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Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons

https://doi.org/10.1093/molbev/msx277
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Description of a new species of Hoolock gibbon (Primates: Hylobatidae) based on integrative taxonomy
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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Estimating the pattern of nucleotide substitution
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The behavioral regulation of monogamy in gibbons (Hylobates muelleri)
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Ancestral Population Sizes and Species Divergence Times in the Primate Lineage on the Basis of Intron and BAC End Sequences
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Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
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Chromosomal phylogeny and evolution of gibbons (Hylobatidae)
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Mammalian Protein Metabolism
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Evolution of Protein Molecules
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Multilocus Resolution of Phylogeny and Timescale in the Extant Adaptive Radiation of Hawaiian Honeycreepers
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Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
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Book review
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Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
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A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3–ND4 gene sequences
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Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera
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Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
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The gene tree delusion
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
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An attempt to estimate the effective size of the ancestral species common to two extant species from which homologous genes are sequenced
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The effect of recombination on background selection
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Duet‐splitting and the evolution of gibbon songs
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Inferring ancient divergences requires genes with strong phylogenetic signals
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Gibbon genome and the fast karyotype evolution of small apes
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Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
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High-resolution species trees without concatenation
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Effects of linkage on rates of molecular evolution.
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Age and rate of diversification of the Hawaiian silversword alliance (Compositae)
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Phylogeny of the Lake Tanganyika Cichlid Species Flock and Its Relationship to the Central and East African Haplochromine Cichlid Fish Faunas
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Computing Bayes Factors Using Thermodynamic Integration
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Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
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Molecular Evolution
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APE: Analyses of Phylogenetics and Evolution in R language
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BEST: Bayesian estimation of species trees under the coalescent model
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ASTRAL: genome-scale coalescent-based species tree estimation
inferredcites →https://doi.org/10.1093/bioinformatics/btu530openalex-snapshot
Quartet Inference from SNP Data Under the Coalescent Model
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
inferredcites →https://doi.org/10.1093/czoolo/61.5.854openalex-snapshot
The BPP program for species tree estimation and species delimitation
inferredcites →https://doi.org/10.1093/genetics/134.4.1289openalex-snapshot
The effect of deleterious mutations on neutral molecular variation.
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Deleterious background selection with recombination.
inferredcites →https://doi.org/10.1093/genetics/147.2.915openalex-snapshot
Statistical Tests of Neutrality of Mutations Against Population Growth, Hitchhiking and Background Selection
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Likelihood and Bayes Estimation of Ancestral Population Sizes in Hominoids Using Data From Multiple Loci
inferredcites →https://doi.org/10.1093/genetics/164.4.1645openalex-snapshot
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msm156openalex-snapshot
Mapping Human Genetic Ancestry
inferredcites →https://doi.org/10.1093/molbev/msn148openalex-snapshot
Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/msp296openalex-snapshot
Isolation with Migration Models for More Than Two Populations
inferredcites →https://doi.org/10.1093/molbev/msr048openalex-snapshot
Testing for Ancient Admixture between Closely Related Populations
inferredcites →https://doi.org/10.1093/molbev/mss118openalex-snapshot
Maximum Likelihood Implementation of an Isolation-with-Migration Model with Three Species for Testing Speciation with Gene Flow
inferredcites →https://doi.org/10.1093/molbev/mss149openalex-snapshot
An Alu-Based Phylogeny of Gibbons (Hylobatidae)
inferredcites →https://doi.org/10.1093/molbev/msu279openalex-snapshot
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msw079openalex-snapshot
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
inferredcites →https://doi.org/10.1093/oso/9780198505235.001.0001openalex-snapshot
The Ecology of Adaptive Radiation
inferredcites →https://doi.org/10.1093/sysbio/syp047openalex-snapshot
What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/sysbio/syr128openalex-snapshot
Is Recombination a Problem for Species-Tree Analyses?
inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
inferredcites →https://doi.org/10.1093/sysbio/sys063openalex-snapshot
From Trajectories to Averages: An Improved Description of the Heterogeneity of Substitution Rates Along Lineages
inferredcites →https://doi.org/10.1093/sysbio/syt049openalex-snapshot
The Influence of Gene Flow on Species Tree Estimation: A Simulation Study
inferredcites →https://doi.org/10.1093/sysbio/syu063openalex-snapshot
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/sysbio/syv029openalex-snapshot
The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews
inferredcites →https://doi.org/10.1093/sysbio/syw063openalex-snapshot
Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species
inferredcites →https://doi.org/10.1093/sysbio/syw119openalex-snapshot
Efficient Bayesian Species Tree Inference under the Multispecies Coalescent
inferredcites →https://doi.org/10.1101/gr.6052507openalex-snapshot
Molecular refinement of gibbon genome rearrangements
inferredcites →https://doi.org/10.1111/j.1365-294x.2005.02632.xopenalex-snapshot
Comparative landscape genetics and the adaptive radiation of Darwin's finches: the role of peripheral isolation
inferredcites →https://doi.org/10.1111/nyas.12747openalex-snapshot
Estimating phylogenetic trees from genome‐scale data
inferredcites →https://doi.org/10.1126/science.193.4249.235openalex-snapshot
Gibbons and Their Territorial Songs
inferredcites →https://doi.org/10.1146/annurev.an.21.100192.002203openalex-snapshot
Primate Limb Bone Structural Adaptations
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2148-10-74openalex-snapshot
Mitochondrial evidence for multiple radiations in the evolutionary history of small apes
inferredcites →https://doi.org/10.1186/1471-2148-12-150openalex-snapshot
A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons
inferredcites →https://doi.org/10.1186/1471-2148-9-259openalex-snapshot
Estimating the phylogeny and divergence times of primates using a supermatrix approach
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s2openalex-snapshot
A comparative study of SVDquartets and other coalescent-based species tree estimation methods
inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.1371/journal.pgen.1000471openalex-snapshot
Widespread Genomic Signatures of Natural Selection in Hominid Evolution
inferredcites →https://doi.org/10.1371/journal.pone.0000073openalex-snapshot
The Syntax and Meaning of Wild Gibbon Songs
inferredcites →https://doi.org/10.1371/journal.pone.0053682openalex-snapshot
Incomplete Lineage Sorting Is Common in Extant Gibbon Genera
inferredcites →https://doi.org/10.1525/9780520943735openalex-snapshot
Lizards in an Evolutionary Tree
inferredcites →https://doi.org/10.1534/genetics.111.129569openalex-snapshot
A General Method for Calculating Likelihoods Under the Coalescent Process
inferredcites →https://doi.org/10.1534/genetics.111.130575openalex-snapshot
The Joint Effects of Background Selection and Genetic Recombination on Local Gene Genealogies
inferredcites →https://doi.org/10.1534/genetics.115.174425openalex-snapshot
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach
inferredcites →https://doi.org/10.1534/genetics.116.190173openalex-snapshot
Challenges in Species Tree Estimation Under the Multispecies Coalescent Model
inferredcites →https://doi.org/10.1554/04-385openalex-snapshot
GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS
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Handbook of the Mammals of the World
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Lizards in an evolutionary tree: ecology and adaptive radiation of anoles

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks
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Composite Likelihood Adjustment in Bayesian Inference for Estimating Species Tree Parameters Under the Multispecies Coalescent
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Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski’s scorpion (Scorpiones: Buthidae) in arid Asian inland
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Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome
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Improvement to GLASS/Maximum Tree Method of Species Tree Inference Using Measurement Error Modified Single Linkage Clustering
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From Evolutionary Genomics to Conservation Action: Gibbon as a System for Integrative Primate Genomics
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A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model
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Gene tree quality affects empirical coalescent branch length estimation
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Phylogenomic analyses provide insights into primate evolution
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Phylogeny and species delimitation of ciliates in the genus Spirostomum (class Heterotrichea) using single-cell transcriptomes
inferred← citeshttps://doi.org/10.1186/s42483-020-00076-5openalex-snapshot
Fungal species associated with apple Valsa canker in East Asia
inferred← citeshttps://doi.org/10.32942/osf.io/9pz6mopenalex-snapshot
Notes on a tree: reframing the relevance of primate choruses, duets, and solo songs
inferred← citeshttps://doi.org/10.3390/genes9030123openalex-snapshot
Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets
inferred← citeshttps://doi.org/10.3390/life8020020openalex-snapshot
phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R
inferred← citeshttps://doi.org/10.3951/sobim.44.2_84openalex-snapshot
テナカサルとヒトのフラキエーション
inferred← citeshttps://doi.org/10.6084/m9.figshare.13316770openalex-snapshot
Additional file 1 of Fungal species associated with apple Valsa canker in East Asia
inferred← citeshttps://doi.org/10.7287/peerj.6399v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.6399v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.6399v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.6399v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.6399v0.2/reviews/3openalex-snapshot
Peer Review #3 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.2)"
inferred← citeshttps://doi.org/10.7554/elife.90656openalex-snapshot
Major patterns in the introgression history of Heliconius butterflies
inferred← citeshttps://doi.org/10.7554/elife.90656.1openalex-snapshot
Major patterns in the introgression history of Heliconius butterflies
inferred← citeshttps://doi.org/10.7554/elife.90656.2openalex-snapshot
Major patterns in the introgression history of Heliconius butterflies
inferred← citeshttps://doi.org/10.7554/elife.90656.3openalex-snapshot
Major patterns in the introgression history of Heliconius butterflies
inferred← citeshttps://doi.org/10.7717/peerj.6399openalex-snapshot
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.