Inference of selective sweep parameters through supervised learning

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

Published: July 20, 2022

Abstract A selective sweep occurs when positive selection drives an initially rare allele to high population frequency. In nature, the precise parameters of a are seldom known: How strong was selection? Did involve only single adaptive (hard sweep) or were multiple alleles at locus sweeping same time (soft sweep)? If soft, did these originate from recurrent new mutations (RNM) standing genetic variation (SGV)? Here, we present method based on supervised machine learning infer such patterns observed around given locus. Our is trained data simulated with SLiM, fast and flexible framework that allows us generate training across wide spectrum evolutionary scenarios can be tailored towards specific interest. Inferences summary statistics describing nucleotide diversity, haplotype structure, linkage disequilibrium, which estimated systematically varying genomic window sizes capture sweeps range strengths. We show our accurately coefficients in 0.01 < s 100 classify types between hard sweeps, RNM soft SGV accuracy 69 % 95 depending strength. also infers correct three empirical loci known associated recent evolution pesticide resistance Drosophila melanogaster . study demonstrates power for inferring present-day genotyping samples, opening door better understanding modes nature. Author Adaptation often involves rapid spread beneficial variant through process called sweep. develop strength driving sweep, distinguish whether it involved (a so-called several variants independent origin simultaneously rising frequency position sweep). requires sampled point time. To address challenge simulating realistic datasets training, explore behavior under variety testing scenarios, including where history interest misspecified. Finally, illustrate method, apply have contributed

Language: Английский

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Hard versus soft selective sweeps during domestication and improvement in soybean

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(11), P. 3137 - 3153

Published: April 2, 2022

Genome scans for selection can provide an efficient way to dissect the genetic basis of domestication traits and understand mechanisms adaptation during crop evolution. Selection involving soft sweeps (simultaneous multiple alleles) is probably common in plant genomes but under-studied, few if any studies have systematically scanned context domestication. Using genome resequencing data from 302 wild domesticated soybean accessions, we conducted using five widely employed statistics identify candidates under classical (hard) sweeps. Across genome, inferred hard are predominant landraces improved varieties, whereas more prevalent a representative subpopulation ancestor. Six domestication-related genes, representing both different stages domestication, were used as positive controls assess detectability domestication-associated Performance various test suggests that differentiation-based (FST ) methods robust detecting complete sweeps, LD-based strategies perform well identifying recent/ongoing sweeps; however, none detected known sweep previously documented at gene Dt1. yielded set 66 candidate loci identified by (iHH) methods; notably, this shared overlaps with many QTLs domestication/improvement traits. Collectively, our results will help advance characterizations shed light on modes involved species.

Language: Английский

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Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls

Published: Jan. 29, 2024

A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in variation linked regions. However, despite this expectation, identifying clear footprints of beneficial passage has proven to be surprisingly challenging. We addressed the basic premise underlying expectation by estimating ages large numbers and deleterious a human genomic data set. Deleterious were found young, on average, given their frequency. older average than non-coding, non-regulatory same This finding not consistent with instead indicates some type balancing selection. Among derived alleles, those fixed show higher local recombination rates still segregating, model which new experience an initial period due linkage disequilibrium recessive alleles. Alleles ultimately fix following will leave modest ‘soft’ sweep impact variation, overall paucity species-wide ‘hard’ sweeps genomes.Analyses age evolutionary reveal are often neutral controls, suggesting role for adaptation.

Language: Английский

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Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species

Genetics, Journal Year: 2024, Volume and Issue: 226(4)

Published: Feb. 16, 2024

Abstract The X chromosome, being hemizygous in males, is exposed one-third of the time increasing visibility new mutations to natural selection, potentially leading different evolutionary dynamics than autosomes. Recently, we found an enrichment hard selective sweeps over soft on chromosome relative autosomes a North American population Drosophila melanogaster. To understand whether this universal feature evolution analyze diversity patterns across 6 commonly studied species. We find increased proportion regions with steep reductions and elevated homozygosity compared assess if these signatures are consistent positive simulate wide variety scenarios spanning variations demography, mutation rate, recombination background sweeps, that observed most sweeps. Our findings highlight importance sex chromosomes driving processes suggest have played significant role shaping multiple

Language: Английский

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Signatures of selective sweeps in continuous-space populations

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

Published: July 26, 2024

Selective sweeps describe the process by which an adaptive mutation arises and rapidly fixes in population, thereby removing genetic variation its genomic vicinity. The expected signatures of selective are relatively well understood panmictic population models, yet natural populations often extend across larger geographic ranges where individuals more likely to mate with those born nearby. To investigate how such spatial structure can affect sweep dynamics signatures, we simulated inhabiting a two-dimensional continuous landscape. maximum dispersal distance offspring from their parents be varied our simulations essentially scenarios increasingly limited dispersal. We find that low-dispersal populations, mutations spread slowly than ones, while recombination becomes less effective at breaking up linkage around locus. Together, these factors result trough reduced diversity locus looks very similar rates. also site frequency spectrum hard enriched for intermediate-frequency variants, making appear softer they are. Furthermore, haplotype heterozygosity tends elevated as compared panmixia, contrary what observe neutral without sweeps. patterns generated resemble soft standing arose substantially older alleles. Our results highlight need better accounting when inferences about

Language: Английский

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