1
|
Liu D, Zhang S, Zuo X, Zheng Y, Li J. Evaluation of genetic diversity and population structure in Leptobotiamicrophthalma Fu & Ye, 1983 (Cypriniformes, Cobitidae). Zookeys 2022; 1121:83-95. [PMID: 36760761 PMCID: PMC9848613 DOI: 10.3897/zookeys.1121.85953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/29/2022] [Indexed: 11/12/2022] Open
Abstract
This paper reports the first account about dynamic changes on genetic diversity and population structure of Leptobotiamicrophthalma in the Yangtze River drainage due to dam constructions. The genetic diversity and population structure of twelve populations of L.microphthalma collected in 2010 and 2020 were estimated using 12 nuclear microsatellite markers. Reduction of genetic diversity between 2010 and 2020 was not significant in a paired t-test (p > 0.05), but population structure of L.microphthalma had a tendency to change: the genetic differentiation (Fst) among the five populations collected in 2010 were all insignificant (p > 0.05). However, differentiation (Fst) among some populations collected in 2020 were significant (p < 0.05), which indicated the population structure of L.microphthalma was changing. Correlation analysis indicated that negative correlations between the genetic diversities and geographical elevations among populations were significant for seven populations collected in 2020 (r = -0.819, p = 0.039), which means that populations of L.microphthalma in high elevation regions were more vulnerable than those in low elevation regions. Finally, some suggestions for conservation and restoration are proposed, such as artificial propagation, to prevent the further reduction of genetic diversity and population resources.
Collapse
Affiliation(s)
- Dongqi Liu
- Sichuan Province Key Laboratory of Characteristic Biological Resources of Dry and Hot River Valley, School of Biological and Chemical Engineering, Panzhihua University, Panzhihua, 617000, ChinaPanzhihua UniversityPanzhihuaChina
| | - Shiming Zhang
- Upper Changjiang River Bureau of Hydrological and Water Resources Survey, Chongqing, 400000, ChinaUpper Changjiang River Bureau of Hydrological and Water Resources SurveyChongqingChina
| | - Xinyu Zuo
- Upper Changjiang River Bureau of Hydrological and Water Resources Survey, Chongqing, 400000, ChinaUpper Changjiang River Bureau of Hydrological and Water Resources SurveyChongqingChina
| | - Yi Zheng
- Sichuan Province Key Laboratory of Characteristic Biological Resources of Dry and Hot River Valley, School of Biological and Chemical Engineering, Panzhihua University, Panzhihua, 617000, ChinaPanzhihua UniversityPanzhihuaChina
| | - Jing Li
- Sichuan Province Key Laboratory of Characteristic Biological Resources of Dry and Hot River Valley, School of Biological and Chemical Engineering, Panzhihua University, Panzhihua, 617000, ChinaPanzhihua UniversityPanzhihuaChina
| |
Collapse
|
3
|
Shi Y, Bouska KL, McKinney GJ, Dokai W, Bartels A, McPhee MV, Larson WA. Gene flow influences the genomic architecture of local adaptation in six riverine fish species. Mol Ecol 2021; 32:1549-1566. [PMID: 34878685 DOI: 10.1111/mec.16317] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/15/2021] [Accepted: 12/01/2021] [Indexed: 11/30/2022]
Abstract
Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from recombination and thus be selected for, but few studies have tested it with empirical data. Here, we used restriction site-associated sequencing to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We used four differentiation-based outlier tests and three genotype-environment association analyses to define neutral single nucleotide polymorphisms (SNPs) and outlier SNPs that were putatively under selection. We then examined the distribution of outlier SNPs along the genome and investigated whether these SNPs were found in genomic islands of differentiation and inversions. We found that gene flow varied among species, and outlier SNPs were clustered more tightly in species with higher gene flow. The two species with the highest overall FST (0.0303-0.0720) and therefore lowest gene flow showed little evidence of clusters of outlier SNPs, with outlier SNPs in these species spreading uniformly across the genome. In contrast, nearly all outlier SNPs in the species with the lowest FST (0.0003) were found in a single large putative inversion. Two other species with intermediate gene flow (FST ~ 0.0025-0.0050) also showed clustered genomic architectures, with most islands of differentiation clustered on a few chromosomes. Our results provide important empirical evidence to support the hypothesis that increasingly clustered architecture of local adaptation is associated with high gene flow.
Collapse
Affiliation(s)
- Yue Shi
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA.,Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, USA
| | - Kristen L Bouska
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, USA
| | - Garrett J McKinney
- NRC Research Associateship Program, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - William Dokai
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA.,Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, USA
| | - Andrew Bartels
- Long Term Resource Monitoring Program, Wisconsin Department of Natural Resources, La Crosse, Wisconsin, USA
| | - Megan V McPhee
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA
| | - Wesley A Larson
- National Oceanographic and Atmospheric Administration, Auke Bay Laboratories, National Marine Fisheries Service, Alaska Fisheries Science Center, Juneau, Alaska, USA.,U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, USA
| |
Collapse
|
4
|
Gehri RR, Gruenthal K, Larson WA. It's complicated: Heterogeneous patterns of genetic structure in five fish species from a fragmented river suggest multiple processes can drive differentiation. Evol Appl 2021; 14:2079-2097. [PMID: 34429750 PMCID: PMC8372089 DOI: 10.1111/eva.13268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
Fragmentation of river systems by dams can have substantial genetic impacts on fish populations. However, genetic structure can exist naturally at small scales through processes other than isolation by physical barriers. We sampled individuals from five native fish species with varying life histories above and below a dam in the lower Boardman River, Michigan, USA, and used RADseq to investigate processes influencing genetic structure in this system. Species assessed were white sucker Catostomus commersonii, yellow perch Perca flavescens, walleye Sander vitreus, smallmouth bass Micropterus dolomieu, and rock bass Ambloplites rupestris. We detected significant differentiation within each species, but patterns of population structure varied substantially. Interestingly, genetic structure did not appear to be solely the result of fragmentation by the dam. While genetic structure in yellow perch and walleye generally coincided with "above dam" and "below dam" sampling locations, samples from our other three species did not. Specifically, samples from rock bass, smallmouth bass, and, to a much lesser extent, white sucker, aligned with a putative Great Lakes (GL) group that contained mostly individuals sampled below the dam and a putative Boardman River (BR) group that contained individuals sampled both above and below the dam, with some evidence of admixture among groups. We hypothesize that the GL and BR groups formed prior to dam construction and our samples largely represent a mixed stock that was sampled sympatrically outside of the spawning season. Support for this hypothesis is especially strong in smallmouth bass, where GL fish were 151 mm smaller than BR fish on average, suggesting a potential ontogenetic habitat shift of young GL fish into the lower river for feeding and/or refuge. Our study illuminates the complex dynamics shaping genetic structure in fragmented river systems and indicates that conclusions drawn for a single species cannot be generalized.
Collapse
Affiliation(s)
- Rebecca R. Gehri
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Kristen Gruenthal
- Office of Applied ScienceWisconsin Department of Natural ResourcesCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Alaska Department of Fish and GameGene Conservation LaboratoryJuneauAKUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- National Oceanographic and Atmospheric AdministrationNational Marine Fisheries ServiceAlaska Fisheries Science CenterAuke Bay LaboratoriesJuneauAKUSA
| |
Collapse
|
5
|
Biesack EE, Dang BT, Ackiss AS, Bird CE, Chheng P, Phounvisouk L, Truong OT, Carpenter KE. Evidence for population genetic structure in two exploited Mekong River fishes across a natural riverine barrier. JOURNAL OF FISH BIOLOGY 2020; 97:696-707. [PMID: 32557668 DOI: 10.1111/jfb.14424] [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: 01/28/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Impacts of urban development on aquatic populations are often complex and difficult to ascertain, but population genetic analysis has allowed researchers to monitor and estimate gene flow in the context of existing and future hydroelectric projects. The Lower Mekong Basin is undergoing rapid hydroelectric development with around 50 completed and under-construction dams and 95 planned dams. The authors investigated the baseline genetic diversity of two exploited migratory fishes, the mud carp Henicorhynchus lobatus (five locations), and the rat-faced pangasiid catfish, Helicophagus leptorhynchus (two locations), in the Lower Mekong Basin using the genomic double digest restriction site-associated DNA (ddRAD) sequencing method. In both species, fish sampled upstream of Khone Falls were differentiated from those collected at other sites, and Ne estimates at the site above the falls were lower than those at other sites. This was the first study to utilize thousands of RAD-generated single nucleotide polymorphisms to indicate that the Mekong's Khone Falls are a potential barrier to gene flow for these two moderately migratory species. The recent completion of the Don Sahong dam across one of the only channels for migratory fishes through Khone Falls may further exacerbate signatures of isolation and continue to disrupt the migration patterns of regionally vital food fishes. In addition, H. lobatus populations downstream of Khone Falls, including the 3S Basin and Tonle Sap system, displayed robust connectivity. Potential obstruction of migration pathways between these river systems resulting from future dam construction may limit dispersal, which has led to elevated inbreeding rates and even local extirpation in other fragmented riverine species.
Collapse
Affiliation(s)
- Ellen E Biesack
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, USA
| | - Binh T Dang
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Amanda S Ackiss
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, USA
| | - Christopher E Bird
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, Texas, USA
| | - Phen Chheng
- Fisheries Administration, Inland Fisheries Research and Development Institute, Phnom Penh, Cambodia
| | | | - Oanh T Truong
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Kent E Carpenter
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, USA
| |
Collapse
|