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Christensen KA, Flores AM, Sakhrani D, Biagi CA, Devlin RH, Sutherland BJG, Withler RE, Rondeau EB, Koop BF. Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing. G3 (BETHESDA, MD.) 2024; 14:jkae169. [PMID: 39041834 DOI: 10.1093/g3journal/jkae169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 04/29/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available.
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Affiliation(s)
- Kris A Christensen
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1H2, Canada
| | - Carlo A Biagi
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1H2, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1H2, Canada
| | - Ben J G Sutherland
- Sutherland Bioinformatics, Lantzville, BC V0R 2H0, Canada
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada
| | - Ruth E Withler
- Pacific Salmon Foundation, Vancouver, BC V6H 3V9, Canada
| | - Eric B Rondeau
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
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2
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Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. J Evol Biol 2024; 37:677-692. [PMID: 38629140 DOI: 10.1093/jeb/voae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 03/25/2024] [Accepted: 04/15/2024] [Indexed: 06/30/2024]
Abstract
The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species' demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.
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Affiliation(s)
- Lauric Reynes
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
| | - Louise Fouqueau
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
| | - Didier Aurelle
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France
- Institut de Systématique Évolution Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Paris, France
| | - Stéphane Mauger
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
| | - Christophe Destombe
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
| | - Myriam Valero
- IRL 3614, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, Roscoff 29688, France
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3
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Bernardi G, Azzurro E, Bariche M, Jimenez C, Kalogirou S, Kleitou P. Invasion genomics of lionfish in the Mediterranean Sea. Ecol Evol 2024; 14:e11087. [PMID: 38450316 PMCID: PMC10915480 DOI: 10.1002/ece3.11087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
The rate of biological invasions is steadily increasing, with major ecological and economic impacts accounting for billions of dollars in damage as a result. One spectacular example is the western Atlantic invasion by lionfishes. In the Mediterranean Sea, invasions from the Red Sea via the Suez Canal (termed Lessepsian invasions) comprise more than 100 fish species, including a recent invasion by lionfish. In light of the devastating effects of lionfish in the Caribbean Sea, understanding the dynamics of Mediterranean lionfish invasion is crucial. The Lessepsian lionfish invasion started in 2012, and rapidly spread to the central Mediterranean. Here, we used thousands of RAD seq genomic markers to study the population dynamics of this invasion. While we did not find a reduction in genetic diversity between source (Red Sea) and invasive (Mediterranean) populations (i.e., bottleneck effects), we found evidence of population structure within the invasive range in the Mediterranean Sea. We found that loci that are potentially under selection may play an important role in invasion success (in particular, genes involved in osmoregulation and fin spine sizes). Genomic approaches proved powerful in examining the ecological and evolutionary patterns of successful invaders and may be used as tools to understand and potentially mitigate future invasions.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
| | - Ernesto Azzurro
- CNR‐IRBIM, National Research CouncilInstitute of Biological Resources and Marine BiotechnologiesAnconaItaly
- Zoological Station A. DohrnNaplesItaly
| | - Michel Bariche
- Department of BiologyAmerican University of BeirutBeirutLebanon
| | - Carlos Jimenez
- Enalia Physis Environmental Research Centre (ENALIA)NicosiaCyprus
- The Cyprus InstituteEnergy Environment and Water Research CenterNicosiaCyprus
| | - Stefanos Kalogirou
- Hellenic Centre for Marine Research, Institute for Marine Biological Resources and Inland WatersHydrobiological Station of RhodesRhodesGreece
| | - Periklis Kleitou
- Marine & Environmental Research (MER) LabLimassolCyprus
- School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
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4
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Diniz FDA, Moura JDO, Bajay MM, Branco LC, Bezerra RD, de Araújo AM. Capra hircus outliers markers in Brazil: Searching for genomic regions under the action of natural selection. Genet Mol Biol 2023; 46:e20230084. [PMID: 37882366 PMCID: PMC10594045 DOI: 10.1590/1678-4685-gmb-2023-0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/21/2023] [Indexed: 10/27/2023] Open
Abstract
Identifying genome regions subject to selection in local breeds of Brazil is an opportunity to elucidate the C. hircus genome plasticity, flowing the colonization history of the country. Using SNP Bead Chip Illumina 50K genotyping of Brazilian Anglo-Nubian (standardized breed) and Marota (local endangered population from the semiarid area of Brazil) to show outliers loci in genome regions subject to selection. After applying data quality control, 45,600 SNPs were included in this investigation. Principal component analysis (PCAdapt) and FDIST2 analysis signalized 14 genomic regions more affected by selection in the Brazilian dry zone environment. The genome study signalized regions that are close to the sequences of genes related to growth and embryonic skeletal development (FGF12, AMPD2, OSTN). In addition, flagged regions close to the genes UTSB2 and SLC5A2 contribute to research on functional adaptation with low water needs and poor nutritive diet to survive. Both genes encode proteins that act on osmotic pathways and avoid cell flooding on stress cell responses. Further studies on the genetic role and involvement of these outliers' genomic regions, building a robust conceptual high-resolution map of natural selection drives, help to achieve hardiness candidate genes linked to the evolutionary history of Capra hircus in the semiarid area of Brazil.
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Affiliation(s)
- Francisco de A. Diniz
- Universidade Federal do Piauí, Teresina, PI, Brazil
- Instituto Federal do Piauí, Teresina, PI, Brazil
| | | | - Miklos M. Bajay
- Universidade do Estado de Santa Catarina, Laguna, SC, Brazil
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5
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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6
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Roux C, Vekemans X, Pannell J. Inferring the Demographic History and Inheritance Mode of Tetraploid Species Using ABC. Methods Mol Biol 2023; 2545:325-348. [PMID: 36720821 DOI: 10.1007/978-1-0716-2561-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Genomic patterns of diversity and divergence are impacted by certain life history traits, reproductive systems, and demographic history. The latter is characterized by fluctuations in population sizes over time, as well as by temporal patterns of introgression. For a given organism, identifying a demographic history that deviates from the standard neutral model allows a better understanding of its evolution but also helps to reduce the risk of false positives when screening for molecular targets of natural selection. Tetraploid organisms and beyond have demographic histories that are complicated by the mode of polyploidization, the mode of inheritance, and different scenarios of gene flow between sub-genomes and diploid parental species. Here we provide guidelines for experimenters wishing to address these issues through a flexible statistical framework: approximate Bayesian computation (ABC). The emphasis is on the general philosophy of the approach to encourage future users to exploit the enormous flexibility of ABC beyond the limitations imposed by generalist data analysis pipelines.
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Affiliation(s)
- Camille Roux
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France.
| | | | - John Pannell
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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7
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Rougemont Q, Xuereb A, Dallaire X, Moore JS, Normandeau E, Perreault-Payette A, Bougas B, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon. Mol Ecol 2023; 32:542-559. [PMID: 35000273 DOI: 10.1111/mec.16339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 01/25/2023]
Abstract
Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.
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Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier, Montpellier, France
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Xavier Dallaire
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Alysse Perreault-Payette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Bérénice Bougas
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada.,Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Ruth E Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, USA
| | - Penelope A Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - John Carlos Garza
- Department of Ocean Sciences and Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Terry D Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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8
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Li L, Milesi P, Tiret M, Chen J, Sendrowski J, Baison J, Chen Z, Zhou L, Karlsson B, Berlin M, Westin J, Garcia‐Gil MR, Wu HX, Lascoux M. Teasing apart the joint effect of demography and natural selection in the birth of a contact zone. THE NEW PHYTOLOGIST 2022; 236:1976-1987. [PMID: 36093739 PMCID: PMC9828440 DOI: 10.1111/nph.18480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/23/2022] [Indexed: 05/26/2023]
Abstract
Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.
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Affiliation(s)
- Lili Li
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Mathieu Tiret
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Jun Chen
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
- College of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Janek Sendrowski
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - John Baison
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Zhi‐qiang Chen
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Linghua Zhou
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | | | - Mats Berlin
- SkogforskUppsala Science Park751 83UppsalaSweden
| | - Johan Westin
- Unit for Field‐Based Forest ResearchSwedish University of Agricultural SciencesSE‐922 91VindelnSweden
| | - Maria Rosario Garcia‐Gil
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Harry X. Wu
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
- CSIRO National Collection Research AustraliaBlack Mountain LaboratoryCanberraACT2601Australia
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
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9
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Szép E, Trubenová B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Mol Ecol Resour 2022; 22:2941-2955. [PMID: 35765749 PMCID: PMC9796524 DOI: 10.1111/1755-0998.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 01/01/2023]
Abstract
Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST , a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST . Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.
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Affiliation(s)
- Enikő Szép
- IST Austria (Institute of Science and Technology Austria)KlosterneuburgAustria
| | - Barbora Trubenová
- IST Austria (Institute of Science and Technology Austria)KlosterneuburgAustria,Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Katalin Csilléry
- Biodiversity and Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
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10
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Gunn JC, Berkman LK, Koppelman J, Taylor AT, Brewer SK, Long JM, Eggert LS. Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex. Ecol Evol 2022; 12:e9370. [PMID: 36225830 PMCID: PMC9534746 DOI: 10.1002/ece3.9370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/05/2022] Open
Abstract
The Neosho Bass (Micropterus velox), a former subspecies of the keystone top-predator and globally popular Smallmouth Bass (M. dolomieu), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single-nucleotide polymorphisms (SNPs) obtained through ddRAD-seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.
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Affiliation(s)
- Joe C. Gunn
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
| | | | | | - Andrew T. Taylor
- Department of BiologyUniversity of Central OklahomaEdmondOklahomaUSA
- Department of BiologyUniversity of North GeorgiaDahlonegaGeorgiaUSA
| | - Shannon K. Brewer
- U.S. Geological Survey, Alabama Cooperative Fish and Wildlife Research Unit, School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - James M. Long
- U.S. Geological Survey, Oklahoma Cooperative Fish and Wildlife Research Unit, Department of Natural Resource Ecology and ManagementOklahoma State UniversityStillwaterOklahomaUSA
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMissouriUSA
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11
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Sherwin WB. Bray-Curtis (AFD) differentiation in molecular ecology: Forecasting, an adjustment ( A A), and comparative performance in selection detection. Ecol Evol 2022; 12:e9176. [PMID: 36110882 PMCID: PMC9465203 DOI: 10.1002/ece3.9176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/07/2022] Open
Abstract
Geographic genetic differentiation measures are used for purposes such as assessing genetic diversity and connectivity, and searching for signals of selection. Confirmation by unrelated measures can minimize false positives. A popular differentiation measure, Bray-Curtis, has been used increasingly in molecular ecology, renamed AFD (hereafter called BCAFD). Critically, BCAFD is expected to be partially independent of the commonly used Hill "Q-profile" measures. BCAFD needs scrutiny for potential biases, by examining limits on its value, and comparing simulations against expectations. BCAFD has two dependencies on within-population (alpha) variation, undesirable for a between-population (beta) measure. The first dependency is derived from similarity toG ST andF ST . The second dependency is that BCAFD cannot be larger than the highest allele proportion in either location (alpha variation), which can be overcome by data-filtering or by a modified statistic A A or "Adjusted AFD". The first dependency does not forestall applications such as assessing connectivity or selection, if we know the measure's null behavior under selective neutrality with specified conditions-which is shown in this article for A A, for equilibrium, and nonequilibrium, for the commonly used data type of single-nucleotide-polymorphisms (SNPs) in two locations. Thus, A A can be used in tandem with mathematically contrasting differentiation measures, with the aim of reducing false inferences. For detecting adaptive loci, the relative performance of A A and other measures was evaluated, showing that it is best to use two mathematically different measures simultaneously, and that A A is in one of the best such pairwise criteria. For any application, using A A, rather than BCAFD, avoids the counterintuitive limitation by maximum allele proportion within localities.
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Affiliation(s)
- William B. Sherwin
- Evolution and Ecology Research Centre, School of BEESUNSW‐SydneySydneyNew South WalesAustralia
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12
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Kvistad L, Falk S, Austin L. Widespread genomic signatures of reproductive isolation and sex-specific selection in the Eastern Yellow Robin, Eopsaltria australis. G3 GENES|GENOMES|GENETICS 2022; 12:6605223. [PMID: 35686912 PMCID: PMC9438485 DOI: 10.1093/g3journal/jkac145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/31/2022] [Indexed: 11/16/2022]
Abstract
How new species evolve is one of the most fundamental questions in biology. Population divergence, which may lead to speciation, may be occurring in the Eastern Yellow Robin, a common passerine that lives along the eastern coast of Australia. This species is composed of 2 parapatric lineages that have highly divergent mitochondrial DNA; however, similar levels of divergence have not been observed in the nuclear genome. Here we re-examine the nuclear genomes of these mitolineages to test potential mechanisms underlying the discordance between nuclear and mitochondrial divergence. We find that nuclear admixture occurs in a narrow hybrid zone, although the majority of markers across the genome show evidence of reproductive isolation between populations of opposing mitolineages. There is an 8 MB section of a previously identified putative neo-sex chromosome that is highly diverged between allopatric but not parapatric populations, which may be the result of a chromosomal inversion. The neo-sex chromosomal nature of this region, as well as the geographic patterns in which it exhibits divergence, suggest it is unlikely to be contributing to reproductive isolation through mitonuclear incompatibilities as reported in earlier studies. In addition, there are sex differences in the number of markers that are differentiated between populations of opposite mitolineages, with greater differentiation occurring in females, which are heterozygous, than males. These results suggest that, despite the absence of previously observed assortative mating, mitolineages of Eastern Yellow Robin experience at least some postzygotic isolation from each other, in a pattern consistent with Haldane’s Rule.
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Affiliation(s)
- Lynna Kvistad
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
| | - Stephanie Falk
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
- Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics , Freiburg D-79108, Germany
| | - Lana Austin
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
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13
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Abstract
The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of 10 populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation-by-distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼650,000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.
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Affiliation(s)
- Takahiro Maruki
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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14
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Gabián M, Morán P, Saura M, Carvajal-Rodríguez A. Detecting Local Adaptation between North and South European Atlantic Salmon Populations. BIOLOGY 2022; 11:933. [PMID: 35741456 PMCID: PMC9219887 DOI: 10.3390/biology11060933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection.
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Affiliation(s)
- María Gabián
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - Paloma Morán
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - María Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain;
| | - Antonio Carvajal-Rodríguez
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
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15
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Climate Adaptation, Drought Susceptibility, and Genomic-Informed Predictions of Future Climate Refugia for the Australian Forest Tree Eucalyptus globulus. FORESTS 2022. [DOI: 10.3390/f13040575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Understanding the capacity of forest tree species to adapt to climate change is of increasing importance for managing forest genetic resources. Through a genomics approach, we modelled spatial variation in climate adaptation within the Australian temperate forest tree Eucalyptus globulus, identified putative climate drivers of this genomic variation, and predicted locations of future climate refugia and populations at-risk of future maladaptation. Using 812,158 SNPs across 130 individuals from 30 populations (i.e., localities) spanning the species’ natural range, a gradientForest algorithm found 1177 SNPs associated with locality variation in home-site climate (climate-SNPs), putatively linking them to climate adaptation. Very few climate-SNPs were associated with population-level variation in drought susceptibility, signalling the multi-faceted nature and complexity of climate adaptation. Redundancy analysis (RDA) showed 24% of the climate-SNP variation could be explained by annual precipitation, isothermality, and maximum temperature of the warmest month. Spatial predictions of the RDA climate vectors associated with climate-SNPs allowed mapping of genomically informed climate selective surfaces across the species’ range under contemporary and projected future climates. These surfaces suggest over 50% of the current distribution of E. globulus will be outside the modelled adaptive range by 2070 and at risk of climate maladaptation. Such surfaces present a new integrated approach for natural resource managers to capture adaptive genetic variation and plan translocations in the face of climate change.
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16
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Vera M, Maroso F, Wilmes SB, Hermida M, Blanco A, Fernández C, Groves E, Malham SK, Bouza C, Robins PE, Martínez P. Genomic survey of edible cockle ( Cerastoderma edule) in the Northeast Atlantic: A baseline for sustainable management of its wild resources. Evol Appl 2022; 15:262-285. [PMID: 35233247 PMCID: PMC8867702 DOI: 10.1111/eva.13340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (F ST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.
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Affiliation(s)
- Manuel Vera
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Department of Life Sciences and BiotechnologiesUniversity of FerraraFerraraItaly
| | - Sophie B. Wilmes
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Emily Groves
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Shelagh K. Malham
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | | | - Peter E. Robins
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
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17
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Azzurro E, Nourigat M, Cohn F, Ben Souissi J, Bernardi G. Right out of the gate: the genomics of Lessepsian invaders in the vicinity of the Suez Canal. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02704-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractMarine organisms that enter the Mediterranean from the Red Sea via the Suez Canal are known as Lessepsian bioinvaders. In general, genetic studies of Lessepsian fishes have shown little structure between Red Sea and Mediterranean populations. Yet notable exceptions suggest the importance of life-history factors that may influence patterns of spatial genetic variation. In this study, by sampling two invasive fishes with different life histories (the rabbitfish Siganus rivulatus and the filefish Stephanolepis diaspros), we looked at evidence of population structure and selection at the boundary between the Red Sea and the Mediterranean (the Suez Canal), using thousands of molecular markers. Results illustrate two divergent patterns of genetic patterns, with little genetic structure in S. rivulatus and strong population structure in S. diaspros, even at such small spatial scale. We discuss differences in ecological characteristics between the two species to account for such differences. In addition, we report that in the face of both high (S. rivulatus) and low (S. diaspros) gene flow, loci under selection were uncovered, and some protein coding genes were identified as being involved with osmoregulation, which seems to be an important feature of individuals crossing the salinity-variable Suez Canal. The presence of genes under selection in populations near the Suez Canal supports the idea that selection may be active and essential for successful invasions right out of the gate.
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18
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Hardy BM, Pope KL, Latch EK. Genomic signatures of demographic declines in an imperiled amphibian inform conservation action. Anim Conserv 2021. [DOI: 10.1111/acv.12695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- B. M. Hardy
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - K. L. Pope
- United States Forest Service Pacific Southwest Research Station Arcata CA USA
| | - E. K. Latch
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
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19
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Yin X, Martinez AS, Sepúlveda MS, Christie MR. Rapid genetic adaptation to recently colonized environments is driven by genes underlying life history traits. BMC Genomics 2021; 22:269. [PMID: 33853517 PMCID: PMC8048285 DOI: 10.1186/s12864-021-07553-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Background Uncovering the mechanisms underlying rapid genetic adaptation can provide insight into adaptive evolution and shed light on conservation, invasive species control, and natural resource management. However, it can be difficult to experimentally explore rapid adaptation due to the challenges associated with propagating and maintaining species in captive environments for long periods of time. By contrast, many introduced species have experienced strong selection when colonizing environments that differ substantially from their native range and thus provide a “natural experiment” for studying rapid genetic adaptation. One such example occurred when sea lamprey (Petromyzon marinus), native to the northern Atlantic, naturally migrated into Lake Champlain and expanded their range into the Great Lakes via man-made shipping canals. Results Utilizing 368,886 genome-wide single nucleotide polymorphisms (SNPs), we calculated genome-wide levels of genetic diversity (i.e., heterozygosity and π) for sea lamprey collected from native (Connecticut River), native but recently colonized (Lake Champlain), and invasive (Lake Michigan) populations, assessed genetic differentiation between all populations, and identified candidate genes that responded to selection imposed by the novel environments. We observed a 14 and 24% reduction in genetic diversity in Lake Michigan and Lake Champlain populations, respectively, compared to individuals from the Connecticut River, suggesting that sea lamprey populations underwent a genetic bottleneck during colonization. Additionally, we identified 121 and 43 outlier genes in comparisons between Lake Michigan and Connecticut River and between Lake Champlain and Connecticut River, respectively. Six outlier genes that contained synonymous SNPs in their coding regions and two genes that contained nonsynonymous SNPs may underlie the rapid evolution of growth (i.e., GHR), reproduction (i.e., PGR, TTC25, STARD10), and bioenergetics (i.e., OXCT1, PYGL, DIN4, SLC25A15). Conclusions By identifying the genomic basis of rapid adaptation to novel environments, we demonstrate that populations of invasive species can be a useful study system for understanding adaptive evolution. Furthermore, the reduction in genome-wide levels of genetic diversity associated with colonization coupled with the identification of outlier genes underlying key life history traits known to have changed in invasive sea lamprey populations (e.g., growth, reproduction) illustrate the utility in applying genomic approaches for the successful management of introduced species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07553-x.
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Affiliation(s)
- Xiaoshen Yin
- Department of Biological Sciences, Purdue University, 915 W. State St., West Lafayette, Indiana, 47907-2054, USA
| | - Alexander S Martinez
- Department of Biological Sciences, Purdue University, 915 W. State St., West Lafayette, Indiana, 47907-2054, USA
| | - Maria S Sepúlveda
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, Indiana, 47907-2054, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, 915 W. State St., West Lafayette, Indiana, 47907-2054, USA. .,Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, Indiana, 47907-2054, USA.
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20
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Abstract
Birds are one of the most recognizable and diverse groups of organisms on earth. This group has played an important role in many fields, including the development of methods in behavioral ecology and evolutionary theory. The use of population genomics took off following the advent of high-throughput sequencing in various taxa. Several features of avian genomes make them particularly amenable for work in this field, including their nucleated red blood cells permitting easy DNA extraction and small, compact genomes. We review the latest findings in the population genomics of birds here, emphasizing questions related to behavior, ecology, evolution, and conservation. Additionally, we include insights in trait mapping and the ability to obtain accurate estimates of important summary statistics for conservation (e.g., genetic diversity and inbreeding). We highlight roadblocks that will need to be overcome in order to advance work on the population genomics of birds and prospects for future work. Roadblocks include the assembly of more contiguous reference genomes using long-reads and optical mapping. Prospects include the integration of population genomics with additional fields (e.g., landscape genetics, phylogeography, and genomic mapping) along with studies beyond genetic variants (e.g., epigenetics).
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21
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Leroy T, Rougemont Q. Introduction to Population Genomics Methods. Methods Mol Biol 2021; 2222:287-324. [PMID: 33301100 DOI: 10.1007/978-1-0716-0997-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput sequencing technologies have provided an unprecedented opportunity to study the different evolutionary forces that have shaped present-day patterns of genetic diversity, with important implications for many directions in plant biology research. To manage such massive quantities of sequencing data, biologists, however, need new additional skills in informatics and statistics. In this chapter, our objective is to introduce population genomics methods to beginners following a learning-by-doing strategy in order to help the reader to analyze the sequencing data by themselves. Conducted analyses cover several main areas of evolutionary biology, such as an initial description of the evolutionary history of a given species or the identification of genes targeted by natural or artificial selection. In addition to the practical advices, we performed re-analyses of two cases studies with different kind of data: a domesticated cereal (African rice) and a non-domesticated tree species (sessile oak). All the code needed to replicate this work is publicly available on github ( https://github.com/ThibaultLeroyFr/Intro2PopGenomics/ ).
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Affiliation(s)
- Thibault Leroy
- Montpellier Institute of Evolutionary Sciences (ISEM), Université de Montpellier, Montpellier, France. .,Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
| | - Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC, Canada
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22
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Schneider K, White TJ, Mitchell S, Adams CE, Reeve R, Elmer KR. The pitfalls and virtues of population genetic summary statistics: Detecting selective sweeps in recent divergences. J Evol Biol 2020; 34:893-909. [DOI: 10.1111/jeb.13738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Tom J. White
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Sonia Mitchell
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Colin E. Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
- Scottish Centre for Ecology and the Natural Environment Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Richard Reeve
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
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23
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Popovic I, Bierne N, Gaiti F, Tanurdžić M, Riginos C. Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels. J Evol Biol 2020; 34:175-192. [PMID: 33251632 DOI: 10.1111/jeb.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 11/01/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
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Affiliation(s)
- Iva Popovic
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution UMR 5554, Université de Montpellier, CNRS-IRD-EPHE-UM, Montpellier, France
| | - Federico Gaiti
- Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
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24
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Genitoni J, Vassaux D, Delaunay A, Citerne S, Portillo Lemus L, Etienne MP, Renault D, Stoeckel S, Barloy D, Maury S. Hypomethylation of the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala mimics the adaptive transition into the terrestrial morphotype. PHYSIOLOGIA PLANTARUM 2020; 170:280-298. [PMID: 32623739 DOI: 10.1111/ppl.13162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Ongoing global changes affect ecosystems and open up new opportunities for biological invasion. The ability of invasive species to rapidly adapt to new environments represents a relevant model for studying short-term adaptation mechanisms. The aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala, is classified as harmful in European rivers. In French wet meadows, this species has shown a rapid transition from aquatic to terrestrial environments with emergence of two distinct morphotypes in 5 years. To understand the heritable mechanisms involved in adjustment to such a new environment, we investigate both genetic and epigenetic as possible sources of flexibility involved in this fast terrestrial transition. We found a low overall genetic differentiation between the two morphotypes arguing against the possibility that terrestrial morphotype emerged from a new adaptive genetic capacity. Artificial hypomethylation was induced on both morphotypes to assess the epigenetic hypothesis. We analyzed global DNA methylation, morphological changes, phytohormones and metabolite profiles of both morphotype responses in both aquatic and terrestrial conditions in shoot and root tissues. Hypomethylation significantly affected morphological variables, phytohormone levels and the amount of some metabolites. The effects of hypomethylation depended on morphotypes, conditions and plant tissues, which highlighted differences among the morphotypes and their plasticity. Using a correlative integrative approach, we showed that hypomethylation of the aquatic morphotype mimicked the characteristics of the terrestrial morphotype. Our data suggest that DNA methylation rather than a new adaptive genetic capacity is playing a key role in L. grandiflora subsp. hexapetala plasticity during its rapid aquatic to terrestrial transition.
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Affiliation(s)
- Julien Genitoni
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Danièle Vassaux
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Alain Delaunay
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Luis Portillo Lemus
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Marie-Pierre Etienne
- Institut Agro, CNRS, Université Rennes, IRMAR (Institut de Recherche Mathématique de Rennes) - UMR 6625, Rennes, F-35000, France
| | - David Renault
- UMR CNRS 6553 EcoBio, University of Rennes 1, Rennes, France
- Institut Universitaire de France, 1 rue Descartes, Paris, France
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université Rennes, Le Rheu, 35653, France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
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Robinet T, Roussel V, Cheze K, Gagnaire PA. Spatial gradients of introgressed ancestry reveal cryptic connectivity patterns in a high gene flow marine fish. Mol Ecol 2020; 29:3857-3871. [PMID: 32853456 DOI: 10.1111/mec.15611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 01/18/2023]
Abstract
Assessing genetic connectivity among populations in high gene flow species is sometimes insufficient to evaluate demographic connectivity. Genetic differentiation quickly becomes zero as soon as a few dozen migrants are exchanged per generation. This provides little information to determine whether migration can ensure demographic coupling. The resulting difficulties in delineating conservation units for the management of commercially exploited marine fish species are well illustrated in the case of the European sea bass (Dicentrarchus labrax). Previous attempts to assess connectivity patterns in the northeast Atlantic have been hampered by a lack of spatial genetic structure. In contrast, mark-recapture data suggested low migration rates between regional spawning areas. Here, we show how a spatial gradient of introgressed Mediterranean ancestry across the northeast Atlantic reflects cryptic patterns of genetic and demographic connectivity. Using a 1K SNP chip data set in 827 individuals sampled from Portugal to the North Sea, we found null overall genetic differentiation across the northeast Atlantic. We however detected a subtle latitudinal admixture gradient originating at the edge of the contact zone with the Mediterranean sea bass lineage. Two significant breaks in the ancestry gradient at the tip of Galicia and northern Brittany indicated barriers to effective dispersal between demographically distinct units. Moreover, a northward expansion signal in Irish and North Seas was revealed by the surfing of rare Mediterranean alleles at the edge of the species range. Our results show that introgressed ancestry gradients offer a powerful alternative to assess genetic and demographic connectivity when the neutral migration-drift balance is not informative.
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Affiliation(s)
- Tony Robinet
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum National d'Histoire Naturelle, CNRS, IRD, SU, UCN, UA, Station marine, Concarneau, France
| | - Valérie Roussel
- Institut GéoArchi EA7462, Université de Bretagne Occidentale, Brest, France
| | - Karine Cheze
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum National d'Histoire Naturelle, CNRS, IRD, SU, UCN, UA, Station marine, Concarneau, France
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Perrier C, Rougemont Q, Charmantier A. Demographic history and genomics of local adaptation in blue tit populations. Evol Appl 2020; 13:1145-1165. [PMID: 32684952 PMCID: PMC7359843 DOI: 10.1111/eva.13035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 12/24/2022] Open
Abstract
Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio‐temporal variations in population demography and variations in recombination rate and in diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests, and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.003 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long‐lasting gene flow between populations inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migration, followed by isolation since the end of the last glaciation. Effective population sizes were large, yet smaller on the island than on the mainland. Weak and nonparallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds and were more often found in regions of low recombination, as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8 Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.
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Affiliation(s)
- Charles Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France.,Centre de Biologie pour la Gestion des Populations UMR CBGP INRAE CIRAD IRD Montpellier SupAgro Univ Montpellier Montpellier France
| | - Quentin Rougemont
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France
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Gagnaire PA. Comparative genomics approach to evolutionary process connectivity. Evol Appl 2020; 13:1320-1334. [PMID: 32684961 PMCID: PMC7359831 DOI: 10.1111/eva.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/01/2023] Open
Abstract
The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses of species to anthropogenic landscape alterations. Genetic connectivity and its evolutionary outcomes depend on a variety of spatially dependent evolutionary processes, such as population structure, local adaptation, genetic admixture, and speciation. Over the last years, population genomic studies have been interrogating these processes with increasing resolution, revealing a large diversity of species responses to spatially structured landscapes. In parallel, multispecies meta-analyses usually based on low-genome coverage data have provided fundamental insights into the ecological determinants of genetic connectivity, such as the influence of key life history traits on population structure. However, comparative studies still lack a thorough integration of macro- and micro-evolutionary scales to fully realize their potential. Here, I present how a comparative genomics framework may provide a deeper understanding of evolutionary process connectivity. This framework relies on coupling the inference of long-term demographic and selective history with an assessment of the contemporary consequences of genetic connectivity. Standardizing this approach across several species occupying the same landscape should help understand how spatial environmental heterogeneity has shaped the diversity of historical and contemporary connectivity patterns in different taxa with contrasted life history traits. I will argue that a reasonable amount of genome sequence data can be sufficient to resolve and connect complex macro- and micro-evolutionary histories. Ultimately, implementing this framework in varied taxonomic groups is expected to improve scientific guidelines for conservation and management policies.
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28
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Hudson J, Johannesson K, McQuaid CD, Rius M. Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrate. Evol Appl 2020; 13:600-612. [PMID: 32431738 PMCID: PMC7045719 DOI: 10.1111/eva.12893] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/30/2019] [Accepted: 10/16/2019] [Indexed: 01/03/2023] Open
Abstract
Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here, we used genotyping-by-sequencing to study both native and introduced ranges of the amphiatlantic marine invertebrate Ciona intestinalis. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using 1,653 single nucleotide polymorphisms (SNPs) from newly collected samples (285 individuals), we first confirmed the presence of this depth-defined genomic divergence along the Swedish coast. We then used approximate Bayesian computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e., deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonization of C. intestinalis in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonizations of C. intestinalis. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridization and by altering both colonization patterns and their ecological effects in the introduced range.
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Affiliation(s)
- Jamie Hudson
- School of Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
| | - Kerstin Johannesson
- Department of Marine SciencesTjärnö Marine LaboratoryUniversity of GothenburgStrömstadSweden
| | - Christopher D. McQuaid
- Department of Zoology and EntomologyCoastal Research GroupRhodes UniversityGrahamstownSouth Africa
| | - Marc Rius
- School of Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
- Department of ZoologyCentre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgAuckland ParkSouth Africa
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29
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Garcia E, Simison WB, Bernardi G. Patterns of Genomic Divergence and Signals of Selection in Sympatric and Allopatric Northeastern Pacific and Sea of Cortez Populations of the Sargo (Anisotremus davidsonii) and Longjaw Mudsucker (Gillichthys mirabilis). J Hered 2020; 111:57-69. [DOI: 10.1093/jhered/esz071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractStudying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, United States, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. Statistically significant differentiation is seen across Point Conception in mudsucker (FST = 0.15), Punta Eugenia in Sargo (FST = 0.02), and on either side of the Baja California peninsula in both species (FST = 0.11 and 0.23, in Sargo and mudsucker, respectively). Each species shows structure using neutral and non-neutral loci. Finally, higher population divergence yields a more even distribution of outliers along their differentiation range but does not always translate into higher outlier proportions or higher rates in which outliers are matched to coding regions. If repeated in similar systems, observed genomic patterns might reveal speciation signatures in diverse networks of population isolation.
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Affiliation(s)
- Eric Garcia
- Ecology and Evolutionary Biology Department, Long Marine Laboratory, University of California Santa Cruz, Santa Cruz, CA
- Department of Biological Sciences, Old Dominion University, Norfolk, VA
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA
| | - Giacomo Bernardi
- Ecology and Evolutionary Biology Department, Long Marine Laboratory, University of California Santa Cruz, Santa Cruz, CA
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30
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Borrell JS, Zohren J, Nichols RA, Buggs RJA. Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow. Evol Appl 2020; 13:161-175. [PMID: 31892950 PMCID: PMC6935589 DOI: 10.1111/eva.12883] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
When populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide restriction site-associated single nucleotide polymorphism (SNP) data, we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.
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Affiliation(s)
| | - Jasmin Zohren
- Sex Chromosome Biology LabThe Francis Crick InstituteLondonUK
| | - Richard A. Nichols
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Richard J. A. Buggs
- Jodrell LaboratoryRoyal Botanic Gardens, KewSurreyUK
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
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31
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Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps. PLoS Comput Biol 2019; 15:e1007426. [PMID: 31710623 PMCID: PMC6872172 DOI: 10.1371/journal.pcbi.1007426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 11/21/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
Selective sweeps, the genetic footprint of positive selection, have been extensively studied in the past decades, with dozens of methods developed to identify swept regions. However, these methods suffer from both false positive and false negative reports, and the candidates identified with different methods are often inconsistent with each other. We propose that a biological cause of this problem can be population subdivision, and a technical cause can be incomplete, or inaccurate, modeling of the dynamic process associated with sweeps. Here we used simulations to show how these effects interact and potentially cause bias. In particular, we show that sweeps maybe misclassified as either hard or soft, when the true time stage of a sweep and that implied, or pre-supposed, by the model do not match. We call this "temporal misclassification". Similarly, "spatial misclassification (softening)" can occur when hard sweeps, which are imported by migration into a new subpopulation, are falsely identified as soft. This can easily happen in case of local adaptation, i.e. when the sweeping allele is not under positive selection in the new subpopulation, and the underlying model assumes panmixis instead of substructure. The claim that most sweeps in the evolutionary history of humans were soft, may have to be reconsidered in the light of these findings.
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32
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Rifkin JL, Castillo AS, Liao IT, Rausher MD. Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). Mol Ecol 2019; 28:1709-1729. [PMID: 30451335 DOI: 10.1111/mec.14945] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 09/03/2018] [Accepted: 11/01/2018] [Indexed: 02/03/2023]
Abstract
Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I. lacunosa to I. cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I. cordatotriloba being substantially more different than sympatric and allopatric I. lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I. cordatotriloba traits become much more like those of I. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.
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Affiliation(s)
- Joanna L Rifkin
- Department of Biology, Duke University, Durham, North Carolina
| | | | - Irene T Liao
- Department of Biology, Duke University, Durham, North Carolina
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina
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Galtier N. Delineating species in the speciation continuum: A proposal. Evol Appl 2019; 12:657-663. [PMID: 30976300 PMCID: PMC6439491 DOI: 10.1111/eva.12748] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/08/2018] [Indexed: 12/18/2022] Open
Abstract
Delineating species is a difficult and seemingly uninteresting issue that is still essential to address. Taxonomic methodology is heterogeneous according to the taxa and scientists involved due to the disparate data quality and quantity and disagreements over the species concept. This has negative impacts on basic and applied research. Genomic data substantially enhance our understanding of the speciation process but do not provide a ubiquitous solution to the species problem. The relevance of comparative approaches in speciation research has nevertheless recently been demonstrated. I suggest moving towards a more unified taxonomic classification through a reference-based decision procedure.
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Affiliation(s)
- Nicolas Galtier
- UMR 5554 – Institut des Sciences de l'EvolutionCNRS – University of Montpellier – IRD – EPHEMontpellierFrance
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34
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Bernardi G, Nelson P, Paddack M, Rulmal J, Crane N. Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes. Ecol Evol 2018; 8:8676-8685. [PMID: 30271536 PMCID: PMC6157655 DOI: 10.1002/ece3.4417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/15/2022] Open
Abstract
The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCalifornia
| | | | | | - John Rulmal
- Ulithi Falalop Community Action ProgramYapFederated States of Micronesia
| | - Nicole Crane
- Department of BiologyCabrillo CollegeAptosCalifornia
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35
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do Prado FD, Vera M, Hermida M, Bouza C, Pardo BG, Vilas R, Blanco A, Fernández C, Maroso F, Maes GE, Turan C, Volckaert FAM, Taggart JB, Carr A, Ogden R, Nielsen EE, Martínez P. Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot ( Scophthalmus maximus). Evol Appl 2018; 11:1322-1341. [PMID: 30151043 PMCID: PMC6099829 DOI: 10.1111/eva.12628] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/23/2018] [Indexed: 12/16/2022] Open
Abstract
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.
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Affiliation(s)
- Fernanda Dotti do Prado
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
- CAPES FoundationMinistry of Education of BrazilBrasíliaBrazil
| | - Manuel Vera
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Belén G. Pardo
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Román Vilas
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Gregory E. Maes
- Laboratory of Biodiversity and Evolutionary GenomicsUniversity of LeuvenLeuvenBelgium
- Center for Human GeneticsUZ Leuven‐Genomics Core, KU LeuvenLeuvenBelgium
- Comparative Genomics CentreCollege of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | - Cemal Turan
- Faculty of Marine Science and TechnologyIskenderun Technical UniversityIskenderunTurkey
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary GenomicsUniversity of LeuvenLeuvenBelgium
- Center for Human GeneticsUZ Leuven‐Genomics Core, KU LeuvenLeuvenBelgium
- Comparative Genomics CentreCollege of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | | | | | - Rob Ogden
- Trace Wildlife Forensics NetworkRoyal Zoological Society of ScotlandEdinburghUK
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Paulino Martínez
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
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Improving conservation policy with genomics: a guide to integrating adaptive potential into U.S. Endangered Species Act decisions for conservation practitioners and geneticists. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1096-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kess T, Galindo J, Boulding EG. Genomic divergence between Spanish Littorina saxatilis ecotypes unravels limited admixture and extensive parallelism associated with population history. Ecol Evol 2018; 8:8311-8327. [PMID: 30250705 PMCID: PMC6145028 DOI: 10.1002/ece3.4304] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/23/2022] Open
Abstract
The rough periwinkle, Littorina saxatilis, is a model system for studying parallel ecological speciation in microparapatry. Phenotypically parallel wave-adapted and crab-adapted ecotypes that hybridize within the middle shore are replicated along the northwestern coast of Spain and have likely arisen from two separate glacial refugia. We tested whether greater geographic separation corresponding to reduced opportunity for contemporary or historical gene flow between parallel ecotypes resulted in less parallel genomic divergence. We sequenced double-digested restriction-associated DNA (ddRAD) libraries from individual snails from upper, mid, and low intertidal levels of three separate sites colonized from two separate refugia. Outlier analysis of 4256 SNP markers identified 34.4% sharing of divergent loci between two geographically close sites; however, these sites each shared only 9.9%-15.1% of their divergent loci with a third more-distant site. STRUCTURE analysis revealed that genotypes from only three of 166 phenotypically intermediate mid-shore individuals appeared to result from recent hybridization, suggesting that hybrids cannot be reliably identified using shell traits. Hierarchical AMOVA indicated that the primary source of genomic differentiation was geographic separation, but also revealed greater similarity of the same ecotype across the two geographically close sites than previously estimated with dominant markers. These results from a model system for ecological speciation suggest that genomic parallelism is affected by the opportunity for historical or contemporary gene flow between populations.
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Affiliation(s)
- Tony Kess
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Juan Galindo
- Departamento de BioquímicaGenética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- Centro de Investigación Mariña da Universidade de Vigo (CIM‐UVIGO)VigoSpain
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Pazmiño DA, Maes GE, Green ME, Simpfendorfer CA, Hoyos-Padilla EM, Duffy CJA, Meyer CG, Kerwath SE, Salinas-de-León P, van Herwerden L. Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers. Heredity (Edinb) 2018; 120:407-421. [PMID: 29321624 PMCID: PMC5889387 DOI: 10.1038/s41437-017-0025-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/07/2017] [Accepted: 10/17/2017] [Indexed: 12/15/2022] Open
Abstract
The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise ΦST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (FST = 0.023-0.035), mtDNA exhibited more divergence (ΦST = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.
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Affiliation(s)
- Diana A Pazmiño
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Universidad San Francisco de Quito - Galápagos Science Center, Quito, Ecuador.
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Leuven, Belgium
- Laboratory for Cytogenetics and Genome Research, Center for Human Genetics, Genomics Core, KU Leuven, Leuven, Belgium
| | - Madeline E Green
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, Australia
- CSIRO Oceans & Atmosphere, Castray Esplanade, Battery Point, Hobart, TAS, Australia
| | - Colin A Simpfendorfer
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | | | - Clinton J A Duffy
- Auckland War Memorial Museum, The Domain, Auckland, New Zealand
- Department of Conservation, Private Bag 68908, Newton, Auckland, New Zealand
| | - Carl G Meyer
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Coconut Island, Kaneohe, HI, USA
| | - Sven E Kerwath
- Department of Biological Sciences, University of Cape Town, Private Bag × 3, Rondebosch, South Africa
- Department of Agriculture, Forestry and Fisheries: Fisheries Branch, Private Bag × 2, Vlaeberg, Cape Town, South Africa
| | - Pelayo Salinas-de-León
- Department of Marine Sciences, Charles Darwin Research Station. Av Charles Darwin s/n, Puerto Ayora, Galapagos Islands, Santa Cruz, Ecuador
- Pristine Seas, National Geographic Society, Washington, D. C., USA
| | - Lynne van Herwerden
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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39
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40
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Fahrenkrog AM, Neves LG, Resende MFR, Dervinis C, Davenport R, Barbazuk WB, Kirst M. Population genomics of the eastern cottonwood ( Populus deltoides). Ecol Evol 2017; 7:9426-9440. [PMID: 29187979 PMCID: PMC5696417 DOI: 10.1002/ece3.3466] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/30/2022] Open
Abstract
Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural P. deltoides population showed low levels of subpopulation differentiation (FST = 0.022–0.106), high genetic diversity (θW = 0.00100, π = 0.00170), a large effective population size (Ne ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D), subpopulation differentiation (XTX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.
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Affiliation(s)
- Annette M Fahrenkrog
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA
| | - Leandro G Neves
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.,Present address: RAPiD Genomics LLC756 2nd Avenue Gainesville FL 32601 USA
| | - Márcio F R Resende
- Horticultural Sciences Department University of Florida Gainesville FL USA
| | - Christopher Dervinis
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
| | - Ruth Davenport
- Biology Department University of Florida Gainesville FL USA
| | - W Brad Barbazuk
- Biology Department University of Florida Gainesville FL USA.,University of Florida Genetics Institute University of Florida Gainesville FL USA
| | - Matias Kirst
- School of Forest Resources and Conservation University of Florida Gainesville FL USA.,University of Florida Genetics Institute University of Florida Gainesville FL USA
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41
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Matsubayashi KW, Kohyama TI, Kobayashi N, Yamasaki S, Kuwajima M, Katakura H. Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna. J Evol Biol 2017; 30:1110-1123. [PMID: 28306172 DOI: 10.1111/jeb.13071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/12/2017] [Indexed: 12/12/2022]
Abstract
Adaptation to different environments can promote population divergence via natural selection even in the presence of gene flow - a phenomenon that typically occurs during ecological speciation. To elucidate how natural selection promotes and maintains population divergence during speciation, we investigated the population genetic structure, degree of gene flow and heterogeneous genomic divergence in three closely related Japanese phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and H. yasutomii. These species act as a generalist, a wild thistle (Cirsium spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist, respectively, and their ranges differ accordingly. The two specialist species widely co-occur but are reproductively isolated solely due to their high specialization to a particular host plant. Genomewide amplified fragment-length polymorphism (AFLP) markers and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious genomewide divergence associated with both geographic distance and ecological divergence. However, a hybridization assessment for both AFLP loci and the mitochondrial sequences revealed a certain degree of unidirectional gene flow between the two sympatric specialist species. Principal coordinates analysis (PCoA) based on all of the variable AFLP loci demonstrated that there are genetic similarities between populations from adjacent localities irrespective of the species (i.e. host range). However, a further comparative genome scan identified a few fractions of loci representing approximately 1% of all loci as different host-associated outliers. These results suggest that these three species had a complex origin, which could be obscured by current gene flow, and that ecological divergence can be maintained with only a small fraction of the genome is related to different host use even when there is a certain degree of gene flow between sympatric species pairs.
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Affiliation(s)
- K W Matsubayashi
- The Faculty of Arts and Science, Kyushu University, Fukuoka, Fukuoka, Japan
| | - T I Kohyama
- Faculty of Earth and Environmental Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - N Kobayashi
- Saitama Prefecture University, Koshigaya, Saitama, Japan
| | - S Yamasaki
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - M Kuwajima
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - H Katakura
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
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42
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Carvajal-Rodríguez A. HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations. PLoS One 2017; 12:e0175944. [PMID: 28423003 PMCID: PMC5397020 DOI: 10.1371/journal.pone.0175944] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/03/2017] [Indexed: 01/10/2023] Open
Abstract
The detection of genomic regions involved in local adaptation is an important topic in current population genetics. There are several detection strategies available depending on the kind of genetic and demographic information at hand. A common drawback is the high risk of false positives. In this study we introduce two complementary methods for the detection of divergent selection from populations connected by migration. Both methods have been developed with the aim of being robust to false positives. The first method combines haplotype information with inter-population differentiation (FST). Evidence of divergent selection is concluded only when both the haplotype pattern and the FST value support it. The second method is developed for independently segregating markers i.e. there is no haplotype information. In this case, the power to detect selection is attained by developing a new outlier test based on detecting a bimodal distribution. The test computes the FST outliers and then assumes that those of interest would have a different mode. We demonstrate the utility of the two methods through simulations and the analysis of real data. The simulation results showed power ranging from 60-95% in several of the scenarios whilst the false positive rate was controlled below the nominal level. The analysis of real samples consisted of phased data from the HapMap project and unphased data from intertidal marine snail ecotypes. The results illustrate that the proposed methods could be useful for detecting locally adapted polymorphisms. The software HacDivSel implements the methods explained in this manuscript.
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43
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Almeida P, Barbosa R, Bensasson D, Gonçalves P, Sampaio JP. Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites. Mol Ecol 2017; 26:2167-2182. [PMID: 28231394 DOI: 10.1111/mec.14071] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/17/2022]
Abstract
In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives.
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Affiliation(s)
- Pedro Almeida
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Raquel Barbosa
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Douda Bensasson
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Paula Gonçalves
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José Paulo Sampaio
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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44
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Luu K, Bazin E, Blum MGB. pcadapt: an R package to perform genome scans for selection based on principal component analysis. Mol Ecol Resour 2017; 17:67-77. [PMID: 27601374 DOI: 10.1101/056135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 05/23/2023]
Abstract
The R package pcadapt performs genome scans to detect genes under selection based on population genomic data. It assumes that candidate markers are outliers with respect to how they are related to population structure. Because population structure is ascertained with principal component analysis, the package is fast and works with large-scale data. It can handle missing data and pooled sequencing data. By contrast to population-based approaches, the package handle admixed individuals and does not require grouping individuals into populations. Since its first release, pcadapt has evolved in terms of both statistical approach and software implementation. We present results obtained with robust Mahalanobis distance, which is a new statistic for genome scans available in the 2.0 and later versions of the package. When hierarchical population structure occurs, Mahalanobis distance is more powerful than the communality statistic that was implemented in the first version of the package. Using simulated data, we compare pcadapt to other computer programs for genome scans (BayeScan, hapflk, OutFLANK, sNMF). We find that the proportion of false discoveries is around a nominal false discovery rate set at 10% with the exception of BayeScan that generates 40% of false discoveries. We also find that the power of BayeScan is severely impacted by the presence of admixed individuals whereas pcadapt is not impacted. Last, we find that pcadapt and hapflk are the most powerful in scenarios of population divergence and range expansion. Because pcadapt handles next-generation sequencing data, it is a valuable tool for data analysis in molecular ecology.
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Affiliation(s)
- Keurcien Luu
- Laboratoire TIMC-IMAG, UMR 5525, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Eric Bazin
- Laboratoire d'Ecologie Alpine UMR 5553, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Michael G B Blum
- Laboratoire TIMC-IMAG, UMR 5525, CNRS, Université Grenoble Alpes, Grenoble, France
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45
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Bertin A, Gouin N, Baumel A, Gianoli E, Serratosa J, Osorio R, Manel S. Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat. Mol Ecol 2016; 26:431-443. [PMID: 27862542 DOI: 10.1111/mec.13923] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 10/18/2016] [Accepted: 10/25/2016] [Indexed: 02/04/2023]
Abstract
Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species-genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species-genetic diversity relationships.
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Affiliation(s)
- Angeline Bertin
- Departamento de Biología, Facultad de Ciencias, Universidad de La Serena, Av. Raúl Bitrán 1305, Casilla 554, La Serena, Chile
| | - Nicolas Gouin
- Departamento de Biología, Facultad de Ciencias, Universidad de La Serena, Av. Raúl Bitrán 1305, Casilla 554, La Serena, Chile.,Centro de Estudios Avanzados en Zonas Áridas, Raúl Bitrán 1305, La Serena, Chile.,Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, Casilla 554, La Serena, Chile
| | - Alex Baumel
- Aix Marseille Univ, IMBE, UMR CNRS, IRD, Avignon Univ, Technopole Environm Arbois Mediterrane, BP 80, F-13545 Aix En Provence 04, France
| | - Ernesto Gianoli
- Departamento de Biología, Facultad de Ciencias, Universidad de La Serena, Av. Raúl Bitrán 1305, Casilla 554, La Serena, Chile.,Departamento de Botánica, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Juan Serratosa
- Facultad de Ciencias del Mar, Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
| | - Rodomiro Osorio
- Departamento de Biología, Facultad de Ciencias, Universidad de La Serena, Av. Raúl Bitrán 1305, Casilla 554, La Serena, Chile
| | - Stephanie Manel
- CNRS, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, EPHE, PSL Research University, F-34293, Montpellier, France
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Bierne N, Bonhomme F, Arnaud-Haond S. Dedicated population genomics for the silent world: the specific questions of marine population genetics. Curr Zool 2016; 62:545-550. [PMID: 29491944 PMCID: PMC5804263 DOI: 10.1093/cz/zow107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Nicolas Bierne
- Université de Montpellier, Montpellier, France
- CNRS – Institut des Sciences de l’Evolution Montpellier, UMR 5554 UM – CNRS
– IRD – EPHE, Station Marine OREME, Sète, France
| | - François Bonhomme
- Université de Montpellier, Montpellier, France
- CNRS – Institut des Sciences de l’Evolution Montpellier, UMR 5554 UM – CNRS
– IRD – EPHE, Station Marine OREME, Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier, Montpellier, France
- Ifremer – MARine Biodiversity, Exploitation and Conservation, UMR 9190 IRD –
IFREMER – UM – CNRS, Sète, France
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47
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Bernatchez L. On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes. JOURNAL OF FISH BIOLOGY 2016; 89:2519-2556. [PMID: 27687146 DOI: 10.1111/jfb.13145] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/23/2016] [Indexed: 05/18/2023]
Abstract
The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some circumstances. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.
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Affiliation(s)
- L Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1Y 2T8, Canada
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48
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Cadzow M, Merriman TR, Boocock J, Dalbeth N, Stamp LK, Black MA, Visscher PM, Wilcox PL. Lack of direct evidence for natural selection at the candidate thrifty gene locus, PPARGC1A. BMC MEDICAL GENETICS 2016; 17:80. [PMID: 27846814 PMCID: PMC5111290 DOI: 10.1186/s12881-016-0341-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/01/2016] [Indexed: 12/12/2022]
Abstract
Background The gene PPARGC1A, in particular the Gly482Ser variant (rs8192678), had been proposed to be subject to natural selection, particularly in recent progenitors of extant Polynesian populations. Reasons include high levels of population differentiation and increased frequencies of the derived type 2 diabetes (T2D) risk 482Ser allele, and association with body mass index (BMI) in a small Tongan population. However, no direct statistical tests for selection have been applied. Methods Using a range of Polynesian populations (Tongan, Māori, Samoan) we re-examined evidence for association between Gly482Ser with T2D and BMI as well as gout. Using also Asian, European, and African 1000 Genome Project samples a range of statistical tests for selection (FST, integrated haplotype score (iHS), cross population extended haplotype homozygosity (XP-EHH), Tajima’s D and Fay and Wu’s H) were conducted on the PPARGC1A locus. Results No statistically significant evidence for association between Gly482Ser and any of BMI, T2D or gout was found. Population differentiation (FST) was smallest between Asian and Pacific populations (New Zealand Māori ≤ 0.35, Samoan ≤ 0.20). When compared to European (New Zealand Māori ≤ 0.40, Samoan ≤ 0.25) or African populations (New Zealand Māori ≤ 0.80, Samoan ≤ 0.66) this differentiation was larger. We did not find any strong evidence for departure from neutral evolution at this locus when applying any of the other statistical tests for selection. However, using the same analytical methods, we found evidence for selection in specific populations at previously identified loci, indicating that lack of selection was the most likely explanation for the lack of evidence of selection in PPARGC1A. Conclusion We conclude that there is no compelling evidence for selection at this locus, and that this gene should not be considered a candidate thrifty gene locus in Pacific populations. High levels of population differentiation at this locus and the reported absence of the derived 482Ser allele in some Melanesian populations, can alternatively be explained by multiple out-of-Africa migrations by ancestral progenitors, and subsequent genetic drift during colonisation of Polynesia. Intermediate 482Ser allele frequencies in extant Western Polynesian populations could therefore be due to recent admixture with Melanesian progenitors. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0341-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Murray Cadzow
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Virtual Institute of Statistical Genetics (www.visg.co.nz), Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Virtual Institute of Statistical Genetics (www.visg.co.nz), Dunedin, New Zealand
| | - James Boocock
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Virtual Institute of Statistical Genetics (www.visg.co.nz), Dunedin, New Zealand
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Virtual Institute of Statistical Genetics (www.visg.co.nz), Dunedin, New Zealand
| | - Peter M Visscher
- Virtual Institute of Statistical Genetics (www.visg.co.nz), Dunedin, New Zealand.,The Queensland Brain Institute, University of Queensland, Brisbane, Australia.,University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute (TRI), Brisbane, Australia
| | - Phillip L Wilcox
- Department of Biochemistry, University of Otago, Dunedin, New Zealand. .,Virtual Institute of Statistical Genetics (www.visg.co.nz), Dunedin, New Zealand. .,formerly Scion (New Zealand Forest Research Institute Ltd), 49 Sala Street, Rotorua, New Zealand. .,Department of Mathematics and Statistics, University of Otago, Science III Building, 730 Cumberland St, Dunedin, 9016, New Zealand.
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Population genomics applications for conservation: the case of the tropical dry forest dweller Peromyscus melanophrys. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0907-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Liu Z, Ji Z, Wang G, Chao T, Hou L, Wang J. Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions. BMC Genomics 2016; 17:863. [PMID: 27809776 PMCID: PMC5094087 DOI: 10.1186/s12864-016-3212-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
Abstract
Background Throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. Mongolian sheep is the common ancestor of the Chinese short fat-tailed sheep. Migration to different ecoregions leads to changes in selection pressures and results in microevolution. Mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. Genome-wide intraspecific variation is required to dissect the genetic basis of these traits. Results This research resequenced 3 short fat-tailed sheep breeds with a 43.2-fold coverage of the sheep genome. We report more than 17 million single nucleotide polymorphisms and 2.9 million indels and identify 143 genomic regions with reduced pooled heterozygosity or increased genetic distance to each other breed that represent likely targets for selection during the migration. These regions harbor genes related to developmental processes, cellular processes, multicellular organismal processes, biological regulation, metabolic processes, reproduction, localization, growth and various components of the stress responses. Furthermore, we examined the haplotype diversity of 3 genomic regions involved in reproduction and found significant differences in TSHR and PRL gene regions among 8 sheep breeds. Conclusions Our results provide useful genomic information for identifying genes or causal mutations associated with important economic traits in sheep and for understanding the genetic basis of adaptation to different ecological environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3212-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhaohua Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Lei Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China.
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