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Van Der Wal C, Ahyong ST, Adams MWD, Ewart KM, Ho SYW, Lo N. Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Mol Phylogenet Evol 2023; 178:107629. [PMID: 36191898 DOI: 10.1016/j.ympev.2022.107629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastacus, which exhibits large variations in colour and spination throughout its putative range. To understand this variation, we investigated the genetic diversity, population structure, phylogeny, and evolutionary timescale of the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Our data set is sampled from over 70 individuals from across the ∼600 km range of the species, and includes a combination of two mitochondrial markers and more than 7000 single-nucleotide polymorphisms (SNPs) from the nuclear genome. Data were also obtained for representatives of the close relative, Euastacus vesper McCormack and Ahyong, 2017. Genomic SNP analyses revealed strong population structure, with multiple distinct populations showing little evidence of gene flow or migration. Phylogenetic analyses of mitochondrial data revealed similar structure between populations. Taken together, our analyses suggest that E. spinifer, as currently understood, represents a species complex, of which E. vesper is a member. Molecular clock estimates place the divergences within this group during the Pleistocene. The isolated and highly fragmented populations identified in our analyses probably represent relict populations of a previously widespread ancestral species. Periodic flooding events during the Pleistocene are likely to have facilitated the movement of these otherwise restricted freshwater crayfish within and between drainage basins, including the Murray-Darling and South East Coast Drainages. We present evidence supporting the recognition of populations in the southern parts of the range of E. spinifer as one or two separate species, which would raise the number of species within the E. spinifer complex to at least three. Our results add to the growing body of evidence that many freshwater crayfish exhibit highly fragmented, range-restricted distributions. In combination with the life-history traits of these species, the restricted distributions exacerbate the threats already placed on freshwater crayfish, which are among the five most endangered animal groups globally.
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Affiliation(s)
- Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia.
| | - Shane T Ahyong
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maxim W D Adams
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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Marshall IR, Brauer CJ, Wedderburn SD, Whiterod NS, Hammer MP, Barnes TC, Attard CRM, Möller LM, Beheregaray LB. Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13889. [PMID: 35023224 DOI: 10.1111/cobi.13889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Restoration programs in the form of ex-situ breeding combined with reintroductions are becoming critical to counteract demographic declines and species losses. Such programs are increasingly using genetic management to improve conservation outcomes. However, the lack of long-term monitoring of genetic indicators following reintroduction prevents assessments of the trajectory and persistence of reintroduced populations. We carried out an extensive monitoring program in the wild for a threatened small-bodied fish (southern pygmy perch, Nannoperca australis) to assess the long-term genomic effects of its captive breeding and reintroduction. The species was rescued prior to its extirpation from the terminal lakes of Australia's Murray-Darling Basin, and then used for genetically informed captive breeding and reintroductions. Subsequent annual or biannual monitoring of abundance, fitness, and occupancy over a period of 11 years, combined with postreintroduction genetic sampling, revealed survival and recruitment of reintroduced fish. Genomic analyses based on data from the original wild rescued, captive born, and reintroduced cohorts revealed low inbreeding and strong maintenance of neutral and candidate adaptive genomic diversity across multiple generations. An increasing trend in the effective population size of the reintroduced population was consistent with field monitoring data in demonstrating successful re-establishment of the species. This provides a rare empirical example that the adaptive potential of a locally extinct population can be maintained during genetically informed ex-situ conservation breeding and reintroduction into the wild. Strategies to improve biodiversity restoration via ex-situ conservation should include genetic-based captive breeding and longitudinal monitoring of standing genomic variation in reintroduced populations.
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Affiliation(s)
- Imogen R Marshall
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Scotte D Wedderburn
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Nick S Whiterod
- Aquasave-Nature Glenelg Trust, Victor Harbor, South Australia, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - Thomas C Barnes
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Nelson Bay, New South Wales, Australia
- Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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Buckley SJ, Brauer CJ, Unmack PJ, Hammer MP, Beheregaray LB. Variation in intraspecific demography drives localised concordance but species-wide discordance in response to past climatic change. BMC Ecol Evol 2022; 22:35. [PMID: 35317750 PMCID: PMC8941757 DOI: 10.1186/s12862-022-01990-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/11/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Understanding how species biology may facilitate resilience to climate change remains a critical factor in detecting and protecting species at risk of extinction. Many studies have focused on the role of particular ecological traits in driving species responses, but less so on demographic history and levels of standing genetic variation. Additionally, spatial variation in the interaction of demographic and adaptive factors may further complicate prediction of species responses to environmental change. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes, the southern (Nannoperca australis) and Yarra (N. obscura) pygmy perches, to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. We described contemporary genetic diversity, phylogenetic histories, demographic histories, and historical species distributions across both species, and statistically evaluated the degree of concordance in co-occurring populations. RESULTS Marked differences in contemporary genetic diversity, historical distribution changes and historical migration were observed across the species, with a distinct lack of genetic diversity and historical range expansion suggested for N. obscura. Although several co-occurring populations within a shared climatic refugium demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species. Discordant responses between species were associated with low standing genetic variation in peripheral populations. This might have hindered adaptive potential, as documented in recent demographic declines and population extinctions for the two species. CONCLUSION Our results highlight both the role of spatial scale in the degree of concordance in species responses to climate change, and the importance of standing genetic variation in facilitating range shifts. Even when ecological traits are similar between species, long-term genetic diversity and historical population demography may lead to discordant responses to ongoing and future climate change.
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Affiliation(s)
- Sean James Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT, 0801, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia.
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Morales‐González S, Giles EC, Quesada‐Calderón S, Saenz‐Agudelo P. Fine-scale hierarchical genetic structure and kinship analysis of the ascidian Pyura chilensis in the southeastern Pacific. Ecol Evol 2019; 9:9855-9868. [PMID: 31534699 PMCID: PMC6745665 DOI: 10.1002/ece3.5526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Studying population structure and genetic diversity at fine spatial scales is key for a better understanding of demographic processes that influence population connectivity. This is particularly important in marine benthic organisms that rely on larval dispersal to maintain connectivity among populations. Here, we report the results of a genetic survey of the ascidian Pyura chilensis from three localities along the southeastern Pacific. This study follows up on a previous report that described a genetic break in this region among localities only 20 km apart. By implementing a hierarchical sampling design at four spatial levels and using ten polymorphic microsatellite markers, we test whether differences in fine-scale population structure explain the previously reported genetic break. We compared genetic spatial autocorrelations, as well as kinship and relatedness distributions within and among localities adjacent to the genetic break. We found no evidence of significant autocorrelation at the scale up to 50 m despite the low dispersal potential of P. chilensis that has been reported in the literature. We also found that the proportion of related individuals in close proximity (<1 km) was higher than the proportion of related individuals further apart. These results were consistent in the three localities. Our results suggest that the spatial distribution of related individuals can be nonrandom at small spatial scales and suggests that dispersal might be occasionally limited in this species or that larval cohorts can disperse in the plankton as clustered groups. Overall, this study sheds light on new aspects of the life of this ascidian as well as confirms the presence of a genetic break at 39°S latitude. Also, our data indicate there is not enough evidence to confirm that this genetic break can be explained by differences in fine-scale genetic patterns among localities.
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Affiliation(s)
- Sarai Morales‐González
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Magister en Ciencias Mención GenéticaEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Emily C. Giles
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Doctorado en Ciencias Mención Ecología y EvoluciónEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Suany Quesada‐Calderón
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Doctorado en Ciencias Mención Ecología y EvoluciónEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
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Pontes PRM, Cavalcante RBL, Sahoo PK, Silva Júnior ROD, da Silva MS, Dall'Agnol R, Siqueira JO. The role of protected and deforested areas in the hydrological processes of Itacaiúnas River Basin, eastern Amazonia. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 235:489-499. [PMID: 30711834 DOI: 10.1016/j.jenvman.2019.01.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/07/2019] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
To protect indigenous land and avoid the spread of deforestation in the Amazon, state and federal Brazilian agencies recognized several protected areas since the 1990s. However, the importance of these protected areas in the water cycle and the hydrologic connection with surrounding landscapes is little analyzed. In this study, we evaluated the role of preserved and deforested areas in the water balance in the Itacaiúnas River Basin using the MGB hydrological model. We estimated the impacts of land cover changes on evapotranspiration and discharge for four scenarios: Preserved (1984 land cover), Recent (2013 land cover, with 50% deforestation), Hypothetical deforestation of protected areas (70% deforestation) and complete deforestation of protected areas (79% deforestation). We showed that deforestation of the remaining preserved area could be responsible for a decrease of 23% (3.5 km³/year) in water transfer to the atmosphere by evapotranspiration. Furthermore, we showed that each 15% of deforestation occurring between the Preserved and Recent scenarios increased the average discharges by 5.4% (40 m³/s). Additionally, past land cover changes in the headwaters of the Itacaiúnas River Basin caused statistically significant changes in discharges inside the protected areas. This insight is considered important due to the association between increases in discharges and water quality issues. The results suggest that headwater areas of secondary drainages that run into the forested domains should be prioritized for reforestation programs. Likewise, the reforestation of nonprotected areas could be responsible for restoring ecosystem services, including hydrological functions, biodiversity and water quality.
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Affiliation(s)
- Paulo R M Pontes
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Brazil.
| | | | - Prafulla K Sahoo
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Brazil
| | | | | | - Roberto Dall'Agnol
- Instituto Tecnológico Vale - Desenvolvimento Sustentável (ITV-DS), Brazil
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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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7
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Buckley SJ, Domingos FMCB, Attard CRM, Brauer CJ, Sandoval-Castillo J, Lodge R, Unmack PJ, Beheregaray LB. Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172125. [PMID: 30110415 PMCID: PMC6030323 DOI: 10.1098/rsos.172125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east-west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east-west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.
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Affiliation(s)
- Sean J. Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Fabricius M. C. B. Domingos
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso, Pontal do Araguaia, MT 78698-000, Brazil
| | - Catherine R. M. Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Chris J. Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Ryan Lodge
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Peter J. Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2601, Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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Schmidt BV, Schaefer JF. Comparative genetic isolation patterns for multiple headwater fishes in three geographic regions. JOURNAL OF FISH BIOLOGY 2018; 92:1090-1109. [PMID: 29479689 DOI: 10.1111/jfb.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Headwater-resident fishes may be prone to a high rate of isolation and a pronounced hierarchical genetic structure due to a combination of niche preference and dendritic effects of river networks. Genetic isolation patterns were compared using microsatellites in six headwater fishes, Fundulus olivaceus, Semotilus atromaculatus, Erimyzon claviformis, Etheostoma artesiae, Etheostoma whipplei and Etheostoma parvipinne, in three geographic regions that included drainages of small, medium and large sizes in the southern United States. All species showed hierarchical nesting of genetic populations and there were clear and mostly consistent differences between species and regions that were identified through summary statistics derived from two independent analyses. For species comparisons, a high isolation grouping (increased number of isolated genetic clusters or sites within regions) and a low-isolation grouping (decreased number of clusters or sites) were identified. Species group placement was related to niche breadth along the river continuum and presumed abundance and variability of preferred microhabitats, with increased headwater specialization among species being associated with placement in the high-isolation grouping. There was a weakly significant positive effect of drainage size on the number of isolated clusters or sites across all species. Regional patterns were shared in two species, with the region containing the smallest drainages having lower rates of isolation in both datasets. This study shows the effects of regional and species characteristics on genetic isolation for headwater species, which are especially prone to isolation due to spatial, dendritic effects of river networks.
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Affiliation(s)
- B V Schmidt
- The University of Southern Mississippi, 118 College Dr, Box # 5018, Hattiesburg, Mississippi 39406, U.S.A
| | - J F Schaefer
- The University of Southern Mississippi, 118 College Dr, Box # 5018, Hattiesburg, Mississippi 39406, U.S.A
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9
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Attard CRM, Brauer CJ, Sandoval-Castillo J, Faulks LK, Unmack PJ, Gilligan DM, Beheregaray LB. Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): Implications for management and resilience to climate change. Mol Ecol 2017; 27:196-215. [PMID: 29165848 DOI: 10.1111/mec.14438] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 01/01/2023]
Abstract
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia, using a genome-wide SNP data set. The MDB spans across arid to wet and temperate to subtropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.
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Affiliation(s)
- Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Leanne K Faulks
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.,Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Peter J Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Dean M Gilligan
- New South Wales Department of Primary Industries, Batemans Bay Fisheries Centre, Batemans Bay, NSW, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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Pavlova A, Beheregaray LB, Coleman R, Gilligan D, Harrisson KA, Ingram BA, Kearns J, Lamb AM, Lintermans M, Lyon J, Nguyen TTT, Sasaki M, Tonkin Z, Yen JDL, Sunnucks P. Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow. Evol Appl 2017; 10:531-550. [PMID: 28616062 PMCID: PMC5469170 DOI: 10.1111/eva.12484] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/29/2017] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity underpins the ability of populations to persist and adapt to environmental changes. Substantial empirical data show that genetic diversity rapidly deteriorates in small and isolated populations due to genetic drift, leading to reduction in adaptive potential and fitness and increase in inbreeding. Assisted gene flow (e.g. via translocations) can reverse these trends, but lack of data on fitness loss and fear of impairing population "uniqueness" often prevents managers from acting. Here, we use population genetic and riverscape genetic analyses and simulations to explore the consequences of extensive habitat loss and fragmentation on population genetic diversity and future population trajectories of an endangered Australian freshwater fish, Macquarie perch Macquaria australasica. Using guidelines to assess the risk of outbreeding depression under admixture, we develop recommendations for population management, identify populations requiring genetic rescue and/or genetic restoration and potential donor sources. We found that most remaining populations of Macquarie perch have low genetic diversity, and effective population sizes below the threshold required to retain adaptive potential. Our simulations showed that under management inaction, smaller populations of Macquarie perch will face inbreeding depression within a few decades, but regular small-scale translocations will rapidly rescue populations from inbreeding depression and increase adaptive potential through genetic restoration. Despite the lack of data on fitness loss, based on our genetic data for Macquarie perch populations, simulations and empirical results from other systems, we recommend regular and frequent translocations among remnant populations within catchments. These translocations will emulate the effect of historical gene flow and improve population persistence through decrease in demographic and genetic stochasticity. Increasing population genetic connectivity within each catchment will help to maintain large effective population sizes and maximize species adaptive potential. The approach proposed here could be readily applicable to genetic management of other threatened species to improve their adaptive potential.
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Affiliation(s)
- Alexandra Pavlova
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
| | | | - Rhys Coleman
- Applied ResearchMelbourne WaterDocklandsVICAustralia
| | - Dean Gilligan
- Freshwater Ecosystems ResearchNSW Department of Primary Industries – FisheriesBatemans BayNSWAustralia
| | - Katherine A. Harrisson
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
- Department of Ecology Environment and EvolutionSchool of Life Sciences, La Trobe UniversityBundoora, Victoria3083Australia
| | - Brett A. Ingram
- Department of Economic DevelopmentJobs, Transport and ResourcesFisheries VictoriaAlexandraVICAustralia
| | - Joanne Kearns
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Annika M. Lamb
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
| | - Mark Lintermans
- Institute for Applied EcologyUniversity of CanberraCanberraACTAustralia
| | - Jarod Lyon
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Thuy T. T. Nguyen
- Agriculture VictoriaAgriBio, Centre for AgriBioscienceBundooraVICAustralia
| | - Minami Sasaki
- School of Biological SciencesFlinders UniversityAdelaideSAAustralia
| | - Zeb Tonkin
- Department of Environment, Land Water and PlanningArthur Rylah Institute, Land, Fire and EnvironmentHeidelbergVICAustralia
| | - Jian D. L. Yen
- School of Physics and AstronomyClayton Campus, Monash UniversityClaytonVICAustralia
| | - Paul Sunnucks
- School of Biological SciencesClayton Campus, Monash UniversityClaytonVICAustralia
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11
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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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12
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Attard CRM, Möller LM, Sasaki M, Hammer MP, Bice CM, Brauer CJ, Carvalho DC, Harris JO, Beheregaray LB. A novel holistic framework for genetic-based captive-breeding and reintroduction programs. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:1060-1069. [PMID: 26892747 DOI: 10.1111/cobi.12699] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
Research in reintroduction biology has provided a greater understanding of the often limited success of species reintroductions and highlighted the need for scientifically rigorous approaches in reintroduction programs. We examined the recent genetic-based captive-breeding and reintroduction literature to showcase the underuse of the genetic data gathered. We devised a framework that takes full advantage of the genetic data through assessment of the genetic makeup of populations before (past component of the framework), during (present component), and after (future component) captive-breeding and reintroduction events to understand their conservation potential and maximize their success. We empirically applied our framework to two small fishes: Yarra pygmy perch (Nannoperca obscura) and southern pygmy perch (Nannoperca australis). Each of these species has a locally adapted and geographically isolated lineage that is endemic to the highly threatened lower Murray-Darling Basin in Australia. These two populations were rescued during Australia's recent decade-long Millennium Drought, when their persistence became entirely dependent on captive-breeding and subsequent reintroduction efforts. Using historical demographic analyses, we found differences and similarities between the species in the genetic impacts of past natural and anthropogenic events that occurred in situ, such as European settlement (past component). Subsequently, successful maintenance of genetic diversity in captivity-despite skewed brooder contribution to offspring-was achieved through carefully managed genetic-based breeding (present component). Finally, genetic monitoring revealed the survival and recruitment of released captive-bred offspring in the wild (future component). Our holistic framework often requires no additional data collection to that typically gathered in genetic-based breeding programs, is applicable to a wide range of species, advances the genetic considerations of reintroduction programs, and is expected to improve with the use of next-generation sequencing technology.
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Affiliation(s)
- C R M Attard
- School of Biological Sciences, Flinders University, Adelaide, SA, 5042, Australia
| | - L M Möller
- School of Biological Sciences, Flinders University, Adelaide, SA, 5042, Australia
| | - M Sasaki
- School of Biological Sciences, Flinders University, Adelaide, SA, 5042, Australia
| | - M P Hammer
- Museum and Art Gallery of the Northern Territory, P.O. Box 4646, Darwin, NT, 0801, Australia
| | - C M Bice
- Inland Waters and Catchment Ecology Program, SARDI Aquatic Sciences, P.O. Box 120, Henley Beach, SA, 5022, Australia
| | - C J Brauer
- School of Biological Sciences, Flinders University, Adelaide, SA, 5042, Australia
| | - D C Carvalho
- School of Biological Sciences, Flinders University, Adelaide, SA, 5042, Australia
- Pontificia Universidade Catolica de Minas Gerais, Belo Horizonte, MG, 30535-610, Brazil
| | - J O Harris
- School of Biological Sciences, Flinders University, Adelaide, SA, 5042, Australia
| | - L B Beheregaray
- School of Biological Sciences, Flinders University, Adelaide, SA, 5042, Australia.
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13
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Brauer CJ, Hammer MP, Beheregaray LB. Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin. Mol Ecol 2016; 25:5093-5113. [DOI: 10.1111/mec.13830] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory School of Biological Sciences Flinders University Adelaide SA 5042 Australia
| | - Michael P. Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory Darwin NT 0801 Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory School of Biological Sciences Flinders University Adelaide SA 5042 Australia
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14
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Attard CRM, Brauer CJ, Van Zoelen JD, Sasaki M, Hammer MP, Morrison L, Harris JO, Möller LM, Beheregaray LB. Multi-generational evaluation of genetic diversity and parentage in captive southern pygmy perch (Nannoperca australis). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0873-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Cole TL, Hammer MP, Unmack PJ, Teske PR, Brauer CJ, Adams M, Beheregaray LB. Range-wide fragmentation in a threatened fish associated with post-European settlement modification in the Murray–Darling Basin, Australia. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0868-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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Weeks AR, Stoklosa J, Hoffmann AA. Conservation of genetic uniqueness of populations may increase extinction likelihood of endangered species: the case of Australian mammals. Front Zool 2016; 13:31. [PMID: 27398088 PMCID: PMC4939060 DOI: 10.1186/s12983-016-0163-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/28/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND As increasingly fragmented and isolated populations of threatened species become subjected to climate change, invasive species and other stressors, there is an urgent need to consider adaptive potential when making conservation decisions rather than focussing on past processes. In many cases, populations identified as unique and currently managed separately suffer increased risk of extinction through demographic and genetic processes. Other populations currently not at risk are likely to be on a trajectory where declines in population size and fitness soon appear inevitable. RESULTS Using datasets from natural Australian mammal populations, we show that drift processes are likely to be driving uniqueness in populations of many threatened species as a result of small population size and fragmentation. Conserving and managing such remnant populations separately will therefore often decrease their adaptive potential and increase species extinction risk. CONCLUSIONS These results highlight the need for a paradigm shift in conservation biology practise; strategies need to focus on the preservation of genetic diversity at the species level, rather than population, subspecies or evolutionary significant unit. The introduction of new genetic variants into populations through in situ translocation needs to be considered more broadly in conservation programs as a way of decreasing extinction risk by increasing neutral genetic diversity which may increase the adaptive potential of populations if adaptive variation is also increased.
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Affiliation(s)
- Andrew R. Weeks
- />School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Jakub Stoklosa
- />School of Mathematics & Statistics and Evolution & Ecology Research Centre, The University of New South Wales, Kensington, NSW 2052 Australia
| | - Ary A. Hoffmann
- />School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010 Australia
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Population genetics of a widely distributed small freshwater fish with varying conservation concerns: the southern purple-spotted gudgeon, Mogurnda adspersa. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0829-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Bracamonte SE, Smith S, Hammer M, Pavey SA, Sunnucks P, Beheregaray LB. Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations. FISH & SHELLFISH IMMUNOLOGY 2015; 46:468-476. [PMID: 26093210 DOI: 10.1016/j.fsi.2015.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/04/2015] [Accepted: 06/07/2015] [Indexed: 06/04/2023]
Abstract
Genetic diversity is an essential aspect of species viability, and assessments of neutral genetic diversity are regularly implemented in captive breeding and conservation programs. Despite their importance, information from adaptive markers is rarely included in such programs. A promising marker of significance in fitness and adaptive potential is the major histocompatibility complex (MHC), a key component of the adaptive immune system. Populations of Australian freshwater fishes are generally declining in numbers due to human impacts and the introduction of exotic species, a scenario of particular concern for members of the family Percichthyidae, several of which are listed as nationally vulnerable or endangered, and hence subject to management plans, captive breeding, and restoration plans. We used a next-generation sequencing approach to characterize the MHC IIB locus and provide a conservative description of its levels of diversity in four endangered percichthyids: Gadopsis marmoratus, Macquaria australasica, Nannoperca australis, and Nannoperca obscura. Evidence is presented for a duplicated MHC IIB locus, positively selected sites and recombination of MHC alleles. Relatively moderate levels of diversity were detected in the four species, as well as in different ecotypes within each species. Phylogenetic analyses revealed genus specific clustering of alleles and no allele sharing among species. There were also no shared alleles observed between two ecotypes within G. marmoratus and within M. australasica, which might be indicative of ecologically-driven divergence and/or long divergence times. This represents the first characterization and assessment of MHC diversity for Percichthyidae, and also for Australian freshwater fishes in general, providing key genetic resources for a vertebrate group of increasing conservation concern.
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Affiliation(s)
- Seraina E Bracamonte
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Steve Smith
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Michael Hammer
- Evolutionary Biology Unit, South Australian Museum, North Terrace Adelaide, South Australia 5000 and Curator of Fishes, Museum and Art Gallery of the Northern Territory, PO Box 4646, Darwin, Northern Territory 0801, Australia
| | - Scott A Pavey
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec QC G1V 0A6, Canada
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne 3800, Victoria, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia.
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19
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Takács P, Erős T, Specziár A, Sály P, Vitál Z, Ferincz Á, Molnár T, Szabolcsi Z, Bíró P, Csoma E. Population Genetic Patterns of Threatened European Mudminnow (Umbra krameri Walbaum, 1792) in a Fragmented Landscape: Implications for Conservation Management. PLoS One 2015; 10:e0138640. [PMID: 26393510 PMCID: PMC4578892 DOI: 10.1371/journal.pone.0138640] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/27/2015] [Indexed: 11/18/2022] Open
Abstract
The European mudminnow (Umbra krameri) is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs) and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80-90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed.
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Affiliation(s)
- Péter Takács
- Balaton Limnological Institute, Centre for Ecological Research, MTA, Tihany, Hungary
- * E-mail:
| | - Tibor Erős
- Balaton Limnological Institute, Centre for Ecological Research, MTA, Tihany, Hungary
| | - András Specziár
- Balaton Limnological Institute, Centre for Ecological Research, MTA, Tihany, Hungary
| | - Péter Sály
- Balaton Limnological Institute, Centre for Ecological Research, MTA, Tihany, Hungary
| | - Zoltán Vitál
- Balaton Limnological Institute, Centre for Ecological Research, MTA, Tihany, Hungary
| | - Árpád Ferincz
- Department of Aquaculture, Szent István University, Gödöllő, Hungary
| | - Tamás Molnár
- Department of Nature Conservation, Kaposvár University, Kaposvár, Hungary
| | - Zoltán Szabolcsi
- Institute of Forensic Medicine, Network of Forensic Science Institutes, Budapest, Hungary
| | - Péter Bíró
- Balaton Limnological Institute, Centre for Ecological Research, MTA, Tihany, Hungary
| | - Eszter Csoma
- Department of Medical Microbiology, University of Debrecen, Debrecen, Hungary
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Miller AD, Sweeney OF, Whiterod NS, Van Rooyen AR, Hammer M, Weeks AR. Critically low levels of genetic diversity in fragmented populations of the endangered Glenelg spiny freshwater crayfish Euastacus bispinosus. ENDANGER SPECIES RES 2014. [DOI: 10.3354/esr00609] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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