Ghost admixture in eastern gorillas DOI Creative Commons
Harvinder Pawar, Aigerim Rymbekova, Sebastián Cuadros-Espinoza

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 19, 2022

Abstract Archaic admixture has had a significant impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. Within the great apes archaic been identified in chimpanzees bonobos, but possibility of not explored other species. Here, we address this question using high-coverage whole genome sequences all four extant gorilla subspecies, six newly sequenced eastern gorillas previously unsampled geographic regions. Using Approximate Bayesian Computation (ABC) neural networks to model demographic history gorillas, find signature an ‘ghost’ lineage common ancestor western gorillas. We infer that up 3% these individuals is introgressed diverged more than 3 million years ago This introgression event took place before split mountain lowland likely 40 thousand ago, may have influenced perception bitter taste When comparing landscapes humans consistent depletion fragments X chromosome However, protein-coding content detectable possibly consequence stronger genetic drift

Language: Английский

Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants DOI Creative Commons

Zhaoxing Wu,

Claudia Solís‐Lemus

Bioinformatics Advances, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

The abundance of gene flow in the Tree Life challenges notion that evolution can be represented with a fully bifurcating process which cannot capture important biological realities like hybridization, introgression, or horizontal transfer. Coalescent-based network methods are increasingly popular, yet not scalable for big data, because they need to perform heuristic search space networks as well numerical optimization NP-hard. Here, we introduce novel method reconstruct phylogenetic based on algebraic invariants. While there is long tradition using invariants phylogenetics, our work first define concordance factors (frequencies four-taxon splits input trees) identify level-1 under multispecies coalescent model.

Language: Английский

Citations

1
Uncovering Ghost Introgression Through Genomic Analysis of a Distinct East Asian Hickory Species DOI Creative Commons
Wei‐Ping Zhang, Ya‐Mei Ding, Yu Cao

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 27, 2023

ABSTRACT Although the possibility of introgression from ghost lineages (all unsampled extant and extinct taxa) is now widely recognized, detecting characterizing remains a challenge. Here, we propose combined use popular D -statistic method, which tests for presence introgression, full-likelihood method BPP, determines possible gene-flow scenarios, including truly responsible. We illustrate utility this approach by investigating reticulation bifurcation history genus Carya (Juglandaceae), beaked hickory sinensis . To achieve goal, generated two chromosome-level reference genomes respectively C. cathayensis Furthermore, re-sequenced whole 43 individuals one individual each 11 diploid species The latter dataset with per used to reconstruct phylogenetic networks estimate divergence time Our results unambiguously demonstrate an lineage into hickory, dispelling certain misconceptions about also discuss profound implications historical biogeography species. [BPP; ; -statistic; gene flow; introgression]

Language: Английский

Citations

2
A Cautionary Note on Using STRUCTURE to Detect Hybridization in a Phylogenetic Context DOI Creative Commons

Xiao‐Xu Pang,

Da‐Yong Zhang

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 8, 2024

Abstract Population genetic clustering methods are widely used to detect hybridization events between closely related populations within species, as well deeply diverged lineages across phylogenetic time-scales, although their strengths and limitations in the latter cases remain poorly explored. This study presents first systematic evaluation of performance most popular population method, STRUCTURE, under a variety cross-species scenarios, including hybrid speciation, introgression involving ghost (i.e., extinct or unsampled) otherwise. Our simulations demonstrate that STRUCTURE performs identifying hybrids parental donors only when admixture happens very recently sampled extant lineages. However, generally fails signals occurs deep time gene flow stems from We find symmetrical contribution speciation will often be revealed extremely asymmetrical especially event occurred more than some ago. results suggest population-genetic may inefficient for detecting either ancient admixtures, partly explaining why has escaped attention evolutionary biologists until recently.

Language: Английский

Citations

0
Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics DOI
Zhihui Zhang, Meizhen Wang, Zhaoping Yang

et al.

Published: Oct. 3, 2024

Abstract Background: Phylogenetic research in Tulipa (Liliaceae), a genus of significant economic and horticultural value, has relied on limited nuclear (mostly nrITS) plastid gene sequences, resulting low-resolution phylogenetic trees uncertain intrageneric classifications. The genus, noted for its large genome, presents discordant relationships among Amana, Erythronium, Tulipa, likely due to incomplete lineage sorting (ILS) and/or reticulate evolution. Thus, phylogenomic approaches are needed clarify these the conflicting signals within tribe Tulipeae. Results: We newly sequenced 50 transcriptomes 46 species Tulipeae (including multiple accessions all four genera) one outgroup Lilieae (Notholirion campanulatum), downloaded 15 previously published supplement sampling. One dataset (74 protein coding genes, PCGs) (2,594 orthologous OGs) were constructed, with latter used tree inference based maximum likelihood (ML) multi-species coalescent (MSC) methods. To investigate causes discordance, ‘site con/discordance factors’ (sCF sDF1/sDF2) calculated first, after which nodes displaying high or imbalanced sDF1/2 selected network analyses polytomy tests determine whether ILS evolution best explain incongruence. Key not resolved by this technique, especially those Erythronium further investigated applying D-statistics QuIBL. Conclusions: failed reconstruct reliable unambiguous evolutionary history pervasive evolution, caused either obscured minority signal differing genomic compartments. However, we confirmed monophyly most subgenera, exception two small subgenus Orithyia, heterophylla was recovered as sister remainder whereas T. sinkiangensis clustered Tulipa. In contrast, traditional sections found be non-monophyletic.

Language: Английский

Citations

0
Phylogeny Inference Under Time-Decaying Migration and Varying Information Content DOI Creative Commons
Zaynab Shaik, Nicola G. Bergh, G. Anthony Verboom

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 23, 2023

A bstract Postspeciation gene flow is widespread across the Tree of Life but ignored as a cause tree discordance under standard multispecies coalescent. Where interspecific migration has occurred not modelled explicitly, effective population sizes, divergence times and topology can be seriously misestimated. Isolation-with-migration coalescent-with-introgression models explicitly model include additional parameters that limit their computational viability with even moderately sized molecular data sets. Here we simulate evolution sequences which vary in information content coalescent while allowing continuous, tree-wide flow/migration between contemporaneous branches, rate decreases time since divergence. Using simulated sequences, evaluate performance DENIM rapidly to gradually time-decaying benchmark its against MSC method StarBeast3. consistently outperforms StarBeast3, both phylogenetic accuracy per core. Rapidly decaying associated improved estimates While species estimation by increasing number loci from 30 60 either method, convergence slowed considerably. By contrast, sequence length 10,000 bp no clear effect on rates, shows tendency towards increased DENIM. We apply StarBeast3 36-locus empirical bat set recover trees identical those obtained 12,931 loci. Our work demonstrates deliver accurate presence deep coalescence empirically realistic patterns using few single-core runtimes 2-3 days.

Language: Английский

Citations

0
Ghost admixture in eastern gorillas DOI Creative Commons
Harvinder Pawar, Aigerim Rymbekova, Sebastián Cuadros-Espinoza

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 19, 2022

Abstract Archaic admixture has had a significant impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. Within the great apes archaic been identified in chimpanzees bonobos, but possibility of not explored other species. Here, we address this question using high-coverage whole genome sequences all four extant gorilla subspecies, six newly sequenced eastern gorillas previously unsampled geographic regions. Using Approximate Bayesian Computation (ABC) neural networks to model demographic history gorillas, find signature an ‘ghost’ lineage common ancestor western gorillas. We infer that up 3% these individuals is introgressed diverged more than 3 million years ago This introgression event took place before split mountain lowland likely 40 thousand ago, may have influenced perception bitter taste When comparing landscapes humans consistent depletion fragments X chromosome However, protein-coding content detectable possibly consequence stronger genetic drift

Language: Английский

Citations

0