1,738,459 research outputs found
Allo-triploid Sphagnum <sup>x</sup>falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers
No full textBackground and Aims. Allopolyploids exhibit both different levels and patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum ×falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations.
Methods. Studying populations from three disjunct regions (South Island [New Zealand]; Tierra de Fuego archipelago [Chile, Argentia]; Tasmania [Australia]) we examine genetic information for five highly stable microsatellite markers that differ among the three (ancestral) monoploid genomes. We partition the holoploid information into separate components for individuals within and among single sites and regions, as well as within and among the three monoploid genomes, and then convert those information components into corresponding diversity measures.
Key Results. The majority (76%) of alleles detected across these five markers appear to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent alloploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83% of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5% of the total information.
Conclusions. Sphagnum ×falcatulum appears to have inherited the great majority of its genetic diversity at these markers by reticulation, rather than by subsequent evolutionary radiation. However, some post hybridization genetic diversification has become fixed in at least one regional population. Methodology allowing statistical analysis of any ploidy level is presented.Peer reviewed
Information Theory Broadens the Spectrum of Molecular Ecology and Evolution
No full textInformation or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or ‘q-profile’) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q=0), Shannon information (q=1), and heterozygosity (q=2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q=2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and non-genetic inheritance.Peer reviewe
Converting quadratic entropy to diversity: both animals and alleles are diverse, but some are more diverse than others
No full textThe use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1] - scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.The Antechinus data are archived in Excel workbook form, along with listings of the QDIVER results extracted from GenAlEx6.51 (http://biology.anu.edu.au/GenAlEx/). DC data and analyses are presented in S5 Appendix, and DR data and analyses are presented in S6 Appendix; these latter are ANU's to enable, and will be available with the paper as PLOS ONE access Supplements.Peer reviewe
Peter-E-Martin/HeCalc: HeCalc 0.0.1 alpha
No full text<p>This is the initial release for HeCalc, a package to perform (U-Th)/He data reduction and uncertainty propagation. It includes functionality though a GUI, the command line, or via the individual functions contained within the package. Future releases will include executable binary files as well to permit straightforward use of the GUI.</p>
<p>Some minor testing has been performed, but this version should be considered to be in alpha. The statistical portions of the software consistently yield the correct outputs, but unexpected bugs may cause crashes, particularly for running the GUI.</p>
Cladal Divergence in Fungal Ophiognomonia (Gnomoniaceae, Diaporthales) Shows Evidence of Climatic Niche Vicariance
No full textWe used the globally widespread genus Ophiognomonia as a model system to investigate climatic niche patterns in fungi, characterizing the climatic profiles of 28 species with seven temperature and seven precipitation variables. Using a novel version of Spatial Evolutionary and Ecological Vicariance Analysis (SEEVA), designed to deal with continuous and correlated variables, we examined well-sampled phyletic splits of a multi-gene phylogeny. We evaluated the degree to which phyletic divergence has been associated with climatic niche divergence between sister lineages, permitting elucidation of climatic associations in evolutionary context. From the 14 inter-correlated climatic variables, we extracted four principal axes, accounting for 93.2% of the climatic variation, with axes broadly labeled as: polarity, tropicality, winter mildness, and aridity. We also analyzed the two single variables maximum monthly temperature and precipitation. We detected climatic associations that were compatible with both niche-conservatism and niche-divergence within the phylogeny, and different cladistic bifurcations associated with different climatic splits. As might have been anticipated, geographic separation (or lack thereof) of phylogenetic splits was correlated with climate niche divergence (or conservation). This elaborated SEEVA method provides a visual and statistically solid basis for characterizing climatic niche divergence that should prove useful for elucidation of many other taxonomic groups.Peer reviewe
Impact of Violated High-Dose Refuge Assumptions on Evolution of Bt-Resistance
No full textTransgenic crops expressing Bacillus thuringiensis (Bt) toxins have been widely and successfully deployed for the control of target pests, while allowing a substantial reduction of insecticide use. The evolution of resistance (a heritable decrease in susceptibility to Bt toxins) can pose a threat to sustained control of target pests, but a high-dose refuge (HDR) management strategy has been key to delaying countervailing evolution of Bt resistance. The HDR strategy relies on the mating frequency between susceptible and resistant individuals, so either partial dominance of resistant alleles or non-random mating in the pest population itself could elevate the pace of resistance evolution. Using classic Wright-Fisher genetic models, we investigated the impact of deviations from standard refuge model assumptions on resistance evolution in the pest populations. We show that when Bt selection is strong, even deviations from random mating and/or strictly recessive resistance that are below the threshold of detection can yield dramatic increases in the pace of resistance evolution. Resistance evolution is hastened whenever the order of magnitude of model violations exceeds the initial frequency of resistant alleles. We also show that existence of a fitness cost for resistant individuals on the refuge crop cannot easily overcome the effect of violated HDR assumptions. We propose a parametrically explicit framework that enables both comparison of various field situations and model inference. Using this model, we propose novel empiric estimators of the pace of resistance evolution (and time to loss of control), whose simple calculation relies on the observed change in resistance allele frequency.Peer reviewe
The Peter E. Love family
No full textThe Peter E. Love family,13x17.5cm Front row: 1. Annie 2. John 3. Peter E. 4. Mrs. Peter E. 5. Charley Property of F.B. Lamberthttps://mds.marshall.edu/lambert_papers/2195/thumbnail.jp
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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