1
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Wang X, Reid K, Chen Y, Dudgeon D, Merilä J. Ecological genetics of isolated loach populations indicate compromised adaptive potential. Heredity (Edinb) 2024; 133:88-98. [PMID: 38961235 PMCID: PMC11286901 DOI: 10.1038/s41437-024-00695-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (Oreonectes platycephalus), a small noemacheilid fish, is widely across southern China, but only in the headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of O. platycephalus to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity, signs of inbreeding, and had small contemporary effective population sizes. Estimates of average observed heterozygosity (HO = 0.0473), average weighted nucleotide diversity (πw = 0.0546) and contemporary effective population sizes (Ne = 10.2 ~ 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average FST = 0.668), even over short geographic distances (<1.5 km), with clear patterns of isolation by distance. These results suggest that Hong Kong populations of O. platycephalus have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and contemporary effective population sizes within O. platycephalus populations are lower than most other freshwater fishes, suggests that they face high local extinction risk and have limited capacity for future adaptation.
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Affiliation(s)
- Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Kerry Reid
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Chen
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - David Dudgeon
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Juha Merilä
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, FI-00014 University of Helsinki, Helsinki, Finland.
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2
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Zeitler L, Gilbert KJ. Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates. Genome Biol Evol 2024; 16:evae139. [PMID: 38935434 PMCID: PMC11245710 DOI: 10.1093/gbe/evae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024] Open
Abstract
Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also create long ROHs. While ROHs are frequently used to understand inbreeding in the context of conservation and selective breeding, as well as for consanguinity of populations and their demographic history, it remains unclear how ROH characteristics are altered by selfing and if this confounds expected signatures of inbreeding due to demographic change. Using simulations, we study the impact of the mode of reproduction and demographic history on ROHs. We apply random forests to identify unique characteristics of ROHs, indicative of different sources of inbreeding. We pinpoint distinct features of ROHs that can be used to better characterize the type of inbreeding the population was subjected to and to predict outcrossing rates and complex demographic histories. Using additional simulations and four empirical datasets, two from highly selfing species and two from mixed-maters, we predict the selfing rate and validate our estimations. We find that self-fertilization rates are successfully identified even with complex demography. Population genetic summary statistics improve algorithm accuracy particularly in the presence of additional inbreeding, e.g. from population bottlenecks. Our findings highlight the importance of ROHs in disentangling confounding factors related to various sources of inbreeding and demonstrate situations where such sources cannot be differentiated. Additionally, our random forest models provide a novel tool to the community for inferring selfing rates using genomic data.
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Affiliation(s)
- Leo Zeitler
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland
| | - Kimberly J Gilbert
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland
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3
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Zeng ZH, Zhong L, Sun HY, Wu ZK, Wang X, Wang H, Li DZ, Barrett SCH, Zhou W. Parallel evolution of morphological and genomic selfing syndromes accompany the breakdown of heterostyly. THE NEW PHYTOLOGIST 2024; 242:302-316. [PMID: 38214455 DOI: 10.1111/nph.19522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures and can involve parallel evolution within related lineages. Adaptive evolution of morphological traits is often assumed to evolve faster than nonadaptive features of the genomic selfing syndrome. We investigated phenotypic and genomic changes associated with transitions from distyly to homostyly in the Primula oreodoxa complex. We determined whether the transition to selfing occurred more than once and investigated stages in the evolution of morphological and genomic selfing syndromes using 22 floral traits and both nuclear and plastid genomic data from 25 populations. Two independent transitions were detected representing an earlier and a more recently derived selfing lineage. The older lineage exhibited classic features of the morphological and genomic selfing syndrome. Although features of both selfing syndromes were less developed in the younger selfing lineage, they exhibited parallel development with the older selfing lineage. This finding contrasts with the prediction that some genomic changes should lag behind adaptive changes to morphological traits. Our findings highlight the value of comparative studies on the timing and extent of transitions from outcrossing to selfing between related lineages for investigating the tempo of morphological and molecular evolution.
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Affiliation(s)
- Zhi-Hua Zeng
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhong
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua-Ying Sun
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, China
| | - Zhi-Kun Wu
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550002, China
| | - Xin Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Wei Zhou
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, 674100, China
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4
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Kent TV, Schrider DR, Matute DR. Demographic history and the efficacy of selection in the globally invasive mosquito Aedes aegypti. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.584008. [PMID: 38559089 PMCID: PMC10979846 DOI: 10.1101/2024.03.07.584008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Aedes aegypti is the main vector species of yellow fever, dengue, zika and chikungunya. The species is originally from Africa but has experienced a spectacular expansion in its geographic range to a large swath of the world, the demographic effects of which have remained largely understudied. In this report, we examine whole-genome sequences from 6 countries in Africa, North America, and South America to investigate the demographic history of the spread of Ae. aegypti into the Americas its impact on genomic diversity. In the Americas, we observe patterns of strong population structure consistent with relatively low (but probably non-zero) levels of gene flow but occasional long-range dispersal and/or recolonization events. We also find evidence that the colonization of the Americas has resulted in introduction bottlenecks. However, while each sampling location shows evidence of a past population contraction and subsequent recovery, our results suggest that the bottlenecks in America have led to a reduction in genetic diversity of only ~35% relative to African populations, and the American samples have retained high levels of genetic diversity (expected heterozygosity of ~0.02 at synonymous sites) and have experienced only a minor reduction in the efficacy of selection. These results evoke the image of an invasive species that has expanded its range with remarkable genetic resilience in the face of strong eradication pressure.
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Affiliation(s)
- Tyler V. Kent
- Department of Biology, College of Arts and Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel R. Schrider
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel R. Matute
- Department of Biology, College of Arts and Sciences, University of North Carolina, Chapel Hill, NC, USA
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5
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La Rocca LA, Frank J, Bentzen HB, Pantel JT, Gerischer K, Bovier A, Krawitz PM. Understanding recessive disease risk in multi-ethnic populations with different degrees of consanguinity. Am J Med Genet A 2024; 194:e63452. [PMID: 37921563 DOI: 10.1002/ajmg.a.63452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
Population medical genetics aims at translating clinically relevant findings from recent studies of large cohorts into healthcare for individuals. Genetic counseling concerning reproductive risks and options is still mainly based on family history, and consanguinity is viewed to increase the risk for recessive diseases regardless of the demographics. However, in an increasingly multi-ethnic society with diverse approaches to partner selection, healthcare professionals should also sharpen their intuition for the influence of different mating schemes in non-equilibrium dynamics. We, therefore, revisited the so-called out-of-Africa model and studied in forward simulations with discrete and not overlapping generations the effect of inbreeding on the average number of recessive lethals in the genome. We were able to reproduce in both frameworks the drop in the incidence of recessive disorders, which is a transient phenomenon during and after the growth phase of a population, and therefore showed their equivalence. With the simulation frameworks, we also provide the means to study and visualize the effect of different kin sizes and mating schemes on these parameters for educational purposes.
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Affiliation(s)
- Luis A La Rocca
- Institute for Applied Mathematics, University of Bonn, Bonn, Germany
| | - Julia Frank
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Heidi Beate Bentzen
- Centre for Medical Ethics, Faculty of Medicine, Univeristy of Oslo, Oslo, Norway
| | - Jean Tori Pantel
- Department of Digitalization and General Practice, University Hospital RWTH Aachen, Aachen, Germany
| | - Konrad Gerischer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Anton Bovier
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute for Applied Mathematics, University of Bonn, Bonn, Germany
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6
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Urquhart-Cronish M, Angert AL, Otto SP, MacPherson A. Density-Dependent Selection during Range Expansion Affects Expansion Load in Life History Traits. Am Nat 2024; 203:382-392. [PMID: 38358811 DOI: 10.1086/728599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractModels of range expansion have independently explored fitness consequences of life history trait evolution and increased rates of genetic drift-or "allele surfing"-during spatial spread, but no previous model has examined the interactions between these two processes. Here, using spatially explicit simulations, we explore an ecologically complex range expansion scenario that combines density-dependent selection with allele surfing to asses the genetic and fitness consequences of density-dependent selection on the evolution of life history traits. We demonstrate that density-dependent selection on the range edge acts differently depending on the life history trait and can either diminish or enhance allele surfing. Specifically, we show that selection at the range edge is always weaker at sites affecting competitive ability (K-selected traits) than at sites affecting birth rate (r-selected traits). We then link differences in the frequency of deleterious mutations to differences in the efficacy of selection and rate of mutation accumulation across distinct life history traits. Finally, we demonstrate that the observed fitness consequences of allele surfing depend on the population density in which expansion load is measured. Our work highlights the complex relationship between ecology and expressed genetic load, which will be important to consider when interpreting both experimental and field studies of range expansion.
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7
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Kyriazis CC, Robinson JA, Lohmueller KE. Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations. Am Nat 2023; 202:737-752. [PMID: 38033186 PMCID: PMC10897732 DOI: 10.1086/726736] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).
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8
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Sandler G, Agrawal AF, Wright SI. Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha. Genome Biol Evol 2023; 15:evad196. [PMID: 37883717 PMCID: PMC10667032 DOI: 10.1093/gbe/evad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
The population genomics of facultatively sexual organisms are understudied compared with their abundance across the tree of life. We explore patterns of genetic diversity in two subspecies of the facultatively sexual liverwort Marchantia polymorpha using samples from across Southern Ontario, Canada. Despite the ease with which M. polymorpha should be able to propagate asexually, we find no evidence of strictly clonal descent among our samples and little to no signal of isolation by distance. Patterns of identity-by-descent tract sharing further showed evidence of recent recombination and close relatedness between geographically distant isolates, suggesting long distance gene flow and at least a modest frequency of sexual reproduction. However, the M. polymorpha genome contains overall very low levels of nucleotide diversity and signs of inefficient selection evidenced by a relatively high fraction of segregating deleterious variants. We interpret these patterns as possible evidence of the action of linked selection and a small effective population size due to past generations of asexual propagation. Overall, the M. polymorpha genome harbors signals of a complex history of both sexual and asexual reproduction.
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Affiliation(s)
- George Sandler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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9
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Rougemont Q, Leroy T, Rondeau EB, Koop B, Bernatchez L. Allele surfing causes maladaptation in a Pacific salmon of conservation concern. PLoS Genet 2023; 19:e1010918. [PMID: 37683018 PMCID: PMC10545117 DOI: 10.1371/journal.pgen.1010918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 10/02/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations, is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.
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Affiliation(s)
- Quentin Rougemont
- Centre d’Ecologie Fonctionnelle et Evolutive, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de Toulouse, Auzeville- Tolosane, France
| | - Eric B. Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, Canada
| | - Ben Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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10
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Zeitler L, Parisod C, Gilbert KJ. Purging due to self-fertilization does not prevent accumulation of expansion load. PLoS Genet 2023; 19:e1010883. [PMID: 37656747 PMCID: PMC10501686 DOI: 10.1371/journal.pgen.1010883] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/14/2023] [Accepted: 07/25/2023] [Indexed: 09/03/2023] Open
Abstract
As species expand their geographic ranges, colonizing populations face novel ecological conditions, such as new environments and limited mates, and suffer from evolutionary consequences of demographic change through bottlenecks and mutation load accumulation. Self-fertilization is often observed at species range edges and, in addition to countering the lack of mates, is hypothesized as an evolutionary advantage against load accumulation through increased homozygosity and purging. We study how selfing impacts the accumulation of genetic load during range expansion via purging and/or speed of colonization. Using simulations, we disentangle inbreeding effects due to demography versus due to selfing and find that selfers expand faster, but still accumulate load, regardless of mating system. The severity of variants contributing to this load, however, differs across mating system: higher selfing rates purge large-effect recessive variants leaving a burden of smaller-effect alleles. We compare these predictions to the mixed-mating plant Arabis alpina, using whole-genome sequences from refugial outcrossing populations versus expanded selfing populations. Empirical results indicate accumulation of expansion load along with evidence of purging in selfing populations, concordant with our simulations, suggesting that while purging is a benefit of selfing evolving during range expansions, it is not sufficient to prevent load accumulation due to range expansion.
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Affiliation(s)
- Leo Zeitler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Christian Parisod
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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11
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Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. Deleterious Variation in Natural Populations and Implications for Conservation Genetics. Annu Rev Anim Biosci 2023; 11:93-114. [PMID: 36332644 PMCID: PMC9933137 DOI: 10.1146/annurev-animal-080522-093311] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.
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Affiliation(s)
- Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, California, USA;
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Stella C Yuan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , , .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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12
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Samuk K, Noor MAF. Gene flow biases population genetic inference of recombination rate. G3 GENES|GENOMES|GENETICS 2022; 12:6698695. [PMID: 36103705 PMCID: PMC9635666 DOI: 10.1093/g3journal/jkac236] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 08/30/2022] [Indexed: 11/21/2022]
Abstract
Accurate estimates of the rate of recombination are key to understanding a host of evolutionary processes as well as the evolution of the recombination rate itself. Model-based population genetic methods that infer recombination rates from patterns of linkage disequilibrium in the genome have become a popular method to estimate rates of recombination. However, these linkage disequilibrium-based methods make a variety of simplifying assumptions about the populations of interest that are often not met in natural populations. One such assumption is the absence of gene flow from other populations. Here, we use forward-time population genetic simulations of isolation-with-migration scenarios to explore how gene flow affects the accuracy of linkage disequilibrium-based estimators of recombination rate. We find that moderate levels of gene flow can result in either the overestimation or underestimation of recombination rates by up to 20–50% depending on the timing of divergence. We also find that these biases can affect the detection of interpopulation differences in recombination rate, causing both false positives and false negatives depending on the scenario. We discuss future possibilities for mitigating these biases and recommend that investigators exercise caution and confirm that their study populations meet assumptions before deploying these methods.
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Affiliation(s)
- Kieran Samuk
- Department of Biology, Duke University , Durham, NC 27708, USA
- Department of Evolution, Ecology, and Organismal Biology, The University of California, Riverside ,Riverside, CA 92521, USA
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13
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Abstract
We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone-Lewontin's Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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14
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Robinson JA, Kyriazis CC, Nigenda-Morales SF, Beichman AC, Rojas-Bracho L, Robertson KM, Fontaine MC, Wayne RK, Lohmueller KE, Taylor BL, Morin PA. The critically endangered vaquita is not doomed to extinction by inbreeding depression. Science 2022; 376:635-639. [PMID: 35511971 PMCID: PMC9881057 DOI: 10.1126/science.abm1742] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality from gillnet fishing have driven Mexico's vaquita porpoise (Phocoena sinus) to ~10 remaining individuals. We analyzed whole-genome sequences from 20 vaquitas and integrated genomic and demographic information into stochastic, individual-based simulations to quantify the species' recovery potential. Our analysis suggests that the vaquita's historical rarity has resulted in a low burden of segregating deleterious variation, reducing the risk of inbreeding depression. Similarly, genome-informed simulations suggest that the vaquita can recover if bycatch mortality is immediately halted. This study provides hope for vaquitas and other naturally rare endangered species and highlights the utility of genomics in predicting extinction risk.
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Affiliation(s)
- Jacqueline A. Robinson
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
| | - Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
| | - Sergio F. Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav); Irapuato, Guanajuato, Mexico
| | | | - Lorenzo Rojas-Bracho
- Comisión Nacional de Áreas Naturales Protegidas/SEMARNAT; Ensenada, Mexico
- PNUD-Sinergia en la Comisión Nacional de Áreas Naturales Protegidas, Ensenada, B.C., México
| | - Kelly M. Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
| | - Michael C. Fontaine
- MIVEGEC, Université de Montpellier, CNRS, IRD; Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES); Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen; Groningen, The Netherlands
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles; Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, USA
| | - Barbara L. Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
| | - Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA ; La Jolla, CA, USA
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15
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Hunt DAGA, DiBattista JD, Hendry AP. Effects of insularity on genetic diversity within and among natural populations. Ecol Evol 2022; 12:e8887. [PMID: 35571757 PMCID: PMC9077629 DOI: 10.1002/ece3.8887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 04/15/2022] [Indexed: 11/27/2022] Open
Abstract
We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen-particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same study system-suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.
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Affiliation(s)
- David A. G. A. Hunt
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
| | - Joseph D. DiBattista
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
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16
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Chen J, Bataillon T, Glémin S, Lascoux M. What does the distribution of fitness effects of new mutations reflect? Insights from plants. THE NEW PHYTOLOGIST 2022; 233:1613-1619. [PMID: 34704271 DOI: 10.1111/nph.17826] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
The distribution of fitness effects (DFE) of new mutations plays a central role in molecular evolution. It is therefore crucial to be able to estimate it accurately from genomic data and to understand the factors that shape it. After a rapid overview of available methods to characterize the fitness effects of mutations, we review what is known on the factors affecting them in plants. Available data indicate that life history traits (e.g. mating system and longevity) have a major effect on the DFE. By contrast, the impact of demography within species appears to be more limited. These results remain to be confirmed, and methods to estimate the joint evolution of demography, life history traits, and the DFE need to be developed.
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Affiliation(s)
- Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, C.F. Möllers Allé 8, Aarhus C, DK-8000, Denmark
| | - Sylvain Glémin
- Centre National de la Recherche Scientifique (CNRS), ECOBIO (Ecosystèmes, Biodiversité, Evolution) - Unité Mixte de Recherche (UMR) 6553, Université de Rennes, Rennes, F-35000, France
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 75236, Sweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 75236, Sweden
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17
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Conover JL, Wendel JF. Deleterious Mutations Accumulate Faster in Allopolyploid than Diploid Cotton (Gossypium) and Unequally between Subgenomes. Mol Biol Evol 2022; 39:6517786. [PMID: 35099532 PMCID: PMC8841602 DOI: 10.1093/molbev/msac024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Whole genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs in polyploids relative to diploids is an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster in allopolyploids than diploids due to the masking effect of redundant gene copies, but this prediction is hitherto unconfirmed. Here, we use the cotton genus (Gossypium), which contains seven allopolyploids derived from a single polyploidization event 1-2 million years ago, to investigate deleterious mutation accumulation. We use two methods of identifying deleterious mutations at the nucleotide and amino acid level, along with whole-genome resequencing of 43 individuals spanning six allopolyploid species and their two diploid progenitors, to demonstrate that deleterious mutations accumulate faster in allopolyploids than in their diploid progenitors. We find that, unlike what would be expected under models of demographic changes alone, strongly deleterious mutations show the biggest difference between ploidy levels, and this effect diminishes for moderately and mildly deleterious mutations. We further show that the proportion of nonsynonymous mutations that are deleterious differs between the two co-resident subgenomes in the allopolyploids, suggesting that homoeologous masking acts unequally between subgenomes. Our results provide a genome-wide perspective on classic notions of the significance of gene duplication that likely are broadly applicable to allopolyploids, with implications for our understanding of the evolutionary fate of deleterious mutations. Finally, we note that some measures of selection (e.g. dN/dS, πN/πS) may be biased when species of different ploidy levels are compared.
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Affiliation(s)
- Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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18
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Vecchyo DOD, Lohmueller KE, Novembre J. Haplotype-based inference of the distribution of fitness effects. Genetics 2022; 220:6501446. [PMID: 35100400 PMCID: PMC8982047 DOI: 10.1093/genetics/iyac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/18/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
Recent genome sequencing studies with large sample sizes in humans have discovered a vast quantity of low-frequency variants, providing an important source of information to analyze how selection is acting on human genetic variation. In order to estimate the strength of natural selection acting on low-frequency variants, we have developed a likelihood-based method that uses the lengths of pairwise identity-by-state between haplotypes carrying low-frequency variants. We show that in some non-equilibrium populations (such as those that have had recent population expansions) it is possible to distinguish between positive or negative selection acting on a set of variants. With our new framework, one can infer a fixed selection intensity acting on a set of variants at a particular frequency, or a distribution of selection coefficients for standing variants and new mutations. We show an application of our method to the UK10K phased haplotype dataset of individuals.
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Affiliation(s)
- Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, 76230, México
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, 90095, United States of America
| | - Kirk E Lohmueller
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, 90095, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, 90095, United States of America
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, 60637, United States of America
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19
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Abstract
The nearly neutral theory is a common framework to describe natural selection at the molecular level. This theory emphasizes the importance of slightly deleterious mutations by recognizing their ability to segregate and eventually get fixed due to genetic drift in spite of the presence of purifying selection. As genetic drift is stronger in smaller than in larger populations, a correlation between population size and molecular measures of natural selection is expected within the nearly neutral theory. However, this hypothesis was originally formulated under equilibrium conditions. As most natural populations are not in equilibrium, testing the relationship empirically may lead to confounded outcomes. Demographic nonequilibria, for instance following a change in population size, are common scenarios that are expected to push the selection–drift relationship off equilibrium. By explicitly modeling the effects of a change in population size on allele frequency trajectories in the Poisson random field framework, we obtain analytical solutions of the nonstationary allele frequency spectrum. This enables us to derive exact results of measures of natural selection and effective population size in a demographic nonequilibrium. The study of their time-dependent relationship reveals a substantial deviation from the equilibrium selection–drift balance after a change in population size. Moreover, we show that the deviation is sensitive to the combination of different measures. These results therefore constitute relevant tools for empirical studies to choose suitable measures for investigating the selection–drift relationship in natural populations. Additionally, our new modeling approach extends existing population genetics theory and can serve as foundation for methodological developments.
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Affiliation(s)
- Rebekka Müller
- Department of Mathematics, Uppsala University, 752 37 Uppsala, Sweden
| | - Ingemar Kaj
- Department of Mathematics, Uppsala University, 752 37 Uppsala, Sweden
| | - Carina F. Mugal
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
- Corresponding author: E-mail:
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20
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Lucena-Perez M, Kleinman-Ruiz D, Marmesat E, Saveljev AP, Schmidt K, Godoy JA. Bottleneck-associated changes in the genomic landscape of genetic diversity in wild lynx populations. Evol Appl 2021; 14:2664-2679. [PMID: 34815746 PMCID: PMC8591332 DOI: 10.1111/eva.13302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 01/06/2023] Open
Abstract
Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic diversity following a bottleneck by comparing whole-genome diversity patterns in populations with and without severe recent documented declines of Iberian (Lynx pardinus, n = 31) and Eurasian lynx (Lynx lynx, n = 29). As expected, overall genomic diversity correlated negatively with bottleneck intensity and/or duration. Correlations of genetic diversity with divergence, chromosome size, gene or functional site content, GC content, or recombination were observed in nonbottlenecked populations, but were weaker in bottlenecked populations. Also, functional features under intense purifying selection and the X chromosome showed an increase in the observed density of variants, even resulting in higher θ W diversity than in nonbottlenecked populations. Increased diversity seems to be related to both a higher mutational input in those regions creating a large collection of low-frequency variants, a few of which increase in frequency during the bottleneck to the point they become detectable with our limited sample, and the reduced efficacy of purifying selection, which affects not only protein structure and function but also the regulation of gene expression. The results of this study alert to the possible reduction of fitness and adaptive potential associated with the genomic erosion in regulatory elements. Further, the detection of a gain of diversity in ultra-conserved elements can be used as a sensitive and easy-to-apply signature of genetic erosion in wild populations.
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Affiliation(s)
- Maria Lucena-Perez
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Daniel Kleinman-Ruiz
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
- Departamento de Genética Facultad de Biología Universidad Complutense Madrid Spain
| | - Elena Marmesat
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Alexander P Saveljev
- Department of Animal Ecology Russian Research Institute of Game Management and Fur Farming Kirov Russia
| | - Krzysztof Schmidt
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - José A Godoy
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
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21
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Bisschop G, Lohse K, Setter D. Sweeps in time: leveraging the joint distribution of branch lengths. Genetics 2021; 219:iyab119. [PMID: 34849880 PMCID: PMC8633083 DOI: 10.1093/genetics/iyab119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/10/2021] [Indexed: 11/14/2022] Open
Abstract
Current methods of identifying positively selected regions in the genome are limited in two key ways: the underlying models cannot account for the timing of adaptive events and the comparison between models of selective sweeps and sequence data is generally made via simple summaries of genetic diversity. Here, we develop a tractable method of describing the effect of positive selection on the genealogical histories in the surrounding genome, explicitly modeling both the timing and context of an adaptive event. In addition, our framework allows us to go beyond analyzing polymorphism data via the site frequency spectrum or summaries thereof and instead leverage information contained in patterns of linked variants. Tests on both simulations and a human data example, as well as a comparison to SweepFinder2, show that even with very small sample sizes, our analytic framework has higher power to identify old selective sweeps and to correctly infer both the time and strength of selection. Finally, we derived the marginal distribution of genealogical branch lengths at a locus affected by selection acting at a linked site. This provides a much-needed link between our analytic understanding of the effects of sweeps on sequence variation and recent advances in simulation and heuristic inference procedures that allow researchers to examine the sequence of genealogical histories along the genome.
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Affiliation(s)
- Gertjan Bisschop
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Derek Setter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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22
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North HL, McGaughran A, Jiggins CD. Insights into invasive species from whole-genome resequencing. Mol Ecol 2021; 30:6289-6308. [PMID: 34041794 DOI: 10.1111/mec.15999] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals can increase the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies applied. To date whole-genome resequencing has only been used in a handful of invasive systems, but these studies have confirmed the importance of processes such as balancing selection and hybridization in allowing invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.
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Affiliation(s)
- Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
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23
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Takou M, Hämälä T, Koch EM, Steige KA, Dittberner H, Yant L, Genete M, Sunyaev S, Castric V, Vekemans X, Savolainen O, de Meaux J. Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population. Mol Biol Evol 2021; 38:1820-1836. [PMID: 33480994 PMCID: PMC8097302 DOI: 10.1093/molbev/msaa322] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European subspecies Arabidopsis lyrata ssp. petraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that nonsynonymous variants segregate at higher frequencies. We detect a 4.9% excess of derived nonsynonymous variants per individual in the range-edge population, suggesting an increase of the genomic burden of deleterious mutations. Inference of the fitness effects of mutations and modeling of allele frequencies under the explicit demographic history of each population predicts a depletion of rare deleterious variants in the range-edge population, but an enrichment for fixed ones, consistent with the bottleneck effect. However, the demographic history of the range-edge population predicts a small net decrease in per-individual fitness. Consistent with this prediction, the range-edge population is not impaired in its growth and survival measured in a common garden experiment. We further observe that the allelic diversity at the self-incompatibility locus, which ensures strict outcrossing and evolves under negative frequency-dependent selection, has remained unchanged. Genomic footprints indicative of selective sweeps are broader in the Northern population but not less frequent. We conclude that the outcrossing species A. lyrata ssp. petraea shows a strong resilience to the effect of range expansion.
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Affiliation(s)
- Margarita Takou
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Evan M Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kim A Steige
- Institute of Botany, University of Cologne, Cologne, Germany
| | | | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Mathieu Genete
- CNRS, UMR 8198 – Evo-Eco-Paleo, University of Lille, Lille, France
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Vincent Castric
- CNRS, UMR 8198 – Evo-Eco-Paleo, University of Lille, Lille, France
| | - Xavier Vekemans
- CNRS, UMR 8198 – Evo-Eco-Paleo, University of Lille, Lille, France
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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24
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Hirata M, Mitsuyuki C, Moritsuka E, Chhang P, Tagane S, Toyama H, Sokh H, Rueangruea S, Suddee S, Suyama Y, Yahara T, Teshima KM, Tachida H, Kusumi J. Evaluating the genetic diversity in two tropical leguminous trees, Dalbergia cochinchinensis and D. nigrescens, in lowland forests in Cambodia and Thailand using MIG-seq. Genes Genet Syst 2021; 96:41-53. [PMID: 33731512 DOI: 10.1266/ggs.20-00026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
It is vital to measure the levels of genetic diversity and differentiation between populations in a species to understand the current genetic structure and evolution of the species. Here, MIG-seq (multiplexed inter-simple sequence repeat genotyping by sequencing) was employed to assess the genetic variation in two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data for 255-618 loci, each with an approximate length of 100 bp, were obtained, and the nucleotide diversity, Tajima's D and FST were computed. The estimates calculated from the data obtained by MIG-seq were compared to those obtained by Sanger sequencing of nine nuclear coding genes in D. cochinchinensis in our previous study. The nucleotide diversity at the MIG-seq loci was slightly higher than that at silent sites in the coding loci, whereas the FST values at the MIG-seq loci were generally lower than those at the coding loci, although the differences were not significant. Moreover, nucleotide diversities within populations of the two species were similar to each other, at approximately 0.005. Three and four population clusters were genetically recognized in D. cochinchinensis and D. nigrescens, respectively. Although the populations were differentiated from each other, the levels of differentiation among them, as measured by FST, were higher in D. cochinchinensis than in D. nigrescens. This indicates higher levels of gene flow between the populations in the latter species. We recommend using MIG-seq for quick surveys of genetic variation because it is cost-effective and results in smaller variance in the estimates of population genetic parameters.
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Affiliation(s)
- Moeko Hirata
- Graduate School of Systems Life Sciences, Kyushu University
| | | | - Etsuko Moritsuka
- Department of Biology, Faculty of Science, Kyushu University.,Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University
| | - Phourin Chhang
- Institute of Forest and Wildlife Research Development, Forestry Administration
| | - Shuichiro Tagane
- Department of Biology, Faculty of Science, Kyushu University.,The Kagoshima University Museum, Kagoshima University
| | - Hironori Toyama
- Department of Biology, Faculty of Science, Kyushu University.,Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies
| | - Heng Sokh
- Institute of Forest and Wildlife Research Development, Forestry Administration
| | - Sukid Rueangruea
- The Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation
| | - Somran Suddee
- The Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation
| | | | | | | | | | - Junko Kusumi
- Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University
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25
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James J, Eyre-Walker A. Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes. Genome Biol Evol 2020; 12:2441-2449. [PMID: 33095231 PMCID: PMC7719226 DOI: 10.1093/gbe/evaa222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 01/19/2023] Open
Abstract
What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.
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Affiliation(s)
- Jennifer James
- School of Life Sciences, University of Sussex, Brighton, United Kingdom.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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26
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Phylomitogenomics provides new perspectives on the Euphasmatodea radiation (Insecta: Phasmatodea). Mol Phylogenet Evol 2020; 155:106983. [PMID: 33059069 DOI: 10.1016/j.ympev.2020.106983] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/11/2020] [Accepted: 10/06/2020] [Indexed: 11/20/2022]
Abstract
Phasmatodea species diversity lies almost entirely within its suborder Euphasmatodea, which exhibits a pantropical distribution and is considered to derive from a recent and rapid evolutionary radiation. To shed light on Euphasmatodea origins and diversification, we assembled the mitogenomes of 17 species from transcriptomic sequencing data and analysed them along with 22 already available Phasmatodea mitogenomes and 33 mitogenomes representing most of the Polyneoptera lineages. Maximum Likelihood and Bayesian Inference approaches retrieved consistent topologies, both showing the widespread conflict between phylogenetic approaches and traditional systematics. We performed a divergence time analysis leveraging ten fossil specimens representative of most polyneopteran lineages: the time tree obtained supports an older radiation of the clade with respect to previous hypotheses. Euphasmatodea diversification is inferred to have started ~ 187 million years ago, suggesting that the Triassic-Jurassic mass extinction and the breakup of Pangea could have contributed to the process. We also investigated Euphasmatodea mitogenomes patterns of dN, dS and dN/dS ratio throughout our time-tree, trying to characterize the selective regime which may have shaped the clade evolution.
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27
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Galtier N, Rousselle M. How Much Does Ne Vary Among Species? Genetics 2020; 216:559-572. [PMID: 32839240 PMCID: PMC7536855 DOI: 10.1534/genetics.120.303622] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
Genetic drift is an important evolutionary force of strength inversely proportional to Ne , the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a difficult task. Here we assess the magnitude of variation in drift power among species of animals via its effect on the mutation load - which implies also inferring the distribution of fitness effects of deleterious mutations. To this aim, we analyze the nonsynonymous (amino-acid changing) and synonymous (amino-acid conservative) allele frequency spectra in a large sample of metazoan species, with a focus on the primates vs. fruit flies contrast. We show that a Gamma model of the distribution of fitness effects is not suitable due to strong differences in estimated shape parameters among taxa, while adding a class of lethal mutations essentially solves the problem. Using the Gamma + lethal model and assuming that the mean deleterious effects of nonsynonymous mutations is shared among species, we estimate that the power of drift varies by a factor of at least 500 between large-Ne and small-Ne species of animals, i.e., an order of magnitude more than the among-species variation in genetic diversity. Our results are relevant to Lewontin's paradox while further questioning the meaning of the Ne parameter in population genomics.
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Affiliation(s)
- Nicolas Galtier
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
| | - Marjolaine Rousselle
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
- Bioinformatics Research Centre, Aarhus University, DK Aarhus, Denmark
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28
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Chen J, Glémin S, Lascoux M. From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta's Slightly Deleterious Model of Molecular Evolution? Genetics 2020; 214:1005-1018. [PMID: 32015019 PMCID: PMC7153929 DOI: 10.1534/genetics.119.302869] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/26/2020] [Indexed: 12/18/2022] Open
Abstract
Since its inception in 1973, the slightly deleterious model of molecular evolution, also known as the nearly neutral theory of molecular evolution, remains a central model to explain the main patterns of DNA polymorphism in natural populations. This is not to say that the quantitative fit to data are perfect. A recent study used polymorphism data from Drosophila melanogaster to test whether, as predicted by the nearly neutral theory, the proportion of effectively neutral mutations depends on the effective population size (Ne ). It showed that a nearly neutral model simply scaling with Ne variation across the genome could not alone explain the data, but that consideration of linked positive selection improves the fit between observations and predictions. In the present article, we extended the work in two main directions. First, we confirmed the observed pattern on a set of 59 species, including high-quality genomic data from 11 animal and plant species with different mating systems and effective population sizes, hence a priori different levels of linked selection. Second, for the 11 species with high-quality genomic data we also estimated the full distribution of fitness effects (DFE) of mutations, and not solely the DFE of deleterious mutations. Both Ne and beneficial mutations contributed to the relationship between the proportion of effectively neutral mutations and local Ne across the genome. In conclusion, the predictions of the slightly deleterious model of molecular evolution hold well for species with small Ne , but for species with large Ne , the fit is improved by incorporating linked positive selection to the model.
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Affiliation(s)
- Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Sylvain Glémin
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
- Université de Rennes, Centre National de la Recherche Scientifique (CNRS), ECOBIO (Ecosystèmes, Biodiversité, Evolution) - Unité Mixte de Recherche (UMR) 6553, F-35000 Rennes, France
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
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The Temporal Dynamics of Background Selection in Nonequilibrium Populations. Genetics 2020; 214:1019-1030. [PMID: 32071195 DOI: 10.1534/genetics.119.302892] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 01/30/2020] [Indexed: 01/06/2023] Open
Abstract
Neutral genetic diversity across the genome is determined by the complex interplay of mutation, demographic history, and natural selection. While the direct action of natural selection is limited to functional loci across the genome, its impact can have effects on nearby neutral loci due to genetic linkage. These effects of selection at linked sites, referred to as genetic hitchhiking and background selection (BGS), are pervasive across natural populations. However, only recently has there been a focus on the joint consequences of demography and selection at linked sites, and some empirical studies have come to apparently contradictory conclusions as to their combined effects. To understand the relationship between demography and selection at linked sites, we conducted an extensive forward simulation study of BGS under a range of demographic models. We found that the relative levels of diversity in BGS and neutral regions vary over time and that the initial dynamics after a population size change are often in the opposite direction of the long-term expected trajectory. Our detailed observations of the temporal dynamics of neutral diversity in the context of selection at linked sites in nonequilibrium populations provide new intuition about why patterns of diversity under BGS vary through time in natural populations and help reconcile previously contradictory observations. Most notably, our results highlight that classical models of BGS are poorly suited for predicting diversity in nonequilibrium populations.
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30
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Mattila TM, Laenen B, Slotte T. Population Genomics of Transitions to Selfing in Brassicaceae Model Systems. Methods Mol Biol 2020; 2090:269-287. [PMID: 31975171 DOI: 10.1007/978-1-0716-0199-0_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many plants harbor complex mechanisms that promote outcrossing and efficient pollen transfer. These include floral adaptations as well as genetic mechanisms, such as molecular self-incompatibility (SI) systems. The maintenance of such systems over long evolutionary timescales suggests that outcrossing is favorable over a broad range of conditions. Conversely, SI has repeatedly been lost, often in association with transitions to self-fertilization (selfing). This transition is favored when the short-term advantages of selfing outweigh the costs, primarily inbreeding depression. The transition to selfing is expected to have major effects on population genetic variation and adaptive potential, as well as on genome evolution. In the Brassicaceae, many studies on the population genetic, gene regulatory, and genomic effects of selfing have centered on the model plant Arabidopsis thaliana and the crucifer genus Capsella. The accumulation of population genomics datasets have allowed detailed investigation of where, when and how the transition to selfing occurred. Future studies will take advantage of the development of population genetics theory on the impact of selfing, especially regarding positive selection. Furthermore, investigation of systems including recent transitions to selfing, mixed mating populations and/or multiple independent replicates of the same transition will facilitate dissecting the effects of mating system variation from processes driven by demography.
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Affiliation(s)
- Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Benjamin Laenen
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
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31
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Castellano D, Eyre-Walker A, Munch K. Impact of Mutation Rate and Selection at Linked Sites on DNA Variation across the Genomes of Humans and Other Homininae. Genome Biol Evol 2020; 12:3550-3561. [PMID: 31596481 PMCID: PMC6944223 DOI: 10.1093/gbe/evz215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2019] [Indexed: 12/23/2022] Open
Abstract
DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise from regional variation in the mutation rate, variation in the intensity and mode of natural selection, and regional variation in the recombination rate. We show that both noncoding and nonsynonymous diversity are positively correlated to a measure of the mutation rate and the recombination rate and negatively correlated to the density of conserved sequences in 50 kb windows across the genomes of humans and nonhuman homininae. Interestingly, we find that although noncoding diversity is equally affected by these three genomic variables, nonsynonymous diversity is mostly dominated by the density of conserved sequences. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggest that selection at linked sites also affect levels of diversity. This is supported by the observation that the ratio of the number of nonsynonymous to noncoding polymorphisms is negatively correlated to a measure of the effective population size across the genome. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by GC biased gene conversion. In conclusion, our comparative analyses describe how recombination rate, gene density, and mutation rate interact to produce the patterns of DNA diversity that we observe along the hominine genomes.
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Affiliation(s)
- David Castellano
- Bioinformatics Research Centre, Aarhus University, Denmark
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, Spain
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Denmark
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32
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Wein T, Dagan T. The Effect of Population Bottleneck Size and Selective Regime on Genetic Diversity and Evolvability in Bacteria. Genome Biol Evol 2019; 11:3283-3290. [PMID: 31688900 PMCID: PMC7145630 DOI: 10.1093/gbe/evz243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2019] [Indexed: 12/20/2022] Open
Abstract
Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity, and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. In this study, we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (small, medium, and large) in two temperature regimes (37 °C and 20 °C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity regardless the bottleneck size; hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.
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Affiliation(s)
- Tanita Wein
- Institute of Microbiology, Kiel University, Germany
| | - Tal Dagan
- Institute of Microbiology, Kiel University, Germany
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33
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Kono TJY, Liu C, Vonderharr EE, Koenig D, Fay JC, Smith KP, Morrell PL. The Fate of Deleterious Variants in a Barley Genomic Prediction Population. Genetics 2019; 213:1531-1544. [PMID: 31653677 PMCID: PMC6893365 DOI: 10.1534/genetics.119.302733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Targeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a "cost of domestication." This includes an increase in the proportion of genetic variants that are likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley lines, we identified 3855 dSNPs among 497,754 total SNPs. We generated whole-genome resequencing data of Hordeum murinum ssp. glaucum as a phylogenetic outgroup to polarize SNPs as ancestral vs. derived. We also observed a higher proportion of dSNPs per synonymous SNPs (sSNPs) in low-recombination regions of the genome. Using 5215 progeny from a genomic prediction experiment, we examined the fate of dSNPs over three breeding cycles. Adjusting for initial frequency, derived alleles at dSNPs reduced in frequency or were lost more often than other classes of SNPs. The highest-yielding lines in the experiment, as chosen by standard genomic prediction approaches, carried fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction had a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.
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Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Emily E Vonderharr
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Justin C Fay
- Department of Biology, University of Rochester, New York 14627
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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34
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Ho EKH, Bartkowska M, Wright SI, Agrawal AF. Population genomics of the facultatively asexual duckweed Spirodela polyrhiza. THE NEW PHYTOLOGIST 2019; 224:1361-1371. [PMID: 31298732 DOI: 10.1111/nph.16056] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Clonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome. We examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually. We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection ineffective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level. The amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such as Arabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.
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Affiliation(s)
- Eddie K H Ho
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Magdalena Bartkowska
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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35
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Castellano D, Macià MC, Tataru P, Bataillon T, Munch K. Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes. Genetics 2019; 213:953-966. [PMID: 31488516 PMCID: PMC6827385 DOI: 10.1534/genetics.119.302494] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
The distribution of fitness effects (DFE) is central to many questions in evolutionary biology. However, little is known about the differences in DFE between closely related species. We use >9000 coding genes orthologous one-to-one across great apes, gibbons, and macaques to assess the stability of the DFE across great apes. We use the unfolded site frequency spectrum of polymorphic mutations (n = 8 haploid chromosomes per population) to estimate the DFE. We find that the shape of the deleterious DFE is strikingly similar across great apes. We confirm that effective population size (Ne ) is a strong predictor of the strength of negative selection, consistent with the nearly neutral theory. However, we also find that the strength of negative selection varies more than expected given the differences in Ne between species. Across species, mean fitness effects of new deleterious mutations covaries with Ne , consistent with positive epistasis among deleterious mutations. We find that the strength of negative selection for the smallest populations, bonobos and western chimpanzees, is higher than expected given their Ne This may result from a more efficient purging of strongly deleterious recessive variants in these populations. Forward simulations confirm that these findings are not artifacts of the way we are inferring Ne and DFE parameters. All findings are replicated using only GC-conservative mutations, thereby confirming that GC-biased gene conversion is not affecting our conclusions.
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Affiliation(s)
- David Castellano
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Moisès Coll Macià
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Paula Tataru
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
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36
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Chen J, Li L, Milesi P, Jansson G, Berlin M, Karlsson B, Aleksic J, Vendramin GG, Lascoux M. Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce. Evol Appl 2019; 12:1539-1551. [PMID: 31462913 PMCID: PMC6708423 DOI: 10.1111/eva.12801] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 12/23/2022] Open
Abstract
Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.
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Affiliation(s)
- Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Lili Li
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gunnar Jansson
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Mats Berlin
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Bo Karlsson
- Forestry Research Institute of Sweden (Skogforsk)EkeboSweden
| | - Jelena Aleksic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
| | - Giovanni G. Vendramin
- Division of Florence, Institute of Biosciences and BioResourcesNational Research Council (IBBR‐CNR)Sesto FiorentinoItaly
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
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37
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Mackintosh A, Laetsch DR, Hayward A, Charlesworth B, Waterfall M, Vila R, Lohse K. The determinants of genetic diversity in butterflies. Nat Commun 2019; 10:3466. [PMID: 31371715 PMCID: PMC6672018 DOI: 10.1038/s41467-019-11308-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/01/2019] [Indexed: 11/09/2022] Open
Abstract
Under the neutral theory, genetic diversity is expected to increase with population size. While comparative analyses have consistently failed to find strong relationships between census population size and genetic diversity, a recent study across animals identified a strong correlation between propagule size and genetic diversity, suggesting that r-strategists that produce many small offspring, have greater long-term population sizes. Here we compare genome-wide genetic diversity across 38 species of European butterflies (Papilionoidea), a group that shows little variation in reproductive strategy. We show that genetic diversity across butterflies varies over an order of magnitude and that this variation cannot be explained by differences in current abundance, propagule size, host or geographic range. Instead, neutral genetic diversity is negatively correlated with body size and positively with the length of the genetic map. This suggests that genetic diversity is determined both by differences in long-term population size and the effect of selection on linked sites.
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Affiliation(s)
- Alexander Mackintosh
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Brian Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Martin Waterfall
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, ESP-08003, Barcelona, Spain
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK.
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38
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Vigué L, Eyre-Walker A. The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae. PeerJ 2019; 7:e7216. [PMID: 31293838 PMCID: PMC6599670 DOI: 10.7717/peerj.7216] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/30/2019] [Indexed: 12/31/2022] Open
Abstract
Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.
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39
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Castellano D, James J, Eyre-Walker A. Nearly Neutral Evolution across the Drosophila melanogaster Genome. Mol Biol Evol 2019; 35:2685-2694. [PMID: 30418639 DOI: 10.1093/molbev/msy164] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Under the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by ∼45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.
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Affiliation(s)
- David Castellano
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Jennifer James
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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40
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Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Sci Rep 2018; 8:16147. [PMID: 30385764 PMCID: PMC6212547 DOI: 10.1038/s41598-018-33897-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
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Affiliation(s)
- María José Rivas
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - María Saura
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Tomas Johansson
- Department of Biology, University of Lund, SE-223 62, Lund, Sweden
| | - Carl André
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Emilio Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain.
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Kim BY, Huber CD, Lohmueller KE. Deleterious variation shapes the genomic landscape of introgression. PLoS Genet 2018; 14:e1007741. [PMID: 30346959 PMCID: PMC6233928 DOI: 10.1371/journal.pgen.1007741] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/13/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022] Open
Abstract
While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how gene flow affects and is affected by the dynamics of deleterious variation. Here we use population genetic simulations to examine how gene flow impacts deleterious variation under a variety of demographic scenarios, mating systems, dominance coefficients, and recombination rates. Our results show that admixture between populations can temporarily reduce the genetic load of smaller populations and cause increases in the frequency of introgressed ancestry, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. Together, these factors lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30–75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models of admixture include both demography and deleterious variation before invoking other mechanisms to explain unusual patterns of genetic variation. Individuals from distinct populations sometimes will produce fertile offspring and will exchange genetic material in a process called hybridization. Genomes of hybrid individuals often show non-random patterns of hybrid ancestry across the genome, where some regions have a high frequency of ancestry from the second population and other regions have less. Typically, this pattern has been attributed to adaptive introgression, where beneficial genetic variants are passed from one population to the other, or to genomic incompatibilities between these distinct species. However, other mechanisms could lead to these heterogeneous patterns of ancestry in hybrids. Here we use simulations to investigate whether deleterious mutations affect the patterns of introgressed ancestry across genomes. We show that when ancestry from a larger population is added to a smaller population, the ancestry from the larger population dramatically increases in frequency because it carries fewer deleterious mutations. This occurs even in the absence of beneficial mutations in either population. Additionally, we show that differences in sex chromosome evolution relative to autosomes, or differences in mating system, can affect patterns of introgression in similar ways. Our study argues that deleterious mutations should be included in population genetic models used to identify unusual regions of the genome that appear to be under selection in hybrids.
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Affiliation(s)
- Bernard Y. Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Christian D. Huber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail:
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42
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Nakamura H, Teshima K, Tachida H. Effects of cyclic changes in population size on neutral genetic diversity. Ecol Evol 2018; 8:9362-9371. [PMID: 30377507 PMCID: PMC6194295 DOI: 10.1002/ece3.4436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/09/2018] [Indexed: 01/29/2023] Open
Abstract
Recurrent changes in population size are often observed in nature, influencing the efficiency of selection and consequently affecting organismal evolution. Thus, it is important to know whether such changes occurred in the past history of a focal population of evolutionary interests. Here, we focused on cyclic changes in population size and investigated the distributional properties of Tajima's D and its power to distinguish a cyclic change model compared with the standard neutral model, changing the frequency and magnitude of the cyclic change. With very low or very high frequencies of the cycle, the distribution of Tajima's D was similar to that in a constant size population, as demonstrated by previous theoretical works. Otherwise, its mean was negative or positive, and its variance was smaller or larger depending on the time of sampling. The detection rate of the cyclic change against the constancy in size by Tajima's D depended on the sample size, the number of loci, and the time of sampling in addition to the frequency and amplitude of the cycle. Using sequence data of several tens of loci, the detection rate was fairly high if the frequency was intermediate and the sampling was made when population size was large; otherwise, the detection rate was not high. We also found that cyclic change could be discriminated from simple expansion or shrinkage of a population by Tajima's D only if the frequency was in a limited range and the sampling was made when the population was large.
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Affiliation(s)
- Haruna Nakamura
- Graduate School of Systems Life SciencesKyushu UniversityFukuokaJapan
| | - Kosuke Teshima
- Department of BiologyFaculty of ScienceKyushu UniversityFukuokaJapan
| | - Hidenori Tachida
- Department of BiologyFaculty of ScienceKyushu UniversityFukuokaJapan
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43
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Gaut BS, Seymour DK, Liu Q, Zhou Y. Demography and its effects on genomic variation in crop domestication. NATURE PLANTS 2018; 4:512-520. [PMID: 30061748 DOI: 10.1038/s41477-018-0210-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 05/20/2023]
Abstract
Over two thousand plant species have been modified morphologically through cultivation and human use. Here, we review three aspects of crop domestication that are currently undergoing marked revisions, due to analytical advancements and their application to whole genome resequencing (WGS) data. We begin by discussing the duration and demographic history of domestication. There has been debate as to whether domestication occurred quickly or slowly. The latter is tentatively supported both by fossil data and application of WGS data to sequentially Markovian coalescent methods that infer the history of effective population size. This history suggests the possibility of extended human impacts on domesticated lineages prior to their purposeful cultivation. We also make the point that demographic history matters, because it shapes patterns and levels of extant genetic diversity. We illustrate this point by discussing the evolutionary processes that contribute to the empirical observation that most crops examined to date have more putatively deleterious alleles than their wild relatives. These deleterious alleles may contribute to genetic load within crops and may be fitting targets for crop improvement. Finally, the same demographic factors are likely to shape the spectrum of structural variants (SVs) within crops. SVs are known to underlie many of the phenotypic changes associated with domestication and crop improvement, but we currently lack sufficient knowledge about the mechanisms that create SVs, their rates of origin, their population frequencies and their phenotypic effects.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Qingpo Liu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, China
| | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
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44
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Wang XJ, Hu QJ, Guo XY, Wang K, Ru DF, German DA, Weretilnyk EA, Abbott RJ, Lascoux M, Liu JQ. Demographic expansion and genetic load of the halophyte model plantEutrema salsugineum. Mol Ecol 2018; 27:2943-2955. [DOI: 10.1111/mec.14738] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/16/2018] [Accepted: 05/24/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Xiao-Juan Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Quan-Jun Hu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Xin-Yi Guo
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Kun Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Da-Fu Ru
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Dmitry A. German
- Department of Biodiversity and Plant Systematics; Centre for Organismal Studies (COS Heidelberg); Heidelberg University; Heidelberg Germany
- South-Siberian Botanical Garden; Altai State University; Barnaul Russia
| | | | | | - Martin Lascoux
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; Uppsala Sweden
| | - Jian-quan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
- State Key Laboratory of Grassland Agro-Ecosystem; College of Life Science; Lanzhou University; Lanzhou China
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45
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Torres R, Szpiech ZA, Hernandez RD. Human demographic history has amplified the effects of background selection across the genome. PLoS Genet 2018; 14:e1007387. [PMID: 29912945 PMCID: PMC6056204 DOI: 10.1371/journal.pgen.1007387] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 07/23/2018] [Accepted: 04/30/2018] [Indexed: 01/22/2023] Open
Abstract
Natural populations often grow, shrink, and migrate over time. Such demographic processes can affect genome-wide levels of genetic diversity. Additionally, genetic variation in functional regions of the genome can be altered by natural selection, which drives adaptive mutations to higher frequencies or purges deleterious ones. Such selective processes affect not only the sites directly under selection but also nearby neutral variation through genetic linkage via processes referred to as genetic hitchhiking in the context of positive selection and background selection (BGS) in the context of purifying selection. While there is extensive literature examining the consequences of selection at linked sites at demographic equilibrium, less is known about how non-equilibrium demographic processes influence the effects of hitchhiking and BGS. Utilizing a global sample of human whole-genome sequences from the Thousand Genomes Project and extensive simulations, we investigate how non-equilibrium demographic processes magnify and dampen the consequences of selection at linked sites across the human genome. When binning the genome by inferred strength of BGS, we observe that, compared to Africans, non-African populations have experienced larger proportional decreases in neutral genetic diversity in strong BGS regions. We replicate these findings in admixed populations by showing that non-African ancestral components of the genome have also been affected more severely in these regions. We attribute these differences to the strong, sustained/recurrent population bottlenecks that non-Africans experienced as they migrated out of Africa and throughout the globe. Furthermore, we observe a strong correlation between FST and the inferred strength of BGS, suggesting a stronger rate of genetic drift. Forward simulations of human demographic history with a model of BGS support these observations. Our results show that non-equilibrium demography significantly alters the consequences of selection at linked sites and support the need for more work investigating the dynamic process of multiple evolutionary forces operating in concert.
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Affiliation(s)
- Raul Torres
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, United States of America
| | - Zachary A. Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States of America
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, United States of America
- * E-mail:
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46
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Prioritization of Variants Detected by Next Generation Sequencing According to the Mutation Tolerance and Mutational Architecture of the Corresponding Genes. Int J Mol Sci 2018; 19:ijms19061584. [PMID: 29861492 PMCID: PMC6032105 DOI: 10.3390/ijms19061584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/09/2018] [Accepted: 05/23/2018] [Indexed: 12/27/2022] Open
Abstract
The biggest challenge geneticists face when applying next-generation sequencing technology to the diagnosis of rare diseases is determining which rare variants, from the dozens or hundreds detected, are potentially implicated in the patient’s phenotype. Thus, variant prioritization is an essential step in the process of rare disease diagnosis. In addition to conducting the usual in-silico analyses to predict variant pathogenicity (based on nucleotide/amino-acid conservation and the differences between the physicochemical features of the amino-acid change), three important concepts should be borne in mind. The first is the “mutation tolerance” of the genes in which variants are located. This describes the susceptibility of a given gene to any functional mutation and depends on the strength of purifying selection acting against it. The second is the “mutational architecture” of each gene. This describes the type and location of mutations previously identified in the gene, and their association with different phenotypes or degrees of severity. The third is the mode of inheritance (inherited vs. de novo) of the variants detected. Here, we discuss the importance of each of these concepts for variant prioritization in the diagnosis of rare diseases. Using real data, we show how genes, rather than variants, can be prioritized by calculating a gene-specific mutation tolerance score. We also illustrate the influence of mutational architecture on variant prioritization using five paradigmatic examples. Finally, we discuss the importance of familial variant analysis as final step in variant prioritization.
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47
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Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina. Proc Natl Acad Sci U S A 2018; 115:816-821. [PMID: 29301967 DOI: 10.1073/pnas.1707492115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.
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48
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Makino T, Rubin CJ, Carneiro M, Axelsson E, Andersson L, Webster MT. Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants. Genome Biol Evol 2018; 10:276-290. [PMID: 29325102 PMCID: PMC5786255 DOI: 10.1093/gbe/evy004] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 12/12/2022] Open
Abstract
A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here, we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken, and silkworm) and two domestic plant species (rice and soybean) compared with their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more single nucleotide polymorphisms in highly conserved elements in domestic species and a tendency for domestic species to harbor a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species.
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Affiliation(s)
- Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Erik Axelsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Sweden
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49
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Amorim CEG, Gao Z, Baker Z, Diesel JF, Simons YB, Haque IS, Pickrell J, Przeworski M. The population genetics of human disease: The case of recessive, lethal mutations. PLoS Genet 2017; 13:e1006915. [PMID: 28957316 PMCID: PMC5619689 DOI: 10.1371/journal.pgen.1006915] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 07/09/2017] [Indexed: 01/08/2023] Open
Abstract
Do the frequencies of disease mutations in human populations reflect a simple balance between mutation and purifying selection? What other factors shape the prevalence of disease mutations? To begin to answer these questions, we focused on one of the simplest cases: recessive mutations that alone cause lethal diseases or complete sterility. To this end, we generated a hand-curated set of 417 Mendelian mutations in 32 genes reported to cause a recessive, lethal Mendelian disease. We then considered analytic models of mutation-selection balance in infinite and finite populations of constant sizes and simulations of purifying selection in a more realistic demographic setting, and tested how well these models fit allele frequencies estimated from 33,370 individuals of European ancestry. In doing so, we distinguished between CpG transitions, which occur at a substantially elevated rate, and three other mutation types. Intriguingly, the observed frequency for CpG transitions is slightly higher than expectation but close, whereas the frequencies observed for the three other mutation types are an order of magnitude higher than expected, with a bigger deviation from expectation seen for less mutable types. This discrepancy is even larger when subtle fitness effects in heterozygotes or lethal compound heterozygotes are taken into account. In principle, higher than expected frequencies of disease mutations could be due to widespread errors in reporting causal variants, compensation by other mutations, or balancing selection. It is unclear why these factors would have a greater impact on disease mutations that occur at lower rates, however. We argue instead that the unexpectedly high frequency of disease mutations and the relationship to the mutation rate likely reflect an ascertainment bias: of all the mutations that cause recessive lethal diseases, those that by chance have reached higher frequencies are more likely to have been identified and thus to have been included in this study. Beyond the specific application, this study highlights the parameters likely to be important in shaping the frequencies of Mendelian disease alleles. What determines the frequencies of disease mutations in human populations? To begin to answer this question, we focus on one of the simplest cases: mutations that cause completely recessive, lethal Mendelian diseases. We first review theory about what to expect from mutation and selection in a population of finite size and generate predictions based on simulations using a plausible demographic scenario of recent human evolution. For a highly mutable type of mutation, transitions at CpG sites, we find that the predictions are close to the observed frequencies of recessive lethal disease mutations. For less mutable types, however, predictions substantially under-estimate the observed frequency. We discuss possible explanations for the discrepancy and point to a complication that, to our knowledge, is not widely appreciated: that there exists ascertainment bias in disease mutation discovery. Specifically, we suggest that alleles that have been identified to date are likely the ones that by chance have reached higher frequencies and are thus more likely to have been mapped. More generally, our study highlights the factors that influence the frequencies of Mendelian disease alleles.
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Affiliation(s)
- Carlos Eduardo G. Amorim
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
- * E-mail:
| | - Ziyue Gao
- Howard Hughes Medical Institution, Stanford University, Stanford, CA, United States of America
| | - Zachary Baker
- Department of Systems Biology, Columbia University, New York, NY, United States of America
| | | | - Yuval B. Simons
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Imran S. Haque
- Counsyl, 180 Kimball Way, South San Francisco, CA, United States of America
| | - Joseph Pickrell
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- New York Genome Center, New York, NY, United States of America
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- Department of Systems Biology, Columbia University, New York, NY, United States of America
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50
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Johri P, Krenek S, Marinov GK, Doak TG, Berendonk TU, Lynch M. Population Genomics of Paramecium Species. Mol Biol Evol 2017; 34:1194-1216. [PMID: 28204679 DOI: 10.1093/molbev/msx074] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium.
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Affiliation(s)
- Parul Johri
- Department of Biology, Indiana University, Bloomington, IN
| | - Sascha Krenek
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | | | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington, IN.,National Center for Genome Analysis Support, Indiana University, Bloomington, IN
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
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