References

Lateral gene transfer as a support for the tree of life

10.1073/pnas.1116871109 · 2012 · External reference

Fossil apes and human evolution

10.1126/science.abb4363 · 2021 · External reference

Changes in life history and population size can explain the relative neutral diversity levels on X and autosomes in extant human populations

10.1073/pnas.1915664117 · 2020 · External reference

HyDe: A Python Package for Genome-Scale Hybridization Detection

10.1093/sysbio/syy023 · 2018 · External reference

Estimating bonobo (Panpaniscus) and chimpanzee (Pantroglodytes) evolutionary history from nucleotide site patterns

10.1073/pnas.2200858119 · 2022 · External reference

Unresolved reference

2004 · External reference

Testing for ancient admixture between closely related populations

10.1093/molbev/msr048 · 2011 · External reference

Ancestral population genomics: the coalescent hidden Markov model approach

10.1534/genetics.109.103010 · 2009 · External reference

Genomic architecture and introgression shape a butterfly radiation

10.1126/science.aaw2090 · 2019 · External reference

The different levels of genetic diversity in sex chromosomes and autosomes

10.1016/j.tig.2009.04.005 · 2009 · External reference

A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

10.1093/molbev/msz296 · 2020 · External reference

Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics

10.1126/science.1258524 · 2015 · External reference

An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla

10.48579/pro/f6kedm · 2023 · External reference

Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes

10.1111/j.1365-294x.2008.04005.x · 2008 · External reference

Pervasive hybridizations in the history of wheat relatives

10.1126/sciadv.aav9188 · 2019 · External reference

A draft sequence of the Neandertal genome

10.1126/science · 2010 · External reference

De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting

10.1093/gbe/evw074 · 2016 · External reference

Sex-biased evolutionary forces shape genomic patterns of human diversity

10.1371/journal.pgen.1000202 · 2008 · External reference

Phylogenomic approaches to detecting and characterizing introgression

10.1093/genetics/iyab173 · 2022 · External reference

Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model

10.1371/journal.pgen.0030007 · 2007 · External reference

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

10.1101/gr.114751.110 · 2011 · External reference

Difficulties in detecting hybridization

10.1080/106351501753462911 · 2001 · External reference

Properties of a neutral allele model with intragenic recombination

10.1016/0040-5809(83)90013-8 · 1983 · External reference

Comparative recombination rates in the rat, mouse, and human genomes

10.1101/gr.1970304 · 2004 · External reference

Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow

10.1093/nsr/nwab127 · 2021 · External reference

A statistical approach for distinguishing hybridization and incomplete lineage sorting

10.1086/600082 · 2009 · External reference

Accelerated genetic drift on chromosome X during the human dispersal out of Africa

10.1038/ng.303 · 2009 · External reference

Is recombination a problem for species-tree analyses?

10.1093/sysbio/syr128 · 2012 · External reference

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

10.1093/bioinformatics/btp368 · 2009 · External reference

The influence of gene flow on species tree estimation: a simulation study

10.1093/sysbio/syt049 · 2014 · External reference

The Effect of Gene Flow on Coalescent-based Species-Tree Inference

10.1093/sysbio/syy020 · 2018 · External reference

A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species

10.1371/journal.pgen.1003125 · 2012 · External reference

Strong male-driven evolution of DNA sequences in humans and apes

10.1038/416624a · 2002 · External reference

How reticulated are species?

10.1002/bies.201500149 · 2016 · External reference

Ancient hybridizations among the ancestral genomes of bread wheat

10.1126/science.1250092 · 2014 · External reference

Evaluating the use of ABBA-BABA statistics to locate introgressed loci

10.1093/molbev/msu269 · 2015 · External reference

Recombination rate variation shapes barriers to introgression across butterfly genomes

10.1371/journal.pbio.2006288 · 2019 · External reference

Widespread genomic signatures of natural selection in hominid evolution

10.1371/journal.pgen.1000471 · 2009 · External reference

Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

10.1093/molbev/msab063 · 2021 · External reference

Gene Tree Discordance Causes Apparent Substitution Rate Variation

10.1093/sysbio/syw018 · 2016 · External reference

Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes

10.1093/sysbio/syw069 · 2017 · External reference

A high-coverage genome sequence from an archaic Denisovan individual

10.1126/science.1224344 · 2012 · External reference

A fine-scale map of recombination rates and hotspots across the human genome

10.1126/science.1117196 · 2005 · External reference

Relationships between gene trees and species trees

10.1093/oxfordjournals.molbev.a040517 · 1988 · External reference

Genetic evidence for complex speciation of humans and chimpanzees

10.1038/nature04789 · 2006 · External reference

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

10.1093/sysbio/syv023 · 2015 · External reference

Doubts about complex speciation between humans and chimpanzees

10.1016/j.tree.2009.04.007 · 2009 · External reference

Efficient Bayesian Species Tree Inference under the Multispecies Coalescent

10.1093/sysbio/syw119 · 2017 · External reference

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci

10.1093/genetics/164.4.1645 · 2003 · External reference

Genetic history of an archaic hominin group from Denisova Cave in Siberia

10.1038/nature09710 · 2010 · External reference

Pervasive incomplete lineage sorting illuminates speciation and selection in primates

10.1126/science.abn4409 · 2023 · External reference

TRAILS: tree reconstruction of ancestry using incomplete lineage sorting

10.1101/2023.06.22.546039 · 2023 · External reference

Legofit: estimating population history from genetic data

10.1186/s12859-019-3154-1 · 2019 · External reference

10.24072/pcjournal.132 · 2022 · Admitted local publication

Aphid: A novel statistical method for dissecting gene flow and lineage sorting in phylogenetic conflict

10.24072/pci.mcb.100199 · 2024 · External reference

Gene flow contributes to diversification of the major fungal pathogen Candida albicans

10.1038/s41467-018-04787-4 · 2018 · External reference

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

10.1371/journal.pbio.2000234 · 2016 · External reference

The genomic landscape of Neanderthal ancestry in present-day humans

10.1038/nature12961 · 2014 · External reference

Insights into hominid evolution from the gorilla genome sequence

10.1038/nature10842 · 2012 · External reference

Consequences of recombination on traditional phylogenetic analysis

10.1093/genetics/156.2.879 · 2000 · External reference

OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes

10.1093/molbev/msz015 · 2019 · External reference

Unresolved reference

2020 · External reference

Incomplete Lineage Sorting in Mammalian Phylogenomics

10.1093/sysbio/syw082 · 2017 · External reference

Do Heliconius butterfly species exchange mimicry alleles?

10.1098/rsbl.2013.0503 · 2013 · External reference

Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques (genus Macaca)

10.24272/j.issn.2095-8137.2021.038 · 2021 · External reference

Widespread introgression across a phylogeny of 155 Drosophila genomes

10.1016/j.cub.2021.10.052 · 2022 · External reference

Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies

10.1093/sysbio/syab063 · 2022 · External reference

Divergence time and population size in the lineage leading to modern humans

10.1006/tpbi.1995.1026 · 1995 · External reference

Estimating the rate of evolution of the rate of molecular evolution

10.1093/oxfordjournals.molbev.a025892 · 1998 · External reference

Ghost Lineages Highly Influence the Interpretation of Introgression Tests

10.1093/sysbio/syac011 · 2022 · External reference

Ghost lineages can invalidate or even reverse findings regarding gene flow

10.1371/journal.pbio.3001776 · 2022 · External reference

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

10.1371/journal.pbio.3000954 · 2020 · External reference

Complex speciation of humans and chimpanzees

10.1038/nature06805 · 2008 · External reference

Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data

10.1093/sysbio/syx085 · 2018 · External reference

Genome analyses substantiate male mutation bias in many species

10.1002/bies.201100091 · 2011 · External reference

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

10.1534/genetics.116.190173 · 2016 · External reference

An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees

10.1093/molbev/msr172 · 2012 · External reference

Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci

10.1093/genetics/162.4.1811 · 2002 · External reference

A likelihood ratio test of speciation with gene flow using genomic sequence data

10.1093/gbe/evq011 · 2010 · External reference

Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability

10.1093/molbev/msac083 · 2022 · External reference

Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow

10.1093/sysbio/syab024 · 2021 · External reference

Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent

10.1093/sysbio/syw097 · 2017 · External reference

A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model

10.1111/mec.16433 · 2022 · External reference