No description available.

BACKGROUND:Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used / however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common.RESULTS:Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci. A consensus of species tree estimation methods supported two species of Alternaria causing citrus brown spot worldwide. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia.CONCLUSIONS:The number of Alternaria species identified as causing brown spot of citrus worldwide using morphological criteria has been overestimated. Little support was found for most of these morphospecies using quantitative species recognition approaches. Correct species delimitation of plant-pathogenic fungi is critical for understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the movement of pathogens to enforce quarantines. This research shows that multilocus phylogenetic methods that allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual species that are morphologically indistinguishable. Two phylogenetic species of Alternaria were identified as causing citrus brown spot worldwide. Further research is needed to determine how these species were introduced worldwide, how they differ phenotypically and how these species are maintained.

As deleterious variants continually arise in a population, they tend to be purged via purifying selection, leading to distortions in the shapes of genealogies relative to neutral expectations. In recent years, a mounting body of evidence has arisen suggesting that this can have significant implications for the patterns of diversity seen in natural populations. However, existing theory has not yet fully characterized the effects of these distortions on the structure of genealogies. The focus of this thesis is on exploring this gap, and developing an analytical description of the distortions that arise in genealogies due to purifying selection. / Physics

<p> This study documents and theorizes the processes behind the coalescence of ancestral Huron-Wendat populations on the north shore of Lake Ontario. A multiscalar analytical approach is employed to examine settlement aggregation at the regional, local and community levels. The study draws upon cross-cultural models of coalescent societies and the archaeology of communities while being theoretically situated within an historical-processual approach. </p> <p> The settlement data presented demonstrate that during the fifteenth century AD, small, previously distinct communities came together into large village aggregates. Through an examination of settlement relocation sequences and the occupational histories of individual villages, the transformations in social and political organization that accompanied this process are examined. Differences between site sequences suggest that while it is possible to identify similar processes in coalescence, the actual experience of coming together varied at the local level due to particular historical contingencies. </p> <p> A major contribution of the study is a detailed analysis of one village relocation sequence involving the aggregation of several small village communities at the Draper site, during the late fifteenth century. In the early sixteenth century, this coalescent community relocated to establish the Mantle site, the largest Iroquoian village excavated to date in the Lower Great Lakes. A detailed analysis of the occupational history of the Mantle site is presented here. The results point to the increasing integration of the community over time. A comparison of the built environments and other features of the Draper and Mantle sites elucidate practices that directly address the lived experience of coalescence. These community-level processes are ultimately situated in, and form the basis for, the broader sociopolitical realignments that characterized the Late Precontact Lower Great Lakes. </p> / Thesis / Doctor of Philosophy (PhD)

No description available.

We study a natural generalization of the Λ-coalescent to a spatial continuum. We introduce the process, which is known as the Segregated Λ-coalescent, via its connections to the (non-spatial) Λ-coalescent and the Spatial Λ-Fleming-Viot process. The main new results contained in this thesis are as follows. The Segregated Λ-coalescent has a non-trivial construction which we present here in terms of stochastic flows. We describe the qualitative behaviour of the Segregated Λ-coalescent and compare it to the behaviour of the Λ-coalescent, showing in particular that the Segregated Λ-coalescent has an extra phase transition which is directly related to the introduction of space. We finish with some results concerning the rate at which the Segregated Λ-coalescent comes down from infinity.

The inference of species boundaries and phylogenetic relationships are fundamental for evolutionary, ecological, and conservation studies. The resolution of species boundaries and the inference of phylogenetic relationships among species are required to define the units of analysis and to find the most closely related units for evaluating alternative models of speciation. I highlight lizards as model organisms for ecological and evolutionary studies, emphasizing their contributions to advances in understanding linkages between phylogeography and speciation. In this dissertation, I focus on the phylogenetic relationships of the lizards in the Liolaemus darwinii group, and the species boundaries of a nested clade within the group, the L. darwinii complex, because of several advantages that make these taxa ideal for phylogeographic studies of speciation. I infer a phylogeny for the L. darwinii group based on DNA sequences of 20 loci (19 nuclear and 1 mitochondrial) using species trees methods that take into account the incongruence among gene trees. I found the minimum number of loci, number of sequences per species, and number of base pairs per locus that should be included in an analysis for an accurate and precise estimate of the species tree. The species tree based on all available data support a clade of closely related species (L. darwinii, L. grosseorum, and L. laurenti) known as the L. darwinii complex. A new method for species delimitation using Approximate Bayesian Computation is introduced and is shown to accurately delimit species given that limited or no gene flow has occurred after divergence and despite biased estimates of demographic parameters. ABC analyses supported the distinctness of two lineages within L. darwinii under a model of speciation with gene flow. Based on the species tree and the species limits obtained in this dissertation, phylogenetic comparative methods can be carried out to address the morphological and ecological evolution in the L. darwinii group and several sister species can be used for testing the alternative speciation models via correlation analyses of genetic, morphological, and ecological datasets. Future studies should assess the role speciation due to adaptive processes and its association the species' ecological niches and life histories.

The analysis of diverse data sets can yield different phylogenetic estimates that challenge systematists to explain the source of discordance. The Ambystomatidae are a classic example of this phylogenetic conflict. Previous attempts to resolve the ambystomatid species tree using allozymic, morphological, and mitochondrial sequence data have yielded different estimates, making it unclear which data source best approximates ambystomatid phylogeny. We present the first multi-locus DNA sequencebased phylogenetic study of the Ambystomatidae. Because independent loci can contain discordant gene tree histories, concatenating unlinked loci into a single data matrix can lead to strongly supported and erroneous results. Therefore, we utilized a range of analyses, including coalescent-based methods of phylogenetic estimation that account for incomplete lineage sorting and concordance-based methods that estimate the proportion of sampled loci that support a particular clade. We repeated these analyses with the removal of individual loci to determine if any locus has a disproportionate effect on our phylogenetic results. Many deep and relatively shallow clades within Ambystoma were robustly resolved. Analyses that excluded loci produced overlapping posterior distributions, suggesting no disproportionate influence of any particular locus. Our estimates differ from previous hypotheses, although there was greater similarity with previous molecular estimates, relative to morphological estimates.

No description available.

No description available.