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Bruxaux J, Zhao W, Hall D, Curtu AL, Androsiuk P, Drouzas AD, Gailing O, Konrad H, Sullivan AR, Semerikov V, Wang XR. Scots pine - panmixia and the elusive signal of genetic adaptation. THE NEW PHYTOLOGIST 2024; 243:1231-1246. [PMID: 38308133 DOI: 10.1111/nph.19563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/14/2024] [Indexed: 02/04/2024]
Abstract
Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.
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Affiliation(s)
- Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
- Forestry Research Institute of Sweden (Skogforsk), 918 21, Sävar, Sweden
| | | | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Heino Konrad
- Department of Forest Biodiversity and Nature Conservation, Unit of Ecological Genetics, Austrian Research Centre for Forests (BFW), 1140, Vienna, Austria
| | - Alexis R Sullivan
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural Division of Russian Academy of Sciences, 620144, Ekaterinburg, Russia
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
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2
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Modica A, Lalagüe H, Muratorio S, Scotti I. Rolling down that mountain: microgeographical adaptive divergence during a fast population expansion along a steep environmental gradient in European beech. Heredity (Edinb) 2024; 133:99-112. [PMID: 38890557 PMCID: PMC11286953 DOI: 10.1038/s41437-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Forest tree populations harbour high genetic diversity thanks to large effective population sizes and strong gene flow, allowing them to diversify through adaptation to local environmental pressures within dispersal distance. Many tree populations also experienced historical demographic fluctuations, including spatial population contraction or expansions at various temporal scales, which may constrain their ability to adapt to environmental variations. Our aim is to investigate how recent contraction and expansion events interfere with local adaptation, by studying patterns of adaptive divergence between closely related stands undergoing environmentally contrasted conditions, and having or not recently expanded. To investigate genome-wide signatures of local adaptation while accounting for demography, we analysed divergence in a European beech population by testing pairwise differentiation among four tree stands at ~35k Single Nucleotide Polymorphisms from ~9k genomic regions. We applied three divergence outlier search methods resting on different assumptions and targeting either single SNPs or contiguous genomic regions, while accounting for the effect of population size variations on genetic divergence. We found 27 signals of selective signatures in 19 target regions. Putatively adaptive divergence involved all stand pairs. We retrieved signals both when comparing old-growth stands and recently colonised areas and when comparing stands within the old-growth area. Therefore, adaptive divergence processes have taken place both over short time spans, under strong environmental contrasts, and over short ecological gradients, in populations that have been stable in the long term. This suggests that standing genetic variation supports local, microgeographic divergence processes, which can maintain genetic diversity at the landscape level.
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Affiliation(s)
- Andrea Modica
- INRAE, URFM, 228, Route de l'Aérodrome, 84914, Avignon, France
| | - Hadrien Lalagüe
- INRAE, EcoFoG, Campus agronomique, 97310, Kourou, French Guiana
| | - Sylvie Muratorio
- INRAE, EcoBioP, 173, Route de Saint-Jean-de-Luz RD 918, 64310, Saint-Pée-sur-Nivelle, France
| | - Ivan Scotti
- INRAE, URFM, 228, Route de l'Aérodrome, 84914, Avignon, France.
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3
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Weng YM, Kavanaugh DH, Schoville SD. Evidence for Admixture and Rapid Evolution During Glacial Climate Change in an Alpine Specialist. Mol Biol Evol 2024; 41:msae130. [PMID: 38935588 PMCID: PMC11247348 DOI: 10.1093/molbev/msae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/30/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet, despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success surviving in highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. We first tested alternative models of evolutionary divergence in the species complex. Using millions of genome-wide SNP markers from hundreds of beetles, we found evidence that the N. ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We tested several possible genetic pathways involved in adaptation to heterogeneous local environments using genome scan and genotype-environment association approaches. From the identified genes, we found enriched functions associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid demographic change, alpine beetles in the N. ingens complex underwent rapid physiological evolution.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
- Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan
| | - David H Kavanaugh
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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4
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Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. J Evol Biol 2024; 37:677-692. [PMID: 38629140 DOI: 10.1093/jeb/voae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 03/25/2024] [Accepted: 04/15/2024] [Indexed: 06/30/2024]
Abstract
The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species' demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.
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Affiliation(s)
- Lauric Reynes
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
| | - Louise Fouqueau
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
| | - Didier Aurelle
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
- Institut de Systématique Évolution Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Paris, France
| | - Stéphane Mauger
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
| | - Christophe Destombe
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
| | - Myriam Valero
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
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Bastias CC, Estarague A, Vile D, Gaignon E, Lee CR, Exposito-Alonso M, Violle C, Vasseur F. Ecological trade-offs drive phenotypic and genetic differentiation of Arabidopsis thaliana in Europe. Nat Commun 2024; 15:5185. [PMID: 38890286 PMCID: PMC11189578 DOI: 10.1038/s41467-024-49267-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Plant diversity is shaped by trade-offs between traits related to competitive ability, propagule dispersal, and stress resistance. However, we still lack a clear understanding of how these trade-offs influence species distribution and population dynamics. In Arabidopsis thaliana, recent genetic analyses revealed a group of cosmopolitan genotypes that successfully recolonized Europe from its center after the last glaciation, excluding older (relict) lineages from the distribution except for their north and south margins. Here, we tested the hypothesis that cosmopolitans expanded due to higher colonization ability, while relicts persisted at the margins due to higher tolerance to competition and/or stress. We compared the phenotypic and genetic differentiation between 71 European genotypes originating from the center, and the south and north margins. We showed that a trade-off between plant fecundity and seed mass shapes the differentiation of A. thaliana in Europe, suggesting that the success of the cosmopolitan groups could be explained by their high dispersal ability. However, at both north and south margins, we found evidence of selection for alleles conferring low dispersal but highly competitive and stress-resistance abilities. This study sheds light on the role of ecological trade-offs as evolutionary drivers of the distribution and dynamics of plant populations.
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Affiliation(s)
- Cristina C Bastias
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.
- Área de Ecología, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, Córdoba, Spain.
| | - Aurélien Estarague
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Elza Gaignon
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology & Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | | | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Müller M, Leuschner C, Weithmann G, Weigel R, Banzragch BE, Steiner W, Gailing O. A genome-wide genetic association study reveals SNPs significantly associated with environmental variables and specific leaf area in European beech. PHYSIOLOGIA PLANTARUM 2024; 176:e14334. [PMID: 38705836 DOI: 10.1111/ppl.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/07/2024]
Abstract
European beech is negatively affected by climate change and a further growth decline is predicted for large parts of its distribution range. Despite the importance of this species, little is known about its genetic adaptation and especially the genetic basis of its physiological traits. Here, we used genotyping by sequencing to identify SNPs in 43 German European beech populations growing under different environmental conditions. In total, 28 of these populations were located along a precipitation and temperature gradient in northern Germany, and single tree-based hydraulic and morphological traits were available. We obtained a set of 13,493 high-quality SNPs that were used for environmental and SNP-trait association analysis. In total, 22 SNPs were identified that were significantly associated with environmental variables or specific leaf area (SLA). Several SNPs were located in genes related to stress response. The majority of the significant SNPs were located in non-coding (intergenic and intronic) regions. These may be in linkage disequilibrium with the causative coding or regulatory regions. Our study gives insights into the genetic basis of abiotic adaptation in European beech, and provides genetic resources that can be used in future studies on this species. Besides clear patterns of local adaptation to environmental conditions of the investigated populations, the analyzed morphological and hydraulic traits explained most of the explainable genetic variation. Thus, they could successfully be altered in tree breeding programs, which may help to increase the adaptation of European beech to changing environmental conditions in the future.
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Affiliation(s)
- Markus Müller
- University of Göttingen, Forest Genetics and Forest Tree Breeding, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
| | - Christoph Leuschner
- Department Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, Göttingen, Germany
| | - Greta Weithmann
- Department Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
| | - Robert Weigel
- Department Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
- Ecological-Botanical Garden, University of Bayreuth, Bayreuth, Germany
| | - Bat-Enerel Banzragch
- Department Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
- Applied Vegetation Ecology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Wilfried Steiner
- Department Forest Genetic Resources, Northwest German Forest Research Institute, Hann. Münden, Germany
| | - Oliver Gailing
- University of Göttingen, Forest Genetics and Forest Tree Breeding, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, Göttingen, Germany
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7
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Schraiber JG, Edge MD, Pennell M. Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579721. [PMID: 38496530 PMCID: PMC10942266 DOI: 10.1101/2024.02.10.579721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.
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8
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Terasaki Hart DE, Wang IJ. Genomic architecture controls multivariate adaptation to climate change. GLOBAL CHANGE BIOLOGY 2024; 30:e17179. [PMID: 38403891 DOI: 10.1111/gcb.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/11/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024]
Abstract
As climate change advances, environmental gradients may decouple, generating novel multivariate environments that stress wild populations. A commonly invoked mechanism of evolutionary rescue is adaptive gene flow tracking climate shifts, but gene flow from populations inhabiting similar conditions on one environmental axis could cause maladaptive introgression when populations are adapted to different environmental variables that do not shift together. Genomic architecture can play an important role in determining the effectiveness and relative magnitudes of adaptive gene flow and in situ adaptation. This may have direct consequences for how species respond to climate change but is often overlooked. Here, we simulated microevolutionary responses to environmental change under scenarios defined by variation in the polygenicity, linkage, and genetic redundancy of two independent traits, one of which is adapted to a gradient that shifts under climate change. We used these simulations to examine how genomic architecture influences evolutionary outcomes under climate change. We found that climate-tracking (up-gradient) gene flow, though present in all scenarios, was strongly constrained under scenarios of lower linkage and higher polygenicity and redundancy, suggesting in situ adaptation as the predominant mechanism of evolutionary rescue under these conditions. We also found that high polygenicity caused increased maladaptation and demographic decline, a concerning result given that many climate-adapted traits may be polygenic. Finally, in scenarios with high redundancy, we observed increased adaptive capacity. This finding adds to the growing recognition of the importance of redundancy in mediating in situ adaptive capacity and suggests opportunities for better understanding the climatic vulnerability of real populations.
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Affiliation(s)
- Drew E Terasaki Hart
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
- The Nature Conservancy, Arlington, Virginia, USA
- CSIRO Environment, Brisbane, Queensland, Australia
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
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Tanaka T, Hayakawa T, Teshima KM. Power of neutrality tests for detecting natural selection. G3 (BETHESDA, MD.) 2023; 13:jkad161. [PMID: 37481468 PMCID: PMC10542275 DOI: 10.1093/g3journal/jkad161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/09/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023]
Abstract
Detection of natural selection is one of the main interests in population genetics. Thus, many tests have been developed for detecting natural selection using genomic data. Although it is recognized that the utility of tests depends on several evolutionary factors, such as the timing of selection, strength of selection, frequency of selected alleles, demographic events, and initial frequency of selected allele when selection started acting (softness of selection), the relationships between such evolutionary factors and the power of tests are not yet entirely clear. In this study, we investigated the power of 4 tests: Tajiama's D, Fay and Wu's H, relative extended haplotype homozygosity (rEHH), and integrated haplotype score (iHS), under ranges of evolutionary parameters and demographic models to quantitatively expand the understanding of approaches for detecting selection. The results show that each test detects selection within a limited parameter range, and there are still wide ranges of parameters for which none of these tests work effectively. In addition, the parameter space in which each test shows the highest power overlaps the empirical results of previous research. These results indicate that our present perspective of adaptation is limited to only a part of actual adaptation.
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Affiliation(s)
- Tomotaka Tanaka
- Graduate School of System Life Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Toshiyuki Hayakawa
- Graduate School of System Life Science, Kyushu University, Fukuoka 819-0395, Japan
- Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Kosuke M Teshima
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
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10
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Fuhrmann N, Prakash C, Kaiser TS. Polygenic adaptation from standing genetic variation allows rapid ecotype formation. eLife 2023; 12:82824. [PMID: 36852484 PMCID: PMC9977305 DOI: 10.7554/elife.82824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
Adaptive ecotype formation can be the first step to speciation, but the genetic underpinnings of this process are poorly understood. Marine midges of the genus Clunio (Diptera) have recolonized Northern European shore areas after the last glaciation. In response to local tide conditions they have formed different ecotypes with respect to timing of adult emergence, oviposition behavior and larval habitat. Genomic analysis confirms the recent establishment of these ecotypes, reflected in massive haplotype sharing between ecotypes, irrespective of whether there is ongoing gene flow or geographic isolation. QTL mapping and genome screens reveal patterns of polygenic adaptation from standing genetic variation. Ecotype-associated loci prominently include circadian clock genes, as well as genes affecting sensory perception and nervous system development, hinting to a central role of these processes in ecotype formation. Our data show that adaptive ecotype formation can occur rapidly, with ongoing gene flow and largely based on a re-assortment of existing alleles.
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Affiliation(s)
- Nico Fuhrmann
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Celine Prakash
- Max Planck Institute for Evolutionary BiologyPlönGermany
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11
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Lasky JR, Josephs EB, Morris GP. Genotype-environment associations to reveal the molecular basis of environmental adaptation. THE PLANT CELL 2023; 35:125-138. [PMID: 36005926 PMCID: PMC9806588 DOI: 10.1093/plcell/koac267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/23/2022] [Indexed: 06/14/2023]
Abstract
A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.
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Affiliation(s)
- Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily B Josephs
- Department of Plant Biology; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Sciences; Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80526, USA
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Abstract
We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.
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Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Edinburgh EH9 3FL, UK
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, 14627, NY, USA
| | - Emily B Josephs
- Department of Plant Biology and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, 48824, MI, USA
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13
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Tiret M, Olsson L, Grahn T, Karlsson B, Milesi P, Lascoux M, Lundqvist S, García‐Gil MR. Divergent selection predating the Last Glacial Maximum mainly acted on macro-phenotypes in Norway spruce. Evol Appl 2022; 16:163-172. [PMID: 36699125 PMCID: PMC9850012 DOI: 10.1111/eva.13519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of Q ST vs. F ST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.
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Affiliation(s)
- Mathieu Tiret
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden,Department of Forest Genetics and Plant PhysiologySLU, Umeå Plant Science Centre (UPSC)UmeåSweden,IGEPP, INRAE, Institut Agro, Université de RennesDomaine de la MotteLe RheuFrance
| | | | | | | | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala UniversityUppsalaSweden
| | | | - Maria Rosario García‐Gil
- Department of Forest Genetics and Plant PhysiologySLU, Umeå Plant Science Centre (UPSC)UmeåSweden
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14
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Shen Y, Gan Y, Xiao Q, Huang Z, Liu J, Gong S, Wang Y, Yu W, Luo X, Ke C, You W. Divergent Carry-Over Effects of Hypoxia during the Early Development of Abalone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17836-17848. [PMID: 36479946 DOI: 10.1021/acs.est.2c04975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
After being exposed to environmental stimuli during early developmental stages, some organisms may gain or weaken physiological regulating abilities, which would have long-lasting effects on their performance. Environmental hypoxia events can have significant effects on marine organisms, but for breeding programs and other practical applications, it is important to further explore the long-term physiological effects of early hypoxia exposure in economically significant species. In this study, the Pacific abalone Haliotis discus hannai was exposed to moderate hypoxia (∼4 mg/L) from zygote to trochophora, and the assessments of hypoxia tolerance were conducted on the grow-out stage. The results revealed that juvenile abalones exposed to hypoxia at the early development stages were more hypoxia-tolerant but with slower weight growth, a phenomenon called the trade-off between growth and survival. These phenotypic effects driven by the hypoxia exposure were explained by strong selection of genes involved in signal transduction, autophagy, apoptosis, and hormone regulation. Moreover, long non-coding RNA regulation plays an important role modulating carry-over effects by controlling DNA replication and repair, signal transduction, myocardial activity, and hormone regulation. This study revealed that the ability to create favorable phenotypic differentiation through genetic selection and/or epigenetic regulation is important for the survival and development of aquatic animals in the face of rapidly changing environmental conditions.
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Affiliation(s)
- Yawei Shen
- State Key Laboratory of Marine Environmental Science, College of the Environmental and Ecology, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
- Fujian Institute for Sustainable Oceans, Xiamen University, Xiamen361102, China
| | - Yang Gan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Qizhen Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of the Environmental and Ecology, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Junyu Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Shihai Gong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Yi Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Wenchao Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen361102, PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen361102, China
- Fujian Institute for Sustainable Oceans, Xiamen University, Xiamen361102, China
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15
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Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data. Genes (Basel) 2022; 13:genes13122310. [PMID: 36553577 PMCID: PMC9777694 DOI: 10.3390/genes13122310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar (AWB) were selected for 10× deep-genome resequencing. The signatures of the selection were analyzed to explore the genetic basis of their germplasm characteristics and to identify excellent germplasm-related functional genes based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected across the genome in 30 pigs. Most of the genetic variations were synonym mutations and existed in the intergenic region. We identified 275 selected regions (top 1%) harboring 85 genes by applying a crossover approach based on genetic differentiation (FST) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs' breeding. The SMPD4 and DDX18 genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 genes were involved in biological regulation of immune T cells and phagocytes. The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN and HIF1A genes were related to fat deposition and muscle development. Moreover, 138 overlapping regions were detected in selected regions and ROH islands of AQ pigs. Additionally, we found that the QTLs with the most overlapping regions were related to back fat thickness, meat color, pH value, fatty acid content, immune cells, parasitic immunity, and bacterial immunity. Based on functional enrichment analysis and QTLs mapping, we conducted further research on the molecular genetic basis of germplasm traits (disease resistance and excellent meat quality). These results are a reliable resource for conserving germplasm resources and exploiting molecular markers of AQ pigs.
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16
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Reproductive isolation via polygenic local adaptation in sub-divided populations: Effect of linkage disequilibria and drift. PLoS Genet 2022; 18:e1010297. [PMID: 36048903 PMCID: PMC9473638 DOI: 10.1371/journal.pgen.1010297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 09/14/2022] [Accepted: 06/16/2022] [Indexed: 12/01/2022] Open
Abstract
This paper considers how polygenic local adaptation and reproductive isolation between hybridizing populations is influenced by linkage disequilibria (LD) between loci, in scenarios where both gene flow and genetic drift counteract selection. It shows that the combined effects of multi-locus LD and genetic drift on allele frequencies at selected loci and on heterozygosity at neutral loci are predicted accurately by incorporating (deterministic) effective migration rates into the diffusion approximation (for selected loci) and into the structured coalescent (for neutral loci). Theoretical approximations are tested against individual-based simulations and used to investigate conditions for the maintenance of local adaptation on an island subject to one-way migration from a differently adapted mainland, and in an infinite-island population with two habitats under divergent selection. The analysis clarifies the conditions under which LD between sets of locally deleterious alleles allows these to be collectively eliminated despite drift, causing sharper and (under certain conditions) shifted migration thresholds for loss of adaptation. Local adaptation also has counter-intuitive effects on neutral (relative) divergence: FST is highest for a pair of subpopulations belonging to the same (rare) habitat, despite the lack of reproductive isolation between them. Environmental adaptation often involves spatially heterogeneous selection at many genetic loci. Thus, the evolutionary consequences of hybridisation between populations adapted to different environments depend on the coupled dynamics of multiple loci under selection, migration and genetic drift, making them challenging to predict. Here, I introduce theoretical approximations that accurately capture the effect of such coupling on allele frequencies at individual loci, while also accounting for the stochastic effects of genetic drift. I then use these approximations to study hybridisation in a metapopulation consisting of many interconnected subpopulations, where each subpopulation belongs to one of two habitats under divergent selection. The analysis clarifies how subpopulations belonging to a rare habitat can maintain local adaptation despite high levels of migration if net selection against multi-locus genotypes is stronger than a threshold which depends on the relative abundances of the two habitats. Further, local adaptation in a metapopulation can significantly elevate FST between subpopulations belonging to the same habitat, even though these are not reproductively isolated. These findings highlight the importance of carefully considering the genetic architecture and spatial context of divergence when interpreting patterns of genomic differentiation between speciating populations.
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17
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Cooper HF, Best RJ, Andrews LV, Corbin JPM, Garthwaite I, Grady KC, Gehring CA, Hultine KR, Whitham TG, Allan GJ. Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species. Mol Ecol 2022; 31:5024-5040. [PMID: 35947510 DOI: 10.1111/mec.16645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022]
Abstract
Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST -FST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on QST -FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R2 up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.
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Affiliation(s)
- Hillary F Cooper
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca J Best
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Lela V Andrews
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA
| | - Jaclyn P M Corbin
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Iris Garthwaite
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin C Grady
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Catherine A Gehring
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin R Hultine
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, USA
| | - Thomas G Whitham
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Gerard J Allan
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
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18
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Waples RS, Ford MJ, Nichols K, Kardos M, Myers J, Thompson TQ, Anderson EC, Koch IJ, McKinney G, Miller MR, Naish K, Narum SR, O'Malley KG, Pearse DE, Pess GR, Quinn TP, Seamons TR, Spidle A, Warheit KI, Willis SC. Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon. J Hered 2022; 113:121-144. [PMID: 35575083 DOI: 10.1093/jhered/esab069] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/07/2021] [Indexed: 11/13/2022] Open
Abstract
The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California's equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Michael J Ford
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Krista Nichols
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | | | - Jim Myers
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | | | - Eric C Anderson
- Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Ilana J Koch
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Garrett McKinney
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
- Washington Department of Fish and Wildlife, Olympia, WA, USA
| | | | - Kerry Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WAUSA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | | | - Devon E Pearse
- Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - George R Pess
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Thomas P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WAUSA
| | - Todd R Seamons
- Washington Department of Fish and Wildlife, Olympia, WA, USA
| | - Adrian Spidle
- Northwest Indian Fisheries Commission, Olympia, WA, USA
| | | | - Stuart C Willis
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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19
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Brown JI, Harrigan RJ, Lavretsky P. Evolutionary and Ecological Drivers of Local Adaptation and Speciation in a North American Avian Species Complex. Mol Ecol 2022; 31:2578-2593. [PMID: 35263000 DOI: 10.1111/mec.16423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Abstract
Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for non-model organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in a climate refugia arising during a glacial period in in a southwestern North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that likely reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage.
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Affiliation(s)
- Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
| | - Ryan J Harrigan
- Center for Tropical Research, University of California, Los Angeles, La Kretz Hall, Suite 300, Los Angeles, CA, 90095, U.S.A
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
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20
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Cubry P, Oddou-Muratorio S, Scotti I, Lefèvre F. Interactions between microenvironment, selection and genetic architecture drive multiscale adaptation in a simulation experiment. J Evol Biol 2022; 35:451-466. [PMID: 35170114 PMCID: PMC9306464 DOI: 10.1111/jeb.13988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Abstract
When environmental conditions differ both within and among populations, multiscale adaptation results from processes at both scales and interference across scales. We hypothesize that within-population environmental heterogeneity influences the chance of success of migration events, both within and among populations, and maintains within-population adaptive differentiation. We used a simulation approach to analyze the joint effects of environmental heterogeneity patterns, selection intensity and number of QTL controlling a selected trait on local adaptation in a hierarchical metapopulation design. We show the general effects of within-population environmental heterogeneity: (i) it increases occupancy rate at the margins of distribution ranges, under extreme environments and high levels of selection; (ii) it increases the adaptation lag in all environments; (iii) it impacts the genetic variance in each environment, depending on the ratio of within- to between-populations environmental heterogeneity; (iv) it reduces the selection-induced erosion of adaptive gene diversity. Most often, the smaller the number of QTL involved, the stronger are these effects. We also show that both within- and between-populations phenotypic differentiation (QST ) mainly results from covariance of QTL effects rather than QTL differentiation (FSTq ), that within-population QTL differentiation is negligible, and that stronger divergent selection is required to produce adaptive differentiation within populations than among populations. With a high number of QTL, when the difference between environments within populations exceeds the smallest difference between environments across populations, high levels of within-population differentiation can be reached, reducing differentiation among populations. Our study stresses the need to account for within-population environmental heterogeneity when investigating local adaptation.
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Affiliation(s)
- Philippe Cubry
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France.,DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | - Sylvie Oddou-Muratorio
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France.,ECOBIOP, Université de Pau et des Pays de l'Adour, E2S UPPA, INRAE, Saint-Pée-sur-Nivelle, France
| | - Ivan Scotti
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France
| | - François Lefèvre
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France
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21
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Population Analysis of Diospyros lotus in the Northwestern Caucasus Based on Leaf Morphology and Multilocus DNA Markers. Int J Mol Sci 2022; 23:ijms23042192. [PMID: 35216308 PMCID: PMC8877681 DOI: 10.3390/ijms23042192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 01/02/2023] Open
Abstract
Diospyros lotus is the one of the most frost-tolerant species in the Diospyros genera, used as a rootstock for colder regions. Natural populations of D. lotus have a fragmented character of distribution in the Northwestern Caucasus, one of the coldest regions of Diospyros cultivation. To predict the behavior of D. lotus populations in an extreme environment, it is necessary to investigate the intraspecific genetic diversity and phenotypic variability of populations in the colder regions. In this study, we analyzed five geographically distant populations of D. lotus according to 33 morphological leaf traits, and the most informative traits were established, namely, leaf length, leaf width, leaf index (leaf to length ratio) and the length of the fourth veins. Additionally, we evaluated the intraspecific genetic diversity of D. lotus using ISSR and SCoT markers and proposed a new parameter for the evaluation of genetic polymorphism among populations, in order to eliminate the effect of sample number. This new parameter is the relative genetic polymorphism, which is the ratio of polymorphism to the number of samples. Based on morphological and genetic data, the northernmost population from Shkhafit was phenotypically and genetically distant from the other populations. The correspondence between several morphological traits (leaf width, leaf length and first to fifth right vein angles) and several marker bands (SCoT5, SCoT7, SCoT30: 800–1500 bp; ISSR13, ISSR14, ISSR880: 500–1000 bp) were observed for the Shkhafit population. Unique SCoT and ISSR fragments can be used as markers for breeding purposes. The results provide a better understanding of adaptive mechanisms in D. lotus in extreme environments and will be important for the further expansion of the cultivation area for persimmon in colder regions.
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22
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de Miguel M, Rodríguez-Quilón I, Heuertz M, Hurel A, Grivet D, Jaramillo-Correa JP, Vendramin GG, Plomion C, Majada J, Alía R, Eckert AJ, González-Martínez SC. Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait., Pinaceae). Mol Ecol 2022; 31:2089-2105. [PMID: 35075727 DOI: 10.1111/mec.16367] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic, i.e., they have a genetic architecture determined by numerous loci each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyze this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response traits) in a clonal common-garden network, planted in contrasted environments (over 12,500 trees). Most of the analyzed traits showed evidence of local adaptation based on Qst -Fst comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change.
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Affiliation(s)
- Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.,EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Agathe Hurel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Juan-Pablo Jaramillo-Correa
- Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, México City, CDMX 04510, Mexico
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino (FI), Italy
| | | | - Juan Majada
- Sección Forestal, SERIDA, Finca Experimental ''La Mata'', 33820, Grado, Principado de Asturias, Spain
| | - Ricardo Alía
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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23
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Gay L, Dhinaut J, Jullien M, Vitalis R, Navascués M, Ranwez V, Ronfort J. Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift. Ecol Evol 2022; 12:e8555. [PMID: 35127051 PMCID: PMC8794724 DOI: 10.1002/ece3.8555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/10/2022] Open
Abstract
Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes. Here, we used a resurrection study to test for adaptation in a selfing population of Medicago truncatula, by comparing the genetic composition and flowering times across 22 generations. We found evidence for evolution toward earlier flowering times by about two days and a peculiar genetic structure, typical of highly selfing populations, where some multilocus genotypes (MLGs) are persistent through time. We used the change in frequency of the MLGs through time as a multilocus fitness measure and built a selection gradient that suggests evolution toward earlier flowering times. Yet, a simulation model revealed that the observed change in flowering time could be explained by drift alone, provided the effective size of the population is small enough (<150). These analyses suffer from the difficulty to estimate the effective size in a highly selfing population, where effective recombination is severely reduced.
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Affiliation(s)
- Laurène Gay
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Julien Dhinaut
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
Evolutionary Biology and Ecology of AlgaeUPMCUniversity of Paris VI, UC, UACH, UMI 3614CNRSSorbonne UniversitésRoscoffFrance
| | - Margaux Jullien
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
INRAUniv. Paris‐SudCNRSAgroParisTechGQE – Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Renaud Vitalis
- CIRADINRAEInstitut AgroIRDCBGPUniv MontpellierMontpellierFrance
| | | | - Vincent Ranwez
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Joëlle Ronfort
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
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24
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Hartfield M, Poulsen NA, Guldbrandtsen B, Bataillon T. Using singleton densities to detect recent selection in Bos taurus. Evol Lett 2021; 5:595-606. [PMID: 34917399 PMCID: PMC8645200 DOI: 10.1002/evl3.263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/05/2022] Open
Abstract
Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the "Singleton Density Score" (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans-milk protein content, milk fat content, and stature-have been subject to directional selection. Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.
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Affiliation(s)
- Matthew Hartfield
- Bioinformatics Research CentreAarhus UniversityAarhusDK‐8000Denmark
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3FLUnited Kingdom
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and GeneticsAarhus UniversityTjeleDK‐8830Denmark
- Rheinische Friedrich‐Wilhelms‐Universität BonnInstitut für TierwissenschaftenBonnDE‐53115Germany
- Department of Veterinary SciencesCopenhagen UniversityFrederiksberg CDK‐1870Denmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityAarhusDK‐8000Denmark
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25
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Haenel Q, Guerard L, MacColl ADC, Berner D. The maintenance of standing genetic variation: Gene flow vs. selective neutrality in Atlantic stickleback fish. Mol Ecol 2021; 31:811-821. [PMID: 34753205 PMCID: PMC9299253 DOI: 10.1111/mec.16269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022]
Abstract
Adaptation to derived habitats often occurs from standing genetic variation. The maintenance within ancestral populations of genetic variants favourable in derived habitats is commonly ascribed to long‐term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favoured in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish (Gasterosteus aculeatus) to a rare derived habitat—nutrient‐depleted acidic lakes—based on whole‐genome sequence data. Sequencing marine stickleback from six locations across the Atlantic Ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic‐adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of standing genetic variation, and calls for a better understanding of the fitness consequences of adaptive variation across habitats and genomic backgrounds.
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Affiliation(s)
- Quiterie Haenel
- Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Laurent Guerard
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | | | - Daniel Berner
- Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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26
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Abstract
Understanding the genetic architecture of complex traits is a major objective in biology. The standard approach for doing so is genome-wide association studies (GWAS), which aim to identify genetic polymorphisms responsible for variation in traits of interest. In human genetics, consistency across studies is commonly used as an indicator of reliability. However, if traits are involved in adaptation to the local environment, we do not necessarily expect reproducibility. On the contrary, results may depend on where you sample, and sampling across a wide range of environments may decrease the power of GWAS because of increased genetic heterogeneity. In this study, we examine how sampling affects GWAS in the model plant species Arabidopsis thaliana. We show that traits like flowering time are indeed influenced by distinct genetic effects in local populations. Furthermore, using gene expression as a molecular phenotype, we show that some genes are globally affected by shared variants, whereas others are affected by variants specific to subpopulations. Remarkably, the former are essentially all cis-regulated, whereas the latter are predominately affected by trans-acting variants. Our result illustrate that conclusions about genetic architecture can be extremely sensitive to sampling and population structure.
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Affiliation(s)
| | - Stephan Reinert
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
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27
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Rajora OP, Zinck JWR. Genetic Diversity, Structure and Effective Population Size of Old-Growth vs. Second-Growth Populations of Keystone and Long-Lived Conifer, Eastern White Pine ( Pinus strobus): Conservation Value and Climate Adaptation Potential. Front Genet 2021; 12:650299. [PMID: 34456961 PMCID: PMC8388927 DOI: 10.3389/fgene.2021.650299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/21/2021] [Indexed: 11/15/2022] Open
Abstract
Whether old-growth (OG) forests have higher genetic diversity and effective population size, consequently higher conservation value and climate adaptive potential than second-growth (SG) forests, remain an unresolved issue. We have tested the hypothesis that old-growth forest tree populations have higher genetic diversity, effective population size (NE ), climate adaptive potential and conservation value and lower genetic differentiation than second-growth forest tree populations, employing a keystone and long-lived conifer, eastern white pine (EWP; Pinus strobus). Genetic diversity and population structure of old-growth and second-growth populations of eastern white pine (EWP) were examined using microsatellites of the nuclear and chloroplast genomes and single nucleotide polymorphisms (SNPs) in candidate nuclear genes putatively involved in adaptive responses to climate and underlying multilocus genetic architecture of local adaptation to climate in EWP. Old-growth and second-growth EWP populations had statistically similar genetic diversity, inbreeding coefficient and inter-population genetic differentiation based on nuclear microsatellites (nSSRs) and SNPs. However, old-growth populations had significantly higher chloroplast microsatellites (cpSSRs) haploid diversity than second-growth populations. Old-growth EWP populations had significantly higher coalescence-based historical long-term NE than second-growth EWP populations, but the linkage disequilibrium (LD)-based contemporary NE estimates were statistically similar between the old-growth and second-growth EWP populations. Analyses of population genetic structure and inter-population genetic relationships revealed some genetic constitution differences between the old-growth and second-growth EWP populations. Overall, our results suggest that old-growth and second-growth EWP populations have similar genetic resource conservation value. Because old-growth and second-growth EWP populations have similar levels of genetic diversity in genes putatively involved in adaptive responses to climate, old-growth, and second-growth populations may have similar adaptive potential under climate change. Our results could potentially be generalized across most of the boreal and temperate conifer forest trees. Our study contributes to address a long-standing issue, advances research field and knowledge about conservation and ecological and climate adaptation of forest trees.
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Affiliation(s)
- Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada
| | - John W R Zinck
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada
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28
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Meger J, Ulaszewski B, Burczyk J. Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. BMC Genomics 2021; 22:583. [PMID: 34332553 PMCID: PMC8325806 DOI: 10.1186/s12864-021-07907-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. RESULTS We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. CONCLUSIONS Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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29
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Cao LJ, Li BY, Chen JC, Zhu JY, Hoffmann AA, Wei SJ. Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness. Mol Ecol 2021; 30:4204-4219. [PMID: 34278603 DOI: 10.1111/mec.16055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 05/23/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders based on ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate-associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and noninvasive species across their native range.
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Affiliation(s)
- Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Bing-Yan Li
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jin-Cui Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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30
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Farleigh K, Vladimirova SA, Blair C, Bracken JT, Koochekian N, Schield DR, Card DC, Finger N, Henault J, Leaché AD, Castoe TA, Jezkova T. The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos). Mol Ecol 2021; 30:4481-4496. [PMID: 34245067 DOI: 10.1111/mec.16070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/30/2022]
Abstract
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP data set, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations.
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Affiliation(s)
- Keaka Farleigh
- Department of Biology, Miami University, Oxford, Ohio, USA
| | | | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, New York, USA.,Biology PhD Program, CUNY Graduate Center, New York, New York, USA
| | | | | | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Nicholas Finger
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, New York, USA
| | | | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, Oxford, Ohio, USA
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31
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Walters SJ, Robinson TP, Byrne M, Wardell‐Johnson GW, Nevill P. Association of putatively adaptive genetic variation with climatic variables differs between a parasite and its host. Evol Appl 2021; 14:1732-1746. [PMID: 34295360 PMCID: PMC8288004 DOI: 10.1111/eva.13234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 11/28/2022] Open
Abstract
Parasitism is a pervasive phenomenon in nature with the relationship between species driving evolution in both parasite and host. Due to their host-dependent lifestyle, parasites may adapt to the abiotic environment in ways that differ from their hosts or from free-living relatives; yet rarely has this been assessed. Here, we test two competing hypotheses related to whether putatively adaptive genetic variation in a specialist mistletoe associates with the same, or different, climatic variables as its host species. We sampled 11 populations of the specialist mistletoe Amyema gibberula var. tatei (n = 154) and 10 populations of its associated host Hakea recurva subsp. recurva (n = 160). Reduced-representation sequencing was used to obtain genome-wide markers and putatively adaptive variation detected using genome scan methods. Climate associations were identified using generalized dissimilarity modelling, and these were mapped geographically to visualize the spatial patterns of genetic composition. Our results supported the hypothesis of parasites and host species responding differently to climatic variables. Temperature was relatively more important in predicting allelic turnover in the specialist mistletoe while precipitation was more important for the host. This suggests that parasitic plants and host species may respond differently to selective pressures, potentially as a result of differing nutrient acquisition strategies. Specifically, mistletoes acquire water from hosts (rather than the abiotic environment), which may provide a buffer to precipitation as a selective pressure. This work deepens and complements the physiological and other ecological studies of adaptation and provides a window into the evolutionary processes that underlie previously observed phenomena. Applying these methods to a comparative study in a host-parasite system has also highlighted factors that affect the study of selection pressure on nonmodel organisms, such as differing adaptation rates and lack of reference genomes.
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Affiliation(s)
- Sheree J. Walters
- ARC Centre for Mine Site RestorationSchool of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | - Todd P. Robinson
- School of Earth and Planetary ScienceCurtin UniversityBentleyWAAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentleyWAAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | - Grant W. Wardell‐Johnson
- ARC Centre for Mine Site RestorationSchool of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | - Paul Nevill
- ARC Centre for Mine Site RestorationSchool of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
- Trace and Environmental DNA LaboratorySchool of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
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32
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Zhou C, Feng Y, Li G, Wang M, Jian J, Wang Y, Zhang W, Song Z, Li L, Lu B, Yang J. The New Is Old: Novel Germination Strategy Evolved From Standing Genetic Variation in Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:699464. [PMID: 34234803 PMCID: PMC8256273 DOI: 10.3389/fpls.2021.699464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/28/2021] [Indexed: 06/01/2023]
Abstract
Feralization of crop plants has aroused an increasing interest in recent years, not only for the reduced yield and quality of crop production caused by feral plants but also for the rapid evolution of novel traits that facilitate the evolution and persistence of weedy forms. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, with separate and independent origins. The weedy rice distributed in eastern and northeastern China did not diverge from their cultivated ancestors by reverting to the pre-domestication trait of seed dormancy during feralization. Instead, they developed a temperature-sensing mechanism to control the timing of seed germination. Subsequent divergence in the minimum critical temperature for germination has been detected between northeastern and eastern populations. An integrative analysis was conducted using combinations of phenotypic, genomic and transcriptomic data to investigate the genetic mechanism underlying local adaptation and feralization. A dozen genes were identified, which showed extreme allele frequency differences between eastern and northeastern populations, and high correlations between allele-specific gene expression and feral phenotypes. Trancing the origin of potential adaptive alleles based on genomic sequences revealed the presence of most selected alleles in wild and cultivated rice genomes, indicating that weedy rice drew upon pre-existing, "conditionally neutral" alleles to respond to the feral selection regimes. The cryptic phenotype was exposed by activating formerly silent alleles to facilitate the transition from cultivation to wild existence, promoting the evolution and persistence of weedy forms.
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Affiliation(s)
- Chengchuan Zhou
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Yang Feng
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Gengyun Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Mengli Wang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Jinjing Jian
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Yuguo Wang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Wenju Zhang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Zhiping Song
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Linfeng Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Baorong Lu
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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33
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Kess T, Dempson JB, Lehnert SJ, Layton KKS, Einfeldt A, Bentzen P, Salisbury SJ, Messmer AM, Duffy S, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop BF, O'Connell MF, Bradbury IR. Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs. Mol Ecol 2021; 30:4415-4432. [PMID: 34152667 DOI: 10.1111/mec.16033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/30/2022]
Abstract
The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (FST = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.
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Affiliation(s)
- Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - J Brian Dempson
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Sarah J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Kara K S Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Anthony Einfeldt
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | | | - Amber M Messmer
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Steven Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | | | - Cameron M Nugent
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Moira M Ferguson
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Michael F O'Connell
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Ian R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
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Sherpa S, Després L. The evolutionary dynamics of biological invasions: A multi-approach perspective. Evol Appl 2021; 14:1463-1484. [PMID: 34178098 PMCID: PMC8210789 DOI: 10.1111/eva.13215] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 01/02/2023] Open
Abstract
Biological invasions, the establishment and spread of non-native species in new regions, can have extensive economic and environmental consequences. Increased global connectivity accelerates introduction rates, while climate and land-cover changes may decrease the barriers to invasive populations spread. A detailed knowledge of the invasion history, including assessing source populations, routes of spread, number of independent introductions, and the effects of genetic bottlenecks and admixture on the establishment success, adaptive potential, and further spread, is crucial from an applied perspective to mitigate socioeconomic impacts of invasive species, as well as for addressing fundamental questions on the evolutionary dynamics of the invasion process. Recent advances in genomics together with the development of geographic information systems provide unprecedented large genetic and environmental datasets at global and local scales to link population genomics, landscape ecology, and species distribution modeling into a common framework to study the invasion process. Although the factors underlying population invasiveness have been extensively reviewed, analytical methods currently available to optimally combine molecular and environmental data for inferring invasive population demographic parameters and predicting further spreading are still under development. In this review, we focus on the few recent insect invasion studies that combine different datasets and approaches to show how integrating genetic, observational, ecological, and environmental data pave the way to a more integrative biological invasion science. We provide guidelines to study the evolutionary dynamics of invasions at each step of the invasion process, and conclude on the benefits of including all types of information and up-to-date analytical tools from different research areas into a single framework.
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Affiliation(s)
- Stéphanie Sherpa
- CNRSLECAUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
| | - Laurence Després
- CNRSLECAUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
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35
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Flanagan BA, Krueger-Hadfield SA, Murren CJ, Nice CC, Strand AE, Sotka EE. Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader. Mol Ecol 2021; 30:1962-1978. [PMID: 33604965 DOI: 10.1111/mec.15854] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/18/2021] [Accepted: 02/01/2021] [Indexed: 12/20/2022]
Abstract
The genomic variation of an invasive species may be affected by complex demographic histories and evolutionary changes during the invasion. Here, we describe the relative influence of bottlenecks, clonality, and population expansion in determining genomic variability of the widespread red macroalga Agarophyton vermiculophyllum. Its introduction from mainland Japan to the estuaries of North America and Europe coincided with shifts from predominantly sexual to partially clonal reproduction and rapid adaptive evolution. A survey of 62,285 SNPs for 351 individuals from 35 populations, aligned to 24 chromosome-length scaffolds indicate that linkage disequilibrium (LD), observed heterozygosity (Ho ), Tajima's D, and nucleotide diversity (Pi) were greater among non-native than native populations. Evolutionary simulations indicate LD and Tajima's D were consistent with a severe population bottleneck. Also, the increased rate of clonal reproduction in the non-native range could not have produced the observed patterns by itself but may have magnified the bottleneck effect on LD. Elevated marker diversity in the genetic source populations could have contributed to the increased Ho and Pi observed in the non-native range. We refined the previous invasion source region to a ~50 km section of northeastern Honshu Island. Outlier detection methods failed to reveal any consistently differentiated loci shared among invaded regions, probably because of the complex A. vermiculophyllum demographic history. Our results reinforce the importance of demographic history, specifically founder effects, in driving genomic variation of invasive populations, even when localized adaptive evolution and reproductive system shifts are observed.
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Affiliation(s)
- Ben A Flanagan
- Department of Biology, College of Charleston, Charleston, SC, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stacy A Krueger-Hadfield
- Department of Biology, College of Charleston, Charleston, SC, USA.,Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Chris C Nice
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, TX, USA
| | - Allan E Strand
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Erik E Sotka
- Department of Biology, College of Charleston, Charleston, SC, USA
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36
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Bothwell HM, Evans LM, Hersch-Green EI, Woolbright SA, Allan GJ, Whitham TG. Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02254. [PMID: 33159398 DOI: 10.1002/eap.2254] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/17/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here, we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) P. angustifolia is differentiated into six genetic groups across its range from México to Canada and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, P. fremontii. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.
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Affiliation(s)
- Helen M Bothwell
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, 617 South Beaver Street, PO Box 5640, Flagstaff, Arizona, 86011, USA
| | - Luke M Evans
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, 617 South Beaver Street, PO Box 5640, Flagstaff, Arizona, 86011, USA
| | - Erika I Hersch-Green
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, 617 South Beaver Street, PO Box 5640, Flagstaff, Arizona, 86011, USA
| | - Scott A Woolbright
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, 617 South Beaver Street, PO Box 5640, Flagstaff, Arizona, 86011, USA
| | - Gerard J Allan
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, 617 South Beaver Street, PO Box 5640, Flagstaff, Arizona, 86011, USA
- Merriam-Powell Center for Environmental Research, Northern Arizona University, 800 South Beaver Street, PO Box 6077, Flagstaff, Arizona, 86011, USA
| | - Thomas G Whitham
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, 617 South Beaver Street, PO Box 5640, Flagstaff, Arizona, 86011, USA
- Merriam-Powell Center for Environmental Research, Northern Arizona University, 800 South Beaver Street, PO Box 6077, Flagstaff, Arizona, 86011, USA
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37
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Depardieu C, Gérardi S, Nadeau S, Parent GJ, Mackay J, Lenz P, Lamothe M, Girardin MP, Bousquet J, Isabel N. Connecting tree-ring phenotypes, genetic associations and transcriptomics to decipher the genomic architecture of drought adaptation in a widespread conifer. Mol Ecol 2021; 30:3898-3917. [PMID: 33586257 PMCID: PMC8451828 DOI: 10.1111/mec.15846] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/15/2021] [Accepted: 01/27/2021] [Indexed: 01/02/2023]
Abstract
As boreal forests face significant threats from climate change, understanding evolutionary trajectories of coniferous species has become fundamental to adapting management and conservation to a drying climate. We examined the genomic architecture underlying adaptive variation related to drought tolerance in 43 populations of a widespread boreal conifer, white spruce (Piceaglauca [Moench] Voss), by combining genotype–environment associations, genotype–phenotype associations, and transcriptomics. Adaptive genetic variation was identified by correlating allele frequencies for 6,153 single nucleotide polymorphisms from 2,606 candidate genes with temperature, precipitation and aridity gradients, and testing for significant associations between genotypes and 11 dendrometric and drought‐related traits (i.e., anatomical, growth response and climate‐sensitivity traits) using a polygenic model. We identified a set of 285 genes significantly associated with a climatic factor or a phenotypic trait, including 110 that were differentially expressed in response to drought under greenhouse‐controlled conditions. The interlinked phenotype–genotype–environment network revealed eight high‐confidence genes involved in white spruce adaptation to drought, of which four were drought‐responsive in the expression analysis. Our findings represent a significant step toward the characterization of the genomic basis of drought tolerance and adaptation to climate in conifers, which is essential to enable the establishment of resilient forests in view of new climate conditions. see also the Perspective by Lars Opgenoorth and Christian Rellstab
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Affiliation(s)
- Claire Depardieu
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
| | - Sébastien Gérardi
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
| | - Simon Nadeau
- Natural Resources CanadaCanadian Forest ServiceCanadian Wood Fibre CenterQuébecQCCanada
| | - Geneviève J. Parent
- Laboratory of GenomicsMaurice‐Lamontagne Institute, Fisheries and Oceans CanadaMont‐JoliQCCanada
| | - John Mackay
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Patrick Lenz
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceCanadian Wood Fibre CenterQuébecQCCanada
| | - Manuel Lamothe
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
| | - Martin P. Girardin
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
- Centre for Forest ResearchUniversité du Québec à MontréalMontréalQCCanada
| | - Jean Bousquet
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
| | - Nathalie Isabel
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
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38
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Ehrlich MA, Wagner DN, Oleksiak MF, Crawford DL. Polygenic Selection within a Single Generation Leads to Subtle Divergence among Ecological NichesINc. Genome Biol Evol 2021; 13:evaa257. [PMID: 33313716 PMCID: PMC7875003 DOI: 10.1093/gbe/evaa257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/09/2020] [Accepted: 12/09/2020] [Indexed: 11/23/2022] Open
Abstract
Selection on standing genetic variation may be effective enough to allow for adaptation to distinct niche environments within a single generation. Minor allele frequency changes at multiple, redundant loci of small effect can produce remarkable phenotypic shifts. Yet, demonstrating rapid adaptation via polygenic selection in the wild remains challenging. Here we harness natural replicate populations that experience similar selection pressures and harbor high within-, yet negligible among-population genetic variation. Such populations can be found among the teleost Fundulus heteroclitus that inhabits marine estuaries characterized by high environmental heterogeneity. We identify 10,861 single nucleotide polymorphisms in F. heteroclitus that belong to a single, panmictic population yet reside in environmentally distinct niches (one coastal basin and three replicate tidal ponds). By sampling at two time points within a single generation, we quantify both allele frequency change within as well as spatial divergence among niche subpopulations. We observe few individually significant allele frequency changes yet find that the "number" of moderate changes exceeds the neutral expectation by 10-100%. We find allele frequency changes to be significantly concordant in both direction and magnitude among all niche subpopulations, suggestive of parallel selection. In addition, within-generation allele frequency changes generate subtle but significant divergence among niches, indicative of local adaptation. Although we cannot distinguish between selection and genotype-dependent migration as drivers of within-generation allele frequency changes, the trait/s determining fitness and/or migration likelihood appear to be polygenic. In heterogeneous environments, polygenic selection and polygenic, genotype-dependent migration offer conceivable mechanisms for within-generation, local adaptation to distinct niches.
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Affiliation(s)
- Moritz A Ehrlich
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, FL, USA
| | - Dominique N Wagner
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, FL, USA
| | - Marjorie F Oleksiak
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, FL, USA
| | - Douglas L Crawford
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, FL, USA
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39
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De La Torre AR, Wilhite B, Puiu D, St. Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir. Genes (Basel) 2021; 12:110. [PMID: 33477542 PMCID: PMC7831106 DOI: 10.3390/genes12010110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species' predictions under climate change.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Benjamin Wilhite
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Daniela Puiu
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - John Bradley St. Clair
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331, USA;
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Steven L. Salzberg
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Brian Allen
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
| | - David B. Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
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40
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Shryock DF, Washburn LK, DeFalco LA, Esque TC. Harnessing landscape genomics to identify future climate resilient genotypes in a desert annual. Mol Ecol 2021; 30:698-717. [PMID: 33007116 DOI: 10.1111/mec.15672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/16/2022]
Abstract
Local adaptation features critically in shaping species responses to changing environments, complicating efforts to revegetate degraded areas. Rapid climate change poses an additional challenge that could reduce fitness of even locally sourced seeds in restoration. Predictive restoration strategies that apply seeds with favourable adaptations to future climate may promote long-term resilience. Landscape genomics is increasingly used to assess spatial patterns in local adaption and may represent a cost-efficient approach for identifying future-adapted genotypes. To demonstrate such an approach, we genotyped 760 plants from 64 Mojave Desert populations of the desert annual Plantago ovata. Genome scans on 5,960 SNPs identified 184 potentially adaptive loci related to climate and satellite vegetation metrics. Causal modelling indicated that variation in potentially adaptive loci was not confounded by isolation by distance or isolation by habitat resistance. A generalized dissimilarity model (GDM) attributed spatial turnover in potentially adaptive loci to temperature, precipitation and NDVI amplitude, a measure of vegetation green-up potential. By integrating a species distribution model (SDM), we find evidence that summer maximum temperature may both constrain the range of P. ovata and drive adaptive divergence in populations exposed to higher temperatures. Within the species' current range, warm-adapted genotypes are predicted to experience a fivefold expansion in climate niche by midcentury and could harbour key adaptations to cope with future climate. We recommend eight seed transfer zones and project each zone into its relative position in future climate. Prioritizing seed collection efforts on genotypes with expanding future habitat represents a promising strategy for restoration practitioners to address rapidly changing climates.
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Affiliation(s)
- Daniel F Shryock
- U.S. Geological Survey, Western Ecological Research Center, Henderson, NV, USA
| | | | - Lesley A DeFalco
- U.S. Geological Survey, Western Ecological Research Center, Henderson, NV, USA
| | - Todd C Esque
- U.S. Geological Survey, Western Ecological Research Center, Henderson, NV, USA
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41
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Melo WA, Vieira LD, Novaes E, Bacon CD, Collevatti RG. Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm. Front Genet 2020; 11:596662. [PMID: 33424928 PMCID: PMC7786001 DOI: 10.3389/fgene.2020.596662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 01/21/2023] Open
Abstract
Despite the global importance of tropical ecosystems, few studies have identified how natural selection has shaped their megadiversity. Here, we test for the role of adaptation in the evolutionary success of the widespread, highly abundant Neotropical palm Mauritia flexuosa. We used a genome scan framework, sampling 16,262 single-nucleotide polymorphisms (SNPs) with target sequence capture in 264 individuals from 22 populations in rainforest and savanna ecosystems. We identified outlier loci as well as signal of adaptation using Bayesian correlations of allele frequency with environmental variables and detected both selective sweeps and genetic hitchhiking events. Functional annotation of SNPs with selection footprints identified loci affecting genes related to adaptation to environmental stress, plant development, and primary metabolic processes. The strong differences in climatic and soil variables between ecosystems matched the high differentiation and low admixture in population Bayesian clustering. Further, we found only small differences in allele frequency distribution in loci putatively under selection among widespread populations from different ecosystems, with fixation of a single allele in most populations. Taken together, our results indicate that adaptive selective sweeps related to environmental stress shaped the spatial pattern of genetic diversity in M. flexuosa, leading to high similarity in allele frequency among populations from different ecosystems.
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Affiliation(s)
- Warita A Melo
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Lucas D Vieira
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Lavras, Brazil
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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42
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Josephs EB. Gene expression links genotype and phenotype during rapid adaptation. Mol Ecol 2020; 30:30-32. [PMID: 33187015 DOI: 10.1111/mec.15729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/06/2020] [Indexed: 12/27/2022]
Abstract
Natural environments can change quickly and organisms living in these environments can either move, go extinct, or persist through rapid adaptation. Understanding the genetic and phenotypic changes that occur during rapid adaptation is crucial for predicting how populations will respond to sudden environmental changes. Since gene expression links genotype to phenotype, determining how rapid adaptation shapes the transcriptome will be useful for identifying both the traits and the genes important for adaptation, especially in cases where adaptation involves changes in quantitative traits. However, we lack a clear understanding of how rapid adaptation can cause and be caused by changes in gene expression. In this issue of Molecular Ecology, Hamann et al. (2020) investigate how gene expression has evolved during rapid adaptation to drought in two populations of the plant species Brassica rapa.
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Affiliation(s)
- Emily B Josephs
- Department of Plant Biology and the Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
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43
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Blanco-Pastor JL, Barre P, Keep T, Ledauphin T, Escobar-Gutiérrez A, Roschanski AM, Willner E, Dehmer KJ, Hegarty M, Muylle H, Veeckman E, Vandepoele K, Ruttink T, Roldán-Ruiz I, Manel S, Sampoux JP. Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass. Mol Ecol Resour 2020; 21:849-870. [PMID: 33098268 DOI: 10.1111/1755-0998.13289] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/10/2020] [Accepted: 10/12/2020] [Indexed: 11/28/2022]
Abstract
Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA-GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry winter versus mild-wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.
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Affiliation(s)
| | - Philippe Barre
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | - Thomas Keep
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | | | - Anna Maria Roschanski
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Evelyn Willner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Klaus J Dehmer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Malchow/Poel, Germany
| | - Matthew Hegarty
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium
| | - Elisabeth Veeckman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Klaas Vandepoele
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, Melle, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stéphanie Manel
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier, Montpellier, France
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44
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Varying Levels of Genetic Control and Phenotypic Plasticity in Timing of Bud Burst, Flower Opening, Leaf Senescence and Leaf Fall in Two Common Gardens of Prunus padus L.
. FORESTS 2020. [DOI: 10.3390/f11101070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Several phenological phases mark the seasonal growth pattern in temperate woody perennials. To gain further insight into the way these phases react on an altering growth environment, we tested whether vegetative and reproductive phenophases in a shrub species respond differentially among different genetic entities and between two different planting sites. We scored leaf bud burst, flower opening, leaf senescence and leaf fall on 267 ramets of Prunus padus L. belonging to 53 genotypes that were sampled in 9 local populations, and that were planted in 2 common gardens in the northern part of Belgium. The data were processed with cumulative logistic regression. The contribution of genetic and non-genetic components to the total variability varied between the four studied seasonal phenophases. The timing of flower opening displayed the smallest relative amount of intragenotypic variance (between ramets), suggesting a stronger genetic control and a lesser need at the individual plant level for plastic fine tuning to the micro-environment. In addition, whereas leaf bud burst showed the highest relative variance at the interpopulation level among all phenophases, probably at least partly attributable to local adaptation, flower opening displayed the highest intergenotypic variance, which may have been promoted more by assortative mating. Spring phenophases were strongly correlated (r = 0.89) as well as the autumnal phenophases (r = 0.72). Flower opening was not correlated with the autumnal phenophases. Timing of leaf bud burst and leaf senescence were negatively correlated, demonstrating that the length of the growing season enlarged or diminished among the studied genotypes. Although the two planting sites were only 24 km apart, all phenophases were advanced at the less exposed site, indicating a phenotypic plastic response. Together, our results suggest that in P. padus, flowering is less sensitive to environmental variation than leaf bud break and may show a lesser impact of a changing environment on this reproductive phenophase.
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Brousseau L, Fine PVA, Dreyer E, Vendramin GG, Scotti I. Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae). Mol Ecol 2020; 30:1136-1154. [PMID: 32786115 DOI: 10.1111/mec.15595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023]
Abstract
Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees-whose large and undisturbed populations often span a variety of environmental conditions and local habitats-are particularly good models to study this process. Here, we explore patterns of adaptive divergence from large (i.e., regional) to small (i.e., microgeographic) spatial scales in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae) under a replicated design involving two microhabitats (~300 m apart) in two study sites (~300 km apart). A three-year reciprocal transplant illustrates that, beyond strong maternal effects and phenotypic plasticity, genetically driven divergence in seedling growth and leaf traits was detected both between seedlings originating from different regions, and between seedlings from different microhabitats. In parallel, a complementary genome scan for selection was carried out through whole-genome sequencing of tree population pools. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier-surrounding genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence of microgeographic divergence in functional traits, the discovery of genomic candidates for microgeographic adaptive divergence represents a promising advance in our understanding of local adaptation, which probably operates across multiple spatial scales and underpins divergence and diversification in Neotropical trees.
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Affiliation(s)
- Louise Brousseau
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles, Kourou Cedex, France.,AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Paul V A Fine
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Erwin Dreyer
- Université de Lorraine, AgroParisTech, INRAE, Silva, Nancy, France
| | - Giovanni G Vendramin
- Institute of Biosciences and BioResources (IBBR-CNR), National Research Council, Division of Florence, Sesto Fiorentino, Italy
| | - Ivan Scotti
- UR629 Ecologie des Forêts Méditerranéennes (URFM), INRAE, Avignon, France
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DeSilva R, Dodd RS. Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture-related gradients. Ecol Evol 2020; 10:10619-10632. [PMID: 33072284 PMCID: PMC7548164 DOI: 10.1002/ece3.6716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 11/12/2022] Open
Abstract
Uncovering the genetic basis of local adaptation is a major goal of evolutionary biology and conservation science alike. In an era of climate change, an understanding of how environmental factors shape adaptive diversity is crucial to predicting species response and directing management. Here, we investigate patterns of genomic variation in giant sequoia, an iconic and ecologically important tree species, using 1,364 bi-allelic single nucleotide polymorphisms (SNPs). We use an F ST outlier test and two genotype-environment association methods, latent factor mixed models (LFMMs) and redundancy analysis (RDA), to detect complex signatures of local adaptation. Results indicate 79 genomic regions of potential adaptive importance, with limited overlap between the detection methods. Of the 58 loci detected by LFMM, 51 showed strong correlations to a precipitation-driven composite variable and seven to a temperature-related variable. RDA revealed 24 outlier loci with association to climate variables, all of which showed strongest relationship to summer precipitation. Nine candidate loci were indicated by two methods. After correcting for geographic distance, RDA models using climate predictors accounted for 49% of the explained variance and showed significant correlations between SNPs and climatic factors. Here, we present evidence of local adaptation in giant sequoia along gradients of precipitation and provide a first step toward identifying genomic regions of adaptive significance. The results of this study will provide information to guide management strategies that seek to maximize adaptive potential in the face of climate change.
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Affiliation(s)
- Rainbow DeSilva
- Department of Environmental Science, Policy, and Management University of California at Berkeley Berkeley California USA
| | - Richard S Dodd
- Department of Environmental Science, Policy, and Management University of California at Berkeley Berkeley California USA
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Napier JD, de Lafontaine G, Hu FS. Exploring genomic variation associated with drought stress in Picea mariana populations. Ecol Evol 2020; 10:9271-9282. [PMID: 32953060 PMCID: PMC7487243 DOI: 10.1002/ece3.6614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/01/2020] [Accepted: 07/08/2020] [Indexed: 01/05/2023] Open
Abstract
Predicted increases in drought and heat stress will likely induce shifts in species bioclimatic envelopes. Genetic variants adapted to water limitation may prove pivotal for species response under scenarios of increasing drought. In this study, we aimed to explore this hypothesis by investigating genetic variation in 16 populations of black spruce (Picea mariana) in relation to climate variables in Alaska. A total of 520 single nucleotide polymorphisms (SNPs) were genotyped for 158 trees sampled from areas of contrasting climate regimes. We used multivariate and univariate genotype-by-environment approaches along with available gene annotations to investigate the relationship between climate and genetic variation among sampled populations. Nine SNPs were identified as having a significant association with climate, of which five were related to drought stress response. Outlier SNPs with respect to the overall environment were significantly overrepresented for several biological functions relevant for coping with variable hydric regimes, including osmotic stress response. This genomic imprint is consistent with local adaptation of black spruce to drought stress. These results suggest that natural selection acting on standing variation prompts local adaptation in forest stands facing water limitation. Improved understanding of possible adaptive responses could inform our projections about future forest dynamics and help prioritize populations that harbor valuable genetic diversity for conservation.
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Affiliation(s)
- Joseph D. Napier
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
| | - Guillaume de Lafontaine
- Department of Plant BiologyUniversity of IllinoisUrbanaILUSA
- Canada Research Chair in Integrative Biology of Northern FloraUniversité du Québec à RimouskiRimouskiQCCanada
| | - Feng Sheng Hu
- Department of GeologyUniversity of IllinoisUrbanaILUSA
- Department of BiologyWashington UniversitySt. LouisMOUSA
- Department of Earth and Planetary SciencesWashington UniversitySt. LouisMOUSA
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Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting. G3-GENES GENOMES GENETICS 2020; 10:2683-2696. [PMID: 32546502 PMCID: PMC7407466 DOI: 10.1534/g3.120.401285] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.
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Cortinovis G, Di Vittori V, Bellucci E, Bitocchi E, Papa R. Adaptation to novel environments during crop diversification. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:203-217. [PMID: 32057695 DOI: 10.1016/j.pbi.2019.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 06/10/2023]
Abstract
In the context of the global challenge of climate change, mitigation strategies are needed to adapt crops to novel environments. The main goal to address this is an understanding of the genetic basis of crop adaptation to different agro-ecological conditions. The movement of crops during the Colombian Exchange that started with the travels of Columbus in 1492 is an example of rapid adaptation to novel environments. Many diversification-related traits have been characterised in multiple crop species, and association-mapping analyses have identified loci involved in these. Here, we present an overview of current knowledge regarding the molecular basis related to the complex patterns of crop adaptation and dissemination, particularly outside their centres of origin. Investigation of the genomic basis of crop expansion offers a powerful contribution to the development of tools to identify and exploit valuable genetic diversity and to improve and design novel resilient crop varieties.
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Affiliation(s)
- Gaia Cortinovis
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Valerio Di Vittori
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
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Moreira LR, Hernandez-Baños BE, Smith BT. Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis). Mol Ecol 2020; 29:3085-3102. [PMID: 32621770 DOI: 10.1111/mec.15536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 06/08/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Spatial patterns of intraspecific variation are shaped by geographical distance among populations, historical changes in gene flow and interactions with local environments. Although these factors are not mutually exclusive and operate on both genomic and phenotypic variation, it is unclear how they affect these two axes of variation. We address this question by exploring the predictors of genomic and phenotypic divergence in Icterus gularis, a broadly distributed Middle American bird that exhibits marked geographical variation in body size across its range. We combined a comprehensive single nucleotide polymorphism and phenotypic data set to test whether genome-wide genetic and phenotypic differentiation are best explained by (i) isolation by distance, (ii) isolation by history or (iii) isolation by environment. We find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow, phenotypic diversity can be best predicted by contemporary environmental heterogeneity. Our genomic analyses reveal strong phylogeographical structure coinciding with the Chivela Pass at the Isthmus of Tehuantepec that was formed during the Pleistocene, when populations were isolated in north-south refugia. In contrast, we found a strong association between body size and environmental variables, such as temperature and precipitation. The relationship between body size and local climate is consistent with a pattern produced by either natural selection or environmental plasticity. Overall, these results provide empirical evidence for why phenotypic and genomic data are often in conflict in taxonomic and phylogeographical studies.
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Affiliation(s)
- Lucas R Moreira
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | | | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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