Tomáš Flouri
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View article: The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model
The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model Open
The multispecies coalescent (MSC) model accounts for genealogical fluctuations across the genome and provides a framework for analyzing genomic data from closely related species to estimate species phylogenies and divergence times, infer i…
View article: Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified
Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified Open
Thanks to genomic data, interspecific gene flow is increasingly recognized as a major evolutionary force that shapes biodiversity. Two models have been developed in the multispecies coalescent (MSC) framework to infer gene flow from genomi…
View article: Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in <i>Drosophila</i>
Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in <i>Drosophila</i> Open
Analysis of genomic data in the past two decades has highlighted the prevalence of introgression as an important evolutionary force in both plants and animals. The genus Drosophila has received much attention recently, with an analysis of …
View article: Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration Open
The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer the history of specie…
View article: Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences
Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences Open
Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nu…
View article: Inference of continuous gene flow between species under misspecified models
Inference of continuous gene flow between species under misspecified models Open
Gene flow between species is increasingly recognized as an important evolutionary process with potential adaptive consequences. Recent methodological advances make it possible to infer different modes of gene flow from genome-scale data, i…
View article: Efficient Bayesian inference under the multispecies coalescent with migration
Efficient Bayesian inference under the multispecies coalescent with migration Open
Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical …
View article: Hierarchical heuristic species delimitation under the multispecies coalescent model with migration
Hierarchical heuristic species delimitation under the multispecies coalescent model with migration Open
The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data to infer the history of species divergence and gene flow. G…
View article: Inferring the Direction of Introgression Using Genomic Sequence Data
Inferring the Direction of Introgression Using Genomic Sequence Data Open
Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. However, gene flow in opposite directions generates similar patterns in multilocu…
View article: European Reference Genome Atlas Community - Phase 1 Members - 2020-2023
European Reference Genome Atlas Community - Phase 1 Members - 2020-2023 Open
This dataset presents a comprehensive list of members registered as part of the European Reference Genome Atlas (ERGA, erga-biodiversity.eu) Community during ERGA Phase 1, which spanned from 2020 to 2023. The dataset includes information o…
View article: European Reference Genome Atlas Community - Phase 1 Members - 2020-2023
European Reference Genome Atlas Community - Phase 1 Members - 2020-2023 Open
This dataset presents a comprehensive list of members registered as part of the European Reference Genome Atlas (ERGA, erga-biodiversity.eu) Community during ERGA Phase 1, which spanned from 2020 to 2023. The dataset includes information o…
View article: Inferring the direction of introgression using genomic sequence data
Inferring the direction of introgression using genomic sequence data Open
Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. However, gene flow in opposite directions generates similar patterns in multilocu…
View article: European Reference Genome Atlas Community - Phase 1 Members - 2020-2023
European Reference Genome Atlas Community - Phase 1 Members - 2020-2023 Open
This dataset presents a comprehensive list of members registered as part of the European Reference Genome Atlas (ERGA, erga-biodiversity.eu) Community during ERGA Phase 1, which spanned from 2020 to 2023. The dataset includes information o…
View article: Estimation of species divergence times in presence of cross-species gene flow
Estimation of species divergence times in presence of cross-species gene flow Open
Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estim…
View article: Inference of Gene Flow between Species under Misspecified Models
Inference of Gene Flow between Species under Misspecified Models Open
Genomic sequence data provide a rich source of information about the history of species divergence and interspecific hybridization or introgression. Despite recent advances in genomics and statistical methods, it remains challenging to inf…
View article: A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source
A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source Open
Uropeltidae is a clade of small fossorial snakes (ca. 64 extant species) endemic to peninsular India and Sri Lanka. Uropeltid taxonomy has been confusing, and the status of some species has not been revised for over a century. Attempts to …
View article: Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent
Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent Open
The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC mode…
View article: Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability
Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability Open
Full-likelihood implementations of the multispecies coalescent with introgression (MSci) model treat genealogical fluctuations across the genome as a major source of information to infer the history of species divergence and gene flow usin…
View article: Genome-scale data reveal deep lineage divergence and a complex demographic history in the Texas horned lizard (Phrynosoma cornutum) throughout the southwestern and central US
Genome-scale data reveal deep lineage divergence and a complex demographic history in the Texas horned lizard (Phrynosoma cornutum) throughout the southwestern and central US Open
The southern US and northern Mexico serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate …
View article: A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model
A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model Open
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 differen…
View article: Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (<i>Phrynosoma cornutum</i>) throughout the Southwestern and Central United States
Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (<i>Phrynosoma cornutum</i>) throughout the Southwestern and Central United States Open
The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoc…
View article: Estimation of Cross-Species Introgression Rates using Genomic Data Despite Model Unidentifiability
Estimation of Cross-Species Introgression Rates using Genomic Data Despite Model Unidentifiability Open
Full likelihood implementations of the multispecies coalescent with introgression (MSci) model takes the genealogical fluctuation across the genome as a major source of information to infer the history of species divergence and gene flow u…
View article: SPART: A versatile and standardized data exchange format for species partition information
SPART: A versatile and standardized data exchange format for species partition information Open
A wide range of data types can be used to delimit species and various computer‐based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species…
View article: Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow
Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow Open
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 po…
View article: Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model
Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model Open
Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phylogenomic …
View article: Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model
Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model Open
A bstract Genome sequencing projects routinely generate haploid consensus sequences from diploid genomes, which are effectively chimeric sequences with the phase at heterozygous sites resolved at random. The impact of phasing errors on phy…
View article: SPART, a versatile and standardized data exchange format for species partition information
SPART, a versatile and standardized data exchange format for species partition information Open
A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of SD unde…
View article: Output files from ipyrad
Output files from ipyrad Open
All output files generated by running the raw GBS data through the ipyad pipeline.
View article: cornutum_ND1_aligned_renamed_full_CB-Aug2020.nexus
cornutum_ND1_aligned_renamed_full_CB-Aug2020.nexus Open
Multiple sequence alignment for all mtDNA sequences used to examine the phylogeography and demographic history of the Texas horned lizard.
View article: cornutum_ND1_aligned_renamed_full_CB-Aug2020.nexus
cornutum_ND1_aligned_renamed_full_CB-Aug2020.nexus Open
Multiple sequence alignment for all mtDNA sequences used to examine the phylogeography and demographic history of the Texas horned lizard.