1
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Saatoglu D, Lundregan SL, Fetterplace E, Goedert D, Husby A, Niskanen AK, Muff S, Jensen H. The genetic basis of dispersal in a vertebrate metapopulation. Mol Ecol 2024; 33:e17295. [PMID: 38396362 DOI: 10.1111/mec.17295] [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: 08/18/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Dispersal affects evolutionary processes by changing population size and genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbour adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal among successfully recruited individuals in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological data set and high-density single-nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), and found a relationship between dispersal probability and a SNP located near genes known to regulate circadian rhythm, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (σA 2 ), which composes 10% of the total variation in dispersal probability. Finally, we investigated differences in σA 2 across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic groups animal model. We found different adaptive potentials across habitats, with higher mean breeding value, σA 2 , and heritability for the habitat presenting lower dispersal rates, suggesting also different roles of environmental variation. Our results suggest a complex genetic architecture of dispersal and demonstrate that adaptive potential may be environment dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment dependence and consequent spatial variation are likely to become ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.
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Affiliation(s)
- Dilan Saatoglu
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sarah L Lundregan
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Evelyn Fetterplace
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Debora Goedert
- 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
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Alina K Niskanen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Stefanie Muff
- Department of Mathematical Sciences, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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2
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Westergren M, Archambeau J, Bajc M, Damjanić R, Theraroz A, Kraigher H, Oddou-Muratorio S, González-Martínez SC. Low but significant evolutionary potential for growth, phenology and reproduction traits in European beech. Mol Ecol 2023. [PMID: 37962106 DOI: 10.1111/mec.17196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/23/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.
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Affiliation(s)
| | | | - Marko Bajc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Rok Damjanić
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | | | | | - Sylvie Oddou-Muratorio
- INRAE, URFM, Avignon, France
- INRAE, Univ. de Pau et des Pays de l'Adour, E2S UPPA, ECOBIOP, Saint-Pée-sur-Nivelle, France
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3
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Oakley CG, Schemske DW, McKay JK, Ågren J. Ecological genetics of local adaptation in Arabidopsis: An 8-year field experiment. Mol Ecol 2023; 32:4570-4583. [PMID: 37317048 DOI: 10.1111/mec.17045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic trade-offs? Here we address these questions in the self-pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RILs) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first 3 years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found 10 adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden, respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The 8-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous 3-year study, identifying one new genetic trade-off and resolving one genetic trade-off into two conditionally adaptive QTL.
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Affiliation(s)
- Christopher G Oakley
- Department of Botany and Plant Pathology, and the Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Douglas W Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, Michigan, USA
| | - John K McKay
- College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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4
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Sinclair-Waters M, Nome T, Wang J, Lien S, Kent MP, Sægrov H, Florø-Larsen B, Bolstad GH, Primmer CR, Barson NJ. Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods. Heredity (Edinb) 2022; 129:356-365. [PMID: 36357776 PMCID: PMC9709158 DOI: 10.1038/s41437-022-00570-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 11/12/2022] Open
Abstract
Characterizing the role of different mutational effect sizes in the evolution of fitness-related traits has been a major goal in evolutionary biology for a century. Such characterization in a diversity of systems, both model and non-model, will help to understand the genetic processes underlying fitness variation. However, well-characterized genetic architectures of such traits in wild populations remain uncommon. In this study, we used haplotype-based and multi-SNP Bayesian association methods with sequencing data for 313 individuals from wild populations to test the mutational composition of known candidate regions for sea age at maturation in Atlantic salmon (Salmo salar). We detected an association at five loci out of 116 candidates previously identified in an aquaculture strain with maturation timing in wild Atlantic salmon. We found that at four of these five loci, variation explained by the locus was predominantly driven by a single SNP suggesting the genetic architecture of this trait includes multiple loci with simple, non-clustered alleles and a locus with potentially more complex alleles. This highlights the diversity of genetic architectures that can exist for fitness-related traits. Furthermore, this study provides a useful multi-SNP framework for future work using sequencing data to characterize genetic variation underlying phenotypes in wild populations.
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Affiliation(s)
- Marion Sinclair-Waters
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences University of Helsinki, Helsinki, Finland.
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Torfinn Nome
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jing Wang
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Key laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew P Kent
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Geir H Bolstad
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), 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
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5
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Prapas D, Scalone R, Lee J, Nurkowski KA, Bou‐assi S, Rieseberg L, Battlay P, Hodgins KA. Quantitative trait loci mapping reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed. Evol Appl 2022; 15:1249-1263. [PMID: 36051461 PMCID: PMC9423086 DOI: 10.1111/eva.13453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 01/09/2023] Open
Abstract
Biological invasions offer a unique opportunity to investigate evolution over contemporary timescales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasive common ragweed (Ambrosia artemisiifolia). Flowering time adaptation is key to this annual species' invasion success, so much so that it has evolved repeated latitudinal clines in size and phenology across its native and introduced ranges despite high gene flow among populations. Here, we produced a high-density linkage map (4493 SNPs) and paired this with phenotypic data from an F2 mapping population (n = 336) to identify one major and two minor quantitative trait loci (QTL) underlying flowering time and height differentiation in this species. Within each QTL interval, several candidate flowering time genes were also identified. Notably, the major flowering time QTL detected in this study was found to overlap with a previously identified haploblock (putative inversion). Multiple genetic maps of this region identified evidence of suppressed recombination in specific genotypes, consistent with inversions. These discoveries support the expectation that a concentrated genetic architecture with fewer, larger, and more tightly linked alleles should underlie rapid local adaptation during invasion, particularly when divergently adapting populations experience high levels of gene flow.
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Affiliation(s)
- Diana Prapas
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology CenterSwedish University of Agricultural SciencesUppsalaSweden
- Department of Grapevine BreedingHochschule Geisenheim UniversityGeisenheimGermany
| | - Jacqueline Lee
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kristin A. Nurkowski
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Sarah Bou‐assi
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Loren Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Paul Battlay
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kathryn A. Hodgins
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
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6
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Kitano J, Ishikawa A, Ravinet M, Courtier-Orgogozo V. Genetic basis of speciation and adaptation: from loci to causative mutations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200503. [PMID: 35634921 PMCID: PMC9149796 DOI: 10.1098/rstb.2020.0503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Does evolution proceed in small steps or large leaps? How repeatable is evolution? How constrained is the evolutionary process? Answering these long-standing questions in evolutionary biology is indispensable for both understanding how extant biodiversity has evolved and predicting how organisms and ecosystems will respond to changing environments in the future. Understanding the genetic basis of phenotypic diversification and speciation in natural populations is key to properly answering these questions. The leap forward in genome sequencing technologies has made it increasingly easier to not only investigate the genetic architecture but also identify the variant sites underlying adaptation and speciation in natural populations. Furthermore, recent advances in genome editing technologies are making it possible to investigate the functions of each candidate gene in organisms from natural populations. In this article, we discuss how these recent technological advances enable the analysis of causative genes and mutations and how such analysis can help answer long-standing evolutionary biology questions. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Laboratory of Molecular Ecological Genetics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Chiba 277-8562, Japan
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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7
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Thompson KA, Peichel CL, Rennison DJ, McGee MD, Albert AYK, Vines TH, Greenwood AK, Wark AR, Brandvain Y, Schumer M, Schluter D. Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent. PLoS Biol 2022; 20:e3001469. [PMID: 35007278 PMCID: PMC8746713 DOI: 10.1371/journal.pbio.3001469] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/04/2021] [Indexed: 12/25/2022] Open
Abstract
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
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Affiliation(s)
- Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
| | - Catherine L. Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diana J. Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Timothy H. Vines
- DataSeer Research Data Services, Vancouver, British Columbia, Canada
| | | | - Abigail R. Wark
- Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Maryland, United States of America
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
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8
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Connallon T, Hodgins KA. Allen Orr and the genetics of adaptation. Evolution 2021; 75:2624-2640. [PMID: 34606622 DOI: 10.1111/evo.14372] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023]
Abstract
Over most of the 20th century, evolutionary biologists predominantly subscribed to a strong form of "micro-mutationism," in which adaptive phenotypic divergence arises from allele frequency changes at many loci, each with a small effect on the phenotype. To be sure, there were well-known examples of large-effect alleles contributing to adaptation, yet such cases were generally regarded as atypical and unrepresentative of evolutionary change in general. In 1998, Allen Orr published a landmark theoretical paper in Evolution, which showed that both small- and large-effect mutations are likely to contribute to "adaptive walks" of a population to an optimum. Coupled with a growing set of empirical examples of large-effect alleles contributing to divergence (e.g., from QTL studies), Orr's paper provided a mathematical formalism that converted many evolutionary biologists from micro-mutationism to a more pluralistic perspective on the genetic basis of evolutionary change. We revisit the theoretical insights emerging from Orr's paper within the historical context leading up to 1998, and track the influence of this paper on the field of evolutionary biology through an examination of its citations over the last two decades and an analysis of the extensive body of theoretical and empirical research that Orr's pioneering paper inspired.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Australia
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9
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Twining CW, Bernhardt JR, Derry AM, Hudson CM, Ishikawa A, Kabeya N, Kainz MJ, Kitano J, Kowarik C, Ladd SN, Leal MC, Scharnweber K, Shipley JR, Matthews B. The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification. Ecol Lett 2021; 24:1709-1731. [PMID: 34114320 DOI: 10.1111/ele.13771] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/20/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022]
Abstract
The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.
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Affiliation(s)
- Cornelia W Twining
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Limnological Institute, University of Konstanz, Konstanz-Egg, Germany
| | - Joey R Bernhardt
- Department of Biology, McGill University, Montréal, QC, Canada.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Cameron M Hudson
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology (TUMSAT, Tokyo, Japan
| | - Martin J Kainz
- WasserCluster Lunz-Inter-university Center for Aquatic Ecosystems Research, Lunz am See, Austria
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Carmen Kowarik
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Sarah Nemiah Ladd
- Ecosystem Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Miguel C Leal
- ECOMARE and CESAM - Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Kristin Scharnweber
- Department of Ecology and Genetics; Limnology, Uppsala University, Uppsala, Sweden.,University of Potsdam, Plant Ecology and Nature Conservation, Potsdam-Golm, Germany
| | - Jeremy R Shipley
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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10
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Coughlan JM, Brown MW, Willis JH. The genetic architecture and evolution of life-history divergence among perennials in the Mimulus guttatus species complex. Proc Biol Sci 2021; 288:20210077. [PMID: 33823671 PMCID: PMC8059554 DOI: 10.1098/rspb.2021.0077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
Ecological divergence is a fundamental source of phenotypic diversity between closely related species, yet the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial divergent selection on both complex, correlated suites of traits (such as life-history), as well as novel adaptations. We use the Mimulus guttatus species complex to assess if the divergence in elevation is accompanied by trait divergence in a group of closely related perennials and determine the genetic architecture of this divergence. We find that divergence in elevation is associated with differences in life-history, as well as a unique trait, the production of rhizomes. The divergence between two perennials is largely explained by few mid-to-large effect quantitative trait loci (QTLs). However, the presence of QTLs with correlated, but opposing effects on multiple traits leads to some hybrids with transgressive trait combinations. Lastly, we find that the genetic architecture of the ability to produce rhizomes changes through development, wherein most hybrids produce rhizomes, but only later in development. Our results suggest that elevational differences may shape life-history divergence between perennials, but aspects of the genetic architecture of divergence may have implications for hybrid fitness in nature.
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Affiliation(s)
- Jenn M. Coughlan
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
- Biology Department, University of North Carolina, 250 Bell Tower Dr., Chapel Hill, NC 27599, USA
| | - Maya Wilson Brown
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI 48824, USA
| | - John H. Willis
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
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11
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Monroe JG, McKay JK, Weigel D, Flood PJ. The population genomics of adaptive loss of function. Heredity (Edinb) 2021; 126:383-395. [PMID: 33574599 PMCID: PMC7878030 DOI: 10.1038/s41437-021-00403-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 12/23/2022] Open
Abstract
Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.
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Affiliation(s)
- J Grey Monroe
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA.
| | - John K McKay
- College of Agriculture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Pádraic J Flood
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Department of Plant Breeding, Wageningen University, Wageningen, The Netherlands
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12
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Leon RG, Dunne JC, Gould F. The role of population and quantitative genetics and modern sequencing technologies to understand evolved herbicide resistance and weed fitness. PEST MANAGEMENT SCIENCE 2021; 77:12-21. [PMID: 32633005 PMCID: PMC7754128 DOI: 10.1002/ps.5988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 05/11/2023]
Abstract
Evolution of resistance to multiple herbicides with different sites of action and of nontarget site resistance (NTSR) often involves multiple genes. Thus, single-gene analyses, typical in studies of target site resistance, are not sufficient for understanding the genetic architecture and dynamics of NTSR and multiple resistance. The genetics of weed adaptation to varied agricultural environments is also generally expected to be polygenic. Recent advances in whole-genome sequencing as well as bioinformatic and statistical tools have made it possible to use population and quantitative genetics methods to expand our understanding of how resistance and other traits important for weed adaptation are genetically controlled at the individual and population levels, and to predict responses to selection pressure by herbicides and other environmental factors. The use of tools such as quantitative trait loci mapping, genome-wide association studies, and genomic prediction will allow pest management scientists to better explain how pests adapt to control tools and how specific genotypes thrive and spread across agroecosystems and other human-disturbed systems. The challenge will be to use this knowledge in developing integrated weed management systems that inhibit broad resistance to current and future weed-control methods. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ramon G Leon
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Jeffrey C Dunne
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Fred Gould
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNCUSA
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13
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Sanderson BJ, Park S, Jameel MI, Kraft JC, Thomashow MF, Schemske DW, Oakley CG. Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual. AMERICAN JOURNAL OF BOTANY 2020; 107:250-261. [PMID: 31762012 PMCID: PMC7065183 DOI: 10.1002/ajb2.1385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/14/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Italy and Sweden provides an essential foundation for uncovering the genotype-phenotype-fitness map for an adaptive response to a key environmental stress. METHODS We examined the consequences of a naturally occurring loss-of-function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing-tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing the Italian CBF2 allele, and two contained deletions created using CRISPR-Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression before and after cold acclimation. RESULTS Freezing tolerance was lower in the Italian (11%) compared to the Swedish (72%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified 10 genes for which all CBF2 LOF lines, and the IT ecotype had similar patterns of reduced cold responsive expression compared to the SW ecotype. CONCLUSIONS We identified 10 genes that are at least partially regulated by CBF2 that may contribute to the differences in cold-acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.
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Affiliation(s)
- Brian J. Sanderson
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Sunchung Park
- MSU‐DOE Plant Research Laboratory and the Plant Resilience InstituteMichigan State UniversityEast LansingMIUSA
- Present address:
USDA ARS SalinasCAUSA
| | - M. Inam Jameel
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
- Present address:
Department of GeneticsUniversity of GeorgiaAthensGAUSA
| | - Joshua C. Kraft
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Michael F. Thomashow
- MSU‐DOE Plant Research Laboratory and the Plant Resilience InstituteMichigan State UniversityEast LansingMIUSA
| | - Douglas W. Schemske
- Department of Plant Biology, and W. K. Kellogg Biological StationMichigan State UniversityEast LansingMIUSA
| | - Christopher G. Oakley
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
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14
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Marshall MM, Remington DL, Lacey EP. Two reproductive traits show contrasting genetic architectures in Plantago lanceolata. Mol Ecol 2019; 29:272-291. [PMID: 31793079 DOI: 10.1111/mec.15320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/25/2022]
Abstract
In many species, temperature-sensitive phenotypic plasticity (i.e., an individual's phenotypic response to temperature) displays a positive correlation with latitude, a pattern presumed to reflect local adaptation. This geographical pattern raises two general questions: (a) Do a few large-effect genes contribute to latitudinal variation in a trait? (b) Is the thermal plasticity of different traits regulated pleiotropically? To address the questions, we crossed individuals of Plantago lanceolata derived from northern and southern European populations. Individuals naturally exhibited high and low thermal plasticity in floral reflectance and flowering time. We grew parents and offspring in controlled cool- and warm-temperature environments, mimicking what plants would encounter in nature. We obtained genetic markers via genotype-by-sequencing, produced the first recombination map for this ecologically important nonmodel species, and performed quantitative trait locus (QTL) mapping of thermal plasticity and single-environment values for both traits. We identified a large-effect QTL that largely explained the reflectance plasticity differences between northern and southern populations. We identified multiple smaller-effect QTLs affecting aspects of flowering time, one of which affected flowering time plasticity. The results indicate that the genetic architecture of thermal plasticity in flowering is more complex than for reflectance. One flowering time QTL showed strong cytonuclear interactions under cool temperatures. Reflectance and flowering plasticity QTLs did not colocalize, suggesting little pleiotropic genetic control and freedom for independent trait evolution. Such genetic information about the architecture of plasticity is environmentally important because it informs us about the potential for plasticity to offset negative effects of climate change.
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Affiliation(s)
- Matthew M Marshall
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - David L Remington
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Elizabeth P Lacey
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA
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15
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MacQueen A, Tian D, Chang W, Holub E, Kreitman M, Bergelson J. Population Genetics of the Highly Polymorphic RPP8 Gene Family. Genes (Basel) 2019; 10:E691. [PMID: 31500388 PMCID: PMC6771003 DOI: 10.3390/genes10090691] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.
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Affiliation(s)
- Alice MacQueen
- Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210008, China.
| | - Wenhan Chang
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| | - Eric Holub
- School of Life Sciences, Wellesbourne Innovation Campus, University of Warwick, Wellesbourne CV359EF, UK.
| | - Martin Kreitman
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| | - Joy Bergelson
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
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16
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Tian L, Rahman SR, Ezray BD, Franzini L, Strange JP, Lhomme P, Hines HM. A homeotic shift late in development drives mimetic color variation in a bumble bee. Proc Natl Acad Sci U S A 2019; 116:11857-11865. [PMID: 31043564 PMCID: PMC6575597 DOI: 10.1073/pnas.1900365116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural phenotypic radiations, with their high diversity and convergence, are well-suited for informing how genomic changes translate to natural phenotypic variation. New genomic tools enable discovery in such traditionally nonmodel systems. Here, we characterize the genomic basis of color pattern variation in bumble bees (Hymenoptera, Apidae, Bombus), a group that has undergone extensive convergence of setal color patterns as a result of Müllerian mimicry. In western North America, multiple species converge on local mimicry patterns through parallel shifts of midabdominal segments from red to black. Using genome-wide association, we establish that a cis-regulatory locus between the abdominal fate-determining Hox genes, abd-A and Abd-B, controls the red-black color switch in a western species, Bombus melanopygus Gene expression analysis reveals distinct shifts in Abd-B aligned with the duration of setal pigmentation at the pupal-adult transition. This results in atypical anterior Abd-B expression, a late developmental homeotic shift. Changing expression of Hox genes can have widespread effects, given their important role across segmental phenotypes; however, the late timing reduces this pleiotropy, making Hox genes suitable targets. Analysis of this locus across mimics and relatives reveals that other species follow independent genetic routes to obtain the same phenotypes.
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Affiliation(s)
- Li Tian
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | | | - Briana D Ezray
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - Luca Franzini
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - James P Strange
- United States Department of Agriculture-Agricultural Research Service Pollinating Insects Research Unit, Utah State University, Logan, UT 84322
| | - Patrick Lhomme
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Biodiversity and Crop Improvement Program, International Center of Agricultural Research in the Dry Areas, 10112 Rabat, Morocco
| | - Heather M Hines
- Department of Biology, The Pennsylvania State University, University Park, PA 16802;
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
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17
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A major role for noncoding regulatory mutations in the evolution of enzyme activity. Proc Natl Acad Sci U S A 2019; 116:12383-12389. [PMID: 31152141 PMCID: PMC6589674 DOI: 10.1073/pnas.1904071116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study investigates how evolutionary changes in enzyme activity occur. Multiple species of Drosophila flies have adapted to food with different levels of alcohol. This study uncovers genetic changes responsible for these repeated adaptive events, focusing on the main enzyme responsible for alcohol metabolism, Alcohol dehydrogenase. Better alcohol metabolism could be achieved either through changes to the enzyme itself or through changes in DNA regulatory sequences that affect how many enzyme molecules are produced. In four different cases, it was found that regulatory changes were the most frequent contributors to evolution. These findings have important implications because most studies of enzyme evolution focus exclusively on changes to protein sequence, and thus a significant source of adaptive changes may be overlooked. The quantitative evolution of protein activity is a common phenomenon, yet we know little about any general mechanistic tendencies that underlie it. For example, an increase (or decrease) in enzyme activity may evolve from changes in protein sequence that alter specific activity, or from changes in gene expression that alter the amount of protein produced. The latter in turn could arise via mutations that affect gene transcription, posttranscriptional processes, or copy number. Here, to determine the types of genetic changes underlying the quantitative evolution of protein activity, we dissected the basis of ecologically relevant differences in Alcohol dehydrogenase (Adh) enzyme activity between and within several Drosophila species. By using recombinant Adh transgenes to map the functional divergence of ADH enzyme activity in vivo, we find that amino acid substitutions explain only a minority (0 to 25%) of between- and within-species differences in enzyme activity. Instead, noncoding substitutions that occur across many parts of the gene (enhancer, promoter, and 5′ and 3′ untranslated regions) account for the majority of activity differences. Surprisingly, one substitution in a transcriptional Initiator element has occurred in parallel in two species, indicating that core promoters can be an important natural source of the tuning of gene activity. Furthermore, we show that both regulatory and coding substitutions contribute to fitness (resistance to ethanol toxicity). Although qualitative changes in protein specificity necessarily derive from coding mutations, these results suggest that regulatory mutations may be the primary source of quantitative changes in protein activity, a possibility overlooked in most analyses of protein evolution.
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18
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Dayan DI, Du X, Baris TZ, Wagner DN, Crawford DL, Oleksiak MF. Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents. BMC Evol Biol 2019; 19:61. [PMID: 30808292 PMCID: PMC6390305 DOI: 10.1186/s12862-019-1392-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Examples of rapid evolution are common in nature but difficult to account for with the standard population genetic model of adaptation. Instead, selection from the standing genetic variation permits rapid adaptation via soft sweeps or polygenic adaptation. Empirical evidence of this process in nature is currently limited but accumulating. RESULTS We provide genome-wide analyses of rapid evolution in Fundulus heteroclitus populations subjected to recently elevated temperatures due to coastal power station thermal effluents using 5449 SNPs across two effluent-affected and four reference populations. Bayesian and multivariate analyses of population genomic structure reveal a substantial portion of genetic variation that is most parsimoniously explained by selection at the site of thermal effluents. An FST outlier approach in conjunction with additional conservative requirements identify significant allele frequency differentiation that exceeds neutral expectations among exposed and closely related reference populations. Genomic variation patterns near these candidate loci reveal that individuals living near thermal effluents have rapidly evolved from the standing genetic variation through small allele frequency changes at many loci in a pattern consistent with polygenic selection on the standing genetic variation. CONCLUSIONS While the ultimate trajectory of selection in these populations is unknown and we survey only a minority of genomic loci, our findings suggest that polygenic models of adaptation may play important roles in large, natural populations experiencing recent selection due to environmental changes that cause broad physiological impacts.
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Affiliation(s)
- David I. Dayan
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Xiao Du
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Tara Z. Baris
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Dominique N. Wagner
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Douglas L. Crawford
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Marjorie F. Oleksiak
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
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19
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Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, Lovell JT, McKay JK. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. eLife 2018; 7:41038. [PMID: 30520727 PMCID: PMC6326724 DOI: 10.7554/elife.41038] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/06/2018] [Indexed: 11/26/2022] Open
Abstract
Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses seven times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops. Water shortages caused by droughts lead to crop losses that affect billions of people around the world each year. By discovering how wild plants adapt to drought, it may be possible to identify traits and genes that help to improve the growth of crop plants when water is scarce. It has been suggested that plants have adapted to droughts by flowering at times of the year when droughts are less likely to occur. For example, if droughts are more likely to happen in spring, the plants may delay flowering until the summer. Arabidopsis thaliana is a small plant that is found across Eurasia, Africa and North America, including in areas that are prone to drought at different times of the year. Individual plants of the same species may carry different versions of the same gene (known as alleles). Some of these alleles may not work properly and are referred to as loss-of-function alleles. Monroe et al. investigated whether A. thaliana plants carry any loss-of-function alleles that are associated with droughts happening in the spring or summer, and whether they are linked to when those plants will flower. Monroe et al. analyzed satellite images collected over the last 30 years to measure when droughts have occurred. Next, they searched genome sequences of Arabidopsis thaliana for alleles that might help the plants to adapt to droughts in the spring or summer. Combining the two approaches revealed that loss-of-function alleles associated with spring droughts were strongly predicted to be associated with the plants flowering later in the year. Similarly, loss-of-function alleles associated with summer droughts were predicted to be associated with the plants flowering earlier in the year. These findings support the idea that plants can adapt to drought by changing when they produce flowers, and suggest that loss-of-function alleles play a major role in this process. New techniques for editing genes mean it is easier than ever to generate new loss-of-function alleles in specific genes. Therefore, the results presented by Monroe et al. may help researchers to develop new varieties of crop plants that are better adapted to droughts.
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Affiliation(s)
- J Grey Monroe
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, United States
| | - Tyler Powell
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Department of Biology, Colorado State University, Fort Collins, United States
| | - Nicholas Price
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Jack L Mullen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Anne Howard
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Kyle Evans
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - John K McKay
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, United States
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20
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Mack KL, Ballinger MA, Phifer-Rixey M, Nachman MW. Gene regulation underlies environmental adaptation in house mice. Genome Res 2018; 28:1636-1645. [PMID: 30194096 PMCID: PMC6211637 DOI: 10.1101/gr.238998.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022]
Abstract
Changes in cis-regulatory regions are thought to play a major role in the genetic basis of adaptation. However, few studies have linked cis-regulatory variation with adaptation in natural populations. Here, using a combination of exome and RNA-seq data, we performed expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses to study the genetic architecture of regulatory variation in wild house mice (Mus musculus domesticus) using individuals from five populations collected along a latitudinal cline in eastern North America. Mice in this transect showed clinal patterns of variation in several traits, including body mass. Mice were larger in more northern latitudes, in accordance with Bergmann's rule. We identified 17 genes where cis-eQTLs were clinal outliers and for which expression level was correlated with latitude. Among these clinal outliers, we identified two genes (Adam17 and Bcat2) with cis-eQTLs that were associated with adaptive body mass variation and for which expression is correlated with body mass both within and between populations. Finally, we performed a weighted gene co-expression network analysis (WGCNA) to identify expression modules associated with measures of body size variation in these mice. These findings demonstrate the power of combining gene expression data with scans for selection to identify genes involved in adaptive phenotypic evolution, and also provide strong evidence for cis-regulatory elements as essential loci of environmental adaptation in natural populations.
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Affiliation(s)
- Katya L Mack
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA
| | - Mallory A Ballinger
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA
| | - Megan Phifer-Rixey
- Department of Biology, Monmouth University, West Long Branch, New Jersey 07764, USA
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA
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21
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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
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22
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Genetic Basis of Body Color and Spotting Pattern in Redheaded Pine Sawfly Larvae ( Neodiprion lecontei). Genetics 2018; 209:291-305. [PMID: 29496749 DOI: 10.1534/genetics.118.300793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/22/2018] [Indexed: 11/18/2022] Open
Abstract
Pigmentation has emerged as a premier model for understanding the genetic basis of phenotypic evolution, and a growing catalog of color loci is starting to reveal biases in the mutations, genes, and genetic architectures underlying color variation in the wild. However, existing studies have sampled a limited subset of taxa, color traits, and developmental stages. To expand the existing sample of color loci, we performed QTL mapping analyses on two types of larval pigmentation traits that vary among populations of the redheaded pine sawfly (Neodiprion lecontei): carotenoid-based yellow body color and melanin-based spotting pattern. For both traits, our QTL models explained a substantial proportion of phenotypic variation and suggested a genetic architecture that is neither monogenic nor highly polygenic. Additionally, we used our linkage map to anchor the current N. lecontei genome assembly. With these data, we identified promising candidate genes underlying (1) a loss of yellow pigmentation in populations in the mid-Atlantic/northeastern United States [C locus-associated membrane protein homologous to a mammalian HDL receptor-2 gene (Cameo2) and lipid transfer particle apolipoproteins II and I gene (apoLTP-II/I)], and (2) a pronounced reduction in black spotting in Great Lakes populations [members of the yellow gene family, tyrosine hydroxylase gene (pale), and dopamine N-acetyltransferase gene (Dat)]. Several of these genes also contribute to color variation in other wild and domesticated taxa. Overall, our findings are consistent with the hypothesis that predictable genes of large effect contribute to color evolution in nature.
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23
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Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive variation. Proc Biol Sci 2017; 284:rspb.2016.2864. [PMID: 28566483 DOI: 10.1098/rspb.2016.2864] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/04/2017] [Indexed: 12/16/2022] Open
Abstract
The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Nicholas H Barton
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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24
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Gervais O, Pong-Wong R, Navarro P, Haley CS, Nagamine Y. Antagonistic genetic correlations for milking traits within the genome of dairy cattle. PLoS One 2017; 12:e0175105. [PMID: 28380033 PMCID: PMC5381921 DOI: 10.1371/journal.pone.0175105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 03/21/2017] [Indexed: 01/18/2023] Open
Abstract
Genome-wide association studies can be applied to identify useful SNPs associated with complex traits. Furthermore, regional genomic mapping can be used to estimate regional variance and clarify the genomic relationships within and outside regions but has not previously been applied to milk traits in cattle. We applied both single SNP analysis and regional genomic mapping to investigate SNPs or regions associated with milk yield traits in dairy cattle. The de-regressed breeding values of three traits, total yield (kg) of milk (MLK), fat (FAT), and protein (PRT) in 305 days, from 2,590 Holstein sires in Japan were analyzed. All sires were genotyped with 40,646 single-nucleotide polymorphism (SNP) markers. A genome-wide significant region (P < 0.01) common to all three traits was identified by regional genomic mapping on chromosome (BTA) 14. In contrast, single SNP analysis identified significant SNPs only for MLK and FAT (P < 0.01), but not PRT in the same region. Regional genomic mapping revealed an additional significant region (P < 0.01) for FAT on BTA5 that was not identified by single SNP analysis. The additive whole-genomic effects estimated in the regional genomic mapping analysis for the three traits were positively correlated with one another (0.830–0.924). However, the regional genomic effects obtained by using a window size of 20 SNPs for FAT on BTA14 were negatively correlated (P < 0.01) with the regional genomic effect for MLK (–0.940) and PRT (–0.878). The BTA14 regional effect for FAT also showed significant negative correlations (P < 0.01) with the whole genomic effects for MLK (–0.153), FAT (–0.172), and PRT (–0.181). These negative genomic correlations between loci are consistent with the negative linkage disequilibrium expected for traits under directional selection. Such antagonistic correlations may hamper the fixation of the FAT increasing alleles on BTA14. In summary, regional genomic mapping found more regions associated with milk production traits than did single SNP analysis. In addition, the existence of non-zero covariances between regional and whole genomic effects may influence the detection of regional effects, and antagonistic correlations could hamper the fixation of major genes under intensive selection.
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Affiliation(s)
- Olivier Gervais
- Kyoto University, Graduate School of Informatics, Kyoto Japan
| | - Ricardo Pong-Wong
- The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Chris S. Haley
- The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, United Kingdom
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
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25
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Vertacnik KL, Linnen CR. Evolutionary genetics of host shifts in herbivorous insects: insights from the age of genomics. Ann N Y Acad Sci 2017; 1389:186-212. [DOI: 10.1111/nyas.13311] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/16/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022]
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26
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Ågren J, Oakley CG, Lundemo S, Schemske DW. Adaptive divergence in flowering time among natural populations of
Arabidopsis thaliana
: Estimates of selection and QTL mapping. Evolution 2016; 71:550-564. [DOI: 10.1111/evo.13126] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Jon Ågren
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre Uppsala University Norbyvägen 18 D SE‐752 36 Uppsala Sweden
| | | | - Sverre Lundemo
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre Uppsala University Norbyvägen 18 D SE‐752 36 Uppsala Sweden
- WWF Norway Postboks 6784, St. Olavs Plass 0130 Oslo Norway
| | - Douglas W. Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station Michigan State University East Lansing Michigan 48824
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27
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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.
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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
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28
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Olsson S, Seoane-Zonjic P, Bautista R, Claros MG, González-Martínez SC, Scotti I, Scotti-Saintagne C, Hardy OJ, Heuertz M. Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers. Mol Ecol Resour 2016; 17:614-630. [PMID: 27718316 DOI: 10.1111/1755-0998.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain
| | - Pedro Seoane-Zonjic
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Rocío Bautista
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France
| | - Ivan Scotti
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Caroline Scotti-Saintagne
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Olivier J Hardy
- Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France.,Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
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29
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Ferris KG, Barnett LL, Blackman BK, Willis JH. The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex. Mol Ecol 2016; 26:208-224. [PMID: 27439150 DOI: 10.1111/mec.13763] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 01/05/2023]
Abstract
The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M. guttatus. These three traits are probably involved in M. laciniatus' adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them 'magic traits'. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects.
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Affiliation(s)
- Kathleen G Ferris
- Department of Biology, Duke University, 125 Science Drive, Durham, NC, 27705, USA
| | - Laryssa L Barnett
- Department of Biology, Duke University, 125 Science Drive, Durham, NC, 27705, USA
| | - Benjamin K Blackman
- Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, VA, 22904, USA
| | - John H Willis
- Department of Biology, Duke University, 125 Science Drive, Durham, NC, 27705, USA
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30
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Konczal M, Koteja P, Orlowska-Feuer P, Radwan J, Sadowska ET, Babik W. Genomic Response to Selection for Predatory Behavior in a Mammalian Model of Adaptive Radiation. Mol Biol Evol 2016; 33:2429-40. [PMID: 27401229 DOI: 10.1093/molbev/msw121] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
If genetic architectures of various quantitative traits are similar, as studies on model organisms suggest, comparable selection pressures should produce similar molecular patterns for various traits. To test this prediction, we used a laboratory model of vertebrate adaptive radiation to investigate the genetic basis of the response to selection for predatory behavior and compare it with evolution of aerobic capacity reported in an earlier work. After 13 generations of selection, the proportion of bank voles (Myodes [=Clethrionomys] glareolus) showing predatory behavior was five times higher in selected lines than in controls. We analyzed the hippocampus and liver transcriptomes and found repeatable changes in allele frequencies and gene expression. Genes with the largest differences between predatory and control lines are associated with hunger, aggression, biological rhythms, and functioning of the nervous system. Evolution of predatory behavior could be meaningfully compared with evolution of high aerobic capacity, because the experiments and analyses were performed in the same methodological framework. The number of genes that changed expression was much smaller in predatory lines, and allele frequencies changed repeatably in predatory but not in aerobic lines. This suggests that more variants of smaller effects underlie variation in aerobic performance, whereas fewer variants of larger effects underlie variation in predatory behavior. Our results thus contradict the view that comparable selection pressures for different quantitative traits produce similar molecular patterns. Therefore, to gain knowledge about molecular-level response to selection for complex traits, we need to investigate not only multiple replicate populations but also multiple quantitative traits.
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Affiliation(s)
- Mateusz Konczal
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Paweł Koteja
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Patrycja Orlowska-Feuer
- Department of Neurophysiology and Chronobiology, Institute of Zoology, Jagiellonian University, Kraków, Poland
| | - Jacek Radwan
- Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Edyta T Sadowska
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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31
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Monroe JG, McGovern C, Lasky JR, Grogan K, Beck J, McKay JK. Adaptation to warmer climates by parallel functional evolution of
CBF
genes in
Arabidopsis thaliana. Mol Ecol 2016; 25:3632-44. [DOI: 10.1111/mec.13711] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/20/2016] [Indexed: 01/05/2023]
Affiliation(s)
- J. Grey Monroe
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO 80523 USA
| | - Cullen McGovern
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
| | - Jesse R. Lasky
- Department of Biology Pennsylvania State University University Park PA 16802 USA
| | - Kelsi Grogan
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
| | - James Beck
- Department of Biological Sciences Wichita State University Wichita KS 67260 USA
- Botanical Research Institute of Texas Fort Worth TX 76107 USA
| | - John K. McKay
- Department of Bioagricultural Sciences and Pest Management Colorado State University Fort Collins CO 80523 USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO 80523 USA
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32
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Dittmar EL, Oakley CG, Conner JK, Gould BA, Schemske DW. Factors influencing the effect size distribution of adaptive substitutions. Proc Biol Sci 2016; 283:20153065. [PMID: 27053750 PMCID: PMC4843649 DOI: 10.1098/rspb.2015.3065] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/15/2016] [Indexed: 12/17/2022] Open
Abstract
The distribution of effect sizes of adaptive substitutions has been central to evolutionary biology since the modern synthesis. Early theory proposed that because large-effect mutations have negative pleiotropic consequences, only small-effect mutations contribute to adaptation. More recent theory suggested instead that large-effect mutations could be favoured when populations are far from their adaptive peak. Here we suggest that the distributions of effect sizes are expected to differ among study systems, reflecting the wide variation in evolutionary forces and ecological conditions experienced in nature. These include selection, mutation, genetic drift, gene flow, and other factors such as the degree of pleiotropy, the distance to the phenotypic optimum, whether the optimum is stable or moving, and whether new mutation or standing genetic variation provides the source of adaptive alleles. Our goal is to review how these factors might affect the distribution of effect sizes and to identify new research directions. Until more theory and empirical work is available, we feel that it is premature to make broad generalizations about the effect size distribution of adaptive substitutions important in nature.
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Affiliation(s)
- Emily L Dittmar
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Christopher G Oakley
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jeffrey K Conner
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Billie A Gould
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Douglas W Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
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33
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Mizrachi E, Myburg AA. Systems genetics of wood formation. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:94-100. [PMID: 26943939 DOI: 10.1016/j.pbi.2016.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/12/2016] [Accepted: 02/15/2016] [Indexed: 05/02/2023]
Abstract
In woody plants, xylogenesis is an exceptionally strong carbon sink requiring robust transcriptional control and dynamic coordination of cellular and metabolic processes directing carbon allocation and partitioning into secondary cell wall biosynthesis. As a biological process, wood formation is an excellent candidate for systems modeling due to the strong correlation patterns and interconnectedness observed for transcriptional and metabolic component traits contributing to complex phenotypes such as cell wall chemistry and ultrastructure. Genetic variation in undomesticated tree populations provides abundant perturbation of systems components, adding another dimension to plant systems biology (besides spatial and temporal variation). High-throughput analysis of molecular component traits in adult trees has provided the first insights into the systems genetics of wood, an important renewable feedstock for biomaterials and bioenergy.
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Affiliation(s)
- Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
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