1
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Charlesworth B. The fitness consequences of genetic divergence between polymorphic gene arrangements. Genetics 2024; 226:iyad218. [PMID: 38147527 PMCID: PMC11090464 DOI: 10.1093/genetics/iyad218] [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: 10/15/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023] Open
Abstract
Inversions restrict recombination when heterozygous with standard arrangements, but often have few noticeable phenotypic effects. Nevertheless, there are several examples of inversions that can be maintained polymorphic by strong selection under laboratory conditions. A long-standing model for the source of such selection is divergence between arrangements with respect to recessive or partially recessive deleterious mutations, resulting in a selective advantage to heterokaryotypic individuals over homokaryotypes. This paper uses a combination of analytical and numerical methods to investigate this model, for the simple case of an autosomal inversion with multiple independent nucleotide sites subject to mildly deleterious mutations. A complete lack of recombination in heterokaryotypes is assumed, as well as constancy of the frequency of the inversion over space and time. It is shown that a significantly higher mutational load will develop for the less frequent arrangement. A selective advantage to heterokaryotypes is only expected when the two alternative arrangements are nearly equal in frequency, so that their mutational loads are very similar in size. The effects of some Drosophila pseudoobscura polymorphic inversions on fitness traits seem to be too large to be explained by this process, although it may contribute to some of the observed effects. Several population genomic statistics can provide evidence for signatures of a reduced efficacy of selection associated with the rarer of two arrangements, but there is currently little published data that are relevant to the theoretical predictions.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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2
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Dussex N, Morales HE, Grossen C, Dalén L, van Oosterhout C. Purging and accumulation of genetic load in conservation. Trends Ecol Evol 2023; 38:961-969. [PMID: 37344276 DOI: 10.1016/j.tree.2023.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and computational approaches. Yet, considerable confusion remains around the definitions of the genetic load and its dynamics, and how they impact individual fitness and population viability. We illustrate how both selective purging and drift affect the distribution of deleterious mutations during population size decline and recovery. We show how this impacts the composition of the genetic load, and how this affects the extinction risk and recovery potential of populations. We propose a framework to examine load dynamics and advocate for the introduction of load estimates in the management of endangered populations.
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Affiliation(s)
- Nicolas Dussex
- Department of Natural History, NTNU University Museum, Erling Skakkes Gate 47A, 7012 Trondheim, Norway.
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christine Grossen
- WSL Swiss Federal Research Institute, CH-8903 Birmensdorf, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91 Stockholm, Sweden
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
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3
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Shults P, Zhang X, Moran M, Cohnstaedt LW, Gerry AC, Vargo EL, Eyer PA. Immigration and seasonal bottlenecks: high inbreeding despite high genetic diversity in an oscillating population of Culicoides sonorensis (Diptera: Ceratopogonidae). JOURNAL OF MEDICAL ENTOMOLOGY 2023; 60:987-997. [PMID: 37417303 DOI: 10.1093/jme/tjad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/01/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
Abstract
Most population genetic studies concern spatial genetic differentiation, but far fewer aim at analyzing the temporal genetic changes that occur within populations. Vector species, including mosquitoes and biting midges, are often characterized by oscillating adult population densities, which may affect their dispersal, selection, and genetic diversity over time. Here, we used a population of Culicoides sonorensis from a single site in California to investigate short-term (intra-annual) and long-term (inter-annual) temporal variation in genetic diversity over a 3 yr period. This biting midge species is the primary vector of several viruses affecting both wildlife and livestock, thus a better understanding of the population dynamics of this species can help inform epidemiological studies. We found no significant genetic differentiation between months or years, and no correlation between adult populations and the inbreeding coefficient (FIS). However, we show that repeated periods of low adult abundance during cooler winter months resulted in recurring bottleneck events. Interestingly, we also found a high number of private and rare alleles, which suggests both a large, stable population, as well as a constant influx of migrants from nearby populations. Overall, we showed that the high number of migrants maintains a high level of genetic diversity by introducing new alleles, while this increased diversity is counterbalanced by recurrent bottleneck events potentially purging unfit alleles each year. These results highlight the temporal influences on population structure and genetic diversity in C. sonorensis and provide insight into factors effecting genetic variation that may occur in other vector species with fluctuating populations.
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Affiliation(s)
- Phillip Shults
- USDA-ARS, Foreign Arthropod-Borne Animal Diseases Research Unit (FABADRU), 1515 College Avenue, Manhattan, KS 66502, USA
| | - Xinmi Zhang
- Department of Entomology, University of California Riverside, Riverside, CA 92521, USA
| | - Megan Moran
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Lee W Cohnstaedt
- USDA-ARS, Foreign Arthropod-Borne Animal Diseases Research Unit (FABADRU), 1515 College Avenue, Manhattan, KS 66502, USA
| | - Alec C Gerry
- Department of Entomology, University of California Riverside, Riverside, CA 92521, USA
| | - Edward L Vargo
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Pierre-Andre Eyer
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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4
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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: 0] [Impact Index Per Article: 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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5
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Tschol M, Reid JM, Bocedi G. Environmental variance in male mating success modulates the positive versus negative impacts of sexual selection on genetic load. J Evol Biol 2023; 36:1242-1254. [PMID: 37497848 DOI: 10.1111/jeb.14202] [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: 11/26/2022] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023]
Abstract
Sexual selection on males is predicted to increase population fitness, and delay population extinction, when mating success negatively covaries with genetic load across individuals. However, such benefits of sexual selection could be counteracted by simultaneous increases in genome-wide drift resulting from reduced effective population size caused by increased variance in fitness. Resulting fixation of deleterious mutations could be greatest in small populations, and when environmental variation in mating traits partially decouples sexual selection from underlying genetic variation. The net consequences of sexual selection for genetic load and population persistence are therefore likely to be context dependent, but such variation has not been examined. We use a genetically explicit individual-based model to show that weak sexual selection can increase population persistence time compared to random mating. However, for stronger sexual selection such positive effects can be overturned by the detrimental effects of increased genome-wide drift. Furthermore, the relative strengths of mutation-purging and drift critically depend on the environmental variance in the male mating trait. Specifically, increasing environmental variance caused stronger sexual selection to elevate deleterious mutation fixation rate and mean selection coefficient, driving rapid accumulation of drift load and decreasing population persistence times. These results highlight an intricate balance between conflicting positive and negative consequences of sexual selection on genetic load, even in the absence of sexually antagonistic selection. They imply that environmental variances in key mating traits, and intrinsic genetic drift, should be properly factored into future theoretical and empirical studies of the evolution of population fitness under sexual selection.
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Affiliation(s)
| | - Jane M Reid
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- Centre for Biodiversity Dynamics, Institutt for Biologi, NTNU, Trondheim, Norway
| | - Greta Bocedi
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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6
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Dwivedi SL, Heslop-Harrison P, Spillane C, McKeown PC, Edwards D, Goldman I, Ortiz R. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. TRENDS IN PLANT SCIENCE 2023; 28:685-697. [PMID: 36764870 DOI: 10.1016/j.tplants.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/03/2022] [Accepted: 01/18/2023] [Indexed: 05/13/2023]
Abstract
Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.
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Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Irwin Goldman
- Department of Horticulture, College of Agricultural and Life Sciences, University of Wisconsin Madison, WI 53706, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SE 23053, Sweden.
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7
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Epigenetic Changes Occurring in Plant Inbreeding. Int J Mol Sci 2023; 24:ijms24065407. [PMID: 36982483 PMCID: PMC10048984 DOI: 10.3390/ijms24065407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.
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8
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Blüml C, Ramm SA, van Benthem KJ, Wittmann MJ. Waiting for love but not forever: Modeling the evolution of waiting time to selfing in hermaphrodites. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1002475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Although mixed mating systems involving both selfing and outcrossing are fairly common in hermaphrodites, the mechanisms maintaining mixed mating are still unknown in many cases. In some species, individuals that have not yet found a mating partner delay self-fertilization for some time. This “waiting time” to selfing (WT) can exhibit heritable variation between individuals and is subject to two opposing selection pressures: waiting longer increases the density-dependent probability to encounter a mate within that time and thereby the chance to avoid inbreeding depression (ID) in offspring, but also increases the risk of dying before reproduction. It has long been hypothesized that fluctuations in population density and thus mate availability can lead to stable intermediate WTs, but to our knowledge there are so far no quantitative models that also take into account the joint evolutionary dynamics of ID. We use an individual-based model and a mathematical approximation to explore how delayed selfing evolves in response to density and density fluctuations. We find that at high density, when individuals meet often, WT evolution is dominated by genetic drift; at intermediate densities, strong ID causes WT to increase; and at low densities, ID is purged and WT approaches zero. Positive feedback loops drive the system to either complete selfing or complete outcrossing. Fluctuating density can slow down convergence to these alternative stable states. However, mixed mating, in the sense of either a stable polymorphism in WT, or stable intermediate waiting times, was never observed. Thus, additional factors need to be explored to explain the persistence of delayed selfing.
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9
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Charmouh AP, Reid JM, Bilde T, Bocedi G. Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations. Evolution 2022; 76:2482-2497. [PMID: 36117269 PMCID: PMC9828521 DOI: 10.1111/evo.14620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/01/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting local extinction, and recolonization through evolving dispersal facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favor increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.
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Affiliation(s)
- Anders P. Charmouh
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUnited Kingdom
| | - Jane M. Reid
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUnited Kingdom,Centre for Biodiversity DynamicsInstitutt for Biologi, NTNUTrondheim7491Norway
| | - Trine Bilde
- Department of BiologyAarhus UniversityAarhus C8000Denmark
| | - Greta Bocedi
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUnited Kingdom
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10
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Xu K. Mutation accumulation in inbreeding populations under evolution of the selfing rate. J Evol Biol 2021; 35:23-39. [PMID: 34860448 DOI: 10.1111/jeb.13968] [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] [Received: 09/14/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 11/28/2022]
Abstract
It is theoretically established that self-fertilization can facilitate mutation accumulation, thus increasing extinction risk. However, in previous studies, selfing rates are often set as fixed parameters, but in natural systems, evolution of selfing rates and deleterious mutations may mutually affect each other. I carried out simulations to investigate the dynamics of selfing rates and mutation accumulation, by allowing deleterious mutations to coevolve with alleles that modify the selfing rate (selfing modifiers). I found that selfing rates will often fluctuate over time, due to successive invasion of alleles that increase selfing and outcrossing. Since mutation fixation is mainly caused by Muller's ratchet, its rate is sensitive to the change of the selfing rate mutations will accumulate in a punctuated pattern. The dynamics are influenced by several factors, such as recombination and the selfing rate effects of selfing modifier loci. Also, such temporal variation produces variation of selfing rates and mutation accumulation rates between multiple conspecific populations, which can increase the average fitness across populations. As factors, such as the genomic mutation rate of deleterious mutations, can simultaneously influence the selfing rate and mutation fixation, effects of these factors on mutation accumulation rates can be complicated and non-monotonic.
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Affiliation(s)
- Kuangyi Xu
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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11
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Signatures of Selection and Genomic Diversity of Muskellunge ( Esox masquinongy) from Two Populations in North America. Genes (Basel) 2021; 12:genes12071021. [PMID: 34209092 PMCID: PMC8303616 DOI: 10.3390/genes12071021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.
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12
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Stoffel MA, Johnston SE, Pilkington JG, Pemberton JM. Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal. Nat Commun 2021; 12:2972. [PMID: 34016997 PMCID: PMC8138023 DOI: 10.1038/s41467-021-23222-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/29/2021] [Indexed: 02/03/2023] Open
Abstract
Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.
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Affiliation(s)
- M A Stoffel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - S E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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13
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Lesaffre T, Billiard S. On Deleterious Mutations in Perennials: Inbreeding Depression, Mutation Load, and Life-History Evolution. Am Nat 2021; 197:E143-E155. [PMID: 33908825 DOI: 10.1086/713499] [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] [Indexed: 11/03/2022]
Abstract
AbstractIn angiosperms, perennials typically present much higher levels of inbreeding depression than annuals. One hypothesis to explain this pattern stems from the observation that inbreeding depression is expressed across multiple life stages in angiosperms. It posits that increased inbreeding depression in more long-lived species could be explained by differences in the way mutations affect fitness, through the life stages at which they are expressed. In this study, we investigate this hypothesis. We combine a physiological growth model and multilocus population genetics approaches to describe a full genotype-to-phenotype-to-fitness map. We study the behavior of mutations affecting growth or survival and explore their consequences in terms of inbreeding depression and mutation load. Although our results agree with empirical data only within a narrow range of conditions, we argue that they may point us toward the type of traits capable of generating high inbreeding depression in long-lived species-that is, traits under sufficiently strong selection, on which selection decreases sharply as life expectancy increases. Then we study the role deleterious mutations maintained at mutation-selection balance may play in the joint evolution of growth and survival strategies.
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14
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Kyriazis CC, Wayne RK, Lohmueller KE. Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression. Evol Lett 2021; 5:33-47. [PMID: 33552534 PMCID: PMC7857301 DOI: 10.1002/evl3.209] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/10/2020] [Accepted: 11/21/2020] [Indexed: 11/08/2022] Open
Abstract
Human-driven habitat fragmentation and loss have led to a proliferation of small and isolated plant and animal populations with high risk of extinction. One of the main threats to extinction in these populations is inbreeding depression, which is primarily caused by recessive deleterious mutations becoming homozygous due to inbreeding. The typical approach for managing these populations is to maintain high genetic diversity, increasingly by translocating individuals from large populations to initiate a "genetic rescue." However, the limitations of this approach have recently been highlighted by the demise of the gray wolf population on Isle Royale, which declined to the brink of extinction soon after the arrival of a migrant from the large mainland wolf population. Here, we use a novel population genetic simulation framework to investigate the role of genetic diversity, deleterious variation, and demographic history in mediating extinction risk due to inbreeding depression in small populations. We show that, under realistic models of dominance, large populations harbor high levels of recessive strongly deleterious variation due to these mutations being hidden from selection in the heterozygous state. As a result, when large populations contract, they experience a substantially elevated risk of extinction after these strongly deleterious mutations are exposed by inbreeding. Moreover, we demonstrate that, although genetic rescue is broadly effective as a means to reduce extinction risk, its effectiveness can be greatly increased by drawing migrants from small or moderate-sized source populations rather than large source populations due to smaller populations harboring lower levels of recessive strongly deleterious variation. Our findings challenge the traditional conservation paradigm that focuses on maximizing genetic diversity in small populations in favor of a view that emphasizes minimizing strongly deleterious variation. These insights have important implications for managing small and isolated populations in the increasingly fragmented landscape of the Anthropocene.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
| | - Robert K. Wayne
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
- Interdepartmental Program in BioinformaticsUniversity of CaliforniaLos AngelesCalifornia90095
- Department of Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCalifornia90095
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15
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Ceballos FC, Hazelhurst S, Clark DW, Agongo G, Asiki G, Boua PR, Xavier Gómez-Olivé F, Mashinya F, Norris S, Wilson JF, Ramsay M. Autozygosity influences cardiometabolic disease-associated traits in the AWI-Gen sub-Saharan African study. Nat Commun 2020; 11:5754. [PMID: 33188201 PMCID: PMC7666169 DOI: 10.1038/s41467-020-19595-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/12/2020] [Indexed: 11/10/2022] Open
Abstract
The analysis of the effects of autozygosity, measured as the change of the mean value of a trait among offspring of genetic relatives, reveals the existence of directional dominance or overdominance. In this study we detect evidence of the effect of autozygosity in 4 out of 13 cardiometabolic disease-associated traits using data from more than 10,000 sub-Saharan African individuals recruited from Ghana, Burkina Faso, Kenya and South Africa. The effect of autozygosity on these phenotypes is found to be sex-related, with inbreeding having a significant decreasing effect in men but a significant increasing effect in women for several traits (body mass index, subcutaneous adipose tissue, low-density lipoproteins and total cholesterol levels). Overall, the effect of inbreeding depression is more intense in men. Differential effects of inbreeding depression are also observed between study sites with different night-light intensity used as proxy for urban development. These results suggest a directional dominant genetic component mediated by environmental interactions and sex-specific differences in genetic architecture for these traits in the Africa Wits-INDEPTH partnership for Genomic Studies (AWI-Gen) cohort.
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Affiliation(s)
- Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - David W Clark
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Godfred Agongo
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Navrongo Health Research Centre, Navrongo, Ghana
| | - Gershim Asiki
- African Population and Health Research Center, Nairobi, Kenya
| | - Palwende R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Faculty of Health Sciences University of the Witwatersrand, Division of Human Genetics, National Health Laboratory Service and School of Pathology, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Felistas Mashinya
- Department of Pathology and Medical Science, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - Shane Norris
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Faculty of Health Sciences University of the Witwatersrand, Division of Human Genetics, National Health Laboratory Service and School of Pathology, Johannesburg, South Africa
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Faculty of Health Sciences University of the Witwatersrand, Division of Human Genetics, National Health Laboratory Service and School of Pathology, Johannesburg, South Africa.
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16
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Effects of Long-Term Selection in the Border Collie Dog Breed: Inbreeding Purge of Canine Hip and Elbow Dysplasia. Animals (Basel) 2020; 10:ani10101743. [PMID: 32992858 PMCID: PMC7601391 DOI: 10.3390/ani10101743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 11/23/2022] Open
Abstract
Simple Summary For dog breeders, health is one of the main criteria when choosing a breeding animal; thus, selection for good anatomy is the key to reduce orthopedic disorders. In many dog breeds, radiographic screening for canine hip and elbow dysplasia is a compulsory test for breeding; however, these multifactorial traits are determined by genetic and environmental factors. Therefore, it is extremely difficult to eliminate these disorders from the population. In natural selection, such traits can be “purged” out of the population with inbreeding. The study aimed to examine the inbreeding-purge of canine hip and elbow dysplasia in the border collie breed. The main conclusion was that over-representation of homozygous individuals may have a positive effect on hip and elbow conformation. Abstract Pedigree data of 13,339 border collie dog was collected along with canine hip dysplasia (CHD) and canine elbow dysplasia (CED) records (1352 CHD and 524 CED), and an inbreeding–purging (IP) model was created. Ancestral inbreeding coefficients were calculated by using a gene dropping simulation method with GRain 2.2 software. Cumulative logit models (CLM) for CHD and CED were fitted using a logit-link Poisson distribution and the classical (F_W), and ancestral inbreeding (F_BAL, F_KAL, and F_KAL_NEW) coefficients as linear regression coefficients. The effective population size was calculated from F_W and decreased in the examined period along with an increase of F_W; however, slight differences were found as a consequence of breeding dog imports. CHD values were lowered by the expansion of F_BAL, as the alleles had been inbred in the past. For CHD, signs of purging were obtained. There was a positive trend regarding the breeding activity (both sire and dam of the future litters should be screened and certified free from CHD and CED), as years of selection increased the frequency of alleles with favorable hip and elbow conformation. Division of the ancestral inbreeding coefficient showed that alleles that had been identical by descent (IBD) for the first time (F_KAL_NEW) had a negative effect on both traits, while F_KAL has shown favorable results for alleles IBD in past generations. Some authors had proven this phenomenon in captive populations or experimental conditions; however, no evidence of inbreeding purge has ever been described in dog populations. Despite the various breeding practices, it seems that alleles of these polygenic disorders could be successfully purged out of the population with long-term selection.
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Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces. G3-GENES GENOMES GENETICS 2020; 10:2497-2506. [PMID: 32467127 PMCID: PMC7341142 DOI: 10.1534/g3.120.401196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here, we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift and document losses of shared haplotypes. We find evidence consistent with selection at functional sites that are potentially involved in the diversity differences between landrace and DH populations. Although we were unable to uncover more details about the mode of selection, we conclude that landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs but come at the cost of decreased genetic diversity.
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18
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Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex. Nat Commun 2020; 11:1001. [PMID: 32081890 PMCID: PMC7035315 DOI: 10.1038/s41467-020-14803-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species. Although there is extensive theory predicting the effects of population bottlenecks on mutation load, there is little empirical evidence from recent bottlenecks. Here, Grossen et al. compare the consequences of population bottlenecks in six ibex species for genome-wide variation and mutation load.
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19
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Baldwin SJ, Schoen DJ. Inbreeding depression is difficult to purge in self-incompatible populations of Leavenworthia alabamica. THE NEW PHYTOLOGIST 2019; 224:1330-1338. [PMID: 31131900 DOI: 10.1111/nph.15963] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 05/20/2019] [Indexed: 06/09/2023]
Abstract
The extent to which inbreeding depression can be purged is a major determinant of mating system evolution and is important to conservation and crop improvement. Studies of inbreeding depression purging have not been conducted in self-incompatible plants before. An experimental ('ancestral') treatment was first created from self-incompatible plants of Leavenworthia alabamica. Lines derived from this population were maintained by self-pollination for three generations in the attempt to create a 'purged' population with fewer recessive, deleterious mutations of large effect. Fitness components and the frequency of malformed phenotypes were monitored in progeny derived from selfing and outcrossing in the ancestral and purged treatments. Fitness component means and inbreeding depression were largely unchanged by three generations of forced self-pollination, and there was no reduction in the frequency of plants exhibiting malformed phenotypes. Our findings indicate that inbreeding depression in this species is largely a result of mutations of mild effect, consistent with the observation that self-incompatibility is maintained in most populations of L. alabamica, despite the presence of genetic variants with weaker self-incompatibility. Moreover, although population theory suggests that deleterious mutations of large effect should be sheltered from selection in the region of self-incompatibility locus, our results do not support this prediction.
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Affiliation(s)
- Sarah J Baldwin
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montreal, QC, H3A 1B1, Canada
| | - Daniel J Schoen
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montreal, QC, H3A 1B1, Canada
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20
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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: 22] [Impact Index Per Article: 4.4] [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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21
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Koski MH, Layman NC, Prior CJ, Busch JW, Galloway LF. Selfing ability and drift load evolve with range expansion. Evol Lett 2019; 3:500-512. [PMID: 31636942 PMCID: PMC6791181 DOI: 10.1002/evl3.136] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/09/2019] [Accepted: 08/11/2019] [Indexed: 12/16/2022] Open
Abstract
Colonization at expanding range edges often involves few founders, reducing effective population size. This process can promote the evolution of self-fertilization, but implicating historical processes as drivers of trait evolution is often difficult and requires an explicit model of biogeographic history. In plants, contemporary limits to outcrossing are often invoked as evolutionary drivers of self-fertilization, but historical expansions may shape mating system diversity, with leading-edge populations evolving elevated selfing ability. In a widespread plant, Campanula americana, we identified a glacial refugium in the southern Appalachian Mountains from spatial patterns of genetic drift among 24 populations. Populations farther from this refugium have smaller effective sizes and fewer rare alleles. They also displayed elevated heterosis in among-population crosses, reflecting the accumulation of deleterious mutations during range expansion. Although populations with elevated heterosis had reduced segregating mutation load, the magnitude of inbreeding depression lacked geographic pattern. The ability to self-fertilize was strongly positively correlated with the distance from the refugium and mutation accumulation-a pattern that contrasts sharply with contemporary mate and pollinator limitation. In this and other species, diversity in sexual systems may reflect the legacy of evolution in small, colonizing populations, with little or no relation to the ecology of modern populations.
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Affiliation(s)
- Matthew H Koski
- Department of Biology University of Virginia Charlottesville Virginia 22902.,Current Address: Department of Biological Sciences Clemson University Clemson SC 29631
| | - Nathan C Layman
- School of Biological Sciences Washington State University Pullman Washington 99164
| | - Carly J Prior
- School of Biological Sciences Washington State University Pullman Washington 99164
| | - Jeremiah W Busch
- School of Biological Sciences Washington State University Pullman Washington 99164
| | - Laura F Galloway
- Department of Biology University of Virginia Charlottesville Virginia 22902
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22
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Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution 2019; 73:1729-1745. [PMID: 31339550 PMCID: PMC6771878 DOI: 10.1111/evo.13812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/11/2019] [Indexed: 01/30/2023]
Abstract
This article analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the inbreeding history model to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple nonidentical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection is discussed.
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Affiliation(s)
- Himani Sachdeva
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, 3400, Austria
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23
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Yuan ML, White KN, Rothermel BB, Zamudio KR, Tuberville TD. Close-kin mating, but not inbred parents, reduces hatching rates and offspring quality in a threatened tortoise. J Evol Biol 2019; 32:1152-1162. [PMID: 31397924 DOI: 10.1111/jeb.13518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 11/29/2022]
Abstract
Inbreeding depression, the reduction in fitness due to mating of related individuals, is of particular conservation concern in species with small, isolated populations. Although inbreeding depression is widespread in natural populations, long-lived species may be buffered from its effects during population declines due to long generation times and thus are less likely to have evolved mechanisms of inbreeding avoidance than species with shorter generation times. However, empirical evidence of the consequences of inbreeding in threatened, long-lived species is limited. In this study, we leverage a well-studied population of gopher tortoises, Gopherus polyphemus, to examine the role of inbreeding depression and the potential for behavioural inbreeding avoidance in a natural population of a long-lived species. We tested the hypothesis that increased parental inbreeding leads to reduced hatching rates and offspring quality. Additionally, we tested for evidence of inbreeding avoidance. We found that high parental relatedness results in offspring with lower quality and that high parental relatedness is correlated with reduced hatching success. However, we found that hatching success and offspring quality increase with maternal inbreeding, likely due to highly inbred females mating with more distantly related males. We did not find evidence for inbreeding avoidance in males and outbred females, suggesting sex-specific evolutionary trade-offs may have driven the evolution of mating behaviour. Our results demonstrate inbreeding depression in a long-lived species and that the evolution of inbreeding avoidance is shaped by multiple selective forces.
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Affiliation(s)
- Michael L Yuan
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA, USA.,Archbold Biological Station, Venus, FL, USA
| | - K Nicole White
- Archbold Biological Station, Venus, FL, USA.,Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, USA.,Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| | | | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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24
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Rougemont Q, Carrier A, Le Luyer J, Ferchaud A, Farrell JM, Hatin D, Brodeur P, Bernatchez L. Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge ( Esox masquinongy) from the St. Lawrence River basin. Evol Appl 2019; 12:902-922. [PMID: 31080504 PMCID: PMC6503833 DOI: 10.1111/eva.12765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/17/2018] [Indexed: 01/03/2023] Open
Abstract
Understanding the genetic and evolutionary impacts of stocking on wild fish populations has long been of interest as negative consequences such as reduced fitness and loss of genetic diversity are commonly reported outcomes. In an attempt to sustain a fishery, managers implemented nearly five decades of extensive stocking of over a million Muskellunge (Esox masquinongy), a native species in the Lower St. Lawrence River (Québec, Canada). We investigated the effect of this stocking on population genetic structure and allelic diversity in the St. Lawrence River in addition to tributaries and several stocked inland lakes. Using genotype by sequencing, we genotyped 643 individuals representing 22 locations and combined this information with forward simulations to investigate the genetic consequences of long-term stocking. Individuals native to the St. Lawrence watershed were genetically differentiated from stocking sources and tributaries, and inland lakes were naturally differentiated from the main river. Empirical data and simulations within the St. Lawrence River revealed weak stocking effects on admixture patterns. Our data suggest that the genetic structure associated with stocked fish was diluted into its relatively large effective population size. This interpretation is also consistent with a hypothesis that selection against introgression was in operation and relatively efficient within the large St. Lawrence River system. In contrast, smaller populations from adjacent tributaries and lakes displayed greater stocking-related admixture that resulted in comparatively higher heterozygosity than the St. Lawrence. Finally, individuals from inland lakes that were established by stocking maintained a close affinity with their source populations. This study illustrated a benefit of combining extensive genomic data with forward simulations for improved inference regarding population-level genetic effects of long-term stocking, and its relevance for fishery management decision making.
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Affiliation(s)
- Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Anne Carrier
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Jeremy Le Luyer
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
- IFREMER, Unité Ressources Marines en Polynésie, Centre Océanologique du PacifiqueTaravao, TahitiFrench Polynesia
| | - Anne‐Laure Ferchaud
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - John M. Farrell
- Department of Environmental and Forest Biology, College of Environmental Science and ForestryState University of New YorkSyracuseNew York
| | - Daniel Hatin
- Ministère des Forêts, de la Faune et des Parcs, Direction de la Gestion de la FauneEstrie‐Montréal‐Montérégie‐LavalLongueuilQuébecCanada
| | - Philippe Brodeur
- Ministère des Forêts, de la Faune et des ParcsDirection de la gestion de la faune de la Mauricie et du Centre‐du‐QuébecTrois‐RivièresQuebecCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
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25
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Oakley CG, Lundemo S, Ågren J, Schemske DW. Heterosis is common and inbreeding depression absent in natural populations of
Arabidopsis thaliana. J Evol Biol 2019; 32:592-603. [DOI: 10.1111/jeb.13441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/23/2019] [Accepted: 03/11/2019] [Indexed: 01/09/2023]
Affiliation(s)
| | - Sverre Lundemo
- Plant Ecology and Evolution Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Jon Ågren
- Plant Ecology and Evolution Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Douglas W. Schemske
- Department of Plant Biology W. K. Kellogg Biological Station Michigan State University East Lansing Michigan
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26
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Charlesworth B. Mutational load, inbreeding depression and heterosis in subdivided populations. Mol Ecol 2018; 27:4991-5003. [DOI: 10.1111/mec.14933] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Brian Charlesworth
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
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27
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Abu Awad D, Coron C. Effects of demographic stochasticity and life-history strategies on times and probabilities to fixation. Heredity (Edinb) 2018; 121:374-386. [PMID: 30050060 PMCID: PMC6134033 DOI: 10.1038/s41437-018-0118-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/09/2018] [Accepted: 06/18/2018] [Indexed: 11/08/2022] Open
Abstract
How life-history strategies influence the evolution of populations is not well understood. Most existing models stem from the Wright-Fisher model which considers discrete generations and a fixed population size, thus not taking into account any potential consequences of overlapping generations and demographic stochasticity on allelic frequencies. We introduce an individual-based model in which both population size and genotypic frequencies at a single bi-allelic locus are emergent properties of the model. Demographic parameters can be defined so as to represent a large range of r and K life-history strategies in a stable environment, and appropriate fixed effective population sizes are calculated so as to compare our model to the Wright-Fisher diffusion. Our results indicate that models with fixed population size that stem from the Wright-Fisher diffusion cannot fully capture the consequences of demographic stochasticity on allele fixation in long-lived species with low reproductive rates. This discrepancy is accentuated in the presence of demo-genetic feedback. Furthermore, we predict that populations with K life-histories should maintain lower genetic diversity than those with r life-histories.
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Affiliation(s)
- Diala Abu Awad
- INRA, UMR 1334 AGAP, 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
- Section of Population Genetics, Technical University of Munich, Liesel-Beckmann Strasse 2, 85354, Freising, Germany.
| | - Camille Coron
- Laboratoire de Mathématiques d'Orsay, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 91405, Orsay, France
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28
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Layman NC, Busch JW. Bottlenecks and inbreeding depression in autotetraploids. Evolution 2018; 72:2025-2037. [PMID: 30136722 DOI: 10.1111/evo.13587] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/14/2018] [Indexed: 12/30/2022]
Abstract
Inbreeding depression is dependent on the ploidy of populations and can inhibit the evolution of selfing. While polyploids should generally harbor less inbreeding depression than diploids at equilibrium, it has been unclear whether this pattern holds in non-equilibrium conditions following bottlenecks. We use stochastic individual-based simulations to determine the effects of population bottlenecks on inbreeding depression in diploids and autotetraploids, in addition to cases where neo-autotetraploids form from the union of unreduced gametes. With a ploidy-independent dominance function based on enzyme kinetics, inbreeding depression is generally lower in autotetraploids for fully and partially recessive mutations. Due to the sampling of more chromosomes during reproduction, bottlenecks generally reduce inbreeding depression to a lesser extent in autotetraploids. All else being equal, population bottlenecks may have ploidy-dependent effects for another reason-in some cases matings between close relatives temporarily increase inbreeding depression in autotetraploids by increasing the frequency of the heterozygous genotype harboring the most harmful mutations. When neo-autotetraploids are formed by few individuals, inbreeding depression is dramatically reduced, given extensive masking of harmful mutations following whole genome duplication. This effect persists as nascent tetraploids reach mutation-selection-drift balance, providing a transient period of permissive conditions favoring the evolution of selfing.
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Affiliation(s)
- Nathan C Layman
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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29
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Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Nonself-Recognition System. Genetics 2018; 209:861-883. [PMID: 29716955 DOI: 10.1534/genetics.118.300748] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/28/2018] [Indexed: 11/18/2022] Open
Abstract
Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self-recognition (SR) and nonself-recognition (NSR). Most work has focused on diversification within SR systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic NSR [SRNase/S Locus F-box (SLF)] SI system. For this model, the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and, in general, is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate-to-high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a NSR SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a recognition system common in flowering plants.
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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: 39] [Impact Index Per Article: 6.5] [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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García-Dorado A. An explicit model for the inbreeding load in the evolutionary analysis of selfing. Evolution 2017; 71:1381-1389. [DOI: 10.1111/evo.13231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/03/2017] [Accepted: 03/09/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Aurora García-Dorado
- Universidad Complutense, Departamento de Genetica; Ciudad Universitaria; Madrid 28040 Spain
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32
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Abu Awad D, Billiard S, Tran V. Perenniality induces high inbreeding depression in self-fertilising species. Theor Popul Biol 2016; 112:43-51. [DOI: 10.1016/j.tpb.2016.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/19/2016] [Accepted: 08/09/2016] [Indexed: 11/30/2022]
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33
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Spigler RB, Theodorou K, Chang S. Inbreeding depression and drift load in small populations at demographic disequilibrium. Evolution 2016; 71:81-94. [DOI: 10.1111/evo.13103] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Rachel B. Spigler
- Department of Biology Temple University 1900 N. 12th Street Philadelphia Pennsylvania 19122
| | - Konstantinos Theodorou
- Biodiversity Conservation Laboratory, Department of Environment, University of the Aegean University Hill 81100 Mytilene Greece
| | - Shu‐Mei Chang
- Department of Plant Biology University of Georgia 2502 Miller Plant Sciences Athens Georgia 30602–7271
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34
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Samis KE, López-Villalobos A, Eckert CG. Strong genetic differentiation but not local adaptation toward the range limit of a coastal dune plant. Evolution 2016; 70:2520-2536. [DOI: 10.1111/evo.13047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Karen E. Samis
- Department of Biology; Queen's University; Kingston Ontario K7L 3N6 Canada
- Current Address: Department of Biology; University of Prince Edward Island; Charlottetown Prince Edward Island C1A 4P3 Canada
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Laugier GJM, Le Moguédec G, Su W, Tayeh A, Soldati L, Serrate B, Estoup A, Facon B. Reduced population size can induce quick evolution of inbreeding depression in the invasive ladybird Harmonia axyridis. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1179-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Porcher E, Lande R. Inbreeding depression under mixed outcrossing, self-fertilization and sib-mating. BMC Evol Biol 2016; 16:105. [PMID: 27188583 PMCID: PMC4869318 DOI: 10.1186/s12862-016-0668-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/25/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Biparental inbreeding, mating between two relatives, occurs at a low frequency in many natural plant populations, which also often have substantial rates of self-fertilization. Although biparental inbreeding is likely to influence the dynamics of inbreeding depression and the evolution of selfing rates, it has received limited theoretical attention in comparison to selfing. The only previous model suggested that biparental inbreeding can favour the maintenance of stable intermediate selfing rates, but made unrealistic assumptions about the genetic basis of inbreeding depression. Here we extend a genetic model of inbreeding depression, describing nearly recessive lethal mutations at a very large number of loci, to incorporate sib-mating. We also include a constant component of inbreeding depression modelling the effects of mildly deleterious, nearly additive alleles. We analyze how observed rates of sib-mating influence the mean number of heterozygous lethals alleles and inbreeding depression in a population reproducing by a mixture of self-fertilization, sib-mating and outcrossing. We finally use the ensuing relationship between equilibrium inbreeding depression and population selfing rate to infer the evolutionarily stable selfing rates expected under such a mixed mating system. RESULTS We show that for a given rate of inbreeding, sib-mating is more efficient at purging inbreeding depression than selfing, because homozygosity of lethals increases more gradually through sib-mating than through selfing. Because sib-mating promotes the purging of inbreeding depression and the evolution of selfing, our genetic model of inbreeding depression also predicts that sib-mating is unlikely to maintain stable intermediate selfing rates. CONCLUSIONS Our results imply that even low rates of sib-mating affect plant mating system evolution, by facilitating the evolution of selfing via more efficient purging of inbreeding depression. Alternative mechanisms, such as pollination ecology, are necessary to explain stable mixed selfing and outcrossing.
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Affiliation(s)
- Emmanuelle Porcher
- Centre d'Ecologie et des Sciences de la Conservation (UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, 57 rue Cuvier, Paris, 75005, France.
| | - Russell Lande
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
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38
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Busch V, Reisch C. Population size and land use affect the genetic variation and performance of the endangered plant species Dianthus seguieri ssp. glaber. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0794-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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39
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Lohr JN, Haag CR. Genetic load, inbreeding depression, and hybrid vigor covary with population size: An empirical evaluation of theoretical predictions. Evolution 2015; 69:3109-22. [PMID: 26497949 DOI: 10.1111/evo.12802] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 10/07/2015] [Accepted: 10/14/2015] [Indexed: 11/26/2022]
Abstract
Reduced population size is thought to have strong consequences for evolutionary processes as it enhances the strength of genetic drift. In its interaction with selection, this is predicted to increase the genetic load, reduce inbreeding depression, and increase hybrid vigor, and in turn affect phenotypic evolution. Several of these predictions have been tested, but comprehensive studies controlling for confounding factors are scarce. Here, we show that populations of Daphnia magna, which vary strongly in genetic diversity, also differ in genetic load, inbreeding depression, and hybrid vigor in a way that strongly supports theoretical predictions. Inbreeding depression is positively correlated with genetic diversity (a proxy for Ne ), and genetic load and hybrid vigor are negatively correlated with genetic diversity. These patterns remain significant after accounting for potential confounding factors and indicate that, in small populations, a large proportion of the segregation load is converted into fixed load. Overall, the results suggest that the nature of genetic variation for fitness-related traits differs strongly between large and small populations. This has large consequences for evolutionary processes in natural populations, such as selection on dispersal, breeding systems, ageing, and local adaptation.
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Affiliation(s)
- Jennifer N Lohr
- Department of Biology, Ecology and Evolution, University of Fribourg, 1700, Fribourg, Switzerland. .,Zoological Institute and Zoological Museum, Biocenter Grindel, Hamburg University, Hamburg, Germany. .,Tvärminne Zoological Station, FIN-10900, Hanko, Finland.
| | - Christoph R Haag
- Department of Biology, Ecology and Evolution, University of Fribourg, 1700, Fribourg, Switzerland.,Zoological Institute and Zoological Museum, Biocenter Grindel, Hamburg University, Hamburg, Germany.,Centre d'Ecologie Fonctionnelle et Evolutive - UMR 5175, 34293, Montpellier Cedex 5, France
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40
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Hartfield M. Evolutionary genetic consequences of facultative sex and outcrossing. J Evol Biol 2015; 29:5-22. [DOI: 10.1111/jeb.12770] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023]
Affiliation(s)
- M. Hartfield
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto ON Canada
- Bioinformatics Research Centre; University of Aarhus; Aarhus Denmark
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41
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Oakley CG, Spoelhof JP, Schemske DW. Increased heterosis in selfing populations of a perennial forb. AOB PLANTS 2015; 7:plv122. [PMID: 26507567 PMCID: PMC4671326 DOI: 10.1093/aobpla/plv122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/09/2015] [Indexed: 06/05/2023]
Abstract
Quantifying the importance of random genetic drift in natural populations is central to understanding the potential limits to natural selection. One approach is to estimate the magnitude of heterosis, the increased fitness of progeny derived from crosses between populations relative to crosses within populations caused by the heterozygous masking of deleterious recessive or nearly recessive alleles that have been fixed by drift within populations. Self-fertilization is expected to reduce the effective population size by half relative to outcrossing, and population bottlenecks may be common during the transition to selfing. Therefore, chance fixation of deleterious alleles due to drift in selfing populations should increase heterosis between populations. Increased homozygosity due to fixation or loss of alleles should also decrease inbreeding depression within populations. Most populations of the perennial herb Arabidopsis lyrata ssp. lyrata are self-incompatible (SI), but several have evolved self-compatibility and are highly selfing. We quantified heterosis and inbreeding depression in two predominantly self-compatible (SC) and seven SI populations in a field common garden experiment within the species' native range and examined the correlation between these metrics to gauge the similarity in their genetic basis. We measured proportion germination in the lab, and survival and fecundity (flower and seed production) for 2 years in the field, and calculated estimates of cumulative fitness. We found 7.2-fold greater heterosis in SC compared with SI populations, despite substantial heterosis in SI populations (56 %). Inbreeding depression was >61 %, and not significantly different between SC and SI populations. There was no correlation between population estimates of heterosis and inbreeding depression, suggesting that they have somewhat different genetic bases. Combined with other sources of information, our results suggest a history of bottlenecks in all of these populations. The bottlenecks in SC populations may have been severe, but their strong inbreeding depression remains enigmatic.
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Affiliation(s)
- Christopher G Oakley
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA
| | - Jonathan P Spoelhof
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA
| | - Douglas W Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
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42
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Effects of Interference Between Selected Loci on the Mutation Load, Inbreeding Depression, and Heterosis. Genetics 2015; 201:745-57. [PMID: 26269503 DOI: 10.1534/genetics.115.178533] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/07/2015] [Indexed: 11/18/2022] Open
Abstract
A classical prediction from single-locus models is that inbreeding increases the efficiency of selection against partially recessive deleterious alleles (purging), thereby decreasing the mutation load and level of inbreeding depression. However, previous multilocus simulation studies found that increasing the rate of self-fertilization of individuals may not lead to purging and argued that selective interference among loci causes this effect. In this article, I derive simple analytical approximations for the mutation load and inbreeding depression, taking into account the effects of interference between pairs of loci. I consider two classical scenarios of nonrandomly mating populations: a single population undergoing partial selfing and a subdivided population with limited dispersal. In the first case, correlations in homozygosity between loci tend to reduce mean fitness and increase inbreeding depression. These effects are stronger when deleterious alleles are more recessive, but only weakly depend on the strength of selection against deleterious alleles and on recombination rates. In subdivided populations, interference increases inbreeding depression within demes, but decreases heterosis between demes. Comparisons with multilocus, individual-based simulations show that these analytical approximations are accurate as long as the effects of interference stay moderate, but fail for high deleterious mutation rates and low dominance coefficients of deleterious alleles.
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43
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Genetic and fitness consequences of interpopulation mating in Dianthus guliae Janka: conservation implications for severely depleted and isolated plant populations. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0727-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Knief U, Hemmrich-Stanisak G, Wittig M, Franke A, Griffith SC, Kempenaers B, Forstmeier W. Quantifying realized inbreeding in wild and captive animal populations. Heredity (Edinb) 2015; 114:397-403. [PMID: 25585923 DOI: 10.1038/hdy.2014.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 11/10/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022] Open
Abstract
Most molecular measures of inbreeding do not measure inbreeding at the scale that is most relevant for understanding inbreeding depression-namely the proportion of the genome that is identical-by-descent (IBD). The inbreeding coefficient FPed obtained from pedigrees is a valuable estimator of IBD, but pedigrees are not always available, and cannot capture inbreeding loops that reach back in time further than the pedigree. We here propose a molecular approach to quantify the realized proportion of the genome that is IBD (propIBD), and we apply this method to a wild and a captive population of zebra finches (Taeniopygia guttata). In each of 948 wild and 1057 captive individuals we analyzed available single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four different genomic regions in each population. This allowed us to determine whether any of these four regions was completely homozygous within an individual, which indicates IBD with high confidence. In the highly nomadic wild population, we did not find a single case of IBD, implying that inbreeding must be extremely rare (propIBD=0-0.00094, 95% CI). In the captive population, a five-generation pedigree strongly underestimated the average amount of realized inbreeding (FPed=0.013<propIBD=0.064), as expected given that pedigree founders were already related. We suggest that this SNP-based technique is generally useful for quantifying inbreeding at the individual or population level, and we show analytically that it can capture inbreeding loops that reach back up to a few hundred generations.
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Affiliation(s)
- U Knief
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - G Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - M Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - A Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - S C Griffith
- 1] Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia [2] School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - B Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - W Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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45
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Gervais C, Awad DA, Roze D, Castric V, Billiard S. GENETIC ARCHITECTURE OF INBREEDING DEPRESSION AND THE MAINTENANCE OF GAMETOPHYTIC SELF-INCOMPATIBILITY. Evolution 2014; 68:3317-24. [DOI: 10.1111/evo.12495] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 07/02/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Camille Gervais
- UMI 3614; Evolutionary Biology and Ecology of Algae; CNRS; 29680 Roscoff France
- Sorbonne Universités; UPMC University Paris 06 29680 Roscoff France
| | - Diala Abu Awad
- Laboratoire de Génétique et Evolution des Populations Végétales; UMR CNRS 8198; Université Lille 1 - Sciences et Technologies; 59655 Villeneuve d'Ascq France
| | - Denis Roze
- UMI 3614; Evolutionary Biology and Ecology of Algae; CNRS; 29680 Roscoff France
- Sorbonne Universités; UPMC University Paris 06 29680 Roscoff France
| | - Vincent Castric
- Laboratoire de Génétique et Evolution des Populations Végétales; UMR CNRS 8198; Université Lille 1 - Sciences et Technologies; 59655 Villeneuve d'Ascq France
| | - Sylvain Billiard
- Laboratoire de Génétique et Evolution des Populations Végétales; UMR CNRS 8198; Université Lille 1 - Sciences et Technologies; 59655 Villeneuve d'Ascq France
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46
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Vekemans X, Poux C, Goubet PM, Castric V. The evolution of selfing from outcrossing ancestors in Brassicaceae: what have we learned from variation at the S-locus? J Evol Biol 2014; 27:1372-85. [PMID: 24725152 DOI: 10.1111/jeb.12372] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/06/2014] [Accepted: 03/10/2014] [Indexed: 12/01/2022]
Abstract
Evolutionary transitions between mating systems have occurred repetitively and independently in flowering plants. One of the most spectacular advances of the recent empirical literature in the field was the discovery of the underlying genetic machinery, which provides the opportunity to retrospectively document the scenario of the outcrossing to selfing transitions in a phylogenetic perspective. In this review, we explore the literature describing patterns of polymorphism and molecular evolution of the locus controlling self-incompatibility (S-locus) in selfing species of the Brassicaceae family in order to document the transition from outcrossing to selfing, a retrospective approach that we describe as the 'mating system genes approach'. The data point to strikingly contrasted scenarios of transition from outcrossing to selfing. We also perform original analyses of the fully sequenced genomes of four species showing self-compatibility, to compare the orthologous S-locus region with that of functional S-locus haplotypes. Phylogenetic analyses suggest that all species we investigated evolved independently towards loss of self-incompatibility, and in most cases almost intact sequences of either of the two S-locus genes suggest that these transitions occurred relatively recently. The S-locus region in Aethionema arabicum, representing the most basal lineage of Brassicaceae, showed unusual patterns so that our analysis could not determine whether self-incompatibility was lost secondarily, or evolved in the core Brassicaceae after the split with this basal lineage. Although the approach we detail can only be used when mating system genes have been identified in a clade, we suggest that its integration with phylogenetic and population genetic approaches should help determine the main routes of this predominant mating system shift in plants.
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Affiliation(s)
- X Vekemans
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université Lille 1, Villeneuve d'Ascq Cedex, France
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47
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Kamran-Disfani A, Agrawal AF. Selfing, adaptation and background selection in finite populations. J Evol Biol 2014; 27:1360-71. [PMID: 24601989 DOI: 10.1111/jeb.12343] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/23/2013] [Accepted: 01/11/2014] [Indexed: 01/28/2023]
Abstract
Classic deterministic genetic models of the evolution of selfing predict species should be either completely outcrossing or completely selfing. However, even species considered high selfers outcross to a small degree (e.g. Arabidopsis thaliana and Caenorhabditis elegans). This discrepancy between theory and data may exist because the classic models ignore the effects of drift interacting with selection, that is, Hill-Robertson effects. High selfing rates make the effective rate of recombination near zero, which is expected to cause the build-up of negative disequilibria in finite populations. Despite the transmission advantage associated with complete selfing, low levels of outcrossing may be favoured because of the benefits of increasing the effective rate of recombination to dissipate negative disequilibria. Using multilocus simulations, we confirm that selfing reduces effective population size through background selection and causes negative disequilibria between selected sites. Consequently, the rate of adaptation is substantially reduced in strong selfers. When selfing rate is allowed to evolve, populations evolve to be either strong outcrossers or strong selfers, depending on the parameter values. Amongst selfers, low, but nonzero, levels of outcrossing can be maintained by selection even when all mutations are deleterious; more outcrossing is maintained with higher rates of deleterious mutation. The addition of beneficial mutations can (i) lead to a quantitative increase in the degree of outcrossing amongst stronger selfers but (ii) may cause outcrossing species to evolve into stronger selfers.
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Affiliation(s)
- A Kamran-Disfani
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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48
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Plech M, de Visser JAGM, Korona R. Heterosis is prevalent among domesticated but not wild strains of Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2014; 4:315-23. [PMID: 24347627 PMCID: PMC3931565 DOI: 10.1534/g3.113.009381] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/11/2013] [Indexed: 11/18/2022]
Abstract
Crosses between inbred but unrelated individuals often result in an increased fitness of the progeny. This phenomenon is known as heterosis and has been reported for wild and domesticated populations of plants and animals. Analysis of heterosis is often hindered by the fact that the genetic relatedness between analyzed organisms is only approximately known. We studied a collection of Saccharomyces cerevisiae isolates from wild and human-created habitats whose genomes were sequenced and thus their relatedness was fully known. We reasoned that if these strains accumulated different deleterious mutations at an approximately constant rate, then heterosis should be most visible in F1 heterozygotes from the least related parents. We found that heterosis was substantial and positively correlated with sequence divergence, but only in domesticated strains. More than 80% of the heterozygous hybrids were more fit than expected from the mean of their homozygous parents, and approximately three-quarters of those exceeded even the fittest parent. Our results support the notion that domestication brings about relaxation of selection and accumulation of deleterious mutations. However, other factors may have contributed as well. In particular, the observed build-up of genetic load might be facilitated by a decrease, and not increase, in the rate of inbreeding.
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Affiliation(s)
- Marcin Plech
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Krakow, Poland
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands
| | | | - Ryszard Korona
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Krakow, Poland
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49
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Awad DA, Gallina S, Bonamy C, Billiard S. The interaction between selection, demography and selfing and how it affects population viability. PLoS One 2014; 9:e86125. [PMID: 24465911 PMCID: PMC3897648 DOI: 10.1371/journal.pone.0086125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/07/2013] [Indexed: 11/18/2022] Open
Abstract
Population extinction due to the accumulation of deleterious mutations has only been considered to occur at small population sizes, large sexual populations being expected to efficiently purge these mutations. However, little is known about how the mutation load generated by segregating mutations affects population size and, eventually, population extinction. We propose a simple analytical model that takes into account both the demographic and genetic evolution of populations, linking population size, density dependence, the mutation load, and self-fertilisation. Analytical predictions were found to be relatively good predictors of population size and probability of population viability when verified using an explicit individual based stochastic model. We show that initially large populations do not always reach mutation-selection balance and can go extinct due to the accumulation of segregating deleterious mutations. Population survival depends not only on the relative fitness and demographic stochasticity, but also on the interaction between the two. When deleterious mutations are recessive, self-fertilisation affects viability non-monotonically and genomic cold-spots could favour the viability of outcrossing populations.
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Affiliation(s)
- Diala Abu Awad
- UMR-CNRS 8198, Laboratoire Génétique et Évolution des Populations Végétales, Université Lille 1, Villeneuve d'Ascq, France
- * E-mail:
| | - Sophie Gallina
- UMR-CNRS 8198, Laboratoire Génétique et Évolution des Populations Végétales, Université Lille 1, Villeneuve d'Ascq, France
| | - Cyrille Bonamy
- Centre de Ressources Informatiques (CRI), Université Lille 1, Villeneuve d'Ascq, France
| | - Sylvain Billiard
- UMR-CNRS 8198, Laboratoire Génétique et Évolution des Populations Végétales, Université Lille 1, Villeneuve d'Ascq, France
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50
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Vitales D, Pellicer J, Vallès J, Garnatje T. Estructura genética y germinación de semillas en poblaciones portuguesas de Cheirolophus uliginosus (Asteraceae): Implicaciones para su conservación. COLLECTANEA BOTANICA 2013. [DOI: 10.3989/collectbot.2013.v32.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Cheirolophus uliginosus es una especie amenazada endémica de la costa atlántica de la península ibérica, donde ocupa unas pocas y reducidas localidades. En nuestro estudio, analizamos los patrones de variación de los haplotipos de ADN cloroplástico y el éxito reproductivo —capacidad germinativa— en siete poblaciones portuguesas de diferente tamaño. El éxito reproductivo de Ch. uliginosus se ha examinado en relación con la estructura genética y el tamaño de sus poblaciones. Los resultados indican una variabilidad intrapoblacional muy baja para los marcadores cloroplásticos utilizados. Nuestro estudio muestra una tasa de germinación significativamente reducida en las poblaciones pequeñas (< 50 individuos) respecto a aquellas de tamaño mediano (50-250 individuos) o grande (> 250 individuos). Para explicar este fenómeno, se deben tomar en consideración las limitaciones ecológicas y el aislamiento genético. Por otro lado, en las poblaciones de Ch. uliginosus de mayor tamaño (> 250 individuos) se ha observado una incidencia más acusada de la depredación de semillas antes de su dispersión, lo cual podría estar afectando a su respuesta reproductiva. Finalmente, las poblaciones más pequeñas —que presentan un reducido éxito reproductivo— contienen los haplotipos más distantes evolutivamente y su conservación debería ser, por tanto, prioritaria.
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