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Campbell MA, Hammer MP, Adams M, Raadik TA, Unmack PJ. Evolutionary relationships and fine-scale geographic structuring in the temperate percichthyid genus Gadopsis (blackfishes) to support fisheries and conservation management. Mol Phylogenet Evol 2024; 199:108159. [PMID: 39029548 DOI: 10.1016/j.ympev.2024.108159] [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: 05/14/2024] [Revised: 07/04/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
Gadopsis (Percichthyidae) is a freshwater genus distributed in south-eastern Australia, including Tasmania, and comprises two recognized species. Previous molecular phylogenetic investigations of the genus, mostly conducted in the pre-genomics era and reflecting a range of geographic and molecular sampling intensities, have supported the recognition of up to seven candidate species. Here we analyze a genome-wide SNP dataset that provides comprehensive geographic and genomic coverage of Gadopsis to produce a robust hypothesis of species boundaries and evolutionary relationships. We then leverage the SNP dataset to characterize relationships within candidate species that lack clear intraspecific phylogenetic relationships. We find further support for the seven previously identified candidate species of Gadopsis and evidence that the Bass Strait centered candidate species (SBA) originated from ancient hybridization. The SNP dataset permits a high degree of intraspecific resolution, providing improvements over previous studies, with numerous candidate species showing intraspecific divisions in phylogenetic analysis. Further population genetic analysis of the Murray-Darling candidate species (NMD) and SBA finds support for K = 6 and K = 7 genetic clusters, respectively. The SNP data generated for this study have diverse applications in natural resource management for these fishes of conservation concern.
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Affiliation(s)
- Matthew A Campbell
- The University of California Davis, Davis, California, USA; University of Alaska Museum of the North, Fairbanks, Alaska, USA.
| | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - Mark Adams
- South Australian Museum, Adelaide, South Australia, Australia; School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Tarmo A Raadik
- Arthur Rylah Institute for Environmental Research, Department of Energy, Environment and Climate Action, Heidelberg, Victoria, Australia
| | - Peter J Unmack
- University of Canberra, Canberra, Australian Capital Territory, Australia
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2
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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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3
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De Araujo Barbosa V, Graham SE, Smith BJ, Hogg ID, McGaughran A. Assessing population genetic structure of three New Zealand stream insects using mitochondrial and nuclear DNA markers. Genome 2022; 65:427-441. [PMID: 35785969 DOI: 10.1139/gen-2022-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Assessing genetic differentiation among natural populations can aid understanding of dispersal patterns and connectivity among habitats. Several molecular markers have become increasingly popular in determining population genetic structure for this purpose. Here, we compared the resolution of mitochondrial cytochrome c oxidase subunit I (COI) and nuclear single nucleotide polymorphism (SNP) markers for detecting population structure among stream insects at small spatial scales. Individuals of three endemic taxa - Coloburiscus humeralis (Ephemeroptera), Zelandobius confusus (Plecoptera), and Hydropsyche fimbriata (Trichoptera) - were collected from forested streams that flow across open pasture in the North Island of New Zealand. Both COI and SNP data indicated limited population structure across the study area, and small differences observed among these species were likely related to their putative dispersal abilities. For example, fine-scale genetic differentiation between and among neighbouring stream populations for H. fimbriata suggests that gene flow, and hence dispersal, may be more limited for this species relative to the others. Based on the generally similar results provided by both types of markers, we suggest that either COI or SNP markers can provide suitable initial estimates of fine-scale population genetic differentiation in stream insects.
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Affiliation(s)
| | - S Elizabeth Graham
- National Institute of Water and Atmospheric Research Hamilton, 418394, Hamilton, Waikato, New Zealand;
| | - Brian J Smith
- National Institute of Water and Atmospheric Research Hamilton, 418394, Hamilton, New Zealand;
| | - Ian D Hogg
- University of Waikato, 3717, Department of Science, Hamilton, New Zealand.,Polar Knowledge Canada, 513970, Canadian High Arctic Research Station, Cambridge Bay, Nunavut, Canada;
| | - Angela McGaughran
- University of Waikato, 3717, School of Science, Hamilton, Waikato, New Zealand;
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4
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Schwarz S, Roe KJ. Population structure and gene flow in the Sheepnose mussel (
Plethobasus cyphyus
) and their implications for conservation. Ecol Evol 2022; 12:e8630. [PMID: 35222980 PMCID: PMC8854780 DOI: 10.1002/ece3.8630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/20/2022] [Accepted: 01/26/2022] [Indexed: 11/07/2022] Open
Abstract
North American freshwater mussel species have experienced substantial range fragmentation and population reductions. These impacts have the potential to reduce genetic connectivity among populations and increase the risk of losing genetic diversity. Thirteen microsatellite loci and an 883 bp fragment of the mitochondrial ND1 gene were used to assess genetic diversity, population structure, contemporary migration rates, and population size changes across the range of the Sheepnose mussel (Plethobasus cyphyus). Population structure analyses reveal five populations, three in the Upper Mississippi River Basin and two in the Ohio River Basin. Sampling locations exhibit a high degree of genetic diversity and contemporary migration estimates indicate that migration within river basins is occurring, although at low rates, but there is no migration is occurring between the Ohio and Mississippi river basins. No evidence of bottlenecks was detected, and almost all locations exhibited the signature of population expansion. Our results indicate that although anthropogenic activity has altered the landscape across the range of the Sheepnose, these activities have yet to be reflected in losses of genetic diversity. Efforts to conserve Sheepnose populations should focus on maintaining existing habitats and fostering genetic connectivity between extant demes to conserve remaining genetic diversity for future viable populations.
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Affiliation(s)
- Sara Schwarz
- Department of Natural Resources Ecology and Management Iowa State University Ames Iowa USA
- Ecology and Evolutionary Biology Program Iowa State University Ames Iowa USA
| | - Kevin J. Roe
- Department of Natural Resources Ecology and Management Iowa State University Ames Iowa USA
- Ecology and Evolutionary Biology Program Iowa State University Ames Iowa USA
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6
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Mussmann SM, Douglas MR, Chafin TK, Douglas ME. BA3‐SNPs: Contemporary migration reconfigured in BayesAss for next‐generation sequence data. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13252] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven M. Mussmann
- Department of Biological Sciences University of Arkansas Fayetteville Arkansas
| | - Marlis R. Douglas
- Department of Biological Sciences University of Arkansas Fayetteville Arkansas
| | - Tyler K. Chafin
- Department of Biological Sciences University of Arkansas Fayetteville Arkansas
| | - Michael E. Douglas
- Department of Biological Sciences University of Arkansas Fayetteville Arkansas
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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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Carvalho DC, Beheregaray LB. Conservation genetics of the threatened catfish Conorhynchos conirostris (Siluriformes: incertae sedis), an evolutionary relict endemic to the São Francisco River Basin, Brazil. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1090-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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9
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Jaisuk C, Senanan W. Effects of landscape features on population genetic variation of a tropical stream fish, Stone lapping minnow, Garra cambodgiensis, in the upper Nan River drainage basin, northern Thailand. PeerJ 2018; 6:e4487. [PMID: 29568710 PMCID: PMC5845392 DOI: 10.7717/peerj.4487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/20/2018] [Indexed: 11/20/2022] Open
Abstract
Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly affected by glaciation. Thus, spatial genetic variation of tropical fish populations should look very different from the pattern observed in temperate fish populations. These data are becoming important for designing appropriate management and conservation plans, as these aquatic systems are undergoing intense development and exploitation. This study evaluated the effects of landscape features on population genetic diversity of Garra cambodgiensis, a stream cyprinid, in eight tributary streams in the upper Nan River drainage basin (n = 30–100 individuals/location), Nan Province, Thailand. These populations are under intense fishing pressure from local communities. Based on 11 microsatellite loci, we detected moderate genetic diversity within eight population samples (average number of alleles per locus = 10.99 ± 3.00; allelic richness = 10.12 ± 2.44). Allelic richness within samples and stream order of the sampling location were negatively correlated (P < 0.05). We did not detect recent bottleneck events in these populations, but we did detect genetic divergence among populations (Global FST = 0.022, P < 0.01). The Bayesian clustering algorithms (TESS and STRUCTURE) suggested that four to five genetic clusters roughly coincide with sub-basins: (1) headwater streams/main stem of the Nan River, (2) a middle tributary, (3) a southeastern tributary and (4) a southwestern tributary. We observed positive correlation between geographic distance and linearized FST (P < 0.05), and the genetic differentiation pattern can be moderately explained by the contemporary stream network (STREAMTREE analysis, R2 = 0.75). The MEMGENE analysis suggested genetic division between northern (genetic clusters 1 and 2) and southern (clusters 3 and 4) sub-basins. We observed a high degree of genetic admixture in each location, highlighting the importance of natural flooding patterns and possible genetic impacts of supplementary stocking. Insights obtained from this research advance our knowledge of the complexity of a tropical stream system, and guide current conservation and restoration efforts for this species in Thailand.
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Affiliation(s)
- Chaowalee Jaisuk
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand.,Department of Animal Science and Fisheries, Faculty of Science and Agricultural Technology, Rajamangala University of Technology Lanna Nan Campus, Nan, Thailand
| | - Wansuk Senanan
- Department of Aquatic Science, Faculty of Science, Burapha University, Chon Buri, Thailand
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Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish. Heredity (Edinb) 2018; 120:515-532. [PMID: 29326479 PMCID: PMC5943333 DOI: 10.1038/s41437-017-0008-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 11/08/2022] Open
Abstract
Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (<13 km) genetic structure within reaches unimpeded by barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (FST = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (<100). Our study highlights that, in structured populations, the ability to detect short-term genetic effects from barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.
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11
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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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