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Li Y, Li M, Xing T, Liu J. Resolving the origins of invertebrate colonists in the Yangtze River Estuary with molecular markers: Implications for ecological connectivity. Ecol Evol 2021; 11:13898-13911. [PMID: 34707826 PMCID: PMC8525129 DOI: 10.1002/ece3.8095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding connectivity over different spatial and temporal scales is fundamental for managing of ecological systems. However, controversy exists for wintertime ecological connectivity between the Yangtze River Estuary (YRE) and inner southwestern Yellow Sea. Here, we investigated ecological connectivity between the YRE and inner southwestern Yellow Sea in wintertime by precisely pinpointing the source of the newly colonized populations of a winter-spawning rocky intertidal invertebrate, Littorina brevicula (Philippi, 1844), on artificial structures along the coast of the Yangtze River Delta (YRD) using mitochondrial ND6 sequences and microsatellite data. Clear phylogeographic and genetic differentiation were detected between natural rocky populations south and north of the YRE, which resulted from the lack of hard substrate for rocky invertebrates in the large YRD coast. For the newly colonized populations on the coast of YRD, most individuals (98%) to the south of ~33.5°N were from natural rocky populations to the south of the YRE and most of those (94%) to the north of ~33.5°N were from the northern natural rocky populations, which demonstrated strong ecological connectivity between the inner southwestern Yellow Sea and the YRE in winter time. We presented the first genetic evidence that demonstrated a northward wintertime coastal current in the inner southwestern Yellow Sea, and precisely illustrated the boundary of the coastal current recently proposed by numerical experiment. These results indicated that the YRE serves as an important source of materials and energy for the inner southwestern Yellow Sea in winter, which can be crucial for the function of the Yellow Sea ecosystem.
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Affiliation(s)
- Yu‐Qiang Li
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of OceanologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Meng‐Yu Li
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of OceanologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Teng‐Fei Xing
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of OceanologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jin‐Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of OceanologyChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Ecology and Environmental ScienceQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
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Chew PC, Christianus A, Zudaidy JM, Ina-Salwany MY, Chong CM, Tan SG. Microsatellite Characterization of Malaysian Mahseer ( Tor spp.) for Improvement of Broodstock Management and Utilization. Animals (Basel) 2021; 11:ani11092633. [PMID: 34573599 PMCID: PMC8471032 DOI: 10.3390/ani11092633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei's genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.
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Affiliation(s)
- Poh Chiang Chew
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Freshwater Fisheries Research Division, Fisheries Research Institute Glami Lemi, Jelebu 71650, Malaysia;
| | - Annie Christianus
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: ; Tel.: +60-3-8947-4884
| | - Jaapar M. Zudaidy
- Freshwater Fisheries Research Division, Fisheries Research Institute Glami Lemi, Jelebu 71650, Malaysia;
| | - Md Yasin Ina-Salwany
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Chou Min Chong
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Soon Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
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Porto-Hannes I, Burlakova LE, Zanatta DT, Lasker HR. Boundaries and hybridization in a secondary contact zone between freshwater mussel species (Family:Unionidae). Heredity (Edinb) 2021; 126:955-973. [PMID: 33883699 PMCID: PMC8178349 DOI: 10.1038/s41437-021-00424-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
Correct species identification and delineation are crucial for effective conservation and management. However, species delineation can be problematic in the presence of morphological ambiguities due to phenotypic plasticity, convergence, and/or interspecific hybridization. Here, we investigated the degree of hybridization between two closely related freshwater mussel species [Bivalvia: Unionidae; Lampsilis siliquoidea (Barnes) and L. radiata (Gmelin)] that present intermediate forms in areas of sympatry. Unionids have a distinct form of mitochondrial DNA (mtDNA) inheritance, termed doubly uniparental inheritance (DUI) where female mtDNA (F-type) is transmitted to all progeny but male mtDNA (M-type) is mostly inherited by the males resulting in mostly homoplasmic females and heteroplasmic males. An individual was identified as hybrid when F-type and M-type mtDNA of the two different species were found in the same individual. Twelve out of 116 sequenced males were identified as hybrids indicating that these species hybridize where their geographic range overlaps in the lower Great Lakes and St. Lawrence basins. Microsatellite analyses further support the occurrence of hybridization but at a larger spatial scale than indicated by the mitochondrial analyses. We also found that strong within-species population genetic structure affects the detection of purebred individuals overestimating the number of hybrids. Given the large geographic scale and proportion of hybrids found in this study, natural hybridization and introgression need to be considered when implementing local biodiversity inventories, identifying waterbodies as source of organisms for relocation and restoration projects and when setting appropriate conservation policies.
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Affiliation(s)
- Isabel Porto-Hannes
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA.
| | | | - David T Zanatta
- Institute for Great Lakes Research, Biology Department, Central Michigan University, Mount Pleasant, MI, USA
| | - Howard R Lasker
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA
- Department of Environment and Sustainability, University at Buffalo, Buffalo, NY, USA
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Sunny A, Duarte-deJesus L, Aguilera-Hernández A, Ramírez-Corona F, Suárez-Atilano M, Percino-Daniel R, Manjarrez J, Monroy-Vilchis O, González-Fernández A. Genetic diversity and demography of the critically endangered Roberts' false brook salamander (Pseudoeurycea robertsi) in Central Mexico. Genetica 2019; 147:149-164. [PMID: 30879155 DOI: 10.1007/s10709-019-00058-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/11/2019] [Indexed: 11/28/2022]
Abstract
Land use changes are threatening the maintenance of biodiversity. Genetic diversity is one of the main indicators of biological diversity and is highly important as it shapes the capability of populations to respond to environmental changes. We studied eleven populations of Pseudoeurycea robertsi, a micro-endemic and critically endangered species from the Nevado de Toluca Volcano, a mountain that is part of the Trans-Mexican Volcanic Belt, Mexico. We sequenced the mitochondrial cytochrome b gene from 71 individuals and genotyped 9 microsatellites from 150 individuals. Our results based on the cytochrome b showed two divergent lineages, with moderate levels of genetic diversity and a recently historical demographic expansion. Microsatellite-based results indicated low levels of heterozygosity for all populations and few alleles per locus, as compared with other mole salamander species. We identified two genetically differentiated subpopulations with a significant level of genetic structure. These results provide fundamental data for the development of management plans and conservation efforts for this critically endangered species.
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Affiliation(s)
- Armando Sunny
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico.
| | - Luis Duarte-deJesus
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Arlene Aguilera-Hernández
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Fabiola Ramírez-Corona
- Taller de Sistemática y Biogeografía, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Marco Suárez-Atilano
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Ruth Percino-Daniel
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Javier Manjarrez
- Laboratorio de Biología Evolutiva, Facultad de Ciencias, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Octavio Monroy-Vilchis
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
| | - Andrea González-Fernández
- Laboratorio de Biología Evolutiva, Facultad de Ciencias, Universidad Autónoma del Estado de México, Instituto Literario #100, Colonia Centro, 50000, Toluca, Mexico State, Mexico
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Rico C, Cuesta JA, Drake P, Macpherson E, Bernatchez L, Marie AD. Null alleles are ubiquitous at microsatellite loci in the Wedge Clam ( Donax trunculus). PeerJ 2017; 5:e3188. [PMID: 28439464 PMCID: PMC5398275 DOI: 10.7717/peerj.3188] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/15/2017] [Indexed: 12/17/2022] Open
Abstract
Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.
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Affiliation(s)
- Ciro Rico
- School of Marine Studies, Molecular Analytics Laboratory (MOANA), Faculty of Science Technology and Environment, The University of the South Pacific, Suva, Fiji.,Estación Biológica de Doñana, (EBD, CSIC), Sevilla, Spain
| | - Jose Antonio Cuesta
- Instituto de Ciencias Marinas de Andalucía (ICMAN, CSIC), Puerto Real (Cádiz), Spain
| | - Pilar Drake
- Instituto de Ciencias Marinas de Andalucía (ICMAN, CSIC), Puerto Real (Cádiz), Spain
| | | | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Pavillon Charles-Eugène-Marchand, Laval University, Quebec, Canada
| | - Amandine D Marie
- School of Marine Studies, Molecular Analytics Laboratory (MOANA), Faculty of Science Technology and Environment, The University of the South Pacific, Suva, Fiji
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Marie AD, Lejeusne C, Karapatsiou E, Cuesta JA, Drake P, Macpherson E, Bernatchez L, Rico C. Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries. Sci Rep 2016; 6:39152. [PMID: 27991535 DOI: 10.1038/srep39152] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/18/2016] [Indexed: 01/25/2023] Open
Abstract
In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics.
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