dx.doi.org/10.1007/BF00186538
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    Evidence on primate phylogeny from ε-globin gene sequences and flanking regions (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 30-55 
    Details
    ISSN: 1432-1432
    Keywords: Primates ; Strepsirhines ; Aye-aye ; Lemurs ; Phylogeny ; ε-globin gene ; Molecular evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic relationships among various primate groups were examined based on sequences of ε-globin genes. ε-globin genes were sequenced from five species of strepsirhine primates. These sequences were aligned and compared with other known primate ε-globin sequences, including data from two additional strepsirhine species, one species of tarsier, 19 species of New World monkeys (representing all extant genera), and five species of catarrhines. In addition, a 2-kb segment upstream of the ε-globin gene was sequenced in two of the five strepsirhines examined. This upstream sequence was aligned with five other species of primates for which data are available in this segment. Domestic rabbit and goat were used as outgroups. This analysis supports the monophyly of order Primates but does not support the traditional prosimian grouping of tarsiers, lorisoids, and lemuroids; rather it supports the sister grouping of tarsiers and anthropoids into Haplorhini and the sister grouping of lorisoids and lemuroids into Strepsirhini. The mouse lemur (Microcebus murinus) and dwarf lemur (Cheirogaleus medius) appear to be most closely related to each other, forming a clade with the lemuroids, and are probably not closely related to the lorisoids, as suggested by some morphological studies. Analysis of the ε-globin data supports the hypothesis that the aye-aye (Daubentonia madagascariensis) shares a sister-group relationship with other Malagasy strepsirhines (all being classified as lemuroids). Relationships among ceboids agree with findings from a previous ε-globin study in which fewer outgroup taxa were employed. Rates of molecular evolution were higher in lorisoids than in lemuroids.
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    Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: Preliminary report (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 359-365 
    Details
    ISSN: 1432-1432
    Keywords: Gibbons ; Mitochondrial DNA ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We analyzed the 896 base-pair (bp) mitochondrial DNA (mtDNA) sequences for seven gibbons, representative of three out of four subgenera. The result from our molecular analysis is consistent with previous studies as to the monophyly of subgenus Hylobates species, yet the relationship among subgenera remains slightly ambiguous. A striking result of the analysis is the phylogenetic location of Kloss's gibbon (H. klossii). Kloss's gibbon has been considered to be an initial off-shoot of the subgenus Hylobates because of its morphological primitiveness. However, our molecular data strongly suggest that Kloss's gibbon speciated most recently within the subgenus Hylobates.
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    URL: http://dx.doi.org/10.1007/BF00186548
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    DNA polymerase δ of Physarum polycephalum (1995)
    Springer
    Current genetics 28 (1995), S. 534-545 
    Details
    ISSN: 1432-0983
    Keywords: DNA polymerase δ ; PCNA ; Phylogeny ; Physarum polycephalum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract DNA polymerase δ from the phylogenetically ancient slime mold Physarum polycephalum has been 380-fold enriched from amoebae. It was found to have the properties typical for this type of DNA polymerase from higher eukaryotes with regard to effectors, template-primer acceptance, co-purification with 3′–5′-exonuclease activity, as well as the effect of endogenous proliferating cell nuclear antigen (PCNA) from amoebae on the stimulation and processivity of DNA synthesis. An identified cDNA fragment shows 65.5% identical amino acides with DNA polymerase δ from Saccharomyces pombe. The molecular mass of the polymerase is 125 kDa while that of PCNA is 35 kDa. During size-exclusion chromatography, the highly purified polymerase eluted in the position of 125 kDa, suggesting that no other proteins were tightly complexed with the enzyme. The DNA polymerases from the (mononucleate) amoebae and from the (multinucleate) plasmodia of P. polycephalum have very similar properties in contrast to their differences in phenotype and their mode of nuclear division. The polymerase shows a higher degree of similarity than DNA polymerase α, and especially the β-like DNA polymerase, with the corresponding polymerases of higher eukaryotes. According to antibody staining, DNA polymerase δ is readily fragmented by proteases, even in the presence of inhibitor cocktails. Including freshly prepared cell lysates, proteolytic fragments are reproducible, the most abundant being 50 kDa in size. The DNA polymerase is recognized by the antisera against two peptides which have been derived by PCR-screening of plasmodial cDNA. One of the proteolytic splitting sites is located within an eight amino-acid stretch between the two antigenic sequences.
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    URL: http://dx.doi.org/10.1007/BF00518166
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    Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria (1995)
    Springer
    Archives of microbiology 163 (1995), S. 96-103 
    Details
    ISSN: 1432-072X
    Keywords: Anaerobic degradation ; Aromatic hydrocarbons ; Alkylbenzenes ; Ethylbenzene ; Crude oil ; Denitrifying bacteria ; Phylogeny ; Thauera selenatis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Anaerobic degradation of alkylbenzenes with side chains longer than that of toluene was studied in freshwater mud samples in the presence of nitrate. Two new denitrifying strains, EbN1 and PbN1, were isolated on ethylbenzene and n-propylbenzene, respectively. For comparison, two further denitrifying strains, ToN1 and mXyN1, were isolated from the same mud with toluene and m-xylene, respectively. Sequencing of 16SrDNA revealed a close relationship of the new isolates to Thauera selenatis. The strains exhibited different specific capacities for degradation of alkylbenzenes. In addition to ethylbenzene, strain EbN1 utilized toluence, but not propylbenzene. In contrast, propylbenzene-degrading strain PbN1 did not grow on toluene, but was able to utilize ethylbenzene. Strain ToN1 used toluene as the only hydrocarbon substrate, whereas strain mXyN1 utilized both toluene and m-xylene. Measurement of the degradation balance demonstrated complete oxidation of ethylbenzene to CO2 by strain EbN1. Further characteristic substrates of strains EbN1 and PbN1 were 1-phenylethanol and acetophenone. In contrast to the other isolates, strain mXyN1 did not grow on benzyl alcohol. Benzyl alcohol (also m-methylbenzyl alcohol) was even a specific inhibitor of toluene and m-xylene utilization by strain mXyN1. None of the strains was able to grow on any of the alkylbenzenes with oxygen as electron acceptor. However, polar aromatic compounds such as benzoate were utilized under both oxic and anoxic conditions. All four isolates grew anaerobically on crude oil. Gas chromatographic analysis of crude oil after growth of strain ToN1 revealed specific depletion of toluene.
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    Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria (1995)
    Springer
    Archives of microbiology 163 (1995), S. 96-103 
    Details
    ISSN: 1432-072X
    Keywords: Key words Anaerobic degradation ; Aromatic ; hydrocarbons ; Alkylbenzenes ; Ethylbenzene ; Crude oil ; Denitrifying bacteria ; Phylogeny ; Thauera selenatis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Anaerobic degradation of alkylbenzenes with side chains longer than that of toluene was studied in freshwater mud samples in the presence of nitrate. Two new denitrifying strains, EbN1 and PbN1, were isolated on ethylbenzene and n-propylbenzene, respectively. For comparison, two further denitrifying strains, ToN1 and mXyN1, were isolated from the same mud with toluene and m-xylene, respectively. Sequencing of 16S rDNA revealed a close relat ionship of the new isolates to Thauera selenatis. The strains exhibited different specific capacities for degradation of alkylbenzenes. In addition to ethylbenzene, strain EbN1 utilized toluene, but not propylbenzene. In contrast, propylbenzene-degrading strain PbN1 did not grow on toluene, but was able to utilize ethylbenzene. Strain ToN1 used toluene as the only hydrocarbon substrate, whereas strain mXyN1 utilized both toluene and m-xylene. Measurement of the degradation balance demonstr ated complete oxidation of ethylbenzene to CO2 by strain EbN1. Further characteristic substrates of strains EbN1 and PbN1 were 1-phenylethanol and acetophenone. In contrast to the other isolates, strain mXyN1 did not grow on benzyl alcohol. Benzyl alcohol (also m-methylbenzyl alcohol) was even a specific inhibitor of toluene and m-xylene utilization by strain mXyN1. None of the strains was able to grow on any of the alkylbenzenes with oxygen as electron acceptor. However, polar aromatic compounds such as benzoate were utilized under both oxic and anoxic conditions. All four isolates grew anaerobically on crude oil. Gas chromatographic analysis of crude oil after growth of strain ToN1 revealed specific depletion of toluene.
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    Heliobacterium modesticaldum, sp. nov., a thermophilic heliobacterium of hot springs and volcanic soils (1995)
    Springer
    Archives of microbiology 163 (1995), S. 259-267 
    Details
    ISSN: 1432-072X
    Keywords: Key words Anoxygenic phototrophic bacteria ; Heliobacteria ; Heliobacterium modesticaldum ; Thermophily ; Hot springs ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Enrichment cultures for heliobacteria at 50°C yielded several strains of a thermophilic heliobacterium species from Yellowstone hot spring microbial mats and volcanic soils from Iceland. The novel organisms grew optimally above 50°C, contained bacteriochlorophyll g, and lacked intracytoplasmic membranes. All isolates were strict anaerobes and grew best as photoheterotrophs, although chemotrophic dark growth on pyruvate was also possible. These thermophilic heliobacteria were diazotrophic and fixed N2 up to their growth temperature limit of 56°C. Phylogenetic studies showed the new isolates to be specific relatives of Heliobacterium gestii and, as has been found in H. gestii, they produce heat-resistant endospores. The unique assemblage of properties found in these thermophilic heliobacteria implicate them as a new species of this group, and we describe them herein as a new species of the genus Heliobacterium, Heliobacterium modesticaldum.
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    Heliobacterium modesticaldum, sp. nov., a thermophilic heliobacterium of hot springs and volcanic soils (1995)
    Springer
    Archives of microbiology 163 (1995), S. 259-267 
    Details
    ISSN: 1432-072X
    Keywords: Anoxygenic phototrophic bacteria ; Heliobacteria ; Heliobacterium modesticaldum ; Thermophily ; Hot springs ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Enrichment cultures for heliobacteria at 50°C yielded several strains of a thermophilic heliobacterium species from Yellowstone hot spring microbial mats and volcanic soils from Iceland. The novel organisms grew optimally above 50°C, contained bacteriochlorophyll g, and lacked intracytoplasmic membranes. All isolates were strict anaerobes and grew best as photoheterotrophs, although chemotrophic dark growth on pyruvate was also possible. These thermophilic heliobacteria were diazotrophic and fixed N2 up to their growth temperature limit of 56°C. Phylogenetic studies showed the new isolates to be specific relatives of Heliobacterium gestii and, as has been found in H. gestii, they produce heat-resistant endospores. The unique assemblage of properties found in these thermophilic heliobacteria implicate them as a new species of this group, and we describe them herein as a new species of the genus Heliobacterium, Heliobacterium modesticaldum.
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    Relationships among cultivated and wild lentils revealed by RAPD analysis (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 647-654 
    Details
    ISSN: 1432-2242
    Keywords: Lens ; RAPD ; Cluster analysis ; Diversity ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RAPD markers were used to distinguish between six different Lens taxa, representing cultivated lentil and its wild relatives. Twenty-four arbitrary sequence 10-mer primers were identified which revealed robust and easily interpretable amplification-product profiles. These generated a total of 88 polymorphic bands in 54 accessions and were used to partition variation within and among Lens taxa. The data showed that, of the taxa examined, ssp. orientalis is most similar to cultivated lentil. L. ervoides was the most divergent wild taxon followed by L. nigricans. The genetic similarity between the latter two species was of the same magnitude as between ssp. orientalis and cultivated lentil. In addition, species-diagnostic amplification products specific to L. odemensis, L. ervoides and L. nigricans were identified. These results correspond well with previous isozyme and RFLP studies. RAPDs, however, appear to provide a greater degree of resolution at a sub-species level. The level of variation detected within cultivated lentils suggests that RAPD markers may be an appropriate technology for the construction of genetic linkage maps between closely related Lens accessions.
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    URL: http://dx.doi.org/10.1007/BF00223292
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    Phylogenetic relationships within Hevea brasiliensis as deduced from a polymorphic mitochondrial DNA region (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 876-884 
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    ISSN: 1432-2242
    Keywords: Hevea brasiliensis ; Mitochondrial DNA ; Phylogeny ; Hypervariable sequence ; Hot spot
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have cloned a 4.5-kb mtDNA fragment showing a high RFLP polymorphism between various Hevea genotypes. Subcloning and sequencing of a 1.4-kb segment of this clone allowed us to design PCR amplification primers to isolate homologous mtDNA segments of about 0.9 kb from 23 representative genotypes of Hevea. Complete sequences from 4 genotypes showed between 6.7% and 20.2% of nucleotide diversity, suggesting the presence of a hypervariable, or hotspot, region. A sequence of 345 nucleotides within this region was determined for the 23 genotypes. The phylogenetic relationships inferred from the sequence comparison are in general agreement with the results obtained from mtDNA RFLP analysis, indicating that this polymorphic mtDNA region is a useful molecular marker for phylogenetic analysis within Hevea.
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    Phylogenetic relationships of cultivated Prunus species from an analysis of chloroplast DNA variation (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 1035-1041 
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    ISSN: 1432-2242
    Keywords: Chloroplast ; Phylogeny ; DNA ; PCR ; Prunus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Chloroplast DNA (cpDNA) restriction-site mutations in seven cultivated Prunus species were compared to establish the phylogenetic relationships among them. Mutations were detected in 3.2-kb and 2.1-kb amplified regions of variable cpDNA, cut with 21 and 10 restriction endonucleases, respectively, to reveal polymorphisms. Parsimony and cluster analyses were performed. The species pairs P. persica-P. dulcis, P. domestica-P. salicina, and P.cerasus-P. fruticosa were completely monophyletic. All of the species were grouped with conventional subgenus classifications. The subgenus Cerasus was the most diverged. Cerasus ancestors separated from the remainder of Prunus relatively early in the development of the genus. P. persica-P. dulcis, P. domestica-P. salicina and P. armeniaca formed a second monophyletic group. Prunophora species were less diverged than Amygdalus species. The results also suggest that the rate of mutation in Cerasus spp. chloroplast genomes is significantly greater than for the other subgenera sampled.
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    Mitochondrial gene variation and phylogenetic relationships in the genus Beta (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 914-919 
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    ISSN: 1432-2242
    Keywords: Sugarbeet ; Beta species ; Mitochondrial gene ; Taxonomy ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Restriction fragment length polymorphisms (RFLPs) for three mitochondrial genes, coxI, coxII and atpA, were used to determine mitochondrial (mt) DNA diversity in 21 accessions of the genus Beta representing wild and cultivated species. On the basis of distribution of the RFLP patterns these Beta genotypes were assigned into six distinct chondriome groups. A high degree of heterogeneity was found to exist between the mitochondrial genomes of the sugarbeet cultivar and the wild species of Procumbentes section. The polymorphic fragments from wild Beta species were cloned and subjected to fine mapping. We found that most of the RFLPs are due to sequence rearrangements rather than point mutations. Our data also suggest that the close linkage between coxII and coxI is taxonomically localized to an evolutionary lineage that led to Vulgares and Corollinae species but not to Procumbentes species. This linkage is most likely to have arisen via the mutation(s) that inserted the DNA segment containing coxI downstream of coxII in the common ancestor of Vulgares and Corollinae species. The results are discussed with regard to the taxonomic and phylogenetic relationships of the Beta species.
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    Genetic variation within and among different cultivars and landraces of Brassica campestris L. and B. oleracea L. based on isozymes (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 346-352 
    Details
    ISSN: 1432-2242
    Keywords: Brassica campestris ; Brassica oleracea ; Isozymes ; Genetic variation ; Heterozygosity ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genetic variation based on isozymes was studied in 43 landraces and cultivars of Brassica campestris from China, 4 cultivars of B. campestris from Sweden and 1 from India, and 5 cultivars of B. oleracea from Sweden and 1 from China (B. alboglabra). A total of 17 isozyme loci was studied, 10 of these were polymorphic in B. campestris and 6 were polymorphic in B. oleracea. The level of heterozygosity seemed to be reduced in the Swedish cultivars compared to the Chinese landraces and cultivars of B. campestris. The level of heterozygosity in B. oleracea was even lower than that in the Swedish cultivars of B. campestris. A phylogeny of the cultivars and landraces of B. campestris showed that the B. campestris var ‘yellow sarson’ cultivar, originating from India, deviated significantly from the other cultivars of B. campestris. A phylogeny of the cultivars of B. oleracea confirmed the expectations that the cultivar B. alboglabra was not closely related to the cultivated forms of B. oleracea.
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    Inheritance of isozymes in Brassica campestris L. and genetic divergence among different species of Brassiceae (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 353-360 
    Details
    ISSN: 1432-2242
    Keywords: Brassica species ; Sinapis species ; Isozymes ; Inheritance ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Electrophoretic investigations of Brassica campestris revealed 8 polymorphic loci that had not been described earlier. The inheritance of 7 of them was determined by crosses between different accessions of B. campestris. A phylogeny of B. campestris, B. nigra, B. alboglabra, Sinapis arvensis and S. alba was estimated from the analysis of 15 isozyme loci. The phylogeny showed a close relationship between B. nigra and S. arvensis and a less close relationship between B. campestris and B. oleracea. S. alba was remotely-related to all of the other species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220899
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    A single nuclear locus phylogeny of soybean based on DNA sequence (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 991-999 
    Details
    ISSN: 1432-2242
    Keywords: Glycininae ; Soybean ; Phylogeny ; DNA sequence ; Genomic donors ; Glycine ; Phaseoleae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Soybean [Glycine max (L.) Merr.] evolution was examined by sequencing portions of the restriction fragment length polymorphism (RFLP) locus A-199a of 21 taxa from the Glycininae and 1 from the Phaseoleae. Four hundred nucleotides were determined in each, aligned, and then compared for these taxa. Within the annual soybean subgenus (Soja), the four accessions differed at as many as 2.2% of the nucleotides. Among 13 perennial soybean species (subgenus Glycine), nucleotide variation ranged from 1.7% to 8.4%. The nucleotide difference between the two soybean subgenera was 3.0–7.0%. Nucleotide variation between the genus Glycine and the related genera of Neonotonia, Amphicarpa, Teramnus, and Phaseolus ranged from 8.2% to 16.4%. In addition to nucleotide substitutions, insertions/deletions (indels) differences were also observed and were consistent with nucleotide-based analysis. Cladistic analysis of the A-199a sequences was performed using Wagner parsimony to construct a soybean phylogeny. Sixteen equally parsimonious trees were produced from these data. The trees were 246 steps in length with a consistency index of 0.78. Indels distribution upon the consensus topology revealed a pattern congruent with the nucleotide-based phylogeny. The current taxonomic status of the soybean subgenera and the related genera of Neonotonia, Amphicarpa, and Teramnus were well-supported and appear monophyletic in this analysis. Homoplasy within the subgenus Glycine led to a lack of resolved topology for many of these 13 taxa. However, the Glycine clade topology was consistent with phylogenies proposed using crossing experiments and cpDNA RFLPs. These genera were arranged from ancestral to derived as: Teramnus, Amphicarpa, Neonotonia, and Glycine when Phaseolus vulgaris was used as an outgroup.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222912
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    Noncoding chloroplast DNA variation in Mexican pines (1995)
    Springer
    Theoretical and applied genetics 91 (1995), S. 1101-1106 
    Details
    ISSN: 1432-2242
    Keywords: Pinus ; Noncoding cpDNA ; Genetic variation ; Phylogeny ; Conservation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Universal primers were used for PCR amplification of three noncoding regions of chloroplast DNA in order to study restriction site variation in 12 Mexican pine species. Two length mutations were identified that are of diagnostic value for two subgenera or sections of the genus. Phylogenetic analysis of the restriction site and length variation showed patterns of variation largely consistent with previous arrangements of these pines, except for the position of Pinus nelsonii, indicating that Pinus section Parraya Mayr, as circumscribed by Little and Critchfield (1969) and later authors, is not a monophyletic group.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223926
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    Easel, a gypsy LTR-retrotransposon in the Salmonidae (1995)
    Springer
    Molecular genetics and genomics 249 (1995), S. 229-236 
    Details
    ISSN: 1617-4623
    Keywords: gypsy ; LTR-retrotransposon ; Fish ; Phylogeny ; Vertebrate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Despite the close similarities between retroviruses and the gypsy/Ty3 group of LTR-retrotransposons their host ranges are largely distinct: the retroviruses are found only in vertebrates, whereas the gypsy LTR-retrotransposons are almost exclusively restricted to invertebrates, plants and fungi. Here we report the amplification by PCR, and characterisation, of one of the first LTR-retrotransposons to be discovered in vertebrates - in several members of the piscine family Salmonidae. Phylogenetic analysis of this retroelement, termed easel, indicates that it is probably a phylogeneticaly basal member of the gypsy group of LTR-retrotransposons and occurs in some of the same species from which retroviruses have previously been isolated. Thus some members of the Salmonidae are the first organisms known to harbour both retroviral branch elements and the gypsy LTR-retrotransposon branch elements. This creates an overlap in the host ranges of the two retroelement families.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00290370
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    A phylogenetic study of titi monkeys, genusCallicebus, based on cranial measurements: I. Phyletic groups ofCallicebus (1995)
    Springer
    Primates 36 (1995), S. 101-120 
    Details
    ISSN: 0032-8332
    Keywords: Callicebus ; Multivariate analysis ; Cranial measurements ; Shape factor ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Examinations of 23 forms ofCallicebus were made to elucidate their phylogenetic relationships based on cranial measurements. Multivariate statistical methods of distance analysis utilizing Q-mode correlation coefficients and principal component analysis were employed. As a result, the following five distinct groups were recognized morphometrically among the 23 species and subspecies: theDonacophilus, Cupreus, Moloch, Personatus, andTorquatus groups. Moreover, the phenetic characters of cranial size, karyotype, pelage coloration, and geographic range were consistent with the results of this group classification. It could be safely concluded therefore that these groups represented phylogenetically independent groups, in view of the fact that the rate of character differentiation was not appreciably different among closely related groups. Of the five groups, thePersonatus andTorquatus groups were respectively considered to maintain a higher peculiarity of character differentiation within theCallicebus phylogeny, since these two groups individually displayed the higher magnitudes of differentiation in both their craniometric shape and some phenetic features. Conversely, the other three groups were considered to be closer to each other in theCallicebus phylogeny.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02381918
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    Ecomorphological diversification and convergence in fluvial cichlid fishes (1995)
    Springer
    Environmental biology of fishes 44 (1995), S. 235-261 
    Details
    ISSN: 1573-5133
    Keywords: Adaptive radiation ; Convergent evolution ; Costa Rica ; Diet ; Phylogeny ; Venezuela ; Zambia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis We compared ecological and morphological patterns among cichlid faunas from three different biotic regions: the Río Tortuguero/Rio Sarapiquf in Costa Rica, the Río Apure drainage in Venezuela, and the Upper Zambezi drainage in Zambia. Cichlids comprise 19 percent of the fish fauna in the Tortuguero and Upper Zambezi drainages and 6.5 percent in the Apure drainage. Cichlid faunas exhibited similar patterns of habitat and food resource utilization, although vegetation-dwelling is more common and detritivory and herbivory are rarer in the Apure fauna. We hypothesize that South American ostariophysan fishes were more preadapted than cichlids to exploit detritivore and herbivore niches. The Zambezi cichlid fauna shows less ecomorphological diversification than the other two faunas, even though the degree of dietary diversification is similar among faunas. Chaetobranchus flavescens from the Venezuelan fauna is the only species that specializes on zooplankton as an adult, and algae grazing (Neetroplus nematopus) and specialized fruit feeding (‘Cichlasoma’ tuba) were represented only in the Costa Rican fauna. Based on the most recent hypothesized phylogeny for the family Cichlidae, we identified numerous interfaunal ecomorphological and feeding niche convergences. Patterns of ecomorphological divergence in relation to cladogenesis indicate a faster rate of evolutionary niche diversification in Central American cichlids compared with the two other faunas.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00005919
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    The phylogenetic relationships ofEeniella nana Smith, Batenburg-van der Vegte et Scheffers based on the partial sequences of 18S and 26S ribosomal RNAs (Candidaceae) (1995)
    Springer
    Journal of industrial microbiology and biotechnology 14 (1995), S. 456-460 
    Details
    ISSN: 1476-5535
    Keywords: Eeniella nana ; rRNA partial sequences ; Taxonomy ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Two strains ofEeniella nana were examined for their partial base sequences of 18S and 26S rRNAs. In the partial base sequences of 18S rRNA (prositions 1451 through 1618, 168 bases) the strains ofE. nana have five, five, four and eleven base differences with those ofDekkera bruxellensis (type species).D. anomala (andBrettanomyces anomalus),D. naardenensis andD. custersiana, respectively. In the 26S rRNA partial base sequencings (positions 1611 through 1835, 225 bases and positions 493 through 622, 130 bases) the base differences were 46, 43, 34 and 40 and the percent similarities were 53–54, 51–54, 56–57 and 51–53, respectively. The sequence data obtained are discussed phylogenetically and taxonomically, especially on retention of the generic nameEeniella.
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    URL: http://dx.doi.org/10.1007/BF01573957
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    Ecomorphological correlates in ten species of subtropical seagrass fishes: diet and microhabitat utilization (1995)
    Springer
    Environmental biology of fishes 44 (1995), S. 37-60 
    Details
    ISSN: 1573-5133
    Keywords: Tampa Bay ; Morphology ; Feeding ; Phylogeny ; Convergence ; Specialization Synopsis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Ecomorphological correlates were sought among ten species of distantly related subtropical seagrass fishes. Morphometric data associated with feeding and microhabitat utilization were compared by principal components analysis, cluster analysis, and canonical correspondence analysis to dietary data. Morphology was generally a poor predictor of diet except for a group of mid-water planktotrophic filter feeders. Separation of the species along morphological axes appears to be related more to microhabitat utilization resulting in three major groups: (1) a group of planktotrophic, mid-water fishes specialized for cruising and seeking out evasive prey characterized by a compressed fusiform body, forked caudal fin, long, closely spaced gill rakers, short to intermediate! length pectoral fin, pointed pectoral fin, large lateral eye, short head, and a terminal or subterminal mouth; (2) slow swimming, less maneuverable epibenthic fishes that pick or suck their prey off the substrate. They are united by more rounded caudal and pectoral fins, and short or no gill rakers; and (3) a group of more mobile and maneuverable epibenthic foragers characterized by a more compressed, sub-gibbose body, long, pointed pectoral fins, forked caudal fins, large lateral eyes, subterminal mouth, and greater jaw protrusibility. Cases of convergence in trophic and microhabitat utilization characters were apparent in some of the groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00005906
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    Perspectives on the ecomorphology of bony fishes (1995)
    Springer
    Environmental biology of fishes 44 (1995), S. 11-20 
    Details
    ISSN: 1573-5133
    Keywords: Morphology ; Ecology ; Form ; Biological role ; Performance ; Ontogeny ; Optimization ; Phylogeny ; Constraints ; Adaptation ; Fundamental niche ; Realized niche
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis The field of ecomorphology has a long history with early roots in Europe. In this half of the century the application of ecomorphology to the biology of fishes has developed in the former Soviet Union, Poland and Czechoslovakia, The Netherlands, and in North America. While the specific approaches vary among countries, many North American studies begin by comparing morphological variation with variation in ecological characteristics at the intra or interspecific levels. These initial correlative studies form the ground work for hypotheses that explore the mechanistic underpinnings of the observed ecomorphological associations. Supporting these mechanistic hypotheses are insights from functional studies which demonstrate the limits to potential resource use resulting from a particular morphology; however, the actual resource use is likely to be more limited due to additional constraints provided by internal (e.g., behavior, physiology) and external (e.g., resource abundance, predator distribution) factors. The results from performance studies in the laboratory or field can be used to test specific ecomorphological hypotheses developed from the initial correlational and functional studies. Such studies may, but rarely do, incorporate an ontogenetic analysis of the ecomorphological association to determine their effect on performance. Finally, input from phylogenetic analyses allow an investigator to examine the evolution of specific features and to assess the rates and directionality of character evolution. The structural and ecological diversity of fishes provides a fertile ground to investigate these interactions. The contributions in this volume highlight some of the specific directions for ecomorphological research covering a variety of biological processes in fishes. These include foraging, locomotion, reproduction, respiration, and sensory systems. Running through these papers are new insights into universal ecomorphological issues, i.e., the relationships between form and ecological role and the factors that modify these relationships.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00005904
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