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Amoutchi AI, Kersten P, Vogt A, Kohlmann K, Kouamelan EP, Mehner T. Population genetics of the African snakehead fish Parachanna obscura along West Africa's water networks: Implications for sustainable management and conservation. Ecol Evol 2023; 13:e9724. [PMID: 36694547 PMCID: PMC9842884 DOI: 10.1002/ece3.9724] [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: 09/07/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023] Open
Abstract
An essential factor for aquatic conservation is genetic diversity or population divergence, which in natural populations reflects the interplay between geographical isolation with restricted gene flow and local evolution of populations. The long geological history of Africa may induce stronger among-population divergence and lower within-population divergence in fish populations of African watersheds. As an example, we studied population structure of the African snakehead fish Parachanna obscura. Our study aimed: (1) to develop a set of highly polymorphic microsatellite markers suitable for the analysis of genetic diversity among P. obscura and (2) to study the genetic diversity and structure of P. obscura populations from the West Africa region and mostly from Côte d'Ivoire, with respect to the effects of climate region and geographical distance on the genetic differentiation. A total of 259 specimens from 15 locations of P. obscura were collected over the West Africa region reflecting a high variability of pairwise geographical distances and variability of hydrological connectivity of the area. We developed a set of 21 polymorphic microsatellite markers for studying population genetics of the fish. The results showed relatively low intragenetic diversity for all the 15 locations, certainly attributable to confinement of fish in segregated catchments, resulting in limited gene flow. We also found evidence for local adaptation processes, suggested by five out of 21 microsatellite loci being under putative selection, according to BAYESCAN analysis. In turn, there was strong genetic differentiation (F ST > 0.5) among fish from most locations, reflecting the allopatric development in watersheds without hydraulic connectivity. Neighbor-joining dendrogram, Principal Coordinate Analysis, and analysis of ancestral groups by STRUCTURE suggested that the 15 locations can be divided into three clusters, mainly matching the dominant climate zones and the segregation of the watersheds in the region. The distinct genetic structure of the fish from the 15 locations obtained in this study suggests that conservation and sustainable management actions of this fish resource should avoid genetic mixing of potentially locally adapted populations.
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Affiliation(s)
- Amien Isaac Amoutchi
- West African Science Service Centre on Climate Change and Adapted Land Use (WASCAL) Graduate Research Program on Climate Change and BiodiversityUniversité Felix Houphouet‐BoignyAbidjanCôte d'Ivoire,Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Petra Kersten
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Asja Vogt
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Klaus Kohlmann
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Essetchi Paul Kouamelan
- Laboratoire d'Hydrobiologie, UFR BiosciencesUniversité Felix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Thomas Mehner
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
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Abdulmalik-Labe OP, Quilang JP. Genetic diversity of lacustrine populations of the snakehead gudgeon Giuris laglaizei (Gobiiformes: Eleotridae) in the Philippines based on mitochondrial DNA control region. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01257-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Franklin TW, Dysthe JC, Neville H, Young MK, McKelvey KM, Schwartz MK. Lahontan Cutthroat Trout (Oncorhynchus clarkii henshawi) and Paiute Cutthroat Trout (Oncorhynchus clarkii seleniris) Detection from Environmental DNA Samples: A Dual-Purpose Assay. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Thomas W. Franklin
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| | - Joseph C. Dysthe
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| | | | - Michael K. Young
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| | - Kevin M. McKelvey
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| | - Michael K. Schwartz
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
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Meyer KA, Hillyard RW, Campbell MR. Detecting Rainbow Trout Introgression in Bonneville Cutthroat Trout of the Bear River Basin Using Field-Based Phenotypic Characteristics. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Kevin A. Meyer
- Idaho Department of Fish and Game, 1414 E. Locust Lane, Nampa, ID 83686
| | - Ryan W. Hillyard
- Idaho Department of Fish and Game, 1345 Barton Rd., Pocatello, ID 83204
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Weitemier K, Penaluna BE, Hauck LL, Longway LJ, Garcia T, Cronn R. Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding. Mol Ecol 2021; 30:4970-4990. [PMID: 33594756 PMCID: PMC8597136 DOI: 10.1111/mec.15811] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/23/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
Genetic diversity underpins species conservation and management goals, and ultimately determines a species' ability to adapt. Using freshwater environmental DNA (eDNA) samples, we examined mitochondrial genetic diversity using multigene metabarcode sequence data from four Oncorhynchus species across 16 sites in Oregon and northern California. Our multigene metabarcode panel included targets commonly used in population genetic NADH dehydrogenase 2 (ND2), phylogenetic cytochrome c oxidase subunit 1 (COI) and eDNA (12S ribosomal DNA) screening. The ND2 locus showed the greatest within-species haplotype diversity for all species, followed by COI and then 12S rDNA for all species except Oncorhynchus kisutch. Sequences recovered for O. clarkii clarkii were either identical to, or one mutation different from, previously characterized haplotypes (95.3% and 4.5% of reads, respectively). The greatest diversity in O. c. clarkii was among coastal watersheds, and subsets of this diversity were shared with fish in inland watersheds. However, coastal streams and the Umpqua River watershed appear to harbour unique haplotypes. Sequences from O. mykiss revealed a disjunction between the Willamette watershed and southern watersheds suggesting divergent histories. We also identified similarities between populations in the northern Deschutes and southern Klamath watersheds, consistent with previously hypothesized connections between the two via inland basins. Oncorhynchus kisutch was only identified in coastal streams and the Klamath River watershed, with most diversity concentrated in the coastal Coquille watershed. Oncorhynchus tshawytscha was only observed at one site, but contained multiple haplotypes at each locus. The characterization of genetic diversity at multiple loci expands the knowledge gained from eDNA sampling and provides crucial information for conservation actions and genetic management.
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Affiliation(s)
- Kevin Weitemier
- Department of Fisheries and WildlifeOregon State UniversityCorvallisORUSA
| | - Brooke E. Penaluna
- U.S. Department of Agriculture, Forest ServicePacific Northwest Research StationCorvallisORUSA
| | - Laura L. Hauck
- U.S. Department of Agriculture, Forest ServicePacific Northwest Research StationCorvallisORUSA
| | - Lucas J. Longway
- Department of Fisheries and WildlifeOregon State UniversityCorvallisORUSA
| | - Tiffany Garcia
- Department of Fisheries and WildlifeOregon State UniversityCorvallisORUSA
| | - Richard Cronn
- U.S. Department of Agriculture, Forest ServicePacific Northwest Research StationCorvallisORUSA
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Beltrán-López RG, Domínguez-Domínguez O, Piller KR, Mejía-Mojica H, Mar-Silva AF, Doadrio I. Genetic differentiation among populations of the blackfin goodea Goodea atripinnis (Cyprinodontiformes: Goodeidae): implications for its evolutionary history. JOURNAL OF FISH BIOLOGY 2021; 98:1253-1266. [PMID: 33350467 DOI: 10.1111/jfb.14654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Central Mexico is characterized by a complex topography that is the result of historic and contemporary tectonic and climatic factors. These events have influenced the evolutionary history of numerous freshwater fishes in the region. Nonetheless, recent studies have shown that life-history traits and ecological characteristics of species may influence dispersal capabilities and the degree of genetic connectivity. Goodea (Cyprinodontiformes: Goodeidae) is one of the most widely distributed and environmentally tolerant genera of goodeids. In this study, the authors analysed variation in the mitochondrial cytochrome b gene to evaluate the phylogeographic relationships, genetic structure, genetic diversity and demographic history of Goodea from across its distribution range. They found low genetic differentiation and identified shared haplotypes among several regions. Geographic segregation was found in samples southwest and northeast of the Lower Lerma region, with some internal isolated groups showing phylogeographic differentiation and unique haplotypes. The AMOVA best explained genetic structure when grouped by haplogroups rather than when grouped by recognized biogeographic regions. Several regions showed null genetic diversity, raising the possibility of dispersal mediated by humans. Finally, Bayesian Skyline Plot analysis showed a population expansion for the Southwest haplogroup, except for the Armería population and sub-group II of the Northeast haplogroup. All this suggests a recent colonization of Goodea atripinnis throughout some of the biogeographic regions currently inhabited by this species.
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Affiliation(s)
- Rosa Gabriela Beltrán-López
- Programa Institucional de Doctorado en Ciencias Biológicas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
- Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
- Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Kyle R Piller
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, USA
| | - Humberto Mejía-Mojica
- Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Adán Fernando Mar-Silva
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
- Programa Institucional de Maestría en Ciencias Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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Keeley ER, Loxterman JL, Matsaw SL, Njoroge ZM, Seiler MB, Seiler SM. Morphological and genetic concordance of cutthroat trout ( Oncorhynchus clarkii) diversification from western North America. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cutthroat trout (Oncorhynchus clarkii (Richardson, 1836)) is one of the most widely distributed species of freshwater fish in western North America. Occupying a diverse range of habitats, they exhibit significant phenotypic variability that is often recognized by intraspecific taxonomy. Recent molecular phylogenies have described phylogenetic diversification across cutthroat trout populations, but no study has provided a range-wide morphological comparison of taxonomic divisions. In this study, we used linear- and geometric-based morphometrics to determine if phylogenetic and subspecies divisions correspond to morphological variation in cutthroat trout, using replicate populations from throughout the geographic range of the species. Our data indicate significant morphological divergence of intraspecific categories in some, but not all, cutthroat trout subspecies. We also compare morphological distance measures with distance measures of mtDNA sequence divergence. DNA sequence divergence was positively correlated with morphological distance measures, indicating that morphologically more similar subspecies have lower sequence divergence in comparison to morphologically distant subspecies. Given these results, integrating both approaches to describing intraspecific variation may be necessary for developing a comprehensive conservation plan in wide-ranging species.
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Affiliation(s)
- Ernest R. Keeley
- Department of Biological Sciences, Mail Stop 8007, Idaho State University, Pocatello, ID 83209, USA
| | - Janet L. Loxterman
- Department of Biological Sciences, Mail Stop 8007, Idaho State University, Pocatello, ID 83209, USA
| | - Sammy L. Matsaw
- Department of Biological Sciences, Mail Stop 8007, Idaho State University, Pocatello, ID 83209, USA
| | - Zacharia M. Njoroge
- Department of Biological Sciences, Mail Stop 8007, Idaho State University, Pocatello, ID 83209, USA
| | | | - Steven M. Seiler
- Department of Biology, Lock Haven University, Lock Haven, PA 17745, USA
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8
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Wu H, Gu Q, Zhou C, Tang Y, Husemann M, Meng X, Zhang J, Nie G, Li X. Molecular phylogeny and biogeography of Triplophysa stone loaches in the Central Chinese Mountains. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractThe geological structure and history of mountains often cause highly complex patterns of evolution. The origin and diversity of the genus Triplophysa is considered to be closely associated with the rapid and persistent rise of the Qinghai-Tibet Plateau (QTP). Species of the genus are widely distributed in the QTP and adjacent regions, and are strongly adapted to its extreme environments. However, the Central Chinese Mountains (CCM), which are far apart from the QTP, also have many Triplophysa populations and yet their taxonomy, phylogeny and origin are unknown. We used three mitochondrial genes of 266 individuals from 29 sites in the CCM to shed light on the evolution of these Triplophysa populations. Phylogenetic analyses and species delimitation revealed seven distinct molecular operational taxonomic units (mOTUs) in the CCM, each with low genetic diversity. Molecular clock and biogeographic analyses suggested that vicariance events resulting from the rapid uplifting of the Qinling and Taihang Mountains initialized diversification in the Pliocene. During the early Pleistocene, dispersal events in the central parts of the Yellow River drainage altered genetic diversity and led to the currently observed biogeographic patterns. Our results suggest the presence of at least six species of Triplophysa in the CCM and more are likely to be discovered in the future.
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Affiliation(s)
- Huihui Wu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Qianhong Gu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, P.R. China
| | - Chuanjiang Zhou
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Yongtao Tang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Martin Husemann
- Centrum für Naturkunde, Universität Hamburg, Hamburg, Germany
| | - Xiaolin Meng
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Jianxin Zhang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Guoxing Nie
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
| | - Xuejun Li
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, P.R. China
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Simmons JB, Campbell T, Jerde CL, Chandra S, Cowan W, Hogan Z, Saenz J, Shoemaker K. Population dynamics of threatened Lahontan cutthroat trout in Summit Lake, Nevada. Sci Rep 2020; 10:9184. [PMID: 32513963 PMCID: PMC7280232 DOI: 10.1038/s41598-020-65992-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/04/2020] [Indexed: 11/24/2022] Open
Abstract
Summit Lake, Nevada (USA) is the last high-desert terminal lake to have a native self-sustaining population of threatened Lahontan cutthroat trout (Oncorhynchus clarkii henshawi). From spring 2015 to fall 2017, we quantified adult abundance and survival and the total annual spawning run. Abundance and survival were estimated with mark-recapture using PIT tags, and the annual spawning run was estimated with PIT tag detections and counts of spawners. Adult abundance fluctuated from 830 (95% CI 559–1248) to 1085 (95% CI 747–1614), with no overall temporal trend, as a decrease in male abundance was generally offset by an equal increase in female abundance. Estimated mean adult survival was 0.51 (95% CI 0.44–0.58). The spawning run increased from 645 (2015) to 868 (2016), but then decreased slightly to 824 (2017, mean = 789 ± 118). Female spawners increased in 2016 but decreased slightly in 2017, whereas male spawners decreased each year. In addition, the proportion of adults that spawned each year increased overall. Our study suggests that the adult population remained stable although most of the study period included the recent, severe regional drought in the western United States (2012–2016).
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Affiliation(s)
- James B Simmons
- University of Nevada, Global Water Center, Department of Biology, Reno, Nevada, United States of America.
| | - Teresa Campbell
- University of Nevada, Global Water Center, Department of Biology, Reno, Nevada, United States of America
| | - Christopher L Jerde
- University of Nevada, Global Water Center, Department of Biology, Reno, Nevada, United States of America.,University of California, Marine Science Institute, Santa Barbara, California, United States of America
| | - Sudeep Chandra
- University of Nevada, Global Water Center, Department of Biology, Reno, Nevada, United States of America
| | - William Cowan
- Summit Lake Paiute Tribe, Sparks, Nevada, United States of America
| | - Zeb Hogan
- University of Nevada, Global Water Center, Department of Biology, Reno, Nevada, United States of America
| | - Jessica Saenz
- Summit Lake Paiute Tribe, Sparks, Nevada, United States of America.,The Great Basin Institute, Reno, Nevada, United States of America
| | - Kevin Shoemaker
- University of Nevada, Department of Natural Resources and Environmental Science, Reno, Nevada, United States of America
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Aguilar C, Miller MJ, Loaiza JR, González R, Krahe R, De León LF. Tempo and mode of allopatric divergence in the weakly electric fish Sternopygus dariensis in the Isthmus of Panama. Sci Rep 2019; 9:18828. [PMID: 31827183 PMCID: PMC6906317 DOI: 10.1038/s41598-019-55336-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/27/2019] [Indexed: 01/12/2023] Open
Abstract
Spatial isolation is one of the main drivers of allopatric speciation, but the extent to which spatially-segregated populations accumulate genetic differences relevant to speciation is not always clear. We used data from ultraconserved elements (UCEs) and whole mitochondrial genomes (i.e., mitogenomes) to explore genetic variation among allopatric populations of the weakly electric fish Sternopygus dariensis across the Isthmus of Panama. We found strong genetic divergence between eastern and western populations of S. dariensis. Over 77% of the UCE loci examined were differentially fixed between populations, and these loci appear to be distributed across the species' genome. Population divergence occurred within the last 1.1 million years, perhaps due to global glaciation oscillations during the Pleistocene. Our results are consistent with a pattern of genetic differentiation under strict geographic isolation, and suggest the presence of incipient allopatric species within S. dariensis. Genetic divergence in S. dariensis likely occurred in situ, long after the closure of the Isthmus of Panama. Our study highlights the contribution of spatial isolation and vicariance to promoting rapid diversification in Neotropical freshwater fishes. The study of spatially-segregated populations within the Isthmus of Panama could reveal how genetic differences accumulate as allopatric speciation proceeds.
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Affiliation(s)
- Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Matthew J Miller
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Jose R Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Panamá, República de Panamá
| | - Rigoberto González
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
| | - Rüdiger Krahe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Luis F De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá.
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá.
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
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11
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Eaton KR, Loxterman JL, Keeley ER. Connections and containers: Using genetic data to understand how watershed evolution and human activities influence cutthroat trout biogeography. PLoS One 2018; 13:e0202043. [PMID: 30096159 PMCID: PMC6086439 DOI: 10.1371/journal.pone.0202043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/26/2018] [Indexed: 11/19/2022] Open
Abstract
Species with large geographic distributions often exhibit complex patterns of diversity that can be further complicated by human activities. Cutthroat trout (Oncorhynchus clarkii) are one of the most widely distributed freshwater fish species in western North America exhibiting substantial phenotypic and genetic variability; however, fish stocking practices have translocated populations outside of their native range and may have obscured intraspecific boundaries. This study focuses on cutthroat trout populations representing three distinct evolutionary clades that are found intermixed within a contact zone between the Bonneville and upper Snake River watersheds in the western United States. We used mitochondrial and microsatellite genetic data, as well as historical stocking records, to evaluate whether populations of cutthroat trout in the contact zone are native or are introduced. We found significant genetic differentiation and fine-scale genetic population structure that was organized primarily by watershed boundaries. While we detected increased genetic diversity in some areas in close proximity to the greatest number of stocking events, the highly organized population structure both within and between areas of the contact zone indicates that the populations are native to the watersheds. Intermixing of distinct evolutionary lineages of cutthroat trout appears to be the result of historical connections between paleodrainages. Our analyses provide a context for understanding how genetic data can be used to assess the status of populations as native or introduced.
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Affiliation(s)
- Kendra R. Eaton
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Janet L. Loxterman
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Ernest R. Keeley
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
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12
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McKelvey KS, Young MK, Wilcox TM, Bingham DM, Pilgrim KL, Schwartz MK. Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams. Ecol Evol 2016; 6:688-706. [PMID: 26865958 PMCID: PMC4739558 DOI: 10.1002/ece3.1887] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/09/2015] [Accepted: 11/23/2015] [Indexed: 01/17/2023] Open
Abstract
Introgressive hybridization between native and introduced species is a growing conservation concern. For native cutthroat trout and introduced rainbow trout in western North America, this process is thought to lead to the formation of hybrid swarms and the loss of monophyletic evolutionary lineages. Previous studies of this phenomenon, however, indicated that hybrid swarms were rare except when native and introduced forms of cutthroat trout co‐occurred. We used a panel of 86 diagnostic, single nucleotide polymorphisms to evaluate the genetic composition of 3865 fish captured in 188 locations on 129 streams distributed across western Montana and northern Idaho. Although introgression was common and only 37% of the sites were occupied solely by parental westslope cutthroat trout, levels of hybridization were generally low. Of the 188 sites sampled, 73% contained ≤5% rainbow trout alleles and 58% had ≤1% rainbow trout alleles. Overall, 72% of specimens were nonadmixed westslope cutthroat trout, and an additional 3.5% were nonadmixed rainbow trout. Samples from seven sites met our criteria for hybrid swarms, that is, an absence of nonadmixed individuals and a random distribution of alleles within the sample; most (6/7) were associated with introgression by Yellowstone cutthroat trout. In streams with multiple sites, upstream locations exhibited less introgression than downstream locations. We conclude that although the widespread introduction of nonnative trout within the historical range of westslope cutthroat trout has increased the incidence of introgression, sites containing nonadmixed populations of this taxon are common and broadly distributed.
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Affiliation(s)
- Kevin S McKelvey
- USDA Forest Service Rocky Mountain Research Station National Genomics Center for Wildlife and Fish Conservation 800 East Beckwith Avenue Missoula Montana 59801
| | - Michael K Young
- USDA Forest Service Rocky Mountain Research Station National Genomics Center for Wildlife and Fish Conservation 800 East Beckwith Avenue Missoula Montana 59801
| | - Taylor M Wilcox
- USDA Forest Service Rocky Mountain Research Station National Genomics Center for Wildlife and Fish Conservation 800 East Beckwith Avenue Missoula Montana 59801; Division of Biological Sciences University of Montana Missoula Montana 59812
| | - Daniel M Bingham
- Rogue Biological Consultants 215 NW 22nd Pl Suite 207 Portland OR 97217
| | - Kristine L Pilgrim
- USDA Forest Service Rocky Mountain Research Station National Genomics Center for Wildlife and Fish Conservation 800 East Beckwith Avenue Missoula Montana 59801
| | - Michael K Schwartz
- USDA Forest Service Rocky Mountain Research Station National Genomics Center for Wildlife and Fish Conservation 800 East Beckwith Avenue Missoula Montana 59801
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Huang X, Li F, Chen J. Reserve network planning for fishes in the middle and lower Yangtze River basin by systematic conservation approaches. SCIENCE CHINA-LIFE SCIENCES 2016; 59:312-24. [PMID: 26749039 DOI: 10.1007/s11427-015-4950-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/14/2015] [Indexed: 11/27/2022]
Abstract
Although China has established more than 600 wetland nature reserves, conservation gaps still exist for many species, especially for freshwater fishes. Underlying this problem is the fact that top-level planning is missing in the construction of nature reserves. To promote the development of nature reserves for fishes, this study took the middle and lower reaches of the Yangtze River basin (MLYRB) as an example to carry out top-level reserve network planning for fishes using approaches of systematic conservation planning. Typical fish species living in freshwater habitats were defined and considered in the planning. Based on sample data collected from large quantities of literatures, continuous distribution patterns of 142 fishes were obtained with species distribution modeling and subsequent processing, and the distributions of another eleven species were artificially designated. With the distribution pattern of species, Marxan was used to carry out conservation planning. To obtain ideal solutions with representativeness, persistence, and efficiency, parameters were set with careful consideration regarding existing wetland reserves, human disturbances, hydrological connectivity, and representation targets of species. Marxan produced the selection frequency of planning units (PUs) and a best solution. Selection frequency indicates the relative protection importance of a PU. The best solution is a representative of ideal fish reserve networks. Both of the PUs with high selection frequency and those in the best solution have low proportions included in existing wetland nature reserves, suggesting that there are significant conservation gaps for fish species in MLYRB. The best solution could serve as a reference for establishing a fish reserve network in the MLYRB. There is great flexibility for replacing selected PUs in the solution, and such flexibility facilitates the implementation of the solution in reality in case of unexpected obstacles. Further, we suggested adopting a freshwater management framework in the implementation of such solution.
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Affiliation(s)
- Xinyi Huang
- Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China
| | - Fan Li
- Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China
| | - Jiakuan Chen
- Institute of Biodiversity Science, Fudan University, Shanghai, 200438, China.
- Center for Watershed Ecology, Institute of Life Science, Nanchang University, Nanchang, 330031, China.
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Sproul JS, Houston DD, Nelson CR, Evans RP, Crandall KA, Shiozawa DK. Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America. BMC Evol Biol 2015; 15:279. [PMID: 26653183 PMCID: PMC4676849 DOI: 10.1186/s12862-015-0553-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 11/27/2015] [Indexed: 11/12/2022] Open
Abstract
Background Phylogeographic studies of aquatic insects provide valuable insights into mechanisms that shape the genetic structure of communities, yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of the least salmonfly Pteronarcella badia (Plecoptera) across western North America. We tested hypotheses related to mode of dispersal and the influence of historic climate oscillations on population genetic structure. In order to generate a larger mitochondrial data set, we used 454 sequencing to reconstruct the complete mitochondrial genome in the early stages of the project. Results Our analysis revealed high levels of population structure with several deeply divergent clades present across the sample area. Evidence from five mitochondrial genes and one nuclear locus identified a potentially cryptic lineage in the Pacific Northwest. Gene flow estimates and geographic clade distributions suggest that overland flight during the winged adult stage is an important dispersal mechanism for this taxon. We found evidence of multiple glacial refugia across the species distribution and signs of secondary contact within and among major clades. Conclusions This study provides a basis for future studies of aquatic insect phylogeography at the inter-basin scale in western North America. Our findings add to an understanding of the role of historical climate isolations in shaping assemblages of aquatic insects in this region. We identified several geographic areas that may have historical importance for other aquatic organisms with similar distributions and dispersal strategies as P. badia. This work adds to the ever-growing list of studies that highlight the potential of next-generation DNA sequencing in a phylogenetic context to improve molecular data sets from understudied groups. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0553-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John S Sproul
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR, 97333, USA.
| | - Derek D Houston
- Department of Ecology, Evolution and Organismal Biology, 251 Bessey Hall, Ames, IA, 50011, USA.
| | - C Riley Nelson
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA. .,M.L Bean Life Science Museum, Brigham Young University, 645 East 1430 North, Provo, UT, 84602, USA.
| | - R Paul Evans
- Department of Microbiology and Molecular Biology, Brigham Young University, 4007 Life Science Building, Provo, UT, 84602, USA.
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Innovation Hall, Ashburn, VA, 20147, USA.
| | - Dennis K Shiozawa
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA. .,M.L Bean Life Science Museum, Brigham Young University, 645 East 1430 North, Provo, UT, 84602, USA.
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The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus. PLoS One 2015; 10:e0142008. [PMID: 26536367 PMCID: PMC4633235 DOI: 10.1371/journal.pone.0142008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/15/2015] [Indexed: 11/29/2022] Open
Abstract
Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi), Yellowstone cutthroat trout (O. clarkii bouvieri), and rainbow trout (O. mykiss), which are of conservation interest both as native species and as invasive species across each other’s native ranges. We found that local polymorphisms within westslope cutthroat trout and rainbow trout posed a challenge to designing assays that are generally applicable across the range of these widely-distributed species. Further, poorly-resolved taxonomies of Yellowstone cutthroat trout and Bonneville cutthroat trout (O. c. utah) prevented design of an assay that distinguishes these recognized taxa. The issues of intraspecific polymorphism and unresolved taxonomy for eDNA assay design addressed in this study are likely to be general problems for closely-related taxa. Prior to field application, we recommend that future studies sample populations and test assays more broadly than has been typical of published eDNA assays to date.
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Liu HP, Hovingh P, Hershler R. Genetic Evidence for Recent Spread of Springsnails (Hydrobiidae:Pyrgulopsis) across the Wasatch Divide. WEST N AM NATURALIST 2015. [DOI: 10.3398/064.075.0309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Range-wide comparisons of northern leatherside chub populations reveal historical and contemporary patterns of genetic variation. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0576-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Page TJ, Hughes JM. Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12231] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Timothy J. Page
- Australian Rivers Institute; Griffith University; Nathan Qld 4111 Australia
| | - Jane M. Hughes
- Australian Rivers Institute; Griffith University; Nathan Qld 4111 Australia
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Kim D, Conway KW. Phylogeography ofRhinichthys cataractae(Teleostei: Cyprinidae): pre-glacial colonization across the Continental Divide and Pleistocene diversification within the Rio Grande drainage. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Daemin Kim
- Graduate Degree Program; Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall, 2258 TAMU College Station TX 77843 USA
| | - Kevin W. Conway
- Department of Wildlife and Fisheries Sciences & Biodiversity Research and Teaching Collections; Texas A&M University; 210 Nagle Hall, 2258 TAMU College Station TX 77843 USA
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Roberts JJ, Fausch KD, Peterson DP, Hooten MB. Fragmentation and thermal risks from climate change interact to affect persistence of native trout in the Colorado River basin. GLOBAL CHANGE BIOLOGY 2013; 19:1383-98. [PMID: 23505098 DOI: 10.1111/gcb.12136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/28/2012] [Indexed: 05/23/2023]
Abstract
Impending changes in climate will interact with other stressors to threaten aquatic ecosystems and their biota. Native Colorado River cutthroat trout (CRCT; Oncorhynchus clarkii pleuriticus) are now relegated to 309 isolated high-elevation (>1700 m) headwater stream fragments in the Upper Colorado River Basin, owing to past nonnative trout invasions and habitat loss. Predicted changes in climate (i.e., temperature and precipitation) and resulting changes in stochastic physical disturbances (i.e., wildfire, debris flow, and channel drying and freezing) could further threaten the remaining CRCT populations. We developed an empirical model to predict stream temperatures at the fragment scale from downscaled climate projections along with geomorphic and landscape variables. We coupled these spatially explicit predictions of stream temperature with a Bayesian Network (BN) model that integrates stochastic risks from fragmentation to project persistence of CRCT populations across the upper Colorado River basin to 2040 and 2080. Overall, none of the populations are at risk from acute mortality resulting from high temperatures during the warmest summer period. In contrast, only 37% of populations have a ≥90% chance of persistence for 70 years (similar to the typical benchmark for conservation), primarily owing to fragmentation. Populations in short stream fragments <7 km long, and those at the lowest elevations, are at the highest risk of extirpation. Therefore, interactions of stochastic disturbances with fragmentation are projected to be greater threats than warming for CRCT populations. The reason for this paradox is that past nonnative trout invasions and habitat loss have restricted most CRCT populations to high-elevation stream fragments that are buffered from the potential consequences of warming, but at risk of extirpation from stochastic events. The greatest conservation need is for management to increase fragment lengths to forestall these risks.
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Affiliation(s)
- James J Roberts
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA.
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Houston DD, Elzinga DB, Maughan PJ, Smith SM, Kauwe JSK, Evans RP, Stinger RB, Shiozawa DK. Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing. BMC Genomics 2012; 13:724. [PMID: 23259499 PMCID: PMC3549761 DOI: 10.1186/1471-2164-13-724] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 12/19/2012] [Indexed: 11/23/2022] Open
Abstract
Background Salmonids are popular sport fishes, and as such have been subjected to widespread stocking throughout western North America. Historically, stocking was done with little regard for genetic variation among populations and has resulted in genetic mixing among species and subspecies in many areas, thus putting the genetic integrity of native salmonid populations at risk and creating a need to assess the genetic constitution of native salmonid populations. Cutthroat trout is a salmonid species with pronounced geographic structure (there are 10 extant subspecies) and a recent history of hybridization with introduced rainbow trout in many populations. Genetic admixture has also occurred among cutthroat trout subspecies in areas where introductions have brought two or more subspecies into contact. Consequently, management agencies have increased their efforts to evaluate the genetic composition of cutthroat trout populations to identify populations that remain uncompromised and manage them accordingly, but additional genetic markers are needed to do so effectively. Here we used genome reduction, MID-barcoding, and 454-pyrosequencing to discover single nucleotide polymorphisms that differentiate cutthroat trout subspecies and can be used as a rapid, cost-effective method to characterize the genetic composition of cutthroat trout populations. Results Thirty cutthroat and six rainbow trout individuals were subjected to genome reduction and next-generation sequencing. A total of 1,499,670 reads averaging 379 base pairs in length were generated by 454-pyrosequencing, resulting in 569,060,077 total base pairs sequenced. A total of 43,558 putative SNPs were identified, and of those, 125 SNP primers were developed that successfully amplified 96 cutthroat trout and rainbow trout individuals. These SNP loci were able to differentiate most cutthroat trout subspecies using distance methods and Structure analyses. Conclusions Genomic and bioinformatic protocols were successfully implemented to identify 125 nuclear SNPs that are capable of differentiating most subspecies of cutthroat trout from one another. The ability to use this suite of SNPs to identify individuals of unknown genetic background to subspecies can be a valuable tool for management agencies in their efforts to evaluate the genetic structure of cutthroat trout populations prior to constructing and implementing conservation plans.
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Affiliation(s)
- Derek D Houston
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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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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