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Christensen KA, Flores AM, Sakhrani D, Biagi CA, Devlin RH, Sutherland BJG, Withler RE, Rondeau EB, Koop BF. Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing. G3 (BETHESDA, MD.) 2024; 14:jkae169. [PMID: 39041834 PMCID: PMC11457079 DOI: 10.1093/g3journal/jkae169] [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: 04/29/2024] [Revised: 04/29/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available.
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Affiliation(s)
- Kris A Christensen
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1H2, Canada
| | - Carlo A Biagi
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1H2, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1H2, Canada
| | - Ben J G Sutherland
- Sutherland Bioinformatics, Lantzville, BC V0R 2H0, Canada
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada
| | - Ruth E Withler
- Pacific Salmon Foundation, Vancouver, BC V6H 3V9, Canada
| | - Eric B Rondeau
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
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2
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Burbrink FT, Myers EA, Pyron RA. Understanding species limits through the formation of phylogeographic lineages. Ecol Evol 2024; 14:e70263. [PMID: 39364037 PMCID: PMC11446989 DOI: 10.1002/ece3.70263] [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: 06/03/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 10/05/2024] Open
Abstract
The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well-defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype-environment interactions, and genome scans for selected loci. Employing these tests in eight lineage-pairs of snakes in North America, we show that six pairs represent 12 "good" species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid-Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology American Museum of Natural History New York New York USA
| | - Edward A Myers
- Department of Herpetology California Academy of Sciences San Francisco California USA
| | - R Alexander Pyron
- Department of Biological Sciences The George Washington University Washington DC USA
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3
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Folkertsma R, Charbonnel N, Henttonen H, Heroldová M, Huitu O, Kotlík P, Manzo E, Paijmans JLA, Plantard O, Sándor AD, Hofreiter M, Eccard JA. Genomic signatures of climate adaptation in bank voles. Ecol Evol 2024; 14:e10886. [PMID: 38455148 PMCID: PMC10918726 DOI: 10.1002/ece3.10886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.
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Affiliation(s)
- Remco Folkertsma
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Comparative Cognition Unit, Messerli Research InstituteUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | - Marta Heroldová
- Department of Forest Ecology, FFWTMendel University in BrnoBrnoCzech Republic
| | - Otso Huitu
- Natural Resources Institute FinlandHelsinkiFinland
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and GeneticsCzech Academy of SciencesLiběchovCzech Republic
| | - Emiliano Manzo
- Fondazione Ethoikos, Convento dell'OsservanzaRadicondoliItaly
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Present address:
Evolutionary Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | | | - Attila D. Sándor
- HUN‐RENClimate Change: New Blood‐Sucking Parasites and Vector‐Borne Pathogens Research GroupBudapestHungary
- Department of Parasitology and ZoologyUniversity of Veterinary MedicineBudapestHungary
- Department of Parasitology and Parasitic DiseasesUniversity of Agricultural Sciences and Veterinary MedicineCluj‐NapocaRomania
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
| | - Jana A. Eccard
- Animal Ecology, Institute for Biochemistry and Biology, Faculty of ScienceBerlin‐Brandenburg Institute for Biodiversity ResearchUniversity of PotsdamPotsdamGermany
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4
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Keller AG, Dahlhoff EP, Bracewell R, Chatla K, Bachtrog D, Rank NE, Williams CM. Multi-locus genomic signatures of local adaptation to snow across the landscape in California populations of a willow leaf beetle. Proc Biol Sci 2023; 290:20230630. [PMID: 37583321 PMCID: PMC10427825 DOI: 10.1098/rspb.2023.0630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/14/2023] [Indexed: 08/17/2023] Open
Abstract
Organisms living in mountains contend with extreme climatic conditions, including short growing seasons and long winters with extensive snow cover. Anthropogenic climate change is driving unprecedented, rapid warming of montane regions across the globe, resulting in reduced winter snowpack. Loss of snow as a thermal buffer may have serious consequences for animals overwintering in soil, yet little is known about how variability in snowpack acts as a selective agent in montane ecosystems. Here, we examine genomic variation in California populations of the leaf beetle Chrysomela aeneicollis, an emerging natural model system for understanding how organisms respond to climate change. We used a genotype-environment association approach to identify genomic signatures of local adaptation to microclimate in populations from three montane regions with variable snowpack and a coastal region with no snow. We found that both winter-associated environmental variation and geographical distance contribute to overall genomic variation across the landscape. We identified non-synonymous variation in novel candidate loci associated with cytoskeletal function, ion transport and membrane stability, cellular processes associated with cold tolerance in other insects. These findings provide intriguing evidence that variation in snowpack imposes selective gradients in montane ecosystems.
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Affiliation(s)
- Abigail G. Keller
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | | | - Ryan Bracewell
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Nathan E. Rank
- Department of Biology, Sonoma State University, Rohnert Park, CA, USA
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5
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Turbek SP, Funk WC, Ruegg KC. Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa. J Hered 2023; 114:300-311. [PMID: 36815497 DOI: 10.1093/jhered/esad011] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species' range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species' distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.
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Affiliation(s)
- Sheela P Turbek
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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6
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Zhang X, Guo R, Shen R, Landis JB, Jiang Q, Liu F, Wang H, Yao X. The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit. HORTICULTURE RESEARCH 2023; 10:uhad031. [PMID: 37799629 PMCID: PMC10548413 DOI: 10.1093/hr/uhad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/14/2023] [Indexed: 10/07/2023]
Abstract
A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates. Actinidia eriantha is a shade-tolerant species, widely distributed in the southern tropical region of China, occurring in spatially heterogeneous environments. In the present study we combined population genomic, epigenomic, and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient, and to assess genomic offset to climatic change for A. eriantha. The population structure is strongly shaped by geography and influenced by restricted gene flow resulting from isolation by distance due to habitat fragmentation. In total, we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation, which were enriched in functional categories related to development processes and stress response; both temperature and precipitation are important factors driving adaptive variation. In addition to single-nucleotide polymorphisms (SNPs), a total of 27 single-methylation variants (SMVs) had significant correlation with at least one of four climatic variables and 16 SMVs were located in or adjacent to genes, several of which were predicted to be involved in plant response to abiotic or biotic stress. Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change. Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation. Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruinan Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853 USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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7
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Wang Y, Zhang L, Zhou Y, Ma W, Li M, Guo P, Feng L, Fu C. Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China. Front Genet 2023; 14:1150704. [PMID: 37144128 PMCID: PMC10151583 DOI: 10.3389/fgene.2023.1150704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.
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Affiliation(s)
- Yihan Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Lin Zhang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Yuchao Zhou
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Wenxin Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Manyu Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Peng Guo
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Peng Guo, ; Li Feng,
| | - Li Feng
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Peng Guo, ; Li Feng,
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
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8
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Lowell N, Suhrbier A, Tarpey C, May S, Carson H, Hauser L. Population structure and adaptive differentiation in the sea cucumber Apostichopus californicus and implications for spatial resource management. PLoS One 2023; 18:e0280500. [PMID: 36928497 PMCID: PMC10019739 DOI: 10.1371/journal.pone.0280500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/03/2023] [Indexed: 03/18/2023] Open
Abstract
A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species' range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driving two patterns of differentiation: isolation-by-distance and a latitudinal gradient of differentiation. Notably, we found detectable population differences among collection sites within the Salish Sea (pairwise FST = 0.001-0.006). Using FST outlier detection and gene-environment association, we identified 10.2% of total SNPs as putatively adaptive. Environmental variables (e.g., temperature, salinity) from the sea surface were more correlated with genetic variation than those same variables measured near the benthos, suggesting that selection on pelagic larvae may drive adaptive differentiation to a greater degree than selection on adults. Our results were consistent with previous estimates of and patterns in population structure for this species in other extents of the range. Additionally, we found that patterns of neutral and adaptive differentiation co-varied, suggesting that adaptive barriers may limit dispersal. Our study provides guidance to decision-makers regarding the designation of management units for A. californicus and adds to the growing body of literature identifying genetic population differentiation in marine species despite large, nominally connected populations.
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Affiliation(s)
- Natalie Lowell
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Andy Suhrbier
- Pacific Shellfish Institute, Olympia, Washington, United States of America
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Samuel May
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Henry Carson
- Washington Department of Fish and Wildlife, Olympia, Washington, United States of America
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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Sepúlveda‐Espinoza F, Bertin‐Benavides A, Hasbún R, Toro‐Núñez Ó, Varas‐Myrik A, Alarcón D, Guillemin M. The impact of Pleistocene glaciations and environmental gradients on the genetic structure of Embothrium coccineum. Ecol Evol 2022; 12:e9474. [PMID: 36381388 PMCID: PMC9646505 DOI: 10.1002/ece3.9474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/11/2022] Open
Abstract
The South American temperate forests were subjected to drastic topographic and climatic changes during the Pliocene-Pleistocene as a consequence of the Andean orogeny and glacial cycles. Such changes are common drivers of genetic structure and adaptation. Embothrium coccineum (Proteaceae) is an emblematic tree of the South American temperate forest (around 20°S of latitude) that has strongly been affected by topographic and climatic events. Previous studies have shown a marked genetic structure in this species, and distinct ecotypes have been described. Yet, little is known about their adaptive genetic responses. The main goal of this study was to investigate the effects of historical and contemporary landscape features affecting the genetic diversity and connectivity of E. coccineum throughout its current natural distribution. Using over 2000 single nucleotide polymorphisms (SNPs), we identified two genetic groups (a Northern and a Central-Southern group) that diverged around 2.8 million years ago. The level of genetic structure was higher among populations within the Northern genetic group than within the Central-Southern group. We propose that these differences in genetic structure may be due to differences in the assemblages of pollinators and in the evolutionary histories of the two genetic groups. Moreover, the data displayed a strong pattern of isolation by the environment in E. coccineum, suggesting that selection could have led to adaptive divergence among localities. We propose that in the Chilean temperate forest, the patterns of genetic variation in E. coccineum reflect both a Quaternary phylogenetic imprint and signatures of selection as a consequence of a strong environmental gradient.
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Affiliation(s)
- Francisco Sepúlveda‐Espinoza
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
- Facultad de Ciencias, Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Ariana Bertin‐Benavides
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
- ONG Conciencia SurConcepciónChile
- Laboratorio de Genómica Forestal, Centro de BiotecnologíaUniversidad de ConcepciónConcepciónChile
| | - Rodrigo Hasbún
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
| | - Óscar Toro‐Núñez
- Departamento de Botánica, Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
| | - Antonio Varas‐Myrik
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
| | - Diego Alarcón
- Departamento de Ciencias Ecológicas, Instituto de Ecología y BiodiversidadUniversidad de ChileÑuñoaChile
| | - Marie‐Laure Guillemin
- Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Facultad de CienciasUniversidad Austral de ChileValdiviaChile
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRSSorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de ChileRoscoffFrance
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL)ValdiviaChile
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10
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Sękiewicz K, Danelia I, Farzaliyev V, Gholizadeh H, Iszkuło G, Naqinezhad A, Ramezani E, Thomas PA, Tomaszewski D, Walas Ł, Dering M. Past climatic refugia and landscape resistance explain spatial genetic structure in Oriental beech in the South Caucasus. Ecol Evol 2022; 12:e9320. [PMID: 36188519 PMCID: PMC9490144 DOI: 10.1002/ece3.9320] [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: 07/17/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Predicting species-level effects of climatic changes requires unraveling the factors affecting the spatial genetic composition. However, disentangling the relative contribution of historical and contemporary drivers is challenging. By applying landscape genetics and species distribution modeling, we investigated processes that shaped the neutral genetic structure of Oriental beech (Fagus orientalis), aiming to assess the potential risks involved due to possible future distribution changes in the species. Using nuclear microsatellites, we analyze 32 natural populations from the Georgia and Azerbaijan (South Caucasus). We found that the species colonization history is the most important driver of the genetic pattern. The detected west-east gradient of genetic differentiation corresponds strictly to the Colchis and Hyrcanian glacial refugia. A significant signal of associations to environmental variables suggests that the distinct genetic composition of the Azerbaijan and Hyrcanian stands might also be structured by the local climate. Oriental beech retains an overall high diversity; however, in the context of projected habitat loss, its genetic resources might be greatly impoverished. The most affected are the Azerbaijan and Hyrcanian populations, for which the detected genetic impoverishment may enhance their vulnerability to environmental change. Given the adaptive potential of range-edge populations, the loss of these populations may ultimately affect the specie's adaptation, and thus the stability and resilience of forest ecosystems in the Caucasus ecoregion. Our study is the first approximation of the potential risks involved, inducing far-reaching conclusions about the need of maintaining the genetic resources of Oriental beech for a species' capacity to cope with environmental change.
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Affiliation(s)
| | - Irina Danelia
- Faculty of Agricultural Science and Biosystems EngineeringGeorgian Technical UniversityTbilisiGeorgia
- National Botanical Garden of GeorgiaTbilisiGeorgia
| | - Vahid Farzaliyev
- Forest Development ServiceMinistry of Ecology and Natural Resources of AzerbaijanBakuAzerbaijan
| | - Hamid Gholizadeh
- Department of Plant Biology, Faculty of Basic SciencesUniversity of MazandaranBabolsarIran
| | - Grzegorz Iszkuło
- Institute of DendrologyPolish Academy of SciencesKórnikPoland
- Faculty of Biological SciencesUniversity of Zielona GóraZielona GóraPoland
| | - Alireza Naqinezhad
- Department of Plant Biology, Faculty of Basic SciencesUniversity of MazandaranBabolsarIran
| | - Elias Ramezani
- Department of Forestry, Faculty of Natural ResourcesUrmia UniversityUrmiaIran
| | | | | | - Łukasz Walas
- Institute of DendrologyPolish Academy of SciencesKórnikPoland
| | - Monika Dering
- Institute of DendrologyPolish Academy of SciencesKórnikPoland
- Faculty of Forestry and Wood TechnologyPoznań University of Life SciencesPoznańPoland
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11
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Archambeau J, Garzón MB, Barraquand F, Miguel MD, Plomion C, González-Martínez SC. Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree. Am Nat 2022; 200:E141-E159. [DOI: 10.1086/720619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Comparative population genomics in Tabebuia alliance shows evidence of adaptation in Neotropical tree species. Heredity (Edinb) 2022; 128:141-153. [PMID: 35132209 PMCID: PMC8897506 DOI: 10.1038/s41437-021-00491-0] [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: 03/22/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022] Open
Abstract
The role of natural selection in shaping spatial patterns of genetic diversity in the Neotropics is still poorly understood. Here, we perform a genome scan with 24,751 probes targeting 11,026 loci in two Neotropical Bignoniaceae tree species: Handroanthus serratifolius from the seasonally dry tropical forest (SDTF) and Tabebuia aurea from savannas, and compared with the population genomics of H. impetiginosus from SDTF. OutFLANK detected 29 loci in 20 genes with selection signal in H. serratifolius and no loci in T. aurea. Using BayPass, we found evidence of selection in 335 loci in 312 genes in H. serratifolius, 101 loci in 92 genes in T. aurea, and 448 loci in 416 genes in H. impetiginosus. All approaches evidenced several genes affecting plant response to environmental stress and primary metabolic processes. The three species shared no SNPs with selection signal, but we found SNPs affecting the same gene in pair of species. Handroanthus serratifolius showed differences in allele frequencies at SNPs with selection signal among ecosystems, mainly between Caatinga/Cerrado and Atlantic Forest, while H. impetiginosus had one allele fixed across all populations, and T. aurea had similar allele frequency distribution among ecosystems and polymorphism across populations. Taken together, our results indicate that natural selection related to environmental stress shaped the spatial pattern of genetic diversity in the three species. However, the three species have different geographical distribution and niches, which may affect tolerances and adaption, and natural selection may lead to different signatures due to the differences in adaptive landscapes in different niches.
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13
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Muniz AC, Pimenta RJG, Cruz MV, Rodrigues JG, Buzatti RSDO, Heuertz M, Lemos‐Filho JP, Lovato MB. Hybrid zone of a tree in a Cerrado/Atlantic Forest ecotone as a hotspot of genetic diversity and conservation. Ecol Evol 2022; 12:e8540. [PMID: 35127043 PMCID: PMC8803295 DOI: 10.1002/ece3.8540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second-generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Mariana Vargas Cruz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | - José P. Lemos‐Filho
- Departamento de BotânicaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
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14
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Nielsen ES, Henriques R, Beger M, von der Heyden S. Distinct interspecific and intraspecific vulnerability of coastal species to global change. GLOBAL CHANGE BIOLOGY 2021; 27:3415-3431. [PMID: 33904200 DOI: 10.1111/gcb.15651] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Characterising and predicting species responses to anthropogenic global change is one of the key challenges in contemporary ecology and conservation. The sensitivity of marine species to climate change is increasingly being described with forecasted species distributions, yet these rarely account for population level processes such as genomic variation and local adaptation. This study compares inter- and intraspecific patterns of biological composition to determine how vulnerability to climate change, and its environmental drivers, vary across species and populations. We compare species trajectories for three ecologically important southern African marine invertebrates at two time points in the future, both at the species level, with correlative species distribution models, and at the population level, with gradient forest models. Reported range shifts are species-specific and include both predicted range gains and losses. Forecasted species responses to climate change are strongly influenced by changes in a suite of environmental variables, from sea surface salinity and sea surface temperature, to minimum air temperature. Our results further suggest a mismatch between future habitat suitability (where species can remain in their ecological niche) and genomic vulnerability (where populations retain their genomic composition), highlighting the inter- and intraspecific variability in species' sensitivity to global change. Overall, this study demonstrates the importance of considering species and population level climatic vulnerability when proactively managing coastal marine ecosystems in the Anthropocene.
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Affiliation(s)
- Erica S Nielsen
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
- Section for Marine Living Resources, Technical University of Denmark, National Institute of Aquatic Resources, Silkeborg, Denmark
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
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15
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Colicchio JM, Hamm LN, Verdonk HE, Kooyers NJ, Blackman BK. Adaptive and nonadaptive causes of heterogeneity in genetic differentiation across the Mimulus guttatus genome. Mol Ecol 2021; 30:6486-6507. [PMID: 34289200 DOI: 10.1111/mec.16087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Genetic diversity becomes structured among populations over time due to genetic drift and divergent selection. Although population structure is often treated as a uniform underlying factor, recent resequencing studies of wild populations have demonstrated that diversity in many regions of the genome may be structured quite dissimilar to the genome-wide pattern. Here, we explored the adaptive and nonadaptive causes of such genomic heterogeneity using population-level, whole genome resequencing data obtained from annual Mimulus guttatus individuals collected across a rugged environment landscape. We found substantial variation in how genetic differentiation is structured both within and between chromosomes, although, in contrast to other studies, known inversion polymorphisms appear to serve only minor roles in this heterogeneity. In addition, much of the genome can be clustered into eight among-population genetic differentiation patterns, but only two of these clusters are particularly consistent with patterns of isolation by distance. By performing genotype-environment association analysis, we also identified genomic intervals where local adaptation to specific climate factors has accentuated genetic differentiation among populations, and candidate genes in these windows indicate climate adaptation may proceed through changes affecting specialized metabolism, drought resistance, and development. Finally, by integrating our findings with previous studies, we show that multiple aspects of plant reproductive biology may be common targets of balancing selection and that variants historically involved in climate adaptation among populations have probably also fuelled rapid adaptation to microgeographic environmental variation within sites.
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Affiliation(s)
- Jack M Colicchio
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Lauren N Hamm
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Hannah E Verdonk
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Nicholas J Kooyers
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology, University of Louisiana, Lafayette, Lafayette, Louisiana, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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16
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Dallaire X, Normandeau É, Mainguy J, Tremblay J, Bernatchez L, Moore J. Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation. Evol Appl 2021; 14:1880-1897. [PMID: 34295370 PMCID: PMC8287999 DOI: 10.1111/eva.13248] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Abstract
Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure in the wild, and landscape genomics can help identify signatures of adaptation to contrasting environments. Arctic Char (Salvelinus alpinus) is an anadromous salmonid and the most harvested fish species by Inuit people, including in Nunavik (Québec, Canada), one of the most recently deglaciated regions in the world. Unlike many other anadromous salmonids, Arctic Char occupy coastal habitats near their natal rivers during their short marine phase restricted to the summer ice-free period. Our main objective was to document putatively neutral and adaptive genomic variation in anadromous Arctic Char populations from Nunavik and bordering regions to inform local fisheries management. We used genotyping by sequencing (GBS) to genotype 18,112 filtered single nucleotide polymorphisms (SNP) in 650 individuals from 23 sampling locations along >2000 km of coastline. Our results reveal a hierarchical genetic structure, whereby neighboring hydrographic systems harbor distinct populations grouped by major oceanographic basins: Hudson Bay, Hudson Strait, Ungava Bay, and Labrador Sea. We found genetic diversity and differentiation to be consistent both with the expected postglacial recolonization history and with patterns of isolation-by-distance reflecting contemporary gene flow. Results from three gene-environment association methods supported the hypothesis of local adaptation to both freshwater and marine environments (strongest associations with sea surface and air temperatures during summer and salinity). Our results support a fisheries management strategy at a regional scale, and other implications for hatchery projects and adaptation to climate change are discussed.
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Affiliation(s)
- Xavier Dallaire
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Centre d’Études Nordiques (CEN)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Julien Mainguy
- Ministère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Jean‐Éric Tremblay
- Département de Biologie, Université LavalQuébecQCCanada
- Ministère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
| | - Jean‐Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Centre d’Études Nordiques (CEN)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
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17
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Leigh DM, Lischer HEL, Guillaume F, Grossen C, Günther T. Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex. Mol Ecol Resour 2021; 21:2350-2363. [PMID: 34097819 PMCID: PMC8518545 DOI: 10.1111/1755-0998.13442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/25/2023]
Abstract
Identifying local adaptation in bottlenecked species is essential for conservation management. Selection detection methods have an important role in species management plans, assessments of adaptive capacity, and looking for responses to climate change. Yet, the allele frequency changes exploited in selection detection methods are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods have across bottlenecked populations. In this study, simulations were used to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). The meticulously recorded demographic history of the Alpine ibex was used to generate comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in outliers identified in empirical Alpine ibex RADseq derived SNP data. Within the simulated data set, the false positive rates were high for all selection detection methods (FST outlier scans and Genetic‐Environment Association analyses) but fell substantially when two or more methods were combined. True positive rates were consistently low and became negligible with increased stringency. Despite finding many outlier loci in the empirical Alpine ibex SNPs, none could be distinguished from genetic drift‐driven false positives. Unfortunately, the low true positive rate also prevents the exclusion of recent local adaptation within the Alpine ibex. The baselines and stringent approach outlined here should be applied to other bottlenecked species to ensure the risk of false positive, or negative, signals of selection are accounted for in conservation management plans.
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Affiliation(s)
- Deborah M Leigh
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Heidi E L Lischer
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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18
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George J, Schueler S, Grabner M, Karanitsch‐Ackerl S, Mayer K, Stierschneider M, Weissenbacher L, van Loo M. Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir ( Pseudotsuga menziesii). Ecol Evol 2021; 11:8238-8253. [PMID: 34188883 PMCID: PMC8216971 DOI: 10.1002/ece3.7654] [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: 12/03/2020] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 11/24/2022] Open
Abstract
Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.
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Affiliation(s)
- Jan‐Peter George
- Faculty of Science & TechnologyTartu ObservatoryUniversity of TartuTartuEstonia
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| | - Silvio Schueler
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsViennaAustria
| | - Michael Grabner
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Sandra Karanitsch‐Ackerl
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Konrad Mayer
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | | | - Lambert Weissenbacher
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| | - Marcela van Loo
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
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19
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N Di Santo L, Hamilton JA. Using environmental and geographic data to optimize ex situ collections and preserve evolutionary potential. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:733-744. [PMID: 32519757 DOI: 10.1111/cobi.13568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 05/26/2023]
Abstract
Maintenance of biodiversity through seed banks and botanical gardens, where the wealth of species' genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections if trade-offs exist among cost, effort, and conserving species evolutionary potential, particularly when genetic data are not available. We evaluated the genetic consequences of population preservation informed by geographic (isolation by distance [IBD]) and environmental (isolation by environment [IBE]) distance for ex situ collections for which population provenance is available. We used 19 genetic and genomic data sets from 15 plant species to assess the proportion of population genetic differentiation explained by geographic and environmental factors and to simulate ex situ collections prioritizing source populations based on pairwise geographic distance, environmental distance, or both. Specifically, we tested the impact prioritizing sampling based on these distances may have on the capture of neutral, functional, or putatively adaptive genetic diversity and differentiation. Individually, IBD and IBE explained limited population genetic differences across all 3 genetic marker classes (IBD, 10-16%; IBE, 1-5.5%). Together, they explained a substantial proportion of population genetic differences for functional (45%) and adaptive (71%) variation. Simulated ex situ collections revealed that inclusion of IBD, IBE, or both increased allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections based on environmental and geographic distance data can optimize genetic variation captured ex situ. For the vast majority of plant species for which there is no genetic information, these data are invaluable to conservation because they can guide preservation of genetic variation needed to maintain evolutionary potential within collections.
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Affiliation(s)
- Lionel N Di Santo
- Department of Biological Sciences, North Dakota State University, Fargo, ND, U.S.A
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, ND, U.S.A
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20
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Ahrens CW, Jordan R, Bragg J, Harrison PA, Hopley T, Bothwell H, Murray K, Steane DA, Whale JW, Byrne M, Andrew R, Rymer PD. Regarding the F-word: The effects of data filtering on inferred genotype-environment associations. Mol Ecol Resour 2021; 21:1460-1474. [PMID: 33565725 DOI: 10.1111/1755-0998.13351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/05/2023]
Abstract
Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results, negatively affecting management strategies. Here, we investigate the effects of filtering on GEA results and the potential implications for assessment of adaptation to environment. We use empirical and simulated data sets derived from two widespread tree species to assess the effects of filtering on GEA outputs. Critically, we find that the level of filtering of missing data and minor allele frequency affect the identification of true positives. Even slight adjustments to these thresholds can change the rate of true positive detection. Using conservative thresholds for missing data and minor allele frequency substantially reduces the size of the data set, lessening the power to detect adaptive variants (i.e., simulated true positives) with strong and weak strengths of selection. Regardless, strength of selection was a good predictor for GEA detection, but even some SNPs under strong selection went undetected. False positive rates varied depending on the species and GEA method, and filtering significantly impacted the predictions of adaptive capacity in downstream analyses. We make several recommendations regarding filtering for GEA methods. Ultimately, there is no filtering panacea, but some choices are better than others, depending on the study system, availability of genomic resources, and desired objectives.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | | | - Jason Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, NSW, Australia
| | - Peter A Harrison
- School of Natural Sciences and Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tas., Australia
| | - Tara Hopley
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, WA, Australia
| | | | - Kevin Murray
- Australian National University, Acton, ACT, Australia
| | - Dorothy A Steane
- CSIRO Land & Water, Hobart, Tas., Australia.,School of Natural Sciences and Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tas., Australia
| | - John W Whale
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, WA, Australia
| | - Rose Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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21
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Meng X, Liu T, Zhang L, Jin L, Sun K, Feng J. Effects of Colonization, Geography and Environment on Genetic Divergence in the Intermediate Leaf-Nosed Bat, Hipposideros larvatus. Animals (Basel) 2021; 11:733. [PMID: 33800251 PMCID: PMC7998825 DOI: 10.3390/ani11030733] [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: 01/19/2021] [Revised: 02/27/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
Determining the evolutionary history and population drivers, such as past large-scale climatic oscillations, stochastic processes and ecological adaptations, represents one of the aims of evolutionary biology. Hipposideros larvatus is a common bat species in Southern China, including Hainan Island. We examined genetic variation in H. larvatus using mitochondrial DNA and nuclear microsatellites. We found a population structure on both markers with a geographic pattern that corresponds well with the structure on mainland China and Hainan Island. To understand the contributions of geography, the environment and colonization history to the observed population structure, we tested isolation by distance (IBD), isolation by adaptation (IBA) and isolation by colonization (IBC) using serial Mantel tests and RDA analysis. The results showed significant impacts of IBD, IBA and IBC on neutral genetic variation, suggesting that genetic variation in H. larvatus is greatly affected by neutral processes, environmental adaptation and colonization history. This study enriches our understanding of the complex evolutionary forces that shape the distribution of genetic variation in bats.
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Affiliation(s)
- Xiangfeng Meng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China; (X.M.); (T.L.); (L.Z.); (J.F.)
- School of Life Science, Jilin Agricultural University, Changchun 130118, China
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22
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Hall D, Olsson J, Zhao W, Kroon J, Wennström U, Wang XR. Divergent patterns between phenotypic and genetic variation in Scots pine. PLANT COMMUNICATIONS 2021; 2:100139. [PMID: 33511348 PMCID: PMC7816077 DOI: 10.1016/j.xplc.2020.100139] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 12/12/2020] [Accepted: 12/25/2020] [Indexed: 05/06/2023]
Abstract
In boreal forests, autumn frost tolerance in seedlings is a critical fitness component because it determines survival rates during regeneration. To understand the forces that drive local adaptation in this trait, we conducted freezing tests in a common garden setting for 54 Pinus sylvestris (Scots pine) populations (>5000 seedlings) collected across Scandinavia into western Russia, and genotyped 24 of these populations (>900 seedlings) at >10 000 SNPs. Variation in cold hardiness among populations, as measured by QST , was above 80% and followed a distinct cline along latitude and longitude, demonstrating significant adaptation to climate at origin. In contrast, the genetic differentiation was very weak (mean FST 0.37%). Despite even allele frequency distribution in the vast majority of SNPs among all populations, a few rare alleles appeared at very high or at fixation in marginal populations restricted to northwestern Fennoscandia. Genotype-environment associations showed that climate variables explained 2.9% of the genetic differentiation, while genotype-phenotype associations revealed a high marker-estimated heritability of frost hardiness of 0.56, but identified no major loci. Very extensive gene flow, strong local adaptation, and signals of complex demographic history across markers are interesting topics of forthcoming studies on this species to better clarify signatures of selection and demography.
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Affiliation(s)
- David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Jenny Olsson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
- Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Johan Kroon
- The Forestry Research Institute of Sweden (Skogforsk), Uppsala Sweden
| | | | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
- Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Corresponding author
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23
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Hellwig T, Abbo S, Sherman A, Coyne CJ, Saranga Y, Lev-Yadun S, Main D, Zheng P, Ophir R. Limited divergent adaptation despite a substantial environmental cline in wild pea. Mol Ecol 2020; 29:4322-4336. [PMID: 32964548 DOI: 10.1111/mec.15633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 08/09/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
Isolation by environment (IBE) is a widespread phenomenon in nature. It is commonly expected that the degree of difference among environments is proportional to the level of divergence between populations in their respective environments. It is therefore assumed that a species' genetic diversity displays a pattern of IBE in the presence of a strong environmental cline if gene flow does not mitigate isolation. We tested this common assumption by analysing the genetic diversity and demographic history of Pisum fulvum, which inhabits contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations, making it an ideal test case. Ecogeographical and subpopulation structure were analysed and compared. The correlation of genetic with environmental distances was calculated to test the effect of isolation by distance and IBE and detect the main drivers of these effects. Historical effective population size was estimated using stairway plot. Limited overlap of ecogeographical and genetic clustering was observed, and correlation between genetic and environmental distances was statistically significant but small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to a past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive gene flow.
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Affiliation(s)
- Timo Hellwig
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
| | - Shahal Abbo
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
| | | | - Yehoshua Saranga
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Simcha Lev-Yadun
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa-Oranim, Tivon, Israel
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Ron Ophir
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
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24
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Nielsen ES, Henriques R, Beger M, Toonen RJ, von der Heyden S. Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species. BMC Evol Biol 2020; 20:121. [PMID: 32938400 PMCID: PMC7493327 DOI: 10.1186/s12862-020-01679-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). RESULTS Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. CONCLUSION The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.
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Affiliation(s)
- Erica S Nielsen
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.,Technical University of Denmark, National Institute of Aquatic Resources, Section for Marine Living Resources, Velsøvej 39, 8600, Silkeborg, Denmark
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
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25
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Ahrens CW, James EA, Miller AD, Scott F, Aitken NC, Jones AW, Lu-Irving P, Borevitz JO, Cantrill DJ, Rymer PD. Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra. Mol Ecol 2020; 29:3872-3888. [PMID: 32885504 DOI: 10.1111/mec.15614] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/27/2022]
Abstract
Global climate change poses a significant threat to natural communities around the world, with many plant species showing signs of climate stress. Grassland ecosystems are not an exception, with climate change compounding contemporary pressures such as habitat loss and fragmentation. In this study, we assess the climate resilience of Themeda triandra, a foundational species and the most widespread plant in Australia, by assessing the relative contributions of spatial, environmental and ploidy factors to contemporary genomic variation. Reduced-representation genome sequencing on 472 samples from 52 locations was used to test how the distribution of genomic variation, including ploidy polymorphism, supports adaptation to hotter and drier climates. We explicitly quantified isolation by distance (IBD) and isolation by environment (IBE) and predicted genomic vulnerability of populations to future climates based on expected deviation from current genomic composition. We found that a majority (54%) of genomic variation could be attributed to IBD, while an additional 22% (27% when including ploidy information) could be explained by two temperature and two precipitation climate variables demonstrating IBE. Ploidy polymorphisms were common within populations (31/52 populations), indicating that ploidy mixing is characteristic of T. triandra populations. Genomic vulnerabilities were found to be heterogeneously distributed throughout the landscape, and our analysis suggested that ploidy polymorphism, along with other factors linked to polyploidy, reduced vulnerability to future climates by 60% (0.25-0.10). Our data suggests that polyploidy may facilitate adaptation to hotter climates and highlight the importance of incorporating ploidy in adaptive management strategies to promote the resilience of this and other foundation species.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia.,Royal Botanic Gardens Victoria, Melbourne, VIC, Australia
| | | | - Adam D Miller
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Warrnambool, VIC, Australia
| | - Ferguson Scott
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Nicola C Aitken
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ashley W Jones
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Garden, Sydney, NSW, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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26
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Estravis-Barcala M, Mattera MG, Soliani C, Bellora N, Opgenoorth L, Heer K, Arana MV. Molecular bases of responses to abiotic stress in trees. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3765-3779. [PMID: 31768543 PMCID: PMC7316969 DOI: 10.1093/jxb/erz532] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 05/05/2023]
Abstract
Trees are constantly exposed to climate fluctuations, which vary with both time and geographic location. Environmental changes that are outside of the physiological favorable range usually negatively affect plant performance and trigger responses to abiotic stress. Long-living trees in particular have evolved a wide spectrum of molecular mechanisms to coordinate growth and development under stressful conditions, thus minimizing fitness costs. The ongoing development of techniques directed at quantifying abiotic stress has significantly increased our knowledge of physiological responses in woody plants. However, it is only within recent years that advances in next-generation sequencing and biochemical approaches have enabled us to begin to understand the complexity of the molecular systems that underlie these responses. Here, we review recent progress in our understanding of the molecular bases of drought and temperature stresses in trees, with a focus on functional, transcriptomic, epigenetic, and population genomic studies. In addition, we highlight topics that will contribute to progress in our understanding of the plastic and adaptive responses of woody plants to drought and temperature in a context of global climate change.
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Affiliation(s)
- Maximiliano Estravis-Barcala
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, (Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad Nacional del Comahue), San Carlos de Bariloche, Rio Negro, Argentina
| | - María Gabriela Mattera
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
| | - Carolina Soliani
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
| | - Nicolás Bellora
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, (Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad Nacional del Comahue), San Carlos de Bariloche, Rio Negro, Argentina
| | - Lars Opgenoorth
- Department of Ecology, Philipps University Marburg, Marburg, Germany
- Swiss Federal Research Institute WSL, BirmensdorfSwitzerland
| | - Katrin Heer
- Department of Conservation Biology, Philipps University Marburg, Marburg Germany
| | - María Verónica Arana
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
- Correspondence:
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27
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Capblancq T, Morin X, Gueguen M, Renaud J, Lobreaux S, Bazin E. Climate-associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps. J Evol Biol 2020; 33:783-796. [PMID: 32125745 DOI: 10.1111/jeb.13610] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 02/23/2020] [Indexed: 01/04/2023]
Abstract
Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming is predicted to induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could impede the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of Fagus sylvatica along a gradient of populations in the French Alps. Using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. A redundancy analysis (RDA)-derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of F. sylvatica in the Alps. Strong effects of elevation and humidity, which contrast north-western and south-eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings allowed identifying populations at risk for F. sylvatica in the Alps, which could be helpful for future management plans.
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Affiliation(s)
| | - Xavier Morin
- CNRS, EPHE, CEFE UMR 5175, Université de Montpellier, Université Paul-Valéry Montpellier, Montpellier, France
| | - Maya Gueguen
- CNRS, LECA UMR 5553, Université Grenoble Alpes, Grenoble, France
| | - Julien Renaud
- CNRS, LECA UMR 5553, Université Grenoble Alpes, Grenoble, France
| | | | - Eric Bazin
- CNRS, LECA UMR 5553, Université Grenoble Alpes, Grenoble, France
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28
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Jackson JM, Pimsler ML, Oyen KJ, Strange JP, Dillon ME, Lozier JD. Local adaptation across a complex bioclimatic landscape in two montane bumble bee species. Mol Ecol 2020; 29:920-939. [PMID: 32031739 DOI: 10.1111/mec.15376] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 01/21/2020] [Accepted: 02/02/2020] [Indexed: 12/21/2022]
Abstract
Understanding evolutionary responses to variation in temperature and precipitation across species ranges is of fundamental interest given ongoing climate change. The importance of temperature and precipitation for multiple aspects of bumble bee (Bombus) biology, combined with large geographic ranges that expose populations to diverse environmental pressures, make these insects well-suited for studying local adaptation. Here, we analyzed genome-wide sequence data from two widespread bumble bees, Bombus vosnesenskii and Bombus vancouverensis, using multiple environmental association analysis methods to investigate climate adaptation across latitude and altitude. The strongest signatures of selection were observed in B. vancouverensis, but despite unique responses between species for most loci, we detected several shared responses. Genes relating to neural and neuromuscular function and ion transport were especially evident with respect to temperature variables, while genes relating to cuticle formation, tracheal and respiratory system development, and homeostasis were associated with precipitation variables. Our data thus suggest that adaptive responses for tolerating abiotic variation are likely to be complex, but that several parallels among species can emerge even for these complex traits and landscapes. Results provide the framework for future work into mechanisms of thermal and desiccation tolerance in bumble bees and a set of genomic targets that might be monitored for future conservation efforts.
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Affiliation(s)
- Jason M Jackson
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Meaghan L Pimsler
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Kennan J Oyen
- Department of Zoology & Physiology and Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - James P Strange
- Department of Entomology, The Ohio State University, Columbus, OH, USA
| | - Michael E Dillon
- Department of Zoology & Physiology and Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
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29
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Borrell JS, Zohren J, Nichols RA, Buggs RJA. Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow. Evol Appl 2020; 13:161-175. [PMID: 31892950 PMCID: PMC6935589 DOI: 10.1111/eva.12883] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
When populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide restriction site-associated single nucleotide polymorphism (SNP) data, we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.
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Affiliation(s)
| | - Jasmin Zohren
- Sex Chromosome Biology LabThe Francis Crick InstituteLondonUK
| | - Richard A. Nichols
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Richard J. A. Buggs
- Jodrell LaboratoryRoyal Botanic Gardens, KewSurreyUK
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
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30
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Mattingsdal M, Jorde PE, Knutsen H, Jentoft S, Stenseth NC, Sodeland M, Robalo JI, Hansen MM, André C, Blanco Gonzalez E. Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe. Mol Ecol 2019; 29:160-171. [DOI: 10.1111/mec.15310] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Morten Mattingsdal
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
| | | | - Halvor Knutsen
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
- Institute of Marine Research Flødevigen Norway
| | - Sissel Jentoft
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
| | - Nils Christian Stenseth
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
| | - Marte Sodeland
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
| | - Joana I. Robalo
- Marine and Environmental Sciences Centre ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida Lisboa Portugal
| | | | - Carl André
- Department of Marine Sciences‐Tjärnö Göteborg University Strömstad Sweden
| | - Enrique Blanco Gonzalez
- Department of Natural Sciences Centre for Coastal Research University of Agder Kristiansand Norway
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
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31
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Chan KO, Brown RM. Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.
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Affiliation(s)
- Kin Onn Chan
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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32
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Looking for Local Adaptation: Convergent Microevolution in Aleppo Pine ( Pinus halepensis). Genes (Basel) 2019; 10:genes10090673. [PMID: 31487909 PMCID: PMC6771008 DOI: 10.3390/genes10090673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 01/15/2023] Open
Abstract
Finding outlier loci underlying local adaptation is challenging and is best approached by suitable sampling design and rigorous method selection. In this study, we aimed to detect outlier loci (single nucleotide polymorphisms, SNPs) at the local scale by using Aleppo pine (Pinus halepensis), a drought resistant conifer that has colonized many habitats in the Mediterranean Basin, as the model species. We used a nested sampling approach that considered replicated altitudinal gradients for three contrasting sites. We genotyped samples at 294 SNPs located in genomic regions selected to maximize outlier detection. We then applied three different statistical methodologies-Two Bayesian outlier methods and one latent factor principal component method-To identify outlier loci. No SNP was an outlier for all three methods, while eight SNPs were detected by at least two methods and 17 were detected only by one method. From the intersection of outlier SNPs, only one presented an allelic frequency pattern associated with the elevational gradient across the three sites. In a context of multiple populations under similar selective pressures, our results underline the need for careful examination of outliers detected in genomic scans before considering them as candidates for convergent adaptation.
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33
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Ribeiro ÂM, Puetz L, Pattinson NB, Dalén L, Deng Y, Zhang G, da Fonseca RR, Smit B, Gilbert MTP. 31° South: The physiology of adaptation to arid conditions in a passerine bird. Mol Ecol 2019; 28:3709-3721. [PMID: 31291502 DOI: 10.1111/mec.15176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022]
Abstract
Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation probably involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intraspecific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub-robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intraspecific divergence observed in harsh environments.
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Affiliation(s)
- Ângela M Ribeiro
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lara Puetz
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Yuan Deng
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ben Smit
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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34
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Hopley T, Byrne M. Gene Flow and Genetic Variation Explain Signatures of Selection across a Climate Gradient in Two Riparian Species. Genes (Basel) 2019; 10:genes10080579. [PMID: 31370268 PMCID: PMC6723506 DOI: 10.3390/genes10080579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/18/2019] [Accepted: 07/31/2019] [Indexed: 12/26/2022] Open
Abstract
Many species occur across environmental gradients and it is expected that these species will exhibit some signals of adaptation as heterogeneous environments and localized gene flow may facilitate local adaptation. While riparian zones can cross climate gradients, many of which are being impacted by climate change, they also create microclimates for the vegetation, reducing environmental heterogeneity. Species with differing distributions in these environments provide an opportunity to investigate the importance of genetic connectivity in influencing signals of adaptation over relatively short geographical distance. Association analysis with genomic data was used to compare signals of selection to climate variables in two species that have differing distributions along a river traversing a climate gradient. Results demonstrate links between connectivity, standing genetic variation, and the development of signals of selection. In the restricted species, the combination of high gene flow in the middle and lower catchment and occurrence in a microclimate created along riverbanks likely mitigated the development of selection to most climatic variables. In contrast the more widely distributed species with low gene flow showed a stronger signal of selection. Together these results strengthen our knowledge of the drivers and scale of adaptation and reinforce the importance of connectivity across a landscape to maintain adaptive potential of plant species.
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Affiliation(s)
- Tara Hopley
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
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35
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Sherpa S, Blum MGB, Després L. Cold adaptation in the Asian tiger mosquito's native range precedes its invasion success in temperate regions. Evolution 2019; 73:1793-1808. [DOI: 10.1111/evo.13801] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Stéphanie Sherpa
- Université Grenoble Alpes CNRS, UMR 5553 LECA F‐38000 Grenoble France
| | - Michael G. B. Blum
- Université Grenoble Alpes CNRS, UMR 5525 TIMC‐IMAG F‐38000 Grenoble France
| | - Laurence Després
- Université Grenoble Alpes CNRS, UMR 5553 LECA F‐38000 Grenoble France
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36
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Arostegui MC, Quinn TP, Seeb LW, Seeb JE, McKinney GJ. Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout. Mol Ecol 2019; 28:1412-1427. [DOI: 10.1111/mec.15037] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Martin C. Arostegui
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Thomas P. Quinn
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - James E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
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37
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Marshall MM, Batten LC, Remington DL, Lacey EP. Natural selection contributes to geographic patterns of thermal plasticity in Plantago lanceolata. Ecol Evol 2019; 9:2945-2963. [PMID: 30891228 PMCID: PMC6405498 DOI: 10.1002/ece3.4977] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/09/2019] [Accepted: 01/17/2019] [Indexed: 01/01/2023] Open
Abstract
A long-standing debate in evolutionary biology concerns the relative importance of different evolutionary forces in explaining phenotypic diversification at large geographic scales. For example, natural selection is typically assumed to underlie divergence along environmental gradients. However, neutral evolutionary processes can produce similar patterns. We collected molecular genetic data from 14 European populations of Plantago lanceolata to test the contributions of natural selection versus neutral evolution to population divergence in temperature-sensitive phenotypic plasticity of floral reflectance. In P. lanceolata, reflectance plasticity is positively correlated with latitude/altitude. We used population pairwise comparisons between neutral genetic differentiation (F ST and Jost's D) and phenotypic differentiation (P ST) to assess the contributions of geographic distance and environmental parameters of the reproductive season in driving population divergence. Data are consistent with selection having shaped large-scale geographic patterns in thermal plasticity. The aggregate pattern of P ST versus F ST was consistent with divergent selection. F ST explained thermal plasticity differences only when geographic distance was not included in the model. Differences in the extent of cool reproductive season temperatures, and not overall temperature variation, explained plasticity differences independent of distance. Results are consistent with the hypothesis that thermal plasticity is adaptive where growing seasons are shorter and cooler, that is, at high latitude/altitude.
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Affiliation(s)
- Matthew M. Marshall
- Department of BiologyUniversity of North Carolina at GreensboroGreensboroNorth Carolina
| | - Leslie C. Batten
- Department of BiologyUniversity of North Carolina at GreensboroGreensboroNorth Carolina
| | - David L. Remington
- Department of BiologyUniversity of North Carolina at GreensboroGreensboroNorth Carolina
| | - Elizabeth P. Lacey
- Department of BiologyUniversity of North Carolina at GreensboroGreensboroNorth Carolina
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38
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Tso KL, Allan GJ. Environmental variation shapes genetic variation in Bouteloua gracilis: Implications for restoration management of natural populations and cultivated varieties in the southwestern United States. Ecol Evol 2019; 9:482-499. [PMID: 30680130 PMCID: PMC6342110 DOI: 10.1002/ece3.4767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 09/14/2018] [Accepted: 11/02/2018] [Indexed: 11/17/2022] Open
Abstract
With the increasing frequency of large-scale restoration efforts, the need to understand the adaptive genetic structure of natural plant populations and their relation to heavily utilized cultivars is critical. Bouteloua gracilis (blue grama) is a wind-dispersed, perennial grass consisting of several cytotypes (2n = 2×-6×) with a widespread distribution in western North America. The species is locally dominant and used regularly in restoration treatments. Using amplified fragment length polymorphism (AFLP) and cpDNA analyses, we assessed the genetic variability and adaptive genetic structure of blue grama within and among 44 sampling sites that are representative of the species' environmental and habitat diversity in the southwestern United States. Five cultivars were also included to investigate genetic diversity and differentiation in natural versus cultivated populations. Three main findings resulted from this study: (a) Ninety-four polymorphic AFLP markers distinguished two population clusters defined largely by samples on and off the Colorado Plateau; (b) substructure of samples on the Colorado Plateau was indicated by genetic divergence between boundary and interior regions, and was supported by cytotype distribution and cpDNA analysis; and (c) six AFLP markers were identified as "outliers," consistent with being under selection. These loci were significantly correlated to mean annual temperature, mean annual precipitation, precipitation of driest quarter, and precipitation of wettest quarter in natural populations, but not in cultivated samples. Marker × environment relationships were found to be largely influenced by cytotype and cultivar development. Our results demonstrate that blue grama is genetically variable, and exhibits genetic structure, which is shaped, in part, by environmental variability across the Colorado Plateau. Information from our study can be used to guide the selection of seed source populations for commercial development and long-term conservation management of B. gracilis, which could include genetic assessments of diversity and the adaptive potential of both natural and cultivated populations for wildland restoration.
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Affiliation(s)
- Katrina L. Tso
- Department of Biological Sciences, Environmental Genetics & Genomics FacilityNorthern Arizona UniversityFlagstaffArizona
| | - Gerard J. Allan
- Department of Biological Sciences, Environmental Genetics & Genomics FacilityNorthern Arizona UniversityFlagstaffArizona
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39
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Friis G, Fandos G, Zellmer AJ, McCormack JE, Faircloth BC, Milá B. Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird. Mol Ecol 2018; 27:5137-5153. [PMID: 30451354 DOI: 10.1111/mec.14946] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/26/2018] [Accepted: 10/15/2018] [Indexed: 12/25/2022]
Abstract
The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation-by-adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.
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Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Guillermo Fandos
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Amanda J Zellmer
- Department of Biology, Occidental College, Los Angeles, California
| | - John E McCormack
- Department of Biology, Occidental College, Los Angeles, California.,Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, California
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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40
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Xia H, Wang B, Zhao W, Pan J, Mao J, Wang X. Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis. Evol Appl 2018; 11:1931-1945. [PMID: 30459839 PMCID: PMC6231471 DOI: 10.1111/eva.12697] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/17/2018] [Accepted: 08/08/2018] [Indexed: 01/04/2023] Open
Abstract
The phylogeographic histories of plants in East Asia are complex and shaped by both past large-scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping-by-sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among-population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.
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Affiliation(s)
- Hanhan Xia
- Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Wei Zhao
- Department of Ecology and Environmental ScienceUPSCUmeå UniversityUmeåSweden
| | - Jin Pan
- Department of Ecology and Environmental ScienceUPSCUmeå UniversityUmeåSweden
| | - Jian‐Feng Mao
- Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Xiao‐Ru Wang
- Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Department of Ecology and Environmental ScienceUPSCUmeå UniversityUmeåSweden
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41
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Sherpa S, Rioux D, Goindin D, Fouque F, François O, Després L. At the Origin of a Worldwide Invasion: Unraveling the Genetic Makeup of the Caribbean Bridgehead Populations of the Dengue Vector Aedes aegypti. Genome Biol Evol 2018; 10:56-71. [PMID: 29267872 PMCID: PMC5758905 DOI: 10.1093/gbe/evx267] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2017] [Indexed: 12/21/2022] Open
Abstract
Human-driven global environmental changes have considerably increased the risk of biological invasions, especially the spread of human parasites and their vectors. Among exotic species that have major impacts on public health, the dengue fever mosquito Aedes aegypti originating from Africa has spread worldwide during the last three centuries. Although considerable progress has been recently made in understanding the history of this invasion, the respective roles of human and abiotic factors in shaping patterns of genetic diversity remain largely unexplored. Using a genome-wide sample of genetic variants (3,530 ddRAD SNPs), we analyzed the genetic structure of Ae. aegypti populations in the Caribbean, the first introduced territories in the Americas. Fourteen populations were sampled in Guyane and in four islands of the Antilles that differ in climatic conditions, intensity of urbanization, and vector control history. The genetic diversity in the Caribbean was low (He = 0.14–0.17), as compared with a single African collection from Benin (He = 0.26) and site-frequency spectrum analysis detected an ancient bottleneck dating back ∼300 years ago, supporting a founder event during the introduction of Ae. aegypti. Evidence for a more recent bottleneck may be related to the eradication program undertaken on the American continent in the 1950s. Among 12 loci detected as FST-outliers, two were located in candidate genes for insecticide resistance (cytochrome P450 and voltage-gated sodium channel). Genome–environment association tests identified additional loci associated with human density and/or deltamethrin resistance. Our results highlight the high impact of human pressures on the demographic history and genetic variation of Ae. aegypti Caribbean populations.
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Affiliation(s)
- Stéphanie Sherpa
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Grenoble Alpes, Grenoble, France
| | - Delphine Rioux
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Grenoble Alpes, Grenoble, France
| | - Daniella Goindin
- Laboratoire d'Entomologie Médicale, Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Florence Fouque
- Special Programme for Research and Training in Tropical Diseases, World Health Organization, Geneva, Switzerland
| | - Olivier François
- Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité, CNRS UMR 5525, Université Grenoble Alpes, Grenoble, France
| | - Laurence Després
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Grenoble Alpes, Grenoble, France
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42
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Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset. Heredity (Edinb) 2018; 122:276-287. [PMID: 30026534 DOI: 10.1038/s41437-018-0124-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 11/08/2022] Open
Abstract
Studying the genetic population structure of species can reveal important insights into several key evolutionary, historical, demographic, and anthropogenic processes. One of the most important statistical tools for inferring genetic clusters is the program STRUCTURE. Recently, several papers have pointed out that STRUCTURE may show a bias when the sampling design is unbalanced, resulting in spurious joining of underrepresented populations and spurious separation of overrepresented populations. Suggestions to overcome this bias include subsampling and changing the ancestry model, but the performance of these two methods has not yet been tested on actual data. Here, I use a data set of 12 high-alpine plant species to test whether unbalanced sampling affects the STRUCTURE inference of population differentiation between the European Alps and the Carpathians. For four of the 12 species, subsampling of the Alpine populations-to match the sample size between the Alps and the Carpathians-resulted in a drastically different clustering than the full data set. On the other hand, STRUCTURE results with the alternative ancestry model were indistinguishable from the results with the default model. Based on these results, the subsampling strategy seems a more viable approach to overcome the bias than the alternative ancestry model. However, subsampling is only possible when there is an a priori expectation of what constitute the main clusters. Though these results do not mean that the use of STRUCTURE should be discarded, it does indicate that users of the software should be cautious about the interpretation of the results when sampling is unbalanced.
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43
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Klimova A, Ortega‐Rubio A, Vendrami DLJ, Hoffman JI. Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence, and long-distance dispersal in North American palms. Ecol Evol 2018; 8:5873-5890. [PMID: 29938100 PMCID: PMC6010798 DOI: 10.1002/ece3.4125] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Comparative studies can provide powerful insights into processes that affect population divergence and thereby help to elucidate the mechanisms by which contemporary populations may respond to environmental change. Furthermore, approaches such as genotyping by sequencing (GBS) provide unprecedented power for resolving genetic differences among species and populations. We therefore used GBS to provide a genomewide perspective on the comparative population structure of two palm genera, Washingtonia and Brahea, on the Baja California peninsula, a region of high landscape and ecological complexity. First, we used phylogenetic analysis to address taxonomic uncertainties among five currently recognized species. We resolved three main clades, the first corresponding to W. robusta and W. filifera, the second to B. brandegeei and B. armata, and the third to B. edulis from Guadalupe Island. Focusing on the first two clades, we then delved deeper by investigating the underlying population structure. Striking differences were found, with GBS uncovering four distinct Washingtonia populations and identifying a suite of loci associated with temperature, consistent with ecologically mediated divergence. By contrast, individual mountain ranges could be resolved in Brahea and few loci were associated with environmental variables, implying a more prominent role of neutral divergence. Finally, evidence was found for long-distance dispersal events in Washingtonia but not Brahea, in line with knowledge of the dispersal mechanisms of these palms including the possibility of human-mediated dispersal. Overall, our study demonstrates the power of GBS together with a comparative approach to elucidate markedly different patterns of genomewide divergence mediated by multiple effectors.
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Affiliation(s)
- Anastasia Klimova
- Centro de Investigaciones Biologicas del Noroeste S.C.La PazBaja California SurMexico
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
| | - Alfredo Ortega‐Rubio
- Centro de Investigaciones Biologicas del Noroeste S.C.La PazBaja California SurMexico
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44
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Lobo A, Hansen OK, Hansen JK, Erichsen EO, Jacobsen B, Kjær ED. Local adaptation through genetic differentiation in highly fragmented Tilia cordata populations. Ecol Evol 2018; 8:5968-5976. [PMID: 29988427 PMCID: PMC6024143 DOI: 10.1002/ece3.4131] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/30/2022] Open
Abstract
We assessed the level of geographic differentiation of Tilia cordata in Denmark based on tests of 91 trees selected from 12 isolated populations. We used quantitative analysis of spring phenology and population genetic analysis based on SSR markers to infer the likely historical genetic processes within and among populations. High genetic variation within and among populations was observed in spring phenology, which correlated with spring temperatures at the origin of the tested T. cordata trees. The population genetic analysis revealed significant differentiation among the populations, but with no clear sign of isolation by distance. We infer the findings as indications of ongoing fine scale selection in favor of local growth conditions made possible by limited gene flow among the small and fragmented populations. This hypothesis fits well with reports of limited fruiting in the investigated Danish T. cordata populations, while the species is known for its ability to propagate vegetatively by root suckers. Our results suggest that both divergent selection and genetic drift may have played important roles in forming the genetic patterns of T. cordata at its northern distribution limit. However, we also speculate that epigenetic mechanism arising from the original population environment could have created similar patterns in regulating the spring phenology.
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Affiliation(s)
- Albin Lobo
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Ole Kim Hansen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Jon Kehlet Hansen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Eva Ortvald Erichsen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Birgitte Jacobsen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
- Present address:
Ministry of Fisheries and HuntingNuukGreenland
| | - Erik Dahl Kjær
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
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45
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Leigh DM, Lischer HEL, Grossen C, Keller LF. Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths. Mol Ecol Resour 2018; 18:778-788. [DOI: 10.1111/1755-0998.12779] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/11/2022]
Affiliation(s)
- D. M. Leigh
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Swiss Institute of Bioinformatics Quartier Sorge ‐ Batiment Genopode Lausanne Switzerland
- Department of Biology Queen's University Kingston ON Canada
| | - H. E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Swiss Institute of Bioinformatics Quartier Sorge ‐ Batiment Genopode Lausanne Switzerland
| | - C. Grossen
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - L. F. Keller
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Zoological Museum University of Zurich Zurich Switzerland
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46
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Optimizing Conservation Strategies for a Threatened Tree Species: In Situ Conservation of White Ash (Fraxinus americana L.) Genetic Diversity through Insecticide Treatment. FORESTS 2018. [DOI: 10.3390/f9040202] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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47
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Housset JM, Nadeau S, Isabel N, Depardieu C, Duchesne I, Lenz P, Girardin MP. Tree rings provide a new class of phenotypes for genetic associations that foster insights into adaptation of conifers to climate change. THE NEW PHYTOLOGIST 2018; 218:630-645. [PMID: 29314017 PMCID: PMC6079641 DOI: 10.1111/nph.14968] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/21/2017] [Indexed: 05/20/2023]
Abstract
Local adaptation in tree species has been documented through a long history of common garden experiments where functional traits (height, bud phenology) are used as proxies for fitness. However, the ability to identify genes or genomic regions related to adaptation to climate requires the evaluation of traits that precisely reflect how and when climate exerts selective constraints. We combine dendroecology with association genetics to establish a link between genotypes, phenotypes and interannual climatic fluctuations. We illustrate this approach by examining individual tree responses embedded in the annual rings of 233 Pinus strobus trees growing in a common garden experiment representing 38 populations from the majority of its range. We found that interannual variability in growth was affected by low temperatures during spring and autumn, and by summer heat and drought. Among-population variation in climatic sensitivity was significantly correlated with the mean annual temperature of the provenance, suggesting local adaptation. Genotype-phenotype associations using these new tree-ring phenotypes validated nine candidate genes identified in a previous genetic-environment association study. Combining dendroecology with association genetics allowed us to assess tree vulnerability to past climate at fine temporal scales and provides avenues for future genomic studies on functional adaptation in forest trees.
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Affiliation(s)
- Johann M. Housset
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Natural Resources CanadaCanadian Wood Fibre Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Centre d’étude de la forêtUniversité du Québec à MontréalC.P. 8888, succ. Centre‐villeMontréalQCH3C 3P8Canada
| | - Simon Nadeau
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Natural Resources CanadaCanadian Wood Fibre Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
| | - Nathalie Isabel
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Chaire de Recherche du Canada en Génomique ForestièreFaculté de Foresteriede Géographie et de GéomatiqueUniversité LavalQuébecQCG1V 0A6Canada
| | - Claire Depardieu
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Chaire de Recherche du Canada en Génomique ForestièreFaculté de Foresteriede Géographie et de GéomatiqueUniversité LavalQuébecQCG1V 0A6Canada
| | - Isabelle Duchesne
- Natural Resources CanadaCanadian Wood Fibre Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
| | - Patrick Lenz
- Natural Resources CanadaCanadian Wood Fibre Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Chaire de Recherche du Canada en Génomique ForestièreFaculté de Foresteriede Géographie et de GéomatiqueUniversité LavalQuébecQCG1V 0A6Canada
| | - Martin P. Girardin
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry Centre1055 du P.E.P.S, PO Box 10380, Stn. Sainte‐FoyQuébecQCG1V 4C7Canada
- Centre d’étude de la forêtUniversité du Québec à MontréalC.P. 8888, succ. Centre‐villeMontréalQCH3C 3P8Canada
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48
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Lobo A, Hansen JK, Hansen LN, Dahl Kjær E. Differences among six woody perennials native to Northern Europe in their level of genetic differentiation and adaptive potential at fine local scale. Ecol Evol 2018; 8:2231-2239. [PMID: 29468039 PMCID: PMC5817134 DOI: 10.1002/ece3.3824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/13/2017] [Accepted: 12/17/2017] [Indexed: 11/12/2022] Open
Abstract
The ability of perennial species to adapt their phenology to present and future temperature conditions is important for their ability to retain high fitness compared to other competing plant species, pests, and pathogens. Many transplanting studies with forest tree species have previously reported substantial genetic differentiation among populations within their native range. However, the question of "how local is local" is still highly debated in conservation biology because studies on genetic patterns of variation within and among populations at the local scale are limited and scattered. In this study, we compare the level of genetic differentiation among populations of six different perennial plant species based on their variation in spring flushing. We assess the level of additive genetic variation present within the local population. For all six species, we find significant differentiation among populations from sites with mean annual temperature ranging between 7.4°C and 8.4°C. The observed variation can only be partly explained by the climate at the site of origin. Most clear relationship between early flushing and higher average spring temperature is observed for the three wind-pollinated species in the study, while the relations are much less clear for the three insect-pollinated species. This supports that pollination system can influence the balance between genetic drift and natural selection and thereby influence the level of local adaptation in long-lived species. On the positive side, we find that the native populations of woody plant species have maintained high levels of additive genetic variation in spring phenology, although this also differs substantially among the six studied species.
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Affiliation(s)
- Albin Lobo
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Jon Kehlet Hansen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Lars Nørgaard Hansen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Erik Dahl Kjær
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
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49
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Sork VL. Genomic Studies of Local Adaptation in Natural Plant Populations. J Hered 2017; 109:3-15. [DOI: 10.1093/jhered/esx091] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022] Open
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50
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Meirmans PG, Godbout J, Lamothe M, Thompson SL, Isabel N. History rather than hybridization determines population structure and adaptation inPopulus balsamifera. J Evol Biol 2017; 30:2044-2058. [DOI: 10.1111/jeb.13174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 08/10/2017] [Accepted: 08/23/2017] [Indexed: 01/12/2023]
Affiliation(s)
- P. G. Meirmans
- Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam The Netherlands
| | - J. Godbout
- Laurentian Forestry Centre; Canadian Forest Service, Natural Resources Canada; Québec QC Canada
| | - M. Lamothe
- Laurentian Forestry Centre; Canadian Forest Service, Natural Resources Canada; Québec QC Canada
| | - S. L. Thompson
- Laurentian Forestry Centre; Canadian Forest Service, Natural Resources Canada; Québec QC Canada
| | - N. Isabel
- Laurentian Forestry Centre; Canadian Forest Service, Natural Resources Canada; Québec QC Canada
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