1
|
Lindner M, Verhagen I, Mateman AC, van Oers K, Laine VN, Visser ME. Genetic and epigenetic differentiation in response to genomic selection for avian lay date. Evol Appl 2024; 17:e13703. [PMID: 38948539 PMCID: PMC11211926 DOI: 10.1111/eva.13703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 07/02/2024] Open
Abstract
Anthropogenic climate change has led to globally increasing temperatures at an unprecedented pace and, to persist, wild species have to adapt to their changing world. We, however, often fail to derive reliable predictions of species' adaptive potential. Genomic selection represents a powerful tool to investigate the adaptive potential of a species, but constitutes a 'blind process' with regard to the underlying genomic architecture of the relevant phenotypes. Here, we used great tit (Parus major) females from a genomic selection experiment for avian lay date to zoom into this blind process. We aimed to identify the genetic variants that responded to genomic selection and epigenetic variants that accompanied this response and, this way, might reflect heritable genetic variation at the epigenetic level. We applied whole genome bisulfite sequencing to blood samples of individual great tit females from the third generation of bidirectional genomic selection lines for early and late lay date. Genomic selection resulted in differences at both the genetic and epigenetic level. Genetic variants that showed signatures of selection were located within genes mostly linked to brain development and functioning, including LOC107203824 (SOX3-like). SOX3 is a transcription factor that is required for normal hypothalamo-pituitary axis development and functioning, an essential part of the reproductive axis. As for epigenetic differentiation, the early selection line showed hypomethylation relative to the late selection line. Sites with differential DNA methylation were located in genes important for various biological processes, including gonadal functioning (e.g., MSTN and PIK3CB). Overall, genomic selection for avian lay date provided insights into where within the genome the heritable genetic variation for lay date, on which selection can operate, resides and indicates that some of this variation might be reflected by epigenetic variants.
Collapse
Affiliation(s)
- Melanie Lindner
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Irene Verhagen
- Wageningen University & Research (WUR)WageningenThe Netherlands
| | - A. Christa Mateman
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Kees van Oers
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Behavioural Ecology GroupWageningen University & Research (WUR)WageningenThe Netherlands
| | - Veronika N. Laine
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| |
Collapse
|
2
|
Blackburn GS, Keeling CI, Prunier J, Keena MA, Béliveau C, Hamelin R, Havill NP, Hebert FO, Levesque RC, Cusson M, Porth I. Genetics of flight in spongy moths (Lymantria dispar ssp.): functionally integrated profiling of a complex invasive trait. BMC Genomics 2024; 25:541. [PMID: 38822259 PMCID: PMC11140922 DOI: 10.1186/s12864-023-09936-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/22/2023] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND Flight can drastically enhance dispersal capacity and is a key trait defining the potential of exotic insect species to spread and invade new habitats. The phytophagous European spongy moths (ESM, Lymantria dispar dispar) and Asian spongy moths (ASM; a multi-species group represented here by L. d. asiatica and L. d. japonica), are globally invasive species that vary in adult female flight capability-female ASM are typically flight capable, whereas female ESM are typically flightless. Genetic markers of flight capability would supply a powerful tool for flight profiling of these species at any intercepted life stage. To assess the functional complexity of spongy moth flight and to identify potential markers of flight capability, we used multiple genetic approaches aimed at capturing complementary signals of putative flight-relevant genetic divergence between ESM and ASM: reduced representation genome-wide association studies, whole genome sequence comparisons, and developmental transcriptomics. We then judged the candidacy of flight-associated genes through functional analyses aimed at addressing the proximate demands of flight and salient features of the ecological context of spongy moth flight evolution. RESULTS Candidate gene sets were typically non-overlapping across different genetic approaches, with only nine gene annotations shared between any pair of approaches. We detected an array of flight-relevant functional themes across gene sets that collectively suggest divergence in flight capability between European and Asian spongy moth lineages has coincided with evolutionary differentiation in multiple aspects of flight development, execution, and surrounding life history. Overall, our results indicate that spongy moth flight evolution has shaped or been influenced by a large and functionally broad network of traits. CONCLUSIONS Our study identified a suite of flight-associated genes in spongy moths suited to exploration of the genetic architecture and evolution of flight, or validation for flight profiling purposes. This work illustrates how complementary genetic approaches combined with phenotypically targeted functional analyses can help to characterize genetically complex traits.
Collapse
Affiliation(s)
- Gwylim S Blackburn
- Natural Resources Canada, Pacific Forestry Centre, Canadian Forest Service, 506 Burnside Road West, Victoria, BC, V8Z 1M5, Canada.
- Natural Resources Canada, Laurentian Forestry Centre, Canadian Forest Service, 1055 Rue du PEPS, Quebec City, Québec, G1V 4C7, Canada.
- Department of Wood and Forest Sciences, Laval University, 1030 Avenue de La Médecine, Québec, QC, G1V 0A6, Canada.
| | - Christopher I Keeling
- Natural Resources Canada, Laurentian Forestry Centre, Canadian Forest Service, 1055 Rue du PEPS, Quebec City, Québec, G1V 4C7, Canada
- Department of Biochemistry, Microbiology, and Bioinformatics, Laval University, Québec, QC, G1V 0A6, Canada
| | - Julien Prunier
- Department of Wood and Forest Sciences, Laval University, 1030 Avenue de La Médecine, Québec, QC, G1V 0A6, Canada
- Institute of Integrative Biology and Systems, Laval University, Québec, QC, Canada
| | - Melody A Keena
- United States Department of Agriculture, Northern Research Station, Forest Service, 51 Mill Pond Road, Hamden, CT, 06514, USA
| | - Catherine Béliveau
- Natural Resources Canada, Laurentian Forestry Centre, Canadian Forest Service, 1055 Rue du PEPS, Quebec City, Québec, G1V 4C7, Canada
| | - Richard Hamelin
- Forest Sciences Centre, University of British Columbia, 2424 Main Mall, Vancouver, BC, 3032V6T 1Z4, Canada
| | - Nathan P Havill
- United States Department of Agriculture, Northern Research Station, Forest Service, 51 Mill Pond Road, Hamden, CT, 06514, USA
| | | | - Roger C Levesque
- Institute of Integrative Biology and Systems, Laval University, Québec, QC, Canada
| | - Michel Cusson
- Natural Resources Canada, Laurentian Forestry Centre, Canadian Forest Service, 1055 Rue du PEPS, Quebec City, Québec, G1V 4C7, Canada
- Department of Biochemistry, Microbiology, and Bioinformatics, Laval University, Québec, QC, G1V 0A6, Canada
| | - Ilga Porth
- Department of Wood and Forest Sciences, Laval University, 1030 Avenue de La Médecine, Québec, QC, G1V 0A6, Canada
- Institute of Integrative Biology and Systems, Laval University, Québec, QC, Canada
- Centre for Forest Research, Laval University, 2405 Rue de La Terrasse, Québec, QC, G1V 0A6, Canada
| |
Collapse
|
3
|
Fraimout A, Guillaume F, Li Z, Sillanpää MJ, Rastas P, Merilä J. Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing. Mol Ecol 2024; 33:e17299. [PMID: 38380534 DOI: 10.1111/mec.17299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/08/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which, in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (Pungitius pungitius) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild outbred populations with high migration rate can impair the estimation of quantitative genetic parameters and bias heritability estimates downwards. On the other hand, the use of a half-sib/full-sib design allowed precise estimation of genetic variance components and revealed significant additive variance and heritability for all measured traits, with negligible dominance contributions. Genome-partitioning and QTL mapping analyses revealed that most traits had a polygenic basis and were controlled by genes at multiple chromosomes. Furthermore, different QTL contributed to variation in the same traits in different populations suggesting heterogeneous underpinnings of parallel evolution at the phenotypic level. Our results provide important guidelines for future studies aimed at estimating adaptive potential in the wild, particularly for those conducted in outbred large-sized populations.
Collapse
Affiliation(s)
- Antoine Fraimout
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Frédéric Guillaume
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Zitong Li
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Mikko J Sillanpää
- Research Unit of Mathematical Sciences, FI-90014 University of Oulu, Oulu, Finland
| | - Pasi Rastas
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Helsinki, Finland
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
4
|
Pointer MD, Spurgin LG, Gage MJG, McMullan M, Richardson DS. Genetic architecture of dispersal behaviour in the post-harvest pest and model organism Tribolium castaneum. Heredity (Edinb) 2023; 131:253-262. [PMID: 37516814 PMCID: PMC10539327 DOI: 10.1038/s41437-023-00641-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 07/31/2023] Open
Abstract
Dispersal behaviour is an important aspect of the life-history of animals. However, the genetic architecture of dispersal-related traits is often obscure or unknown, even in well studied species. Tribolium castaneum is a globally significant post-harvest pest and established model organism, yet studies of its dispersal have shown ambiguous results and the genetic basis of this behaviour remains unresolved. We combine experimental evolution and agent-based modelling to investigate the number of loci underlying dispersal in T. castaneum, and whether the trait is sex-linked. Our findings demonstrate rapid evolution of dispersal behaviour under selection. We find no evidence of sex-biases in the dispersal behaviour of the offspring of crosses, supporting an autosomal genetic basis of the trait. Moreover, simulated data approximates experimental data under simulated scenarios where the dispersal trait is controlled by one or few loci, but not many loci. Levels of dispersal in experimentally inbred lines, compared with simulations, indicate that a single locus model is not well supported. Taken together, these lines of evidence support an oligogenic architecture underlying dispersal in Tribolium castaneum. These results have implications for applied pest management and for our understanding of the evolution of dispersal in the coleoptera, the world's most species-rich order.
Collapse
|
5
|
van Oers K, van den Heuvel K, Sepers B. The Epigenetics of Animal Personality. Neurosci Biobehav Rev 2023; 150:105194. [PMID: 37094740 DOI: 10.1016/j.neubiorev.2023.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
Animal personality, consistent individual differences in behaviour, is an important concept for understanding how individuals vary in how they cope with environmental challenges. In order to understand the evolutionary significance of animal personality, it is crucial to understand the underlying regulatory mechanisms. Epigenetic marks such as DNA methylation are hypothesised to play a major role in explaining variation in phenotypic changes in response to environmental alterations. Several characteristics of DNA methylation also align well with the concept of animal personality. In this review paper, we summarise the current literature on the role that molecular epigenetic mechanisms may have in explaining personality variation. We elaborate on the potential for epigenetic mechanisms to explain behavioural variation, behavioural development and temporal consistency in behaviour. We then suggest future routes for this emerging field and point to potential pitfalls that may be encountered. We conclude that a more inclusive approach is needed for studying the epigenetics of animal personality and that epigenetic mechanisms cannot be studied without considering the genetic background.
Collapse
Affiliation(s)
- Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands.
| | - Krista van den Heuvel
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
| |
Collapse
|
6
|
Gauzere J, Pemberton JM, Slate J, Morris A, Morris S, Walling CA, Johnston SE. A polygenic basis for birth weight in a wild population of red deer (Cervus elaphus). G3 (BETHESDA, MD.) 2023; 13:jkad018. [PMID: 36652410 PMCID: PMC10085764 DOI: 10.1093/g3journal/jkad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The genetic architecture of traits under selection has important consequences for the response to selection and potentially for population viability. Early QTL mapping studies in wild populations have reported loci with large effect on trait variation. However, these results are contradicted by more recent genome-wide association analyses, which strongly support the idea that most quantitative traits have a polygenic basis. This study aims to re-evaluate the genetic architecture of a key morphological trait, birth weight, in a wild population of red deer (Cervus elaphus), using genomic approaches. A previous study using 93 microsatellite and allozyme markers and linkage mapping on a kindred of 364 deer detected a pronounced QTL on chromosome 21 explaining 29% of the variance in birth weight, suggesting that this trait is partly controlled by genes with large effects. Here, we used data for more than 2,300 calves genotyped at >39,000 SNP markers and two approaches to characterise the genetic architecture of birth weight. First, we performed a genome-wide association (GWA) analysis, using a genomic relatedness matrix to account for population structure. We found no SNPs significantly associated with birth weight. Second, we used genomic prediction to estimate the proportion of variance explained by each SNP and chromosome. This analysis confirmed that most genetic variance in birth weight was explained by loci with very small effect sizes. Third, we found that the proportion of variance explained by each chromosome was slightly positively correlated with its size. These three findings highlight a highly polygenic architecture for birth weight, which contradicts the previous QTL study. These results are probably explained by the differences in how associations are modelled between QTL mapping and GWA. Our study suggests that models of polygenic adaptation are the most appropriate to study the evolutionary trajectory of this trait.
Collapse
Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- AGAP, Université Montpellier, CIRAD, INRAE, Institut Agro, 34090 Montpellier, France
| | | | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alison Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Craig A Walling
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| |
Collapse
|
7
|
Abstract
We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.
Collapse
Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Edinburgh EH9 3FL, UK
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, 14627, NY, USA
| | - Emily B Josephs
- Department of Plant Biology and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, 48824, MI, USA
| |
Collapse
|
8
|
Decomposing phenotypic skew and its effects on the predicted response to strong selection. Nat Ecol Evol 2022; 6:774-785. [PMID: 35422480 DOI: 10.1038/s41559-022-01694-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/08/2022] [Indexed: 12/29/2022]
Abstract
The major frameworks for predicting evolutionary change assume that a phenotype's underlying genetic and environmental components are normally distributed. However, the predictions of these frameworks may no longer hold if distributions are skewed. Despite this, phenotypic skew has never been decomposed, meaning the fundamental assumptions of quantitative genetics remain untested. Here we demonstrate that the substantial phenotypic skew in the body size of juvenile blue tits (Cyanistes caeruleus) is driven by environmental factors. Although skew had little impact on our predictions of selection response in this case, our results highlight the impact of skew on the estimation of inheritance and selection. Specifically, the nonlinear parent-offspring regressions induced by skew, alongside selective disappearance, can strongly bias estimates of heritability. The ubiquity of skew and strong directional selection on juvenile body size imply that heritability is commonly overestimated, which may in part explain the discrepancy between predicted and observed trait evolution.
Collapse
|
9
|
Stuart KC, Sherwin WB, Cardilini AP, Rollins LA. Genetics and Plasticity Are Responsible for Ecogeographical Patterns in a Recent Invasion. Front Genet 2022; 13:824424. [PMID: 35360868 PMCID: PMC8963341 DOI: 10.3389/fgene.2022.824424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/02/2022] [Indexed: 12/02/2022] Open
Abstract
Patterns of covariation between phenotype and environment are presumed to be reflective of local adaptation, and therefore translate to a meaningful influence on an individual’s overall fitness within that specific environment. However, these environmentally driven patterns may be the result of numerous and interacting processes, such as genetic variation, epigenetic variation, or plastic non-heritable variation. Understanding the relative importance of different environmental variables on underlying genetic patterns and resulting phenotypes is fundamental to understanding adaptation. Invasive systems are excellent models for such investigations, given their propensity for rapid evolution. This study uses reduced representation sequencing data paired with phenotypic data to examine whether important phenotypic traits in invasive starlings (Sturnus vulgaris) within Australia appear to be highly heritable (presumably genetic) or appear to vary with environmental gradients despite underlying genetics (presumably non-heritable plasticity). We also sought to determine which environmental variables, if any, play the strongest role shaping genetic and phenotypic patterns. We determined that environmental variables—particularly elevation—play an important role in shaping allelic trends in Australian starlings and may also reinforce neutral genetic patterns resulting from historic introduction regime. We examined a range of phenotypic traits that appear to be heritable (body mass and spleen mass) or negligibly heritable (e.g. beak surface area and wing length) across the starlings’ Australian range. Using SNP variants associated with each of these phenotypes, we identify key environmental variables that correlate with genetic patterns, specifically that temperature and precipitation putatively play important roles shaping phenotype in this species. Finally, we determine that overall phenotypic variation is correlated with underlying genetic variation, and that these interact positively with the level of vegetation variation within a region, suggesting that ground cover plays an important role in shaping selection and plasticity of phenotypic traits within the starlings of Australia.
Collapse
Affiliation(s)
- Katarina C. Stuart
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Katarina C. Stuart,
| | - William B. Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Adam P.A. Cardilini
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Lee A. Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| |
Collapse
|
10
|
On the genetic architecture of rapidly adapting and convergent life history traits in guppies. Heredity (Edinb) 2022; 128:250-260. [PMID: 35256765 PMCID: PMC8986872 DOI: 10.1038/s41437-022-00512-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 12/29/2022] Open
Abstract
The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- and low-predation environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use four independent F2 QTL crosses to examine the genetic basis of seven (five female, two male) guppy life history phenotypes and discuss how these genetic architectures may facilitate or constrain rapid adaptation and convergence. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many loci of small-effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid, repeatable phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but subsequent genetic redundancy may limit gene re-use across populations, in agreement with an absence of strong signatures of genetic convergence from recent analyses of wild guppies.
Collapse
|
11
|
Duntsch L, Brekke P, Ewen JG, Santure AW. Who are you? A framework to identify and report genetic sample mix-ups. Mol Ecol Resour 2021; 22:1855-1867. [PMID: 34907643 DOI: 10.1111/1755-0998.13575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/28/2022]
Abstract
Sample mix-ups occur when samples have accidentally been duplicated, mislabelled or swapped. When samples are subsequently genotyped or sequenced, this can lead to individual IDs being incorrectly linked to genetic data, resulting in incorrect or biased research results, or reduced power to detect true biological patterns. We surveyed the community and found that almost 80% of responding researchers have encountered sample mix-ups. However, many recent studies in the field of molecular ecology do not appear to systematically report individual assignment checks as part of their publications. Although checks may be done, lack of consistent reporting means that it is difficult to assess whether sample mix-ups have occurred or been detected. Here, we present an easy-to-follow sample verification framework that can utilise existing metadata, including species, population structure, sex and pedigree information. We demonstrate its application to a dataset representing individuals of a threatened Aotearoa New Zealand bird species, the hihi, genotyped on a 50K SNP array. We detected numerous incorrect genotype-ID associations when comparing observed and genetic sex or comparing to relationships in a verified microsatellite pedigree. The framework proposed here helped to confirm 488 individuals (39%), correct another 20 bird-genotype links, and detect hundreds of incorrect sample IDs, emphasizing the value of routinely checking genetic and genomic datasets for their accuracy. We therefore promote the implementation and reporting of this simple yet effective sample verification framework as a standardized quality control step for studies in the field of molecular ecology.
Collapse
Affiliation(s)
- Laura Duntsch
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W Santure
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| |
Collapse
|
12
|
Tietgen L, Hagen IJ, Kleven O, Bernardi CD, Kvalnes T, Norén K, Hasselgren M, Wallén JF, Angerbjörn A, Landa A, Eide NE, Flagstad Ø, Jensen H. Fur colour in the Arctic fox: genetic architecture and consequences for fitness. Proc Biol Sci 2021; 288:20211452. [PMID: 34583587 PMCID: PMC8479361 DOI: 10.1098/rspb.2021.1452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.
Collapse
Affiliation(s)
- Lukas Tietgen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Ingerid J Hagen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Oddmund Kleven
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Cecilia Di Bernardi
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway.,Department of Biology and Biotechnologies 'Charles Darwin', University of Rome La Sapienza, Viale dell' Università 32, Rome 00185, Italy
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Malin Hasselgren
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Johan Fredrik Wallén
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden.,Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Arild Landa
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Nina E Eide
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Øystein Flagstad
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| |
Collapse
|
13
|
McFarlane SE, Pemberton JM. Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland. G3 (BETHESDA, MD.) 2021; 11:jkab274. [PMID: 34568926 PMCID: PMC8473967 DOI: 10.1093/g3journal/jkab274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/16/2021] [Indexed: 12/21/2022]
Abstract
We deployed admixture mapping on a sample of 386 deer from a hybrid swarm between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon) sampled in Kintyre, Scotland to search for quantitative trait loci (QTLs) underpinning phenotypic differences between the species. These two species are highly diverged genetically [Fst between pure species, based on 50K single nucleotide polymorphism (SNPs) = 0.532] and phenotypically: pure red have on average twice the carcass mass of pure sika in our sample (38.7 kg vs 19.1 kg). After controlling for sex, age, and population genetic structure, we found 10 autosomal genomic locations with QTL for carcass mass. Effect sizes ranged from 0.191 to 1.839 kg and as expected, in all cases the allele derived from sika conferred lower carcass mass. The sika population was fixed for all small carcass mass alleles, whereas the red deer population was typically polymorphic. GO term analysis of genes lying in the QTL regions are associated with oxygen transport. Although body mass is a likely target of selection, none of the SNPs marking QTL are introgressing faster or slower than expected in either direction.
Collapse
Affiliation(s)
- S Eryn McFarlane
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Department of Biology, Lund University, 22100 Lund, Sweden
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| |
Collapse
|
14
|
Lee KD, Millar CD, Brekke P, Whibley A, Ewen JG, Hingston M, Zhu A, Santure AW. The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi. Mol Ecol Resour 2021; 22:415-429. [PMID: 34323011 DOI: 10.1111/1755-0998.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or "SNP chips", enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.
Collapse
Affiliation(s)
- Kate D Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Melanie Hingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Amy Zhu
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| |
Collapse
|
15
|
Heterogeneous selection on exploration behavior within and among West European populations of a passerine bird. Proc Natl Acad Sci U S A 2021; 118:2024994118. [PMID: 34234017 DOI: 10.1073/pnas.2024994118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterogeneous selection is often proposed as a key mechanism maintaining repeatable behavioral variation ("animal personality") in wild populations. Previous studies largely focused on temporal variation in selection within single populations. The relative importance of spatial versus temporal variation remains unexplored, despite these processes having distinct effects on local adaptation. Using data from >3,500 great tits (Parus major) and 35 nest box plots situated within five West-European populations monitored over 4 to 18 y, we show that selection on exploration behavior varies primarily spatially, across populations, and study plots within populations. Exploration was, simultaneously, selectively neutral in the average population and year. These findings imply that spatial variation in selection may represent a primary mechanism maintaining animal personalities, likely promoting the evolution of local adaptation, phenotype-dependent dispersal, and nonrandom settlement. Selection also varied within populations among years, which may counteract local adaptation. Our study underlines the importance of combining multiple spatiotemporal scales in the study of behavioral adaptation.
Collapse
|
16
|
Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evol Lett 2021; 5:196-213. [PMID: 34136269 PMCID: PMC8190449 DOI: 10.1002/evl3.227] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/06/2021] [Accepted: 03/29/2021] [Indexed: 01/11/2023] Open
Abstract
Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.
Collapse
Affiliation(s)
- Eva L Koch
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Hernán E Morales
- Evolutionary Genetics Section Globe Institute University of Copenhagen Copenhagen Denmark.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Jenny Larsson
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Anja M Westram
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,IST Austria Klosterneuburg Austria
| | - Rui Faria
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida FL 32306-4120
| | - E Moriarty Lemmon
- Department of Biological Science Florida State University Tallahassee Florida FL 32306-4295
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| |
Collapse
|
17
|
van Oers K, Sepers B, Sies W, Gawehns F, Verhoeven KJF, Laine VN. Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird. Integr Comp Biol 2020; 60:1517-1530. [PMID: 33031487 PMCID: PMC7742756 DOI: 10.1093/icb/icaa138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The search for the hereditary mechanisms underlying quantitative traits traditionally focused on the identification of underlying genomic polymorphisms such as single-nucleotide polymorphisms. It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. It is unclear, however, if and how DNA methylation can stably be transferred from one generation to the next and can thereby be a component of the heritable variation of a trait. In this study, we explore whether DNA methylation responds to phenotypic selection using whole-genome and genome-wide bisulfite approaches. We assessed differential erythrocyte DNA methylation patterns between extreme personality types in the Great Tit (Parus major). For this, we used individuals from a four-generation artificial bi-directional selection experiment and siblings from eight F2 inter-cross families. We find no differentially methylated sites when comparing the selected personality lines, providing no evidence for the so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that the genome-wide DNA methylation profiles of individuals are mainly explained by family structure, indicating that the majority of variation in DNA methylation in CpG sites between individuals can be explained by genetic differences. Although we found some candidates explaining behavioral differences between F2 siblings, we could not confirm this with a whole-genome approach, thereby confirming the absence of epialleles in these F2 intercrosses. We conclude that while epigenetic variation may underlie phenotypic variation in behavioral traits, we were not able to find evidence that DNA methylation can explain heritable variation in personality traits in Great Tits.
Collapse
Affiliation(s)
- Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
- Behavioural Ecology Group, Wageningen University & Research, Wageningen, P.O. Box 338, 6700 AH, the Netherlands
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
- Behavioural Ecology Group, Wageningen University & Research, Wageningen, P.O. Box 338, 6700 AH, the Netherlands
| | - William Sies
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Fleur Gawehns
- Bioinformatics Unit, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| |
Collapse
|
18
|
Höglund A, Henriksen R, Fogelholm J, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The methylation landscape and its role in domestication and gene regulation in the chicken. Nat Ecol Evol 2020; 4:1713-1724. [PMID: 32958860 DOI: 10.1038/s41559-020-01310-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 08/26/2020] [Indexed: 01/06/2023]
Abstract
Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.
Collapse
Affiliation(s)
- Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M Guerrero-Bosagna
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.,Evolutionary Biology Centrum, Dept of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.
| |
Collapse
|
19
|
Ruckman SN, Blackmon H. The March of the Beetles: Epistatic Components Dominate Divergence in Dispersal Tendency in Tribolium castaneum. J Hered 2020; 111:498-505. [PMID: 32798223 PMCID: PMC7525825 DOI: 10.1093/jhered/esaa030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/12/2020] [Indexed: 11/14/2022] Open
Abstract
The genetic underpinnings of traits are rarely simple. Most traits of interest are instead the product of multiple genes acting in concert to determine the phenotype. This is particularly true for behavioral traits, like dispersal. Our investigation focuses on the genetic architecture of dispersal tendency in the red flour beetle, Tribolium castaneum. We used artificial selection to generate lines with either high or low dispersal tendency. Our populations responded quickly in the first generations of selection and almost all replicates had higher dispersal tendency in males than in females. These selection lines were used to create a total of 6 additional lines: F1 and reciprocal F1, as well as 4 types of backcrosses. We estimated the composite genetic effects that contribute to divergence in dispersal tendency among lines using line cross-analysis. We found variation in the dispersal tendency of our lines was best explained by autosomal additive and 3 epistatic components. Our results indicate that dispersal tendency is heritable, but much of the divergence in our selection lines was due to epistatic effects. These results are consistent with other life-history traits that are predicted to maintain more epistatic variance than additive variance and highlight the potential for epistatic variation to act as an adaptive reserve that may become visible to selection when a population is subdivided.
Collapse
Affiliation(s)
- Sarah N Ruckman
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX.,Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, 2475 TAMU, College Station, TX
| | - Heath Blackmon
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX.,Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, 2475 TAMU, College Station, TX
| |
Collapse
|
20
|
Duntsch L, Tomotani BM, de Villemereuil P, Brekke P, Lee KD, Ewen JG, Santure AW. Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi ( Notiomystis cincta). Proc Biol Sci 2020; 287:20200948. [PMID: 32842928 PMCID: PMC7482260 DOI: 10.1098/rspb.2020.0948] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.
Collapse
Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études PSL, MNHN, CNRS, Sorbonne Université, Université des Antilles, Paris, France
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Kate D. Lee
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W. Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| |
Collapse
|
21
|
Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout. G3-GENES GENOMES GENETICS 2020; 10:1929-1947. [PMID: 32284313 PMCID: PMC7263693 DOI: 10.1534/g3.120.401184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char (Salvelinus alpinus) are likely differentiated by three or four chromosomal fissions, possibly one chromosomal fusion, and 6 or more large inversions. Combining centromere mapping information with putative inversion coordinates revealed that the majority of detected inversions differentiating lake trout from other salmonids are pericentric and located on acrocentric and telocentric linkage groups. Our results suggest that speciation and adaptive divergence within the genus Salvelinus may have been associated with multiple pericentric inversions occurring primarily on acrocentric and telocentric chromosomes. The linkage map presented here will be a critical resource for advancing conservation oriented genomic research on lake trout and exploring chromosomal evolution within and between salmonid species.
Collapse
|
22
|
Bubac CM, Miller JM, Coltman DW. The genetic basis of animal behavioural diversity in natural populations. Mol Ecol 2020; 29:1957-1971. [PMID: 32374914 DOI: 10.1111/mec.15461] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/17/2020] [Accepted: 05/01/2020] [Indexed: 12/30/2022]
Abstract
Individual differences in animal behaviour influence ecological and evolutionary processes. Much behavioural variation has a heritable component, suggesting that genetics may play a role in its development. Yet, the study of the mechanistic description linking genes to behaviour in nature remains in its infancy, and such research is considered a challenge in contemporary biology. Here, we performed a literature review and meta-analysis to assess trends in analytical approaches used to investigate the relationship between genes and behaviour in natural systems, specifically candidate gene approaches, quantitative trait locus (QTL) mapping, and genome-wide association studies (GWAS). We aimed to determine the efficacy and success of each approach, while also describing which behaviours and species were examined by researchers most often. We found that the majority of QTL mapping and GWAS results revealed a significant or suggestive effect (Zr = 0.3 [95% CI: 0.25:0.35] and Zr = 0.39 [0.33:0.46], respectively) between the trait of interest and genetic marker(s) tested, while over half of candidate gene accounts (Zr = 0.16 [0.11:0.21]) did not find a significant association. Approximately a third of all study estimates investigated animal personality traits; though, reproductive and migratory behaviours were also well-represented. Our findings show that despite widespread accessibility of molecular approaches given current sequencing technologies, efforts to elucidate the genetic basis of behaviour in free-ranging systems has been limited to relatively few species. We discuss challenges encountered by researchers, and recommend integration of novel genomic methods with longitudinal studies to usher in the next wave of behavioural genomic research.
Collapse
Affiliation(s)
- Christine M Bubac
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
23
|
Gienapp P. Opinion: Is gene mapping in wild populations useful for understanding and predicting adaptation to global change? GLOBAL CHANGE BIOLOGY 2020; 26:2737-2749. [PMID: 32108978 DOI: 10.1111/gcb.15058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 05/22/2023]
Abstract
Changing environmental conditions will inevitably alter selection pressures. Over the long term, populations have to adapt to these altered conditions by evolutionary change to avoid extinction. Quantifying the 'evolutionary potential' of populations to predict whether they will be able to adapt fast enough to forecasted changes is crucial to fully assess the threat for biodiversity posed by climate change. Technological advances in sequencing and high-throughput genotyping have now made genomic studies possible in a wide range of species. Such studies, in theory, allow an unprecedented understanding of the genomics of ecologically relevant traits and thereby a detailed assessment of the population's evolutionary potential. Aimed at a wider audience than only evolutionary geneticists, this paper gives an overview of how gene-mapping studies have contributed to our understanding and prediction of evolutionary adaptations to climate change, identifies potential reasons why their contribution to understanding adaptation to climate change may remain limited, and highlights approaches to study and predict climate change adaptation that may be more promising, at least in the medium term.
Collapse
|
24
|
Sinclair-Waters M, Ødegård J, Korsvoll SA, Moen T, Lien S, Primmer CR, Barson NJ. Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon. Genet Sel Evol 2020; 52:9. [PMID: 32050893 PMCID: PMC7017552 DOI: 10.1186/s12711-020-0529-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 01/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturity is an important life history trait that affects factors such as survival, reproductive success, and growth. Furthermore, age at maturity can seriously impact aquaculture production. Therefore, characterizing the genetic architecture that underlies variation in age at maturity is of key interest. RESULTS Here, we refine our understanding of the genetic architecture for age at maturity of male Atlantic salmon using a genome-wide association study of 11,166 males from a single aquaculture strain, using imputed genotypes at 512,397 single nucleotide polymorphisms (SNPs). All individuals were genotyped with a 50K SNP array and imputed to higher density using parents genotyped with a 930K SNP array and pedigree information. We found significant association signals on 28 of 29 chromosomes (P-values: 8.7 × 10-133-9.8 × 10-8), including two very strong signals spanning the six6 and vgll3 gene regions on chromosomes 9 and 25, respectively. Furthermore, we identified 116 independent signals that tagged 120 candidate genes with varying effect sizes. Five of the candidate genes found here were previously associated with age at maturity in other vertebrates, including humans. DISCUSSION These results reveal a mixed architecture of large-effect loci and a polygenic component that consists of multiple smaller-effect loci, suggesting a more complex genetic architecture of Atlantic salmon age at maturity than previously thought. This more complex architecture will have implications for selection on this key trait in aquaculture and for management of wild salmon populations.
Collapse
Affiliation(s)
- Marion Sinclair-Waters
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland. .,Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Jørgen Ødegård
- AquaGen, Trondheim, Norway.,Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Nicola J Barson
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| |
Collapse
|
25
|
Sparks AM, Watt K, Sinclair R, Pilkington JG, Pemberton JM, McNeilly TN, Nussey DH, Johnston SE. The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries). PLoS Genet 2019; 15:e1008461. [PMID: 31697674 PMCID: PMC6863570 DOI: 10.1371/journal.pgen.1008461] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 11/19/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated livestock or laboratory organisms. While the genetic basis of variation in immune responses have been investigated in these systems, there is a poor understanding of how genetic variation influences immunity in natural, untreated populations living in complex environments. Here, we examine the genetic architecture of variation in immune traits in the Soay sheep of St Kilda, an unmanaged population of sheep infected with strongyle gastrointestinal nematodes. We assayed IgA, IgE and IgG antibodies against the prevalent nematode Teladorsagia circumcincta in the blood plasma of > 3,000 sheep collected over 26 years. Antibody levels were significantly heritable (h2 = 0.21 to 0.57) and highly stable over an individual’s lifespan. IgA levels were strongly associated with a region on chromosome 24 explaining 21.1% and 24.5% of heritable variation in lambs and adults, respectively. This region was adjacent to two candidate loci, Class II Major Histocompatibility Complex Transactivator (CIITA) and C-Type Lectin Domain Containing 16A (CLEC16A). Lamb IgA levels were also associated with the immunoglobulin heavy constant loci (IGH) complex, and adult IgE levels and lamb IgA and IgG levels were associated with the major histocompatibility complex (MHC). This study provides evidence of high heritability of a complex immunological trait under natural conditions and provides the first evidence from a genome-wide study that large effect genes located outside the MHC region exist for immune traits in the wild. Understanding how immune responses vary in natural populations can give an insight into how infection affects the ability of hosts and parasites to survive and reproduce, and how this drives evolutionary and ecological dynamics. Yet, very little is known about how immune responses vary over an individual’s lifetime and how genes contribute to this variation under natural conditions. Our study investigates the genetic architecture of variation in three antibody types, IgA, IgE and IgG in a wild population of Soay sheep on the St Kilda archipelago in North-West Scotland. Using data collected over 26 years, we show that antibody levels have a heritable basis in lambs and adults and are stable over an individual’s lifetime. We also identify several genomic regions with large effects on immune responses. Our study offers the first insights into the genetic control of immunity in a wild population, which is essential to understand how immune profiles vary in challenging natural conditions and how natural selection maintains genetic variation in complex immune traits.
Collapse
Affiliation(s)
- Alexandra M. Sparks
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
| | - Kathryn Watt
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rona Sinclair
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jill G. Pilkington
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Josephine M. Pemberton
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, United Kingdom
| | - Daniel H. Nussey
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan E. Johnston
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
26
|
Class B, Brommer JE, van Oers K. Exploratory behavior undergoes genotype-age interactions in a wild bird. Ecol Evol 2019; 9:8987-8994. [PMID: 31462997 PMCID: PMC6706179 DOI: 10.1002/ece3.5430] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 11/06/2022] Open
Abstract
Animal personality traits are often heritable and plastic at the same time. Indeed, behaviors that reflect an individual's personality can respond to environmental factors or change with age. To date, little is known regarding personality changes during a wild animals' lifetime and even less about stability in heritability of behavior across ages. In this study, we investigated age-related changes in the mean and in the additive genetic variance of exploratory behavior, a commonly used measure of animal personality, in a wild population of great tits. Heritability of exploration is reduced in adults compared to juveniles, with a low genetic correlation across these age classes. A random regression animal model confirmed the occurrence of genotype-age interactions (G×A) in exploration, causing a decrease in additive genetic variance before individuals become 1 year old, and a decline in cross-age genetic correlations between young and increasingly old individuals. Of the few studies investigating G×A in behaviors, this study provides rare evidence for this phenomenon in an extensively studied behavior. We indeed demonstrate that heritability and cross-age genetic correlations in this behavior are not stable over an individual's lifetime, which can affect its potential response to selection. Because G×A is likely to be common in behaviors and have consequences for our understanding of the evolution of animal personality, more attention should be turned to this phenomenon in the future work.
Collapse
Affiliation(s)
- Barbara Class
- Department of BiologyUniversity of TurkuTurkuFinland
| | | | - Kees van Oers
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| |
Collapse
|
27
|
Gompert Z, Brady M, Chalyavi F, Saley TC, Philbin CS, Tucker MJ, Forister ML, Lucas LK. Genomic evidence of genetic variation with pleiotropic effects on caterpillar fitness and plant traits in a model legume. Mol Ecol 2019; 28:2967-2985. [DOI: 10.1111/mec.15113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 04/17/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Zachariah Gompert
- Department of Biology Utah State University Logan Utah USA
- Ecology Center Utah State University Logan Utah USA
| | - Megan Brady
- Department of Biology Utah State University Logan Utah USA
| | | | - Tara C. Saley
- Department of Biology Utah State University Logan Utah USA
- Ecology Center Utah State University Logan Utah USA
| | | | | | | | | |
Collapse
|
28
|
Bosse M, Spurgin LG, Laine VN, Cole EF, Firth JA, Gienapp P, Gosler AG, McMahon K, Poissant J, Verhagen I, Groenen MAM, van Oers K, Sheldon BC, Visser ME, Slate J. Response to Perrier and Charmantier: On the importance of time scales when studying adaptive evolution. Evol Lett 2019; 3:248-253. [PMID: 31171980 PMCID: PMC6546378 DOI: 10.1002/evl3.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/13/2019] [Indexed: 11/26/2022] Open
Affiliation(s)
- Mirte Bosse
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Wageningen University and Research—Animal Breeding and GenomicsWageningenThe Netherlands
| | - Lewis G. Spurgin
- School of Biological SciencesUniversity of East AngliaUnited Kingdom
| | - Veronika N. Laine
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Ella F. Cole
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Josh A. Firth
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Phillip Gienapp
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Andrew G. Gosler
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Keith McMahon
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Jocelyn Poissant
- Department of Ecosystem and Public Health, Faculty of Veterinary MedicineUniversity of CalgaryCanada
| | - Irene Verhagen
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Martien A. M. Groenen
- Wageningen University and Research—Animal Breeding and GenomicsWageningenThe Netherlands
| | - Kees van Oers
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Ben C. Sheldon
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Wageningen University and Research—Animal Breeding and GenomicsWageningenThe Netherlands
| | - Jon Slate
- Department of Animal and Plant SciencesUniversity of SheffieldUnited Kingdom
| |
Collapse
|
29
|
Kemppainen P, Husby A. Accounting for heteroscedasticity and censoring in chromosome partitioning analyses. Evol Lett 2018; 2:599-609. [PMID: 30564443 PMCID: PMC6292708 DOI: 10.1002/evl3.88] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 01/02/2023] Open
Abstract
A fundamental assumption in quantitative genetics is that traits are controlled by many loci of small effect. Using genomic data, this assumption can be tested using chromosome partitioning analyses, where the proportion of genetic variance for a trait explained by each chromosome (h2c), is regressed on its size. However, as h2c‐estimates are necessarily positive (censoring) and the variance increases with chromosome size (heteroscedasticity), two fundamental assumptions of ordinary least squares (OLS) regression are violated. Using simulated and empirical data we demonstrate that these violations lead to incorrect inference of genetic architecture. The degree of bias depends mainly on the number of chromosomes and their size distribution and is therefore specific to the species; using published data across many different species we estimate that not accounting for this effect overall resulted in 28% false positives. We introduce a new and computationally efficient resampling method that corrects for inflation caused by heteroscedasticity and censoring and that works under a large range of dataset sizes and genetic architectures in empirical datasets. Our new method substantially improves the robustness of inferences from chromosome partitioning analyses.
Collapse
Affiliation(s)
- Petri Kemppainen
- Organismal and Evolutionary Biology Research Programme University of Helsinki 00014 Helsinki Finland
| | - Arild Husby
- Organismal and Evolutionary Biology Research Programme University of Helsinki 00014 Helsinki Finland.,Department of Ecology and Genetics Uppsala University 75236 Uppsala Sweden
| |
Collapse
|
30
|
Santure AW, Garant D. Wild GWAS-association mapping in natural populations. Mol Ecol Resour 2018; 18:729-738. [PMID: 29782705 DOI: 10.1111/1755-0998.12901] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/27/2022]
Abstract
The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such "gene mapping" studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment. These studies are also allowing us to gain insight into the evolutionary processes maintaining variation in natural populations, to better understand genotype-by-environment and epistatic interactions and to track the dynamics of allele frequency change at loci contributing to traits under selection. Gene mapping in the wild using genomewide association scans (GWAS) do, however, come with a number of methodological challenges, not least the population structure in space and time inherent to natural populations. We here provide an overview of these challenges, summarize the exciting methodological advances and applications of association mapping in natural populations reported in this special issue and provide some guidelines for future "wild GWAS" research.
Collapse
Affiliation(s)
- Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Dany Garant
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| |
Collapse
|
31
|
Lundregan SL, Hagen IJ, Gohli J, Niskanen AK, Kemppainen P, Ringsby TH, Kvalnes T, Pärn H, Rønning B, Holand H, Ranke PS, Båtnes AS, Selvik LK, Lien S, Saether BE, Husby A, Jensen H. Inferences of genetic architecture of bill morphology in house sparrow using a high-density SNP array point to a polygenic basis. Mol Ecol 2018; 27:3498-3514. [DOI: 10.1111/mec.14811] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/15/2018] [Accepted: 06/28/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Sarah L. Lundregan
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Ingerid J. Hagen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Norwegian Institute for Nature Research; Trondheim Norway
| | - Jostein Gohli
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
| | - Alina K. Niskanen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Department of Ecology and Genetics; University of Oulu; Oulu Finland
| | - Petri Kemppainen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
| | - Thor Harald Ringsby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Thomas Kvalnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Henrik Pärn
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Bernt Rønning
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Håkon Holand
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Peter S. Ranke
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Anna S. Båtnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Linn-Karina Selvik
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics; Department of Animal and Aquacultural Sciences; Faculty of Life Sciences; Norwegian University of Life Sciences; Ås Norway
| | - Bernt-Erik Saether
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Arild Husby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
- Department of Ecology and Genetics; EBC; Uppsala University; Uppsala Sweden
| | - Henrik Jensen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| |
Collapse
|
32
|
Leroy G, Carroll EL, Bruford MW, DeWoody JA, Strand A, Waits L, Wang J. Next-generation metrics for monitoring genetic erosion within populations of conservation concern. Evol Appl 2018; 11:1066-1083. [PMID: 30026798 PMCID: PMC6050182 DOI: 10.1111/eva.12564] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/11/2017] [Indexed: 12/26/2022] Open
Abstract
Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large-effect detrimental alleles, maladaptation and loss of adaptability). Technological advances in genomics now allow the production of data the can be measured by new metrics with improved precision, increased efficiency and the potential to discriminate between neutral diversity (shaped mainly by population size and gene flow) and functional/adaptive diversity (shaped mainly by selection), allowing the assessment of management-relevant genetic markers. The requirements of such studies in terms of sample size and marker density largely depend on the kind of population monitored, the questions to be answered and the metrics employed. We discuss prospects for the integration of this new information and metrics into conservation monitoring programmes.
Collapse
Affiliation(s)
- Gregoire Leroy
- Food and Agriculture Organization (FAO) of the United Nations, Animal Production and Health DivisionRomeItaly
| | - Emma L. Carroll
- Scottish Oceans Institute and School of BiologyUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places InstituteCardiff UniversityCardiffUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Allan Strand
- Department of BiologyGrice Marine Laboratory, College of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
| |
Collapse
|
33
|
Ramakers JJC, Culina A, Visser ME, Gienapp P. Environmental coupling of heritability and selection is rare and of minor evolutionary significance in wild populations. Nat Ecol Evol 2018; 2:1093-1103. [PMID: 29915341 PMCID: PMC6027994 DOI: 10.1038/s41559-018-0577-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/15/2018] [Indexed: 01/01/2023]
Abstract
Predicting the rate of adaptation to environmental change in wild populations is important for understanding evolutionary change. However, predictions may be unreliable if the two key variables affecting the rate of evolutionary change-heritability and selection-are both affected by the same environmental variable. To determine how general such an environmentally induced coupling of heritability and selection is, and how this may influence the rate of adaptation, we made use of freely accessible, open data on pedigreed wild populations to answer this question at the broadest possible scale. Using 16 populations from 10 vertebrate species, which provided data on 50 traits (relating to body mass, morphology, physiology, behaviour and life history), we found evidence for an environmentally induced relationship between heritability and selection in only 6 cases, with weak evidence that this resulted in an increase or decrease in the expected selection response. We conclude that such a coupling of heritability and selection is unlikely to strongly affect evolutionary change, even though both heritability and selection are commonly postulated to be dependent on the environment.
Collapse
Affiliation(s)
- Jip J C Ramakers
- Department of Animal Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands.
| | - Antica Culina
- Department of Animal Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| |
Collapse
|
34
|
Perrier C, Delahaie B, Charmantier A. Heritability estimates from genomewide relatedness matrices in wild populations: Application to a passerine, using a small sample size. Mol Ecol Resour 2018; 18:838-853. [DOI: 10.1111/1755-0998.12886] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 01/16/2023]
Affiliation(s)
- C. Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS‐UMR5175 CEFE Montpellier France
| | - B. Delahaie
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS‐UMR5175 CEFE Montpellier France
| | - A. Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS‐UMR5175 CEFE Montpellier France
| |
Collapse
|
35
|
Hansson B, Sigeman H, Stervander M, Tarka M, Ponnikas S, Strandh M, Westerdahl H, Hasselquist D. Contrasting results from GWAS and QTL mapping on wing length in great reed warblers. Mol Ecol Resour 2018; 18:867-876. [DOI: 10.1111/1755-0998.12785] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Martin Stervander
- Department of Biology Lund University Lund Sweden
- Institute of Ecology and Evolution University of Oregon Eugene Oregon
| | - Maja Tarka
- Department of Biology Lund University Lund Sweden
| | | | | | | | | |
Collapse
|
36
|
Schielzeth H, Rios Villamil A, Burri R. Success and failure in replication of genotype-phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations? Mol Ecol Resour 2018; 18:739-754. [PMID: 29575806 DOI: 10.1111/1755-0998.12780] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 12/29/2022]
Abstract
Recent developments in sequencing technologies have facilitated genomewide mapping of phenotypic variation in natural populations. Such mapping efforts face a number of challenges potentially leading to low reproducibility. However, reproducible research forms the basis of scientific progress. We here discuss the options for replication and the reasons for potential nonreproducibility. We then review the evidence for reproducible quantitative trait loci (QTL) with a focus on natural animal populations. Existing case studies of replication fall into three categories: (i) traits that have been mapped to major effect loci (including chromosomal inversion and supergenes) by independent research teams; (ii) QTL fine-mapped in discovery populations; and (iii) attempts to replicate QTL across multiple populations. Major effect loci, in particular those associated with inversions, have been successfully replicated in several cases within and across populations. Beyond such major effect variants, replication has been more successful within than across populations, suggesting that QTL discovered in natural populations may often be population-specific. This suggests that biological causes (differences in linkage patterns, allele frequencies or context-dependencies of QTL) contribute to nonreproducibility. Evidence from other fields, notably animal breeding and QTL mapping in humans, suggests that a significant fraction of QTL is indeed reproducible in direction and magnitude at least within populations. However, there is also a large number of QTL that cannot be easily reproduced. We put forward that more studies should explicitly address the causes and context-dependencies of QTL signals, in particular to disentangle linkage differences, allele frequency differences and gene-by-environment interactions as biological causes of nonreproducibility of QTL, especially between populations.
Collapse
Affiliation(s)
- Holger Schielzeth
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Alejandro Rios Villamil
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Reto Burri
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| |
Collapse
|
37
|
Kim JM, Santure AW, Barton HJ, Quinn JL, Cole EF, Visser ME, Sheldon BC, Groenen MAM, van Oers K, Slate J. A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour. Mol Ecol Resour 2018; 18:877-891. [PMID: 29573186 DOI: 10.1111/1755-0998.12778] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 12/25/2022]
Abstract
High-density SNP microarrays ("SNP chips") are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high-density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.
Collapse
Affiliation(s)
- J-M Kim
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, Korea
| | - A W Santure
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - H J Barton
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
| | - J L Quinn
- School of Biological, Earth and Environmental Science (BEES), University College Cork, Cork, Ireland
| | - E F Cole
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | | | - M E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - B C Sheldon
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - M A M Groenen
- Wageningen University and Research - Animal Breeding and Genomics, Wageningen, Netherlands
| | - K van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - J Slate
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
| |
Collapse
|
38
|
Lucas LK, Nice CC, Gompert Z. Genetic constraints on wing pattern variation in
Lycaeides
butterflies: A case study on mapping complex, multifaceted traits in structured populations. Mol Ecol Resour 2018. [DOI: 10.1111/1755-0998.12777] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Chris C. Nice
- Department of Biology Texas State University San Marcos TX USA
| | - Zachariah Gompert
- Department of Biology Utah State University Logan UT USA
- Ecology Center Utah State University Logan UT USA
| |
Collapse
|
39
|
Kemppainen P, Husby A. Inference of genetic architecture from chromosome partitioning analyses is sensitive to genome variation, sample size, heritability and effect size distribution. Mol Ecol Resour 2018. [DOI: 10.1111/1755-0998.12774] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Petri Kemppainen
- Metapopulation Research Centre Department of Biosciences University of Helsinki Helsinki Finland
| | - Arild Husby
- Metapopulation Research Centre Department of Biosciences University of Helsinki Helsinki Finland
- Department of Ecology and Genetics (Evolutionary Biology) EBC Uppsala University Uppsala Sweden
| |
Collapse
|
40
|
Guðbrandsson J, Franzdóttir SR, Kristjánsson BK, Ahi EP, Maier VH, Kapralova KH, Snorrason SS, Jónsson ZO, Pálsson A. Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs. PeerJ 2018; 6:e4345. [PMID: 29441236 PMCID: PMC5807978 DOI: 10.7717/peerj.4345] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/19/2018] [Indexed: 02/06/2023] Open
Abstract
Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3'-bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and translin (tsn). The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.
Collapse
Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Freshwater Division, Marine and Freshwater Research Institute, Reykjavík, Iceland
| | - Sigríður Rut Franzdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | - Ehsan Pashay Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Karl-Franzens-Universität, Graz, Austria
| | - Valerie Helene Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | | | - Zophonías Oddur Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| |
Collapse
|
41
|
Gienapp P, Fior S, Guillaume F, Lasky JR, Sork VL, Csilléry K. Genomic Quantitative Genetics to Study Evolution in the Wild. Trends Ecol Evol 2017; 32:897-908. [PMID: 29050794 DOI: 10.1016/j.tree.2017.09.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022]
Abstract
Quantitative genetic theory provides a means of estimating the evolutionary potential of natural populations. However, this approach was previously only feasible in systems where the genetic relatedness between individuals could be inferred from pedigrees or experimental crosses. The genomic revolution opened up the possibility of obtaining the realized proportion of genome shared among individuals in natural populations of virtually any species, which could promise (more) accurate estimates of quantitative genetic parameters in virtually any species. Such a 'genomic' quantitative genetics approach relies on fewer assumptions, offers a greater methodological flexibility, and is thus expected to greatly enhance our understanding of evolution in natural populations, for example, in the context of adaptation to environmental change, eco-evolutionary dynamics, and biodiversity conservation.
Collapse
Affiliation(s)
- Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
| | - Simone Fior
- Plant Ecological Genetics, ETH Zurich, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Katalin Csilléry
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland; Biodiversity and Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| |
Collapse
|
42
|
Sutherland BJG, Rico C, Audet C, Bernatchez L. Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis. G3 (BETHESDA, MD.) 2017; 7:2749-2762. [PMID: 28626004 PMCID: PMC5555479 DOI: 10.1534/g3.117.040915] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/13/2017] [Indexed: 02/06/2023]
Abstract
Whole-genome duplication (WGD) can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e., heterochiasmy), which is also poorly understood. The family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have nonhomologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species and four genera). Although nonhomology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify quantitative trait loci (QTL) for 21 unique growth, reproductive, and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.
Collapse
Affiliation(s)
- Ben J G Sutherland
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Ciro Rico
- School of Marine Studies, Molecular Diagnostics Laboratory, University of the South Pacific, Suva, Fiji
- Department of Wetland Ecology, Estación Biológica de Doñana (EBD-CSIC), 41092 Sevilla, Spain
| | - Céline Audet
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Quebec G5L 3A1, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| |
Collapse
|
43
|
Saastamoinen M, Bocedi G, Cote J, Legrand D, Guillaume F, Wheat CW, Fronhofer EA, Garcia C, Henry R, Husby A, Baguette M, Bonte D, Coulon A, Kokko H, Matthysen E, Niitepõld K, Nonaka E, Stevens VM, Travis JMJ, Donohue K, Bullock JM, Del Mar Delgado M. Genetics of dispersal. Biol Rev Camb Philos Soc 2017; 93:574-599. [PMID: 28776950 PMCID: PMC5811798 DOI: 10.1111/brv.12356] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 12/12/2022]
Abstract
Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal‐related phenotypes or evidence for the micro‐evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment‐dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non‐additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non‐equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context‐dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.
Collapse
Affiliation(s)
- Marjo Saastamoinen
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Greta Bocedi
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K
| | - Julien Cote
- Laboratoire Évolution & Diversité Biologique UMR5174, CNRS, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Delphine Legrand
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Christopher W Wheat
- Population Genetics, Department of Zoology, Stockholm University, S-10691 Stockholm, Sweden
| | - Emanuel A Fronhofer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland
| | - Cristina Garcia
- CIBIO-InBIO, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Roslyn Henry
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K.,School of GeoSciences, University of Edinburgh, Edinburgh EH89XP, U.K
| | - Arild Husby
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Michel Baguette
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France.,Museum National d'Histoire Naturelle, Institut Systématique, Evolution, Biodiversité, UMR 7205, F-75005 Paris, France
| | - Dries Bonte
- Department of Biology, Ghent University, B-9000 Ghent, Belgium
| | - Aurélie Coulon
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Biogéographie et Ecologie des Vertébrés, 34293 Montpellier, France.,CESCO UMR 7204, Bases écologiques de la conservation, Muséum national d'Histoire naturelle, 75005 Paris, France
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Kristjan Niitepõld
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Etsuko Nonaka
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Virginie M Stevens
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France
| | - Justin M J Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K
| | | | - James M Bullock
- NERC Centre for Ecology & Hydrology, Wallingford OX10 8BB, U.K
| | | |
Collapse
|
44
|
Silva CNS, McFarlane SE, Hagen IJ, Rönnegård L, Billing AM, Kvalnes T, Kemppainen P, Rønning B, Ringsby TH, Sæther BE, Qvarnström A, Ellegren H, Jensen H, Husby A. Insights into the genetic architecture of morphological traits in two passerine bird species. Heredity (Edinb) 2017; 119:197-205. [PMID: 28613280 DOI: 10.1038/hdy.2017.29] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/08/2017] [Accepted: 05/04/2017] [Indexed: 01/15/2023] Open
Abstract
Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (VP), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of VP). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.
Collapse
Affiliation(s)
- C N S Silva
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland
| | - S E McFarlane
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - I J Hagen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - L Rönnegård
- School of Technology and Business Studies, Dalarna University, Falun, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A M Billing
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - T Kvalnes
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - P Kemppainen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - B Rønning
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - T H Ringsby
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - B-E Sæther
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - H Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - H Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Husby
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
45
|
Delahaie B, Charmantier A, Chantepie S, Garant D, Porlier M, Teplitsky C. Conserved G-matrices of morphological and life-history traits among continental and island blue tit populations. Heredity (Edinb) 2017; 119:76-87. [PMID: 28402327 DOI: 10.1038/hdy.2017.15] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/31/2022] Open
Abstract
The genetic variance-covariance matrix (G-matrix) summarizes the genetic architecture of multiple traits. It has a central role in the understanding of phenotypic divergence and the quantification of the evolutionary potential of populations. Laboratory experiments have shown that G-matrices can vary rapidly under divergent selective pressures. However, because of the demanding nature of G-matrix estimation and comparison in wild populations, the extent of its spatial variability remains largely unknown. In this study, we investigate spatial variation in G-matrices for morphological and life-history traits using long-term data sets from one continental and three island populations of blue tit (Cyanistes caeruleus) that have experienced contrasting population history and selective environment. We found no evidence for differences in G-matrices among populations. Interestingly, the phenotypic variance-covariance matrices (P) were divergent across populations, suggesting that using P as a substitute for G may be inadequate. These analyses also provide the first evidence in wild populations for additive genetic variation in the incubation period (that is, the period between last egg laid and hatching) in all four populations. Altogether, our results suggest that G-matrices may be stable across populations inhabiting contrasted environments, therefore challenging the results of previous simulation studies and laboratory experiments.
Collapse
Affiliation(s)
- B Delahaie
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-UMR5175 CEFE, Montpellier, France
| | - A Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-UMR5175 CEFE, Montpellier, France
| | - S Chantepie
- Laboratoire d'Écologie Alpine, Université Grenoble Alpes, Unité Mixte de Recherche 5533 CNRS, Grenoble, France
| | - D Garant
- Département de biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - M Porlier
- Département de biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - C Teplitsky
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-UMR5175 CEFE, Montpellier, France
| |
Collapse
|
46
|
Huisman J. Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond. Mol Ecol Resour 2017; 17:1009-1024. [PMID: 28271620 PMCID: PMC6849609 DOI: 10.1111/1755-0998.12665] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/02/2016] [Accepted: 02/24/2017] [Indexed: 11/30/2022]
Abstract
Data on hundreds or thousands of single nucleotide polymorphisms (SNPs) provide detailed information about the relationships between individuals, but currently few tools can turn this information into a multigenerational pedigree. I present the r package sequoia, which assigns parents, clusters half-siblings sharing an unsampled parent and assigns grandparents to half-sibships. Assignments are made after consideration of the likelihoods of all possible first-, second- and third-degree relationships between the focal individuals, as well as the traditional alternative of being unrelated. This careful exploration of the local likelihood surface is implemented in a fast, heuristic hill-climbing algorithm. Distinction between the various categories of second-degree relatives is possible when likelihoods are calculated conditional on at least one parent of each focal individual. Performance was tested on simulated data sets with realistic genotyping error rate and missingness, based on three different large pedigrees (N = 1000-2000). This included a complex pedigree with overlapping generations, occasional close inbreeding and some unknown birth years. Parentage assignment was highly accurate down to about 100 independent SNPs (error rate <0.1%) and fast (<1 min) as most pairs can be excluded from being parent-offspring based on opposite homozygosity. For full pedigree reconstruction, 40% of parents were assumed nongenotyped. Reconstruction resulted in low error rates (<0.3%), high assignment rates (>99%) in limited computation time (typically <1 h) when at least 200 independent SNPs were used. In three empirical data sets, relatedness estimated from the inferred pedigree was strongly correlated to genomic relatedness.
Collapse
Affiliation(s)
- Jisca Huisman
- Ashworth Laboratories, School of Biological Sciences, Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| |
Collapse
|
47
|
Knief U, Schielzeth H, Backström N, Hemmrich‐Stanisak G, Wittig M, Franke A, Griffith SC, Ellegren H, Kempenaers B, Forstmeier W. Association mapping of morphological traits in wild and captive zebra finches: reliable within, but not between populations. Mol Ecol 2017; 26:1285-1305. [DOI: 10.1111/mec.14009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 12/05/2016] [Accepted: 12/21/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Holger Schielzeth
- Department of Population Ecology Friedrich Schiller University Jena 07743 Jena Germany
| | - Niclas Backström
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | | | - Michael Wittig
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Simon C. Griffith
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
- School of Biological, Earth & Environmental Sciences University of New South Wales Sydney NSW 2057 Australia
| | - Hans Ellegren
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| |
Collapse
|
48
|
Hughes KA, Leips J. Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses. Ann N Y Acad Sci 2017; 1389:76-91. [PMID: 27936291 PMCID: PMC5318229 DOI: 10.1111/nyas.13256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/10/2016] [Accepted: 08/22/2016] [Indexed: 12/20/2022]
Abstract
Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.
Collapse
Affiliation(s)
- Kimberly A. Hughes
- Department of Biological Science, Florida State University, Tallahassee, Florida
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland
| |
Collapse
|
49
|
Gagnaire PA, Gaggiotti OE. Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches. Curr Zool 2016; 62:603-616. [PMID: 29491948 PMCID: PMC5804256 DOI: 10.1093/cz/zow088] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/21/2016] [Indexed: 12/27/2022] Open
Abstract
Highly fecund marine species with dispersive life-history stages often display large population sizes and wide geographic distribution ranges. Consequently, they are expected to experience reduced genetic drift, efficient selection fueled by frequent adaptive mutations, and high migration loads. This has important consequences for understanding how local adaptation proceeds in the sea. A key issue in this regard, relates to the genetic architecture underlying fitness traits. Theory predicts that adaptation may involve many genes but with a high variance in effect size. Therefore, the effect of selection on allele frequencies may be substantial for the largest effect size loci, but insignificant for small effect genes. In such a context, the performance of population genomic methods to unravel the genetic basis of adaptation depends on the fraction of adaptive genetic variance explained by the cumulative effect of outlier loci. Here, we address some methodological challenges associated with the detection of local adaptation using molecular approaches. We provide an overview of genome scan methods to detect selection, including those assuming complex demographic models that better describe spatial population structure. We then focus on quantitative genetics approaches that search for genotype-phenotype associations at different genomic scales, including genome-wide methods evaluating the cumulative effect of variants. We argue that the limited power of single locus tests can be alleviated by the use of polygenic scores to estimate the joint contribution of candidate variants to phenotypic variation.
Collapse
Affiliation(s)
- Pierre-Alexandre Gagnaire
- Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
- ISEM – CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète, 34200, France
| | - Oscar E. Gaggiotti
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, KY16 9LB, UK
| |
Collapse
|
50
|
Poissant J, Morrissey MB, Gosler AG, Slate J, Sheldon BC. Multivariate selection and intersexual genetic constraints in a wild bird population. J Evol Biol 2016; 29:2022-2035. [PMID: 27338121 DOI: 10.1111/jeb.12925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/03/2016] [Accepted: 06/22/2016] [Indexed: 01/18/2023]
Abstract
When selection differs between the sexes for traits that are genetically correlated between the sexes, there is potential for the effect of selection in one sex to be altered by indirect selection in the other sex, a situation commonly referred to as intralocus sexual conflict (ISC). While potentially common, ISC has rarely been studied in wild populations. Here, we studied ISC over a set of morphological traits (wing length, tarsus length, bill depth and bill length) in a wild population of great tits (Parus major) from Wytham Woods, UK. Specifically, we quantified the microevolutionary impacts of ISC by combining intra- and intersex additive genetic (co)variances and sex-specific selection estimates in a multivariate framework. Large genetic correlations between homologous male and female traits combined with evidence for sex-specific multivariate survival selection suggested that ISC could play an appreciable role in the evolution of this population. Together, multivariate sex-specific selection and additive genetic (co)variance for the traits considered accounted for additive genetic variance in fitness that was uncorrelated between the sexes (cross-sex genetic correlation = -0.003, 95% CI = -0.83, 0.83). Gender load, defined as the reduction in a population's rate of adaptation due to sex-specific effects, was estimated at 50% (95% CI = 13%, 86%). This study provides novel insights into the evolution of sexual dimorphism in wild populations and illustrates how quantitative genetics and selection analyses can be combined in a multivariate framework to quantify the microevolutionary impacts of ISC.
Collapse
Affiliation(s)
- J Poissant
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK. .,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
| | - M B Morrissey
- School of Biology, University of St Andrews, St Andrews, UK
| | - A G Gosler
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - J Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - B C Sheldon
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| |
Collapse
|