Documenting homoploid hybrid speciation

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: May 23, 2024

Abstract Homoploid hybrid speciation is challenging to document because hybridization can lead outcomes other than speciation. Thus, some authors have argued that establishment of homoploid should include evidence reproductive barriers isolating the neo‐species from its parental species were derived hybridization. While this criterion difficult satisfy, several recent papers successfully employed a common pipeline identify candidate genes underlying such and (in one case) validate their function. We describe pipeline, application plant animal what we learned about as consequence. argue – given ubiquity admixture polygenic basis isolation could be much more protracted suggested by earlier conceptual arguments theoretical studies.

Language: Английский

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Rapid establishment of species barriers in plants compared to animals

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

Published: Oct. 20, 2023

Speciation, the process by which new reproductively isolated species arise from ancestral populations, occurs because of genetic changes that accumulate over time. To date, notion interspecific exchange more frequently between plant than animals has gained a strong footing in scientific discourse, albeit primarily relying on verbal arguments centered mating behavior. By examining dynamics gene flow across continuum divergence both kingdoms, we observe opposite relationship: plants experience less introgression at same level divergence, suggesting barriers are established rapidly plants. This pattern questions differences microevolutionary processes and impact macroevolutionary scale. One Sentence Summary Genetic is frequent animal plants, challenging historical views.

Language: Английский

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Distinguishing between histories of speciation and introgression using genomic data

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

Published: Sept. 9, 2022

Abstract Introgression creates complex, non-bifurcating relationships among species. At individual loci and across the genome, both introgression incomplete lineage sorting interact to produce a wide range of different gene tree topologies. These processes can obscure history speciation lineages, and, as result, identifying vs. remains challenge. Here, we use theory simulation investigate how mislead multiple approaches species inference. We find that arbitrarily low amounts methods parsimony if rate is sufficiently high. also show an alternative approach based on minimum node heights inconsistent depends genome. To distinguish between introgression, apply supervised machine learning models set features easily be obtained from phylogenomic datasets. these are highly accurate in classifying simulated that, histories identified, PhyloNet will return estimates contribution each data (i.e. edge weights). Overall, our results highlight promise potentially powerful complement phylogenetic analysis genomic data.

Language: Английский

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Recurrent selection and reduction in recombination shape the genomic landscape of divergence across multiple population pairs of Green-backed Tit

Evolution Letters, Journal Year: 2023, Volume and Issue: 7(2), P. 99 - 111

Published: March 16, 2023

Speciation is fundamental for building and maintaining biodiversity. The formation of the highly differentiated genomic regions between diverging taxa has been interpreted as a result divergence with gene flow, linked selection, reduction in recombination. It challenging to unravel these nonexclusive processes shaping divergence. Here, we investigate relative roles differentiation montane bird, Green-backed Tit (Parus monticolus). Our genetic structure demographic analyses identify that four lineages diverge 838 113 thousand years ago there evidence secondary flow. divergent do not increase time, found old show relatively fewer numbers smaller sizes than young (numbers, 118-138 vs. 156-289; sizes, 5.9-6.9 7.8-14.5 megabase). Across genome, outlier windows nucleotide diversity, absolute divergence, recombination rate, suggesting recurrent selection low being major driver Finally, flow tends affect if are less likely be targets selection. Altogether, our study shows how common ancestry, have contributed emergence islands at different stages speciation.

Language: Английский

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Notes from the taxonomic disaster zone: Evolutionary drivers of intractable species boundaries in an Australian lizard clade (Scincidae: Ctenotus)

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(20)

Published: July 17, 2023

Abstract Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative others. To understand the processes that underlie taxonomic intractability, we dissect speciation history of an Australian lizard clade arguably represents a “worst‐case” scenario for delimitation within vertebrates: Ctenotus inornatus group, beset with decoupled genetic phenotypic breaks, uncertain geographic ranges, parallelism purportedly diagnostic morphological characters. We sampled hundreds localities generate genomic perspective on population divergence, structure, admixture. Our results revealed rampant paraphyly nominate taxa lineages are either morphologically cryptic or polytypic. Isolation‐by‐distance patterns reflect spatially continuous differentiation among certain pairs putative species, yet distances other pairs. Comparisons mitochondrial nuclear gene trees, tests introgression, historical demographic modelling identified flow between divergent candidate species. Levels admixture from phylogenetic relatedness; is often higher sympatric than parapatric populations same Such idiosyncratic introgression contribute fuzzy while also varying fuzziness. suggest “taxonomic disaster zones” like C. group result spatial variation porosity resulting variation. This study raises questions about origin persistence hybridizing highlights unique insights provided by long eluded straightforward categorization.

Language: Английский

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Uncovering Ghost Introgression Through Genomic Analysis of a Distinct East Asian Hickory Species

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

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Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance

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

Published: Nov. 15, 2022

Abstract Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for inferences the tempo and mode trait evolution across species while accounting their common ancestry. These analyses typically assume single, bifurcating phylogenetic tree that describes shared history among species. However, modern phylogenomic shown genomes are often composed mosaic different histories can disagree both with each other—so-called discordant gene trees. trees describe not captured by tree, therefore unaccounted in classic approaches. The application standard to containing discordance leads incorrect about timing, direction, rate evolution. Here, we develop two approaches incorporating into methods: one involves constructing fuller variance-covariance matrix includes relationships found another applies Felsenstein’s pruning algorithm over set calculate likelihoods. Both agnostic biological causes discordance, which may include incomplete lineage sorting introgression. Using simulation, demonstrate our new generate much more accurate estimates tree-wide rates than methods. We apply clades wild tomato genus Solanum varying demonstrating contribution variation floral traits ability provide inferences. Our potential be applied broad range inference problems phylogenetics, including ancestral state reconstruction lineage-specific shifts.

Language: Английский

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Five millennia of mitochondrial introgression in Atlantic bluefin tuna identified using ancient DNA

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

Published: March 27, 2024

Abstract Mitogenomic (MT) introgression between species is readily documented in marine fishes. Such events may either be long-term natural phenomena or the result of human-driven shifts spatial distributions previously separated species. Determining drivers behind MT stymied by difficulty directly observing patterns interbreeding over long timescales. Using ancient DNA spanning five millennia, we here investigate presence from Pacific bluefin tuna ( Thunnus orientalis ) and albacore alalunga into Atlantic thynnus ), a with extensive exploitation history observed abundance, demographic distribution. Comparing (n=130) modern (n=78) mitogenomes specimens covering most range detect no significant temporal population structure. This lack spatiotemporal genomic differentiation indicative ongoing gene flow populations large effective sizes millennia. Moreover, identify introgressed genomes up to 5000 years old find that this rate has remained similar through time. We therefore conclude date unaffected anthropogenic impacts. By providing oldest example environment, our results highlight utility obtain insights persistence such phenomena.

Language: Английский

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Surprise hybrid origins of a butterfly species

Nature, Journal Year: 2024, Volume and Issue: 628(8009), P. 723 - 724

Published: April 17, 2024

Language: Английский

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Comparative approaches to understanding speciation: a case study in Xantusia lizards

Evolutionary Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 1, 2024

Abstract The diversity of life forms that surround us formed through a variety processes. Speciation researchers use suite comparative approaches to understand both the generalities and variance underpinning this diversification. Here, we summarize these what they have taught us, then apply them speciation in night lizards Xantusia, genus small found arid regions western North America. Although Xantusia species span range phenotypic genetic divergence, find appears be predictable consequence divergence extended periods allopatry. We conclude by identifying possible areas growth for studies speciation.

Language: Английский

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