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Mitochondrial genetic diversity, phylogeography and historical demography of Moroccan native freshwater fishes: a case study of the genus Luciobarbus Heckel, 1843. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01107-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Chen Z, Grossfurthner L, Loxterman JL, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies. Evol Appl 2022; 15:3-21. [PMID: 35126645 PMCID: PMC8792483 DOI: 10.1111/eva.13335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research InstituteUniversity of IdahoHagermanIdahoUSA
| | - Lukas Grossfurthner
- Bioinformatics and Computational Biology Graduate ProgramUniversity of IdahoHagermanIdahoUSA
| | - Janet L. Loxterman
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | | | | | - Travis Seaborn
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Brandy Smith
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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Beltrán-López RG, González-Díaz AA, Soria-Barreto M, Garduño-Sánchez MA, Xochitla-Castrejón C, Rodiles-Hernández R, Ornelas-García CP. Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units. PeerJ 2021; 9:e11952. [PMID: 34532157 PMCID: PMC8404570 DOI: 10.7717/peerj.11952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
The endangered Chiapas killifish Tlaloc hildebrandi is an endemic freshwater species that lives in four subbasins of the Grijalva and Usumacinta basins, and one of the most geographically restricted species of the Produndulidae family. The species was originally described as endemic to springs in the high limestone plateau in San Cristóbal de Las Casas in the Río Amarillo subbasin (upper Grijalva basin). However, it was recently recorded in the Jataté and Tzaconejá subbasins in the upper Usumacinta basin, thereby expanding its known distribution range. The discovery of these populations is relevant not only for the conservation of the species but also for a better understanding of its evolutionary history. Currently, the scarce populations of T. hildebrandi, found in only a few localities in the Grijalva and Usumacinta basins, are fragmented and living under unfavorable conditions. Here, we analyzed three mitochondrial (mt-atp8&6 and mt-nd2) and one nuclear (nuc-s7) marker in order to assess the genetic diversity and population structure of T. hildebrandi. We found that, in comparison with other endangered freshwater fish species from Mexico, T. hildebrandi showed a lower level of genetic diversity (mt-nd2: h = 0.469, π = 0.0009; mt-atp8&6: h = 0.398, π = 0.001; and nuc-S7: h = 0.433, π = 0.001). Moreover, the analyzed populations exhibited a strong genetic structure in accordance with their geographic distribution, and can be placed into three genetic clusters: (1) Amarillo plus Chenhaló in the upper Grijalva basin, (2) Jataté, and (3) Tzaconejá, both in the upper Usumacinta basin. On the basis of our results, we propose the recognition of at least three evolutionarily significant units (ESUs) for the species and the urgent implementation of ex situ and in situ conservation and management efforts that consider the genetic background of the species.
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Affiliation(s)
- Rosa G Beltrán-López
- Colección Nacional de Peces, Departamento de Zoología. Instituto de Biología, Ciudad de México, Mexico
| | - Alfonso A González-Díaz
- Colección de Peces, Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, Mexico
| | - Miriam Soria-Barreto
- Centro de Investigación de Ciencias Ambientales, Facultad de Ciencias Naturales, Ciudad del Carmen, Campeche, Mexico.,Cátedra CONACYT. El Colegio de la Frontera Sur-Unidad San Cristóbal de Las Casas, San Cristobál de Las Casas, Chiapas, Mexico
| | | | - Carmela Xochitla-Castrejón
- Colección de Peces, Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, Mexico
| | - Rocío Rodiles-Hernández
- Colección de Peces, Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, Mexico
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Khedkar GD, Jamdade R, Kalyankar A, Tiknaik A, Ron TB, Haymer D. Genetic fragmentation in India's third longest river system, the Narmada. SPRINGERPLUS 2014; 3:385. [PMID: 25126486 PMCID: PMC4130967 DOI: 10.1186/2193-1801-3-385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 06/24/2014] [Indexed: 11/24/2022]
Abstract
India’s third longest river, the Narmada, is studied here for the potential effects on native fish populations of river fragmentation due to various barriers including dams and a waterfall. The species we studied include a cyprinid fish, Catla catla, and a mastacembelid, Mastacembelus armatus, both of which are found in the Narmada. Our goal was to use DNA sequence information from the D-loop region of the mitochondrial DNA to explore how this fragmentation could impact the genetic structure of these fish populations. Our results clearly show that these barriers can contribute to the fragmentation of the genetic structure of these fish communities, Furthermore, these barriers enhance the effects of natural isolation by distance and the asymmetry of dispersal flows. This may be a slow process, but it can create significant isolation and result in genetic disparity. In particular, populations furthest upstream having low migration rates could be even more subject to genetic impoverishment. This study serves as a first report of its kind for a river system on the Indian subcontinent. The results of this study also emphasize the need for appropriate attention towards the creation of fish passages across the dams and weirs that could help in maintaining biodiversity.
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Affiliation(s)
- Gulab D Khedkar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, 431004 India ; Department of Cell and Molecular Biology, University of Hawaii, 1960 East-West Rd, Honolulu, HI 96822 USA
| | - Rahul Jamdade
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, 431004 India
| | - Amol Kalyankar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, 431004 India
| | - Anita Tiknaik
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, 431004 India
| | - Tetsuzan Benny Ron
- College of Tropical Agriculture and Human Resources, Department of Human Nutrition, Food and Animal Sciences, University of Hawaii, Honolulu, HI USA
| | - David Haymer
- Department of Cell and Molecular Biology, University of Hawaii, 1960 East-West Rd, Honolulu, HI 96822 USA
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Limborg MT, Blankenship SM, Young SF, Utter FM, Seeb LW, Hansen MHH, Seeb JE. Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss. Ecol Evol 2012; 2:1-18. [PMID: 22408722 PMCID: PMC3297173 DOI: 10.1002/ece3.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/27/2011] [Accepted: 09/27/2011] [Indexed: 12/21/2022] Open
Abstract
Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies
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Gutiérrez-Rodríguez C, Shearer AE, Morris MR, de Queiroz K. Phylogeography and monophyly of the swordtail fish species Xiphophorus birchmanni (Cyprinodontiformes, Poeciliidae). ZOOL SCR 2008. [DOI: 10.1111/j.1463-6409.2007.00311.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and man-made barriers in the Russian River, California. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9183-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gutiérrez-Rodríguez C, Morris MR, Dubois NS, Queiroz KD. Genetic variation and phylogeography of the swordtail fish Xiphophorus cortezi (Cyprinodontiformes, Poeciliidae). Mol Phylogenet Evol 2006; 43:111-23. [PMID: 17194605 DOI: 10.1016/j.ympev.2006.10.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Revised: 09/27/2006] [Accepted: 10/20/2006] [Indexed: 11/25/2022]
Abstract
Swordtail fish have been studied extensively in relation to diverse aspects of biology; however, little attention has been paid to the patterns of genetic variation within and among populations of swordtails. In this study, we sequenced the mtDNA control region from 65 individuals and 10 populations of Xiphophorus cortezi to investigate the genetic variation within and among populations, including tests for correlations between genetic and geographic distances and tests for species monophyly. We found low gene and nucleotide diversity within populations and high degrees of genetic differentiation among populations. Significant and positive correlations between genetic distance and both river and straight-line geographic distance indicate that genetic differentiation among X. cortezi populations can be explained, to some extent, by an isolation-by-distance model and provide evidence of stream capture. Phylogenetic analyses suggest that X. cortezi is paraphyletic relative to X. malinche, raising questions concerning the status of these taxa as separate species.
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Microsatellite DNA analysis of rainbow trout (Oncorhynchus mykiss) from western Alberta, Canada: native status and evolutionary distinctiveness of “Athabasca” rainbow trout. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9142-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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McCusker MR, Parkinson E, Taylor EB. Mitochondrial DNA variation in rainbow trout (Oncorhynchus mykiss) across its native range: testing biogeographical hypotheses and their relevance to conservation. Mol Ecol 2000; 9:2089-108. [PMID: 11123621 DOI: 10.1046/j.1365-294x.2000.01121.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
North-western North America has been repeatedly glaciated over most of the past two million years, with the most recent glaciation occurring between 60 000 and 10 000 years ago. Intraspecific genetic variation in many species has been shaped by where they survived glaciation and what postglacial recolonization routes were used. In this study, molecular techniques were used to investigate biogeographical, taxonomic and conservation issues in rainbow trout, Oncorhynchus mykiss. Mitochondrial DNA (mtDNA) variation was assessed using a restriction fragment length polymorphism (RFLP) analysis, focusing mainly on the previously understudied northern extent of the species' range. Two phylogenetically distinct mitochondrial lineages were found that differed from each other by up to 1.8% in sequence. Although the geographical distributions of the two clades overlap extensively, diversity and distributional analyses strongly suggest that trout survived glaciation in both coastal and inland refugia followed by postglacial gene flow and secondary contact. Postglacial dispersal into British Columbia most likely occurred from the Queen Charlotte Islands and the Columbia River. Although trout most likely also survived glaciation along the coast of Washington, Oregon and California, as well as near the Bering Strait, evidence suggests that dispersal into British Columbia from these areas was limited. Sequence analysis of mitochondrial haplotypes revealed higher diversity in California than in the northern part of the species' range, indicating an ancient presence of the species in the south. Phylogeographic divergence probably predates adaptive variation in the species as suggested by evidence for parallel evolution of life history types across the range of O. mykiss.
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Affiliation(s)
- M R McCusker
- Department of Zoology and Native Fish Research Group, University of British Columbia, 6270 University Blvd., Vancouver, B.C., Canada
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Genetic consequences of an artificial introduction of guppies
(Poecilia reticulata)
in N. Trinidad. Proc Biol Sci 1997. [DOI: 10.1098/rspb.1992.0049] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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LARGIADER CR, SCHOLL A. Genetic introgression between native and introduced brown troutSalmo truttaL. populations in the Rhone River Basin. Mol Ecol 1996. [DOI: 10.1046/j.1365-294x.1996.00099.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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LARGIADER CR, SCHOLL A. Genetic introgression between native and introduced brown trout Salmo trutta L. populations in the Rhone River Basin. Mol Ecol 1996. [DOI: 10.1111/j.1365-294x.1996.tb00331.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Coppes Z. Isozymes of glucosephosphate isomerase (PGI) in fishes of the subclass actinopterygii. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1986; 84:575-88. [PMID: 3757487 DOI: 10.1016/0305-0491(86)90126-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A compilation of the species of fishes of the subclass Actinopterygii for the study of the PGI isozyme system is given. PGI appears to be codified by more than one locus in fishes; 65% of the species analysed here have two loci for PGI. PGI duplication in fishes and the relationship of isozymes of PGI with temperature and metabolism are discussed.
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