Adaptive and maladaptive introgression in grapevine domestication

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(24)

Published: June 5, 2023

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild cultivated grapes in Europe, but the time, mode, pattern, and biological effects these events not been investigated. Here, we studied resequencing data 345 samples spanning distributional range (Vitis vinifera ssp. sylvestris) (V. vinifera) grapes. Based on machine learning-based population genetic analyses, detected evidence for a single domestication grapevine, followed by continuous gene flow between European (EU) over past ~2,000 y, especially EU wine We also inferred that soft-selective sweeps were dominant artificial selection. Gene pathways associated with synthesis aromatic compounds enriched regions both selected introgressed, suggesting an important resource improving flavor Despite potential benefits grape improvement, introgressed fragments introduced higher deleterious burden, most SNPs structural variants hidden heterozygous state. Cultivated benefited adaptive grapes, has increased load. In general, our study beneficial harmful is critical breeding grapevine take advantage resources.

Language: Английский

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Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features

Science, Journal Year: 2024, Volume and Issue: 383(6685)

Published: Feb. 22, 2024

In some mammals, notably humans, recombination occurs almost exclusively where the protein PRDM9 binds, whereas in vertebrates lacking an intact

Language: Английский

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Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(2), P. e1010615 - e1010615

Published: Feb. 23, 2023

The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic from 154 breeds, and 69 wild seven Ovis species. On average, detected 6.8%, 1.0% 0.2% introgressed sequence in originating Iranian mouflon, urial argali, respectively, with rare introgressions other Interestingly, several haplotypes contributed to differentiations across such as RXFP2 haplotype mouflon conferring spiral horn trait, MSRB3 argali strongly associated ear morphology, VPS13B probably possibly facial traits. Our results reveal that introgression events species high rate differentiation but also individual variation within We propose long divergent are ubiquitous source phenotypic allows adaptation variable environment, remain intact receiving due reduced recombination.

Language: Английский

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The Role of Hybridization in Species Formation and Persistence

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: 16(12), P. a041445 - a041445

Published: March 4, 2024

Joshua V. Peñalba1, Anna Runemark2, Joana I. Meier3,4, Pooja Singh5,6, Guinevere O.U. Wogan7, Rosa Sánchez-Guillén8, James Mallet9, Sina J. Rometsch10,11, Mitra Menon12, Ole Seehausen5,6, Jonna Kulmuni13,14,16 and Ricardo Pereira15,16 1Museum für Naturkunde, Leibniz Institute for Evolution Biodiversity Science, Center Integrative Discovery, 10115 Berlin, Germany 2Department of Biology, Lund University, 22632 Lund, Sweden 3Tree Life, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom 4Department Zoology, University Cambridge, CB2 3EJ, 5Department Aquatic Ecology, Ecology Evolution, Bern, 3012 Switzerland 6Center & Biogeochemistry, Swiss Federal Science Technology (EAWAG), CH-8600 Kastanienbaum, 7Department Oklahoma State Stillwater, 74078, USA 8Red de Biología Evolutiva, INECOL, Xalapa, Veracruz, CP 91073, Mexico 9Organismal Evolutionary Harvard Massachusetts 02138, 10Department Yale New Haven, Connecticut 06511, 11Yale Biospheric Studies, 12Department California Davis, 95616, 13Department Population Ecosystem Dynamics, Amsterdam, 1098 XH The Netherlands 14Organismal Biology Research Programme, Helsinki, Biocenter 3, Finland 15Department Museum Natural History Stuttgart, Stuttgart 70191, Correspondence: ricardojn.pereira{at}gmail.com ↵16 These authors contributed equally to this work.

Language: Английский

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The temporal and genomic scale of selection following hybridization

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(12)

Published: March 15, 2024

Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks understanding evolutionary dynamics within hybrid populations that underlie these have been lacking. Due to clock-like effect recombination hybrids breaking up parental haplotypes, drift and produce predictable ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on Discrete Wavelet Transform study scale local its association with rates show capture temporal genome-wide after hybridization. We apply published datasets from swordtail fish ( Xiphophorus ) baboons Papio inferred Neanderthal modern humans. Across systems, upward 20% broadest can be attributed systematic against introgressed alleles, consistent strong acting early-generation hybrids. Signatures fine suggest over longer time scales; however, our ability confidently infer is likely limited by inherent biases current estimating contiguous segments similarity. approaches will become widely applicable as data systems increasingly available help shed light generalities consequences interspecific

Language: Английский

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Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(8), P. e1010717 - e1010717

Published: Aug. 7, 2023

Reshuffling of genetic variation occurs both by independent assortment chromosomes and homologous recombination. Such reshuffling can generate novel allele combinations break linkage between advantageous deleterious variants which increases the potential efficacy natural selection. Here we used high-density maps to characterize global regional recombination rate in two populations wood white butterfly (Leptidea sinapis) that differ considerably their karyotype as a consequence at least 27 chromosome fissions fusions. The data were compared estimates diversity measures selection assess relationship chromosomal rearrangements, crossing over, maintenance adaptation. Our show is influenced size number, but difference number crossovers karyotypes reduced higher frequency double larger chromosomes. As expected from effects on linked sites, observed an overall positive association populations. results also revealed significant effect rearrangements intergenic change populations, limited polymorphisms coding sequence. We conclude have considerable landscape consequently influence efficiency

Language: Английский

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Fisher's Geometric Model as a Tool to Study Speciation

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: 16(7), P. a041442 - a041442

Published: Jan. 22, 2024

Hilde Schneemann1, Bianca De Sanctis1,2 and John J. Welch1 1Department of Genetics, University Cambridge, Cambridge CB2 3EH, United Kingdom 2Department Zoology, 3EJ, Correspondence: hilde.schneemann{at}evobio.eu

Language: Английский

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Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(8), P. e3002742 - e3002742

Published: Aug. 26, 2024

Over the past 2 decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common-not just in particular lineages but taxonomic groups across tree of life. As a result, genomes many modern species harbor regions inherited from related species. This observation has raised fundamental questions about degree which genomic outcomes hybridization are repeatable and natural selection drives such repeatability. However, lack appropriate systems answer these limited empirical progress this area. Here, we leverage independently formed hybrid populations swordtail fish Xiphophorus birchmanni X. cortezi address question. We find local ancestry one population predictive another, demographically independent population. Applying newly developed methods, can attribute much repeatability strong earliest generations after initial hybridization. complement analyses with time-series data demonstrates at under remained stable over approximately 40 evolution. Finally, compare our results well-studied × malinche conclude deeper evolutionary divergence resulted stronger higher patterns hybrids cortezi.

Language: Английский

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Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(2)

Published: Feb. 1, 2024

Advances in genomic studies have revealed that hybridization nature is pervasive and raised questions about the dynamics of different genetic evolutionary factors following initial event. While recent research has proposed outcomes might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated introgression between 2 divergent lineages 9-spined sticklebacks (Pungitius pungitius) Baltic Sea. We found intensity direction selection on introgressed variation varied across elements: while functionally important regions displayed reduced rates introgression, promoter showed enrichment. Despite general trend negative selection, identified specific were enriched for variants, within these regions, detected footprints indicating adaptive introgression. Geographically, against functional changes strongest vicinity secondary contact zone weaken as a function distance from contact. Altogether, results suggest stabilization genomes complex, multistage process involving both positive selection. In spite predominance also evidence variants likely associated with adaptation Sea environmental conditions.

Language: Английский

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The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location

PLoS Biology, Journal Year: 2023, Volume and Issue: 21(7), P. e3002185 - e3002185

Published: July 17, 2023

The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature evolution. Examples both adaptive and deleterious introgression exist in variety systems. What unclear how fitness an introgressing haplotype changes as species diverge size changes. In simple model, we show may more easily occur into parts genome which have not diverged heavily from ancestor. key insight alleles shared background are likely to positive epistatic interactions, increasing larger block. regions where few existing substitutions disrupted, this epistasis can be than incompatibilities with recipient genome. Further, early process divergence, large haplotypes favored individual alleles. This model consistent observations relationship recombination rate frequency across genome; however, it generates several novel predictions. First, suggests exist, negative, recently pairs. Furthermore, replaces derived variation will at sites carrying ancestral variants. These predictions tested example Drosophila melanogaster , some support for both. Finally, provides potential alternative explanation asymmetry direction expectations higher rapidly populations slowly evolving ones.

Language: Английский

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