Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Mathematical Biology"
DOI: 10.1007/s00285-016-1034-0
Abstract: The focus of this article is a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using molecular sequences from multiple loci. The species delimitation requires no a priori… read more here.
Keywords: algorithmic improvements; delimitation phylogeny; phylogeny estimation; species delimitation ... See more keywords
A simulation study to examine the information content in phylogenomic datasets under the multispecies coalescent model.
Sign Up to like & getrecommendations! Published in 2020 at "Molecular biology and evolution"
DOI: 10.1093/molbev/msaa166
Abstract: We use computer simulation to examine the information content in multilocus datasets for inference under the multispecies coalescent (MSC) model. Inference problems considered include estimation of evolutionary parameters (such as species divergence times, population sizes,… read more here.
Keywords: information content; examine information; simulation; multispecies coalescent ... See more keywords
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
Sign Up to like & getrecommendations! Published in 2018 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msy147
Abstract: Abstract The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-likelihood implementation… read more here.
Keywords: tree inference; inference bpp; bpp using; species tree ... See more keywords
A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis
Sign Up to like & getrecommendations! Published in 2019 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msz296
Abstract: Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity… read more here.
Keywords: genomic sequence; sequence data; introgression; coalescent model ... See more keywords
Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow
Sign Up to like & getrecommendations! Published in 2021 at "National Science Review"
DOI: 10.1093/nsr/nwab127
Abstract: Multispecies coalescent (MSC) is the extension of the single-population coalescent model to multiple species. It integrates the phylogenetic process of species divergences and the population genetic process of coalescent, and provides a powerful framework for… read more here.
Keywords: cross species; species gene; multispecies coalescent; gene ... See more keywords
The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution.
Sign Up to like & getrecommendations! Published in 2020 at "Systematic biology"
DOI: 10.1093/sysbio/syaa084
Abstract: Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently,… read more here.
Keywords: gene family; new model; multilocus multispecies; multispecies coalescent ... See more keywords
StarBeast3: Adaptive Parallelised Bayesian Inference under the Multispecies Coalescent.
Sign Up to like & getrecommendations! Published in 2022 at "Systematic biology"
DOI: 10.1093/sysbio/syac010
Abstract: As genomic sequence data becomes increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution… read more here.
Keywords: multispecies coalescent; bayesian inference; inference; adaptive parallelised ... See more keywords
A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model
Sign Up to like & getrecommendations! Published in 2022 at "Molecular Ecology"
DOI: 10.1111/mec.16433
Abstract: Phylogenomic analyses under the multispecies coalescent model assume no recombination within locus and free recombination among loci. Yet, in real data sets intralocus recombination causes different sites of the same locus to have different genealogical… read more here.
Keywords: recombination; impact recombination; coalescent model; multispecies coalescent ... See more keywords
Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology
Sign Up to like & getrecommendations! Published in 2017 at "PeerJ"
DOI: 10.7717/peerj.3724
Abstract: While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily… read more here.
Keywords: validation description; rainbow skinks; two new; species delimitation ... See more keywords