1,721,026 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
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
Corolla size and temporal displacement of flowering times among sympatric diploid and tetraploid highbush blueberry (Vaccinium corymbosum)
No full textPolyploidy (whole-genome duplication) is common in vascular plants, but the modes of establishment and persistence, as well as the ecological consequences, of polyploidy remain vague. Highbush blueberry (Vaccinium corymbosum L.) is an ecologically and economically important understory shrub with an unclear species definition, coexisting in sympatric populations of diploid and tetraploid cytotypes. This study analyzes differences in bloom time between sympatric diploid and tetraploid V. corymbosum in natural populations, testing the potential for these cytotypes to interbreed and contributing to the formation and continuity of ploidy-level diversification within this species. Ploidal level was confirmed through DNA flow cytometry of sympatric plants from two populations in New Jersey, USA. Flower bloom date and corolla size were recorded over a three-year period. Diploid corollas were 32% smaller than tetraploid corollas, making them easily identifiable in the field. Ploidy accounted for 55-69% of the variation in bloom date, with diploids flowering about one week before tetraploids, and the remaining variation distributed among plants, among branches, and within branches. Notwithstanding these differences, there was modest overlap in flowering time between cytotypes, suggesting that cross-pollination is possible. This contributes evidence to the most current species definition of V. corymbosum as a single (mixed ploidy) species.Poster's Graduate Student Thesis Publication.Peer reviewed
Influences of host community characteristics on Borrelia burgdorferi infection prevalence in Blacklegged ticks
No full textLyme disease is a major vector-borne bacterial disease in the USA. The disease is caused by Borrelia burgdorferi, and transmitted among hosts and humans, primarily by blacklegged ticks (Ixodes scapularis). The ~25 B. burgdorferi genotypes, based on genotypic variation of their outer surface protein C (ospC), can be phenotypically separated as strains that primarily cause human diseases – human invasive strains (HIS) – or those that rarely do – and are non-randomly associated with host species. The goal of this study was to examine the extent to which phenotypic outcomes of B. burgdorferi could be explained by the host communities fed upon by blacklegged ticks. In 2006 and 2009, we determined the host community composition based on abundance estimates of the vertebrate hosts, and collected host-seeking nymphal ticks in 2007 and 2010 to determine the ospC genotypes within infected ticks. We regressed instances of B. burgdorferi phenotypes on site-specific characteristics of host communities by constructing Bayesian hierarchical models that properly handled missing data. The models provided quantitative support for the relevance of host composition on Lyme disease risk pertaining to B. burgdorferi prevalence (i.e., overall nymphal infection prevalence, or NIPAll) and HIS prevalence among the infected ticks (NIPHIS). In 2006, we found positive associations of the relative abundances of mice, of chipmunks, and of shrews with NIPAll. We also found positive associations of NIPHIS with shrews, and with host community diversity (H’), but negative associations with mice, and with chipmunks. In 2009, the relative abundance of mice showed a positive association with NIPAll, whereas the relative abundance of shrews and of H’ showed a negative association. With NIPHIS, only H’ showed a positive association, whereas the relative abundances of mice, of chipmunks, and of shrews, had negative associations. Our study highlights the variability between two years in the effects of host composition on B. burgdorferi genotypes. More importantly, our results highlight how disease risk inference, based on the role of host community, changes when we examine risk overall or at the phenotypic level. Long-term studies will be necessary to detect any consistent effects of host community composition on genotypic variation in the Lyme disease spirochetes
Correlated Morphological and Genetic Patterns in Embothrium coccineum (Proteaceae) Across Climate and Geography: Can Embothrium Survive Patagonian Climate Change?
Full text linkAdaptive radiation and reproductive isolation can determine the biogeographic structure of any species. We examine patterns of biotic variation in Embothrium coccineum, a Proteaceae tree that spans 20º of latitude and is both morphologically and genetically highly variable. We aim to: (1) explore the correspondence between these biotic patterns and current geographic and climatic gradients, and (2) determine whether and how those patterns are likely to respond to changing climate. We conducted separate Principal Components Analysis on biotic and abiotic sets of variables for 34 populations of Embothrium coccineum, accounting for a large fraction of the total variation in each. We then used canonical correlation analyses to optimize the match of those gradients onto each other. Smaller, rounder leaves and particular alleles typify the colder-drier parts of the range, while larger, lanceolate leaves and other alleles typify warmer-moister areas. Finally we mapped biotic profiles onto a predicted climatic landscape, based on doubling of CO2 projections. The climatic regime is predicted to shift geographically, but this lineage has successfully responded to repeated and dramatic climatic shifts since the Oligocene, and it should also be able to move and adapt quickly enough to meet the present challenge. More generally, our analytic approach can be extended to analysis of biotic and abiotic patterns in other species facing climatic challenges. Where there is enough biogeographic variation to provide adaptively relevant substrate, and where propagule dispersal is sufficiently extensive to keep up with the pace of spatial climatic shift, such taxa should be able to cope with shifting climate.Fil: Souto, Cintia Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación En Biodiversidad y Medioambiente; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche. Laboratorio de Ecotono; ArgentinaFil: Smouse, Peter E.. Rutgers University. Department of Ecology, Evolution and Natural Resources; Estados Unido
The relationship between heterozygosity and growth rate in pitch pine (Pinus rigida Mill.) and loblolly pine (Pinus taeda L.).
No full textThe phenomena of inbreeding depression and hybrid vigor have been known for 250 years; the causal mechanisms remain unclear. Two genetic hypotheses were offered in the early 1900's: inbreeding depression and overdominance. The premise of the overdominance model is that inbreeding depression is a reflection of heterotic selection; the dominance hypothesis is based on the effects of deleterious recessives. I examined the relationship between electrophoretic heterozygosity and growth rate in eight populations of Pinus rigida Mill. That study provides some evidence for overdominance, but suffers from the usual limitations of uncontrolled field surveys. I next examined a plantation of Pinus taeda L., progeny from a 1968 study of genetic load. Survival of the selfed progeny over the 19 years of the study was about 8% of that for the outcrossed trees. Among surviving progeny, selfs have grown much more slowly than outcrosses. There is a considerable fitness loss associated with genomic homozygosity in this normally outbred species, but either hypothesis could explain it equally well. The selfed progeny of heterozygous mothers showed a 70% deficit of the rarer alleles. In addition, the common homozygote always has a net survival advantage over homozygotes for the rarer alleles. The effects of genotype on growth were not as clear as the survival differentials, but outcrossed progeny having rare genotypes grew more poorly than did common homozygotes, which grew slower than common heterozygotes. The corresponding correlation in the selfs was in the reverse direction and very small. The asymmetry of selection is contrary to predictions of the dominance model but in keeping with those of the overdominance model. The major question emerging from the survivorship data is how the rarer alleles are maintained in the face of severe selection against them. The growth data suggest that there may be some heterozygous advantage for the more common but not for the rarer alleles. The fecundity advantage of the heterozygous mothers seems insufficient to counterbalance the survival disadvantages of the rare alleles, but there is clear evidence for countervailing selective pressures that could lead to the maintenance of genetic variation.PhDBotanyGeneticsUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/162021/1/8907006.pd
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