ArticleSystematic biology2023
Estimation of species divergence times in presence of cross-species gene flow.
Article in Systematic biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- The Complex Interplay between Evolutionary Flexibility and Diversification in a Family of Spiders.Systematic biology · 2026Article
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- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi's paleo-archipelago.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Timing and Pattern of Early Diversification in Drosophilidae (Diptera).Molecular biology and evolution · 2025Article
- Genomic identification of conservation areas amid lineage divergence and admixture in a threatened island gecko.BMC biology · 2025Article
- Pervasive and recurrent hybridization prevents inbreeding in Europe's most threatened seabird.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Synergies between speciation and conservation science yield novel insights for mitigating the biodiversity crisis of the Anthropocene.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 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
- Phylogenomics, historical biogeography, and diversification of leaf traits in the Malagasy-endemic genus Uncarina (Pedaliaceae).American journal of botany · 2025Article
- Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species.The Plant journal : for cell and molecular biology · 2024Article
- Morphometrics and Phylogenomics of Coca (Erythroxylum spp.) Illuminate Its Reticulate Evolution, With Implications for Taxonomy.Molecular biology and evolution · 2024Article
- Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information.Systematic biology · 2024Article
- Interspecific transfer of genetic information through polyploid bridges.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa.Annals of botany · 2024Article
- Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family.Scientific reports · 2024Article
- Divergent dynamics of sexual and habitat isolation at the transition between stick insect populations and species.Nature communications · 2024Article
- Inclusion of highly admixed genotypes in grapevine genomic analyses leads to an equivocal reconstruction of its domestication history.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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Abstract
Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent].
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