An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla DOI Creative Commons
Nicolas Galtier

Peer Community Journal, Journal Year: 2024, Volume and Issue: 4

Published: Jan. 22, 2024

Gene flow and incomplete lineage sorting are two distinct sources of phylogenetic conflict, i.e., gene trees that differ in topology from each other the species tree. Distinguishing between processes is a key objective current evolutionary genomics. This most often pursued via so-called ABBA-BABA type method, which relies on prediction symmetry tree discordance made by hypothesis. flow, however, need not be asymmetric, when it not, approaches do properly measure prevalence flow. I introduce Aphid, an approximate maximum-likelihood method aimed at quantifying conflict branch length analysis three-species trees. Aphid draws information fact affected tend to have shorter branches, longer than average Accounting for among-loci variance mutation rate time, returns estimates speciation times ancestral effective population size, posterior assessment contribution conflict. Simulations suggest reasonably robust wide range conditions. Analysis coding non-coding data primates illustrates potential approach reveals substantial fraction human/chimpanzee/gorilla due ancient also predicts older smaller estimated size this group, compared existing analyses assuming no

Language: Английский

Phylogenetic tree building in the genomic age DOI
Paschalia Kapli, Ziheng Yang, Maximilian J. Telford

et al.

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(7), P. 428 - 444

Published: May 18, 2020

Language: Английский

Citations

397
Widespread introgression across a phylogeny of 155 Drosophila genomes DOI Creative Commons
Anton Suvorov, Bernard Kim, Jeremy Wang

et al.

Current Biology, Journal Year: 2021, Volume and Issue: 32(1), P. 111 - 123.e5

Published: Nov. 16, 2021

Language: Английский

Citations

229
Prevalence and Adaptive Impact of Introgression DOI
Nathaniel B. Edelman, James Mallet

Annual Review of Genetics, Journal Year: 2021, Volume and Issue: 55(1), P. 265 - 283

Published: Sept. 28, 2021

Alleles that introgress between species can influence the evolutionary and ecological fate of exposed to novel environments. Hybrid offspring different are often unfit, yet it has long been argued introgression be a potent force in evolution, especially plants. Over last two decades, genomic data have increasingly provided evidence is critically important source genetic variation this additional useful adaptive evolution both animals Here, we review factors probability foreign variants provide long-term benefits (so-called introgression) discuss their potential benefits. We find plays an role particularly when far from its fitness optimum, such as they expand range or subject changing

Language: Английский

Citations

164
Phylogenomic approaches to detecting and characterizing introgression DOI Creative Commons
Mark S. Hibbins, Matthew W. Hahn

Genetics, Journal Year: 2021, Volume and Issue: 220(2)

Published: Nov. 11, 2021

Abstract Phylogenomics has revealed the remarkable frequency with which introgression occurs across tree of life. These discoveries have been enabled by rapid growth methods designed to detect and characterize from whole-genome sequencing data. A large class phylogenomic makes use data species infer based on expectations multispecies coalescent. range simple tests, such as D-statistic, model-based approaches for inferring phylogenetic networks. Here, we provide a detailed overview various signals that different modes are expected leave in genome, how current them. We discuss strengths pitfalls these identify areas future development, highlighting introgression, power each method conclude discussion challenges they could potentially be addressed.

Language: Английский

Citations

145
Hybrid speciation driven by multilocus introgression of ecological traits DOI Creative Commons
Neil Rosser, Fernando Seixas, Lucie M. Queste

et al.

Nature, Journal Year: 2024, Volume and Issue: 628(8009), P. 811 - 817

Published: April 17, 2024

Abstract Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species 1,2 . However, convincing examples homoploid hybrid speciation remain rare because it is challenging demonstrate that hybridization was crucial in generating reproductive isolation 3 Here we combine population genomic analysis with quantitative trait locus mapping species-specific traits examine a case Heliconius butterflies. We show elevatus sympatric both parents has persisted as an independently evolving lineage for at least 180,000 years. This despite pervasive ongoing gene flow one parent, pardalinus , which homogenizes 99% their genomes. The remaining 1% introgressed from other melpomene scattered widely across H. genome islands divergence These contain multiple are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones mate choice. Collectively, these place on its own adaptive peak permit coexistence parents. Our results driven by introgression ecological traits, possible multilocus genetic architecture.

Language: Английский

Citations

25
The evolution of insect biodiversity DOI Creative Commons
Erik Tihelka, Chenyang Cai, Mattia Giacomelli

et al.

Current Biology, Journal Year: 2021, Volume and Issue: 31(19), P. R1299 - R1311

Published: Oct. 1, 2021

Language: Английский

Citations

85
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow DOI Creative Commons
Dezhi Zhang, Frank E. Rheindt, Huishang She

et al.

Systematic Biology, Journal Year: 2021, Volume and Issue: 70(5), P. 961 - 975

Published: March 30, 2021

Abstract Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction species phylogenies is gene flow, especially if interspecific flow has affected large parts genome. We investigated phylogenetic relationships within clade comprising eight passerine birds (Phylloscopidae, Phylloscopus, leaf warblers) using one de novo genome assembly and 78 resequenced genomes. On basis hypothesis-exclusion trials D-statistics, network analysis, demographic inference we identified ancient affecting between ancestral lineage sister pair. This consistently caused erroneous phylogeny when amounts data. In contrast, were captured smaller analyzed, showing “winner-takes-all democratic majority tree” necessarily tree. Under this condition, sometimes avoid effects due stochastic sampling, as hidden reticulation histories are more likely emerge from use larger sets, whole-genome sets. addition, also found genomic regions by generally exhibited higher differentiation but lower recombination rate nucleotide diversity. Our study highlights importance considering in reconstructions era.[Bifurcation; introgression; recombination; reticulation; Phylloscopus.]

Language: Английский

Citations

61
Multispecies Coalescent: Theory and Applications in Phylogenetics DOI
Siavash Mirarab, Luay Nakhleh, Tandy Warnow

et al.

Annual Review of Ecology Evolution and Systematics, Journal Year: 2021, Volume and Issue: 52(1), P. 247 - 268

Published: Aug. 20, 2021

Species tree estimation is a basic part of many biological research projects, ranging from answering evolutionary questions (e.g., how did group species adapt to their environments?) addressing in functional biology. Yet, very challenging, due processes such as incomplete lineage sorting, gene duplication and loss, horizontal transfer, hybridization, which can make trees differ each other the overall history species. Over last 10–20 years, there has been tremendous growth methods mathematical theory for estimating phylogenetic networks, some these are now wide use. In this survey, we provide an overview current state art, identify limitations existing theory, propose additional problems directions.

Language: Английский

Citations

60
Estimation of species divergence times in presence of cross-species gene flow DOI Creative Commons
George P. Tiley, Tomáš Flouri,

Xiyun Jiao

et al.

Systematic Biology, Journal Year: 2023, Volume and Issue: 72(4), P. 820 - 836

Published: March 24, 2023

Abstract Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence even a small amount bias time estimates when gene flow is ignored in analysis. Using advances analytical methods under multispecies coalescent (MSC) model, demonstrate that by accounting for incomplete lineage sorting and using large data sets this problem be avoided. The multispecies-coalescent-with-introgression (MSci) model capable accurately estimating both times ancestral effective population sizes, only single diploid individual per sampled. We characterize some general expectations biases estimation three different scenarios: 1) between sister species, 2) non-sister 3) from an unsampled (i.e., ghost) outgroup lineage. also conducted isolation-with-migration (IM) found MSci assuming episodic was able estimate despite high levels continuous flow. estimated MSC models two published empirical datasets with previous evidence introgression, one 372 target-enrichment loci baobabs (Adansonia), another 1000 transcriptome 14 tomato relative, Jaltomata. analyses not confirm our findings simulations, demonstrating reliably but robust amounts extensive taxon sampling. [divergence time; flow; hybridization; introgression; model; coalescent]

Language: Английский

Citations

28
Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow DOI Creative Commons

Xiyun Jiao,

Tomáš Flouri, Ziheng Yang

et al.

National Science Review, Journal Year: 2021, Volume and Issue: 8(12)

Published: July 13, 2021

Multispecies coalescent (MSC) is the extension of single-population model to multiple species. It integrates phylogenetic process species divergences and population genetic coalescent, provides a powerful framework for number inference problems using genomic sequence data from species, including estimation divergence times sizes, trees accommodating discordant gene trees, cross-species flow delimitation. In this review, we introduce major features MSC model, discuss full-likelihood heuristic methods tree summarize recent methodological advances in flow. We statistical computational challenges field research directions where breakthroughs may be likely next few years.

Language: Английский

Citations

53