ArticleMolecular biology and evolution2018
Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 96 citations in OpenAlex.
- On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection.Molecular biology and evolution · 2026Article
- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Phylogeny and species delimitation of ciliates in the genus Spirostomum (class Heterotrichea) using single-cell transcriptomes.BMC ecology and evolution · 2025Article
- Dance displays in gibbons: biological and linguistic perspectives on structured, intentional, and rhythmic body movement.Primates; journal of primatology · 2025Article
- Phylogeny and species delimitation of ciliates in the genusbioRxiv : the preprint server for biology · 2024Article
- Major patterns in the introgression history ofeLife · 2023Article
- Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation.Systematic biology · 2023Article
- Estimation of species divergence times in presence of cross-species gene flow.Systematic biology · 2023Article
- Phylogeography of the desert scorpion illuminates a route out of Central Asia.Current zoology · 2023Article
- Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks.Systematic biology · 2023Article
- Recombination Variation Shapes Phylogeny and Introgression in Wild Diploid Strawberries.Molecular biology and evolution · 2023Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
- Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies.Systematic biology · 2022Article
- Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent.Molecular biology and evolution · 2022Article
- Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability.Molecular biology and evolution · 2022Article
- A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model.Molecular ecology · 2022Article
- Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model.Systematic biology · 2022Article
- Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow.National science review · 2021Article
- PRANC: ML species tree estimation from the ranked gene trees under coalescence.Bioinformatics (Oxford, England) · 2020Article
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2 authors at 1 institution in 3 countries.
Funding
Abstract
The phylogenetic relationships among extant gibbon species remain unresolved despite numerous efforts using morphological, behavorial, and genetic data and the sequencing of whole genomes. A major challenge in reconstructing the gibbon phylogeny is the radiative speciation process, which resulted in extremely short internal branches in the species phylogeny and extensive incomplete lineage sorting with extensive gene-tree heterogeneity across the genome. Here, we analyze two genomic-scale data sets, with ∼10,000 putative noncoding and exonic loci, respectively, to estimate the species tree for the major groups of gibbons. We used the Bayesian full-likelihood method bpp under the multispecies coalescent model, which naturally accommodates incomplete lineage sorting and uncertainties in the gene trees. For comparison, we included three heuristic coalescent-based methods (mp-est, SVDQuartets, and astral) as well as concatenation. From both data sets, we infer the phylogeny for the four extant gibbon genera to be (Hylobates, (Nomascus, (Hoolock, Symphalangus))). We used simulation guided by the real data to evaluate the accuracy of the methods used. Astral, while not as efficient as bpp, performed well in estimation of the species tree even in presence of excessive incomplete lineage sorting. Concatenation, mp-est and SVDQuartets were unreliable when the species tree contains very short internal branches. Likelihood ratio test of gene flow suggests a small amount of migration from Hylobates moloch to H. pileatus, while cross-genera migration is absent or rare. Our results highlight the utility of coalescent-based methods in addressing challenging species tree problems characterized by short internal branches and rampant gene tree-species tree discordance.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.