Introgression between highly divergent fungal sister species

Journal of Evolutionary Biology, Journal Year: 2023, Volume and Issue: 36(8), P. 1133 - 1149

Published: June 26, 2023

To understand how species evolve and adapt to changing environments, it is important study gene flow introgression due their influence on speciation radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The based two fungal sister with morphological ecological similarities occurring in overlapping habitats. We examined between by conducting whole genome sequencing of individuals from populations North America Europe. assessed genome-wide nucleotide divergence performed crossing experiments reproductive barriers. further used ABBA-BABA statistics together network analysis investigate introgression, conducted demographic modelling gain insight into times results revealed that the are highly divergent incompatible vitro. Despite this, small regions were scattered throughout genomes one event likely involves ghost population (extant or extinct). This demonstrates can be found among histories studied without collections all involved. Moreover, shown useful tool research isolation

Language: Английский

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Context‐dependent evolution of high trophic position drives functional disparity in subterranean crustaceans

Functional Ecology, Journal Year: 2023, Volume and Issue: 37(9), P. 2523 - 2534

Published: July 23, 2023

Abstract Species performance depends on the concerted interplay of their functional traits. Natural selection acts species and influences entire suits interdependent traits, thereby driving evolution diversity (FD) within a clade. In given habitat, traits are expected to integrate into only few adaptive combinations. When clade diversifies in different habitats, FD habitats (herein called α ‐FD) response local selections, while between alternative combinations that specific habitat emerge. This multivariate leads two hypotheses. First, realized ‐FD one represents small fraction variation second, FDs across (hereafter β equal or greater than would be absence interdependence We tested these hypotheses using 185 highly diverse subterranean amphipod genus Niphargus living three habitats: river interstitial, cave lakes, streams. (i) explored integration related locomotion feeding biology (ii) if each is lower it without trait interdependence, (iii) pairwise comparisons higher interdependence. all length appendages as proxy speed was positively correlated with trophic position species. On contrary, body shape correlations were dependent: high positions slender, stout invariant streams respectively. Using null models, we show whereas expectations. The results indicate preserved potential for diversification habitats. can through hybridization drive radiations. Moreover, this perspective compatible several central ecological evolutionary concepts, such landscape niche theory. Read free Plain Language Summary article Journal blog.

Language: Английский

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Inferring phylogenetic structure, taxa hybridization, and divergence times within rock voles of subgenus Aschizomys (Cricetidae: Alticola) using quaddRAD sequencing and a cytb dataset

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(12)

Published: Dec. 1, 2023

Abstract The subgenus Aschizomys belongs to the genus Alticola (Central Asian mountain vole) and consists of two species: macrotis lemminus. Phylogenetic relationships within remain obscure due limited sampling, an insufficient number molecular markers used in phylogenetic studies, paraphyly observed on mitochondrial trees. In this work, infer reliable evaluate putative scenarios ancient hybridization subgenus, we applied double‐digest restriction site‐associated DNA paired‐end (quaddRAD) sequencing 20 samples (20 individuals), including five species , dated divergence cytochrome b ( cytb ) lineages using a “second calibration” approach. We showed monophyly basis thousands nuclear loci demonstrated traces introgression also genome. Observed could be explained by event rather than incomplete lineage sorting. This explanation was confirmed analysis time. Overall, our results support hypothesis extensive migration during Late Pleistocene, with leading population introgression. expect article become starting point for series rigorous studies history as whole.

Language: Английский

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Localizing post-admixture adaptive variants with object detection on ancestry-painted chromosomes

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

Published: Sept. 5, 2022

Abstract Gene flow between previously isolated populations during the founding of an admixed or hybrid population has potential to introduce adaptive alleles into new population. If allele is common in one source population, but not other, then as rises frequency genetic ancestry from containing will increase nearby well. Patterns have therefore been used identify post-admixture positive selection humans and other animals, including examples immunity, metabolism, animal coloration. A method identifies regions genome that local ‘outliers’ compared distribution across rest genome, considering each locus independently. However, we lack theoretical models for expected distributions under various demographic scenarios, resulting false positives negatives. Further, patterns distant sites are often independent. As a result, current methods tend infer wide genomic many genes selection, limiting biological interpretation. Instead, develop deep learning object detection applied images generated ancestry-painted genomes. This approach preserves information surrounding context avoids pitfalls user-defined summary statistics. We find the-method robust variety misspecifications using simulated data. Applied human genotype data Cabo Verde, localize known single narrow region multiple long windows obtained two ancestry-based methods.

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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