201
|
Leveraging GWAS for complex traits to detect signatures of natural selection in humans. Curr Opin Genet Dev 2018; 53:9-14. [PMID: 29913353 DOI: 10.1016/j.gde.2018.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 02/08/2023]
Abstract
Natural selection can shape the genetic architecture of complex traits. In human populations, signals of positive selection at genetic loci have been detected through a variety of genome-wide scanning approaches without the knowledge of how genes affect traits or fitness. In the past decade, genome-wide association studies (GWAS) have provided unprecedented insights into the genetic basis of quantitative variation in complex traits. Summary statistics generated from these GWAS have been shown to be an extraordinary data source that can be utilized to detect and quantify natural selection in the genetic architecture of complex traits. In this review, we focus on recent discoveries about selection on genetic variants associated with human complex traits based on GWAS-facilitated methods.
Collapse
|
202
|
de Lafontaine G, Napier JD, Petit RJ, Hu FS. Invoking adaptation to decipher the genetic legacy of past climate change. Ecology 2018; 99:1530-1546. [PMID: 29729183 DOI: 10.1002/ecy.2382] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 12/31/2022]
Abstract
Persistence of natural populations during periods of climate change is likely to depend on migration (range shifts) or adaptation. These responses were traditionally considered discrete processes and conceptually divided into the realms of ecology and evolution. In a milestone paper, Davis and Shaw (2001) Science 292:673 argued that the interplay of adaptation and migration was central to biotic responses to Quaternary climate, but since then there has been no synthesis of efforts made to set up this research program. Here we review some of the salient findings from molecular genetic studies assessing ecological and evolutionary responses to Quaternary climate change. These studies have revolutionized our understanding of population processes associated with past species migration. However, knowledge remains limited about the role of natural selection for local adaptation of populations to Quaternary environmental fluctuations and associated range shifts, and for the footprints this might have left on extant populations. Next-generation sequencing technologies, high-resolution paleoclimate analyses, and advances in population genetic theory offer an unprecedented opportunity to test hypotheses about adaptation through time. Recent population genomics studies have greatly improved our understanding of the role of contemporary adaptation to local environments in shaping spatial patterns of genetic diversity across modern-day landscapes. Advances in this burgeoning field provide important conceptual and methodological bases to decipher the historical role of natural selection and assess adaptation to past environmental variation. We suggest that a process called "temporal conditional neutrality" has taken place: some alleles favored in glacial environments become selectively neutral in modern-day conditions, whereas some alleles that had been neutral during glacial periods become under selection in modern environments. Building on this view, we present a new integrative framework for addressing the interplay of demographic and adaptive evolutionary responses to Quaternary climate dynamics, the research agenda initially envisioned by Davis and Shaw (2001) Science 292:673.
Collapse
Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of Northern Flora, Université du Québec à Rimouski, Rimouski, Québec, G5L 3A1, Canada.,Department of Plant Biology, University of Illinois, Urbana, Illinois, 61801, USA
| | - Joseph D Napier
- Department of Plant Biology, University of Illinois, Urbana, Illinois, 61801, USA
| | - Rémy J Petit
- Biogeco, INRA, Univ. Bordeaux, Cestas, 33610, France
| | - Feng Sheng Hu
- Department of Plant Biology, University of Illinois, Urbana, Illinois, 61801, USA.,Department of Geology, University of Illinois, Urbana, Illinois, 61801, USA
| |
Collapse
|
203
|
Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
Collapse
Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
204
|
Pritchard VL, Mäkinen H, Vähä JP, Erkinaro J, Orell P, Primmer CR. Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes. Mol Ecol 2018; 27:2560-2575. [DOI: 10.1111/mec.14705] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Hannu Mäkinen
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute; University of Turku; Turku Finland
| | | | - Panu Orell
- Natural Resources Institute Finland (LUKE); Oulu Finland
| | - Craig R. Primmer
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
| |
Collapse
|
205
|
Waterhouse MD, Erb LP, Beever EA, Russello MA. Adaptive population divergence and directional gene flow across steep elevational gradients in a climate-sensitive mammal. Mol Ecol 2018; 27:2512-2528. [DOI: 10.1111/mec.14701] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/29/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Matthew D. Waterhouse
- Department of Biology; University of British Columbia; Kelowna British Columbia Canada
| | - Liesl P. Erb
- Departments of Biology and Environmental Studies; Warren Wilson College; Asheville North Carolina
| | - Erik A. Beever
- U.S. Geological Survey; Northern Rocky Mountain Science Center; Bozeman Montana
- Department of Ecology; Montana State University; Bozeman Montana
| | - Michael A. Russello
- Department of Biology; University of British Columbia; Kelowna British Columbia Canada
| |
Collapse
|
206
|
Cheng JY, Mailund T, Nielsen R. Fast admixture analysis and population tree estimation for SNP and NGS data. Bioinformatics 2018; 33:2148-2155. [PMID: 28334108 DOI: 10.1093/bioinformatics/btx098] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/16/2017] [Indexed: 01/05/2023] Open
Abstract
Motivation Structure methods are highly used population genetic methods for classifying individuals in a sample fractionally into discrete ancestry components. Contribution We introduce a new optimization algorithm for the classical STRUCTURE model in a maximum likelihood framework. Using analyses of real data we show that the new method finds solutions with higher likelihoods than the state-of-the-art method in the same computational time. The optimization algorithm is also applicable to models based on genotype likelihoods, that can account for the uncertainty in genotype-calling associated with Next Generation Sequencing (NGS) data. We also present a new method for estimating population trees from ancestry components using a Gaussian approximation. Using coalescence simulations of diverging populations, we explore the adequacy of the STRUCTURE-style models and the Gaussian assumption for identifying ancestry components correctly and for inferring the correct tree. In most cases, ancestry components are inferred correctly, although sample sizes and times since admixture can influence the results. We show that the popular Gaussian approximation tends to perform poorly under extreme divergence scenarios e.g. with very long branch lengths, but the topologies of the population trees are accurately inferred in all scenarios explored. The new methods are implemented together with appropriate visualization tools in the software package Ohana. Availability and Implementation Ohana is publicly available at https://github.com/jade-cheng/ohana . In addition to source code and installation instructions, we also provide example work-flows in the project wiki site. Contact jade.cheng@birc.au.dk. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jade Yu Cheng
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.,Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA, USA.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA, USA.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
207
|
Kreiner JM, Stinchcombe JR, Wright SI. Population Genomics of Herbicide Resistance: Adaptation via Evolutionary Rescue. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:611-635. [PMID: 29140727 DOI: 10.1146/annurev-arplant-042817-040038] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The evolution of herbicide resistance in weed populations is a highly replicated example of adaptation surmounting the race against extinction, but the factors determining its rate and nature remain poorly understood. Here, we explore theory and empirical evidence for the importance of population genetic parameters-including effective population size, dominance, mutational target size, and gene flow-in influencing the probability and mode of herbicide resistance adaptation and its variation across species. We compiled data on the number of resistance mutations across populations for 79 herbicide-resistant species. Our findings are consistent with theoretical predictions that self-fertilization reduces resistance adaptation from standing variation within populations, but increases independent adaptation across populations. Furthermore, we provide evidence for a ploidy-mating system interaction that may reflect trade-offs in polyploids between increased effective population size and greater masking of beneficial mutations. We highlight the power of population genomic approaches to provide insights into the evolutionary dynamics of herbicide resistance with important implications for understanding the limits of adaptation.
Collapse
Affiliation(s)
- Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; , ,
| | | | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; , ,
| |
Collapse
|
208
|
Kay KM, Woolhouse S, Smith BA, Pope NS, Rajakaruna N. Sympatric serpentine endemic
Monardella
(Lamiaceae) species maintain habitat differences despite hybridization. Mol Ecol 2018; 27:2302-2316. [DOI: 10.1111/mec.14582] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/09/2018] [Accepted: 02/20/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Kathleen M. Kay
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California
| | - Suzie Woolhouse
- Department of Biological Sciences San José State University San José California
| | - Brett A. Smith
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California
| | - Nathaniel S. Pope
- Department of Integrative Biology The University of Texas at Austin Austin Texas
| | - Nishanta Rajakaruna
- Biological Sciences Department California Polytechnic State University San Luis Obispo California
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
| |
Collapse
|
209
|
Theodorou P, Radzevičiūtė R, Kahnt B, Soro A, Grosse I, Paxton RJ. Genome-wide single nucleotide polymorphism scan suggests adaptation to urbanization in an important pollinator, the red-tailed bumblebee ( Bombus lapidarius L.). Proc Biol Sci 2018; 285:20172806. [PMID: 29669900 PMCID: PMC5936727 DOI: 10.1098/rspb.2017.2806] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/26/2018] [Indexed: 01/24/2023] Open
Abstract
Urbanization is considered a global threat to biodiversity; the growth of cities results in an increase in impervious surfaces, soil and air pollution, fragmentation of natural vegetation and invasion of non-native species, along with numerous environmental changes, including the heat island phenomenon. The combination of these effects constitutes a challenge for both the survival and persistence of many native species, while also imposing altered selective regimes. Here, using 110 314 single nucleotide polymorphisms generated by restriction-site-associated DNA sequencing, we investigated the genome-wide effects of urbanization on putative neutral and adaptive genomic diversity in a major insect pollinator, Bombus lapidarius, collected from nine German cities and nine paired rural sites. Overall, genetic differentiation among sites was low and there was no obvious genome-wide genetic structuring, suggesting the absence of strong effects of urbanization on gene flow. We nevertheless identified several loci under directional selection, a subset of which was associated with urban land use, including the percentage of impervious surface surrounding each sampling site. Overall, our results provide evidence of local adaptation to urbanization in the face of gene flow in a highly mobile insect pollinator.
Collapse
Affiliation(s)
- Panagiotis Theodorou
- General Zoology, Institute of Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Rita Radzevičiūtė
- General Zoology, Institute of Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, 10257 Vilnius, Lithuania
| | - Belinda Kahnt
- General Zoology, Institute of Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Antonella Soro
- General Zoology, Institute of Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Ivo Grosse
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany
| | - Robert J Paxton
- General Zoology, Institute of Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| |
Collapse
|
210
|
Forester BR, Lasky JR, Wagner HH, Urban DL. Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations. Mol Ecol 2018; 27:2215-2233. [DOI: 10.1111/mec.14584] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Brenna R. Forester
- Nicholas School of the Environment; Duke University; Durham North Carolina
| | - Jesse R. Lasky
- Department of Biology; Pennsylvania State University; University Park Pennsylvania
| | - Helene H. Wagner
- Department of Biology; University of Toronto Mississauga; Mississauga ON Canada
| | - Dean L. Urban
- Nicholas School of the Environment; Duke University; Durham North Carolina
| |
Collapse
|
211
|
Garner AG, Goulet BE, Farnitano MC, Molina-Henao YF, Hopkins R. Genomic Signatures of Reinforcement. Genes (Basel) 2018; 9:E191. [PMID: 29614048 PMCID: PMC5924533 DOI: 10.3390/genes9040191] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement's characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.
Collapse
Affiliation(s)
- Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Benjamin E Goulet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Matthew C Farnitano
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Y Franchesco Molina-Henao
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
- Department of Biology, Universidad del Valle, Cali 760032, Colombia.
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| |
Collapse
|
212
|
Racimo F, Berg JJ, Pickrell JK. Detecting Polygenic Adaptation in Admixture Graphs. Genetics 2018; 208:1565-1584. [PMID: 29348143 PMCID: PMC5887149 DOI: 10.1534/genetics.117.300489] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/16/2018] [Indexed: 01/09/2023] Open
Abstract
An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred. To address this, we created a method to detect polygenic adaptation in an admixture graph, which is a representation of the historical divergences and admixture events relating different populations through time. We developed a Markov chain Monte Carlo (MCMC) algorithm to infer branch-specific parameters reflecting the strength of selection in each branch of a graph. Additionally, we developed a set of summary statistics that are fast to compute and can indicate which branches are most likely to have experienced polygenic adaptation. We show via simulations that this method-which we call PolyGraph-has good power to detect polygenic adaptation, and applied it to human population genomic data from around the world. We also provide evidence that variants associated with several traits, including height, educational attainment, and self-reported unibrow, have been influenced by polygenic adaptation in different populations during human evolution.
Collapse
Affiliation(s)
- Fernando Racimo
- New York Genome Center, New York, New York 10013
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350, Denmark
| | - Jeremy J Berg
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Joseph K Pickrell
- New York Genome Center, New York, New York 10013
- Department of Biological Sciences, Columbia University, New York, New York 10027
| |
Collapse
|
213
|
Housset JM, Nadeau S, Isabel N, Depardieu C, Duchesne I, Lenz P, Girardin MP. Tree rings provide a new class of phenotypes for genetic associations that foster insights into adaptation of conifers to climate change. THE NEW PHYTOLOGIST 2018; 218:630-645. [PMID: 29314017 PMCID: PMC6079641 DOI: 10.1111/nph.14968] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/21/2017] [Indexed: 05/20/2023]
Abstract
Local adaptation in tree species has been documented through a long history of common garden experiments where functional traits (height, bud phenology) are used as proxies for fitness. However, the ability to identify genes or genomic regions related to adaptation to climate requires the evaluation of traits that precisely reflect how and when climate exerts selective constraints. We combine dendroecology with association genetics to establish a link between genotypes, phenotypes and interannual climatic fluctuations. We illustrate this approach by examining individual tree responses embedded in the annual rings of 233 Pinus strobus trees growing in a common garden experiment representing 38 populations from the majority of its range. We found that interannual variability in growth was affected by low temperatures during spring and autumn, and by summer heat and drought. Among-population variation in climatic sensitivity was significantly correlated with the mean annual temperature of the provenance, suggesting local adaptation. Genotype-phenotype associations using these new tree-ring phenotypes validated nine candidate genes identified in a previous genetic-environment association study. Combining dendroecology with association genetics allowed us to assess tree vulnerability to past climate at fine temporal scales and provides avenues for future genomic studies on functional adaptation in forest trees.
Collapse
Affiliation(s)
- Johann M. Housset
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Natural Resources CanadaCanadian Wood Fibre Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Centre d’étude de la forêtUniversité du Québec à MontréalC.P. 8888, succ. Centre‐villeMontréalQCH3C 3P8Canada
| | - Simon Nadeau
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Natural Resources CanadaCanadian Wood Fibre Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
| | - Nathalie Isabel
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Chaire de Recherche du Canada en Génomique ForestièreFaculté de Foresteriede Géographie et de GéomatiqueUniversité LavalQuébecQCG1V 0A6Canada
| | - Claire Depardieu
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Chaire de Recherche du Canada en Génomique ForestièreFaculté de Foresteriede Géographie et de GéomatiqueUniversité LavalQuébecQCG1V 0A6Canada
| | - Isabelle Duchesne
- Natural Resources CanadaCanadian Wood Fibre Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
| | - Patrick Lenz
- Natural Resources CanadaCanadian Wood Fibre Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Chaire de Recherche du Canada en Génomique ForestièreFaculté de Foresteriede Géographie et de GéomatiqueUniversité LavalQuébecQCG1V 0A6Canada
| | - Martin P. Girardin
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Centre d’étude de la forêtUniversité du Québec à MontréalC.P. 8888, succ. Centre‐villeMontréalQCH3C 3P8Canada
| |
Collapse
|
214
|
Ahrens CW, Rymer PD, Stow A, Bragg J, Dillon S, Umbers KDL, Dudaniec RY. The search for loci under selection: trends, biases and progress. Mol Ecol 2018. [PMID: 29524276 DOI: 10.1111/mec.14549] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics.
Collapse
Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Adam Stow
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Jason Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Shannon Dillon
- Diversity and Adaptation, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Kate D L Umbers
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia.,School of Science and Health, Western Sydney University, Richmond, NSW, Australia
| | - Rachael Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
215
|
Storfer A, Patton A, Fraik AK. Navigating the Interface Between Landscape Genetics and Landscape Genomics. Front Genet 2018; 9:68. [PMID: 29593776 PMCID: PMC5859105 DOI: 10.3389/fgene.2018.00068] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/15/2018] [Indexed: 11/13/2022] Open
Abstract
As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used.
Collapse
Affiliation(s)
- Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| |
Collapse
|
216
|
Sani SGAS, Chang PL, Zubair A, Carrasquilla-Garcia N, Cordeiro M, Penmetsa RV, Munis MFH, Nuzhdin SV, Cook DR, von Wettberg EJ. Genetic Diversity, Population Structure, and Genetic Correlation with Climatic Variation in Chickpea ( Cicer arietinum) Landraces from Pakistan. THE PLANT GENOME 2018; 11:170067. [PMID: 29505627 DOI: 10.3835/plantgenome2017.08.0067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chickpea ( L.) production in arid regions, such as those predominant in Pakistan, faces immense challenges of drought and heat stress. Addressing these challenges is made more difficult by the lack of genetic and phenotypic characterization of available cultivated varieties and breeding materials. Genotyping-by-sequencing offers a rapid and cost-effective means to identify genome-wide nucleotide variation in crop germplasm. When combined with extended crop phenotypes deduced from climatic variation at sites of collection, the data can predict which portions of genetic variation might have roles in climate resilience. Here we use 8113 single nucleotide polymorphism markers to determine genetic variation and compare population structure within a previously uncharacterized collection of 77 landraces and 5 elite cultivars, currently grown in situ on farms throughout the chickpea growing regions of Pakistan. The compiled landraces span a striking aridity gradient into the Thal Desert of the Punjab. Despite low levels of variation across the collection and limited genetic structure, we found some differentiation between accessions from arid, semiarid, irrigated, and coastal areas. In a subset of 232 markers, we found evidence of differentiation along gradients of elevation and isothermality. Our results highlight the utility of exploring large germplasm collections for nucleotide variation associated with environmental extremes, and the use of such data to nominate germplasm accessions with the potential to improve crop drought tolerance and other environmental traits.
Collapse
|
217
|
Van Wyngaarden M, Snelgrove PVR, DiBacco C, Hamilton LC, Rodríguez‐Ezpeleta N, Zhan L, Beiko RG, Bradbury IR. Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus. Ecol Evol 2018; 8:2824-2841. [PMID: 29531698 PMCID: PMC5838053 DOI: 10.1002/ece3.3846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 01/03/2023] Open
Abstract
Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus, to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and we hypothesized that climatic variation significantly drives clinal trends in allele frequency. Using a large environmental dataset, including temperature, salinity, chlorophyll a, and nutrient concentrations, we identified a suite of SNPs (285-621, depending on analysis and environmental dataset) potentially under selection through correlations with environmental variation. Principal components analysis of different outlier SNPs and environmental datasets revealed similar northern and southern clusters, with significant associations between the first axes of each (R2adj = .66-.79). Multivariate redundancy analysis of outlier SNPs and the environmental principal components indicated that environmental factors explained more than 32% of the variance. Similarly, multiple linear regressions and random-forest analysis identified winter average and minimum ocean temperatures as significant parameters in the link between genetic and environmental variation. This work indicates that oceanographic variation is associated with the observed genomic cline in this species and that seasonal periods of extreme cold may restrict gene flow along a latitudinal gradient in this marine benthic bivalve. Incorporating this finding into management may improve accuracy of management strategies and future predictions.
Collapse
Affiliation(s)
| | - Paul V. R. Snelgrove
- Department of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
| | | | | | | | - Luyao Zhan
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
| | - Robert G. Beiko
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
| | - Ian R. Bradbury
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| |
Collapse
|
218
|
Kanitz R, Guillot EG, Antoniazza S, Neuenschwander S, Goudet J. Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses. PLoS One 2018; 13:e0192460. [PMID: 29466398 PMCID: PMC5821356 DOI: 10.1371/journal.pone.0192460] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 12/21/2022] Open
Abstract
Although it is generally accepted that geography is a major factor shaping human genetic differentiation, it is still disputed how much of this differentiation is a result of a simple process of isolation-by-distance, and if there are factors generating distinct clusters of genetic similarity. We address this question using a geographically explicit simulation framework coupled with an Approximate Bayesian Computation approach. Based on six simple summary statistics only, we estimated the most probable demographic parameters that shaped modern human evolution under an isolation by distance scenario, and found these were the following: an initial population in East Africa spread and grew from 4000 individuals to 5.7 million in about 132 000 years. Subsequent simulations with these estimates followed by cluster analyses produced results nearly identical to those obtained in real data. Thus, a simple diffusion model from East Africa explains a large portion of the genetic diversity patterns observed in modern humans. We argue that a model of isolation by distance along the continental landmasses might be the relevant null model to use when investigating selective effects in humans and probably many other species.
Collapse
Affiliation(s)
- Ricardo Kanitz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Elsa G. Guillot
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Samuel Neuenschwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
219
|
Tataru P, Simonsen M, Bataillon T, Hobolth A. Statistical Inference in the Wright-Fisher Model Using Allele Frequency Data. Syst Biol 2018; 66:e30-e46. [PMID: 28173553 PMCID: PMC5837693 DOI: 10.1093/sysbio/syw056] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/31/2016] [Accepted: 06/06/2016] [Indexed: 11/14/2022] Open
Abstract
The Wright–Fisher model provides an elegant mathematical framework for understanding allele frequency data. In particular, the model can be used to infer the demographic history of species and identify loci under selection. A crucial quantity for inference under the Wright–Fisher model is the distribution of allele frequencies (DAF). Despite the apparent simplicity of the model, the calculation of the DAF is challenging. We review and discuss strategies for approximating the DAF, and how these are used in methods that perform inference from allele frequency data. Various evolutionary forces can be incorporated in the Wright–Fisher model, and we consider these in turn. We begin our review with the basic bi-allelic Wright–Fisher model where random genetic drift is the only evolutionary force. We then consider mutation, migration, and selection. In particular, we compare diffusion-based and moment-based methods in terms of accuracy, computational efficiency, and analytical tractability. We conclude with a brief overview of the multi-allelic process with a general mutation model.
Collapse
Affiliation(s)
- Paula Tataru
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Maria Simonsen
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Asger Hobolth
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| |
Collapse
|
220
|
Zhao Y, Peng W, Guo H, Chen B, Zhou Z, Xu J, Zhang D, Xu P. Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:45-59. [PMID: 29256104 DOI: 10.1007/s10126-017-9786-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/21/2017] [Indexed: 06/07/2023]
Abstract
The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.
Collapse
Affiliation(s)
- Yunfeng Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing, Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
| | - Wenzhu Peng
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Huayang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Baohua Chen
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Zhixiong Zhou
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jian Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing, Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Dianchang Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Peng Xu
- Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China.
| |
Collapse
|
221
|
Hohenlohe PA, Hand BK, Andrews KR, Luikart G. Population Genomics Provides Key Insights in Ecology and Evolution. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_20] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
222
|
|
223
|
Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
224
|
Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
225
|
Seeholzer GF, Brumfield RT. Isolation by distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae:
Cranioleuca antisiensis,
Line‐cheeked Spinetail) despite near threefold body size change across an environmental gradient. Mol Ecol 2017; 27:279-296. [DOI: 10.1111/mec.14429] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/18/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Glenn F. Seeholzer
- Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge LA USA
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge LA USA
| |
Collapse
|
226
|
Li Y, Zhang XX, Mao RL, Yang J, Miao CY, Li Z, Qiu YX. Ten Years of Landscape Genomics: Challenges and Opportunities. FRONTIERS IN PLANT SCIENCE 2017; 8:2136. [PMID: 29312391 PMCID: PMC5733015 DOI: 10.3389/fpls.2017.02136] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/01/2017] [Indexed: 05/06/2023]
Abstract
Landscape genomics is a relatively new discipline that aims to reveal the relationship between adaptive genetic imprints in genomes and environmental heterogeneity among natural populations. Although the interest in landscape genomics has increased since this term was coined, studies on this topic remain scarce. Landscape genomics has become a powerful method to scan and determine the genes responsible for the complex adaptive evolution of species at population (mostly) and individual (more rarely) level. This review outlines the sampling strategies, molecular marker types and research categories in 37 articles published during the first 10 years of this field (i.e., 2007-2016). We also address major challenges and future directions for landscape genomics. This review aims to promote interest in conducting additional studies in landscape genomics.
Collapse
Affiliation(s)
- Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Xue-Xia Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Run-Li Mao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Jie Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Cai-Yun Miao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Zhuo Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
227
|
Abstract
Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures-both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.
Collapse
|
228
|
Micheletti SJ, Matala AR, Matala AP, Narum SR. Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss). Mol Ecol 2017; 27:128-145. [PMID: 29110354 DOI: 10.1111/mec.14407] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 01/03/2023]
Abstract
Organisms typically show evidence of adaptation to features within their local environment. However, many species undergo long-distance dispersal or migration across larger geographic regions that consist of highly heterogeneous habitats. Therefore, selection may influence adaptive genetic variation associated with landscape features at residing sites and along migration routes in migratory species. We tested for genomic adaptation to landscape features at natal spawning sites and along migration paths to the ocean of anadromous steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin. Results from multivariate ordination, gene-environment association and outlier analyses using 24,526 single nucleotide polymorphisms (SNPs) provided evidence that adaptive allele frequencies were more commonly associated with landscape features along migration paths than features at natal sites (91.8% vs. 8.2% of adaptive loci, respectively). Among the 45 landscape variables tested, migration distance to the ocean and mean annual precipitation along migration paths were significantly associated with adaptive genetic variation in three distinct genetic groups. Additionally, variables such as minimum migration water temperature and mean migration slope were significant only in inland stocks of steelhead that migrate up to 1,200 km farther than those near the coast, indicating regional differences in migratory selective pressures. This study provides novel approaches for investigating migratory corridors and some of the first evidence that environment along migration paths can lead to substantial divergent selection. Consequently, our approach to understand genetic adaptation to migration conditions can be applied to other migratory species when migration or dispersal paths are generally known.
Collapse
Affiliation(s)
- Steven J Micheletti
- Columbia River Inter-Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, ID, USA
| | - Amanda R Matala
- Columbia River Inter-Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, ID, USA
| | - Andrew P Matala
- Columbia River Inter-Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, ID, USA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, ID, USA
| |
Collapse
|
229
|
Crossley MS, Chen YH, Groves RL, Schoville SD. Landscape genomics of Colorado potato beetle provides evidence of polygenic adaptation to insecticides. Mol Ecol 2017; 26:6284-6300. [DOI: 10.1111/mec.14339] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/21/2017] [Accepted: 08/21/2017] [Indexed: 12/13/2022]
Affiliation(s)
| | - Yolanda H. Chen
- Department of Plant and Soil Sciences University of Vermont Burlington VT USA
| | - Russell L. Groves
- Department of Entomology University of Wisconsin‐Madison Madison WI USA
| | - Sean D. Schoville
- Department of Entomology University of Wisconsin‐Madison Madison WI USA
| |
Collapse
|
230
|
Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/13836_2017_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
231
|
Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis‐Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P. Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity. Mol Ecol 2017; 26:6253-6269. [DOI: 10.1111/mec.14368] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Katherine A. Harrisson
- School of Biological Sciences Monash University Clayton Vic. Australia
- Department of Ecology Environment and Evolution School of Life Sciences La Trobe University Bundoora Vic. Australia
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Stephen J. Amish
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission Hagerman Fish Culture Experiment Station Hagerman IDUSA
| | | | - Meaghan L. Rourke
- Department of Primary Industries DPI Fisheries Narrandera NSW Australia
| | - Jarod Lyon
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Zeb Tonkin
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Dean M. Gilligan
- Department of Primary Industries DPI Fisheries, Batemans Bay Fisheries Office Batemans Bay NSW Australia
| | | | - Mark Lintermans
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Han Ming Gan
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Christopher M. Austin
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Gordon Luikart
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Paul Sunnucks
- School of Biological Sciences Monash University Clayton Vic. Australia
| |
Collapse
|
232
|
He Q, Prado JR, Knowles LL. Inferring the geographic origin of a range expansion: Latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program x-origin. Mol Ecol 2017; 26:6908-6920. [PMID: 29044712 DOI: 10.1111/mec.14380] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/08/2017] [Accepted: 09/18/2017] [Indexed: 01/17/2023]
Abstract
Climatic or environmental change is not only driving distributional shifts in species today, but it has also caused distributions to expand and contract in the past. Inferences about the geographic locations of past populations especially regions that served as refugia (i.e., source populations) and migratory routes are a challenging endeavour. Refugial areas may be evidenced from fossil records or regions of temporal stability inferred from ecological niche models. Genomic data offer an alternative and broadly applicable source of information about the locality of refugial areas, especially relative to fossil data, which are either unavailable or incomplete for most species. Here, we present a pipeline we developed (called x-origin) for statistically inferring the geographic origin of range expansion using a spatially explicit coalescent model and an approximate Bayesian computation testing framework. In addition to assessing the probability of specific latitudinal and longitudinal coordinates of refugial or source populations, such inferences can also be made accounting for the effects of temporal and spatial environmental heterogeneity, which may impact migration routes. We demonstrate x-origin with an analysis of genomic data collected in the Collared pika that underwent postglacial expansion across Alaska, as well as present an assessment of its accuracy under a known model of expansion to validate the approach.
Collapse
Affiliation(s)
- Qixin He
- Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, IL, USA
| | - Joyce R Prado
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, Brazil
| | - Laura Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
233
|
Smouse PE, Banks SC, Peakall R. Converting quadratic entropy to diversity: Both animals and alleles are diverse, but some are more diverse than others. PLoS One 2017; 12:e0185499. [PMID: 29088229 PMCID: PMC5663342 DOI: 10.1371/journal.pone.0185499] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/13/2017] [Indexed: 12/14/2022] Open
Abstract
The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.
Collapse
Affiliation(s)
- Peter E. Smouse
- Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Sam C. Banks
- The Fenner School of Environment and Society, The Australian National University, Acton, ACT, Australia
- * E-mail:
| | - Rod Peakall
- Research School of Biology, The Australian National University, Acton, ACT, Australia
| |
Collapse
|
234
|
Landscape genomics analysis of Achyranthes bidentata reveal adaptive genetic variations are driven by environmental variations relating to ecological habit. POPUL ECOL 2017. [DOI: 10.1007/s10144-017-0599-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
235
|
Harris SE, Munshi-South J. Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus). Mol Ecol 2017; 26:6336-6350. [PMID: 28980357 DOI: 10.1111/mec.14369] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 09/25/2017] [Indexed: 02/06/2023]
Abstract
Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomic approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analysed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP data set under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in New York City are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggests selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.
Collapse
Affiliation(s)
- Stephen E Harris
- The Graduate Center, City University of New York (CUNY), New York, NY, USA
| | - Jason Munshi-South
- Louis Calder Center-Biological Field Station, Fordham University, Armonk, NY, USA
| |
Collapse
|
236
|
Distinguishing Among Modes of Convergent Adaptation Using Population Genomic Data. Genetics 2017; 207:1591-1619. [PMID: 29046403 DOI: 10.1534/genetics.117.300417] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/30/2017] [Indexed: 11/18/2022] Open
Abstract
Geographically separated populations can convergently adapt to the same selection pressure. Convergent evolution at the level of a gene may arise via three distinct modes. The selected alleles can (1) have multiple independent mutational origins, (2) be shared due to shared ancestral standing variation, or (3) spread throughout subpopulations via gene flow. We present a model-based, statistical approach that utilizes genomic data to detect cases of convergent adaptation at the genetic level, identify the loci involved and distinguish among these modes. To understand the impact of convergent positive selection on neutral diversity at linked loci, we make use of the fact that hitchhiking can be modeled as an increase in the variance in neutral allele frequencies around a selected site within a population. We build on coalescent theory to show how shared hitchhiking events between subpopulations act to increase covariance in allele frequencies between subpopulations at loci near the selected site, and extend this theory under different models of migration and selection on the same standing variation. We incorporate this hitchhiking effect into a multivariate normal model of allele frequencies that also accounts for population structure. Based on this theory, we present a composite-likelihood-based approach that utilizes genomic data to identify loci involved in convergence, and distinguishes among alternate modes of convergent adaptation. We illustrate our method on genome-wide polymorphism data from two distinct cases of convergent adaptation. First, we investigate the adaptation for copper toxicity tolerance in two populations of the common yellow monkey flower, Mimulus guttatus We show that selection has occurred on an allele that has been standing in these populations prior to the onset of copper mining in this region. Lastly, we apply our method to data from four populations of the killifish, Fundulus heteroclitus, that show very rapid convergent adaptation for tolerance to industrial pollutants. Here, we identify a single locus at which both independent mutation events and selection on an allele shared via gene flow, either slightly before or during selection, play a role in adaptation across the species' range.
Collapse
|
237
|
Sork VL. Genomic Studies of Local Adaptation in Natural Plant Populations. J Hered 2017; 109:3-15. [DOI: 10.1093/jhered/esx091] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022] Open
|
238
|
Jordan R, Hoffmann AA, Dillon SK, Prober SM. Evidence of genomic adaptation to climate in
Eucalyptus microcarpa
: Implications for adaptive potential to projected climate change. Mol Ecol 2017; 26:6002-6020. [DOI: 10.1111/mec.14341] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Rebecca Jordan
- Bio21 Institute School of BioSciences University of Melbourne Parkville Vic Australia
| | - Ary A. Hoffmann
- Bio21 Institute School of BioSciences University of Melbourne Parkville Vic Australia
| | | | | |
Collapse
|
239
|
Gouy A, Daub JT, Excoffier L. Detecting gene subnetworks under selection in biological pathways. Nucleic Acids Res 2017; 45:e149. [PMID: 28934485 PMCID: PMC5766194 DOI: 10.1093/nar/gkx626] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 12/30/2022] Open
Abstract
Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data. We developed a method to analyse gene networks that is suitable to evidence polygenic selection. The general idea is to search biological pathways for subnetworks of genes that directly interact with each other and that present unusual evolutionary features. Subnetwork search is a typical combinatorial optimization problem that we solve using a simulated annealing approach. We have applied our methodology to find signals of adaptation to high-altitude in human populations. We show that this adaptation has a clear polygenic basis and is influenced by many genetic components. Our approach, implemented in the R package signet, improves on gene-level classical tests for selection by identifying both new candidate genes and new biological processes involved in adaptation to altitude.
Collapse
Affiliation(s)
- Alexandre Gouy
- Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Joséphine T. Daub
- Institute of Evolutionary Biology, Universitat Pompeu Fabra – CSIC, 08003 Barcelona, Spain
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| |
Collapse
|
240
|
Lasky JR, Forester BR, Reimherr M. Coherent synthesis of genomic associations with phenotypes and home environments. Mol Ecol Resour 2017; 18:91-106. [DOI: 10.1111/1755-0998.12714] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Jesse R. Lasky
- Department of Biology; Pennsylvania State University; University Park PA USA
| | | | - Matthew Reimherr
- Department of Statistics; Pennsylvania State University; University Park PA USA
| |
Collapse
|
241
|
|
242
|
Hahn C, Genner MJ, Turner GF, Joyce DA. The genomic basis of cichlid fish adaptation within the deepwater "twilight zone" of Lake Malawi. Evol Lett 2017; 1:184-198. [PMID: 30283648 PMCID: PMC6124600 DOI: 10.1002/evl3.20] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/01/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022] Open
Abstract
Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population‐level RAD‐seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome‐level specialization for life at depth as an important process in cichlid radiation.
Collapse
Affiliation(s)
- Christoph Hahn
- Evolutionary and Environmental Genomics Group (@EvoHull), School of Environmental Sciences University of Hull Hull HU5 7RX United Kingdom.,Institute of Zoology University of Graz A-8010 Graz Austria
| | - Martin J Genner
- School of Biological Sciences University of Bristol Bristol Life Sciences Building, 24 Tyndall Avenue Bristol BS8 1TQ United Kingdom
| | - George F Turner
- School of Biological Sciences Bangor University Bangor Gwynedd LL57 2UW Wales United Kingdom
| | - Domino A Joyce
- Evolutionary and Environmental Genomics Group (@EvoHull), School of Environmental Sciences University of Hull Hull HU5 7RX United Kingdom
| |
Collapse
|
243
|
Aguilar-Rangel MR, Chávez Montes RA, González-Segovia E, Ross-Ibarra J, Simpson JK, Sawers RJ. Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño. PeerJ 2017; 5:e3737. [PMID: 28852597 PMCID: PMC5572453 DOI: 10.7717/peerj.3737] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/04/2017] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Gene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions. METHODS Allele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments. RESULTS A total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates. DISCUSSION Prior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation.
Collapse
Affiliation(s)
- M. Rocío Aguilar-Rangel
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Ricardo A. Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- ABACUS: Laboratorio de Matemáticas Aplicadas y Cómputo de Alto Rendimiento del Departamento de Matemáticas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ocoyoacac, Estado de México, Mexico
| | - Eric González-Segovia
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, Center for Population Biology and Genome Center, University of California, Davis, CA, United States of America
| | - June K. Simpson
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Ruairidh J.H. Sawers
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| |
Collapse
|
244
|
Eoche-Bosy D, Gautier M, Esquibet M, Legeai F, Bretaudeau A, Bouchez O, Fournet S, Grenier E, Montarry J. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida. Mol Ecol 2017; 26:4700-4711. [PMID: 28734070 DOI: 10.1111/mec.14240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 12/30/2022]
Abstract
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.
Collapse
Affiliation(s)
- D Eoche-Bosy
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - M Gautier
- CBGP, INRA, IRD, CIRAD, Montpellier SupAgro, Montferrier-sur-Lez, France.,IBC, Montpellier, France
| | - M Esquibet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - F Legeai
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenScale, INRIA, Rennes, France
| | - A Bretaudeau
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenOuest COre Facility, INRIA, Rennes, France
| | - O Bouchez
- GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.,GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - S Fournet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - E Grenier
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - J Montarry
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| |
Collapse
|
245
|
Termignoni-García F, Jaramillo-Correa JP, Chablé-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante-Pliego P. Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient. Mol Ecol 2017; 26:4483-4496. [DOI: 10.1111/mec.14224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 05/06/2017] [Accepted: 06/12/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Flavia Termignoni-García
- Department of Zoology; National Collection of Birds (CNAV); Institute of Biology; Universidad Nacional Autónoma de México; CdMx México
| | - Juan P. Jaramillo-Correa
- Department of Evolutionary Ecology; Institute of Ecology; Universidad Nacional Autónoma de México; CdMx México
| | - Juan Chablé-Santos
- Department of Zoology; Facultad de Medicina Veterinaria y Zootecnia; Universidad Autónoma de Yucatán; Yucatán México
| | - Mark Liu
- Biodiversity Research Center; Academia Sinica; Taipei Nankang Taiwan
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology (OEB); Harvard University; Cambridge MA USA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology (OEB); Harvard University; Cambridge MA USA
| | - Patricia Escalante-Pliego
- Department of Zoology; National Collection of Birds (CNAV); Institute of Biology; Universidad Nacional Autónoma de México; CdMx México
| |
Collapse
|
246
|
Nuismer SL, Jenkins CE, Dybdahl MF. Identifying coevolving loci using interspecific genetic correlations. Ecol Evol 2017; 7:6894-6903. [PMID: 28904769 PMCID: PMC5587482 DOI: 10.1002/ece3.3107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/16/2023] Open
Abstract
Evaluating the importance of coevolution for a wide range of evolutionary questions, such as the role parasites play in the evolution of sexual reproduction, requires that we understand the genetic basis of coevolutionary interactions. Despite its importance, little progress has been made identifying the genetic basis of coevolution, largely because we lack tools designed specifically for this purpose. Instead, coevolutionary studies are often forced to re-purpose single species techniques. Here, we propose a novel approach for identifying the genes mediating locally adapted coevolutionary interactions that relies on spatial correlations between genetic marker frequencies in the interacting species. Using individual-based multi-locus simulations, we quantify the performance of our approach across a range of coevolutionary genetic models. Our results show that when one species is strongly locally adapted to the other and a sufficient number of populations can be sampled, our approach accurately identifies functionally coupled host and parasite genes. Although not a panacea, the approach we outline here could help to focus the search for coevolving genes in a wide variety of well-studied systems for which substantial local adaptation has been demonstrated.
Collapse
Affiliation(s)
| | | | - Mark F. Dybdahl
- School of Biological SciencesWashington State UniversityPullmanWAUSA
| |
Collapse
|
247
|
Aguirre-Liguori JA, Tenaillon MI, Vázquez-Lobo A, Gaut BS, Jaramillo-Correa JP, Montes-Hernandez S, Souza V, Eguiarte LE. Connecting genomic patterns of local adaptation and niche suitability in teosintes. Mol Ecol 2017; 26:4226-4240. [PMID: 28612956 DOI: 10.1111/mec.14203] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/14/2017] [Accepted: 06/01/2017] [Indexed: 01/04/2023]
Abstract
The central abundance hypothesis predicts that local adaptation is a function of the distance to the centre of a species' geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals of adaptation. We identified candidate adaptive SNPs in each population by combining neutrality tests and cline analyses. By applying linear regression models, we found that the number of candidate SNPs is positively associated with niche suitability, while genetic diversity is reduced at the limits of the geographic distribution. Our results suggest that overall, populations located at the limit of the species' niches are adapting locally. We argue that local adaptation to this limit could initiate ecological speciation processes and facilitate adaptation to global change.
Collapse
Affiliation(s)
- J A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - M I Tenaillon
- Génétique Quantitative et Evolution - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - A Vázquez-Lobo
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - B S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - J P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - S Montes-Hernandez
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato, Mexico
| | - V Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - L E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
248
|
Kang J, Ma X, He S. Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq. Sci Rep 2017; 7:2813. [PMID: 28588195 PMCID: PMC5460224 DOI: 10.1038/s41598-017-02853-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.
Collapse
Affiliation(s)
- Jingliang Kang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuhui Ma
- College of Animal Science, Guizhou University, Guizhou, 550025, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
| |
Collapse
|
249
|
Harrison TL, Wood CW, Borges IL, Stinchcombe JR. No evidence for adaptation to local rhizobial mutualists in the legume Medicago lupulina. Ecol Evol 2017; 7:4367-4376. [PMID: 28649348 PMCID: PMC5478075 DOI: 10.1002/ece3.3012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/15/2017] [Accepted: 03/27/2017] [Indexed: 12/31/2022] Open
Abstract
Local adaptation is a common but not ubiquitous feature of species interactions, and understanding the circumstances under which it evolves illuminates the factors that influence adaptive population divergence. Antagonistic species interactions dominate the local adaptation literature relative to mutualistic ones, preventing an overall assessment of adaptation within interspecific interactions. Here, we tested whether the legume Medicago lupulina is adapted to the locally abundant species of mutualistic nitrogen-fixing rhizobial bacteria that vary in frequency across its eastern North American range. We reciprocally inoculated northern and southern M. lupulina genotypes with the northern (Ensifer medicae) or southern bacterium (E. meliloti) in a greenhouse experiment. Despite producing different numbers of root nodules (the structures in which the plants house the bacteria), neither northern nor southern plants produced more seeds, flowered earlier, or were more likely to flower when inoculated with their local rhizobia. We then used a pre-existing dataset to perform a genome scan for loci that showed elevated differentiation between field-collected plants that hosted different bacteria. None of the loci we identified belonged to the well-characterized suite of legume-rhizobia symbiosis genes, suggesting that the rhizobia do not drive genetic divergence between M. lupulina populations. Our results demonstrate that symbiont local adaptation has not evolved in this mutualism despite large-scale geographic variation in the identity of the interacting species.
Collapse
Affiliation(s)
- Tia L. Harrison
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Corlett W. Wood
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Isabela L. Borges
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
- Centre for Genome Evolution and FunctionUniversity of TorontoTorontoONCanada
| |
Collapse
|
250
|
Lind BM, Friedline CJ, Wegrzyn JL, Maloney PE, Vogler DR, Neale DB, Eckert AJ. Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA. Mol Ecol 2017; 26:3168-3185. [PMID: 28316116 DOI: 10.1111/mec.14106] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/18/2022]
Abstract
Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116 231 SNPs) to describe signatures of fine-scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST = 0.0069), there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures and suggest that ongoing adaptation of many P. albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine-scale adaptation.
Collapse
Affiliation(s)
- Brandon M Lind
- Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Patricia E Maloney
- Department of Plant Pathology and Tahoe Environmental Research Center, University of California, Davis, CA, 95616, USA
| | - Detlev R Vogler
- USDA, Forest Service, Pacific Southwest Research Station, Institute of Forest Genetics, 2480 Carson Road, Placerville, CA, 95667, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| |
Collapse
|