The genomic origins of the world’s first farmers

Cell, Journal Year: 2022, Volume and Issue: 185(11), P. 1842 - 1859.e18

Published: May 1, 2022

The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well processes timing their differentiation, remain largely unknown. Demogenomic modeling high-quality ancient genomes reveals that early farmers Anatolia emerged from a multiphase mixing Asian population with strongly bottlenecked western hunter-gatherer after last glacial maximum. Moreover, ancestors went through period extreme drift during westward range expansion, contributing highly to distinctiveness. This elucidates demographic at root transition leads spatial interpretation history Asia late Pleistocene Holocene.

Language: Английский

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Genome-wide analyses of introgression between two sympatric Asian oak species

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(7), P. 924 - 935

Published: May 5, 2022

Language: Английский

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Deep Learning in Population Genetics

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(2)

Published: Jan. 23, 2023

Abstract Population genetics is transitioning into a data-driven discipline thanks to the availability of large-scale genomic data and need study increasingly complex evolutionary scenarios. With likelihood Bayesian approaches becoming either intractable or computationally unfeasible, machine learning, in particular deep algorithms are emerging as popular techniques for population genetic inferences. These rely on that learn non-linear relationships between input model parameters being estimated through representation learning from training sets. Deep currently employed field comprise discriminative generative models with fully connected, convolutional, recurrent layers. Additionally, wide range powerful simulators generate under scenarios now available. The application empirical sets mostly replicates previous findings demography reconstruction signals natural selection organisms. To showcase feasibility tackle new challenges, we designed branched architecture detect recent balancing temporal haplotypic data, which exhibited good predictive performance simulated data. Investigations interpretability neural networks, their robustness uncertain creative will provide further opportunities technological advancements field.

Language: Английский

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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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The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(4), P. 721 - 731

Published: April 1, 2024

Abstract Coffea arabica , an allotetraploid hybrid of eugenioides and canephora is the source approximately 60% coffee products worldwide, its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies a di-haploid C. accession modern representatives diploid progenitors, . The three species exhibit largely conserved genome structures between parents descendant subgenomes, with no obvious global subgenome dominance. find evidence for founding polyploidy event 350,000–610,000 years ago, followed by pre-domestication bottlenecks, resulting in narrow genetic variation. A split wild cultivar progenitors occurred ~30.5 thousand period migration two populations. Analysis varieties, including lines historically introgressed highlights their breeding histories loci that may contribute to pathogen resistance, laying groundwork future genomics-based

Language: Английский

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The Promise of Inferring the Past Using the Ancestral Recombination Graph

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(2)

Published: Jan. 18, 2024

Abstract The ancestral recombination graph (ARG) is a structure that represents the history of coalescent and events connecting set sequences (Hudson RR. In: Futuyma D, Antonovics J, editors. Gene genealogies process. Oxford Surveys in Evolutionary Biology; 1991. p. 1 to 44.). full ARG can be represented as genealogical trees at every locus genome, annotated with change topology between adjacent loci mutations occurred along branches those (Griffiths RC, Marjoram P. An graph. Donnelly P, Tavare S, Progress population genetics human evolution. Springer; 1997. 257 270.). Valuable insights gained into past evolutionary processes, such demographic or influence natural selection, by studying ARG. It regarded “holy grail” (Hubisz M, Siepel A. Inference graphs using ARGweaver. Dutheil JY, Statistical genomics. New York, NY: Springer US; 2020. 231–266.) since it encodes processes generate all patterns allelic haplotypic variation from which commonly used summary statistics genetic research (e.g. heterozygosity linkage disequilibrium) derived. Many previous inferences relied on extracted genotype matrix. represent significant advancement representation sample shows recombination, coalescence, mutation across particular sequence. This theory contains much information, if not more, than combination independent could derived Consistent this idea, some first ARG-based analyses have proven more powerful statistic-based (Speidel L, Forest Shi Myers SR. A method for genome-wide genealogy estimation thousands samples. Nat Genet. 2019:51(9):1321 1329.; Stern AJ, Wilton PR, Nielsen R. approximate full-likelihood inferring selection allele frequency trajectories DNA sequence data. PLoS 2019:15(9):e1008384.; Hubisz MJ, Williams AL, Mapping gene flow ancient hominins through demography-aware inference 2020:16(8):e1008895.; Fan C, Mancuso N, Chiang CWK. estimate relationships. Am J Hum 2022:109(5):812–824.; Cahoon JL, Dinh BL, Ortega-Del Vecchyo Huber Edge MD, likelihood-based framework trees. bioRxiv. 2023.10.10.561787. 2023.; Hejase HA, Mo Z, Campagna deep-learning approach selective sweeps Mol Biol Evol. 2022:39(1):msab332.; Link V, Schraiber JG, B, CWK, MD. Tree-based QTL mapping expected local relatedness matrices. 2023.04.07.536093. Zhang BC, Biddanda A, Gunnarsson ÁF, Cooper F, Palamara PF. Biobank-scale enables analysis complex traits. 2023:55(5):768–776.). As such, there has been interest field investigate 2 main problems related ARG: (i) How we based genomic data, (ii) how extract information ARG? In perspective, highlight 3 topics pertain these issues: development computational innovations enable ARG; remaining challenges estimating methodological advances deducing forces mechanisms perspective serves introduce readers types questions explored most pressing issues must addressed order make an indispensable tool research.

Language: Английский

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Hybrid speciation driven by multilocus introgression of ecological traits

Nature, Journal Year: 2024, Volume and Issue: 628(8009), P. 811 - 817

Published: April 17, 2024

Abstract Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species 1,2 . However, convincing examples homoploid hybrid speciation remain rare because it is challenging demonstrate that hybridization was crucial in generating reproductive isolation 3 Here we combine population genomic analysis with quantitative trait locus mapping species-specific traits examine a case Heliconius butterflies. We show elevatus sympatric both parents has persisted as an independently evolving lineage for at least 180,000 years. This despite pervasive ongoing gene flow one parent, pardalinus , which homogenizes 99% their genomes. The remaining 1% introgressed from other melpomene scattered widely across H. genome islands divergence These contain multiple are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones mate choice. Collectively, these place on its own adaptive peak permit coexistence parents. Our results driven by introgression ecological traits, possible multilocus genetic architecture.

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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What is reproductive isolation?

Journal of Evolutionary Biology, Journal Year: 2022, Volume and Issue: 35(9), P. 1143 - 1164

Published: Sept. 1, 2022

Abstract Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since modern synthesis and basis by which biological species are defined. Despite this, term used seemingly different ways, attempts to quantify RI have very approaches. After showing that field lacks clear definition term, we attempt clarify key issues, including what is, how it can be quantified principle, measured practice. Following other definitions with genetic focus, propose quantitative measure effect differences between populations on gene flow. Specifically, compares flow neutral alleles presence these without any such differences. thus greater than zero when reduce populations. We show range scenarios. A conclusion depends strongly circumstances—including spatial, temporal genomic context—making difficult compare across systems. reviewing methods for estimating from data, conclude discuss our findings light goals encourage use integrate organismal biology ways efforts data vastly In this paper, issues about RI,

Language: Английский

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Guidelines for standardizing the application of discriminant analysis of principal components to genotype data

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(3), P. 523 - 538

Published: Aug. 30, 2022

Despite the popularity of discriminant analysis principal components (DAPC) for studying population structure, there has been little discussion best practice this method. In work, I provide guidelines standardizing application DAPC to genotype data sets. An often overlooked fact is that generates a model describing genetic differences among set populations defined by researcher. Appropriate parameterization critical obtaining biologically meaningful results. show number leading PC axes used as predictors among-population differences, paxes , should not exceed k-1 informative are expected k effective in set. This criterion specification more appropriate compared widely proportional variance criterion, which results choice ≫ k-1. parameterized with no than axes: (i) parsimonious; (ii) captures maximal variation on relevant predictors; (iii) less sensitive unintended interpretations structure; and (iv) generally applicable independent sample Assessing fit be routine aids interpretation structure. It imperative researchers articulate their study goals, is, testing priori expectations vs. de novo inferred populations, because implications how interpreted. The practical recommendations work molecular ecology community roadmap using investigations.

Language: Английский

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