scholarly journals Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

2015 ◽  
Author(s):  
Florencia Schlamp ◽  
Julian van der Made ◽  
Rebecca Stambler ◽  
Lewis Chesebrough ◽  
Adam R Boyko ◽  
...  
Keyword(s):  
Artificial Selection ◽  
Population Sample ◽  
Population Bottlenecks ◽  
Selective Sweeps ◽  
Nucleotide Polymorphism ◽  
Genomic Signatures ◽  
Population Genomic ◽  
Dog Domestication ◽  
Soft Selective Sweeps ◽  
Positive Controls

Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.

scholarly journals Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data

2020 ◽  
Author(s):  
Nandita Garud ◽  
Philipp W. Messer ◽  
Dmitri Petrov
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Population ◽  
Genomic Data ◽  
Selective Sweeps ◽  
Demographic Models ◽  
Population Genomic ◽  
Free Parameters ◽  
Candidate Loci ◽  
Soft Selective Sweeps ◽  
Positive Controls

AbstractWhether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population of Drosophila melanogaster (DGRP) allowed us to rediscover three known cases of adaptation at the loci Ace, Cyp6g1, and CHKov1 known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harris et al. 2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim, confusingly, that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps in D. melanogaster are first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that the demographic models employed in such analyses are generally necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require fitting a very large number of free parameters.

scholarly journals Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009373 ◽  
Author(s):  
Nandita R. Garud ◽  
Philipp W. Messer ◽  
Dmitri A. Petrov
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Population ◽  
Genomic Data ◽  
Selective Sweeps ◽  
Demographic Models ◽  
Population Genomic ◽  
Free Parameters ◽  
Candidate Loci ◽  
Soft Selective Sweeps ◽  
Positive Controls

Whether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population ofDrosophila melanogaster(DGRP) allowed us to rediscover three known cases of adaptation at the lociAce,Cyp6g1, andCHKov1known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harriset al. 2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and that instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps inD.melanogasterare first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that most demographic models employed in such analyses are necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require a large number of free parameters.

scholarly journals Single nucleotide polymorphism heritability and differential patterns of genetic overlap between inattention and four neurocognitive factors in youth

2020 ◽  
pp. 1-11
Author(s):  
Lauren Micalizzi ◽  
Leslie A. Brick ◽  
Marisa E. Marraccini ◽  
Chelsie E. Benca-Bachman ◽  
Rohan H.C. Palmer ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Executive Function ◽  
Social Cognition ◽  
Genome Wide Association Study ◽  
Population Sample ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Genetic Overlap ◽  
Complex Cognition

Abstract Theoretical models of attention-deficit/hyperactivity disorder implicate neurocognitive dysfunction, yet neurocognitive functioning covers a range of abilities that may not all be linked with inattention. This study (a) investigated the single nucleotide polymorphism (SNP) heritability (h2SNP) of inattention and aspects of neurocognitive efficiency (memory, social cognition, executive function, and complex cognition) based on additive genome-wide effects; (b) examined if there were shared genetic effects among inattention and each aspect of neurocognitive efficiency; and (c) conducted an exploratory genome-wide association study to identify genetic regions associated with inattention. The sample included 3,563 participants of the Philadelphia Neurodevelopmental Cohort, a general population sample aged 8–21 years who completed the Penn Neurocognitive Battery. Data on inattention was obtained with the Kiddie Schedule of Affective Disorders (adapted). Genomic relatedness matrix restricted maximum likelihood was implemented in genome-wide complex trait analysis. Analyses revealed significant h2SNP for inattention (20%, SE = 0.08), social cognition (13%, SE = 0.08), memory (17%, SE = 0.08), executive function (25%, SE = 0.08), and complex cognition (24%, SE = 0.08). There was a positive genetic correlation (0.67, SE = 0.37) and a negative residual covariance (−0.23, SE = 0.06) between inattention and social cognition. No SNPs reached genome-wide significance for inattention. Results suggest specificity in genetic overlap among inattention and different aspects of neurocognitive efficiency.

scholarly journals Targeted re-sequencing reveals the genomic signatures of multiple barley domestications

2016 ◽  
Author(s):  
Artem Pankin ◽  
Janine Altmüller ◽  
Christian Becker ◽  
Maria von Korff
Keyword(s):  
Wild Barley ◽  
Molecular Data ◽  
Molecular Evidence ◽  
List Type ◽  
Selective Sweeps ◽  
Wild Populations ◽  
Genomic Signatures ◽  
Fertile Crescent ◽  
Origin Of Agriculture ◽  
The Relationship

SummaryBarley (Hordeum vulgare L.) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear.To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci.We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts.These findings provided first molecular evidence in favor of multiple barley domestications in the Levantine and Zagros clusters of the origin of agriculture.

scholarly journals Genomic signatures of rapid adaptive divergence in a tropical montane species

2021 ◽  
Vol 17 (7) ◽  
pp. 20210089
Author(s):  
Per G. P. Ericson ◽  
Martin Irestedt ◽  
Huishang She ◽  
Yanhua Qu
Keyword(s):  
Environmental Heterogeneity ◽  
Adaptive Divergence ◽  
Glacial Cycles ◽  
Genomic Signatures ◽  
Tropical Mountain ◽  
Population Genomic ◽  
Allopatric Divergence ◽  
Suitable Habitats ◽  
Genomic Regions ◽  
Two Populations

Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird ( Amblyornis papuensis ). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.

scholarly journals Soft selective sweeps in evolutionary rescue

2016 ◽  
Author(s):  
Benjamin A. Wilson ◽  
Pleuni S. Pennings ◽  
Dmitri A. Petrov
Keyword(s):  
Drug Resistance ◽  
Population Genetics ◽  
Population Genetic ◽  
Genetic Adaptation ◽  
Selective Sweeps ◽  
Adaptive Mutations ◽  
Evolutionary Rescue ◽  
Large Populations ◽  
Genetic Signatures ◽  
Soft Selective Sweeps

AbstractEvolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics. While most population genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when evolutionary rescue is likely, it is often driven by soft selective sweeps where multiple adaptive mutations spread through the population simultaneously. We give full analytic results for the probability of evolutionary rescue and the probability that evolutionary rescue occurs via soft selective sweeps in our model. We expect that these results will find utility in understanding the genetic signatures associated with various evolutionary rescue scenarios in large populations, such as the evolution of drug resistance in viral, bacterial, or eukaryotic pathogens.

scholarly journals Architecture of parallel adaptation to freshwater in multiple populations of threespine stickleback

2018 ◽  
Author(s):  
Nadezhda V. Terekhanova ◽  
Anna E. Barmintseva ◽  
Alexey S. Kondrashov ◽  
Georgii A. Bazykin ◽  
Nikolai S. Mugue
Keyword(s):  
Genetic Architecture ◽  
White Sea ◽  
Core Region ◽  
Selective Sweeps ◽  
The White Sea ◽  
Threespine Sticklebacks ◽  
White Sea Basin ◽  
Soft Selective Sweeps ◽  
Freshwater Environments

AbstractThreespine sticklebacks adapted to freshwater environments all over the Northern Hemisphere. This adaptation involved parallel recruitment of freshwater alleles in clusters of closely linked sites, or divergence islands (DIs). However, it is unclear to what extent the DIs involved in adaptation and the alleles within them coincide between populations adapting to similar environments. Here, we examine 10 freshwater populations of similar ages from the White Sea basin, and study the repeatability of patterns of adaptation in them. Overall, the 65 detected DIs tend to reside in regions of low recombination, underlining the role of reduced recombination in their establishment. Moreover, the DIs are clustered in the genome to the extent that is not explainable by the recombination rate alone, consistent with the divergence hitchhiking model. 21 out of the 65 DIs are universal; i.e., the frequency of freshwater alleles in them is increased in all analyzed populations. Universal DIs tend to have longer core region shared between populations, and the divergence between the marine and the freshwater haplotypes in them is higher, implying that they are older, also consistently with divergence hitchhiking. Within most DIs, the same set of sites distinguished the marine and the freshwater haplotypes in all populations; however, in some of the DIs, the genetic architecture of the freshwater haplotype differed between populations, suggesting that they could have been established by soft selective sweeps.

scholarly journals Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

2018 ◽  
Author(s):  
Patrick Monnahan ◽  
Filip Kolář ◽  
Pierre Baduel ◽  
Christian Sailer ◽  
Jordan Koch ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Genome Duplication ◽  
Purifying Selection ◽  
Theoretical Work ◽  
Deleterious Mutations ◽  
Evolutionary Potential ◽  
Genomic Signatures ◽  
Population Genomic ◽  
Variable Species ◽  
Arabidopsis Arenosa

AbstractPloidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ∼300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find the impacts of polyploidy on population genomic processes are subtle yet pervasive, including reduced efficiency on linked and purifying selection as well as rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution, and interploidy introgression all conspire to shape the evolutionary potential of polyploids.

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