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Sbiba SE, Quintela M, Øyro J, Dahle G, Jurado-Ruzafa A, Iita K, Nikolioudakis N, Bazairi H, Chlaida M. Genetic investigation of population structure in Atlantic chub mackerel, Scomber colias Gmelin, 1789 along the West African coast. PeerJ 2024; 12:e17928. [PMID: 39247552 PMCID: PMC11380841 DOI: 10.7717/peerj.17928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 07/24/2024] [Indexed: 09/10/2024] Open
Abstract
Sustainable management of transboundary fish stocks hinges on accurate delineation of population structure. Genetic analysis offers a powerful tool to identify potential subpopulations within a seemingly homogenous stock, facilitating the development of effective, coordinated management strategies across international borders. Along the West African coast, the Atlantic chub mackerel (Scomber colias) is a commercially important and ecologically significant species, yet little is known about its genetic population structure and connectivity. Currently, the stock is managed as a single unit in West African waters despite new research suggesting morphological and adaptive differences. Here, eight microsatellite loci were genotyped on 1,169 individuals distributed across 33 sampling sites from Morocco (27.39°N) to Namibia (22.21°S). Bayesian clustering analysis depicts one homogeneous population across the studied area with null overall differentiation (F ST = 0.0001ns), which suggests panmixia and aligns with the migratory potential of this species. This finding has significant implications for the effective conservation and management of S. colias within a wide scope of its distribution across West African waters from the South of Morocco to the North-Centre of Namibia and underscores the need for increased regional cooperation in fisheries management and conservation.
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Affiliation(s)
- Salah Eddine Sbiba
- Biodiversity, Ecology and Genome Laboratory, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Research and Development Unit on Marine Biology, National Institute of Fisheries Research, Casablanca, Morocco
| | - María Quintela
- Department of Population Genetics, Institute of Marine Research, Bergen, Norway
| | - Johanne Øyro
- Department of Population Genetics, Institute of Marine Research, Bergen, Norway
| | - Geir Dahle
- Department of Population Genetics, Institute of Marine Research, Bergen, Norway
| | - Alba Jurado-Ruzafa
- Oceanographic Centre of the Canary Islands, Spanish Institute of Oceanography (IEO-CSIC), Tenerife, Spain
| | - Kashona Iita
- National Marine Information and Research Centre (NATMIRC), Ministry of Fisheries and Marine Resources, Swakopmund, Namibia
| | | | - Hocein Bazairi
- Biodiversity, Ecology and Genome Laboratory, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- University of Gibraltar, Europa Point Campus, Natural Sciences and Environment Research Hub, Gibraltar, Gibraltar
| | - Malika Chlaida
- Research and Development Unit on Marine Biology, National Institute of Fisheries Research, Casablanca, Morocco
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Pauly R, Alexander Feltus F. Simplified detection of genetic background admixture using artificial intelligence. Clin Genet 2024; 106:247-257. [PMID: 38561851 DOI: 10.1111/cge.14527] [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] [Received: 12/01/2023] [Revised: 02/14/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
Admixture refers to the mixing of genetic ancestry from different populations. Admixture is important for genomic medicine because it can affect how an individual responds to certain medications, how they metabolize drugs, and susceptibility to certain diseases. For example, some genetic variants associated with drug metabolism and response may be more common in certain populations, and individuals with admixed ancestry may have a different frequency of these variants than individuals from the ancestral populations. Understanding the patterns of admixture in a population can also help researchers identify new genetic variants associated with diseases or traits and develop more personalized and targeted treatments. In this study, we compared and classified the known and self-reported genetic backgrounds from 1000 Genomes Project and admixed samples from GTEx projects using supervised, unsupervised and statistical classification methodologies. We developed a novel tool called Admix-AI that uses a one-dimensional convolutional neural network to understand and classify admixed genetic backgrounds using 213 DNA-marker based genetic background labels. Admix-AI can be used to discover admixed proportions in samples and ultimately aid personalized genomic medicine by identifying specific biomarker systems. We compared Admix-AI to the existing admixture categorization software and found our tool to be computationally faster with 2× speedup and streamlined usage. Admix-AI is available as open-source code under GPL version 3.0 license at https://github.com/rpauly/Admix-AI.
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Affiliation(s)
- Rini Pauly
- Biomedical Data Science & Informatics Program, Clemson University, Clemson, South Carolina, USA
| | - Frank Alexander Feltus
- Biomedical Data Science & Informatics Program, Clemson University, Clemson, South Carolina, USA
- Genetics and Biochemistry Department, Clemson University, Clemson, South Carolina, USA
- Center for Human Genetics, Clemson University, Greenwood, South Carolina, USA
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Abhainn EA, Shirley DL, Stanley RK, Scarpato T, Koch JL, Romero-Severson J. Gene flow from Fraxinus cultivars into natural stands of Fraxinus pennsylvanica occurs range-wide, is regionally extensive, and is associated with a loss of allele richness. PLoS One 2024; 19:e0294829. [PMID: 38753718 PMCID: PMC11098341 DOI: 10.1371/journal.pone.0294829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/30/2024] [Indexed: 05/18/2024] Open
Abstract
In North America, a comparatively small number of Fraxinus (ash) cultivars were planted in large numbers in both urban and rural environments across the entire range of Fraxinus pennsylvanica Marsh (green ash) over the last 80 years. Undetected cultivar gene flow, if extensive, could significantly lower genetic diversity within populations, suppress differentiation between populations, generate interspecific admixture not driven by long-standing natural processes, and affect the impact of abiotic and biotic threats. In this investigation we generated the first range-wide genetic assessment of F. pennsylvanica to detect the extent of cultivar gene flow into natural stands. We used 16 EST-SSR markers to genotype 48 naturally regenerated populations of F. pennsylvanica distributed across the native range (1291 trees), 19 F. pennsylvanica cultivars, and one F. americana L. (white ash) cultivar to detect cultivar propagule dispersal into these populations. We detected first generation cultivar parentage with high confidence in 171 individuals in 34 of the 48 populations and extensive cultivar parentage (23-50%) in eight populations. The incidence of cultivar parentage was negatively associated with allele richness (R2 = 0.151, p = 0.006). The evidence for a locally high frequency of cultivar propagule dispersal and the interspecific admixture in eastern populations will inform Fraxinus gene pool conservation strategies and guide the selection of individuals for breeding programs focused on increasing resistance to the emerald ash borer (Agrilus planipennis Fairmaire), an existential threat to the Fraxinus species of North America.
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Affiliation(s)
- Everett A. Abhainn
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, United States of America
| | - Devin L. Shirley
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, United States of America
| | - Robert K. Stanley
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, United States of America
| | - Tatum Scarpato
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, United States of America
| | - Jennifer L. Koch
- USDA Forest Service, Northern Research Station, Delaware, Ohio, United States of America
| | - Jeanne Romero-Severson
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, United States of America
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Angst P, Ameline C, Haag CR, Ben-Ami F, Ebert D, Fields PD. Genetic Drift Shapes the Evolution of a Highly Dynamic Metapopulation. Mol Biol Evol 2022; 39:msac264. [PMID: 36472514 PMCID: PMC9778854 DOI: 10.1093/molbev/msac264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The dynamics of extinction and (re)colonization in habitat patches are characterizing features of dynamic metapopulations, causing them to evolve differently than large, stable populations. The propagule model, which assumes genetic bottlenecks during colonization, posits that newly founded subpopulations have low genetic diversity and are genetically highly differentiated from each other. Immigration may then increase diversity and decrease differentiation between subpopulations. Thus, older and/or less isolated subpopulations are expected to have higher genetic diversity and less genetic differentiation. We tested this theory using whole-genome pool-sequencing to characterize nucleotide diversity and differentiation in 60 subpopulations of a natural metapopulation of the cyclical parthenogen Daphnia magna. For comparison, we characterized diversity in a single, large, and stable D. magna population. We found reduced (synonymous) genomic diversity, a proxy for effective population size, weak purifying selection, and low rates of adaptive evolution in the metapopulation compared with the large, stable population. These differences suggest that genetic bottlenecks during colonization reduce effective population sizes, which leads to strong genetic drift and reduced selection efficacy in the metapopulation. Consistent with the propagule model, we found lower diversity and increased differentiation in younger and also in more isolated subpopulations. Our study sheds light on the genomic consequences of extinction-(re)colonization dynamics to an unprecedented degree, giving strong support for the propagule model. We demonstrate that the metapopulation evolves differently from a large, stable population and that evolution is largely driven by genetic drift.
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Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | - Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
- Evolutionary Biology, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Christoph R Haag
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier 34293, France
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
| | - Frida Ben-Ami
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
- Tvärminne Zoological Station, University of Helsinki, Hanko 10900, Finland
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Götz J, Rajora OP, Gailing O. Genetic Structure of Natural Northern Range-Margin Mainland, Peninsular, and Island Populations of Northern Red Oak (Quercus rubra L.). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.907414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant populations at the leading edge of the species’ native range often exhibit genetic structure as a result of genetic drift and adaptation to harsh environmental conditions. Hence, they are likely to harbour rare genetic adaptations to local environmental conditions and therefore are of particular interest to understand climate adaptation. We examined genetic structure of nine northern marginal mainland, peninsular and isolated island natural populations of northern red oak (Quercus rubraL.), a valuable long-lived North American hardwood tree species, covering a wide climatic range, using 17 nuclear microsatellites. We found pronounced genetic differentiation of a disjunct isolated island population from all mainland and peninsular populations. Furthermore, we observed remarkably strong fine-scale spatial genetic structure (SGS) in all investigated populations. Such high SGS values are uncommon and were previously solely observed in extreme range-edge marginal oak populations in one other study. We found a significant correlation between major climate parameters and SGS formation in northern range-edge red oak populations, with more pronounced SGS in colder and drier regions. Most likely, the harsh environment in leading edge populations influences the density of reproducing trees within the populations and therefore leads to restricted overlapping of seed shadows when compared to more central populations. Accordingly, SGS was negatively correlated with effective population size and increased with latitude of the population locations. The significant positive association between genetic distances and precipitation differences between populations may be indicative of isolation by adaptation in the observed range-edge populations. However, this association was not confirmed by a multiple regression analysis including geographic distances and precipitation distances, simultaneously. Our study provides new insights in the genetic structure of long-lived tree species at their leading distribution edge.
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Nelson TD, MacDonald ZG, Sperling FAH. Moths passing in the night: Phenological and genomic divergences within a forest pest complex. Evol Appl 2022; 15:166-180. [PMID: 35126654 PMCID: PMC8792478 DOI: 10.1111/eva.13338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Temporal separation of reproductive timing can contribute to species diversification both through allochronic speciation and later reinforcement of species boundaries. Such phenological differences are an enigmatic component of evolutionary divergence between two major forest defoliator species of the spruce budworm complex: Choristoneura fumiferana and C. occidentalis. While these species interbreed freely in laboratory settings, natural hybridization rates have not been reliably quantified due to their indistinguishable morphology. To assess whether temporal isolation is contributing to reproductive isolation, we collected adult individuals throughout their expected zone of sympatry in western Canada at 10-day intervals over two successive years, assigning taxonomic identities using thousands of single nucleotide polymorphisms. We found unexpectedly broad sympatry between C. fumiferana and C. occidentalis biennis and substantial overlap of regional flight periods. However, flight period divergence was much more apparent on a location-by-location basis, highlighting the importance of considering spatial scale in these analyses. Phenological comparisons were further complicated by the biennial life cycle of C. o. biennis, the main subspecies of C. occidentalis in the region, and the occasional occurrence of the annually breeding subspecies C. o. occidentalis. Nonetheless, we demonstrate that biennialism is not a likely contributor to reproductive isolation within the species complex. Overall, interspecific F1 hybrids comprised 2.9% of sequenced individuals, confirming the genomic distinctiveness of C. fumiferana and C. occidentalis, while also showing incomplete reproductive isolation of lineages. Finally, we used F ST-based outlier and genotype-environment association analyses to identify several genomic regions under putative divergent selection. These regions were disproportionately located on the Z linkage region of C. fumiferana, and contained genes, particularly antifreeze proteins, that are likely to be associated with overwintering success and diapause. In addition to temporal isolation, we conclude that other mechanisms, including ecologically mediated selection, are contributing to evolutionary divergence within the spruce budworm species complex.
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Affiliation(s)
- Tyler D. Nelson
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Summerland Research and Development CentreAgriculture and Agri‐Food CanadaSummerlandBritish ColumbiaCanada
| | - Zachary G. MacDonald
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Department of Renewable ResourcesUniversity of AlbertaEdmontonAlbertaCanada
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Ony M, Klingeman WE, Zobel J, Trigiano RN, Ginzel M, Nowicki M, Boggess SL, Everhart S, Hadziabdic D. Genetic diversity in North American Cercis Canadensis reveals an ancient population bottleneck that originated after the last glacial maximum. Sci Rep 2021; 11:21803. [PMID: 34750401 PMCID: PMC8576035 DOI: 10.1038/s41598-021-01020-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding of the present-day genetic diversity, population structure, and evolutionary history of tree species can inform resource management and conservation activities, including response to pressures presented by a changing climate. Cercis canadensis (Eastern Redbud) is an economically valuable understory tree species native to the United States (U.S.) that is also important for forest ecosystem and wildlife health. Here, we document and explain the population genetics and evolutionary history of this deciduous tree species across its distributed range. In this study, we used twelve microsatellite markers to investigate 691 wild-type trees sampled at 74 collection sites from 23 Eastern U.S. states. High genetic diversity and limited gene flow were revealed in wild, natural stands of C. canadensis with populations that are explained by two major genetic clusters. These findings indicate that an ancient population bottleneck occurred coinciding with the last glacial maximum (LGM) in North America. The structure in current populations likely originated from an ancient population in the eastern U.S. that survived LGM and then later diverged into two contemporary clusters. Data suggests that populations have expanded since the last glaciation event from one into several post-glacial refugia that now occupy this species’ current geographic range. Our enhanced understanding benchmarks the genetic variation preserved within this species and can direct future efforts in conservation, and resource utilization of adaptively resilient populations that present the greatest genetic and structural diversity.
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Affiliation(s)
- Meher Ony
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | | | - John Zobel
- Department of Forest Resources, University of Minnesota, St. Paul, MN, USA
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Matthew Ginzel
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Marcin Nowicki
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Sydney Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.
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Ledoux J, Ghanem R, Horaud M, López‐Sendino P, Romero‐Soriano V, Antunes A, Bensoussan N, Gómez‐Gras D, Linares C, Machordom A, Ocaña O, Templado J, Leblois R, Ben Souissi J, Garrabou J. Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: Patterns, processes and conservation implications. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jean‐Baptiste Ledoux
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Institut de Ciències del Mar CSIC Barcelona Spain
| | - Raouia Ghanem
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
| | | | | | | | - Agostinho Antunes
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | | | | | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals Institut de Recerca de la Biodiversitat (IRBIO) Universitat de Barcelona Barcelona Spain
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Oscar Ocaña
- Departamento de Oceanografía Biológica y Biodiversidad Fundación Museo del Mar de Ceuta Ceuta Spain
| | - José Templado
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Raphaêl Leblois
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
- Institut de Biologie Computationnelle University of Montpellier Montpellier France
| | - Jamila Ben Souissi
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
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Kitada S, Nakamichi R, Kishino H. Understanding population structure in an evolutionary context: population-specific FST and pairwise FST. G3-GENES GENOMES GENETICS 2021; 11:6364900. [PMID: 34549777 PMCID: PMC8527463 DOI: 10.1093/g3journal/jkab316] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 08/27/2021] [Indexed: 01/04/2023]
Abstract
Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies.
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Affiliation(s)
- Shuichi Kitada
- Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | | | - Hirohisa Kishino
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.,The Research Institute of Evolutionary Biology, Tokyo 138-0098, Japan
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Distinct genetic clustering in the weakly differentiated polar cod, Boreogadus saida Lepechin, 1774 from East Siberian Sea to Svalbard. Polar Biol 2021. [DOI: 10.1007/s00300-021-02911-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractThe cold-adapted polar cod Boreogadus saida, a key species in Arctic ecosystems, is vulnerable to global warming and ice retreat. In this study, 1257 individuals sampled in 17 locations within the latitudinal range of 75–81°N from Svalbard to East Siberian Sea were genotyped with a dedicated suite of 116 single-nucleotide polymorphic loci (SNP). The overall pattern of isolation by distance (IBD) found was driven by the two easternmost samples (East Siberian Sea and Laptev Sea), whereas no differentiation was registered in the area between the Kara Sea and Svalbard. Eleven SNP under strong linkage disequilibrium, nine of which could be annotated to chromosome 2 in Atlantic cod, defined two genetic groups of distinct size, with the major cluster containing seven-fold larger number of individuals than the minor. No underlying geographic basis was evident, as both clusters were detected throughout all sampling sites in relatively similar proportions (i.e. individuals in the minor cluster ranging between 4 and 19% on the location basis). Similarly, females and males were also evenly distributed between clusters and age groups. A differentiation was, however, found regarding size at age: individuals belonging to the major cluster were significantly longer in the second year. This study contributes to increasing the population genetic knowledge of this species and suggests that an appropriate management should be ensured to safeguard its diversity.
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Xuereb A, D'Aloia CC, Andrello M, Bernatchez L, Fortin MJ. Incorporating putatively neutral and adaptive genomic data into marine conservation planning. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:909-920. [PMID: 32785955 DOI: 10.1111/cobi.13609] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/17/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
The availability of genomic data for an increasing number of species makes it possible to incorporate evolutionary processes into conservation plans. Recent studies show how genetic data can inform spatial conservation prioritization (SCP), but they focus on metrics of diversity and distinctness derived primarily from neutral genetic data sets. Identifying adaptive genetic markers can provide important information regarding the capacity for populations to adapt to environmental change. Yet, the effect of including metrics based on adaptive genomic data into SCP in comparison to more widely used neutral genetic metrics has not been explored. We used existing genomic data on a commercially exploited species, the giant California sea cucumber (Parastichopus californicus), to perform SCP for the coastal region of British Columbia (BC), Canada. Using a RAD-seq data set for 717 P. californicus individuals across 24 sampling locations, we identified putatively adaptive (i.e., candidate) single nucleotide polymorphisms (SNPs) based on genotype-environment associations with seafloor temperature. We calculated various metrics for both neutral and candidate SNPs and compared SCP outcomes with independent metrics and combinations of metrics. Priority areas varied depending on whether neutral or candidate SNPs were used and on the specific metric used. For example, targeting sites with a high frequency of warm-temperature-associated alleles to support persistence under future warming prioritized areas in the southern coastal region. In contrast, targeting sites with high expected heterozygosity at candidate loci to support persistence under future environmental uncertainty prioritized areas in the north. When combining metrics, all scenarios generated intermediate solutions, protecting sites that span latitudinal and thermal gradients. Our results demonstrate that distinguishing between neutral and adaptive markers can affect conservation solutions and emphasize the importance of defining objectives when choosing among various genomic metrics for SCP.
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Affiliation(s)
- Amanda Xuereb
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Cassidy C D'Aloia
- Department of Biological Sciences, University of New Brunswick Saint John, 100 Tucker Park Road, Saint John, NB, E2L 4L5, Canada
| | - Marco Andrello
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 Avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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12
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Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy. Heredity (Edinb) 2021; 126:846-858. [PMID: 33608651 PMCID: PMC8102499 DOI: 10.1038/s41437-021-00413-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Conservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.
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Petrou EL, Fuentes-Pardo AP, Rogers LA, Orobko M, Tarpey C, Jiménez-Hidalgo I, Moss ML, Yang D, Pitcher TJ, Sandell T, Lowry D, Ruzzante DE, Hauser L. Functional genetic diversity in an exploited marine species and its relevance to fisheries management. Proc Biol Sci 2021; 288:20202398. [PMID: 33622133 PMCID: PMC7934995 DOI: 10.1098/rspb.2020.2398] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/28/2021] [Indexed: 01/02/2023] Open
Abstract
The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring (Clupea pallasii) across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particular SYNE2, which influences the development of retinal photoreceptors in vertebrates. SYNE2 is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (Clupea harengus). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.
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Affiliation(s)
- Eleni L. Petrou
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA
| | | | - Luke A. Rogers
- Fisheries and Oceans Canada, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Melissa Orobko
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA
| | - Isadora Jiménez-Hidalgo
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA
| | - Madonna L. Moss
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | - Dongya Yang
- Department of Archaeology, Simon Fraser University, Education Building 9635, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Tony J. Pitcher
- University of British Columbia, Institute for the Oceans and Fisheries, Vancouver, British Columbia, Canada
| | - Todd Sandell
- Washington Department of Fish and Wildlife, 16018 Mill Creek Boulevard, Mill Creek, WA 98012-1541, USA
| | - Dayv Lowry
- Washington Department of Fish and Wildlife, 1111 Washington Street SE, 6th Floor, Olympia, WA 98504-3150, USA
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle WA 98105, USA
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14
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Quintela M, Richter‐Boix À, Bekkevold D, Kvamme C, Berg F, Jansson E, Dahle G, Besnier F, Nash RDM, Glover KA. Genetic response to human-induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway. Ecol Evol 2021; 11:1691-1718. [PMID: 33613998 PMCID: PMC7882954 DOI: 10.1002/ece3.7160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/21/2022] Open
Abstract
Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; that is, Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat, and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant F ST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbor-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (F ST) between marine and brackish sprat is larger in the comparison Norway-Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, that is, 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.
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Affiliation(s)
| | - Àlex Richter‐Boix
- CREAFCampus de BellaterraAutonomous University of BarcelonaBarcelonaSpain
| | - Dorte Bekkevold
- DTU‐Aqua National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | | | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | | | - Richard D. M. Nash
- Centre for EnvironmentFisheries and Aquaculture Science (Cefas)LowestoftUK
| | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
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15
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Ochoa A, Storey JD. Estimating FST and kinship for arbitrary population structures. PLoS Genet 2021; 17:e1009241. [PMID: 33465078 PMCID: PMC7846127 DOI: 10.1371/journal.pgen.1009241] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/29/2021] [Accepted: 11/02/2020] [Indexed: 12/20/2022] Open
Abstract
FST and kinship are key parameters often estimated in modern population genetics studies in order to quantitatively characterize structure and relatedness. Kinship matrices have also become a fundamental quantity used in genome-wide association studies and heritability estimation. The most frequently-used estimators of FST and kinship are method-of-moments estimators whose accuracies depend strongly on the existence of simple underlying forms of structure, such as the independent subpopulations model of non-overlapping, independently evolving subpopulations. However, modern data sets have revealed that these simple models of structure likely do not hold in many populations, including humans. In this work, we analyze the behavior of these estimators in the presence of arbitrarily-complex population structures, which results in an improved estimation framework specifically designed for arbitrary population structures. After generalizing the definition of FST to arbitrary population structures and establishing a framework for assessing bias and consistency of genome-wide estimators, we calculate the accuracy of existing FST and kinship estimators under arbitrary population structures, characterizing biases and estimation challenges unobserved under their originally-assumed models of structure. We then present our new approach, which consistently estimates kinship and FST when the minimum kinship value in the dataset is estimated consistently. We illustrate our results using simulated genotypes from an admixture model, constructing a one-dimensional geographic scenario that departs nontrivially from the independent subpopulations model. Our simulations reveal the potential for severe biases in estimates of existing approaches that are overcome by our new framework. This work may significantly improve future analyses that rely on accurate kinship and FST estimates. Kinship coefficients and FST, which measure relatedness and population structure, respectively, are important quantities needed to accurately perform various analyses on genetic data, including genome-wide association studies and heritability estimation. However, existing estimators require restrictive assumptions of independence that are not met by real human and other datasets. In this work we find that existing estimators can be severely biased under reasonable scenarios, first by theoretically determining their properties, and then using an admixture simulation to illustrate our findings. In particular, we find that existing FST estimators are downwardly biased, and that existing kinship matrix estimators have related biases that are on average downward and of similar magnitude but vary for every pair of individuals. These insights led us to a new estimation framework for kinship and FST that is practically unbiased for any population structure, as demonstrated by theory and simulations. Our new approaches—available as open-source R packages—are easy to use and are more widely applicable than existing approaches, and they are likely to improve downstream analyses that require accurate kinship and FST estimates.
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Affiliation(s)
- Alejandro Ochoa
- Duke Center for Statistical Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - John D. Storey
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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16
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Shaney KJ, Diaz-Ramirez LG, Espindola S, Castañeda-Rico S, Berovides-Álvarez V, Vázquez-Domínguez E. Defining intraspecific conservation units in the endemic Cuban Rock Iguanas (Cyclura nubila nubila). Sci Rep 2020; 10:21607. [PMID: 33303852 PMCID: PMC7729961 DOI: 10.1038/s41598-020-78664-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/27/2020] [Indexed: 11/09/2022] Open
Abstract
Defining conservation units is an important step in species management and requires interpretation of the genetic diversity and ecological function of the taxon being considered. We used the endemic Cuban Rock Iguanas (Cyclura nubila nubila) as a model to highlight this challenge and examined patterns of its intraspecific genetic diversity across Cuba. We evaluated nuclear (microsatellite loci) and mitochondrial diversity across eight populations from the island and its off-shore cays, and applied the population genetics results for assignment of Management Unit (MU) status and Evolutionary Significant Units (ESUs) based on phylogeographic and time of divergence information. We identified at least six distinct Cuban Rock Iguana MUs, encompassing demographically isolated and genetically differentiated populations across Cuba, most with low effective population size, declining populations, and with high risk of inbreeding and genetic drift. Hence, each MU should be considered of urgent conservation priority. Given the key ecological seed dispersal role of C. n. nubila, the disappearance of any MU could trigger the loss of local ecological functional diversity and major negative impacts on their ecosystems. Two divergent ESUs were also identified, exhibiting an historical east-west geographic separation on Cuba. Based on a Caribbean phylogeographic assessment, our findings strengthen the conclusion that all geographically and evolutionarily differentiated Cyclura species and subspecies across the archipelago warrant ESU distinction.
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Affiliation(s)
- Kyle J Shaney
- Departamento de Ecología de La Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - L Grisell Diaz-Ramirez
- Division of Geriatrics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sayra Espindola
- Departamento de Ecología de La Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Susette Castañeda-Rico
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Vicente Berovides-Álvarez
- Facultad de Ciencias Biológicas, Universidad de La Habana, Calle 25, # 455, entre J e I, Vedado, Ciudad Habana, Cuba
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de La Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México.
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17
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Hellwig T, Abbo S, Sherman A, Coyne CJ, Saranga Y, Lev-Yadun S, Main D, Zheng P, Ophir R. Limited divergent adaptation despite a substantial environmental cline in wild pea. Mol Ecol 2020; 29:4322-4336. [PMID: 32964548 DOI: 10.1111/mec.15633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 08/09/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
Isolation by environment (IBE) is a widespread phenomenon in nature. It is commonly expected that the degree of difference among environments is proportional to the level of divergence between populations in their respective environments. It is therefore assumed that a species' genetic diversity displays a pattern of IBE in the presence of a strong environmental cline if gene flow does not mitigate isolation. We tested this common assumption by analysing the genetic diversity and demographic history of Pisum fulvum, which inhabits contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations, making it an ideal test case. Ecogeographical and subpopulation structure were analysed and compared. The correlation of genetic with environmental distances was calculated to test the effect of isolation by distance and IBE and detect the main drivers of these effects. Historical effective population size was estimated using stairway plot. Limited overlap of ecogeographical and genetic clustering was observed, and correlation between genetic and environmental distances was statistically significant but small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to a past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive gene flow.
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Affiliation(s)
- Timo Hellwig
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
| | - Shahal Abbo
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
| | | | - Yehoshua Saranga
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Simcha Lev-Yadun
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa-Oranim, Tivon, Israel
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Ron Ophir
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
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18
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Underwood JN, Richards Z, Berry O, Oades D, Howard A, Gilmour JP. Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote north-west Australia. Evol Appl 2020; 13:2404-2421. [PMID: 33005230 PMCID: PMC7513722 DOI: 10.1111/eva.13033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022] Open
Abstract
Management strategies designed to conserve coral reefs threatened by climate change need to incorporate knowledge of the spatial distribution of inter- and intra-specific genetic diversity. We characterized patterns of genetic diversity and connectivity using single nucleotide polymorphisms (SNPs) in two reef-building corals to explore the eco-evolutionary processes that sustain populations in north-west Australia. Our sampling focused on the unique reefs of the Kimberley; we collected the broadcast spawning coral Acropora aspera (n = 534) and the brooding coral Isopora brueggemanni (n = 612) across inter-archipelago (tens to hundreds of kilometres), inter-reef (kilometres to tens of kilometres) and within-reef (tens of metres to a few kilometres) scales. Initial analysis of A. aspera identified four highly divergent lineages that were co-occurring but morphologically similar. Subsequent population analyses focused on the most abundant and widespread lineage, Acropora asp-c. Although the overall level of geographic subdivision was greater in the brooder than in the spawner, fundamental similarities in patterns of genetic structure were evident. Most notably, limits to gene flow were observed at scales <35 kilometres. Further, we observed four discrete clusters and a semi-permeable barrier to dispersal that were geographically consistent between species. Finally, sites experiencing bigger tides were more connected to the metapopulation and had greater gene diversity than those experiencing smaller tides. Our data indicate that the inshore reefs of the Kimberley are genetically isolated from neighbouring oceanic bioregions, but occasional dispersal between inshore archipelagos is important for the redistribution of evolutionarily important genetic diversity. Additionally, these results suggest that networks of marine reserves that effectively protect reefs from local pressures should be spaced within a few tens of kilometres to conserve the existing patterns of demographic and genetic connectivity.
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Affiliation(s)
- Jim N Underwood
- Australian Institute of Marine Science Indian Oceans Marine Research Centre, Crawley Perth WA Australia
- Western Australian Marine Science Institution Indian Ocean Marine Research Centre Crawley WA Australia
| | - Zoe Richards
- Western Australian Marine Science Institution Indian Ocean Marine Research Centre Crawley WA Australia
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Aquatic Zoology Western Australian Museum Welshpool WA Australia
| | - Oliver Berry
- Western Australian Marine Science Institution Indian Ocean Marine Research Centre Crawley WA Australia
- CSIRO Oceans and Atmosphere Indian Oceans Marine Research Centre, Crawley Perth WA Australia
| | - Daniel Oades
- Bardi Jawi Rangers Kimberley Land Council Broome WA Australia
| | - Azton Howard
- Bardi Jawi Rangers Kimberley Land Council Broome WA Australia
| | - James P Gilmour
- Australian Institute of Marine Science Indian Oceans Marine Research Centre, Crawley Perth WA Australia
- Western Australian Marine Science Institution Indian Ocean Marine Research Centre Crawley WA Australia
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19
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Capblancq T, Butnor JR, Deyoung S, Thibault E, Munson H, Nelson DM, Fitzpatrick MC, Keller SR. Whole-exome sequencing reveals a long-term decline in effective population size of red spruce ( Picea rubens). Evol Appl 2020; 13:2190-2205. [PMID: 33005218 PMCID: PMC7513712 DOI: 10.1111/eva.12985] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/26/2020] [Accepted: 04/09/2020] [Indexed: 01/02/2023] Open
Abstract
Understanding the factors influencing the current distribution of genetic diversity across a species range is one of the main questions of evolutionary biology, especially given the increasing threat to biodiversity posed by climate change. Historical demographic processes such as population expansion or bottlenecks and decline are known to exert a predominant influence on past and current levels of genetic diversity, and revealing this demo-genetic history can have immediate conservation implications. We used a whole-exome capture sequencing approach to analyze polymorphism across the gene space of red spruce (Picea rubens Sarg.), an endemic and emblematic tree species of eastern North America high-elevation forests that are facing the combined threat of global warming and increasing human activities. We sampled a total of 340 individuals, including populations from the current core of the range in northeastern USA and southeastern Canada and from the southern portions of its range along the Appalachian Mountains, where populations occur as highly fragmented mountaintop "sky islands." Exome capture baits were designed from the closely relative white spruce (P. glauca Voss) transcriptome, and sequencing successfully captured most regions on or near our target genes, resulting in the generation of a new and expansive genomic resource for studying standing genetic variation in red spruce applicable to its conservation. Our results, based on over 2 million exome-derived variants, indicate that red spruce is structured into three distinct ancestry groups that occupy different geographic regions of its highly fragmented range. Moreover, these groups show small Ne , with a temporal history of sustained population decline that has been ongoing for thousands (or even hundreds of thousands) of years. These results demonstrate the broad potential of genomic studies for revealing details of the demographic history that can inform management and conservation efforts of nonmodel species with active restoration programs, such as red spruce.
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Affiliation(s)
| | - John R Butnor
- USDA Forest Service Southern Research Station University of Vermont Burlington VT USA
| | - Sonia Deyoung
- Department of Plant Biology University of Vermont Burlington VT USA
| | - Ethan Thibault
- Department of Plant Biology University of Vermont Burlington VT USA
| | - Helena Munson
- Department of Plant Biology University of Vermont Burlington VT USA
| | - David M Nelson
- Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
| | - Matthew C Fitzpatrick
- Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
| | - Stephen R Keller
- Department of Plant Biology University of Vermont Burlington VT USA
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20
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Quintela M, Kvamme C, Bekkevold D, Nash RDM, Jansson E, Sørvik AG, Taggart JB, Skaala Ø, Dahle G, Glover KA. Genetic analysis redraws the management boundaries for the European sprat. Evol Appl 2020; 13:1906-1922. [PMID: 32908594 PMCID: PMC7463317 DOI: 10.1111/eva.12942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 02/03/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Sustainable fisheries management requires detailed knowledge of population genetic structure. The European sprat is an important commercial fish distributed from Morocco to the Arctic circle, Baltic, Mediterranean, and Black seas. Prior to 2018, annual catch advice on sprat from the International Council for the Exploration of the Sea (ICES) was based on five putative stocks: (a) North Sea, (b) Kattegat-Skagerrak and Norwegian fjords, (c) Baltic Sea, (d) West of Scotland-southern Celtic Seas, and (e) English Channel. However, there were concerns that the sprat advice on stock size estimates management plan inadequately reflected the underlying biological units. Here, we used ddRAD sequencing to develop 91 SNPs that were thereafter used to genotype approximately 2,500 fish from 40 locations. Three highly distinct and relatively homogenous genetic groups were identified: (a) Norwegian fjords; (b) Northeast Atlantic including the North Sea, Kattegat-Skagerrak, Celtic Sea, and Bay of Biscay; and (c) Baltic Sea. Evidence of genetic admixture and possibly physical mixing was detected in samples collected from the transition zone between the North and Baltic seas, but not between any of the other groups. These results have already been implemented by ICES with the decision to merge the North Sea and the Kattegat-Skagerrak sprat to be assessed as a single unit, thus demonstrating that genetic data can be rapidly absorbed to align harvest regimes and biological units.
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Affiliation(s)
| | | | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
| | | | | | | | - John B Taggart
- Institute of Aquaculture School of Natural Sciences University of Stirling Stirling UK
| | | | - Geir Dahle
- Institute of Marine Research Bergen Norway
| | - Kevin A Glover
- Institute of Marine Research Bergen Norway
- Institute of Biology University of Bergen Bergen Norway
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21
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MacDonald ZG, Dupuis JR, Davis CS, Acorn JH, Nielsen SE, Sperling FAH. Gene flow and climate-associated genetic variation in a vagile habitat specialist. Mol Ecol 2020; 29:3889-3906. [PMID: 32810893 DOI: 10.1111/mec.15604] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022]
Abstract
Previous work in landscape genetics suggests that geographic isolation is of greater importance to genetic divergence than variation in environmental conditions. This is intuitive when configurations of suitable habitat are a dominant factor limiting dispersal and gene flow, but has not been thoroughly examined for habitat specialists with strong dispersal capability. Here, we evaluate the effects of geographic and environmental isolation on genetic divergence for a vagile invertebrate with high habitat specificity and a discrete dispersal life stage: Dod's Old World swallowtail butterfly, Papilio machaon dodi. In Canada, P. m. dodi are generally restricted to eroding habitat along major river valleys where their larval host plant occurs. A series of causal and linear mixed effects models indicate that divergence of genome-wide single nucleotide polymorphisms is best explained by a combination of environmental isolation (variation in summer temperatures) and geographic isolation (Euclidean distance). Interestingly, least-cost path and circuit distances through a resistance surface parameterized as the inverse of habitat suitability were not supported. This suggests that, although habitat associations of many butterflies are specific due to reproductive requirements, habitat suitability and landscape permeability are not equivalent concepts due to considerable adult vagility. We infer that divergent selection related to variation in summer temperatures has produced two genetic clusters within P. m. dodi, differing in voltinism and diapause propensity. Within the next century, temperatures are predicted to rise by amounts greater than the present-day difference between regions of the genetic clusters, potentially affecting the persistence of the northern cluster under continued climate change.
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Affiliation(s)
- Zachary G MacDonald
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Corey S Davis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - John H Acorn
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Scott E Nielsen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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22
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Li B, Yaegashi S, Carvajal TM, Gamboa M, Chiu M, Ren Z, Watanabe K. Machine-learning-based detection of adaptive divergence of the stream mayfly Ephemera strigata populations. Ecol Evol 2020; 10:6677-6687. [PMID: 32724541 PMCID: PMC7381564 DOI: 10.1002/ece3.6398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/21/2020] [Accepted: 04/30/2020] [Indexed: 11/07/2022] Open
Abstract
Adaptive divergence is a key mechanism shaping the genetic variation of natural populations. A central question linking ecology with evolutionary biology is how spatial environmental heterogeneity can lead to adaptive divergence among local populations within a species. In this study, using a genome scan approach to detect candidate loci under selection, we examined adaptive divergence of the stream mayfly Ephemera strigata in the Natori River Basin in northeastern Japan. We applied a new machine-learning method (i.e., random forest) besides traditional distance-based redundancy analysis (dbRDA) to examine relationships between environmental factors and adaptive divergence at non-neutral loci. Spatial autocorrelation analysis based on neutral loci was employed to examine the dispersal ability of this species. We conclude the following: (a) E. strigata show altitudinal adaptive divergence among the populations in the Natori River Basin; (b) random forest showed higher resolution for detecting adaptive divergence than traditional statistical analysis; and (c) separating all markers into neutral and non-neutral loci could provide full insight into parameters such as genetic diversity, local adaptation, and dispersal ability.
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Affiliation(s)
- Bin Li
- Insititute of Environmental and EcologyShandong Normal UniversityJinanChina
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
| | - Sakiko Yaegashi
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
- Department of Civil and Environmental EngineeringUniversity of YamanashiYamanashiJapan
| | | | - Maribet Gamboa
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
| | - Ming‐Chih Chiu
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
| | - Zongming Ren
- Insititute of Environmental and EcologyShandong Normal UniversityJinanChina
| | - Kozo Watanabe
- Department of Civil and Environmental EngineeringEhime UniversityMatsuyamaJapan
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23
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Seljestad GW, Quintela M, Faust E, Halvorsen KT, Besnier F, Jansson E, Dahle G, Knutsen H, André C, Folkvord A, Glover KA. "A cleaner break": Genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse ( Labrus bergylta). Ecol Evol 2020; 10:6120-6135. [PMID: 32607218 PMCID: PMC7319121 DOI: 10.1002/ece3.6404] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
Capture and long-distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetic structure of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain, using 82 SNP markers. We detected two very distinct genetic groups in Scandinavia, northwestern and southeastern. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat discontinuity for this rocky shore associated benthic egg-laying species. Wrasse from Galicia were highly differentiated from all Scandinavian locations, but more similar to northwestern than southeastern locations. Distinct genetic differences were observed between sympatric spotty and plain phenotypes in Galicia, but not in Scandinavia. The mechanisms underlying the geographic patterns between phenotypes are discussed, but not identified. We conclude that extensive aquaculture-mediated translocation of ballan wrasse from Sweden and southern Norway to western and middle Norway has the potential to mix genetically distinct populations. These results question the sustainability of the current cleaner fish practice.
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Affiliation(s)
- Gaute W. Seljestad
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
| | | | - Ellika Faust
- Department of Marine Sciences—TjärnöUniversity of GothenburgStrömstadSweden
| | - Kim T. Halvorsen
- Institute of Marine ResearchAustevoll Research StationStorebøNorway
| | | | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Halvor Knutsen
- Institute of Marine ResearchFlødevigenNorway
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
| | - Carl André
- Department of Marine Sciences—TjärnöUniversity of GothenburgStrömstadSweden
| | - Arild Folkvord
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
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24
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Austrich A, Mora MS, Mapelli FJ, Fameli A, Kittlein MJ. Influences of landscape characteristics and historical barriers on the population genetic structure in the endangered sand-dune subterranean rodent Ctenomys australis. Genetica 2020; 148:149-164. [PMID: 32451787 DOI: 10.1007/s10709-020-00096-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/20/2020] [Indexed: 11/29/2022]
Abstract
Understanding the processes and patterns of local adaptation and migration involves an exhaustive knowledge of how landscape features and population distances shape the genetic variation at the geographical level. Ctenomys australis is an endangered subterranean rodent characterized by having a restricted geographic range immerse in a highly fragmented sand dune landscape in the Southeast of Buenos Aires province, Argentina. We use 13 microsatellite loci in a total of 194 individuals from 13 sampling sites to assess the dispersal patterns and population structure in the complete geographic range of this endemic species. Our analyses show that populations are highly structured with low rates of gene flow among them. Genetic differentiation among sampling sites was consistent with an isolation by distance pattern, however, an important fraction of the population differentiation was explained by natural barriers such as rivers and streams. Although the individuals were sampled at locations distanced from each other, we also use some landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. These analyses showed that the sand dune habitat availability (the most suitable habitat for the occupation of the species), was one of the main factors that explained the differentiation patterns of the different sampling sites located on both sides of the Quequén Salado River. Finally, habitat availability was directly associated with the width of the sand dune landscape in the Southeast of Buenos Aires province, finding the greatest genetic differentiation among the populations of the Northeast, where this landscape is narrower.
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Affiliation(s)
- Ailin Austrich
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina.
| | - Matías S Mora
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina
| | - Fernando J Mapelli
- Grupo de Genética y Ecología Para la Conservación de la Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Alberto Fameli
- Grupo de Genética y Ecología Para la Conservación de la Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Marcelo J Kittlein
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina
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25
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Chybicki IJ, Iszkuło G, Suszka J. Bayesian quantification of ecological determinants of outcrossing in natural plant populations: Computer simulations and the case study of biparental inbreeding in English yew. Mol Ecol 2019; 28:4077-4096. [DOI: 10.1111/mec.15195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Igor J. Chybicki
- Department of Genetics Kazimierz Wielki University Bydgoszcz Poland
| | - Grzegorz Iszkuło
- Institute of Dendrology Polish Academy of Sciences Kórnik Poland
- Faculty of Biological Sciences University of Zielona Góra Zielona Góra Poland
| | - Jan Suszka
- Institute of Dendrology Polish Academy of Sciences Kórnik Poland
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26
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Grummer JA, Beheregaray LB, Bernatchez L, Hand BK, Luikart G, Narum SR, Taylor EB. Aquatic Landscape Genomics and Environmental Effects on Genetic Variation. Trends Ecol Evol 2019; 34:641-654. [DOI: 10.1016/j.tree.2019.02.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 01/17/2023]
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27
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Cossu P, Scarpa F, Sanna D, Lai T, Dedola GL, Curini-Galletti M, Mura L, Fois N, Casu M. Influence of genetic drift on patterns of genetic variation: The footprint of aquaculture practices in Sparus aurata (Teleostei: Sparidae). Mol Ecol 2019; 28:3012-3024. [PMID: 31125994 DOI: 10.1111/mec.15134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/30/2022]
Abstract
Aquaculture finfish production based on floating cage technology has raised increasing concerns regarding the genetic integrity of natural populations. Accidental mass escapes can induce the loss of genetic diversity in wild populations by increasing genetic drift and inbreeding. Farm escapes probably represent an important issue in the gilthead sea bream (Sparus aurata), which accounted for 76.4% of total escapees recorded in Europe during a 3-year survey. Here, we investigated patterns of genetic variation in farmed and wild populations of gilthead sea bream from the Western Mediterranean, a region of long gilthead sea bream farming. We focused on the role that genetic drift may play in shaping these patterns. Results based on microsatellite markers matched those observed in previous studies. Farmed populations showed lower levels of genetic diversity than wild populations and were genetically divergent from their wild counterparts. Overall, farmed populations showed the smallest effective population size and increased levels of relatedness compared to wild populations. The small broodstock size coupled with breeding practices that may favour the variance in individual reproductive success probably boosted genetic drift. This factor appeared to be a major driver of the genetic patterns observed in the gilthead sea bream populations analysed in the present study. These results further stress the importance of recommendations aimed at maintaining broodstock sizes as large as possible and equal sex-ratios among breeders, as well as avoiding unequal contributions among parents.
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Affiliation(s)
- Piero Cossu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Fabio Scarpa
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tiziana Lai
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Gian Luca Dedola
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Marco Curini-Galletti
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Laura Mura
- AGRIS Sardegna, Servizio Ricerca Prodotti Ittici, Olmedo, Italy
| | - Nicola Fois
- AGRIS Sardegna, Servizio Ricerca Prodotti Ittici, Olmedo, Italy
| | - Marco Casu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
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28
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Sertse D, You FM, Ravichandran S, Cloutier S. The genetic structure of flax illustrates environmental and anthropogenic selections that gave rise to its eco-geographical adaptation. Mol Phylogenet Evol 2019; 137:22-32. [PMID: 30978393 DOI: 10.1016/j.ympev.2019.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 01/15/2023]
Abstract
Flax, one of the eight founder crops of agriculture, has been cultivated for its oil and/or fiber for millennia. Understanding genetic divergence and geographic origins of germplasm in line with their cultivation history and ecological adaptation are essential for conservation and breeding. Here we performed a genome-wide assessment based on more than 51,000 single nucleotide polymorphic sites defining 383 flax accessions from a core collection representing 37 flax growing countries. Population structure analysis resulted in a total of 12 populations that were pooled into four major groups: Temperate, South Asian, Abyssinian and Mediterranean. The vast majority (n = 335) belonged to the Temperate group that comprised eight populations including one dominated by fiber flax. Genetic variation between fiber and oil morphotypes was less pronounced than variation within morphotypes. The genetic variation among groups and populations was attributed in part to eco-geographic and anthropogenic factors. Genetic signatures indicated loci under strong selection by environmental factors such as day length. A high concentration of private haplotypes were observed in the South Asian, Mediterranean and Abyssinian populations despite their low genotype representation, hinting at the long history of the crop in these regions. The addition of genotypes from these three regions would enrich the core collection by capturing a wider genetic breadth for breeding and conservation.
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Affiliation(s)
- Demissew Sertse
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Frank M You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada.
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29
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Rodríguez-Zárate CJ, Sandoval-Castillo J, van Sebille E, Keane RG, Rocha-Olivares A, Urteaga J, Beheregaray LB. Isolation by environment in the highly mobile olive ridley turtle ( Lepidochelys olivacea) in the eastern Pacific. Proc Biol Sci 2019; 285:rspb.2018.0264. [PMID: 29720414 DOI: 10.1098/rspb.2018.0264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/10/2018] [Indexed: 11/12/2022] Open
Abstract
Spatial and temporal scales at which processes modulate genetic diversity over the landscape are usually overlooked, impacting the design of conservation management practices for widely distributed species. We examine processes shaping population divergence in highly mobile species by re-assessing the case of panmixia in the iconic olive ridley turtle from the eastern Pacific. We implemented a biophysical model of connectivity and a seascape genetic analysis based on nuclear DNA variation of 634 samples collected from 27 nesting areas. Two genetically distinct populations largely isolated during reproductive migrations and mating were detected, each composed of multiple nesting sites linked by high connectivity. This pattern was strongly associated with a steep environmental gradient and also influenced by ocean currents. These findings relate to meso-scale features of a dynamic oceanographic interface in the eastern tropical Pacific (ETP) region, a scenario that possibly provides different cost-benefit solutions and selective pressures for sea turtles during both the mating and migration periods. We reject panmixia and propose a new paradigm for olive ridley turtles where reproductive isolation due to assortative mating is linked to its environment. Our study demonstrates the relevance of integrative approaches for assessing the role of environmental gradients and oceanographic currents as drivers of genetic differentiation in widely distributed marine species. This is relevant for the conservation management of species of highly mobile behaviour, and assists the planning and development of large-scale conservation strategies for the threatened olive ridley turtles in the ETP.
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Affiliation(s)
| | | | - Erik van Sebille
- Institute for Marine and Atmospheric Research, Utrecht University, 3584 CC, The Netherlands.,Grantham Institute and Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Robert G Keane
- Geographic Information Systems, Flinders University, Adelaide, South Adelaide 5001, Australia
| | - Axayácatl Rocha-Olivares
- Laboratorio de Ecología Molecular, Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada Baja California 22860, Mexico
| | | | - Luciano B Beheregaray
- Molecular Ecology Laboratory, Flinders University, Adelaide, South Adelaide 5001, Australia
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30
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Brauer CJ, Unmack PJ, Smith S, Bernatchez L, Beheregaray LB. On the roles of landscape heterogeneity and environmental variation in determining population genomic structure in a dendritic system. Mol Ecol 2018; 27:3484-3497. [DOI: 10.1111/mec.14808] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide South Australia Australia
| | - Peter J. Unmack
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia
| | - Steve Smith
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide South Australia Australia
- Department of Integrative Biology and Evolution University of Veterinary Medicine Vienna Austria
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec Québec Quebec Canada
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide South Australia Australia
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31
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Importance of landscape features and fire refuges on genetic diversity of Thuya occidentalis L., in boreal fire dominated landscapes. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1091-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Jackson JM, Pimsler ML, Oyen KJ, Koch‐Uhuad JB, Herndon JD, Strange JP, Dillon ME, Lozier JD. Distance, elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude. Mol Ecol 2018; 27:2926-2942. [DOI: 10.1111/mec.14735] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Jason M. Jackson
- Department of Biological Sciences The University of Alabama Tuscaloosa Alabama
| | - Meaghan L. Pimsler
- Department of Biological Sciences The University of Alabama Tuscaloosa Alabama
| | - Kennan Jeannet Oyen
- Department of Zoology & Physiology and Program in Ecology University of Wyoming Laramie Wyoming
| | - Jonathan B. Koch‐Uhuad
- Tropical Conservation Biology & Environmental Science Graduate Program Department of Biology University of Hawaii at Hilo Hilo Hawaii
| | - James D. Herndon
- USDA‐ARS Pollinating Insect Research Unit Utah State University Logan Utah
| | - James P. Strange
- USDA‐ARS Pollinating Insect Research Unit Utah State University Logan Utah
| | - Michael E. Dillon
- Department of Zoology & Physiology and Program in Ecology University of Wyoming Laramie Wyoming
| | - Jeffrey D. Lozier
- Department of Biological Sciences The University of Alabama Tuscaloosa Alabama
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33
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Islam MRU, Schmidt DJ, Crook DA, Hughes JM. Patterns of genetic structuring at the northern limits of the Australian smelt ( Retropinna semoni) cryptic species complex. PeerJ 2018; 6:e4654. [PMID: 29736331 PMCID: PMC5936633 DOI: 10.7717/peerj.4654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 03/31/2018] [Indexed: 11/20/2022] Open
Abstract
Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S FST = 0.13; SEQ-N FST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units along south east Queensland to guide future conservation management. The present findings at least can assist managers to plan for effective conservation and management of different fish species along coastal drainages of south east Queensland, Australia.
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Affiliation(s)
- Md Rakeb-Ul Islam
- Australian Rivers Institute, Griffith University, Brisbane, Australia
| | - Daniel J Schmidt
- Australian Rivers Institute, Griffith University, Brisbane, Australia
| | - David A Crook
- Research Institute for Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Brisbane, Australia
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34
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Leydet KP, Grupstra CGB, Coma R, Ribes M, Hellberg ME. Host-targeted RAD-Seq reveals genetic changes in the coralOculina patagonicaassociated with range expansion along the Spanish Mediterranean coast. Mol Ecol 2018; 27:2529-2543. [DOI: 10.1111/mec.14702] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Karine Posbic Leydet
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
| | - Carsten G. B. Grupstra
- Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam The Netherlands
- Institut de Ciències del mar; Barcelona Spain
| | - Rafel Coma
- Centre d'Estudis Avançats de Blanes; Blanes Girona Spain
| | - Marta Ribes
- Institut de Ciències del mar; Barcelona Spain
| | - Michael E. Hellberg
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
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35
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Cao YN, Wang IJ, Chen LY, Ding YQ, Liu LX, Qiu YX. Inferring spatial patterns and drivers of population divergence of Neolitsea sericea (Lauraceae), based on molecular phylogeography and landscape genomics. Mol Phylogenet Evol 2018; 126:162-172. [PMID: 29678646 DOI: 10.1016/j.ympev.2018.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 03/02/2018] [Accepted: 04/09/2018] [Indexed: 11/24/2022]
Abstract
The relative roles of geography, climate and ecology in driving population divergence and (incipient) speciation has so far been largely neglected in studies addressing the evolution of East Asia's island flora. Here, we employed chloroplast and ribosomal DNA sequences and restriction site-associated DNA sequencing (RADseq) loci to investigate the phylogeography and drivers of population divergence of Neolitsea sericea. These data sets support the subdivision of N. sericea populations into the Southern and Northern lineages across the 'Tokara gap'. Two distinct sublineages were further identified for the Northern lineage of N. sericea from the RADseq data. RADseq was also used along with approximate Bayesian computation to show that the current distribution and differentiation of N. sericea populations resulted from a combination of relatively ancient migration and successive vicariant events that likely occurred during the mid to late Pleistocene. Landscape genomic analyses showed that, apart from geographic barriers, barrier, potentially local adaptation to different climatic conditions appears to be one of the major drivers for lineage diversification of N. sericea.
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Affiliation(s)
- Ya-Nan Cao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Lu-Yao Chen
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan-Qian Ding
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lu-Xian Liu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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36
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Underwood JN, Richards ZT, Miller KJ, Puotinen ML, Gilmour JP. Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral. Mol Ecol 2018; 27:1586-1602. [DOI: 10.1111/mec.14559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/22/2018] [Accepted: 02/24/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Jim N. Underwood
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Zoe T. Richards
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Aquatic Zoology Western Australian Museum Perth WA Australia
| | - Karen J. Miller
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Marji L. Puotinen
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - James P. Gilmour
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
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37
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Constandinou S, Nikoloudakis N, Kyratzis AC, Katsiotis A. Genetic diversity of Avena ventricosa populations along an ecogeographical transect in Cyprus is correlated to environmental variables. PLoS One 2018. [PMID: 29529086 PMCID: PMC5846772 DOI: 10.1371/journal.pone.0193885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Avena ventricosa Balansa ex Coss. is considered the C-genome donor of the cultivated hexaploid oat and is a ‘priority’ species for conservation, since it has limited geographic distribution and the only recorded populations in Europe are present in Cyprus. The current study attempts to characterize the genetic structure and fragmentation of the species via the application of genotypic markers. It was revealed that the genetic variety was mainly allocated among the populations collected, since clustering obtained was according to the geographic origin of the samples and the habitat. Species distribution modeling showed that the most important climatic variable defining A. ventricosa distribution is the mean diurnal temperature. Furthermore, significant association of the genetic structure to environmental variables was detected; overall, a negative association to precipitation was confirmed, while significant correlations of genetic structure and the temperature at the time of anthesis and germination were established. The safeguarding of this valuable genetic resource is discussed.
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Affiliation(s)
- Stella Constandinou
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Athinon and Anexartisias 57, Limassol, Cyprus
| | - Nikolaos Nikoloudakis
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Athinon and Anexartisias 57, Limassol, Cyprus
| | - Angelos C. Kyratzis
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Athinon and Anexartisias 57, Limassol, Cyprus
- Department of Vegetable Crops, Agricultural Research Institute, Nicosia, Cyprus, Nicosia, Cyprus
| | - Andreas Katsiotis
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Athinon and Anexartisias 57, Limassol, Cyprus
- * E-mail:
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Couvray S, Coupé S. Three-year monitoring of genetic diversity reveals a micro-connectivity pattern and local recruitment in the broadcast marine species Paracentrotus lividus. Heredity (Edinb) 2017; 120:110-124. [PMID: 29180717 DOI: 10.1038/s41437-017-0013-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/14/2017] [Accepted: 09/23/2017] [Indexed: 12/20/2022] Open
Abstract
In conservation and management of marine biological resources, a knowledge of connectivity is necessary to understand how local populations are naturally replenished by the arrival of new recruits from source populations. At small geographical scales, species experiencing moderate to long pelagic larval phases are mostly genetically homogeneous, which hinders inferences about local connectivity. Recent studies demonstrated that assessing genetic relatedness and kinship could provide information about local connectivity in populations with high levels of gene flow. Here, we were interested in deciphering the structure and connectivity of populations of the sea urchin Paracentrotus lividus, by monitoring populations at 11 localities distributed along a 225-km coast-line in the south-eastern French Mediterranean Sea. Using 12 microsatellite loci, we found a weak but significant genetic differentiation and observed a transient genetic differentiation among locations within temporal cohorts, without any correlation with the distance between locations, interpreted as unexplainable chaotic genetic patchiness. Among temporal cohorts, the more related individuals were mainly found within locations and the observed local differentiation (FST) correlated with the proportion of kin within locations, suggesting that larvae dispersed cohesively. Specifically, we could also reveal that populations flanking Cape Sicié were influenced by eastern populations and that local recruitment was a frequent occurrence. Overall, our results contribute to the growing number of studies showing that connectivity can be reliably assessed at a fine spatial scale even in genetically homogenous populations.
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Affiliation(s)
- Sylvain Couvray
- Institut Océanographique Paul Ricard, Ile des Embiez, 83140, Six-Fours-Les-Plages, France
| | - Stéphane Coupé
- Univ Toulon, Aix Marseille Univ, CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, La Garde, France.
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39
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Strugnell JM, Allcock AL, Watts PC. Closely related octopus species show different spatial genetic structures in response to the Antarctic seascape. Ecol Evol 2017; 7:8087-8099. [PMID: 29043058 PMCID: PMC5632630 DOI: 10.1002/ece3.3327] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/18/2017] [Accepted: 07/23/2017] [Indexed: 01/28/2023] Open
Abstract
Determining whether comparable processes drive genetic divergence among marine species is relevant to molecular ecologists and managers alike. Sympatric species with similar life histories might be expected to show comparable patterns of genetic differentiation and a consistent influence of environmental factors in shaping divergence. We used microsatellite loci to quantify genetic differentiation across the Scotia Arc in three species of closely related benthic octopods, Pareledone turqueti, P. charcoti, and Adelieledone polymorpha. The relative importance of environmental factors (latitude, longitude, depth, and temperature) in shaping genetic structure was investigated when significant spatial genetic structure was uncovered. Isolated populations of P. turqueti and A. polymorpha at these species' range margins were genetically different to samples close to mainland Antarctica; however, these species showed different genetic structures at a regional scale. Samples of P. turqueti from the Antarctic Peninsula, Elephant Island, and Signy Island were genetically different, and this divergence was associated primarily with sample collection depth. By contrast, weak or nonsignificant spatial genetic structure was evident across the Antarctic Peninsula, Elephant Island, and Signy Island region for A. polymorpha, and slight associations between population divergence and temperature or depth (and/or longitude) were detected. Pareledone charcoti has a limited geographic range, but exhibited no genetic differentiation between samples from a small region of the Scotia Arc (Elephant Island and the Antarctic Peninsula). Thus, closely related species with similar life history strategies can display contrasting patterns of genetic differentiation depending on spatial scale; moreover, depth may drive genetic divergence in Southern Ocean benthos.
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Affiliation(s)
- Jan M. Strugnell
- Centre for Sustainable Tropical Fisheries and AquacultureMarine Biology and Aquaculture James Cook UniversityTownsvilleQldAustralia
- Department of Ecology, Environment and EvolutionSchool of Life SciencesLa Trobe UniversityMelbourneVic.Australia
| | - A. Louise Allcock
- Ryan Institute and School of Natural SciencesNational University of Ireland GalwayGalwayIreland
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Mora MS, Mapelli FJ, López A, Gómez Fernández MJ, Mirol PM, Kittlein MJ. Landscape genetics in the subterranean rodent Ctenomys "chasiquensis" associated with highly disturbed habitats from the southeastern Pampas region, Argentina. Genetica 2017; 145:575-591. [PMID: 28905157 DOI: 10.1007/s10709-017-9983-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 09/07/2017] [Indexed: 11/29/2022]
Abstract
Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci. We use landscape genetics approaches to assess the relationship between genetic connectivity among populations and environmental attributes. Our analyses show that populations of C. "chasiquensis" are moderately to highly structured at a regional level. This pattern is most likely the outcome of substantial gene flow on the more homogeneous sand dune habitat of the Northwest of its distributional range, in conjunction with an important degree of isolation of eastern and southwestern populations, where the optimal habitat is surrounded by a highly fragmented landscape. Landscape genetics analysis suggests that habitat quality and longitude were the environmental factors most strongly associated with genetic differentiation/uniqueness of populations. In conclusion, our results indicate an important genetic structure in this species, even at a small spatial scale, suggesting that contemporary habitat fragmentation increases population differentiation.
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Affiliation(s)
- Matías Sebastián Mora
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina.
| | - Fernando J Mapelli
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina
| | - Aldana López
- Área de Recursos Naturales, CONICET INTA EEA Bariloche, CC 277 8400, Bariloche, Río Negro, Argentina
| | - María Jimena Gómez Fernández
- Grupo de Genética y Ecología en Conservación y Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Patricia M Mirol
- Grupo de Genética y Ecología en Conservación y Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Marcelo J Kittlein
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Universidad Nacional de Mar del Plata, Funes 3250, 3rd floor, 7600, Mar del Plata, Argentina
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41
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Sylvester EVA, Bentzen P, Bradbury IR, Clément M, Pearce J, Horne J, Beiko RG. Applications of random forest feature selection for fine-scale genetic population assignment. Evol Appl 2017; 11:153-165. [PMID: 29387152 PMCID: PMC5775496 DOI: 10.1111/eva.12524] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 07/11/2017] [Indexed: 01/10/2023] Open
Abstract
Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine‐learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with FST ranking for selection of single nucleotide polymorphisms (SNP) for fine‐scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self‐assignment accuracy of at least 90% using each method to create panels of 50–700 markers Panels of SNPs identified using random forest‐based methods performed up to 7.8 and 11.2 percentage points better than FST‐selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self‐assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using FST‐selected panels. Our results demonstrate a role for machine‐learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.
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Affiliation(s)
| | - Paul Bentzen
- Marine Gene Probe Laboratory Department of Biology Dalhousie University Halifax NS Canada
| | | | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute Memorial University of Newfoundland St. John's NL Canada.,Labrador Institute Memorial University of Newfoundland Happy Valley-Goose Bay NL Canada
| | - Jon Pearce
- Northern SE Regional Aquaculture Association Hidden Falls Hatchery Sitka AK USA
| | - John Horne
- Marine Gene Probe Laboratory Department of Biology Dalhousie University Halifax NS Canada
| | - Robert G Beiko
- Faculty of Computer Science Dalhousie University Halifax NS Canada
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42
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Herrera CM, Medrano M, Bazaga P. Comparative epigenetic and genetic spatial structure of the perennial herb Helleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence. AMERICAN JOURNAL OF BOTANY 2017; 104:1195-1204. [PMID: 28814406 DOI: 10.3732/ajb.1700162] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Epigenetic variation can play a role in local adaptation; thus, there should be associations among epigenetic variation, environmental variation, and functional trait variation across populations. This study examines these relationships in the perennial herb Helleborus foetidus (Ranunculaceae). METHODS Plants from 10 subpopulations were characterized genetically (AFLP, SSR markers), epigenetically (MSAP markers), and phenotypically (20 functional traits). Habitats were characterized using six environmental variables. Isolation-by-distance (IBD) and isolation-by-environment (IBE) patterns of genetic and epigenetic divergence were assessed, as was the comparative explanatory value of geographical and environmental distance as predictors of epigenetic, genetic, and functional differentiation. KEY RESULTS Subpopulations were differentiated genetically, epigenetically, and phenotypically. Genetic differentiation was best explained by geographical distance, while epigenetic differentiation was best explained by environmental distance. Divergence in functional traits was correlated with environmental and epigenetic distances, but not with geographical and genetic distances. CONCLUSIONS Results are compatible with the hypothesis that epigenetic IBE and functional divergence reflected responses to environmental variation. Spatial analyses simultaneously considering epigenetic, genetic, phenotypic and environmental information provide a useful tool to evaluate the role of environmental features as drivers of natural epigenetic variation between populations.
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Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 26, 41092 Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 26, 41092 Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 26, 41092 Sevilla, Spain
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43
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Termignoni-García F, Jaramillo-Correa JP, Chablé-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante-Pliego P. Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient. Mol Ecol 2017; 26:4483-4496. [DOI: 10.1111/mec.14224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 05/06/2017] [Accepted: 06/12/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Flavia Termignoni-García
- Department of Zoology; National Collection of Birds (CNAV); Institute of Biology; Universidad Nacional Autónoma de México; CdMx México
| | - Juan P. Jaramillo-Correa
- Department of Evolutionary Ecology; Institute of Ecology; Universidad Nacional Autónoma de México; CdMx México
| | - Juan Chablé-Santos
- Department of Zoology; Facultad de Medicina Veterinaria y Zootecnia; Universidad Autónoma de Yucatán; Yucatán México
| | - Mark Liu
- Biodiversity Research Center; Academia Sinica; Taipei Nankang Taiwan
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology (OEB); Harvard University; Cambridge MA USA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology (OEB); Harvard University; Cambridge MA USA
| | - Patricia Escalante-Pliego
- Department of Zoology; National Collection of Birds (CNAV); Institute of Biology; Universidad Nacional Autónoma de México; CdMx México
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44
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Nair A, Fountain T, Ikonen S, Ojanen SP, van Nouhuys S. Spatial and temporal genetic structure at the fourth trophic level in a fragmented landscape. Proc Biol Sci 2017; 283:rspb.2016.0668. [PMID: 27226470 DOI: 10.1098/rspb.2016.0668] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/28/2016] [Indexed: 11/12/2022] Open
Abstract
A fragmented habitat becomes increasingly fragmented for species at higher trophic levels, such as parasitoids. To persist, these species are expected to possess life-history traits, such as high dispersal, that facilitate their ability to use resources that become scarce in fragmented landscapes. If a specialized parasitoid disperses widely to take advantage of a sparse host, then the parasitoid population should have lower genetic structure than the host. We investigated the temporal and spatial genetic structure of a hyperparasitoid (fourth trophic level) in a fragmented landscape over 50 × 70 km, using microsatellite markers, and compared it with the known structures of its host parasitoid, and the butterfly host which lives as a classic metapopulation. We found that population genetic structure decreases with increasing trophic level. The hyperparasitoid has fewer genetic clusters (K = 4), than its host parasitoid (K = 15), which in turn is less structured than the host butterfly (K = 27). The genetic structure of the hyperparasitoid also shows temporal variation, with genetic differentiation increasing due to reduction of the population size, which reduces the effective population size. Overall, our study confirms the idea that specialized species must be dispersive to use a fragmented host resource, but that this adaptation has limits.
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Affiliation(s)
- Abhilash Nair
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - Toby Fountain
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - Suvi Ikonen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - Sami P Ojanen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - Saskya van Nouhuys
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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45
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Crisci C, Ledoux JB, Mokhtar-Jamaï K, Bally M, Bensoussan N, Aurelle D, Cebrian E, Coma R, Féral JP, La Rivière M, Linares C, López-Sendino P, Marschal C, Ribes M, Teixidó N, Zuberer F, Garrabou J. Regional and local environmental conditions do not shape the response to warming of a marine habitat-forming species. Sci Rep 2017; 7:5069. [PMID: 28698582 PMCID: PMC5505982 DOI: 10.1038/s41598-017-05220-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/25/2017] [Indexed: 11/20/2022] Open
Abstract
The differential response of marine populations to climate change remains poorly understood. Here, we combine common garden thermotolerance experiments in aquaria and population genetics to disentangle the factors driving the population response to thermal stress in a temperate habitat-forming species: the octocoral Paramuricea clavata. Using eight populations separated from tens of meters to hundreds of kilometers, which were differentially impacted by recent mortality events, we identify 25 °C as a critical thermal threshold. After one week of exposure at this temperature, seven of the eight populations were affected by tissue necrosis and after 30 days of exposure at this temperature, the mean % of affected colonies increased gradually from 3 to 97%. We then demonstrate the weak relation between the observed differential phenotypic responses and the local temperature regimes experienced by each population. A significant correlation was observed between these responses and the extent of genetic drift impacting each population. Local adaptation may thus be hindered by genetic drift, which seems to be the main driver of the differential response. Accordingly, conservation measures should promote connectivity and control density erosion in order to limit the impact of genetic drift on marine populations facing climate change.
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Affiliation(s)
- C Crisci
- Polo de Desarrollo Universitario Modelización y Análisis de Recursos Naturales, Centro Universitario Regional del Este, Universidad de la República, Rocha, 27000, Uruguay.
| | - J-B Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, 4050-123, Portugal
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - K Mokhtar-Jamaï
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M Bally
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
| | - N Bensoussan
- IPSO FACTO, SCOPArl, Pole Océanologie, Marseille, 13001, France
| | - D Aurelle
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - E Cebrian
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, 17300, Spain
- Departament de Ciències Ambientals, Facultat de Ciències, Universitat de Girona, Girona, 17071, Spain
| | - R Coma
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, 17300, Spain
| | - J-P Féral
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M La Rivière
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
| | - C Linares
- Departament d'Ecologia, Universitat de Barcelona, Barcelona, 08028, Spain
| | - P López-Sendino
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - C Marschal
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M Ribes
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - N Teixidó
- Stazione Zoologica Anton Dohrn, Villa Dohrn-Benthic Ecology Center, Punta San Pietro, Ischia, Naples, 80077, Italy
| | - F Zuberer
- Institut Pytheas, UMS 3470, CNRS, Marseille, 13013, France
| | - J Garrabou
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
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46
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Watanabe K, Monaghan MT. Comparative tests of the species-genetic diversity correlation at neutral and nonneutral loci in four species of stream insect. Evolution 2017; 71:1755-1764. [PMID: 28485820 DOI: 10.1111/evo.13261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 03/29/2017] [Accepted: 04/16/2017] [Indexed: 11/30/2022]
Abstract
A fundamental question linking population genetics and community ecology is how adaptive processes (e.g., natural selection) and neutral processes (e.g., drift-migration equilibrium) underpin the species-genetic diversity correlation (SGDC). Here, we combine genome scans and outlier loci detection with community analysis to separately test for neutral and nonneutral SGDCs in four species of stream insect. We sampled 60 localities in Japan and examined the relationships among population AFLP band richness (Br), taxon richness of the total community (S) and of the trophic guild (Str ), and 15 habitat parameters that could potentially drive adaptation and influence richness. Neutral Br was positively correlated with S only in the dominant species of these communities, suggesting Br may be constrained when intraspecific competition is pronounced. Nonneutral Br was correlated with Str in a species restricted to high elevations where habitat heterogeneity was highest. Community distance and genetic distance (β-SGDC) was correlated in two of the four species at both neutral and nonneutral loci. Distance-based redundancy analysis found geographic isolation and elevation to drive divergence of both communities and populations. This suggests that both neutral and adaptive divergence occurred through the shared influences of geographic isolation and local adaptation at the two levels of diversity.
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Affiliation(s)
- Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, 14195, Berlin, Germany
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47
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Delêtre M, Soengas B, Vidaurre PJ, Meneses RI, Delgado Vásquez O, Oré Balbín I, Santayana M, Heider B, Sørensen M. Ecotypic differentiation under farmers' selection: Molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes. Evol Appl 2017; 10:498-513. [PMID: 28515782 PMCID: PMC5427675 DOI: 10.1111/eva.12472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/21/2017] [Indexed: 11/30/2022] Open
Abstract
Understanding the distribution of crop genetic diversity in relation to environmental factors can give insights into the eco‐evolutionary processes involved in plant domestication. Yam beans (Pachyrhizus Rich. ex DC.) are leguminous crops native to South and Central America that are grown for their tuberous roots but are seed‐propagated. Using a landscape genetic approach, we examined correlations between environmental factors and phylogeographic patterns of genetic diversity in Pachyrhizus landrace populations. Molecular analyses based on chloroplast DNA sequencing and a new set of nuclear microsatellite markers revealed two distinct lineages, with strong genetic differentiation between Andean landraces (lineage A) and Amazonian landraces (lineage B). The comparison of different evolutionary scenarios for the diversification history of yam beans in the Andes using approximate Bayesian computation suggests that Pachyrhizus ahipa and Pachyrhizus tuberosus share a progenitor‐derivative relationship, with environmental factors playing an important role in driving selection for divergent ecotypes. The new molecular data call for a revision of the taxonomy of Pachyrhizus but are congruent with paleoclimatic and archeological evidence, and suggest that selection for determinate growth was part of ecophysiological adaptations associated with the diversification of the P. tuberosus–P. ahipa complex during the Mid‐Holocene.
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Affiliation(s)
- Marc Delêtre
- Département Hommes, Natures, Sociétés Muséum National d'Histoire Naturelle Paris France
| | - Beatriz Soengas
- Département Hommes, Natures, Sociétés Muséum National d'Histoire Naturelle Paris France
| | - Prem Jai Vidaurre
- Instituto de Ecologia Universidad Mayor de San Andrés Herbario Nacional de Bolivia La Paz Bolivia.,Museo Nacional de Historia Natural Unidad de Botánica La Paz Bolivia
| | - Rosa Isela Meneses
- Instituto de Ecologia Universidad Mayor de San Andrés Herbario Nacional de Bolivia La Paz Bolivia.,Museo Nacional de Historia Natural Unidad de Botánica La Paz Bolivia
| | | | - Isabel Oré Balbín
- Programa de Investigaciones para el Aprovechamiento Sostenible de la Biodiversidad Instituto de Investigaciones de la Amazonía Peruana Iquitos Perú
| | - Monica Santayana
- Genetics, Genomics and Crop Improvement International Potato Center (CIP) Lima Perú
| | - Bettina Heider
- Genetics, Genomics and Crop Improvement International Potato Center (CIP) Lima Perú
| | - Marten Sørensen
- Department of Plant and Environmental Sciences Kobenhavns Universitet Frederiksberg Denmark
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48
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Meyer L, Causse R, Pernin F, Scalone R, Bailly G, Chauvel B, Délye C, Le Corre V. New gSSR and EST-SSR markers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L. and can be transferred to other invasive Ambrosia species. PLoS One 2017; 12:e0176197. [PMID: 28489870 PMCID: PMC5425025 DOI: 10.1371/journal.pone.0176197] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 04/06/2017] [Indexed: 11/23/2022] Open
Abstract
Ambrosia artemisiifolia L., (common ragweed), is an annual invasive and highly troublesome plant species originating from North America that has become widespread across Europe. New sets of genomic and expressed sequence tag (EST) based simple sequence repeats (SSRs) markers were developed in this species using three approaches. After validation, 13 genomic SSRs and 13 EST-SSRs were retained and used to characterize the genetic diversity and population genetic structure of Ambrosia artemisiifolia populations from the native (North America) and invasive (Europe) ranges of the species. Analysing the mating system based on maternal families did not reveal any departure from complete allogamy and excess homozygosity was mostly due the presence of null alleles. High genetic diversity and patterns of genetic structure in Europe suggest two main introduction events followed by secondary colonization events. Cross-species transferability of the newly developed markers to other invasive species of the Ambrosia genus was assessed. Sixty-five percent and 75% of markers, respectively, were transferable from A. artemisiifolia to Ambrosia psilostachya and Ambrosia tenuifolia. 40% were transferable to Ambrosia trifida, this latter species being seemingly more phylogenetically distantly related to A. artemisiifolia than the former two.
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Affiliation(s)
- Lucie Meyer
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Romain Causse
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Fanny Pernin
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Romain Scalone
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Géraldine Bailly
- Sustainable Agriculture Department, BASF France SAS, Ecully, France
| | - Bruno Chauvel
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Christophe Délye
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Valérie Le Corre
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
- * E-mail:
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Lean J, Hammer MP, Unmack PJ, Adams M, Beheregaray LB. Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system. Heredity (Edinb) 2017; 118:374-384. [PMID: 27876805 PMCID: PMC5345605 DOI: 10.1038/hdy.2016.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 11/09/2022] Open
Abstract
Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray-Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity-a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.
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Affiliation(s)
- J Lean
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - M P Hammer
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia, Australia
- Curator of Fishes, Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - P J Unmack
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - M Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - L B Beheregaray
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
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Gaggiotti OE. Metapopulations of Marine Species with Larval Dispersal: A Counterpoint to Ilkka's Glanville Fritillary Metapopulations. ANN ZOOL FENN 2017. [DOI: 10.5735/086.054.0110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Oscar E. Gaggiotti
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, Fife KY16 8LB, UK
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