Ghost admixture in eastern gorillas

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(9), P. 1503 - 1514

Published: July 27, 2023

Abstract Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic been identified in chimpanzees bonobos but the 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 neural networks to model demographic history gorillas, find signature an ‘ghost’ lineage common ancestor western gorillas. We infer that up 3% genome these individuals is introgressed diverged more than 3 million years ago This introgression event took place before split mountain lowland probably 40 thousand may have influenced perception bitter taste When comparing landscapes humans bonobos, consistent depletion fragments X chromosome However, protein-coding content detectable possibly consequence stronger genetic drift

Language: Английский

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Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

Cladistics, Journal Year: 2024, Volume and Issue: 40(4), P. 357 - 373

Published: Jan. 10, 2024

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex in and observe variations across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution southwest China probably constitute syngameon. In this study, we mapped resequencing from different group Quercus aquifolioides reference genome obtain high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. reconstructed phylogenetic relationships, explored level pattern introgression these investigated tree variation using sliding windows. same or plastomes were found be shared extensively within specific geographical area. Phylogenomic analyses genome-wide SNP that most clade showed genetic coherence, but several connected by introgression. trees obtained windows are highly heterogeneous therefore obscured. Our study all form obscured observed empirically best explained conjunction incomplete lineage sorting.

Language: Английский

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Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(1), P. 207 - 222

Published: Jan. 1, 2024

Abstract In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying introgression, however, presents challenge. To address this issue, we focused on simple cases involving 3 species known phylogenetic tree. Using mathematical analyses simulations, evaluated performance popular methods, including HyDe PhyloNet/MPL, full-likelihood method, Bayesian Phylogenetics Phylogeography (BPP), in detecting introgression. Our findings suggest that heuristic approaches relying site-pattern counts gene-tree topologies struggle differentiate between sampled non-sister species, frequently leading incorrect identification donor recipient species. The method BPP uses multilocus sequence alignments directly—hence taking into account both branch lengths, by contrast, is capable phylogenomic datasets. We analyzed real-world dataset 14 Jaltomata (Solanaceae) showcase potential methods accurate inference

Language: Английский

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Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species

The Plant Journal, Journal Year: 2024, Volume and Issue: 119(3), P. 1386 - 1399

Published: June 6, 2024

SUMMARY Ghost introgression, or the transfer of genetic material from extinct unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost especially in plant remains scarce. Here, we newly assembled chromosome‐level genomes both Carya sinensis and cathayensis , additionally re‐sequenced whole 43 C. individuals as well 11 representing diploid hickory species. These genomic datasets were used investigate reticulation bifurcation patterns within genus (Juglandaceae), with a particular focus on beaked . By combining D ‐statistic BPP methods, obtained compelling that supports occurrence introgression an ancestral lineage. This conclusion was reinforced through phylogenetic network analysis genome scan method VolcanoFinder, latter which can detect signatures adaptive unknown donors. Our results not only dispel certain misconceptions about history but also further refine our understanding 's biogeography via divergence estimates. Moreover, successful integration methods demonstrates their efficacy facilitating more precise identification types.

Language: Английский

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Phylogenomics and species delimitation in the Lepidophyma sylvaticum complex (Squamata: Xantusiidae) using ddRADseq and morphological data

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 108288 - 108288

Published: Jan. 1, 2025

Language: Английский

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Coalescent-based branch length estimation improves dating of species trees

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 28, 2025

Species trees need to be dated for many downstream applications. Typical molecular dating methods take a phylogenetic tree with branch lengths in substitution units as well set of calibrations input and convert the species unit time while being consistent pre-specified calibrations. When from multi-locus genome-scale datasets, sometimes topology are estimated using concatenation. However, concatenation does not address gene heterogeneity across genome. While Bayesian can some forms heterogeneity, such incomplete lineage sorting, they scalable large datasets. In this paper, we introduce new pipeline that addresses discordance both length estimation. The uses discordance-aware account sorting estimating maximum likelihood-based step. Our simulation study on datasets shows produces more accurate less biased dates than pipelines use or unpartitioned methods. Furthermore, it is substantially handle thousands genes. results two biological show improves inference node ages nodes, particular extant taxa, diversification analysis.

Language: Английский

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Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: April 28, 2025

Phylogenetic research in Tulipa (Liliaceae), a genus of significant economic and horticultural value, has relied on limited nuclear (mostly ribosomal internal transcribed spacer, nrITS) plastid DNA 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. We newly sequenced 50 transcriptomes 46 species Tulipeae (including multiple accessions all four genera) one outgroup sister Lilieae (Notholirion campanulatum), downloaded 15 previously published supplement sampling. One dataset (74 protein-coding genes, PCGs) (2594 orthologous OGs) were constructed, with latter used tree inference based maximum likelihood (ML) multi-species coalescent (MSC) methods. To investigate causes gene 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 further investigated applying D-statistics QuIBL. 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 remainder whereas T. sinkiangensis clustered Tulipa. In contrast, traditional sections found be non-monophyletic.

Language: Английский

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Hybridisation has shaped a recent radiation of grass-feeding aphids

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: July 13, 2023

Aphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, aphids give birth to live young that already pregnant. qualities enable rapid population growth and have facilitated the colonisation crops globally. In cases, so-called "super clones" come dominate agricultural systems. However, extent which stage aphid life cycle has shaped global pest populations remained unclear, as origins successful lineages. Here, we used chromosome-scale genome assemblies disentangle evolution two pests cereals-the English (Sitobion avenae) Indian miscanthi) grain aphids.

Language: Английский

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Holocene Climate Change Promoted Allopatric Divergence and Disjunct Geographic Distribution in a Bee Orchid Species

Journal of Biogeography, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 2, 2024

ABSTRACT Aim Species with disjunct geographic distributions provide natural opportunities to investigate incipient or recent allopatric divergence. The combination of both genetic and ecological data may be fruitful decipher the causes such patterns: (i) actual vicariance, (ii) successful colonisation from one source a new range (dispersal, biological introduction) (iii) parallel convergent evolution. Location Southern France Northern Spain. Taxon bee orchid Ophrys aveyronensis (and its two recognised subspecies O. a. subsp. vitorica ) displays distribution subranges separated by 600 km on sides Pyrenees mountain range. Methods As divergence is often complex document in wild, we used population genomics niche modelling (ENM) this intriguing biogeographic pattern. Results genomic demonstrate that all studied populations exhibit similar patterns diversity dramatic decrease effective size compared ancestral population. Significant differentiation reciprocal monophyly exist between , despite very time as young ca. 1500 generations ago. Moreover, paleo‐ENM analyses support consistent split broad range, contraction distinct longitudinal latitudinal shifts response climate warming during Holocene. Main Conclusion congruence results obtained ENM approaches documents how continental initiated speciation system. provides promising opportunity study onset reproductive isolation evolution following an initial stage separation group high diversification rate.

Language: Английский

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Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events”

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(3), P. e3002557 - e3002557

Published: March 19, 2024

In a previous article [1], we used simulations to show how acknowledging the existence of extinct and unsampled lineages, or "ghosts," could substantially influence conclusions regarding gene flow derived from tree branch lengths analyses.We mentioned that this in particular challenge claim by Pittis Gabaldon [2,3] genes alpha-proteobacterial origin are more recently transferred than those originating actinobacteria.Bernabeu colleagues [4] propose critique our results based on 2 additional interesting analyses.The first one, summarized their Fig 1C, is description conditions under which can actually be reversed ("conditions shift" terminology), thus possibility.Bernabeu conclude these "rather restrictive" "highly constrained," suggesting they unlikely.This calls for 3 comments.One list give slightly relaxed.Indeed, it not necessary earlier transfer (from alpha-proteobacteria) originates ghost lineage (as 1C [4]).The shift also obtained if comes directly non-ghost alpha-proteobacteria (α1 1) at an time actinobacteria.This decreases restrictivity shift.Another comment necessarily independent.Constraining events happen limited timeframe (the FECA-to-LECA period) presented as condition chance occurs all [4], but according analyses (Fig 6B [1]) may same increase probability leads shift.A last constrained" vague subjective qualifications.An opposite intuition arguable: consider most microbial diversity unknown [5], observe numerous complete clades (such CPR, represents large part ToL 1A Ref [4]) probably missing such analysis, seem sufficiently plausible question robustness stemlength claims.Further work needed transform intuitions into assess likelihood (or not) when overwhelming presence ghosts.Our [1] were attempt quantify effect.Surely sufficient definitive answer, because indeed informed knowledge have about life.At least, light Bernabeu remains, view, largely open.

Language: Английский

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