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Chen W, Xiang D, Gao S, Zhu S, Wu Z, Li Y, Li J. Whole-genome resequencing confirms the genetic effects of dams on an endangered fish Hemibagrus guttatus (Siluriformes: Bagridae): A case study in a tributary of the Pearl River. Gene 2024; 895:148000. [PMID: 37979951 DOI: 10.1016/j.gene.2023.148000] [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: 09/02/2023] [Revised: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023]
Abstract
Dam construction in riverine ecosystems has fragmented natural aquatic habitats and has altered environmental conditions. As a result, damming has been demonstrated to threaten aquatic biodiversity by reducing species distribution ranges and hindering gene exchange, leading to the inability to adapt to environmental changes. Knowledge of the contemporary genetic diversity and genetic structure of fish populations that are separated by dams is vital to developing effective conservation strategies, particularly for endangered fish species. We chose the Lianjiang River, a tributary of the Pearl River, as a case study to assess the effects of dams on the genetic diversity and genetic structure of an endangered fish species, Hemibagrus guttatus, using whole-genome resequencing data from 63 fish samples. The results indicated low levels of genetic diversity, high levels of inbreeding and decreasing trend of effective population size in fragmented H. guttatus populations. In addition, there were significant genetic structure and genetic differentiation among populations, suggesting that the dams might have affected H. guttatus populations. Our findings may benefit management and conservation practices for this endangered species that is currently suffering from the effects of dam construction.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Denggao Xiang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Shang Gao
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Zhi Wu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China.
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Whitney JL, Coleman RR, Deakos MH. Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian reef Manta Rays. BMC Ecol Evol 2023; 23:31. [PMID: 37422622 PMCID: PMC10329317 DOI: 10.1186/s12862-023-02130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 06/07/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Reef manta rays (Mobula alfredi) are globally distributed in tropical and subtropical seas. Their life history traits (slow growth, late maturity, low reproductive output) make them vulnerable to perturbations and therefore require informed management strategies. Previous studies have reported wide-spread genetic connectivity along continental shelves suggesting high gene flow along continuous habitats spanning hundreds of kilometers. However, in the Hawaiian Islands, tagging and photo-identification evidence suggest island populations are isolated despite proximity, a hypothesis that has not yet been evaluated with genetic data. RESULTS This island-resident hypothesis was tested by analyzing whole mitogenome haplotypes and 2048 nuclear single nucleotide polymorphisms (SNPs) between M. alfredi (n = 38) on Hawai'i Island and Maui Nui (the 4-island complex of Maui, Moloka'i, Lāna'i and Kaho'olawe). Strong divergence in the mitogenome (ΦST = 0.488) relative to nuclear genome-wide SNPs (neutral FST = 0.003; outlier FST = 0.186), and clustering of mitochondrial haplotypes among islands provides robust evidence that female reef manta rays are strongly philopatric and do not migrate between these two island groups. Combined with restricted male-mediated migration, equivalent to a single male moving between islands every 2.2 generations (~ 64 years), we provide evidence these populations are significantly demographically isolated. Estimates of contemporary effective population size (Ne) are 104 (95% CI: 99-110) in Hawai'i Island and 129 (95% CI: 122-136) in Maui Nui. CONCLUSIONS Concordant with evidence from photo identification and tagging studies, these genetic results indicate reef manta rays in Hawai'i have small, genetically-isolated resident island populations. We hypothesize that due to the Island Mass Effect, large islands provide sufficient resources to support resident populations, thereby making crossing deep channels separating island groups unnecessary. Small effective population size, low genetic diversity, and k-selected life history traits make these isolated populations vulnerable to region-specific anthropogenic threats, which include entanglement, boat strikes, and habitat degradation. The long-term persistence of reef manta rays in the Hawaiian Islands will require island-specific management strategies.
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Affiliation(s)
- Jonathan L Whitney
- National Oceanic and Atmospheric Administration, Pacific Islands Fisheries Science Center, Honolulu, Hawai'i, USA.
| | - Richard R Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Sciences, University of Miami, Miami, FL, USA
| | - Mark H Deakos
- Hawai'i Association for Marine Education and Research, Lahaina, Maui, Hawai'i, USA
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Ye Z, Yuan J, Damgaard J, Berchi GM, Cianferoni F, Pintar MR, Olosutean H, Zhu X, Jiang K, Yang X, Fu S, Bu W. Climate Warming Since the Holocene Accelerates West-East Communication for the Eurasian Temperate Water Strider Species Aquarius paludum. Mol Biol Evol 2022; 39:6575397. [PMID: 35482393 PMCID: PMC9087890 DOI: 10.1093/molbev/msac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Holocene climate warming has dramatically altered biological diversity and distributions. Recent human-induced emissions of greenhouse gases will exacerbate global warming and thus induce threats to cold-adapted taxa. However, the impacts of this major climate change on transcontinental temperate species are still poorly understood. Here, we generated extensive genomic datasets for a water strider, Aquarius paludum, which was sampled across its entire distribution in Eurasia and used these datasets in combination with ecological niche modeling (ENM) to elucidate the influence of the Holocene and future climate warming on its population structure and demographic history. We found that A. paludum consisted of two phylogeographic lineages that diverged in the middle Pleistocene, which resulted in a “west–east component” genetic pattern that was probably triggered by Central Asia-Mongoxin aridification and Pleistocene glaciations. The diverged western and eastern lineages had a second contact in the Holocene, which shaped a temporary hybrid zone located at the boundary of the arid–semiarid regions of China. Future predictions detected a potentially novel northern corridor to connect the western and eastern populations, indicating west–east gene flow would possibly continue to intensify under future warming climate conditions. Further integrating phylogeographic and ENM analyses of multiple Eurasian temperate taxa based on published studies reinforced our findings on the “west–east component” genetic pattern and the predicted future northern corridor for A. paludum. Our study provided a detailed paradigm from a phylogeographic perspective of how transcontinental temperate species differ from cold-adapted taxa in their response to climate warming.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Juanjuan Yuan
- College of Life Sciences, Zaozhuang University, 1 Beian Road, Shandong 277000, China
| | - Jakob Damgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Gavril Marius Berchi
- Department of Taxonomy & Ecology, Faculty of Biology & Geology, Babeş-Bolyai University, 5-7 Clinicilor Street, 400015 Cluj-Napoca, Romania.,Institute for Advanced Environmental Research, West University of Timișoara, 4 Oituz Street, 300086 Timișoara, Romania
| | - Fabio Cianferoni
- Research Institute on Terrestrial Ecosystems, National Research Council of Italy, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy.,Zoology, "La Specola", Natural History Museum, University of Florence, Via Romana 17, I-50125 Florence, Italy
| | - Matthew R Pintar
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Horea Olosutean
- Applied Ecology Research Center, Lucian Blaga University of Sibiu, 5-7 Ion Ratiu Street, 550012 Sibiu, Romania
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xin Yang
- School of Sports, Taiyuan University of Science and Technology, 66 Waliu Road, Shanxi 030024, China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
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Qi J, Shi F, Zhang B, Chen X, Jie X, Furumitsu K, Corush JB, Yamaguchi A, Zhang J. Insights into genetic variation and demographic history of sharpnose rays: Examinations of three species of Telatrygon (Elasmobranchii, Dasyatidae) from the Indo-West Pacific. Integr Zool 2021; 17:1063-1077. [PMID: 34932875 DOI: 10.1111/1749-4877.12614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coastal and demersal chondrichthyans (sharks, rays, and skates) are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology. Population genetic studies investigating the extent to which demographic history shapes the genetic structure of these fishes are rare. Here, we combination mitochondrial DNA (Cytb and ND2) and eight nuclear microsatellite loci from 244 individuals to examine the population genetic structure and demographic history of the three Indo-West Pacific species of sharpnose rays (Telatrygon zugei, Telatrygon biasa, and Trygon crozieri). High levels of genetic variation both within and between species was identified. Phylogenetic analysis partitioned haplotypes into two lineages supporting divergence of T. zugei from T. crozieri and T. biasa during the Pleistocene. Furthermore, microsatellite-based clustering analyses identified four genetic groups (i.e., T. zugei from Japan, T. zugei from coastal China, T. biasa from Gulf of Thailand, and T. crozieri from the Andaman Sea. Measurements of genetic differentiation also support these four groups. Additionally, Pleistocene demographic expansions were examined in all genetic groups. The climate oscillations and current hydrologic cycles in the Indo-West Pacific appear to be coincide with the hypothesis regarding speciation and the observed demographic history trends of the sharpnose rays. Considering the species group has, until recently, been thought to be one species, these results are critical for defining management units and guiding conservation efforts to preserve stingray biodiversity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jiwei Qi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fanglei Shi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baowei Zhang
- School of Life Science, Anhui University, Hefei, Anhui, China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xing Jie
- East China Sea Centre of Standard and Metrology, SOA, Shanghai, China
| | | | - Joel B Corush
- Illinois Natural History Survey, University of Illinois Champaign-Urbana, Champaign, IL, 61820
| | | | - Jie Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
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Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus). Sci Rep 2021; 11:13357. [PMID: 34172804 PMCID: PMC8233350 DOI: 10.1038/s41598-021-92905-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
Benthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490-0.900, nucleotide diversity, π = 0.0010-0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118-0.216; π = 0.0004-0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.
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Smith KL, Feldheim K, Carlson JK, Wiley TR, Taylor SS. Female philopatry in smalltooth sawfish Pristis pectinata: conservation and management implications. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Schwanck TN, Schweinsberg M, Lampert KP, Guttridge TL, Tollrian R, O'Shea O. Linking local movement and molecular analysis to explore philopatry and population connectivity of the southern stingray Hypanus americanus. JOURNAL OF FISH BIOLOGY 2020; 96:1475-1488. [PMID: 32191344 DOI: 10.1111/jfb.14325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/05/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Limited data pertaining to life history and population connectivity of the data-deficient southern stingray (Hypanus americanus) are available. To determine potential vulnerabilities of their populations, this study aimed to analyse their movement patterns and genetic variability. A population of southern stingrays encompassing nine sites around Cape Eleuthera, the Bahamas, has been monitored using mark-recapture, spanning a 2.5 year period. Out of 200 individual stingrays, more than a third were encountered again. The home range of the females appears to be restricted, which supports the notion of high site residency. As resident populations of stingrays could suffer from a lack of population connectivity and be predestined for genetic isolation and local extirpation, this study further investigated the genetic connectivity of four sample sites in the central and western Bahamas. A haplotype analysis from the mitochondrial D-loop region showed that no distinct population structure strictly correlated with the sample site. These findings were complemented by five microsatellite loci that revealed high degrees in genotypic variability and little population differentiation. The results suggest gene flow mediated by both males and females.
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Affiliation(s)
- Tanja N Schwanck
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, 44801 Bochum, Germany
- School of Biological Sciences, University of Aberdeen, AB24 2TZ Aberdeen, United Kingdom
| | - Maximilian Schweinsberg
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, 44801 Bochum, Germany
| | - Kathrin P Lampert
- Institute for Zoology, University of Cologne, 50674 Cologne, Germany
| | - Tristan L Guttridge
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, The Bahamas
- Saving the Blue, Kendall, Miami, Florida, USA
| | - Ralph Tollrian
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, 44801 Bochum, Germany
| | - Owen O'Shea
- The Centre for Ocean Research and Education, Gregory Town, Eleuthera, The Bahamas
- Shark Research and Conservation Program, Cape Eleuthera Institute, Eleuthera, The Bahamas
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