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Showing 1 to 20 of 65 for “"Coalescent"”.
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A Comparison of Coalescent Estimation Software
Coalescent theory is a method often used by population geneticists in order to make inferences about evolutionary parameters. The coalescent is a stochastic model that approximates ancestral relationships among genes. An understanding of the coalescent pattern of a sample of sequences, along with …
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Complex population models with coalescent simulations
Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.
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Variational Inference Using Approximate Likelihood Under the Coalescent With Recombination
Coalescent methods are proven and powerful tools for population genetics, phylogenetics, epidemiology, and other fields. The multispecies coalescent (MSC) model has been widely employed by phylogenetic algorithms to construct the species tree while accounting for incomplete lineage sorting (ILS). …
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Genetic inference of deep hominin evolutionary history using the sequentially Markovian coalescent
Whole genome sequencing has allowed researchers to infer human demographic history with unprecedented resolution. Of particular interest are the series of population size changes, admixture events, and adaptations that have occurred over time. Many methods that infer these quantities rely on …
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Speciation and phylogeography: coalescent-based models applied to the Cape plant genus Pauridia
The Cape (CFR) is an exceptional centre plant This diversity is concentrated in a profusion geographically restricted endemic species within a The CFR is a rich and dynamic for the molecular study of speciation, but until recently studies have focused on factors influencing diversification of whole …
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Speciation and phylogeography: coalescent-based models applied to the Cape plant genus Pauridia
The Cape (CFR) is an exceptional centre plant This diversity is concentrated in a profusion geographically restricted endemic species within a The CFR is a rich and dynamic for the molecular study of speciation, but until recently studies have focused on factors influencing diversification of whole …
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A Phylogenetic History of the Tenerife Skink Chalcides viridanus: A multi-locus Coalescent Approach
… study highlights both how using a multi-locus coalescent approach can reveal a greater insight in to a species’ phylogeographical history, but also how factors such as incomplete lineage sorting can severely limit any intraspecific phylogenetic inferences made on recently diverged population …
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Fluctuating asymmetry as a measure of developmental instability in Arikara bioarchaeological assemblages
… represented in archaeological variants of the Coalescent tradition. Specifically, cranial morphometric, cranial nonmetric, and post-cranial metric measurements have been used to determine if meaningful patterns in the magnitude of FA across variants of the Coalescent tradition can be detected. …
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Historical refuges and recolonization routes in the Southern Appalachian Mountains, inferred through phylogeographic analysis of the spotted wintergreen (Chimaphila maculata)
… has recently benefited from incorporation of coalescent modeling to test competing scenarios of population history of a species. Ecological niche modeling has also been useful in inferring areas of likely suitable habitat during past climate conditions. Several studies have examined the …
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Investigation of Craniofacial Morphological Variation at Sully (39SL4)
… from 69 Sully burials attributed to the Extended Coalescent and 305 burials from Extended Coalescent and Post-Contact Coalescent cemeteries from Anton Rygh (39CA4), Mobridge (39WW1), Larson (39WW2), Black Widow Ridge (39ST203), Leavitt (39ST215), Cheyenne River (39ST1), and Indian Creek (39ST15) …
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Investigation of Craniofacial Morphological Variation at Sully (39SL4)
… from 69 Sully burials attributed to the Extended Coalescent and 305 burials from Extended Coalescent and Post-Contact Coalescent cemeteries from Anton Rygh (39CA4), Mobridge (39WW1), Larson (39WW2), Black Widow Ridge (39ST203), Leavitt (39ST215), Cheyenne River (39ST1), and Indian Creek (39ST15) …
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Model-based approaches to discovering diversity : new implementations, tests of adequacy and an empirical application to central American Diptera
… the fit of empirical data to a multispecies coalescent model commonly used in phylogenetic inference. Systematic and phylogeographic studies are generating ever-larger datasets which often range up to the genome scale and often wish to use coalescent models to infer parameters such as …
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Bayesian Inference of Phylogenetic Networks
The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under the MSC, owing mainly to the …
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Inferring Genomic Histories of Structured Populations: Lessons from the Hominids
… of the effects on theoretical distributions of coalescent times. The approach is then applied to examples arising in chimpanzee and human population history, in both cases suggesting effective population size changes are more likely due to changes in census population size, rather than island …
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Seeing Prehistory through New Lenses: Using Geophysical and Statistical Analysis to Identify Fresh Perspectives of a 15th Century Mandan Occupation
… traditions, highlighting new associations with Coalescent groups. A compact system for food capacity was also discovered, with more than 1,500 storage pits visible inside and outside of all structures delineated. Archaeological applications of these new technologies have provided a near-complete …
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Bayesian mixture modelling of migration by founder analysis
… appropriate simulations based on the structured coalescent that previous inferences based on the idea of founder sequences sufer from the fundamental problem that it is assumed that migration events coincide with the nodes (coalescent events) of the reconstructed tree. It is shown that such an …
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Hybridization And Introgression In Marine Invertebrates: Population Genomics Of Phymactis Papillosa And Asterias Sea Stars
… forbes</em>i. For each system, I applied coalescent-based species tree inference using CASTER (Zhang et al., 2025) and introgression analyses using Dsuite (Malinsky et al., 2021). For the <em>Asterias</em> sea stars system only, I applied admixture dating using linkage disequilibrium decay …
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The human molecular clock and mutation process : a characterization using microsatellite DNA
… are accurate molecular clocks for coalescent times of at least two million years. These results raise the prospect of using microsatellite data sets to determine parameters of population history. In order to calibrate genetic distances into time, the mutation rate must be known. …
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Phylogeny and phylogeography of the Chacma Baboon (Papio ursinus): the role of landscape in shaping contemporary genetic structure in the southern African baboon
… and phylogeographic techniques, including coalescent modeling, were used to examine past and present population dynamics of chacma baboon populations. Bayesian tree constructions provide a timeline of diversification for the sample. Although the ecological drivers of ongoing differentiation …
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Evolutionary dynamics of bird populations in Southeast Asia
… a fixed plumage difference (mantle coloration). Coalescent analyses showed that the plumage polymorphism was caused by past genetic introgression between the two parental forms. (2) I sampled 16 lowland rainforest bird species primarily from the Malay Peninsula and Borneo to test the …
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