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Seo D, Lee DH, Jin S, Won JI, Lim D, Park M, Kim TH, Lee HK, Kim S, Choi I, Lee JH, Gondro C, Lee SH. Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure. Sci Rep 2022; 12:6438. [PMID: 35440706 PMCID: PMC9018707 DOI: 10.1038/s41598-022-09425-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/01/2022] [Indexed: 11/09/2022] Open
Abstract
Indigenous Korean breeds such as Hanwoo (Korean) cattle have adapted to their local environment during the past 5000 years. In the 1980s, the National Genetic Improvement Program was established to develop a modern economic breed for beef production in Korea through artificial selection. This process is thought to have altered the genomic structure of breeding traits over time. The detection of genetic variants under selection could help to elucidate the genetic mechanism of artificial selection in modern cattle breeds. Indigenous Hanwoo cattle have adapted in response to local natural and artificial selection during a 40-year breeding program. We analyzed genomic changes in the selection signatures of an unselected population (USP; n = 362) and a selected population (KPN; n = 667) of Hanwoo cattle. Genomic changes due to long-term artificial selection were identified using a genome-wide integrated haplotype score (iHS) and a genome-wide association study (GWAS). Signatures of recent selection were detected as positive (piHS > 6) or negative (piHS < –6) iHS scores spanning more than 46 related genes in KPN cattle, but none in USP cattle. A region adjacent to the PLAG1 gene was found to be under strong selection for carcass weight. The GWAS results also showed a selection signature on BTA14, but none on BTA13. Pathway and quantitative trait locus analysis results identified candidate genes related to energy metabolism, feed efficiency, and reproductive traits in Hanwoo cattle. Strong selection significantly altered Hanwoo cattle genome structural properties such as linkage disequilibrium (LD) and haplotypes through causal mutation for target traits. Haplotype changes of genome structure which are changes of ancestral allele to derived alleles due to selection were clearly identified on BTA13 and BTA14; however, the structure of the LD block was not clearly observed except BTA14. Thus, selection based on EBVs would be working very well in Hanwoo cattle breeding program appears to have been highly successful.
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Affiliation(s)
- Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Doo Ho Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Jung Il Won
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju, Korea
| | - Mina Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, RDA, Seonghwan, South Korea
| | - Tae Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju, Korea
| | - Hak Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, South Korea
| | - Sidong Kim
- Poultry Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea
| | - Inchul Choi
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Cedric Gondro
- Beacon Center for the Study of Evolution in Action and Department of Animal Science, Michigan State University, East Lansing, USA
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea.
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2
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A Faster and More Accurate Algorithm for Calculating Population Genetics Statistics Requiring Sums of Stirling Numbers of the First Kind. G3-GENES GENOMES GENETICS 2020; 10:3959-3967. [PMID: 32900901 PMCID: PMC7642932 DOI: 10.1534/g3.120.401575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Ewen’s sampling formula is a foundational theoretical result that connects probability and number theory with molecular genetics and molecular evolution; it was the analytical result required for testing the neutral theory of evolution, and has since been directly or indirectly utilized in a number of population genetics statistics. Ewen’s sampling formula, in turn, is deeply connected to Stirling numbers of the first kind. Here, we explore the cumulative distribution function of these Stirling numbers, which enables a single direct estimate of the sum, using representations in terms of the incomplete beta function. This estimator enables an improved method for calculating an asymptotic estimate for one useful statistic, Fu’s Fs. By reducing the calculation from a sum of terms involving Stirling numbers to a single estimate, we simultaneously improve accuracy and dramatically increase speed.
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3
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Perdomo-Sabogal Á, Nowick K. Genetic Variation in Human Gene Regulatory Factors Uncovers Regulatory Roles in Local Adaptation and Disease. Genome Biol Evol 2019; 11:2178-2193. [PMID: 31228201 PMCID: PMC6685493 DOI: 10.1093/gbe/evz131] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2019] [Indexed: 01/13/2023] Open
Abstract
Differences in gene regulation have been suggested to play essential roles in the evolution of phenotypic changes. Although DNA changes in cis-regulatory elements affect only the regulation of its corresponding gene, variations in gene regulatory factors (trans) can have a broader effect, because the expression of many target genes might be affected. Aiming to better understand how natural selection may have shaped the diversity of gene regulatory factors in human, we assembled a catalog of all proteins involved in controlling gene expression. We found that at least five DNA-binding transcription factor classes are enriched among genes located in candidate regions for selection, suggesting that they might be relevant for understanding regulatory mechanisms involved in human local adaptation. The class of KRAB-ZNFs, zinc-finger (ZNF) genes with a Krüppel-associated box, stands out by first, having the most genes located on candidate regions for positive selection. Second, displaying most nonsynonymous single nucleotide polymorphisms (SNPs) with high genetic differentiation between populations within these regions. Third, having 27 KRAB-ZNF gene clusters with high extended haplotype homozygosity. Our further characterization of nonsynonymous SNPs in ZNF genes located within candidate regions for selection, suggests regulatory modifications that might influence the expression of target genes at population level. Our detailed investigation of three candidate regions revealed possible explanations for how SNPs may influence the prevalence of schizophrenia, eye development, and fertility in humans, among other phenotypes. The genetic variation we characterized here may be responsible for subtle to rough regulatory changes that could be important for understanding human adaptation.
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Affiliation(s)
- Álvaro Perdomo-Sabogal
- Human Biology Group, Department of Biology, Chemistry and Pharmacy, Institute for Zoology, Freie Universität Berlin, Germany
| | - Katja Nowick
- Human Biology Group, Department of Biology, Chemistry and Pharmacy, Institute for Zoology, Freie Universität Berlin, Germany
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4
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Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 168 Suppl 67:4-26. [PMID: 30408154 DOI: 10.1002/ajpa.23737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.
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Affiliation(s)
- Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Esteban J Parra
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Frida Lona-Durazo
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Khai C Ang
- Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania
| | - Florin Mircea Illiescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Tina Lasisi
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Izzy Starr
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
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5
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Goodswen SJ, Kennedy PJ, Ellis JT. A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen. Front Genet 2018; 9:332. [PMID: 30177953 PMCID: PMC6109633 DOI: 10.3389/fgene.2018.00332] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/02/2018] [Indexed: 11/22/2022] Open
Abstract
Over the last two decades, various in silico approaches have been developed and refined that attempt to identify protein and/or peptide vaccines candidates from informative signals encoded in protein sequences of a target pathogen. As to date, no signal has been identified that clearly indicates a protein will effectively contribute to a protective immune response in a host. The premise for this study is that proteins under positive selection from the immune system are more likely suitable vaccine candidates than proteins exposed to other selection pressures. Furthermore, our expectation is that protein sequence regions encoding major histocompatibility complexes (MHC) binding peptides will contain consecutive positive selection sites. Using freely available data and bioinformatic tools, we present a high-throughput approach through a pipeline that predicts positive selection sites, protein subcellular locations, and sequence locations of medium to high T-Cell MHC class I binding peptides. Positive selection sites are estimated from a sequence alignment by comparing rates of synonymous (dS) and non-synonymous (dN) substitutions among protein coding sequences of orthologous genes in a phylogeny. The main pipeline output is a list of protein vaccine candidates predicted to be naturally exposed to the immune system and containing sites under positive selection. Candidates are ranked with respect to the number of consecutive sites located on protein sequence regions encoding MHCI-binding peptides. Results are constrained by the reliability of prediction programs and quality of input data. Protein sequences from Toxoplasma gondii ME49 strain (TGME49) were used as a case study. Surface antigen (SAG), dense granules (GRA), microneme (MIC), and rhoptry (ROP) proteins are considered worthy T. gondii candidates. Given 8263 TGME49 protein sequences processed anonymously, the top 10 predicted candidates were all worthy candidates. In particular, the top ten included ROP5 and ROP18, which are T. gondii virulence determinants. The chance of randomly selecting a ROP protein was 0.2% given 8263 sequences. We conclude that the approach described is a valuable addition to other in silico approaches to identify vaccines candidates worthy of laboratory validation and could be adapted for other apicomplexan parasite species (with appropriate data).
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Affiliation(s)
- Stephen J Goodswen
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Paul J Kennedy
- School of Software, Faculty of Engineering and Information Technology, Centre for Artificial Intelligence, University of Technology Sydney, Ultimo, NSW, Australia
| | - John T Ellis
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
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6
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Lee KS, Chatterjee P, Choi EY, Sung MK, Oh J, Won H, Park SM, Kim YJ, Yi SV, Choi JK. Selection on the regulation of sympathetic nervous activity in humans and chimpanzees. PLoS Genet 2018; 14:e1007311. [PMID: 29672586 PMCID: PMC5908061 DOI: 10.1371/journal.pgen.1007311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/17/2018] [Indexed: 12/31/2022] Open
Abstract
Adrenergic α2C receptor (ADRA2C) is an inhibitory modulator of the sympathetic nervous system. Knockout mice for this gene show physiological and behavioural alterations that are associated with the fight-or-flight response. There is evidence of positive selection on the regulation of this gene during chicken domestication. Here, we find that the neuronal expression of ADRA2C is lower in human and chimpanzee than in other primates. On the basis of three-dimensional chromatin structure, we identified a cis-regulatory region whose DNA sequences have been significantly accelerated in human and chimpanzee. Active histone modification marks this region in rhesus macaque but not in human and chimpanzee; instead, repressive marks are enriched in various human brain samples. This region contains two neuron-restrictive silencer factor (NRSF) binding motifs, each of which harbours a polymorphism. Our genotyping and analysis of population genome data indicate that at both polymorphic sites, the derived allele has reached fixation in humans and chimpanzees but not in bonobos, whereas only the ancestral allele is present among macaques. Our CRISPR/Cas9 genome editing and reporter assays show that both derived nucleotides repress ADRA2C, most likely by increasing NRSF binding. In addition, we detected signatures of recent positive selection for lower neuronal ADRA2C expression in humans. Our findings indicate that there has been selective pressure for enhanced sympathetic nervous activity in the evolution of humans and chimpanzees.
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Affiliation(s)
- Kang Seon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Paramita Chatterjee
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Eun-Young Choi
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Gyeonggi, Republic of Korea
| | - Min Kyung Sung
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Jaeho Oh
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Hyejung Won
- Department of Neurology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Seong-Min Park
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Gyeonggi, Republic of Korea
| | - Youn-Jae Kim
- Specific Organs Cancer Branch, Research Institute, National Cancer Center, Ilsan, Gyeonggi, Republic of Korea
| | - Soojin V. Yi
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
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7
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Gouy A, Daub JT, Excoffier L. Detecting gene subnetworks under selection in biological pathways. Nucleic Acids Res 2017; 45:e149. [PMID: 28934485 PMCID: PMC5766194 DOI: 10.1093/nar/gkx626] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 12/30/2022] Open
Abstract
Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data. We developed a method to analyse gene networks that is suitable to evidence polygenic selection. The general idea is to search biological pathways for subnetworks of genes that directly interact with each other and that present unusual evolutionary features. Subnetwork search is a typical combinatorial optimization problem that we solve using a simulated annealing approach. We have applied our methodology to find signals of adaptation to high-altitude in human populations. We show that this adaptation has a clear polygenic basis and is influenced by many genetic components. Our approach, implemented in the R package signet, improves on gene-level classical tests for selection by identifying both new candidate genes and new biological processes involved in adaptation to altitude.
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Affiliation(s)
- Alexandre Gouy
- Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Joséphine T. Daub
- Institute of Evolutionary Biology, Universitat Pompeu Fabra – CSIC, 08003 Barcelona, Spain
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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8
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Byars SG, Huang QQ, Gray LA, Bakshi A, Ripatti S, Abraham G, Stearns SC, Inouye M. Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy. PLoS Genet 2017; 13:e1006328. [PMID: 28640878 PMCID: PMC5480811 DOI: 10.1371/journal.pgen.1006328] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.
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Affiliation(s)
- Sean G. Byars
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Qin Qin Huang
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Lesley-Ann Gray
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Bakshi
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Samuli Ripatti
- Institute of Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gad Abraham
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Stephen C. Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Michael Inouye
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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9
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Abstract
Whole genome sequencing of families of Arabidopsis has recently lent strong support to the heterozygote instability (HI) hypothesis that heterozygosity locally increases mutation rate. However, there is an important theoretical difference between the impact on base substitutions, where mutation rate increases in regions surrounding a heterozygous site, and the impact of HI on sequences such as microsatellites, where mutations are likely to occur at the heterozygous site itself. At microsatellite loci, HI should create a positive feedback loop, with heterozygosity and mutation rate mutually increasing each other. Direct support for HI acting on microsatellites is limited and contradictory. I therefore analysed AC microsatellites in 1163 genome sequences from the 1000 genomes project. I used the presence of rare alleles, which are likely to be very recent in origin, as a surrogate measure of mutation rate. I show that rare alleles are more likely to occur at locus-population combinations with higher heterozygosity even when all populations carry exactly the same number of alleles.
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Affiliation(s)
- William Amos
- Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK
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10
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Schrider DR, Kern AD. S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning. PLoS Genet 2016; 12:e1005928. [PMID: 26977894 PMCID: PMC4792382 DOI: 10.1371/journal.pgen.1005928] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/21/2016] [Indexed: 12/17/2022] Open
Abstract
Detecting the targets of adaptive natural selection from whole genome sequencing data is a central problem for population genetics. However, to date most methods have shown sub-optimal performance under realistic demographic scenarios. Moreover, over the past decade there has been a renewed interest in determining the importance of selection from standing variation in adaptation of natural populations, yet very few methods for inferring this model of adaptation at the genome scale have been introduced. Here we introduce a new method, S/HIC, which uses supervised machine learning to precisely infer the location of both hard and soft selective sweeps. We show that S/HIC has unrivaled accuracy for detecting sweeps under demographic histories that are relevant to human populations, and distinguishing sweeps from linked as well as neutrally evolving regions. Moreover, we show that S/HIC is uniquely robust among its competitors to model misspecification. Thus, even if the true demographic model of a population differs catastrophically from that specified by the user, S/HIC still retains impressive discriminatory power. Finally, we apply S/HIC to the case of resequencing data from human chromosome 18 in a European population sample, and demonstrate that we can reliably recover selective sweeps that have been identified earlier using less specific and sensitive methods.
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Affiliation(s)
- Daniel R. Schrider
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- * E-mail:
| | - Andrew D. Kern
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
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11
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Heterochrony as Diachronically Modified Cell-Cell Interactions. BIOLOGY 2016; 5:biology5010004. [PMID: 26784244 PMCID: PMC4810161 DOI: 10.3390/biology5010004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/29/2015] [Accepted: 12/31/2015] [Indexed: 12/31/2022]
Abstract
Heterochrony is an enabling concept in evolution theory that metaphorically captures the mechanism of biologic change due to mechanisms of growth and development. The spatio-temporal patterns of morphogenesis are determined by cell-to-cell signaling mediated by specific soluble growth factors and their cognate receptors on nearby cells of different germline origins. Subsequently, down-stream production of second messengers generates patterns of form and function. Environmental upheavals such as Romer’s hypothesized drying up of bodies of water globally caused the vertebrate water-land transition. That transition caused physiologic stress, modifying cell-cell signaling to generate terrestrial adaptations of the skeleton, lung, skin, kidney and brain. These tissue-specific remodeling events occurred as a result of the duplication of the Parathyroid Hormone-related Protein Receptor (PTHrPR) gene, expressed in mesodermal fibroblasts in close proximity to ubiquitously expressed endodermal PTHrP, amplifying this signaling pathway. Examples of how and why PTHrPR amplification affected the ontogeny, phylogeny, physiology and pathophysiology of the lung are used to substantiate and further our understanding through insights to the heterochronic mechanisms of evolution, such as the fish swim bladder evolving into the vertebrate lung, interrelated by such functional homologies as surfactant and mechanotransduction. Instead of the conventional description of this phenomenon, lung evolution can now be understood as adaptive changes in the cellular-molecular signaling mechanisms underlying its ontogeny and phylogeny.
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12
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Manel S, Perrier C, Pratlong M, Abi-Rached L, Paganini J, Pontarotti P, Aurelle D. Genomic resources and their influence on the detection of the signal of positive selection in genome scans. Mol Ecol 2015; 25:170-84. [DOI: 10.1111/mec.13468] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/06/2015] [Accepted: 11/07/2015] [Indexed: 12/16/2022]
Affiliation(s)
- S. Manel
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier -EPHE; laboratoire Biogéographie et écologie des vertébrés; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - C. Perrier
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier -EPHE; laboratoire Biogéographie et écologie des vertébrés; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - M. Pratlong
- Aix Marseille Université; CNRS; IRD; Avignon Université, IMBE UMR 7263; Station Marine d'Endoume, 13007; Marseille France
- Aix Marseille Université; CNRS; Centrale Marseille; I2M UMR 7373; Evolution Biologique Modélisation; 3 Place Victor Hugo, 13331 Marseille Cedex Case 19 France
| | - L. Abi-Rached
- Equipe ATIP; URMITE UM 63 CNRS 7278 IRD 198 Inserm U1095; IHU Méditerranée Infection; Aix-Marseille Université; 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05 France
| | - J. Paganini
- XEGEN SAS; 15 Rue de la République 13420 Gemenos France
| | - P. Pontarotti
- Aix Marseille Université; CNRS; Centrale Marseille; I2M UMR 7373; Evolution Biologique Modélisation; 3 Place Victor Hugo, 13331 Marseille Cedex Case 19 France
| | - D. Aurelle
- Aix Marseille Université; CNRS; IRD; Avignon Université, IMBE UMR 7263; Station Marine d'Endoume, 13007; Marseille France
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Chen H. Population genetic studies in the genomic sequencing era. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2015; 36:223-32. [PMID: 26228473 DOI: 10.13918/j.issn.2095-8137.2015.4.223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Recent advances in high-throughput sequencing technologies have revolutionized the field of population genetics. Data now routinely contain genomic level polymorphism information, and the low cost of DNA sequencing enables researchers to investigate tens of thousands of subjects at a time. This provides an unprecedented opportunity to address fundamental evolutionary questions, while posing challenges on traditional population genetic theories and methods. This review provides an overview of the recent methodological developments in the field of population genetics, specifically methods used to infer ancient population history and investigate natural selection using large-sample, large-scale genetic data. Several open questions are also discussed at the end of the review.
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Affiliation(s)
- Hua Chen
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101,
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