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  • 1
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    Springer Nature | Springer
    Publication Date: 2024-04-05
    Description: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
    Keywords: Microbial Genetics and Genomics ; Evolutionary Biology ; Genetics and Population Dynamics ; Microbial Ecology ; Human Genetics ; Genetics and Genomics ; Comparative genomics ; Metagenomics ; Microbial Population Analysis ; Pangenome Profile ; Supra-Genome Analysis ; Adaptive Evolution ; Computational Tools ; Bioinformatic Genomics ; Core Dispensable Genome ; Selection, Recombination, Composition ; Acquired Resistance ; Bacterial Species Concept ; Genomic Diversity ; Bacterial Ecology, Microevolution ; Open Access ; Pan-metagenomics ; Pan-microbiomics ; Pan-epigenome ; Gene Transfer ; Pan-phenomes ; Microbiology (non-medical) ; Genetics (non-medical) ; Evolution ; Applied mathematics ; Ecological science, the Biosphere ; Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAJ Evolution ; thema EDItEUR::P Mathematics and Science::PB Mathematics::PBW Applied mathematics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::M Medicine and Nursing::MF Pre-clinical medicine: basic sciences::MFN Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical)
    Language: English
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  • 2
    Publication Date: 2024-01-12
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; General Decision Sciences ; Soil fauna ; Leaf litter ; DNA barcoding ; Biodiversity ; Restoration ecology ; Climate ; change ; Metabarcoding ; Tropical forest ; Systematic conservation planning ; Surveillance monitoring ; Targeted monitoring
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 3
    Publication Date: 2024-01-12
    Description: Caribbean dry forests are among the most endangered tropical ecosystems on earth. Several studies exist on their floristic composition and their recovery after natural or man-made disturbances, but little is known on the small Dutch Caribbean islands. In this study, we present quantitative data on plant species richness and abundance on St. Eustatius, one of the smallest islands of the Lesser Antilles. We collected and identified trees, shrubs, lianas and herbs in 11 plots of 25 x 25 m in different vegetation types. We compared their floristic composition and structure to vegetation surveys from roughly the same locations in the 1990s and 1950s. We found substantial differences among our 11 plots: vegetation types varied from evergreen forests to deciduous shrubland and open woodland. The number of tree species \xe2\x89\xa5 10 cm DBH ranged between one and 17, and their density between three and 82 per plot. In spite that all plots were subject to grazing by free roaming cattle, canopy height and floristic diversity have increased in the last decades. Invasive species are present in the open vegetation types, but not under (partly) closed canopy. Comparison with the earlier surveys showed that the decline of agriculture and conservation efforts resulted in the regeneration of dry forests between the 1950s and 2015. This process has also been reported from nearby islands and offers good opportunities for the future conservation of Caribbean dry forests.
    Keywords: Nature and Landscape Conservation ; Ecology ; Ecology ; Evolution ; Behavior and Systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 4
    Publication Date: 2024-04-18
    Description: Since the introduction of non-native rodents to the Caribbean region, these invaders have successfully occupied many, if not most, islands where they pose tremendous threats to native biodiversity and ecosystems. The objective of our study was to conduct a preliminary assessment of the relative abundance of invasive alien rodents in different vegetation types on the small Caribbean island of St. Eustatius, which has no native rodent species. We used tracking tunnels (baited ink cards placed in tunnels to identify the prints of animals lured to the card) to determine the presence of rodent species. We collected data in 25 x 25 m (n = 13) and 5 x 5m (n = 130) plots to determine whether elevation, number of tree species, canopy cover or other microhabitat components were correlated with rodent relative abundance. Invasive rodents are present in varying relative abundances in rural areas on St. Eustatius. House mice (Mus musculus) were not recorded inside the terrestrial protected areas, whereas black rats (Rattus rattus) were detected in all elevations and all but one vegetation type sampled. We determined significant correlations between some of the habitat characteristics, especially elevation, canopy height, leaf litter cover and number of tree species, which showed significant collinearity with 27 of 45 pairwise comparisons. There was a significant correlation between rodent relative abundance and the number of tree species, but not between elevation, number of living trees, number of shrubs, rainfall, canopy cover, canopy height, leaf litter cover, leaf litter depth, or slope. There was a significant difference within vegetation types for the frequency of traps containing rat versus mouse tracks. Our study was impacted by two major hurricanes in September 2017.
    Keywords: Nature and Landscape Conservation ; Ecology ; Ecology ; Evolution ; Behavior and Systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Sexual plant reproduction 7 (1994), S. 87-94 
    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
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Sexual plant reproduction 9 (1996), S. 357-361 
    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
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Journal of evolutionary economics 3 (1993), S. 199-224 
    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
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of evolutionary economics 6 (1996), S. 1-30 
    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
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of evolutionary economics 7 (1997), S. 339-353 
    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
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of evolutionary economics 9 (1999), S. 109-133 
    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
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