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Cid N, Erős T, Heino J, Singer G, Jähnig SC, Cañedo‐Argüelles M, Bonada N, Sarremejane R, Mykrä H, Sandin L, Paloniemi R, Varumo L, Datry T. From meta-system theory to the sustainable management of rivers in the Anthropocene. FRONTIERS IN ECOLOGY AND THE ENVIRONMENT 2022; 20:49-57. [PMID: 35873359 PMCID: PMC9292669 DOI: 10.1002/fee.2417] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Regional-scale ecological processes, such as the spatial flows of material, energy, and organisms, are fundamental for maintaining biodiversity and ecosystem functioning in river networks. Yet these processes remain largely overlooked in most river management practices and underlying policies. Here, we propose adoption of a meta-system approach, where regional processes acting at different levels of ecological organization - populations, communities, and ecosystems - are integrated into conventional river conservation, restoration, and biomonitoring. We also describe a series of measurements and indicators that could be assimilated into the implementation of relevant biodiversity and environmental policies. Finally, we highlight the need for alternative management strategies that can guide practitioners toward applying recent advances in ecology to preserve and restore river ecosystems and the ecosystem services they provide, in the context of increasing alteration of river network connectivity worldwide.
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Affiliation(s)
- Núria Cid
- INRAEUR RiverLyCentre de Lyon‐VilleurbanneVilleurbanne CedexFrance
| | - Tibor Erős
- Balaton Limnological Research InstituteTihanyHungary
| | - Jani Heino
- Finnish Environment InstituteFreshwater CentreOuluFinland
| | - Gabriel Singer
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Sonja C Jähnig
- Leibniz Institute of Freshwater Ecology and Inland FisheriesDepartment of Ecosystem ResearchBerlinGermany
- Geography DepartmentFaculty of Mathematics and Natural SciencesHumboldt‐Universität zu BerlinBerlinGermany
| | - Miguel Cañedo‐Argüelles
- Freshwater Ecology, Hydrology and Management Research GroupDepartament de Biologia EvolutivaEcologia i Ciències AmbientalsFacultat de BiologiaUniversitat de BarcelonaBarcelonaSpain
- Institut de Recerca de l'AiguaUniversitat de BarcelonaBarcelonaSpain
| | - Núria Bonada
- Freshwater Ecology, Hydrology and Management Research GroupDepartament de Biologia EvolutivaEcologia i Ciències AmbientalsFacultat de BiologiaUniversitat de BarcelonaBarcelonaSpain
- Institut de Recerca de la BiodiversitatUniversitat de BarcelonaBarcelonaSpain
| | | | - Heikki Mykrä
- Finnish Environment InstituteFreshwater CentreOuluFinland
| | | | - Riikka Paloniemi
- Finnish Environment InstituteEnvironmental Policy CentreHelsinkiFinland
| | - Liisa Varumo
- Finnish Environment InstituteEnvironmental Policy CentreHelsinkiFinland
| | - Thibault Datry
- INRAEUR RiverLyCentre de Lyon‐VilleurbanneVilleurbanne CedexFrance
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Mendes SL, Machado MP, Coelho MM, Sousa VC. Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species. Heredity (Edinb) 2021; 127:401-412. [PMID: 34462578 PMCID: PMC8478877 DOI: 10.1038/s41437-021-00466-1] [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] [Received: 04/02/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023] Open
Abstract
Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers-Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis-using a population genomics dataset of 23,562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well-differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage, we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes.
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Affiliation(s)
- Sofia L. Mendes
- grid.9983.b0000 0001 2181 4263cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Miguel P. Machado
- grid.9983.b0000 0001 2181 4263cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Maria M. Coelho
- grid.9983.b0000 0001 2181 4263cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Vitor C. Sousa
- grid.9983.b0000 0001 2181 4263cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
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3
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High genetic differentiation in the endemic and endangered freshwater fish Achondrostoma salmantinum Doadrio and Elvira, 2007 from Spain, as revealed by mitochondrial and SNP markers. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01381-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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4
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Sousa-Santos C, Jesus TF, Fernandes C, Robalo JI, Coelho MM. Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data. Mol Phylogenet Evol 2018; 133:263-285. [PMID: 30583043 DOI: 10.1016/j.ympev.2018.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 01/05/2023]
Abstract
The evolutionary history of western Iberian Leuciscinae, obligatory freshwater fish, is directly linked to the evolution of the hydrographic network of the Iberian Peninsula after its isolation from the rest of Europe, which involved dramatic rearrangements such as the transition from endorheic lakes to open basins draining to the Atlantic. Previous phylogenetic research on western Iberian leuciscines, using mainly mitochondrial DNA and more recently one or two nuclear genes, has found contradictory results and there remain many unresolved issues regarding species relationships, taxonomy, and evolutionary history. Moreover, there is a lack of integration between phylogenetic and divergence time estimates and information on the timing of geomorphological changes and paleobasin rearrangements in the Iberian Peninsula. This study presents the first comprehensive fossil-calibrated multilocus coalescent species tree of western Iberian Leuciscinae (including 14 species of Achondrostoma, Iberochondrostoma, Pseudochondrostoma and Squalius endemic to the Iberian Peninsula, seven of which endemic to Portugal) based on seven nuclear genes, and from which we infer their biogeographic history by comparing divergence time estimates to known dated geological events. The phylogenetic pattern suggests slow-paced evolution of leuciscines during the Early-Middle Miocene endorheic phase of the main Iberian river basins, with the shift to exorheism in the late Neogene-Quaternary allowing westward dispersals that resulted in many cladogenetic events and a high rate of endemism in western Iberia. The results of this study also: (i) confirm the paraphyly of S. pyrenaicus with respect to S. carolitertii, and thus the possible presence of a new taxon in the Portuguese Tagus currently assigned to S. pyrenaicus; (ii) support the taxonomic separation of the Guadiana and Sado populations of S. pyrenaicus; (iii) show the need for further population sampling and taxonomic research to clarify the phylogenetic status of A. arcasii from the Minho basin and of the I. lusitanicum populations in the Sado and Tagus basins; and (iv) indicate that A. occidentale, I. olisiponensis and P. duriensis are the most ancient lineages within their respective genera.
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Affiliation(s)
- C Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - T F Jesus
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisbon, Portugal(2).
| | - C Fernandes
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
| | - J I Robalo
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - M M Coelho
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
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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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Pavinato VAC, Michel AP, de Campos JB, Omoto C, Zucchi MI. Influence of historical land use and modern agricultural expansion on the spatial and ecological divergence of sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae) in Brazil. Heredity (Edinb) 2017; 120:25-37. [PMID: 29234172 DOI: 10.1038/s41437-017-0018-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/02/2017] [Accepted: 09/29/2017] [Indexed: 01/06/2023] Open
Abstract
Human-mediated changes in landscapes can facilitate niche expansion and accelerate the adaptation of insect species. The interaction between the evolutionary history of the sugarcane borer, Diatraea saccharalis Fabricius, and historical and modern agricultural activity in Brazil shaped its spatial genetic structure, facilitating ecological divergence and incipient host shifting. Based on microsatellite data, STRUCTURE analyses identified two (K = 2) and three (K = 3) significant genetic clusters that corresponded to: (a) a strong signal of spatial genetic structure and, (b) a cryptic signal of host differentiation. We inferred that K = 2 reflects the footprint of agricultural activity, such as expansion of crop production (sugarcane and maize), unintentional dispersion of pests, and management practices. In contrast, K = 3 indicated incipient host differentiation between larvae collected from sugarcane or maize. Our estimates of population size changes indicated that a historical bottleneck was associated with a reduction of sugarcane production ≈200 years ago. However, a more recent population expansion was detected (>1950s), associated with agricultural expansion of large crop production into previously unfarmed land. Partial Mantel tests supported our hypothesis of incipient host adaptation, and identified isolation-by-environment (e.g., host plant) in São Paulo and Minas Gerais states, where sugarcane has been traditionally produced in Brazil. The impact of agricultural production on D. saccharalis may continue, as the current population structure may hinder the efficacy of refuge plants in delaying insect resistance evolution to Bt toxin.
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Affiliation(s)
- Vitor A C Pavinato
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, 6109, Campinas, SP, Brazil. .,Department of Entomology, Ohio Agricultural Research and Development Center, Thorne Hall, The Ohio State University, 1680, Madison Avenue, Wooster, OH, USA.
| | - Andrew P Michel
- Department of Entomology, Ohio Agricultural Research and Development Center, Thorne Hall, The Ohio State University, 1680, Madison Avenue, Wooster, OH, USA
| | - Jaqueline B de Campos
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, 6109, Campinas, SP, Brazil
| | - Celso Omoto
- Department of Entomology and Acarology, University of São Paulo, Avenida Pádua Dias 11, CP 9, Piracicaba, SP, Brazil
| | - Maria I Zucchi
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Avenida Bertrand Russel, s/n, Cidade Universitária Zeferino Vaz, 6109, Campinas, SP, Brazil.,Agribusiness Technological Development of São Paulo (APTA), Laboratory of Conservation Genetics and Genomics, Rodovia SP 127 km 30, CP 28, Piracicaba, SP, Brazil
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Cochran-Biederman JL, Wyman KE, French WE, Loppnow GL. Identifying correlates of success and failure of native freshwater fish reintroductions. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:175-86. [PMID: 25115187 DOI: 10.1111/cobi.12374] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 04/22/2014] [Indexed: 05/14/2023]
Abstract
Reintroduction of imperiled native freshwater fish is becoming an increasingly important conservation tool amidst persistent anthropogenic pressures and new threats related to climate change. We summarized trends in native fish reintroductions in the current literature, identified predictors of reintroduction outcome, and devised recommendations for managers attempting future native fish reintroductions. We constructed random forest classifications using data from 260 published case studies of native fish reintroductions to estimate the effectiveness of variables in predicting reintroduction outcome. The outcome of each case was assigned as a success or failure on the basis of the author's perception of the outcome and on whether or not survival, spawning, or recruitment were documented during post-reintroduction monitoring. Inadequately addressing the initial cause of decline was the best predictor of reintroduction failure. Variables associated with habitat (e.g., water quality, prey availability) were also good predictors of reintroduction outcomes, followed by variables associated with stocking (e.g., genetic diversity of stock source, duration of stocking event). Consideration of these variables by managers during the planning process may increase the likelihood for successful outcomes in future reintroduction attempts of native freshwater fish.
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Affiliation(s)
- Jennifer L Cochran-Biederman
- Conservation Biology Graduate Program, 135 Skok Hall, 1980 Folwell Avenue, Saint Paul, MN, 55108, U.S.A.; Biology Department, Winona State University, 175 W. Mark Street, Winona, MN, 55987, U.S.A
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Khedkar GD, Tiknaik A, Kalyankar AD, A CSR, Khedkar CD, Ron TB, Haymer D. Genetic structure of populations and conservation issues relating to an endangered catfish,Clarias batrachus,in India. ACTA ACUST UNITED AC 2014; 27:1181-7. [DOI: 10.3109/19401736.2014.945524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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9
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Genetic and morphological analyses indicate high population mixing in the endangered cichlid Alcolapia flock of East Africa. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0551-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Population structure and conservation genetic assessment of the endangered Pugnose Shiner, Notropis anogenus. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0542-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Metcalf JL, Love Stowell S, Kennedy CM, Rogers KB, McDonald D, Epp J, Keepers K, Cooper A, Austin JJ, Martin AP. Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout. Mol Ecol 2012; 21:5194-207. [DOI: 10.1111/mec.12028] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 07/30/2012] [Accepted: 08/03/2012] [Indexed: 11/29/2022]
Affiliation(s)
| | - S. Love Stowell
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder; CO; 80309; USA
| | - C. M. Kennedy
- U.S. Fish and Wildlife Service; Colorado Fish and Wildlife Conservation Office; Estes Park; CO; 80517; USA
| | - K. B. Rogers
- Aquatic Research Group; Colorado Parks and Wildlife; Steamboat Springs; CO; 80477; USA
| | - D. McDonald
- Department of Chemistry & Biochemistry and Biofrontiers Institute; University of Colorado; Boulder; CO; USA
| | - J. Epp
- Pisces Molecular; LLC; Boulder; CO; 80301; USA
| | - K. Keepers
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder; CO; 80309; USA
| | - A. Cooper
- Australian Centre for Ancient DNA; University of Adelaide; Adelaide; SA; 5005; Australia
| | - J. J. Austin
- Australian Centre for Ancient DNA; University of Adelaide; Adelaide; SA; 5005; Australia
| | - A. P. Martin
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder; CO; 80309; USA
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Zeng L, Cheng Q, Chen X. Microsatellite analysis reveals the population structure and migration patterns of Scomber japonicus (Scombridae) with continuous distribution in the East and South China Seas. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.02.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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LOPES-CUNHA MIGUEL, ABOIM MARIAA, MESQUITA NATACHA, ALVES MJUDITE, DOADRIO IGNACIO, COELHO MMANUELA. Population genetic structure in the Iberian cyprinid fish Iberochondrostoma lemmingii (Steindachner, 1866): disentangling species fragmentation and colonization processes. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01827.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Chiang TY, Lee TW, Hsu KC, Kuo CH, Lin DY, Lin HD. Population Structure in the Endangered Cyprinid FishPararasbora moltrechtiin Taiwan, Based on Mitochondrial and Microsatellite DNAs. Zoolog Sci 2011; 28:642-51. [DOI: 10.2108/zsj.28.642] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Henriques R, Sousa V, Coelho MM. Migration patterns counteract seasonal isolation of Squalius torgalensis, a critically endangered freshwater fish inhabiting a typical Circum-Mediterranean small drainage. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0078-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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