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Joint inference of species histories and gene flow

https://doi.org/10.1101/348391
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What this work says

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

inferredcites →https://doi.org/10.1002/bies.201500149openalex-snapshot
How reticulated are species?
inferredcites →https://doi.org/10.1007/978-0-387-98141-3openalex-snapshot
ggplot2: Elegant Graphics for Data Analysis
inferredcites →https://doi.org/10.1016/j.jtbi.2010.09.010openalex-snapshot
Sampling-through-time in birth–death trees
inferredcites →https://doi.org/10.1016/j.tpb.2007.11.001openalex-snapshot
The distribution of the coalescence time and the number of pairwise nucleotide differences in the “isolation with migration” model
inferredcites →https://doi.org/10.1016/j.tpb.2012.05.003openalex-snapshot
The distribution of the coalescence time and the number of pairwise nucleotide differences in a model of population divergence or speciation with an initial period of gene flow
inferredcites →https://doi.org/10.1016/j.ympev.2009.05.033openalex-snapshot
Coalescent methods for estimating phylogenetic trees
inferredcites →https://doi.org/10.1038/196907a0openalex-snapshot
Anopheles gambiae Complex
inferredcites →https://doi.org/10.1038/nature12228openalex-snapshot
Great ape genetic diversity and population history
inferredcites →https://doi.org/10.1038/nrg3446openalex-snapshot
Understanding the origin of species with genome-scale data: modelling gene flow
inferredcites →https://doi.org/10.1073/pnas.0611164104openalex-snapshot
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
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Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation
inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/bty406openalex-snapshot
MASCOT: parameter and state inference under the marginal structured coalescent approximation
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/158.2.885openalex-snapshot
Distinguishing Migration From Isolation: A Markov Chain Monte Carlo Approach
inferredcites →https://doi.org/10.1093/genetics/161.1.269openalex-snapshot
Larger Genetic Differences Within Africans Than Between Africans and Eurasians
inferredcites →https://doi.org/10.1093/genetics/164.4.1511openalex-snapshot
Low Nucleotide Diversity in Chimpanzees and Bonobos
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/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/msp298openalex-snapshot
The Divergence of Chimpanzee Species and Subspecies as Revealed in Multipopulation Isolation-with-Migration Analyses
inferredcites →https://doi.org/10.1093/molbev/msx126openalex-snapshot
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates
inferredcites →https://doi.org/10.1093/molbev/msx186openalex-snapshot
The Structured Coalescent and Its Approximations
inferredcites →https://doi.org/10.1093/molbev/msy158openalex-snapshot
Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex
inferredcites →https://doi.org/10.1093/molbev/msy162openalex-snapshot
Phylogeny Estimation by Integration over Isolation with Migration Models
inferredcites →https://doi.org/10.1093/sysbio/syab054openalex-snapshot
Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales
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/syx060openalex-snapshot
Taming the BEAST—A Community Teaching Material Resource for BEAST 2
inferredcites →https://doi.org/10.1093/ve/vez030openalex-snapshot
Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations
inferredcites →https://doi.org/10.1101/242875openalex-snapshot
Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales
inferredcites →https://doi.org/10.1101/gr.1933104openalex-snapshot
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
inferredcites →https://doi.org/10.1111/j.1755-0998.2009.02732.xopenalex-snapshot
seqphase : a web tool for interconverting phase input/output files and fasta sequence alignments
inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00169.xopenalex-snapshot
phytools: an R package for phylogenetic comparative biology (and other things)
inferredcites →https://doi.org/10.1126/science.1258524openalex-snapshot
Extensive introgression in a malaria vector species complex revealed by phylogenomics
inferredcites →https://doi.org/10.1126/science.286.5442.1159openalex-snapshot
Extensive Nuclear DNA Sequence Diversity Among Chimpanzees
inferredcites →https://doi.org/10.1126/science.aaa3600openalex-snapshot
Conundrum of jumbled mosquito genomes
inferredcites →https://doi.org/10.1146/annurev-ecolsys-102710-145028openalex-snapshot
Evolution of Anopheles gambiae in Relation to Humans and Malaria
inferredcites →https://doi.org/10.1186/1471-2164-15-53openalex-snapshot
MafFilter: a highly flexible and extensible multiple genome alignment files processor
inferredcites →https://doi.org/10.1371/journal.pcbi.1000520openalex-snapshot
Bayesian Phylogeography Finds Its Roots
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1006650openalex-snapshot
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
inferredcites →https://doi.org/10.1371/journal.pgen.1005421openalex-snapshot
New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation
inferredcites →https://doi.org/10.1371/journal.ppat.1003932openalex-snapshot
Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2
inferredcites →https://doi.org/10.1534/genetics.103.024182openalex-snapshot
Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis
inferredcites →https://doi.org/10.1534/genetics.113.158758openalex-snapshot
Estimation of the Spontaneous Mutation Rate per Nucleotide Site in a Drosophila melanogaster Full-Sib Family
inferredcites →https://doi.org/10.1534/genetics.166.3.1375openalex-snapshot
Nucleotide Diversity in Gorillas

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-3-030-10837-3_13openalex-snapshot
Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization
inferred← citeshttps://doi.org/10.1007/s43994-025-00270-1openalex-snapshot
The influence of gene flow on the genetic diversity of SARS-CoV-2 and its variants (British, South African, and Brazilian)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107270openalex-snapshot
Nuclear phylogenies and genomics of a contact zone establish the species rank of Podarcis lusitanicus (Squamata, Lacertidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108274openalex-snapshot
A straightforward workflow to explore species diversity using the Patagonian lizards of the Diplolaemus genus (Iguania: Leiosauridae) as a study case, with the description of a new species
inferred← citeshttps://doi.org/10.1038/s41559-022-01661-xopenalex-snapshot
Supergene origin and maintenance in Atlantic cod
inferred← citeshttps://doi.org/10.1073/pnas.2410939122openalex-snapshot
Genomics of Neotropical biodiversity indicators: Two butterfly radiations with rampant chromosomal rearrangements and hybridization
inferred← citeshttps://doi.org/10.1093/botlinnean/boad025openalex-snapshot
First dated phylogenetic reconstruction of the genus Tamarix (Tamaricaceae): biogeographical implications and hybridization processes in the Mediterranean Basin
inferred← citeshttps://doi.org/10.1093/gbe/evab260openalex-snapshot
Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States
inferred← citeshttps://doi.org/10.1093/gbe/evae172openalex-snapshot
Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides
inferred← citeshttps://doi.org/10.1101/2023.07.18.549472openalex-snapshot
Mitochondrial variation in Anopheles gambiae and An. coluzzii : phylogeographic legacy of species isolation and mito-nuclear associations with metabolic resistance to pathogens and insecticides
inferred← citeshttps://doi.org/10.1101/2023.11.23.568248openalex-snapshot
Phylogeny Inference Under Time-Decaying Migration and Varying Information Content
inferred← citeshttps://doi.org/10.1111/mec.17099openalex-snapshot
A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales
inferred← citeshttps://doi.org/10.1111/mec.70349openalex-snapshot
Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon
inferred← citeshttps://doi.org/10.1111/syen.12352openalex-snapshot
Species limits in butterflies (Lepidoptera: Nymphalidae): reconciling classical taxonomy with the multispecies coalescent
inferred← citeshttps://doi.org/10.1111/zsc.12725openalex-snapshot
A new gecko (Phyllodactylidae: Homonota whitii group) from the Diaguita highlands, Argentina, with an updated phylogeny for the genus
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006650openalex-snapshot
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
inferred← citeshttps://doi.org/10.33612/diss.824282369openalex-snapshot
Speciation and evolution in the Anopheles gambiae complex in the face of widespread introgressive hybridization
inferred← citeshttps://doi.org/10.5808/gi.2019.17.4.e37openalex-snapshot
Recent advances in Bayesian inference of isolation-with-migration models
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