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Recombination-aware phylogenomics unravels the complex divergence of hybridizing species.

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What this work says

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

inferredcites →https://doi.org/10.1006/geno.1999.5743openalex-snapshot

A Genetic Linkage Map of Microsatellites in the Domestic Cat (Felis catus)

inferredcites →https://doi.org/10.1007/978-94-010-0265-3_2openalex-snapshot

Recombination and the divergence of hybridizing species

inferredcites →https://doi.org/10.1007/s00239-001-0034-9openalex-snapshot

The Effect of Recombination on the Accuracy of Phylogeny Estimation

inferredcites →https://doi.org/10.1007/s10577-009-9079-1openalex-snapshot

Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years

inferredcites →https://doi.org/10.1016/j.cell.2018.05.007openalex-snapshot

SMCHD1 Merges Chromosome Compartments and Assists Formation of Super-Structures on the Inactive X

inferredcites →https://doi.org/10.1016/j.tig.2008.04.007openalex-snapshot

Sex chromosomes and speciation in Drosophila

inferredcites →https://doi.org/10.1016/j.ympev.2010.01.036openalex-snapshot

Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae)

inferredcites →https://doi.org/10.1016/j.ympev.2016.09.017openalex-snapshot

Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification

inferredcites →https://doi.org/10.1016/s0169-5347(00)02027-9openalex-snapshot

How does recombination affect phylogeny estimation?

inferredcites →https://doi.org/10.1017/cbo9780511819049.017openalex-snapshot

Introduction to recombination detection

inferredcites →https://doi.org/10.1038/nature10231openalex-snapshot

Inference of human population history from individual whole-genome sequences

inferredcites →https://doi.org/10.1038/nature14181openalex-snapshot

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

inferredcites →https://doi.org/10.1038/nature18589openalex-snapshot

Structural organization of the inactive X chromosome in the mouse

inferredcites →https://doi.org/10.1038/nature19417openalex-snapshot

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

inferredcites →https://doi.org/10.1038/ncomms3433openalex-snapshot

The tiger genome and comparative analysis with lion and snow leopard genomes

inferredcites →https://doi.org/10.1038/ng.3199openalex-snapshot

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

inferredcites →https://doi.org/10.1038/ng1111openalex-snapshot

Evidence for co-evolution of gene order and recombination rate

inferredcites →https://doi.org/10.1038/nrg1603openalex-snapshot

Phylogenomics and the reconstruction of the tree of life

inferredcites →https://doi.org/10.1038/nrg2712openalex-snapshot

Mammalian recombination hot spots: properties, control and evolution

inferredcites →https://doi.org/10.1038/s41467-018-05479-9openalex-snapshot

Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

inferredcites →https://doi.org/10.1073/pnas.0308513100openalex-snapshot

Exceptional conservation of horse–human gene order on X chromosome revealed by high-resolution radiation hybrid mapping

inferredcites →https://doi.org/10.1073/pnas.1410083111openalex-snapshot

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

inferredcites →https://doi.org/10.1073/pnas.1419306112openalex-snapshot

Extreme selective sweeps independently targeted the X chromosomes of the great apes

inferredcites →https://doi.org/10.1073/pnas.1616744114openalex-snapshot

Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

inferredcites →https://doi.org/10.1086/600082openalex-snapshot

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

inferredcites →https://doi.org/10.1093/gbe/evw179openalex-snapshot

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

inferredcites →https://doi.org/10.1093/gbe/evy085openalex-snapshot

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species

inferredcites →https://doi.org/10.1093/genetics/156.2.879openalex-snapshot

Consequences of Recombination on Traditional Phylogenetic Analysis

inferredcites →https://doi.org/10.1093/jhered/esg008openalex-snapshot

Second-Generation Integrated Genetic Linkage/Radiation Hybrid Maps of the Domestic Cat (Felis catus)

inferredcites →https://doi.org/10.1093/molbev/mst116openalex-snapshot

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

inferredcites →https://doi.org/10.1093/molbev/msw243openalex-snapshot

The composite regulatory basis of the large X-effect in mouse speciation

inferredcites →https://doi.org/10.1093/sysbio/syv023openalex-snapshot

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

inferredcites →https://doi.org/10.1093/sysbio/syv045openalex-snapshot

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

inferredcites →https://doi.org/10.1098/rspb.2012.0683openalex-snapshot

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

inferredcites →https://doi.org/10.1098/rstb.2011.0249openalex-snapshot

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

inferredcites →https://doi.org/10.1101/gr.113985.110openalex-snapshot

Adaptive seeds tame genomic sequence comparison

inferredcites →https://doi.org/10.1101/gr.114751.110openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.114876.110openalex-snapshot

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

inferredcites →https://doi.org/10.1101/gr.125864.111openalex-snapshot

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

inferredcites →https://doi.org/10.1101/gr.186668.114openalex-snapshot

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

inferredcites →https://doi.org/10.1101/gr.7.3.210openalex-snapshot

X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content.

inferredcites →https://doi.org/10.1101/gr.9.12.1223openalex-snapshot

Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping

inferredcites →https://doi.org/10.1111/evo.12118openalex-snapshot

MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING

inferredcites →https://doi.org/10.1111/evo.12712openalex-snapshot

Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05730.xopenalex-snapshot

Genome‐wide patterns of divergence and gene flow across a butterfly radiation

inferredcites →https://doi.org/10.1111/j.1558-5646.2010.01092.xopenalex-snapshot

SPECIATION IN THE EUROPEAN RABBIT (ORYCTOLAGUS CUNICULUS): ISLANDS OF DIFFERENTIATION ON THE X CHROMOSOME AND AUTOSOMES

inferredcites →https://doi.org/10.1111/mec.12716openalex-snapshot

Sympatric Asian felid phylogeography reveals a major Indochinese–Sundaic divergence

inferredcites →https://doi.org/10.1111/mec.13038openalex-snapshot

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

inferredcites →https://doi.org/10.1111/mec.13557openalex-snapshot

A genomic perspective on hybridization and speciation

inferredcites →https://doi.org/10.1111/mec.14777openalex-snapshot

Evaluating genomic signatures of “the large X‐effect” during complex speciation

inferredcites →https://doi.org/10.1126/sciadv.1700299openalex-snapshot

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

inferredcites →https://doi.org/10.1126/science.1122277openalex-snapshot

The Late Miocene Radiation of Modern Felidae: A Genetic Assessment

inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot

A Draft Sequence of the Neandertal Genome

inferredcites →https://doi.org/10.1126/science.1211028openalex-snapshot

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot

Whole-genome analyses resolve early branches in the tree of life of modern birds

inferredcites →https://doi.org/10.1186/1471-2148-14-137openalex-snapshot

The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms

inferredcites →https://doi.org/10.1186/1471-2164-11-159openalex-snapshot

Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot

ANGSD: Analysis of Next Generation Sequencing Data

inferredcites →https://doi.org/10.1186/s12863-014-0148-xopenalex-snapshot

Recombination of the porcine X chromosome: a high density linkage map

inferredcites →https://doi.org/10.1186/s13059-015-0728-8openalex-snapshot

Bipartite structure of the inactive mouse X chromosome

inferredcites →https://doi.org/10.1186/s13059-015-0837-4openalex-snapshot

Genomic legacy of the African cheetah, Acinonyx jubatus

inferredcites →https://doi.org/10.1186/s13059-016-1090-1openalex-snapshot

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot

Relaxed Phylogenetics and Dating with Confidence

inferredcites →https://doi.org/10.1371/journal.pgen.1003519openalex-snapshot

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

inferredcites →https://doi.org/10.1371/journal.pgen.1004410openalex-snapshot

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

inferredcites →https://doi.org/10.1371/journal.pgen.1005451openalex-snapshot

Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence

inferredcites →https://doi.org/10.1534/g3.116.028746openalex-snapshot

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination

inferredcites →https://doi.org/10.1534/genetics.113.152074openalex-snapshot

Purifying Selection Causes Widespread Distortions of Genealogical Structure on the Human X Chromosome

What points at this work

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

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/10.7717/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.