Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(2), P. 584 - 595

Published: Oct. 4, 2020

Patterson's D, also known as the ABBA-BABA statistic, and related statistics such f

Language: Английский

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Widespread introgression across a phylogeny of 155 Drosophila genomes

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

Published: Nov. 16, 2021

Language: Английский

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Prevalence and Adaptive Impact of Introgression

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

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Natural hybridization reduces vulnerability to climate change

Nature Climate Change, Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 30, 2023

Abstract Under climate change, species unable to track their niche via range shifts are largely reliant on genetic variation adapt and persist. Genomic vulnerability predictions used identify populations that lack the necessary variation, particularly at climate-relevant genes. However, hybridization as a source of novel adaptive is typically ignored in genomic studies. We estimated environmental models for closely related rainbowfish ( Melanotaenia spp.) across an elevational gradient Australian Wet Tropics. Hybrid between widespread generalist several narrow endemic exhibited reduced projected climates compared pure endemics. Overlaps introgressed regions were consistent with signal introgression. Our findings highlight often-underappreciated conservation value hybrid indicate introgression may contribute evolutionary rescue ranges.

Language: Английский

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East African cichlid fishes

EvoDevo, Journal Year: 2023, Volume and Issue: 14(1)

Published: Jan. 5, 2023

Cichlid fishes are a very diverse and species-rich family of teleost that inhabit lakes rivers India, Africa, South Central America. Research has largely focused on East African cichlids the Rift Lakes Tanganyika, Malawi, Victoria constitute biodiversity hotspots cichlid fishes. Here, we give an overview study system, research questions, methodologies. spans many disciplines including ecology, evolution, physiology, genetics, development, behavioral biology. In this review, focus range organismal traits, coloration phenotypes, trophic adaptations, appendages like fins scales, sensory systems, sex, brains, behaviors. Moreover, discuss studies phylogenies, plasticity, general evolutionary patterns, ranging from convergence to speciation rates proximate ultimate mechanisms underlying these processes. From methodological viewpoint, last decade brought great advances in fish research, particularly through advent affordable deep sequencing genetic manipulations. The ability integrate across traits disciplines, developmental biology ecology makes fascinating system.

Language: Английский

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Three problems in the genetics of speciation by selection

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(30)

Published: July 18, 2022

Speciation is the process by which barriers to gene flow evolve between populations. Although we now know that speciation largely driven natural selection, knowledge of agents selection and genetic genomic mechanisms facilitate divergence required for a satisfactory theory speciation. In this essay, highlight three advances/problems in our understanding have arisen from studies genes regions underlie evolution reproductive isolation. First, describe how identification “speciation” makes it possible identify causing isolation, while also noting link genetics phenotypic intrinsic postzygotic remains tenuous. Second, discuss important role recombination suppressors facilitating with flow, but point out means timing become associated cold spots uncertain. Third, establish importance ancient variation speciation, although argue focus on evolutionarily young groups may bias conclusions favor relative new mutations.

Language: Английский

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Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(3), P. 526 - 546

Published: July 27, 2021

Abstract Introgression is an important biological process affecting at least 10% of the extant species in animal kingdom. significantly impacts inference phylogenetic relationships where a strictly binary tree model cannot adequately explain reticulate net-like relationships. Here, we use phylogenomic approaches to understand patterns introgression along evolutionary history unique, nonmodel insect system: dragonflies and damselflies (Odonata). We demonstrate that pervasive force across various taxonomic levels within Odonata. In particular, show morphologically “intermediate” Anisozygoptera (one three primary suborders Odonata besides Zygoptera Anisoptera), which retain phenotypic characteristics other two suborders, experienced high likely coming from zygopteran genomes. Additionally, find evidence for multiple cases deep inter-superfamilial ancestral introgression. [Gene flow; Odonata; phylogenomics; evolution.]

Language: Английский

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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Aug. 2, 2022

Adaptive radiations represent some of the most remarkable explosions diversification across tree life. However, constraints to rapid and how they are sometimes overcome, particularly relative roles genetic architecture hybridization, remain unclear. Here, we address these questions in Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals each 22 species belonging six ecologically distinct ecomorph classes several lake-systems. We reveal repeated ecological morphological along common environmental axis is associated with both genome-wide allele frequency shifts specific, larger effect, locus, gene edar. Additionally, highlight possible role introgression between from different lake-systems facilitating evolution persistence unique trait combinations ecology. These results importance genome secondary contact hybridization fuelling adaptive radiation.

Language: Английский

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Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation

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

Published: July 29, 2024

Abstract Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large segregating in benthic subradiation that each suppress recombination over more than half a chromosome. Two were transferred from deepwater pelagic Diplotaxodon via admixture, while others established early deep clade. Introgression haplotypes lineages inside and outside radiation coincided with bursts species diversification. Inversions show evidence for transient sex linkage striking excess protein changing substitutions points towards selection on neuro-sensory, physiological reproductive genes. We conclude repeated interplay between depth adaptation sex-specific has been central evolution this iconic system.

Language: Английский

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Rapid diversification of St-genome-sharing species in wheat grasses (Triticeae: Poaceae) accompanied by diversifying selection of chloroplast genes

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 9, 2025

The St-genome-sharing taxa are highly complex group of the species with St nuclear genome and monophyletic origin in maternal lineages within Triticeae, which contains more than half polyploid that distributed a wide range ecological habitats. While high level genetic heterogeneity plastome DNA due to reticulate evolutionary event has been considered link richness taxa, relationship between dynamics diversification molecular evolution is lack understanding. Here, integrating 106 previously 12 newly sequenced plastomes representing almost all recognized genomic types genus this study applies phylogenetic reconstruction methods combination lineage analyses, estimate sequence evolution, gene expression investigate tribe. Phylogenomic analysis confirmed previous relationships, St/E/V (Pseudoroegneria/Lophopyrum + Thinopyrum/Dasypyrum) being suffered from chloroplast capture prior polyploidization events. Analyses rates detected significant acceleration approximately five million years ago taxa. Molecular tests further indicated radiation accelerated accompanied by adaptive changes few chloroplast-encoded genes directly or indirectly related photosynthesis. Our results support an important role for during diversification. In data, investigations using other genomes, such as genome, urgently needed enhance our understanding history especially determine whether well because represents inheritation angiosperms.

Language: Английский

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