Estimating Time to the Common Ancestor for a Beneficial Allele

Smith, Jeanette M.; Coop, Graham; Stephens, Matthew; Novembre, John

doi:10.1093/molbev/msy006

Cited by 57 publications

(59 citation statements)

References 97 publications

(95 reference statements)

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“…However, these methods typically operate on a discretized timescale [13], utilize only a fraction of the information available in larger sample data, or employ approximations to overcome computational complexity [14,15,25]. Alternate approaches, in particular those that have been used to indicate allele age, are often strongly parameterized and make assumptions about demographic history, selection, or the shape of genealogical trees [26][27][28][29]. Our method is non-parametric and makes no assumptions about the demographic or selective processes that shaped the underlying genealogy.…”

Section: Introductionmentioning

confidence: 99%

Dating genomic variants and shared ancestry in population-scale sequencing data

Albers

McVean

2018

Preprint

118

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The origin and fate of new mutations within species is the fundamental process underlying evolution. However, while much attention has been focused on characterizing the presence, frequency, and phenotypic impact of genetic variation, the evolutionary histories of most variants are largely unexplored. We have developed a nonparametric approach for estimating the date of origin of genetic variants in large-scale sequencing data sets. The accuracy and robustness of the approach is demonstrated through simulation. Using data from two publicly available human genomic diversity resources, we estimated the age of more than 45 million single nucleotide polymorphisms (SNPs) in the human genome and release the Atlas of Variant Age as a public online database. We characterize the relationship between variant age and frequency in different geographical regions, and demonstrate the value of age information in interpreting variants of functional and selective importance. Finally, we use allele age estimates to power a rapid approach for inferring the ancestry shared between individual genomes, to quantify genealogical relationships at different points in the past, as well as describe and explore the evolutionary history of modern human populations.

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Section: Introductionmentioning

confidence: 99%

Dating genomic variants and shared ancestry in population-scale sequencing data

Albers

McVean

2018

Preprint

118

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“…The rate of exponential decrease of linkage disequilibrium can be used to date 944 admixture events [88], and sophisticated haplotype-based methods have been used to 945 characterize admixture and selection in ancestral human populations [89,90]. Positive 946 selection also increases LD [91][92][93], and methods were proposed to employ haplotype 947 structure to date the MRCA of a beneficial allele [94]. Haplotype-based methods are 948 usually powerful at detecting even soft and partial classic selective sweeps [45].…”

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confidence: 99%

VolcanoFinder: genomic scans for adaptive introgression

Setter

Mousset

Cheng

et al. 2019

Preprint

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Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method-VolcanoFinder-to detect recent events of adaptive introgression using polymorphism data from the recipient species only.VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity.Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH -RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder. Author summaryThe process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression. We present an analytically-tractable model for the effects of adaptive introgression on non-adaptive genetic variation in the genomic region surrounding the beneficial allele. The result we describe is a characteristic volcano-shaped pattern of increased variability that arises around the positively-selected site, and we introduce an open-source method VolcanoFinder to detect this signal in genomic data. Importantly, VolcanoFinder is a population-genetic likelihood-based approach, rather than a comparative-genomic approach, and can therefore probe genomic variation data from a single population for footprints of adaptive introgression, even from a priori unknown and possibly extinct donor species. 4 exchange of key adaptations between related species, with potentially important 5 implications for our view of the adaptive process. Indeed, recent studies have brought 6 clear evidence of cross-species introgression of advantageous alleles [3-6].7 Well-documented examples cover a wide range of taxa, including the transfer of 8 wing-pattern mimicry genes in Heliconius butterflies [7], herbivore resistance and abiotic 9tolerance genes in wild sunflowers [8,9], pesticide resistance in mice [10] and 10 mosquitoes [11], and new mating and vegetative incompatibility types in an invasive 11 fungus [12]. Su...

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“…Carneiro et al 2011) and tested an upper and lower estimate for mutation rate in European 307 rabbit (2.02 x 10 -9 and 2.35 x 10 -9 mutations/site/generation;Carneiro et al 2012). We also 308 explored the influence of using a divergent population (homozygous winter-white individuals 309 from MT; n=5 individuals) or a local population (homozygous winter-white individuals from OR 310 and WA; n=19 individuals) to represent the ancestral winter-white haplotype(Smith et al 2018). 311We assumed chr4:5480355 (in oryCun2 coordinates) as the site of the "selected allele", which 312 lies in the center of the association interval between two strong candidate insertion-deletion 313 mutations in the 5' cis-regulatory region of Agouti and is perfectly correlated with winter coat314 color (Jones et al 2018).…”

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The origin and spread of locally adaptive seasonal camouflage in snowshoe hares

Jones

Mills

Jensen

et al. 2019

Preprint

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9Adaptation is central to population persistence in the face of environmental change, yet we rarely 10 precisely understand the origin and spread of adaptive variation in natural populations. Snowshoe 11 hares (Lepus americanus) along the Pacific Northwest (PNW) coast have evolved brown winter 12 camouflage through positive selection on recessive variation at the Agouti pigmentation gene 13 introgressed from black-tailed jackrabbits (L. californicus). Here we combine new and published 14 whole genome and exome sequences with targeted genotyping of Agouti in order to investigate 15 the evolutionary history of local seasonal camouflage adaptation in the PNW. We find evidence 16 of significantly elevated inbreeding and mutational load in coastal winter-brown hares, consistent 17 with a recent range expansion into temperate coastal environments that incurred indirect fitness 18 costs. The genome-wide distribution of introgression tract lengths supports a pulse of 19 hybridization near the end of the last glacial maximum, which may have facilitated range 20 expansion via introgression of winter-brown camouflage variation. However, signatures of a 21 selective sweep at Agouti indicate a much more recent spread of winter-brown camouflage. 22Through simulations we show that the temporal lag between the hybrid origin and subsequent 23 selective sweep of the recessive winter-brown allele can be largely attributed to the limits of 24 natural selection imposed by simple allelic dominance. We argue that while hybridization during 25 periods of environmental change may provide a critical reservoir of adaptive variation at range 26 edges, the probability and pace of local adaptation will strongly depend on population 27 demography and the genetic architecture of introgressed variation. 28 individual inbreeding and mutational load along range edges may also reflect past histories of 52 adaptation and range expansion that result in non-equilibrium population dynamics. For instance, 53 mating between close relatives may increase in founder populations that have recently undergone 54 severe population contractions associated with range expansions (Frankham 1998). Likewise, 55 mutational load may be amplified through the colonization of new environments because 56 population contractions reduce the efficacy of selection against deleterious alleles at the 57 expansion front (i.e., expansion load; Peischl et al. 2013;Henn et al. 2016; González-Martínez et 58 al. 2017;Willi et al. 2018). Thus, when adaptation does occur along range margins it may 59 produce negative feedbacks on population fitness and evolutionary potential. 60Patterns of migration into range edge populations are also pivotal to their fitness and 61 adaptive potential. Larger core populations are expected to produce relatively more migrants 62 than smaller edge populations, leading to asymmetric rates of gene flow between core and 63 peripheral habitats. In extreme scenarios, edge populations with low population growth rates 64 (l<1) can be demographic sinks that ar...

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Estimating Time to the Common Ancestor for a Beneficial Allele

Cited by 57 publications

References 97 publications

Dating genomic variants and shared ancestry in population-scale sequencing data

Dating genomic variants and shared ancestry in population-scale sequencing data

VolcanoFinder: genomic scans for adaptive introgression

The origin and spread of locally adaptive seasonal camouflage in snowshoe hares

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