scholarly journals Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium

2020 ◽  
Vol 37 (12) ◽  
pp. 3642-3653
Author(s):  
Enrique Santiago ◽  
Irene Novo ◽  
Antonio F Pardiñas ◽  
María Saura ◽  
Jinliang Wang ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Recombination Rates ◽  
Animal Populations ◽  
Wide Range ◽  
Demographic Trajectories ◽  
Model Computer ◽  
Conservation Of Endangered Species

Abstract Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.

scholarly journals Unbiased Estimation of Linkage Disequilibrium from Unphased Data

2019 ◽  
Vol 37 (3) ◽  
pp. 923-932 ◽  
Author(s):  
Aaron P Ragsdale ◽  
Simon Gravel
Keyword(s):  
Linkage Disequilibrium ◽  
Unbiased Estimation ◽  
Sequencing Data ◽  
Effective Population ◽  
Island Fox ◽  
Wide Range ◽  
Population Sizes ◽  
The Common ◽  
Genomic Regions ◽  
The Relationship

Abstract Linkage disequilibrium (LD) is used to infer evolutionary history, to identify genomic regions under selection, and to dissect the relationship between genotype and phenotype. In each case, we require accurate estimates of LD statistics from sequencing data. Unphased data present a challenge because multilocus haplotypes cannot be inferred exactly. Widely used estimators for the common statistics r2 and D2 exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, including D2, for both single and multiple randomly mating populations. These unbiased statistics are particularly well suited to estimate effective population sizes from unlinked loci in small populations. We develop a simple inference pipeline and use it to refine estimates of recent effective population sizes of the threatened Channel Island Fox populations.

scholarly journals Unbiased estimation of linkage disequilibrium from unphased data

2019 ◽  
Author(s):  
Aaron P. Ragsdale ◽  
Simon Gravel
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Evolutionary History ◽  
Unbiased Estimation ◽  
Sequencing Data ◽  
Unbiased Estimators ◽  
Population Size Estimates ◽  
Wide Range ◽  
The Common ◽  
Size Estimates

AbstractLinkage disequilibrium is used to infer evolutionary history and to identify regions under selection or associated with a given trait. In each case, we require accurate estimates of linkage disequilibrium from sequencing data. Unphased data presents a challenge because the co-occurrence of alleles at different loci is ambiguous. Commonly used estimators for the common statistics r2 and D2 exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, including D2, for both single and multiple randomly mating populations. These provide accurate estimates over three orders of magnitude in LD. We also use these estimators to construct an estimator for r2 that is less biased than commonly used estimators, but nevertheless argue for using rather than r2 for population size estimates.

Adaptive Radiation Genomics of Two Ecologically Divergent Hawai‘ian Honeycreepers: The ‘akiapōlā‘au and the Hawai‘i ‘amakihi

2019 ◽  
Author(s):  
Michael G Campana ◽  
André Corvelo ◽  
Jennifer Shelton ◽  
Taylor E Callicrate ◽  
Karen L Bunting ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
De Novo ◽  
Demographic History ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Morphology Evolution ◽  
Effective Population ◽  
Island Endemic ◽  
Wide Range ◽  
Bill Morphology

Abstract The Hawai‘ian honeycreepers (drepanids) are a classic example of adaptive radiation: they adapted to a variety of novel dietary niches, evolving a wide range of bill morphologies. Here we investigated genomic diversity, demographic history, and genes involved in bill morphology phenotypes in 2 honeycreepers: the ‘akiapōlā‘au (Hemignathus wilsoni) and the Hawai‘i ‘amakihi (Chlorodrepanis virens). The ‘akiapōlā‘au is an endangered island endemic, filling the “woodpecker” niche by using a unique bill morphology, while the Hawai‘i ‘amakihi is a dietary generalist common on the islands of Hawai‘i and Maui. We de novo sequenced the ‘akiapōlā‘au genome and compared it to the previously sequenced ‘amakihi genome. The ‘akiapōlā‘au is far less heterozygous and has a smaller effective population size than the ‘amakihi, which matches expectations due to its smaller census population and restricted ecological niche. Our investigation revealed genomic islands of divergence, which may be involved in the honeycreeper radiation. Within these islands of divergence, we identified candidate genes (including DLK1, FOXB1, KIF6, MAML3, PHF20, RBP1, and TIMM17A) that may play a role in honeycreeper adaptations. The gene DLK1, previously shown to influence Darwin’s finch bill size, may be related to honeycreeper bill morphology evolution, while the functions of the other candidates remain unknown.

scholarly journals Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

2019 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

Maximum Likelihood Estimation of Recombination Rates From Population Data

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1393-1401 ◽  
Author(s):  
Mary K Kuhner ◽  
Jon Yamato ◽  
Joseph Felsenstein
Keyword(s):  
Population Sample ◽  
Likelihood Estimation ◽  
Population Data ◽  
Molecular Data ◽  
Effective Population ◽  
Recombination Rates ◽  
Wide Range ◽  
Estimate Rate ◽  
Parameter Values ◽  
Neutral Mutation Rate

AbstractWe describe a method for co-estimating r = C/μ (where C is the per-site recombination rate and μ is the per-site neutral mutation rate) and Θ = 4Neμ (where Ne is the effective population size) from a population sample of molecular data. The technique is Metropolis-Hastings sampling: we explore a large number of possible reconstructions of the recombinant genealogy, weighting according to their posterior probability with regard to the data and working values of the parameters. Different relative rates of recombination at different locations can be accommodated if they are known from external evidence, but the algorithm cannot itself estimate rate differences. The estimates of Θ are accurate and apparently unbiased for a wide range of parameter values. However, when both Θ and r are relatively low, very long sequences are needed to estimate r accurately, and the estimates tend to be biased upward. We apply this method to data from the human lipoprotein lipase locus.

scholarly journals Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii

2020 ◽  
Vol 12 (4) ◽  
pp. 370-380 ◽  
Author(s):  
Ahmed R Hasan ◽  
Rob W Ness
Keyword(s):  
Linkage Disequilibrium ◽  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Effective Rate ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Recombination Rates ◽  
Recombination Rate Variation

Abstract Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.

scholarly journals Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three relatedPopulusspecies

2015 ◽  
Author(s):  
Jing Wang ◽  
Nathaniel R Street ◽  
Douglas G Scofield ◽  
Pär K Ingvarsson
Keyword(s):  
Natural Selection ◽  
Rate Variation ◽  
Sequencing Data ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Recombination Rates ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Population Sizes ◽  
Wide Scale

AbstractA central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-scaled recombination rates in three species ofPopulus:P. tremula, P. tremuloidesandP. trichocarpa. We find thatP. tremuloideshas the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereasP. trichocarpaharbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, both due to purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination are largely explaining the disparate magnitudes and signatures of linked selection we observe among species. The present work provides the first phylogenetic comparative study at genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

scholarly journals Models of archaic admixture and recent history from two-locus statistics

2018 ◽  
Author(s):  
Aaron P. Ragsdale ◽  
Simon Gravel
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Evolutionary Models ◽  
Human History ◽  
Wide Range ◽  
Archaic Admixture

AbstractWe learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4-8% genetic ancestry to individuals in world-wide populations.Author SummaryThroughout human history, populations have expanded and contracted, split and merged, and ex-changed migrants. Because these events affected genetic diversity, we can learn about human history by comparing predictions from evolutionary models to genetic data. Here, we show how to rapidly compute such predictions for a wide range of diversity measures within and across populations under complex demographic scenarios. While widely used models of human history accurately predict common measures of diversity, we show that they strongly underestimate the co-occurence of low frequency mutations within human populations in Asia, Europe, and Africa. Models allowing for archaic admixture, the relatively recent mixing of human populations with deeply diverged human lineages, resolve this discrepancy. We use such models to infer demographic models that include both recent and ancient features of human history. We recover the well-characterized admixture of Neanderthals in Eurasian populations, as well as admixture from an as-yet unknown diverged human population within Africa, further suggesting that admixture with deeply diverged lineages occurred multiple times in human history. By simultaneously testing model predictions for a broad range of diversity statistics, we can assess the robustness of common evolutionary models, identify missing historical events, and build more informed models of human demography.

scholarly journals Recent demography drives changes in linked selection across the maize genome

2015 ◽  
Author(s):  
Timothy M. Beissinger ◽  
Li Wang ◽  
Kate Crosby ◽  
Arun Durvasula ◽  
Matthew B. Hufford ◽  
...  
Keyword(s):  
Population Size ◽  
Demographic History ◽  
Purifying Selection ◽  
Rapid Expansion ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Effective Population ◽  
The Impact ◽  
Linked Selection

AbstractGenetic diversity is shaped by the interaction of drift and selection, but the details of this interaction are not well understood. The impact of genetic drift in a population is largely determined by its demographic history, typically summarized by its long-term effective population size (Ne). Rapidly changing population demographics complicate this relationship, however. To better understand how changing demography impacts selection, we used whole-genome sequencing data to investigate patterns of linked selection in domesticated and wild maize (teosinte). We produce the first whole-genome estimate of the demography of maize domestication, showing that maize was reduced to approximately 5% the population size of teosinte before it experienced rapid expansion post-domestication to population sizes much larger than its ancestor. Evaluation of patterns of nucleotide diversity in and near genes shows little evidence of selection on beneficial amino acid substitutions, and that the domestication bottleneck led to a decline in the efficiency of purifying selection in maize. Young alleles, however, show evidence of much stronger purifying selection in maize, reflecting the much larger effective size of present day populations. Our results demonstrate that recent demographic change — a hallmark of many species including both humans and crops — can have immediate and wide-ranging impacts on diversity that conflict with would-be expectations based on Ne alone.

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