151
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Cayuela H, Rougemont Q, Laporte M, Mérot C, Normandeau E, Dorant Y, Tørresen OK, Hoff SNK, Jentoft S, Sirois P, Castonguay M, Jansen T, Praebel K, Clément M, Bernatchez L. Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish. Mol Ecol 2020; 29:2379-2398. [DOI: 10.1111/mec.15499] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Siv Nam Khang Hoff
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Pascal Sirois
- Département des sciences fondamentales Université du Québec à Chicoutimi Chicoutimi QC Canada
| | - Martin Castonguay
- Fisheries and Oceans Canada Institut Maurice‐Lamontagne Mont‐Joli QC Canada
| | - Teunis Jansen
- GINR‐Greenland Institute of Natural Resources Nuuk Greenland
- DTU Aqua‐National Institute of Aquatic Resources Technical University of Denmark Charlottenlund Castle, Charlottenlund Denmark
| | - Kim Praebel
- Norwegian College of Fishery Science Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Marie Clément
- Center for Fisheries Ecosystems Research Fisheries and Marine Institute of Memorial University of Newfoundland St. John's NL Canada
- Labrador Institute of Memorial University of Newfoundland Happy Valley‐Goose Bay NL Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
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152
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Reatini B, Vision TJ. Genetic architecture influences when and how hybridization contributes to colonization. Evolution 2020; 74:1590-1602. [PMID: 32267552 DOI: 10.1111/evo.13972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 01/19/2023]
Abstract
The role of genetic architecture in adaptation to novel environments has received considerable attention when the source of adaptive variation is de novo mutation. Relatively less is known when the source of adaptive variation is inter- or intraspecific hybridization. We model hybridization between divergent source populations and subsequent colonization of an unoccupied novel environment using individual-based simulations to understand the influence of genetic architecture on the timing of colonization and the mode of adaptation. We find that two distinct categories of genetic architecture facilitate rapid colonization but that they do so in qualitatively different ways. For few and/or tightly linked loci, the mode of adaptation is via the recovery of adaptive parental genotypes. With many unlinked loci, the mode of adaptation is via the generation of novel hybrid genotypes. The first category results in the shortest colonization lag phases across the widest range of parameter space, but further adaptation is mutation limited. The second category takes longer and is more sensitive to genetic variance and dispersal rate, but can facilitate adaptation to environmental conditions that exceed the tolerance of parental populations. These findings have implications for understanding the origins of biological invasions and the success of hybrid populations.
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Affiliation(s)
- Bryan Reatini
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, 27599-3280
| | - Todd J Vision
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, 27599-3280
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153
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Sun SJ, Catherall AM, Pascoal S, Jarrett BJM, Miller SE, Sheehan MJ, Kilner RM. Rapid local adaptation linked with phenotypic plasticity. Evol Lett 2020; 4:345-359. [PMID: 32774883 PMCID: PMC7403679 DOI: 10.1002/evl3.176] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/12/2020] [Accepted: 04/29/2020] [Indexed: 11/05/2022] Open
Abstract
Models of "plasticity-first" evolution are attractive because they explain the rapid evolution of new complex adaptations. Nevertheless, it is unclear whether plasticity can facilitate rapid microevolutionary change between diverging populations. Here, we show how plasticity may have generated adaptive differences in fecundity between neighboring wild populations of burying beetles Nicrophorus vespilloides. These populations occupy distinct Cambridgeshire woodlands that are just 2.5 km apart and that probably originated from a common ancestral population about 1000-4000 years ago. We find that populations are divergently adapted to breed on differently sized carrion. Adaptive differences in clutch size and egg size are associated with divergence at loci connected with oogenesis. The populations differ specifically in the elevation of the reaction norm linking clutch size to carrion size (i.e., genetic accommodation), and in the likelihood that surplus offspring will be lost after hatching. We suggest that these two processes may have facilitated rapid local adaptation on a fine-grained spatial scale.
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Affiliation(s)
- Syuan-Jyun Sun
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Andrew M Catherall
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Sonia Pascoal
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Benjamin J M Jarrett
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom.,Department of Entomology Michigan State University East Lansing Michigan 48824
| | - Sara E Miller
- Department of Neurobiology and Behavior Cornell University Ithaca New York 14853
| | - Michael J Sheehan
- Department of Neurobiology and Behavior Cornell University Ithaca New York 14853
| | - Rebecca M Kilner
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
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154
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Mérot C, Oomen RA, Tigano A, Wellenreuther M. A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation. Trends Ecol Evol 2020; 35:561-572. [PMID: 32521241 DOI: 10.1016/j.tree.2020.03.002] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/25/2020] [Accepted: 03/03/2020] [Indexed: 12/12/2022]
Abstract
Structural genomic variants (SVs) are ubiquitous and play a major role in adaptation and speciation. Yet, comparative and population genomics have focused predominantly on gene duplications and large-effect inversions. The lack of a common framework for studying all SVs is hampering progress towards a more systematic assessment of their evolutionary significance. Here we (i) review how different types of SVs affect ecological and evolutionary processes; (ii) suggest unifying definitions and recommendations for future studies; and (iii) provide a roadmap for the integration of SVs in ecoevolutionary studies. In doing so, we lay the foundation for population genomics, theoretical, and experimental approaches to understand how the full spectrum of SVs impacts ecological and evolutionary processes.
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Affiliation(s)
- Claire Mérot
- Université Laval, Institut de Biologie Intégrative des Systèmes, 1030 Avenue de la Médecine, G1V 0A6, Québec, QC, Canada.
| | - Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371 Oslo, Norway; Centre for Coastal Research, University of Agder, Universitetsveien 25, 4630 Kristiansand, Norway.
| | - Anna Tigano
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.
| | - Maren Wellenreuther
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand; The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand.
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155
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Waldvogel A, Feldmeyer B, Rolshausen G, Exposito‐Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. Evolutionary genomics can improve prediction of species' responses to climate change. Evol Lett 2020; 4:4-18. [PMID: 32055407 PMCID: PMC7006467 DOI: 10.1002/evl3.154] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/31/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco-evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large-scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco-evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.
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Affiliation(s)
- Ann‐Marie Waldvogel
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | | | | | - Robert Kofler
- Institute of Population GeneticsVetmeduni ViennaAustria
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwichUnited Kingdom
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe‐UniversityFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
| | | | | | - Alan Bergland
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia
| | - Thomas Flatt
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Frederic Guillaume
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
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156
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Keuler R, Garretson A, Saunders T, Erickson RJ, St Andre N, Grewe F, Smith H, Lumbsch HT, Huang JP, St Clair LL, Leavitt SD. Genome-scale data reveal the role of hybridization in lichen-forming fungi. Sci Rep 2020; 10:1497. [PMID: 32001749 PMCID: PMC6992703 DOI: 10.1038/s41598-020-58279-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Advancements in molecular genetics have revealed that hybridization may be common among plants, animals, and fungi, playing a role in evolutionary dynamics and speciation. While hybridization has been well-documented in pathogenic fungi, the effects of these processes on speciation in fungal lineages with different life histories and ecological niches are largely unexplored. Here we investigated the potential influence of hybridization on the emergence of morphologically and reproductively distinct asexual lichens. We focused on vagrant forms (growing obligately unattached to substrates) within a clade of rock-dwelling, sexually reproducing species in the Rhizoplaca melanophthalma (Lecanoraceae, Ascomycota) species complex. We used phylogenomic data from both mitochondrial and nuclear genomes to infer evolutionary relationships and potential patterns of introgression. We observed multiple instances of discordance between the mitochondrial and nuclear trees, including the clade comprising the asexual vagrant species R. arbuscula, R. haydenii, R. idahoensis, and a closely related rock-dwelling lineage. Despite well-supported phylogenies, we recovered strong evidence of a reticulated evolutionary history using a network approach that incorporates both incomplete lineage sorting and hybridization. These data suggest that the rock-dwelling western North American subalpine endemic R. shushanii is potentially the result of a hybrid speciation event, and introgression may have also played a role in other taxa, including vagrant species R. arbuscula, R. haydenii and R. idahoensis. We discuss the potential roles of hybridization in terms of generating asexuality and novel morphological traits in lichens. Furthermore, our results highlight the need for additional study of reticulate phylogenies when investigating species boundaries and evolutionary history, even in cases with well-supported topologies inferred from genome-scale data.
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Affiliation(s)
- Rachel Keuler
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Alexis Garretson
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Theresa Saunders
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Robert J Erickson
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Nathan St Andre
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Felix Grewe
- Grainger Bioinformatics Center, Science & Education, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Hayden Smith
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - H Thorsten Lumbsch
- Grainger Bioinformatics Center, Science & Education, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, 128 Academia Rd, Section 2, Nankang District, Taipei, 11529, Taiwan
| | - Larry L St Clair
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
- M. L. Bean Life Science Museum, Brigham Young University, 1115 MLBM, Provo, UT, 84602, USA
| | - Steven D Leavitt
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA.
- M. L. Bean Life Science Museum, Brigham Young University, 1115 MLBM, Provo, UT, 84602, USA.
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157
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Kioukis A, Michalopoulou VA, Briers L, Pirintsos S, Studholme DJ, Pavlidis P, Sarris PF. Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection. BMC Genomics 2020; 21:48. [PMID: 31937246 PMCID: PMC6961386 DOI: 10.1186/s12864-019-6439-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/29/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc. RESULTS: We sequenced genomes of four Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data (thus, the parts of the genome that has evolved nearly neutrally), we find the gene flow between different Bc population is recent and its genomic diversity is high. CONCLUSIONS Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected demographic models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement.
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Affiliation(s)
- Antonios Kioukis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, 70013, Crete, Greece
| | - Vassiliki A Michalopoulou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, 70013, Crete, Greece
| | - Laura Briers
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Stergios Pirintsos
- Department of Biology, University of Crete, 714 09, Heraklion, Greece
- Botanical Garden, University of Crete, Gallos Campus, 741 00, Rethymnon, Greece
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, 70013, Crete, Greece
| | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, 70013, Crete, Greece.
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
- Department of Biology, University of Crete, 714 09, Heraklion, Greece.
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158
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Kess T, Bentzen P, Lehnert SJ, Sylvester EVA, Lien S, Kent MP, Sinclair‐Waters M, Morris C, Wringe B, Fairweather R, Bradbury IR. Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish. Ecol Evol 2020; 10:638-653. [PMID: 32015832 PMCID: PMC6988541 DOI: 10.1002/ece3.5828] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023] Open
Abstract
Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
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Affiliation(s)
- Tony Kess
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Paul Bentzen
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Sarah J. Lehnert
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Emma V. A. Sylvester
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Sigbjørn Lien
- Department of Animal and Aquacultural SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Matthew P. Kent
- Department of Animal and Aquacultural SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Marion Sinclair‐Waters
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | - Corey Morris
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Brendan Wringe
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | | | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
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159
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Slatyer RA, Schoville SD, Nufio CR, Buckley LB. Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community? Ecol Evol 2020; 10:980-997. [PMID: 32015859 PMCID: PMC6988534 DOI: 10.1002/ece3.5961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 01/13/2023] Open
Abstract
Species responses to environmental change are likely to depend on existing genetic and phenotypic variation, as well as evolutionary potential. A key challenge is to determine whether gene flow might facilitate or impede genomic divergence among populations responding to environmental change, and if emergent phenotypic variation is dependent on gene flow rates. A general expectation is that patterns of genetic differentiation in a set of codistributed species reflect differences in dispersal ability. In less dispersive species, we predict greater genetic divergence and reduced gene flow. This could lead to covariation in life-history traits due to local adaptation, although plasticity or drift could mirror these patterns. We compare genome-wide patterns of genetic structure in four phenotypically variable grasshopper species along a steep elevation gradient near Boulder, Colorado, and test the hypothesis that genomic differentiation is greater in short-winged grasshopper species, and statistically associated with variation in growth, reproductive, and physiological traits along this gradient. In addition, we estimate rates of gene flow under competing demographic models, as well as potential gene flow through surveys of phenological overlap among populations within a species. All species exhibit genetic structure along the elevation gradient and limited gene flow. The most pronounced genetic divergence appears in short-winged (less dispersive) species, which also exhibit less phenological overlap among populations. A high-elevation population of the most widespread species, Melanoplus sanguinipes, appears to be a sink population derived from low elevation populations. While dispersal ability has a clear connection to the genetic structure in different species, genetic distance does not predict growth, reproductive, or physiological trait variation in any species, requiring further investigation to clearly link phenotypic divergence to local adaptation.
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Affiliation(s)
| | | | - César R. Nufio
- University of Colorado Natural History MuseumUniversity of ColoradoBoulderCOUSA
- National Science FoundationAlexandriaVAUSA
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160
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Schmidt H, Lee Y, Collier TC, Hanemaaijer MJ, Kirstein OD, Ouledi A, Muleba M, Norris DE, Slatkin M, Cornel AJ, Lanzaro GC. Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events. Commun Biol 2019; 2:473. [PMID: 31886413 PMCID: PMC6923408 DOI: 10.1038/s42003-019-0717-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/28/2019] [Indexed: 01/20/2023] Open
Abstract
The mosquito Anopheles gambiae s.s. is distributed across most of sub-Saharan Africa and is of major scientific and public health interest for being an African malaria vector. Here we present population genomic analyses of 111 specimens sampled from west to east Africa, including the first whole genome sequences from oceanic islands, the Comoros. Genetic distances between populations of A. gambiae are discordant with geographic distances but are consistent with a stepwise migration scenario in which the species increases its range from west to east Africa through consecutive founder events over the last ~200,000 years. Geological barriers like the Congo River basin and the East African rift seem to play an important role in shaping this process. Moreover, we find a high degree of genetic isolation of populations on the Comoros, confirming the potential of these islands as candidate sites for potential field trials of genetically engineered mosquitoes for malaria control.
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Affiliation(s)
- Hanno Schmidt
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Travis C. Collier
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Mark J. Hanemaaijer
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Oscar D. Kirstein
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Ahmed Ouledi
- Université des Comores, Grande Comore, Union of the Comoros
| | | | - Douglas E. Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California - Berkeley, Berkeley, CA 94720 USA
| | - Anthony J. Cornel
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
- Mosquito Control Research Laboratory, Department of Entomology and Nematology, University of California - Kearney Research and Extension Center, Parlier, CA 93648 USA
| | - Gregory C. Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
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161
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Homola JJ, Loftin CS, Cammen KM, Helbing CC, Birol I, Schultz TF, Kinnison MT. Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs. J Hered 2019; 110:707-719. [PMID: 31278891 PMCID: PMC6785938 DOI: 10.1093/jhered/esz041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.
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Affiliation(s)
- Jared J Homola
- School of Biology and Ecology, University of Maine, Orono, ME
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Cynthia S Loftin
- the US Geological Survey, Maine Cooperative Fish and Wildlife Research Unit, Orono, ME
| | | | - Caren C Helbing
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Inanc Birol
- the Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Thomas F Schultz
- the Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC
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162
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Quigley KM, Bay LK, van Oppen MJH. The active spread of adaptive variation for reef resilience. Ecol Evol 2019; 9:11122-11135. [PMID: 31641460 PMCID: PMC6802068 DOI: 10.1002/ece3.5616] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
The speed at which species adapt depends partly on the rates of beneficial adaptation generation and how quickly they spread within and among populations. Natural rates of adaptation of corals may not be able to keep pace with climate warming. Several interventions have been proposed to fast-track thermal adaptation, including the intentional translocation of warm-adapted adults or their offspring (assisted gene flow, AGF) and the ex situ crossing of warm-adapted corals with conspecifics from cooler reefs (hybridization or selective breeding) and field deployment of those offspring. The introgression of temperature tolerance loci into the genomic background of cooler-environment corals aims to facilitate adaptation to warming while maintaining fitness under local conditions. Here we use research on selective sweeps and connectivity to understand the spread of adaptive variants as it applies to AGF on the Great Barrier Reef (GBR), focusing on the genus Acropora. Using larval biophysical dispersal modeling, we estimate levels of natural connectivity in warm-adapted northern corals. We then model the spread of adaptive variants from single and multiple reefs and assess if the natural and assisted spread of adaptive variants will occur fast enough to prepare receiving central and southern populations given current rates of warming. We also estimate fixation rates and spatial extent of fixation under multiple release scenarios to inform intervention design. Our results suggest that thermal tolerance is unlikely to spread beyond northern reefs to the central and southern GBR without intervention, and if it does, 30+ generations are needed for adaptive gene variants to reach fixation even under multiple release scenarios. We argue that if translocation, breeding, and reseeding risks are managed, AGF using multiple release reefs can be beneficial for the restoration of coral populations. These interventions should be considered in addition to conventional management and accompanied by strong mitigation of CO2 emissions.
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Affiliation(s)
- Kate M. Quigley
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | - Line K. Bay
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine ScienceTownsvilleQldAustralia
- School of BioSciencesThe University of MelbourneParkvilleVic.Australia
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163
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Cummins D, Kennington WJ, Rudin-Bitterli T, Mitchell NJ. A genome-wide search for local adaptation in a terrestrial-breeding frog reveals vulnerability to climate change. GLOBAL CHANGE BIOLOGY 2019; 25:3151-3162. [PMID: 31273907 DOI: 10.1111/gcb.14703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
Terrestrial-breeding amphibians are likely to be vulnerable to warming and drying climates, as their embryos require consistent moisture for successful development. Adaptation to environmental change will depend on sufficient genetic variation existing within or between connected populations. Here, we use Single Nucleotide Polymorphism (SNP) data to investigate genome-wide patterns in genetic diversity, gene flow and local adaptation in a terrestrial-breeding frog (Pseudophryne guentheri) subject to a rapidly drying climate and recent habitat fragmentation. The species was sampled across 12 central and range-edge populations (192 samples), and strong genetic structure was apparent, as were high inbreeding coefficients. Populations showed differences in genetic diversity, and one population lost significant genetic diversity in a decade. More than 500 SNP loci were putatively under directional selection, and 413 of these loci were correlated with environmental variables such as temperature, rainfall, evaporation and soil moisture. One locus showed homology to a gene involved in the activation of maturation in Xenopus oocytes, which may facilitate rapid development of embryos in drier climates. The low genetic diversity, strong population structuring and presence of local adaptation revealed in this study shows why management strategies such as targeted gene flow may be necessary to assist isolated populations to adapt to future climates.
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Affiliation(s)
- Deanne Cummins
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - W Jason Kennington
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Tabitha Rudin-Bitterli
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Nicola J Mitchell
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
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164
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The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity (Edinb) 2019; 124:1-14. [PMID: 31399719 PMCID: PMC6906368 DOI: 10.1038/s41437-019-0257-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/16/2019] [Accepted: 07/25/2019] [Indexed: 12/22/2022] Open
Abstract
By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on background matching, a particular facet of crypsis that involves the ability of an organism to conceal itself through matching its color to the surrounding environment. While interesting in and of itself, the study of this phenotype has also provided fruitful population genetic insights into the interplay of strong positive selection with other evolutionary processes. Specifically, and predicated upon the findings of previous candidate gene association studies, a primary focus of this recent literature involves the realization that the inference of selection from DNA sequence data first requires a robust model of population demography in order to identify genomic regions which do not conform to neutral expectations. Moreover, these demographic estimates provide crucial information about the origin and timing of the onset of selective pressures associated with, for example, the colonization of a novel environment. Furthermore, such inference has revealed crypsis to be a particularly useful phenotype for investigating the interplay of migration and selection—with examples of gene flow constraining rates of adaptation, or alternatively providing the genetic variants that may ultimately sweep through the population. Here, we evaluate the underlying evidence, review the strengths and weaknesses of the many population genetic methodologies used in these studies, and discuss how these insights have aided our general understanding of the evolutionary process.
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165
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Snell RS, Beckman NG, Fricke E, Loiselle BA, Carvalho CS, Jones LR, Lichti NI, Lustenhouwer N, Schreiber SJ, Strickland C, Sullivan LL, Cavazos BR, Giladi I, Hastings A, Holbrook KM, Jongejans E, Kogan O, Montaño-Centellas F, Rudolph J, Rogers HS, Zwolak R, Schupp EW. Consequences of intraspecific variation in seed dispersal for plant demography, communities, evolution and global change. AOB PLANTS 2019; 11:plz016. [PMID: 31346404 PMCID: PMC6644487 DOI: 10.1093/aobpla/plz016] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/20/2019] [Indexed: 05/22/2023]
Abstract
As the single opportunity for plants to move, seed dispersal has an important impact on plant fitness, species distributions and patterns of biodiversity. However, models that predict dynamics such as risk of extinction, range shifts and biodiversity loss tend to rely on the mean value of parameters and rarely incorporate realistic dispersal mechanisms. By focusing on the mean population value, variation among individuals or variability caused by complex spatial and temporal dynamics is ignored. This calls for increased efforts to understand individual variation in dispersal and integrate it more explicitly into population and community models involving dispersal. However, the sources, magnitude and outcomes of intraspecific variation in dispersal are poorly characterized, limiting our understanding of the role of dispersal in mediating the dynamics of communities and their response to global change. In this manuscript, we synthesize recent research that examines the sources of individual variation in dispersal and emphasize its implications for plant fitness, populations and communities. We argue that this intraspecific variation in seed dispersal does not simply add noise to systems, but, in fact, alters dispersal processes and patterns with consequences for demography, communities, evolution and response to anthropogenic changes. We conclude with recommendations for moving this field of research forward.
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Affiliation(s)
- Rebecca S Snell
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, USA
| | - Noelle G Beckman
- Department of Biology and Ecology Center, Utah State University, Logan, UT, USA
| | - Evan Fricke
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Bette A Loiselle
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
- Center for Latin American Studies, University of Florida, Gainsville, FL, USA
| | | | - Landon R Jones
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | | | - Nicky Lustenhouwer
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Sebastian J Schreiber
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA, USA
| | - Christopher Strickland
- Department of Mathematics and Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Lauren L Sullivan
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Brittany R Cavazos
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Itamar Giladi
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Alan Hastings
- Department of Environmental Science and Policy, University of California, Davis, CA, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | | | - Eelke Jongejans
- Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Oleg Kogan
- Physics Department, California Polytechnic State University, San Luis Obispo, CA, USA
| | | | - Javiera Rudolph
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Haldre S Rogers
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Rafal Zwolak
- Department of Systematic Zoology, Adam Mickiewicz University, Poznań, Poland
| | - Eugene W Schupp
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT, USA
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166
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Yadav S, Stow AJ, Dudaniec RY. Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum). Mol Ecol 2019; 28:3395-3412. [DOI: 10.1111/mec.15146] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Sonu Yadav
- Department of Biological Sciences Macquarie University North Ryde NSW Australia
| | - Adam J. Stow
- Department of Biological Sciences Macquarie University North Ryde NSW Australia
| | - Rachael Y. Dudaniec
- Department of Biological Sciences Macquarie University North Ryde NSW Australia
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167
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Margres MJ, Patton A, Wray KP, Hassinger ATB, Ward MJ, Lemmon EM, Lemmon AR, Rokyta DR. Tipping the Scales: The Migration-Selection Balance Leans toward Selection in Snake Venoms. Mol Biol Evol 2019; 36:271-282. [PMID: 30395254 DOI: 10.1093/molbev/msy207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The migration-selection interaction is the strongest determinant of whether a beneficial allele increases in frequency within a population. Results of empirical studies examining the role of gene flow in an adaptive context, however, have largely been equivocal, with examples of opposing outcomes being repeatedly documented (e.g., local adaptation with high levels of gene flow vs. gene swamping). We compared neutral genomic and venom expression divergence for three sympatric pit vipers with differing ecologies to determine if and how migration-selection disequilibria result in local adaptation. We specifically tested whether neutral differentiation predicted phenotypic differentiation within an isolation-by-distance framework. The decoupling of neutral and phenotypic differentiation would indicate selection led to adaptive divergence irrespective of migration, whereas a significant relationship between neutral and venom expression differentiation would provide evidence in favor of the constraining force of gene flow. Neutral differentiation and geographic distance predicted phenotypic differentiation only in the generalist species, indicating that selection was the predominant mechanism in the migration-selection balance underlying adaptive venom evolution in both specialists. Dispersal is thought to be a stronger influence on genetic differentiation than specialization, but our results suggest the opposite. Greater specialization may lead to greater diversification rates, and extreme spatial and temporal variation in selective pressures can favor generalist phenotypes evolving under strong stabilizing selection. Our results are consistent with these expectations, suggesting that the equivocal findings of studies examining the role of gene flow in an adaptive context may be explained by ecological specialization theory.
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Affiliation(s)
- Mark J Margres
- Department of Biological Science, Florida State University, Tallahassee, FL.,School of Biological Sciences, Washington State University, Pullman, WA.,Department of Biological Sciences, Clemson University, Clemson, SC
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Kenneth P Wray
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Alyssa T B Hassinger
- Department of Biological Science, Florida State University, Tallahassee, FL.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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168
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QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient. Proc Natl Acad Sci U S A 2019; 116:12933-12941. [PMID: 31182579 PMCID: PMC6600931 DOI: 10.1073/pnas.1821543116] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Understanding how individual genetic loci contribute to trait variation across geographic space is of fundamental importance for understanding evolutionary adaptations. Our study demonstrates that most loci underlying locally adaptive trait variation have beneficial effects in some geographic regions while conferring little or no detectable cost in other parts of the geographic range of switchgrass over two field seasons of study. Thus, loci that contribute to local adaptation vary in the degree to which they are costly in alternative environments but typically confer greater benefits than costs. Further, our study suggests that breeding locally adapted varieties of switchgrass will be a boon to the biofuel industry, as locally adaptive loci could be combined to increase local yields in switchgrass. Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify the benefits and costs of locally adaptive loci across 17° of latitude in a four-grandparent outbred mapping population in outcrossing switchgrass (Panicum virgatum L.), an emerging biofuel crop and dominant tallgrass species. We conducted quantitative trait locus (QTL) mapping across 10 sites, ranging from Texas to South Dakota. This analysis revealed that beneficial biomass (fitness) QTL generally incur minimal costs when transplanted to other field sites distributed over a large climatic gradient over the 2 y of our study. Therefore, locally advantageous alleles could potentially be combined across multiple loci through breeding to create high-yielding regionally adapted cultivars.
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169
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Impact of habitat loss and fragmentation on reproduction, dispersal and species persistence for an endangered Chilean tree. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01187-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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170
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Phair NL, Toonen RJ, Knapp I, von der Heyden S. Shared genomic outliers across two divergent population clusters of a highly threatened seagrass. PeerJ 2019; 7:e6806. [PMID: 31106053 PMCID: PMC6497040 DOI: 10.7717/peerj.6806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/18/2019] [Indexed: 12/15/2022] Open
Abstract
The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.
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Affiliation(s)
- Nikki Leanne Phair
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Robert John Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Ingrid Knapp
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Sophie von der Heyden
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
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171
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Zonana DM, Gee JM, Bridge ES, Breed MD, Doak DF. Assessing Behavioral Associations in a Hybrid Zone through Social Network Analysis: Complex Assortative Behaviors Structure Associations in a Hybrid Quail Population. Am Nat 2019; 193:852-865. [PMID: 31094596 DOI: 10.1086/703158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Behavior can strongly influence rates and patterns of hybridization between animal populations and species. Yet few studies have examined reproductive behaviors in natural hybrid zones within the fine-scale social context in which they naturally occur. We use radio-frequency identification tags with social network analyses to test whether phenotypic similarity in plumage and mass correlate with social behavior throughout a breeding season in a California and Gambel's quail hybrid zone. We use a novel approach to partition phenotypic variation in a way that does not confound differences between sexes and species, and we illustrate the complex ways that phenotype and behavior structure the social environment, mating opportunities, and male-male associations. Associations within the admixed population were random with respect to species-specific plumage but showed strong patterns of assortment based on sexually dimorphic plumage, monomorphic plumage, and mass. Weak behavioral reproductive isolation in this admixed population may be the result of complex patterns of phenotypic assortment based on multiple traits rather than a lack of phenotypic discrimination. More generally, our results support the utility of social network analyses for analyzing behavioral factors affecting genetic exchange between populations and species.
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172
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Abstract
Introgression is emerging as an important source of novel genetic variation, alongside standing variation and mutation. It is adaptive when such introgressed alleles are maintained by natural selection. Recently, there has been an explosion in the number of studies on adaptive introgression. In this review, we take a plant perspective centred on four lines of evidence: (i) introgression, (ii) selection, (iii) phenotype and (iv) fitness. While advances in genomics have contributed to our understanding of introgression and porous species boundaries (task 1), and the detection of signatures of selection in introgression (task 2), the investigation of adaptive introgression critically requires links to phenotypic variation and fitness (tasks 3 and 4). We also discuss the conservation implications of adaptive introgression in the face of climate change. Adaptive introgression is particularly important in rapidly changing environments, when standing genetic variation and mutation alone may only offer limited potential for adaptation. We conclude that clarifying the magnitude and fitness effects of introgression with improved statistical techniques, coupled with phenotypic evidence, has great potential for conservation and management efforts.
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Affiliation(s)
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, Canada
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173
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Nelson TC, Jones MR, Velotta JP, Dhawanjewar AS, Schweizer RM. UNVEILing connections between genotype, phenotype, and fitness in natural populations. Mol Ecol 2019; 28:1866-1876. [PMID: 30830713 PMCID: PMC6525050 DOI: 10.1111/mec.15067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/12/2019] [Accepted: 02/27/2019] [Indexed: 12/29/2022]
Abstract
Understanding the links between genetic variation and fitness in natural populations is a central goal of evolutionary genetics. This monumental task spans the fields of classical and molecular genetics, population genetics, biochemistry, physiology, developmental biology, and ecology. Advances to our molecular and developmental toolkits are facilitating integrative approaches across these traditionally separate fields, providing a more complete picture of the genotype-phenotype map in natural and non-model systems. Here, we summarize research presented at the first annual symposium of the UNVEIL Network, an NSF-funded collaboration between the University of Montana and the University of Nebraska, Lincoln, which took place from the 1st to the 3rd of June, 2018. We discuss how this body of work advances basic evolutionary science, what it implies for our ability to predict evolutionary change, and how it might inform novel conservation strategies.
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Affiliation(s)
- Thomas C Nelson
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | - Jonathan P Velotta
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | | | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
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174
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Barth JMI, Villegas-Ríos D, Freitas C, Moland E, Star B, André C, Knutsen H, Bradbury I, Dierking J, Petereit C, Righton D, Metcalfe J, Jakobsen KS, Olsen EM, Jentoft S. Disentangling structural genomic and behavioural barriers in a sea of connectivity. Mol Ecol 2019; 28:1394-1411. [PMID: 30633410 PMCID: PMC6518941 DOI: 10.1111/mec.15010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 12/17/2022]
Abstract
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole‐genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord‐type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord‐type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - David Villegas-Ríos
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, IMEDEA CSIC-UIB, Esporles, Spain.,Department of Ecology and Marine Resources, Institute of Marine Research, (IIM CSIC), Vigo, Spain
| | - Carla Freitas
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway.,Oceanic Observatory of Madeira, Funchal, Portugal
| | - Even Moland
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Ian Bradbury
- Science Branch, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - David Righton
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Julian Metcalfe
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Esben M Olsen
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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175
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Pfeifer SP, Laurent S, Sousa VC, Linnen CR, Foll M, Excoffier L, Hoekstra HE, Jensen JD. The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow. Mol Biol Evol 2019; 35:792-806. [PMID: 29346646 PMCID: PMC5905656 DOI: 10.1093/molbev/msy004] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at the Agouti locus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from 11 sites along a transect spanning the Sand Hills at 660,000 single nucleotide polymorphisms across the genome. Using these genomic data, we found that deer mice first colonized the Sand Hills following the last glacial period. Subsequent high rates of gene flow have served to homogenize the majority of the genome between populations on and off the Sand Hills, with the exception of the Agouti pigmentation locus. Furthermore, mutations at this locus are strongly associated with the pigment traits that are strongly correlated with local soil coloration and thus responsible for cryptic coloration.
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Affiliation(s)
- Susanne P Pfeifer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ
| | - Stefan Laurent
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Vitor C Sousa
- Institute of Ecology & Evolution, University of Berne, Berne, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - Matthieu Foll
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurent Excoffier
- Institute of Ecology & Evolution, University of Berne, Berne, Switzerland
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology and Molecular & Cellular Biology, Museum of Comparative Zoology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Jeffrey D Jensen
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ
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176
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Barley AJ, Nieto-Montes de Oca A, Reeder TW, Manríquez-Morán NL, Arenas Monroy JC, Hernández-Gallegos O, Thomson RC. Complex patterns of hybridization and introgression across evolutionary timescales in Mexican whiptail lizards (Aspidoscelis). Mol Phylogenet Evol 2019; 132:284-295. [DOI: 10.1016/j.ympev.2018.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023]
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177
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Yang M, Xu C, Duchesne P, Ma Q, Yin G, Fang Y, Lu F, Zhang W. Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries. Ecol Evol 2019; 9:3059-3074. [PMID: 30962881 PMCID: PMC6434575 DOI: 10.1002/ece3.4793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/31/2018] [Accepted: 11/12/2018] [Indexed: 12/22/2022] Open
Abstract
Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate-high level of genetic differentiation among populations (range F ST: 0.0310-0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none-liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co-contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.
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Affiliation(s)
- Mei Yang
- College of AgricultureYangtze UniversityJingzhouChina
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Chengyuan Xu
- School of Health, Medical and Applied SciencesCentral Queensland UniversityBundabergQueenslandAustralia
| | | | - Qiang Ma
- Shanghai Chongming Dongtan National Nature ReserveShanghaiChina
| | - Ganqiang Yin
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Yang Fang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Fan Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Coastal Ecosystems Research Station of the Yangtze River EstuaryFudan UniversityShanghaiChina
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178
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Saatkamp A, Cochrane A, Commander L, Guja LK, Jimenez-Alfaro B, Larson J, Nicotra A, Poschlod P, Silveira FAO, Cross AT, Dalziell EL, Dickie J, Erickson TE, Fidelis A, Fuchs A, Golos PJ, Hope M, Lewandrowski W, Merritt DJ, Miller BP, Miller RG, Offord CA, Ooi MKJ, Satyanti A, Sommerville KD, Tangney R, Tomlinson S, Turner S, Walck JL. A research agenda for seed-trait functional ecology. THE NEW PHYTOLOGIST 2019; 221:1764-1775. [PMID: 30269352 DOI: 10.1111/nph.15502] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/17/2018] [Indexed: 06/08/2023]
Abstract
Trait-based approaches have improved our understanding of plant evolution, community assembly and ecosystem functioning. A major challenge for the upcoming decades is to understand the functions and evolution of early life-history traits, across levels of organization and ecological strategies. Although a variety of seed traits are critical for dispersal, persistence, germination timing and seedling establishment, only seed mass has been considered systematically. Here we suggest broadening the range of morphological, physiological and biochemical seed traits to add new understanding on plant niches, population dynamics and community assembly. The diversity of seed traits and functions provides an important challenge that will require international collaboration in three areas of research. First, we present a conceptual framework for a seed ecological spectrum that builds upon current understanding of plant niches. We then lay the foundation for a seed-trait functional network, the establishment of which will underpin and facilitate trait-based inferences. Finally, we anticipate novel insights and challenges associated with incorporating diverse seed traits into predictive evolutionary ecology, community ecology and applied ecology. If the community invests in standardized seed-trait collection and the implementation of rigorous databases, major strides can be made at this exciting frontier of functional ecology.
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Affiliation(s)
- Arne Saatkamp
- Aix Marseille Université, Université d'Avignon, CNRS, IRD, IMBE, Facultés St Jérôme, case 421, 13397, Marseille, France
| | - Anne Cochrane
- Department of Biodiversity, Conservation and Attractions, Science and Conservation, Locked Bag 104, Bentley Delivery Centre, Bentley, WA, 6983, Australia
- Division of Ecology & Evolution, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Lucy Commander
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Lydia K Guja
- Centre for Australian National Biodiversity Research, CSIRO National Research Collections Australia, Clunies Ross St, Acton, ACT, 2601, Australia
- Biodiversity Science Section, Australian National Botanic Gardens, Clunies Ross St, Canberra, ACT, 2601, Australia
| | - Borja Jimenez-Alfaro
- Research Unit of Biodiversity (CSIC/UO/PA), Universidad de Oviedo, Edificio de Investigación, 33600, Mieres, Spain
| | - Julie Larson
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Adrienne Nicotra
- Division of Ecology & Evolution, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
| | - Peter Poschlod
- Ecology & Conservation Biology, Institute of Plant Sciences, University of Regensburg, D-93040, Regensburg, Germany
| | - Fernando A O Silveira
- Department of Botany, Federal University of Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG, Brazil
| | - Adam T Cross
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Emma L Dalziell
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - John Dickie
- Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, RH17 6TN, UK
| | - Todd E Erickson
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Alessandra Fidelis
- Lab of Vegetation Ecology, Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Avenida 24-A 1515, 13506-900, Rio Claro, Brazil
| | - Anne Fuchs
- Centre for Australian National Biodiversity Research, CSIRO National Research Collections Australia, Clunies Ross St, Acton, ACT, 2601, Australia
- Biodiversity Science Section, Australian National Botanic Gardens, Clunies Ross St, Canberra, ACT, 2601, Australia
| | - Peter J Golos
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Michael Hope
- Centre for Australian National Biodiversity Research, CSIRO National Research Collections Australia, Clunies Ross St, Acton, ACT, 2601, Australia
- Atlas of Living Australia, CSIRO, Canberra, ACT, 2601, Australia
| | - Wolfgang Lewandrowski
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - David J Merritt
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ben P Miller
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Russell G Miller
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Catherine A Offord
- The Australian Plant Bank, Royal Botanic Gardens and Domain Trust, Mount Annan, NSW, 2567, Australia
| | - Mark K J Ooi
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Annisa Satyanti
- Division of Ecology & Evolution, The Australian National University, 46 Sullivans Creek Road, Acton, ACT, 2601, Australia
- Biodiversity Science Section, Australian National Botanic Gardens, Clunies Ross St, Canberra, ACT, 2601, Australia
- Center for Plant Conservation, Bogor Botanic Gardens, Indonesian Institute of Sciences, Jalan Ir. H. Juanda, Bogor, West Java, 16001, Indonesia
| | - Karen D Sommerville
- The Australian Plant Bank, Royal Botanic Gardens and Domain Trust, Mount Annan, NSW, 2567, Australia
| | - Ryan Tangney
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Sean Tomlinson
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Shane Turner
- Department of Biodiversity, Conservation and Attractions, Kings Park Science, 1 Kattidj Close, Kings Park, WA, 6005, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Jeffrey L Walck
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37130, USA
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179
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Dayan DI, Du X, Baris TZ, Wagner DN, Crawford DL, Oleksiak MF. Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents. BMC Evol Biol 2019; 19:61. [PMID: 30808292 PMCID: PMC6390305 DOI: 10.1186/s12862-019-1392-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Examples of rapid evolution are common in nature but difficult to account for with the standard population genetic model of adaptation. Instead, selection from the standing genetic variation permits rapid adaptation via soft sweeps or polygenic adaptation. Empirical evidence of this process in nature is currently limited but accumulating. RESULTS We provide genome-wide analyses of rapid evolution in Fundulus heteroclitus populations subjected to recently elevated temperatures due to coastal power station thermal effluents using 5449 SNPs across two effluent-affected and four reference populations. Bayesian and multivariate analyses of population genomic structure reveal a substantial portion of genetic variation that is most parsimoniously explained by selection at the site of thermal effluents. An FST outlier approach in conjunction with additional conservative requirements identify significant allele frequency differentiation that exceeds neutral expectations among exposed and closely related reference populations. Genomic variation patterns near these candidate loci reveal that individuals living near thermal effluents have rapidly evolved from the standing genetic variation through small allele frequency changes at many loci in a pattern consistent with polygenic selection on the standing genetic variation. CONCLUSIONS While the ultimate trajectory of selection in these populations is unknown and we survey only a minority of genomic loci, our findings suggest that polygenic models of adaptation may play important roles in large, natural populations experiencing recent selection due to environmental changes that cause broad physiological impacts.
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Affiliation(s)
- David I. Dayan
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Xiao Du
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Tara Z. Baris
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Dominique N. Wagner
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Douglas L. Crawford
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Marjorie F. Oleksiak
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
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180
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Sonnenberg BR, Branch CL, Pitera AM, Bridge E, Pravosudov VV. Natural Selection and Spatial Cognition in Wild Food-Caching Mountain Chickadees. Curr Biol 2019; 29:670-676.e3. [DOI: 10.1016/j.cub.2019.01.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/05/2018] [Accepted: 01/02/2019] [Indexed: 12/16/2022]
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181
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Evidence for divergent patterns of local selection driving venom variation in Mojave Rattlesnakes (Crotalus scutulatus). Sci Rep 2018; 8:17622. [PMID: 30514908 PMCID: PMC6279745 DOI: 10.1038/s41598-018-35810-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/09/2018] [Indexed: 01/20/2023] Open
Abstract
Snake venoms represent an enriched system for investigating the evolutionary processes that lead to complex and dynamic trophic adaptations. It has long been hypothesized that natural selection may drive geographic variation in venom composition, yet previous studies have lacked the population genetic context to examine these patterns. We leverage range-wide sampling of Mojave Rattlesnakes (Crotalus scutulatus) and use a combination of venom, morphological, phylogenetic, population genetic, and environmental data to characterize the striking dichotomy of neurotoxic (Type A) and hemorrhagic (Type B) venoms throughout the range of this species. We find that three of the four previously identified major lineages within C. scutulatus possess a combination of Type A, Type B, and a ‘mixed’ Type A + B venom phenotypes, and that fixation of the two main venom phenotypes occurs on a more fine geographic scale than previously appreciated. We also find that Type A + B individuals occur in regions of inferred introgression, and that this mixed phenotype is comparatively rare. Our results support strong directional local selection leading to fixation of alternative venom phenotypes on a fine geographic scale, and are inconsistent with balancing selection to maintain both phenotypes within a single population. Our comparisons to biotic and abiotic factors further indicate that venom phenotype correlates with fang morphology and climatic variables. We hypothesize that links to fang morphology may be indicative of co-evolution of venom and other trophic adaptations, and that climatic variables may be linked to prey distributions and/or physiology, which in turn impose selection pressures on snake venoms.
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182
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Breitwieser M, Vigneau E, Viricel A, Becquet V, Lacroix C, Erb M, Huet V, Churlaud C, Le Floch S, Guillot B, Graber M, Thomas H. What is the relationship between the bioaccumulation of chemical contaminants in the variegated scallop Mimachlamys varia and its health status? A study carried out on the French Atlantic coast using the Path ComDim model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:662-670. [PMID: 29870942 DOI: 10.1016/j.scitotenv.2018.05.317] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 05/19/2023]
Abstract
Increasing activity along the French Atlantic coast has led to chronic pollution with, in particular, mixtures of contaminants such as hydrocarbons, phytosanitary products, PCBs and heavy metals. Based on previous research, pollution biomarkers were used in this study as they can indicate health status when monitoring the impact of pollutants on coastal species such as the marine bivalve Mimachlamys varia. Mollusc bivalves were sampled in March 2016, in open and semi-open areas (a harbour zone), from thirteen sites which differed in terms of their level of pollution, and were located along the Atlantic coast from Brittany down to the Nouvelle-Aquitaine region. First, analyses of heavy metals and organic contaminants (e.g. pesticides, polycyclic aromatic hydrocarbons, polychlorobiphenyl) in the digestive gland of bivalves were performed. Second, biochemical assays were used to study defence biomarkers: oxidative stress with Superoxide Dismutase (SOD), detoxification of organic compounds with Glutathione-S Transferase (GST), lipid peroxidation with Malondialdehyde (MDA), and immune processes with Laccase. In addition to the biochemical assays, a genetic approach was used to measure genetic diversity (haplotype and nucleotide diversity) at each site. Biomarker assays and genetic diversity were correlated with the chemical contaminants in bivalves using the Path-ComDim statistical model. Our results showed specific correlations between biochemical assays in the digestive glands with heavy metal contaminants, and between genetic diversity and organic pollution. Blocks of responses were analysed for correlations in order to develop standardized tools and guidelines that could improve our understanding of the short-term and long-term impact of contaminants on physiological parameters.
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Affiliation(s)
- Marine Breitwieser
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS - Université de La Rochelle, 2 rue Olympe de Gouges, F-17042 La Rochelle Cedex 01, France.
| | | | - Amélia Viricel
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS - Université de La Rochelle, 2 rue Olympe de Gouges, F-17042 La Rochelle Cedex 01, France
| | - Vanessa Becquet
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS - Université de La Rochelle, 2 rue Olympe de Gouges, F-17042 La Rochelle Cedex 01, France
| | - Camille Lacroix
- Cedre, Centre de Documentation, de Recherche et d'Expérimentations sur les Pollutions Accidentelles des Eaux, 715 rue Alain Colas, CS 41836, Brest, Cedex 2, France
| | - Marina Erb
- Cedre, Centre de Documentation, de Recherche et d'Expérimentations sur les Pollutions Accidentelles des Eaux, 715 rue Alain Colas, CS 41836, Brest, Cedex 2, France
| | - Valérie Huet
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS - Université de La Rochelle, 2 rue Olympe de Gouges, F-17042 La Rochelle Cedex 01, France
| | - Carine Churlaud
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS - Université de La Rochelle, 2 rue Olympe de Gouges, F-17042 La Rochelle Cedex 01, France
| | - Stéphane Le Floch
- Cedre, Centre de Documentation, de Recherche et d'Expérimentations sur les Pollutions Accidentelles des Eaux, 715 rue Alain Colas, CS 41836, Brest, Cedex 2, France
| | - Benoit Guillot
- UMR CNRS 5805 EPOC-OASU-Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac Cedex, France
| | - Marianne Graber
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS - Université de La Rochelle, 2 rue Olympe de Gouges, F-17042 La Rochelle Cedex 01, France
| | - Hélène Thomas
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS - Université de La Rochelle, 2 rue Olympe de Gouges, F-17042 La Rochelle Cedex 01, France
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183
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Sailer C, Babst-Kostecka A, Fischer MC, Zoller S, Widmer A, Vollenweider P, Gugerli F, Rellstab C. Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils. Sci Rep 2018; 8:16085. [PMID: 30382172 PMCID: PMC6208402 DOI: 10.1038/s41598-018-33938-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022] Open
Abstract
When plants adapt to local environments, strong signatures of selection are expected in the genome, particularly in high-stress environments such as trace metal element enriched (metalliferous) soils. Using Arabidopsis halleri, a model species for metal homeostasis and adaptation to extreme environments, we identifid genes, gene variants, and pathways that are associated with soil properties and may thus contribute to adaptation to high concentrations of trace metal elements. We analysed whole-genome Pool-seq data from two metallicolous (from metalliferous soils) and two non-metallicolous populations (in total 119 individuals) and associated allele frequencies of the identified single-nucleotide polymorphisms (SNPs) with soil variables measured on site. Additionally, we accounted for polygenic adaptation by searching for gene pathways showing enrichment of signatures of selection. Out of >2.5 million SNPs, we identified 57 SNPs in 19 genes that were significantly associated with soil variables and are members of three enriched pathways. At least three of these candidate genes and pathways are involved in transmembrane transport and/or associated with responses to various stresses such as oxidative stress. We conclude that both allocation and detoxification processes play a crucial role in A. halleri for coping with these unfavourable conditions.
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Affiliation(s)
- Christian Sailer
- WSL Swiss Federal Research Institute, Birmensdorf, 8903, Switzerland.
- ETH Zürich, Institute of Integrative Biology, Zürich, 8092, Switzerland.
| | | | - Martin C Fischer
- ETH Zürich, Institute of Integrative Biology, Zürich, 8092, Switzerland
| | - Stefan Zoller
- ETH Zürich, Genetic Diversity Centre, Zürich, 8092, Switzerland
| | - Alex Widmer
- ETH Zürich, Institute of Integrative Biology, Zürich, 8092, Switzerland
| | | | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, 8903, Switzerland
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184
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Inversion frequencies and phenotypic effects are modulated by the environment: insights from a reciprocal transplant study in Coelopa frigida. Evol Ecol 2018. [DOI: 10.1007/s10682-018-9960-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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185
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Knutsen H, Jorde PE, Hutchings JA, Hemmer‐Hansen J, Grønkjær P, Jørgensen KM, André C, Sodeland M, Albretsen J, Olsen EM. Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales. Evol Appl 2018; 11:1527-1539. [PMID: 30344625 PMCID: PMC6183466 DOI: 10.1111/eva.12640] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/09/2018] [Indexed: 12/15/2022] Open
Abstract
Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analysed genetic origin of 6,483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two genetically divergent Atlantic cod ecotypes throughout the study area and study period. A "fjord" ecotype dominated in numbers deep inside fjords while a "North Sea" ecotype was the only type found in offshore North Sea. Both ecotypes coexisted in similar proportions throughout coastal habitats at all spatial scales. The size-at-age of the North Sea ecotype on average exceeded that of the fjord ecotype by 20% in length and 80% in weight across all habitats. Different growth and size among individuals of the two types might be one of several ecologically significant variables that allow for stable coexistence of closely related populations within the same habitat. Management plans, biodiversity initiatives and other mitigation strategies that do not account for the mixture of species ecotypes are unlikely to meet objectives related to the sustainability of fish and fisheries.
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Affiliation(s)
- Halvor Knutsen
- Institute of Marine ResearchFlødevigenHisNorway
- Department of BiosciencesCentre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernOsloNorway
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
| | - Per Erik Jorde
- Institute of Marine ResearchFlødevigenHisNorway
- Department of BiosciencesCentre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernOsloNorway
| | - Jeffrey A. Hutchings
- Institute of Marine ResearchFlødevigenHisNorway
- Department of BiosciencesCentre for Ecological and Evolutionary Synthesis (CEES)University of OsloBlindernOsloNorway
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - Jakob Hemmer‐Hansen
- Section for Marine Living ResourcesNational Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Peter Grønkjær
- Department for BioscienceAarhus UniversityAquatic BiologyAarhusDenmark
| | | | - Carl André
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | - Marte Sodeland
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
| | | | - Esben M. Olsen
- Institute of Marine ResearchFlødevigenHisNorway
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
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186
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Seixas FA, Boursot P, Melo-Ferreira J. The genomic impact of historical hybridization with massive mitochondrial DNA introgression. Genome Biol 2018; 19:91. [PMID: 30056805 PMCID: PMC6065068 DOI: 10.1186/s13059-018-1471-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. RESULTS Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions. CONCLUSIONS General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.
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Affiliation(s)
- Fernando A Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France.
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
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187
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Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja CM, Lemaitre C, Vitalis R, Simon JC. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races. Mol Ecol 2018; 27:3287-3300. [PMID: 30010213 DOI: 10.1111/mec.14799] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host-plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host-plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
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Affiliation(s)
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
| | - Anaïs Gouin
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Fabrice Legeai
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554) - CNRS - IRD - EPHE - CIRAD -Université de Montpellier, Montpellier, France
| | | | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
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188
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Angers B, Chapdelaine V, Deremiens L, Vergilino R, Leung C, Doucet SL, Glémet H, Angers A. Gene flow prevents mitonuclear co-adaptation: A comparative portrait of sympatric wild types and cybrids in the fish Chrosomus eos. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 27:77-84. [PMID: 29986214 DOI: 10.1016/j.cbd.2018.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/26/2022]
Abstract
Allospecific mtDNA can occasionally be beneficial for the fitness of populations. It is, however, difficult to assess the effect of mtDNA in natural conditions due to genetic and/or environmental interactions. In the fish Chrosomus eos, the transfer of C. neogaeus mitochondria occurs in a single generation and results in natural cybrids. For a few lakes in Quebec, C. eos can harbor either a C. eos mtDNA (wild types) or a C. neogaeus mtDNA (cybrids). Moreover, mtDNA of cybrids originated either from Mississippian or Atlantic glacial refuges. Such diversity provides a useful system for in situ assessment of allospecific mtDNA effects. We determined genetic, epigenetic and transcriptomic variation as well as mitochondrial enzymatic activity (complex IV) changes among wild types and cybrids either in sympatry or allopatry. Wild types and cybrids did not segregate spatially within a lake. Moreover, no significant genetic differentiation was detected among wild types and cybrids indicating sustained gene flow. Mitochondrial complex IV activity was higher for cybrids in both sympatry and allopatry while no difference was detected among cybrid haplotypes. Epigenetic and transcriptomic analyses revealed only subtle differences between sympatric wild types and cybrids compared to differences between sites. Altogether, these results indicate a limited influence of allospecific mtDNA in nuclear gene expression when controlling for genetic and environmental effects. The absence of a reproductive barrier between wild types and cybrids results in random association of either C. eos or C. neogaeus mtDNA with C. eos nDNA at each generation, and prevents mitonuclear co-adaptation in sympatry.
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Affiliation(s)
- Bernard Angers
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada.
| | - Vincent Chapdelaine
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Léo Deremiens
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Roland Vergilino
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Christelle Leung
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Simon-Luc Doucet
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Hélène Glémet
- Department of environmental sciences, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - Annie Angers
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
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189
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Young EF, Tysklind N, Meredith MP, de Bruyn M, Belchier M, Murphy EJ, Carvalho GR. Stepping stones to isolation: Impacts of a changing climate on the connectivity of fragmented fish populations. Evol Appl 2018; 11:978-994. [PMID: 29928304 PMCID: PMC5999207 DOI: 10.1111/eva.12613] [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: 10/19/2017] [Accepted: 02/05/2018] [Indexed: 01/02/2023] Open
Abstract
In the marine environment, understanding the biophysical mechanisms that drive variability in larval dispersal and population connectivity is essential for estimating the potential impacts of climate change on the resilience and genetic structure of populations. Species whose populations are small, isolated and discontinuous in distribution will differ fundamentally in their response and resilience to environmental stress, compared with species that are broadly distributed, abundant and frequently exchange conspecifics. Here, we use an individual-based modelling approach, combined with a population genetics projection model, to consider the impacts of a warming climate on the population connectivity of two contrasting Antarctic fish species, Notothenia rossii and Champsocephalus gunnari. Focussing on the Scotia Sea region, sea surface temperatures are predicted to increase significantly by the end of the 21st century, resulting in reduced planktonic duration and increased egg and larval mortality. With shorter planktonic durations, the results of our study predict reduced dispersal of both species across the Scotia Sea, from Antarctic Peninsula sites to islands in the north and east, and increased dispersal among neighbouring sites, such as around the Antarctic Peninsula. Increased mortality modified the magnitude of population connectivity but had little effect on the overall patterns. Whilst the predicted changes in connectivity had little impact on the projected regional population genetic structure of N. rossii, which remained broadly genetically homogeneous within distances of ~1,500 km, the genetic isolation of C. gunnari populations in the northern Scotia Sea was predicted to increase with rising sea temperatures. Our study highlights the potential for increased isolation of island populations in a warming world, with implications for the resilience of populations and their ability to adapt to ongoing environmental change, a matter of high relevance to fisheries and ecosystem-level management.
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Affiliation(s)
| | - Niklas Tysklind
- School of Biological SciencesBangor UniversityBangorGwyneddUK
- Present address:
INRAUMR8172 EcoFoGAgroParisTechCiradCNRSUniversité des AntillesUniversité de GuyaneKourouFrance
| | | | - Mark de Bruyn
- School of Life and Environmental SciencesThe University of SydneySydneyNSWAustralia
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190
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Perrier C, Lozano del Campo A, Szulkin M, Demeyrier V, Gregoire A, Charmantier A. Great tits and the city: Distribution of genomic diversity and gene-environment associations along an urbanization gradient. Evol Appl 2018; 11:593-613. [PMID: 29875805 PMCID: PMC5979639 DOI: 10.1111/eva.12580] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/19/2017] [Indexed: 01/02/2023] Open
Abstract
Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genomewide effects of urbanization on neutral and adaptive genomic diversity in 140 adult great tits Parus major collected in locations with contrasted urbanization levels (from a natural forest to highly urbanized areas of a city; Montpellier, France). Heterozygosity was slightly lower in the more urbanized sites compared to the more rural ones. Low but significant effect of urbanization on genetic differentiation was found, at the site level but not at the nest level, indicative of the geographic scale of urbanization impact and of the potential for local adaptation despite gene flow. Gene-environment association tests identified numerous SNPs with small association scores to urbanization, distributed across the genome, from which a subset of 97 SNPs explained up to 81% of the variance in urbanization, overall suggesting a polygenic response to selection in the urban environment. These findings open stimulating perspectives for broader applications of high-resolution genomic tools on other cities and larger sample sizes to investigate the consistency of the effects of urbanization on the spatial distribution of genetic diversity and the polygenic nature of gene-urbanization association.
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Affiliation(s)
- Charles Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, Campus CNRS, Université de MontpellierMontpellier Cedex 5France
| | - Ana Lozano del Campo
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, Campus CNRS, Université de MontpellierMontpellier Cedex 5France
| | - Marta Szulkin
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, Campus CNRS, Université de MontpellierMontpellier Cedex 5France
- Wild Urban Evolution and Ecology LaboratoryCentre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Virginie Demeyrier
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, Campus CNRS, Université de MontpellierMontpellier Cedex 5France
| | - Arnaud Gregoire
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, Campus CNRS, Université de MontpellierMontpellier Cedex 5France
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, Campus CNRS, Université de MontpellierMontpellier Cedex 5France
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191
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Stapley J, Feulner PGD, Johnston SE, Santure AW, Smadja CM. Variation in recombination frequency and distribution across eukaryotes: patterns and processes. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0455. [PMID: 29109219 PMCID: PMC5698618 DOI: 10.1098/rstb.2016.0455] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 01/04/2023] Open
Abstract
Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Jessica Stapley
- Centre for Adaptation to a Changing Environment, IBZ, ETH Zürich, 8092 Zürich, Switzerland
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JY, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Carole M Smadja
- Institut des Sciences de l'Evolution UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, 3095 Montpellier cedex 05, France
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192
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Waterhouse MD, Erb LP, Beever EA, Russello MA. Adaptive population divergence and directional gene flow across steep elevational gradients in a climate-sensitive mammal. Mol Ecol 2018; 27:2512-2528. [DOI: 10.1111/mec.14701] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/29/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Matthew D. Waterhouse
- Department of Biology; University of British Columbia; Kelowna British Columbia Canada
| | - Liesl P. Erb
- Departments of Biology and Environmental Studies; Warren Wilson College; Asheville North Carolina
| | - Erik A. Beever
- U.S. Geological Survey; Northern Rocky Mountain Science Center; Bozeman Montana
- Department of Ecology; Montana State University; Bozeman Montana
| | - Michael A. Russello
- Department of Biology; University of British Columbia; Kelowna British Columbia Canada
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193
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Garner AG, Goulet BE, Farnitano MC, Molina-Henao YF, Hopkins R. Genomic Signatures of Reinforcement. Genes (Basel) 2018; 9:E191. [PMID: 29614048 PMCID: PMC5924533 DOI: 10.3390/genes9040191] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement's characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.
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Affiliation(s)
- Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Benjamin E Goulet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Matthew C Farnitano
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
| | - Y Franchesco Molina-Henao
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
- Department of Biology, Universidad del Valle, Cali 760032, Colombia.
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 021382, USA.
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA.
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194
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Ahrens CW, Rymer PD, Stow A, Bragg J, Dillon S, Umbers KDL, Dudaniec RY. The search for loci under selection: trends, biases and progress. Mol Ecol 2018. [PMID: 29524276 DOI: 10.1111/mec.14549] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Adam Stow
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Jason Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Shannon Dillon
- Diversity and Adaptation, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Kate D L Umbers
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia.,School of Science and Health, Western Sydney University, Richmond, NSW, Australia
| | - Rachael Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
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195
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Barley AJ, Brown JM, Thomson RC. Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent. Syst Biol 2018; 67:269-284. [PMID: 28945903 DOI: 10.1093/sysbio/syx073] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/31/2017] [Indexed: 11/14/2022] Open
Abstract
The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to fill this gap by using simulation to characterize the sensitivity of inference under the multispecies coalescent (MSC) to several violations of model assumptions thought to be common in empirical data. We also assess the fit of the MSC model to empirical data in the context of species delimitation. Our results show substantial variation in model fit across data sets. Posterior predictive tests find the poorest model performance in data sets that were hypothesized to be impacted by model violations. We also show that while the inferences assuming the MSC are robust to minor model violations, such inferences can be biased under some biologically plausible scenarios. Taken together, these results suggest that researchers can identify individual data sets in which species delimitation under the MSC is likely to be problematic, thereby highlighting the cases where additional lines of evidence to identify species boundaries are particularly important to collect. Our study supports a growing body of work highlighting the importance of model checking in phylogenetics, and the usefulness of tailoring tests of model fit to assess the reliability of particular inferences. [Populations structure, gene flow, demographic changes, posterior prediction, simulation, genetics.].
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Affiliation(s)
- Anthony J Barley
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI 96822, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI 96822, USA
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196
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Sandoval‐Castillo J, Robinson NA, Hart AM, Strain LWS, Beheregaray LB. Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (
Haliotis laevigata
), along a longitudinal environmental gradient. Mol Ecol 2018; 27:1603-1620. [DOI: 10.1111/mec.14526] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 12/05/2017] [Accepted: 12/15/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Jonathan Sandoval‐Castillo
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
| | - Nick A. Robinson
- Nofima Ås Norway
- Sustainable Aquaculture Laboratory School of BioSciences University of Melbourne Parkville Vic Australia
| | - Anthony M. Hart
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Western Australia Hillarys WA Australia
| | - Lachlan W. S. Strain
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Western Australia Hillarys WA Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
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197
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Levänen R, Thulin CG, Spong G, Pohjoismäki JLO. Widespread introgression of mountain hare genes into Fennoscandian brown hare populations. PLoS One 2018; 13:e0191790. [PMID: 29370301 PMCID: PMC5784980 DOI: 10.1371/journal.pone.0191790] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/11/2018] [Indexed: 11/29/2022] Open
Abstract
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
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Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Carl-Gustaf Thulin
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
- * E-mail:
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198
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Attard CRM, Brauer CJ, Sandoval-Castillo J, Faulks LK, Unmack PJ, Gilligan DM, Beheregaray LB. Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): Implications for management and resilience to climate change. Mol Ecol 2017; 27:196-215. [PMID: 29165848 DOI: 10.1111/mec.14438] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 01/01/2023]
Abstract
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia, using a genome-wide SNP data set. The MDB spans across arid to wet and temperate to subtropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.
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Affiliation(s)
- Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Leanne K Faulks
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.,Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Peter J Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Dean M Gilligan
- New South Wales Department of Primary Industries, Batemans Bay Fisheries Centre, Batemans Bay, NSW, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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199
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Blackburn GS, Brunet BMT, Muirhead K, Cusson M, Béliveau C, Levesque RC, Lumley LM, Sperling FAH. Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of aChoristoneurabudworm. Mol Ecol 2017; 26:6666-6684. [DOI: 10.1111/mec.14386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 09/26/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Gwylim S. Blackburn
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Bryan M. T. Brunet
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Kevin Muirhead
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Michel Cusson
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Catherine Béliveau
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Roger C. Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Lisa M. Lumley
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Felix A. H. Sperling
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
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200
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Abstract
Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties.
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