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Hale MC, Pearse DE, Campbell MA. Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (Oncorhynchus mykiss). G3 (BETHESDA, MD.) 2024:jkae100. [PMID: 38885060 DOI: 10.1093/g3journal/jkae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
Multiple studies in a range of taxa have found links between structural variants and the development of ecologically important traits. Such variants are becoming easier to find due, in large part, to the increase in the amount of genome-wide sequence data in nonmodel organisms. The salmonids (salmon, trout, and charr) are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture, fisheries, and variation in multiple ecologically important life-history traits. Previous research on rainbow trout (Oncorhynchus mykiss) has documented a large pericentric (∼55 Mb) chromosomal inversion (CI) on chromosome 5 (Omy05) and a second smaller (∼14 Mb) chromosome inversion on Omy20. While the Omy05 inversion appears to be associated with multiple adaptive traits, the inversion on Omy20 has received far less attention. In this study, we re-analyze RAD-seq and amplicon data from several populations of rainbow trout (O. mykiss) to better document the structure and geographic distribution of variation in the Omy20 CI. Moreover, we utilize phylogenomic techniques to characterize both the age- and the protein-coding gene content of the Omy20 CI. We find that the age of the Omy20 inversion dates to the early stages of O. mykiss speciation and predates the Omy05 inversion by ∼450,000 years. The 2 CIs differ further in terms of the frequency of the homokaryotypes. While both forms of the Omy05 CI are found across the eastern Pacific, the ancestral version of the Omy20 CI is restricted to the southern portion of the species range in California. Furthermore, the Omy20 inverted haplotype is comparable in genetic diversity to the ancestral form, whereas derived CIs typically show substantially reduced genetic diversity. These data contribute to our understanding of the age and distribution of a large CI in rainbow trout and provide a framework for researchers looking to document CIs in other nonmodel species.
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Affiliation(s)
- Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76109, USA
| | - Devon E Pearse
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, CA 95064, USA
| | - Matthew A Campbell
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
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2
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Lázari C, Riva-Rossi C, Ciancio J, Pascual M, Clemento AJ, Pearse DE, Garza JC. Ancestry and genetic structure of resident and anadromous rainbow trout (Oncorhynchus mykiss) in Argentina. JOURNAL OF FISH BIOLOGY 2024; 104:1972-1989. [PMID: 38556852 DOI: 10.1111/jfb.15722] [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: 04/20/2023] [Revised: 12/21/2023] [Accepted: 02/25/2024] [Indexed: 04/02/2024]
Abstract
Since the first introduction from North America more than a century ago, rainbow trout (Oncorhynchus mykiss) have rapidly established self-sustaining populations in major river basins of Patagonia. Many generations later, only the freshwater resident life history is expressed in the Chubut and Negro rivers of northern Argentinian Patagonia, whereas both the resident and anadromous life histories are found in the Santa Cruz River of southern Argentina. Despite previous studies that have tried to identify the sources of these introduced populations, uncertainty still exists. Here we combined data from many single-nucleotide polymorphisms and microsatellite loci in O. mykiss populations from Argentina and North America to evaluate putative source populations, gene flow between Argentinian river basins, and genetic diversity differences between Argentinian and North American populations. We found that populations from northern and southern Patagonia are highly differentiated and have limited gene flow between them. Phylogeographic analysis also confirmed that they have separate origins, with the northern populations most closely related to the domesticated rainbow trout strains that are raised worldwide and the Santa Cruz River populations most closely related to North American populations from California and Oregon that have an anadromous component. In addition, fish with different life histories in the Santa Cruz River were found to constitute a single interbreeding population. No evidence was found of reduced genetic variation in introduced rainbow trout, suggesting multiple contributing sources. In spite of these advances in understanding, significant questions remain regarding the origins and evolution of the introduced O. mykiss in Patagonia.
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Affiliation(s)
- Carolina Lázari
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Carla Riva-Rossi
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Puerto Madryn, Argentina
| | - Javier Ciancio
- Centro para el Estudio de Sistemas Marinos (CESIMAR-CONICET), Puerto Madryn, Argentina
| | - Miguel Pascual
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Puerto Madryn, Argentina
| | - Anthony J Clemento
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, USA
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
| | - Devon E Pearse
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, USA
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
| | - John Carlos Garza
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, USA
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
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3
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Jourdan J, Bundschuh M, Copilaș-Ciocianu D, Fišer C, Grabowski M, Hupało K, Jemec Kokalj A, Kabus J, Römbke J, Soose LJ, Oehlmann J. Cryptic Species in Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1889-1914. [PMID: 37314101 DOI: 10.1002/etc.5696] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Jonas Jourdan
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Denis Copilaș-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michał Grabowski
- Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Kabus
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie, Flörsheim am Main, Germany
| | - Laura J Soose
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
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4
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Post JR, Ward HGM, Wilson KL, Sterling GL, Cantin A, Taylor EB. Assessing conservation status with extensive but low-resolution data: Application of frequentist and Bayesian models to endangered Athabasca River rainbow trout. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13783. [PMID: 34114680 DOI: 10.1111/cobi.13783] [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: 06/03/2020] [Accepted: 05/28/2021] [Indexed: 06/12/2023]
Abstract
Use of extensive but low-resolution abundance data is common in the assessment of species at-risk status based on quantitative decline criteria under International Union for Conservation of Nature (IUCN) and national endangered species legislation. Such data can be problematic for 3 reasons. First, statistical power to reject the null hypothesis of no change is often low because of small sample size and high sampling uncertainty leading to a high frequency of type II errors. Second, range-wide assessments composed of multiple site-specific observations do not effectively weight site-specific trends into global trends. Third, uncertainty in site-specific temporal trends and relative abundance are not propagated at the appropriate spatial scale. A common result is the propensity to underestimate the magnitude of declines and therefore fail to identify the appropriate at-risk status for a species. We used 3 statistical approaches, from simple to more complex, to estimate temporal decline rates for a designatable unit (DU) of rainbow trout in the Athabasca River watershed in western Canada. This DU is considered a native species for purposes of listing because of its genetic composition characterized as >0.95 indigenous origin in the face of continuing introgressive hybridization with introduced populations in the watershed. Analysis of abundance trends from 57 time series with a fixed-effects model identified 33 sites with negative trends, but only 2 were statistically significant. By contrast, a hierarchical linear mixed model weighted by site-specific abundance provided a DU-wide decline estimate of 16.4% per year and a 3-generation decline of 93.2%. A hierarchical Bayesian mixed model yielded a similar 3-generation decline trend of 91.3% and the posterior distribution showed that the estimate had a >99% probability of exceeding thresholds for an endangered listing. We conclude that the Bayesian approach was the most useful because it provided a probabilistic statement of threshold exceedance in support of an at-risk status recommendation.
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Affiliation(s)
- John R Post
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hillary G M Ward
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Ministry of Forests, Lands and Natural Resource Operations, Penticton, British Columbia, Canada
| | - Kyle L Wilson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Central Coast Indigenous Resource Alliance, Campbell River, British Columbia, Canada
| | - George L Sterling
- Fisheries Branch, Operations Division, Alberta Environment and Parks, Edson, Alberta, Canada
| | - Ariane Cantin
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, Canada
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5
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Strowbridge N, Northrup SL, Earhart ML, Blanchard TS, Schulte PM. Acute measures of upper thermal and hypoxia tolerance are not reliable predictors of mortality following environmental challenges in rainbow trout ( Oncorhynchus mykiss). CONSERVATION PHYSIOLOGY 2021; 9:coab095. [PMID: 34987825 PMCID: PMC8710852 DOI: 10.1093/conphys/coab095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/16/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Anthropogenic climate change threatens freshwater biodiversity and poses a challenge for fisheries management, as fish will increasingly be exposed to episodes of high temperature and low oxygen (hypoxia). Here, we examine the extent of variation in tolerance of acute exposure to these stressors within and among five strains of rainbow trout (Oncorhynchus mykiss) currently being used or under consideration for use in stocking programmes in British Columbia, Canada. We used incipient lethal oxygen saturation (ILOS) as an index of acute hypoxia tolerance, critical thermal maximum (CTmax) as an index of acute upper thermal tolerance and mortality following these two acute exposure trials to assess the relative resilience of individuals and strains to climate change-relevant stressors. We measured tolerance across two brood years and two life stages (fry and yearling), using a highly replicated design with hundreds of individuals per strain and life stage. There was substantial within-strain variation in CTmax and ILOS, but differences among strains, although statistically significant, were small. In contrast, there were large differences in post-trial mortality among strains, ranging from less than 2% mortality in the most resilient strain to 55% mortality in the least resilient. There was a statistically significant, but weak, correlation between CTmax and ILOS at both life stages for some strains, with thermally tolerant individuals tending to be hypoxia tolerant. These data indicate that alternative metrics of tolerance may result in different conclusions regarding resilience to climate change stressors, which has important implications for stocking and management decisions for fish conservation in a changing climate.
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Affiliation(s)
- Nicholas Strowbridge
- Department of Zoology University of British Columbia, Vancouver, BC V6T 1 Z4, Canada
| | - Sara L Northrup
- Freshwater Fisheries Society of British Columbia, Abbotsford, BC V9A 7S2, Canada
| | - Madison L Earhart
- Department of Zoology University of British Columbia, Vancouver, BC V6T 1 Z4, Canada
| | - Tessa S Blanchard
- Department of Zoology University of British Columbia, Vancouver, BC V6T 1 Z4, Canada
| | - Patricia M Schulte
- Department of Zoology University of British Columbia, Vancouver, BC V6T 1 Z4, Canada
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6
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Salisbury SJ, Ruzzante DE. Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms. Annu Rev Anim Biosci 2021; 10:81-106. [PMID: 34758272 DOI: 10.1146/annurev-animal-051021-080709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- S J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
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7
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Hoc B, Tomson T, Malumba P, Blecker C, Jijakli MH, Purcaro G, Francis F, Caparros Megido R. Production of rainbow trout (Oncorhynchus mykiss) using black soldier fly (Hermetia illucens) prepupae-based formulations with differentiated fatty acid profiles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 794:148647. [PMID: 34217091 DOI: 10.1016/j.scitotenv.2021.148647] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
The aquaculture sector is expanding rapidly and needs an increasing supply of fishery products. To ensure an ecological transition of this sector, alternative feed ingredients are required for fish nutrition. Potential alternatives include insects, particularly the black soldier fly (BSF, Hermetia illucens L. 1758), which is being increasingly targeted for their nutritional qualities and their sustainable production practices. BSF have a well-balanced amino acid profile; however, their fatty acid profile is not sufficiently balanced for most aquafeed formulations but can be modulated through their feed. In this study, two different batches of BSF prepupae (BSFP) were firstly produced: BSFP with a standard ω3 content (C18:3n-3 ≈ 1.36%) and ω3-enriched BSFP (C18:3n-3 ≈ 9.67%). Then, three isoproteic, -lipidic and -energetic trout feeds were formulated and produced: one control and two feeds containing 75% BSF meal as a substitute for fish meal (standard vs ω3-enriched-BSF). Finally, a trout feeding trial (n = 3 for each feed batch) in a recirculating aquaculture system was carried out for 75 days. BSFP meal inclusion in trout diets did not impact most nutritional and growth parameters of trout compared to the control; however, the coefficient of fatness increased, weight gain decreased and fatty acid profiles of fillets were altered. In conclusion, this study presents a more sustainable model of trout production by including insects from bioconversion of local byproducts in aquafeed.
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Affiliation(s)
- Bertrand Hoc
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech (University of Liège), Passage des Déportés 2, 5030 Gembloux, Belgium.
| | - Thomas Tomson
- Integrated and Urban Plant Pathology, Gembloux Agro-Bio Tech (University of Liège), Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Paul Malumba
- Food Science and Formulation, Gembloux Agro-Bio Tech (University of Liège), Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Christophe Blecker
- Food Science and Formulation, Gembloux Agro-Bio Tech (University of Liège), Passage des Déportés 2, 5030 Gembloux, Belgium
| | - M Haissam Jijakli
- Integrated and Urban Plant Pathology, Gembloux Agro-Bio Tech (University of Liège), Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Giorgia Purcaro
- Laboratory of Analytical Chemistry, Gembloux Agro-Bio Tech (University of Liège), Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Frédéric Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech (University of Liège), Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Rudy Caparros Megido
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech (University of Liège), Passage des Déportés 2, 5030 Gembloux, Belgium.
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8
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Kannry SH, O'Rourke SM, Kelson SJ, Miller MR. On the Ecology and Distribution of Steelhead (Oncorhynchus mykiss) in California's Eel River. J Hered 2020; 111:548-563. [PMID: 33125465 DOI: 10.1093/jhered/esaa043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/28/2020] [Indexed: 11/12/2022] Open
Abstract
The preservation of life history and other phenotypic complexity is central to the resilience of Pacific salmon stocks. Steelhead (Oncorhynchus mykiss) express a diversity of life-history strategies such as the propensity to migrate (anadromy/residency) and the timing and state of maturation upon return to freshwater (run-timing), providing an opportunity to study adaptive phenotypic complexity. Historically, the Eel River supported upwards of 1 million salmon and steelhead, but the past century has seen dramatic declines of all salmonids in the watershed. Here we investigate life-history variation in Eel River steelhead by using Rapture sequencing, on thousands of individuals, to genotype the region diagnostic for run-timing (GREB1L) and the region strongly associated with residency/anadromy (OMY5) in the Eel River and other locations, as well as determine patterns of overall genetic differentiation. Our results provide insight into many conservation-related issues. For example, we found that distinct segregation between winter and summer-run steelhead correlated with flow-dependent barriers in major forks of the Eel, that summer-run steelhead inhabited the upper Eel prior to construction of an impassable dam, and that both life history and overall genetic diversity have been maintained in the resident trout population above; and we found no evidence of the summer-run allele in the South Fork Eel, indicating that summer run-timing cannot be expected to arise from standing genetic variation in this and other populations that lack the summer-run phenotype. The results presented in this study provide valuable information for designing future restoration and management strategies for O. mykiss in Northern California and beyond.
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9
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Weinstein SY, Thrower FP, Nichols KM, Hale MC. A large-scale chromosomal inversion is not associated with life history development in rainbow trout from Southeast Alaska. PLoS One 2019; 14:e0223018. [PMID: 31539414 PMCID: PMC6754156 DOI: 10.1371/journal.pone.0223018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/11/2019] [Indexed: 01/12/2023] Open
Abstract
In studying the causative mechanisms behind migration and life history, the salmonids-salmon, trout, and charr-are an exemplary taxonomic group, as life history development is known to have a strong genetic component. A double inversion located on chromosome 5 in rainbow trout (Oncorhynchus mykiss) is associated with life history development in multiple populations, but the importance of this inversion has not been thoroughly tested in conjunction with other polymorphisms in the genome. To that end, we used a high-density SNP chip to genotype 192 F1 migratory and resident rainbow trout and focused our analyses to determine whether this inversion is important in life history development in a well-studied population of rainbow trout from Southeast Alaska. We identified 4,994 and 436 SNPs-predominantly outside of the inversion region-associated with life history development in the migrant and resident familial lines, respectively. Although F1 samples showed genomic patterns consistent with the double inversion on chromosome 5 (reduced observed and expected heterozygosity and an increase in linkage disequilibrium), we found no statistical association between the inversion and life history development. Progeny produced by crossing resident trout and progeny produced by crossing migrant trout both consisted of a mix of migrant and resident individuals, irrespective of the individuals' inversion haplotype on chromosome 5. This suggests that although the inversion is present at a low frequency, it is not strongly associated with migration as it is in populations of Oncorhynchus mykiss from lower latitudes.
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Affiliation(s)
- Spencer Y. Weinstein
- Department of Biology, Texas Christian University, Fort Worth, United States of America
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute, Alaska Fisheries Center, NOAA, Juneau, AK, United States of America
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA, United States of America
| | - Matthew C. Hale
- Department of Biology, Texas Christian University, Fort Worth, United States of America
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10
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Arostegui MC, Quinn TP, Seeb LW, Seeb JE, McKinney GJ. Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout. Mol Ecol 2019; 28:1412-1427. [DOI: 10.1111/mec.15037] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Martin C. Arostegui
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Thomas P. Quinn
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - James E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
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11
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Genetic mixture analyses in support of restoration of a high value recreational fishery for rainbow trout (Oncorhynchus mykiss) from a large lake in interior British Columbia. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01182-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Pavlov SD, Semenova AV, Melnikova MN. Differentiation of the Kamchatka Rainbow Trout Parasalmo (Oncorhynchus) mykiss Populations by Microsatellite DNA Loci. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019020122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Contemporary and historical river connectivity influence population structure in western brook lamprey in the Columbia River Basin. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1137-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Dibble KL, Yackulic CB, Kennedy TA, Budy P. Flow management and fish density regulate salmonid recruitment and adult size in tailwaters across western North America. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2015; 25:2168-2179. [PMID: 26910947 DOI: 10.1890/14-2211.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Rainbow and brown trout have been intentionally introduced into tailwaters downriver of dams globally and provide billions of dollars in economic benefits. At the same time, recruitment and maximum length of trout populations in tailwaters often fluctuate erratically, which negatively affects the value of fisheries. Large recruitment events may increase dispersal downriver where other fish species may be a priority (e.g., endangered species). There is an urgent need to understand the drivers of trout population dynamics in tailwaters, in particular the role of flow management. Here, we evaluate how flow, fish density, and other physical factors of the river influence recruitment and mean adult length in tailwaters across western North America, using data from 29 dams spanning 1-19 years. Rainbow trout recruitment was negatively correlated with high annual, summer, and spring flow and dam latitude, and positively correlated with high winter flow, subadult brown trout catch, and reservoir storage capacity. Brown trout recruitment was negatively correlated with high water velocity and daily fluctuations in flow (i.e., hydropeaking) and positively correlated with adult rainbow trout catch. Among these many drivers, rainbow trout recruitment was primarily correlated with high winter flow combined with low spring flow, whereas brown trout recruitment was most related to high water velocity. The mean lengths of adult rainbow and brown trout were influenced by similar flow and catch metrics. Length in both species was positively correlated with high annual flow but declined in tailwaters with high daily fluctuations in flow, high catch rates of conspecifics, and when large cohorts recruited to adult size. Whereas brown trout did not respond to the proportion of water allocated between seasons, rainbow trout length increased in rivers that released more water during winter than in spring. Rainbow trout length was primarily related to high catch rates of conspecifics, whereas brown trout length was mainly related to large cohorts recruiting to the adult size class. Species-specific responses to flow management are likely attributable to differences in seasonal timing of key life history events such as spawning, egg hatching, and fry emergence.
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15
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Lea EV, Mee JA, Post JR, Rogers SM, Mogensen S. Rainbow trout in seasonal environments: phenotypic trade-offs across a gradient in winter duration. Ecol Evol 2015; 5:4778-94. [PMID: 26640659 PMCID: PMC4662309 DOI: 10.1002/ece3.1636] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 07/13/2015] [Indexed: 11/09/2022] Open
Abstract
Survival through periods of resource scarcity depends on the balance between metabolic demands and energy storage. The opposing effects of predation and starvation mortality are predicted to result in trade-offs between traits that optimize fitness during periods of resource plenty (e.g., during the growing season) and those that optimize fitness during periods of resource scarcity (e.g., during the winter). We conducted a common environment experiment with two genetically distinct strains of rainbow trout to investigate trade-offs due to (1) the balance of growth and predation risk related to foraging rate during the growing season and (2) the allocation of energy to body size prior to the winter. Fry (age 0) from both strains were stocked into replicate natural lakes at low and high elevation that differed in winter duration (i.e., ice cover) by 59 days. Overwinter survival was lowest in the high-elevation lakes for both strains. Activity rate and growth rate were highest at high elevation, but growing season survival did not differ between strains or between environments. Hence, we did not observe a trade-off between growth and predation risk related to foraging rate. Growth rate also differed significantly between the strains across both environments, which suggests that growth rate is involved in local adaptation. There was not, however, a difference between strains or between environments in energy storage. Hence, we did not observe a trade-off between growth and storage. Our findings suggest that intrinsic metabolic rate, which affects a trade-off between growth rate and overwinter survival, may influence local adaptation in organisms that experience particularly harsh winter conditions (e.g., extended periods trapped beneath the ice in high-elevation lakes) in some parts of their range.
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Affiliation(s)
- Ellen V Lea
- Department of Biological Sciences University of Calgary 2500 University Dr. NW Calgary Alberta Canada T2N 1N4
| | - Jonathan A Mee
- Department of Biological Sciences University of Calgary 2500 University Dr. NW Calgary Alberta Canada T2N 1N4
| | - John R Post
- Department of Biological Sciences University of Calgary 2500 University Dr. NW Calgary Alberta Canada T2N 1N4
| | - Sean M Rogers
- Department of Biological Sciences University of Calgary 2500 University Dr. NW Calgary Alberta Canada T2N 1N4
| | - Stephanie Mogensen
- Department of Biological Sciences University of Calgary 2500 University Dr. NW Calgary Alberta Canada T2N 1N4
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Origin and Genetic Diversity of Lake Trout in the Togiak National Wildlife Refuge, Alaska. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2015. [DOI: 10.3996/032014-jfwm-022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Lake trout Salvelinus namaycush is a slow-growing, late-maturing, cold-water-adapted species whose native distribution is described by the glaciated regions of North America. Southwestern Alaska, the western limit of the species range, has undergone repeated episodes of glacial advance and retreat. In this study, lake trout were sampled from 15 lakes in six drainages on or near Togiak National Wildlife Refuge (TNWR) in southwestern Alaska. Data from 14 microsatellite loci were used to test for genetic evidence that lake trout survived the most recent glacial advance in a local refugium, and to test the effect of habitat size, elevation, and drainage on within- and among-population variation. We could not infer that unglaciated lakes within the TNWR served as a refugium during the most recent glacial maximum. In a neighbor-joining tree, populations largely clustered by drainage, suggesting a single founding source for each drainage. An exception occurred in the Nushagak and Kuskokwim rivers, where evidence for stream capture was detected. Among-population variation, as measured by FST, was 0.35; pairwise FST within drainages ranged from 0.05 to 0.47, indicative of low gene flow, even within drainages, though individual-based analysis detected movement of lake trout among lakes within the Kanektok, Goodnews, and Nushagak rivers. Lake surface area was positively associated with allele richness, and negatively associated with FIS, indicating that smaller lakes in the TNWR harbor less genetic diversity and may have more limited adaptive potential.
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Yamamoto S, Maekawa K, Morita K, Crane PA, Oleinik AG. Phylogeography of the Salmonid Fish, Dolly VardenSalvelinus malma: Multiple Glacial Refugia in the North Pacific Rim. Zoolog Sci 2014; 31:660-70. [DOI: 10.2108/zs130266] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Houston DD, Shiozawa DK, Smith BT, Riddle BR. Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow. BMC Evol Biol 2014; 14:111. [PMID: 24885371 PMCID: PMC4038058 DOI: 10.1186/1471-2148-14-111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/12/2014] [Indexed: 11/29/2022] Open
Abstract
Background Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species that is widely distributed throughout western North America. The species’ native range includes several well-documented Pleistocene refugia. Here we use mitochondrial DNA sequence data to assess phylogeography, and to test two biogeographic hypotheses regarding post-glacial colonization by redside shiner: 1) Redside shiner entered the Bonneville Basin at the time of the Bonneville Flood (Late Pleistocene; 14.5 Ka), and 2) redside shiner colonized British Columbia post-glacially from a single refugium in the Upper Columbia River drainage. Results Genetic diversification in redside shiner began in the mid to late Pleistocene, but was not associated with LGM. Different clades of redside shiner were distributed in multiple glacial age refugia, and each clade retains a signature of population expansion, with clades having secondary contact in some areas. Conclusions Divergence times between redside shiner populations in the Bonneville Basin and the Upper Snake/Columbia River drainage precedes the Bonneville Flood, thus it is unlikely that redside shiner invaded the Bonneville Basin during this flooding event. All but one British Columbia population of redside shiner are associated with the Upper Columbia River drainage with the lone exception being a population near the coast, suggesting that the province as a whole was colonized from multiple refugia, but the inland British Columbia redside shiner populations are affiliated with a refugium in the Upper Columbia River drainage.
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Affiliation(s)
- Derek D Houston
- School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, NV 89154-4004, USA.
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19
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Discovery and characterization of novel genetic markers for coastal cutthroat trout (Oncorhynchus clarkii clarkii). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9863-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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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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Pavlov SD, Semenova AV, Rubtsova GA, Afanasiev KI. Analysis of microsatellite variation in the rainbow trout Parasalmo (Oncorhynchus) mykiss from Kamchatka. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411100139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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ABADÍA-CARDOSO ALICIA, CLEMENTO ANTHONYJ, GARZA JOHNCARLOS. Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout,Oncorhynchus mykiss. Mol Ecol Resour 2011; 11 Suppl 1:31-49. [DOI: 10.1111/j.1755-0998.2010.02971.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Zhao L, Zhang J, Liu Z, Li M. Multiple unrelated founding events for the long-distance Pleistocene dispersal of the Salangid, Neosalanx taihuensis: a general demographic model for inshore-orientated freshwater fish. Mol Phylogenet Evol 2010; 58:142-7. [PMID: 21081172 DOI: 10.1016/j.ympev.2010.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Revised: 10/26/2010] [Accepted: 11/03/2010] [Indexed: 10/18/2022]
Abstract
The Salangid icefish Neosalanx taihuensis (Salangidae) originated from inshore of the East China seas and underwent adaptive freshwater radiation from the mid-Miocene to the early Pleistocene. The distribution of its genetic diversity presents a random pattern inconsistent with contemporary hydrological structure. In the present study, coalescent simulations were used to analyze its Pleistocene dispersal history. Population history simulation supported the hypothesis of long-distance dispersal during the Pleistocene based on multiple unrelated founding events. This analogous genetic pattern has been described for other inshore-orientated freshwater fish, and may represent a general history dispersal model for the phylogeography of these species. From network analysis, three subclades (Clades 1-3) grouped consistently with three probable ancestral haplotypes (H36, H27, and H33). Demographic analysis also revealed that the ancestral haplotype group (Clade 1) dispersed into freshwater during an interglacial age about 0.35Ma, while Clades 2 and 3 dispersed about 0.12 and 0.145Ma, respectively. The N. taihuensis population remained relatively small for a considerable amount of time during the Pleistocene ages, with population expansion events mainly occurring after the last glacial maximum (LGM).
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Affiliation(s)
- Liang Zhao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang, Beijing, China
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BRANNON ERNESTL, POWELL MADISONS, QUINN THOMASP, TALBOT ANDRÉ. Population Structure of Columbia River Basin Chinook Salmon and Steelhead Trout. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/10641260490280313] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Yu JN, Azuma N, Yoon M, Brykov V, Urawa S, Nagata M, Jin DH, Abe S. Population genetic structure and phylogeography of masu salmon (Oncorhynchus masou masou) inferred from mitochondrial and microsatellite DNA analyses. Zoolog Sci 2010; 27:375-85. [PMID: 20443684 DOI: 10.2108/zsj.27.375] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The population genetic structure and phylogeography of masu salmon were investigated by using variation in the mitochondrial NADH dehydrogenase subunit 5 gene (ND5) and six polymorphic microsatellite loci among a total of 895 fish representing 18 populations collected from Japan (9), Russia (7), and Korea (2) from 2000 to 2008. An analysis of ND5 nucleotide sequences revealed 22 variable sites in about 560 bp in the 5' half of the gene, which defined 20 haplotypes, including some associated with geographical regions. Haplotype and nucleotide diversities were greater in the populations in Japan and Korea than in those in Russia, indicating greater genetic diversity in the Japanese and Korean populations than in the Russian populations. All the microsatellite loci examined showed a high level of variation, but the expected heterozygosity indicated a similar level of genetic diversity among the populations of the three regions, contrary to the results for ND5. However, AMOVA and pairwise population F (ST) estimates for both ND5 and the microsatellite markers indicated a similar pattern of moderate genetic differentiation among populations of the three regions, and large population groups on the coasts of the Sea of Japan, Sea of Okhotsk, and Pacific Ocean in the Far East. From a mismatch distribution analysis and neutrality test, the observed genetic structure appears to have been influenced primarily by bottlenecks during glacial periods and population expansions during interglacial periods in the late Pleistocene.
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Affiliation(s)
- Jeong-Nam Yu
- Division of Marine Biociences, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Japan
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Taylor EB, Tamkee P, Keeley ER, Parkinson EA. Conservation prioritization in widespread species: the use of genetic and morphological data to assess population distinctiveness in rainbow trout (Oncorhynchus mykiss) from British Columbia, Canada. Evol Appl 2010; 4:100-15. [PMID: 25567956 PMCID: PMC3352517 DOI: 10.1111/j.1752-4571.2010.00136.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 04/25/2010] [Indexed: 11/30/2022] Open
Abstract
Prioritization of efforts to maintain biodiversity is an important component of conservation, but is more often applied to ecosystems or species than within species. We assessed distinctiveness among 27 populations of rainbow trout (Salmonidae: Oncorhynchus mykiss) from British Columbia, Canada, using microsatellite DNA variation (representing historical or contemporary demography) and morphology (representing adaptive variation). Standardized genetic scores, that is, the average deviation across individuals within populations from the overall genetic score generated by factorial correspondence analysis, ranged from 1.05 to 4.90 among populations. Similar standardized morphological scores, generated by principal components analysis, ranged from 1.19 to 5.35. There was little correlation between genetic and morphological distinctiveness across populations, although one population was genetically and morphologically the most distinctive. There was, however, a significant correlation (r = 0.26, P = 0.008) between microsatellite (FST) and morphological (PST) divergence. We combined measures of allelic richness, genetic variation within, and divergence among, populations and morphological variation to provide a conservation ranking of populations. Our approach can be combined with other measures of biodiversity value (habitat, rarity, human uses, threat status) to rationalize the prioritization of populations, especially for widespread species where geographic isolation across distinct environments promotes intraspecific variability.
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Affiliation(s)
- Eric B Taylor
- Department of Zoology, Beaty Biodiversity Research Centre, and Native Fishes Research Group, University of British Columbia Vancouver, BC, Canada
| | - Patrick Tamkee
- Department of Zoology, Beaty Biodiversity Research Centre, and Native Fishes Research Group, University of British Columbia Vancouver, BC, Canada
| | - Ernest R Keeley
- Department of Biological Sciences, Idaho State University Pocatello, ID, USA
| | - Eric A Parkinson
- British Columbia Ministry of Environment, Biodiversity Branch, University of British Columbia Vancouver, BC, Canada
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Melnikova MN, Pavlov SD, Kolesnikov AA, Petrov NB. Screening of population genetic SCAR markers for mykiss Parasalmo (Oncorhynchus) mykiss from Kamchatka. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410060104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Brunelli JP, Steele CA, Thorgaard GH. Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout. Mol Phylogenet Evol 2010; 56:983-90. [PMID: 20546904 DOI: 10.1016/j.ympev.2010.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 05/14/2010] [Accepted: 05/17/2010] [Indexed: 11/19/2022]
Abstract
Y-chromosome and mitochondrial DNA markers can reveal phylogenetic patterns by allowing tracking of male and female lineages, respectively. We used sequence data from a recently discovered Y-linked marker and a mitochondrial marker to examine phylogeographic structure in the widespread and economically important rainbow trout (Oncorhynchus mykiss). Two distinct geographic groupings that generally correspond to coastal and inland subspecies were evident within the Y-marker network while the mtDNA haplotype network showed little geographic structure. Our results suggest that male-specific behavior has prevented widespread admixture of Y haplotypes and that gene flow between the coastal and inland subspecies has largely occurred through females. This new Y marker may also aid conservation efforts by genetically identifying inland populations that have not hybridized with widely stocked coastal-derived hatchery fish.
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Affiliation(s)
- Joseph P Brunelli
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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Bucking C, Fitzpatrick JL, Nadella SR, Wood CM. Post-prandial metabolic alkalosis in the seawater-acclimated trout: the alkaline tide comes in. ACTA ACUST UNITED AC 2009; 212:2159-66. [PMID: 19561205 DOI: 10.1242/jeb.027862] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The consequences of feeding and digestion on acid-base balance and regulation in a marine teleost (seawater-acclimated steelhead trout; Oncorhynchus mykiss) were investigated by tracking changes in blood pH and [HCO3-], as well as alterations in net acid or base excretion to the water following feeding. Additionally the role of the intestine in the regulation of acid-base balance during feeding was investigated with an in vitro gut sac technique. Feeding did not affect plasma glucose or urea concentrations, however, total plasma ammonia rose during feeding, peaking between 3 and 24 h following the ingestion of a meal, three-fold above resting control values (approximately 300 micromol ml(-1)). This increase in plasma ammonia was accompanied by an increase in net ammonia flux to the water (approximately twofold higher in fed fish versus unfed fish). The arterial blood also became alkaline with increases in pH and plasma [HCO3-] between 3 and 12 h following feeding, representing the first measurement of an alkaline tide in a marine teleost. There was no evidence of respiratory compensation for the measured metabolic alkalosis, as Pa CO2 remained unchanged throughout the post-feeding period. However, in contrast to an earlier study on freshwater-acclimated trout, fed fish did not exhibit a compensating increase in net base excretion, but rather took in additional base from the external seawater, amounting to approximately 8490 micromol kg(-1) over 48 h. In vitro experiments suggest that at least a portion of the alkaline tide was eliminated through increased HCO3- secretion coupled to Cl- absorption in the intestinal tract. This did not occur in the intestine of freshwater-acclimated trout. The marked effects of the external salinity (seawater versus freshwater) on different post-feeding patterns of acid-base balance are discussed.
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Affiliation(s)
- Carol Bucking
- McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.
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30
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Genetic analysis and uncertain taxonomic status of threatened Foskett Spring speckled dace. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9959-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Goebel AM, Ranker TA, Corn PS, Olmstead RG. Mitochondrial DNA evolution in the Anaxyrus boreas species group. Mol Phylogenet Evol 2009; 50:209-25. [DOI: 10.1016/j.ympev.2008.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/10/2008] [Accepted: 06/24/2008] [Indexed: 11/27/2022]
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32
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Zhao L, Zhang J, Liu Z, Funk SM, Wei F, Xu M, Li M. Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences. BMC Evol Biol 2008; 8:201. [PMID: 18625046 PMCID: PMC2483725 DOI: 10.1186/1471-2148-8-201] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Accepted: 07/14/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Salangid icefish Neosalanx taihuensis (Salangidae) is an economically important fish, which is endemic to China, restricted to large freshwater systems (e.g. lakes, large rivers and estuaries) and typically exhibit low vagility. The continuous distribution ranges from the temperate region of the Huai and Yellow River basins to the subtropical region of the Pearl River basin. This wide ranging distribution makes the species an ideal model for the study of palaeoclimatic effects on population genetic structure and phylogeography. Here, we aim to analyze population genetic differentiation within and between river basins and demographic history in order to understand how this species responded to severe climatic oscillations, decline of the sea levels during the Pleistocene ice ages and tectonic activity. RESULTS We obtained the complete mtDNA cytochrome b sequences (1141 bp) of 354 individuals from 13 populations in the Pearl River, the Yangze River and the Huai River basin. Thirty-six haplotypes were detected. Haplotype frequency distributions were strongly skewed, with most haplotypes (n = 24) represented only in single samples each and thus restricted to a single population. The most common haplotype (H36) was found in 49.15% of all individuals. Analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. Significant levels of genetic subdivision were detected among populations within basins rather than between the three basins. Demographic analysis revealed that the population size in the Pearl River basin has remained relatively constant whereas the populations in the Yangze River and the Huai River basins expanded about 221 and 190 kyr ago, respectively, with the majority of mutations occurring after the last glacial maximum (LGM). CONCLUSION The observed complex genetic pattern of N. taihuensis is coherent with a scenario of multiple unrelated founding events by long-distance colonization and dispersal combined with contiguous population expansion and locally restricted gene flow. We also found that this species was likely severely impacted by past glaciations. More favourable climate and the formation of large suitable habitations together facilitated population expansion after the late Quaternary (especially the LGM). We proposed that all populations should be managed and conserved separately, especially for habitat protection.
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Affiliation(s)
- Liang Zhao
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang, Beijing 100101, PR China
- Faculty of biology, Suzhou University, Suzhou, Anhui 234000, PR China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, PR China
| | - Jie Zhang
- Key laboratory of zoological Evolution and Systematics, Institute of Zoology, Chinese Academy of Sciences, Chaoyang, Beijing 100101, PR China
| | - Zhijin Liu
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang, Beijing 100101, PR China
| | | | - Fuwen Wei
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang, Beijing 100101, PR China
| | - Muqi Xu
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang, Beijing 100101, PR China
| | - Ming Li
- Key laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang, Beijing 100101, PR China
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Metcalf JL, Pritchard VL, Silvestri SM, Jenkins JB, Wood JS, Cowley DE, Evans RP, Shiozawa DK, Martin AP. Across the great divide: genetic forensics reveals misidentification of endangered cutthroat trout populations. Mol Ecol 2007; 16:4445-54. [PMID: 17727621 DOI: 10.1111/j.1365-294x.2007.03472.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Accurate assessment of species identity is fundamental for conservation biology. Using molecular markers from the mitochondrial and nuclear genomes, we discovered that many putatively native populations of greenback cutthroat trout (Oncorhynchus clarkii stomias) comprised another subspecies of cutthroat trout, Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus). The error can be explained by the introduction of Colorado River cutthroat trout throughout the native range of greenback cutthroat trout in the late 19th and early 20th centuries by fish stocking activities. Our results suggest greenback cutthroat trout within its native range is at a higher risk of extinction than ever before despite conservation activities spanning more than two decades.
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Affiliation(s)
- Jessica L Metcalf
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
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ZHANG JIE, LI MING, XU MUQI, TAKITA TORU, WEI FUWEN. Molecular phylogeny of icefish Salangidae based on complete mtDNA cytochrome b sequences, with comments on estuarine fish evolution. Biol J Linn Soc Lond 2007. [DOI: 10.1111/j.1095-8312.2007.00785.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Brown JW, van Coeverden de Groot PJ, Birt TP, Seutin G, Boag PT, Friesen VL. Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus. Mol Ecol 2007; 16:327-43. [PMID: 17217348 DOI: 10.1111/j.1365-294x.2007.03151.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peregrine falcon populations underwent devastating declines in the mid-20th century due to the bioaccumulation of organochlorine contaminants, becoming essentially extirpated east of the Great Plains and significantly reduced elsewhere in North America. Extensive re-introduction programs and restrictions on pesticide use in Canada and the United States have returned many populations to predecline sizes. A proper population genetic appraisal of the consequences of this decline requires an appropriate context defined by (i) meaningful demographic entities; and (ii) suitable reference populations. Here we explore the validity of currently recognized subspecies designations using data from the mitochondrial control region and 11 polymorphic microsatellite loci taken from 184 contemporary individuals from across the breeding range, and compare patterns of population genetic structure with historical patterns inferred from 95 museum specimens. Of the three North American subspecies, the west coast marine subspecies Falco peregrinus pealei is well differentiated genetically in both time periods using nuclear loci. In contrast, the partitioning of continental Falco peregrinus anatum and arctic Falco peregrinus tundrius subspecies is not substantiated, as individuals from these subspecies are historically indistinguishable genetically. Bayesian clustering analyses demonstrate that contemporary genetic differentiation between these two subspecies is mainly due to changes within F. p. anatum (specifically the southern F. p. anatum populations). Despite expectations and a variety of tests, no genetic bottleneck signature is found in the identified populations; in fact, many contemporary indices of diversity are higher than historical values. These results are rationalized by the promptness of the recovery and the possible introduction of new genetic material.
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Affiliation(s)
- Joseph W Brown
- Department of Biology, Queen's University, Kingston, Ontario, Canada.
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Hughes AL, Hughes MAK. Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Mol Ecol 2007; 16:1369-76. [PMID: 17391262 DOI: 10.1111/j.1365-294x.2007.03242.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleotide sequence diversity at mitochondrial protein-coding loci from 72 species of birds from different geographical regions was analysed in order to test the hypothesis that temperate zone species show population genetic effects of past glaciation. Temperate zone species showed reduced nucleotide diversity in comparison to tropical mainland species, suggesting that the latter have long-term effective population sizes due to population bottleneck effects during the most recent glaciation. This hypothesis was further supported by evidence of an unusually high estimated rate of population growth in species breeding in North America and wintering in the New World tropics (Nearctic migrants), consistent with population expansion after a bottleneck. Nearctic migrants also showed evidence of an abundance of rare nonsynonymous (amino acid-altering) polymorphisms, a pattern suggesting that slightly deleterious polymorphisms drifted to high frequencies during a bottleneck and are now being eliminated by selection. Because the shape of the North American land mass limited the area available for refugia during glaciation, the bottleneck effects are predicted to have been particularly strong in Nearctic migrants, and this prediction was supported. The reduced genetic diversity of Nearctic migrants provides an additional basis for concern for the survival of these species, which are threatened by loss of habitat in the winter range and by introduced disease.
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Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg., 700 Sumter Street, Columbia, SC 29208, USA.
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BROWN JOSEPHW, VAN COEVERDEN DE GROOT PETERJ, BIRT TIMP, SEUTIN GILLES, BOAG PETERT, FRIESEN VICKIL. Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus. Mol Ecol 2006. [DOI: 10.1111/j.1365-294x.2006.03151.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Steele CA, Storfer A. Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus). Mol Ecol 2006; 15:2477-87. [PMID: 16842421 DOI: 10.1111/j.1365-294x.2006.02950.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species' phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20,000 years ago), mid-Pleistocene (800,000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and 'g' distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.
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Affiliation(s)
- Craig A Steele
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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Abstract
To demonstrate the importance of genetic data for multispecies conservation approaches, we examined the distribution of genetic variation across the range of the mountain whitefish (Prosopium williamsoni) at microsatellite and allozyme loci. The mountain whitefish is a common species that is particularly well suited for accurately revealing historical patterns of genetic structure and differs markedly from previously studied species in habitat requirements and life history characteristics. As such, comparing the population genetic structure of other native fishes to similar data from mountain whitefish could inform management and conservation strategies. Genetic variation for mountain whitefish was hierarchically distributed for both allozymes and microsatellites. We found evidence for a total of five major genetically differentiated assemblages and we observed subdivision among populations within assemblages that generally corresponded to major river basins. We observed little genetic differentiation within major river basins. Geographic patterns of genetic differentiation for mountain whitefish were concordant with other native species in several circumstances, providing information for the designation of conservation units that reflect concordant genetic differentiation of multiple species. Differences in genetic patterns between mountain whitefish and other native fishes reflect either differences in evolutionary histories of the species considered or differences in aspects of their ecology and life history. In addition, mountain whitefish populations appear to exchange genes over a much larger geographic scale than co-occurring salmonids and are likely to be affected differently by disturbances such as habitat fragmentation.
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Affiliation(s)
- Andrew R Whiteley
- University of Montana, Division of Biological Sciences, Missoula, MT 59812, USA.
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40
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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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41
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42
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Genetic divergence of mykizha (Parasalmo (Oncorhynchus) mykiss) from Kamchatka inferred from restriction analysis and sequencing of mtDNA cytochrome b gene. RUSS J GENET+ 2004. [DOI: 10.1007/s11177-005-0072-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Oakey DD, Douglas ME, Douglas MR. Small Fish in a Large Landscape: Diversification of Rhinichthys osculus (Cyprinidae) in Western North America. COPEIA 2004. [DOI: 10.1643/cg-02-264r1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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44
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Dobes CH, Mitchell-Olds T, Koch MA. Extensive chloroplast haplotype variation indicates Pleistocene hybridization and radiation of North American Arabis drummondii, A. x divaricarpa, and A. holboellii (Brassicaceae). Mol Ecol 2004; 13:349-70. [PMID: 14717892 DOI: 10.1046/j.1365-294x.2003.02064.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Arabis drummondii, A. holboellii and their hybrid A. x divaricarpa are widespread perennials of open habitats in North America. A phylogenetic analysis based on noncoding chloroplast DNA sequences (trnL intron and trnL/F intergenic spacer) resolved A. drummondii as a monophyletic taxon, but found A. holboellii to bear chloroplast haplotypes from highly diverged evolutionary lineages. This raised the question of a possible polyphyletic origin of A. holboellii. Arabis x divaricarpa was found to be of recent and polytopic origin, a result consistent with its presumed hybrid origin. One hundred and three chloroplast haplotypes were detected within 719 Arabis accessions investigated. The majority of chloroplast-types were estimated to have arisen prior to the Wisconsin glaciation. Phylogeographical analysis using nested clade analysis, suggested for A. holboellii (i). past fragmentation events, partitioning genetic variation in several instances between the Sierra Nevada, the Southern Rocky Mountains and the Colorado Plateau on the one hand and the Central to Northern Rockies of the United States and adjacent Cascades on the other; and for both parental species (ii). recolonization of major areas formerly covered by the Wisconsin glaciation by three haplotypes; and (iii). restricted gene flow indicating isolation by distance in areas south of the last glacial maximum. Arabis x divaricarpa is closely codistributed with its parental species and resampled their haplotypes. The highest genetic diversity was found in the Rocky Mountains from Idaho and Montana south to Utah and Colorado. This area was further hypothesized to have played a major role in the origin of both parental species and probably represented an important glacial refugium. However, evidence for glacial refugia was also found in arctic and boreal regions of Alaska and near the Great Lakes. In comparison to nuclear ribosomal internal transcribed spacer data, chloroplast DNA divergence was very high and evidently predated the origin of A. drummondii and possibly A. holboellii. Divergence of major chloroplast lineages dates back to the middle of the Pleistocene at least. Extensive hybridization is the most likely evolutionary factor working on A. holboellii to explain the revealed discrepancy in nuclear DNA and chloroplast DNA diversification.
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Affiliation(s)
- C H Dobes
- Institute of Botany, University of Natural Resources and Applied Life Sciences Vienna, Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria
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45
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Wong BBM, Keogh JS, McGlashan DJ. Current and historical patterns of drainage connectivity in eastern Australia inferred from population genetic structuring in a widespread freshwater fish Pseudomugil signifer (Pseudomugilidae). Mol Ecol 2004; 13:391-401. [PMID: 14717894 DOI: 10.1046/j.1365-294x.2003.02085.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Dispersal can play an important role in the genetic structuring of natural populations. In this regard, freshwater fishes often exhibit extensive population genetic subdivision and are ideal subjects for investigating current and historical patterns of connection and dissociation between drainages. We set out to generate a comprehensive molecular phylogeny for a widespread freshwater fish from eastern Australia, the Pacific blue-eye Pseudomugil signifer. Although movement via flood events may be important in the southern end of the species' range, genetic structuring revealed the importance of historical drainage connections and dissociations in mediating or disrupting dispersal. A dominant feature of our phylogeny is a split between northern and southern populations, which appears to be congruent with a biogeographical barrier recently implicated as important for the connectivity of freshwater organisms in eastern Australia. The extent of the split also has taxonomic implications consistent with suggestions that the Pacific blue-eye may represent more than a single species.
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Affiliation(s)
- B B M Wong
- School of Botany and Zoology, Australian National University, Canberra, ACT 0200, Australia.
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46
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McMillen-Jackson AL, Bert TM. Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States. Mol Ecol 2004; 12:2895-905. [PMID: 14629371 DOI: 10.1046/j.1365-294x.2003.01955.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Analysing the population genetic structures of sympatric species provides opportunities to compare patterns of population genetic structure and phylogeography in order to gain insight into the factors that influence the development of the observed patterns. In this study, we compared the population genetic structures and phylogeographies of brown shrimp (Farfantepenaeus aztecus) and white shrimp (Litopenaeus setiferus), two sympatric penaeid shrimp species that inhabit the waters of the eastern USA, using sequence analysis of the mitochondrial DNA control region. Brown shrimp showed no significant phylogenetic structure or population subdivision, and closely related haplotypes were geographically dispersed. Mismatch analysis indicated that brown shrimp experienced a late-Pleistocene era sudden population expansion. In contrast, white shrimp had a complex haplotype phylogeny consisting of two distinct lineages and two less well-defined sublineages, and the haplotypes and lineages were geographically structured. Mismatch analysis for white shrimp also showed evidence of sudden population expansion, albeit for each lineage separately and more recently than in the brown shrimp. These disparate patterns may have developed as a result of species-specific differences in physiological tolerances and habitat preferences that caused greater fluctuations in white shrimp population sizes and reductions in long-term effective population size relative to that of the brown shrimp, and thereby increased the susceptibility of the white shrimp populations to stochastic genetic change.
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Affiliation(s)
- A L McMillen-Jackson
- Florida Marine Research Institute, 100 8th Avenue S.E., St. Petersburg, FL 33701, USA.
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47
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Froufe E, Knizhin I, Koskinen MT, Primmer CR, Weiss S. Identification of reproductively isolated lineages of Amur grayling (Thymallus grubii Dybowski 1869): concordance between phenotypic and genetic variation. Mol Ecol 2003; 12:2345-55. [PMID: 12919473 DOI: 10.1046/j.1365-294x.2003.01901.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We analysed variation at maternally (mitochondrial DNA control region sequences) and bi-parentally (10 microsatellites) inherited genetic markers, as well as across 12 meristic characters in 7 populations of Amur grayling, Thymallus grubii, from eastern Siberia. All three data sets were concordant in supporting the existence of three diagnosable, reciprocally monophyletic, and most probably reproductively isolated, lineages of grayling within the Amur drainage. There was a significant correlation between genetic and phenotypic divergence, both within and among lineages. Two phenotypically distinct forms (with and without an orange spot on the posterior portion of the dorsal fin), found in sympatry in the lower Amur, most likely result from secondary contact, as they demonstrate 4.6% sequence divergence at the mitochondrial DNA control region. This divergence, together with the existence of at least one nearby population of orange spot grayling outside the Amur drainage (0.8% divergence) underscore the palaeo-hydrological complexity of the system, which presumably promoted genetic divergence in a shifting allopatric framework throughout the Pleistocene. Grayling from the upper Amur, corresponding to the type locality for the species, formed a sister group (1.4-1.6% divergent) to the orange spot lineage perhaps diverging in the early Pleistocene (1.4-1.6 Ma).
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Affiliation(s)
- E Froufe
- CIBIO/UP, Campus Agrário de Vairão, Portugal
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48
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Salzburger W, Brandstätter A, Gilles A, Parson W, Hempel M, Sturmbauer C, Meyer A. Phylogeography of the vairone (Leuciscus souffia, Risso 1826) in Central Europe. Mol Ecol 2003; 12:2371-86. [PMID: 12919475 DOI: 10.1046/j.1365-294x.2003.01911.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The vairone Leuciscus souffia is a cyprinid fish that inhabits river systems in and around the Alps. The complete mitochondrial DNA control region (945 bp) was sequenced in 295 vairone from 22 populations in Central Europe. A total of 51 haplotypes were identified with a maximum pairwise distance between haplotypes of 5.6%. Phylogenetic analyses revealed two major clades in L. souffia, an 'Italian' clade, and an 'Alpine' clade. Two hybrid zones exist, in the Mediterranean Alps and in the Soca basin. The position of the sister species of L. souffia, L. turskyi, to the 'Alpine' and the 'Italian' clade could not be resolved unambiguously. However, a linearized tree analysis indicated that L. turskyi represents a third lineage, that originated at the same time as the 'Alpine' and the 'Italian' clades of L. souffia. In the 'Alpine' clade two groups were resolved, a subclade with haplotypes from the Rhône and Var basins and a cluster with haplotypes from the Danube and Rhine systems. Our data suggest a long history of the vairone in Central Europe, predating Pleistocene glacial cycles. Two main refugia during glaciations must have existed, one in Italy and another one most probably in the Danube system. However, age estimates based on molecular clock calibrations suggest the survival of 'Alpine' haplotypes in several drainages during the last glaciation cycles. The Rhine system was only recently colonized.
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Affiliation(s)
- Walter Salzburger
- Department of Biology, University Konstanz, Universitaetsstrasse 10, 78457 Konstanz, Germany.
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49
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Ruckelshaus MH, Levin P, Johnson JB, Kareiva PM. The Pacific Salmon Wars: What Science Brings to the Challenge of Recovering Species. ACTA ACUST UNITED AC 2002. [DOI: 10.1146/annurev.ecolsys.33.010802.150504] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
▪ Abstract Politicians, scientists, government agencies, and the public are all engaged in recovery planning for Pacific salmon. In order for science to fulfill its potential in the arena of salmon recovery planning, several shortcomings of the science and its application to decision-making must be rectified. The definition of conservation units using genetic and phylogenetic inference needs to be sharpened. Ecological analyses must get beyond casting blame for past declines in salmon numbers and examine mixed strategies of management that consider interactions between hatcheries, harvest, hydropower, and habitat factors as well as background natural stresses and invasive species. Glib acceptance of expert opinion and extrapolated or inferred data should be tempered. To deal with uncertainty, recovery teams should engage in scenario analyses in which a wide variety of assumptions are played out. Finally, there is a pressing need for analyses aimed at determining what circumstances and communication strategies give science an effective voice in decision-making.
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Affiliation(s)
- Mary H. Ruckelshaus
- NMFS Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, Washington 98112
- The Nature Conservancy of Washington, 217 Pine Street, Ste. 1100, Seattle, Washington 98101
| | - Phil Levin
- NMFS Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, Washington 98112
- The Nature Conservancy of Washington, 217 Pine Street, Ste. 1100, Seattle, Washington 98101
| | - Jerald B. Johnson
- NMFS Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, Washington 98112
- The Nature Conservancy of Washington, 217 Pine Street, Ste. 1100, Seattle, Washington 98101
| | - Peter M. Kareiva
- NMFS Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, Washington 98112
- The Nature Conservancy of Washington, 217 Pine Street, Ste. 1100, Seattle, Washington 98101
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50
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Grunwald C, Stabile J, Waldman JR, Gross R, Wirgin I. Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences. Mol Ecol 2002; 11:1885-98. [PMID: 12296933 DOI: 10.1046/j.1365-294x.2002.01575.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Shortnose sturgeon is an anadromous North American acipenserid that since 1973 has been designated as federally endangered in US waters. Historically, shortnose sturgeon occurred in as many as 19 rivers from the St. John River, NB, to the St. Johns River, FL, and these populations ranged in census size from 10(1) to 10(4), but little is known of their population structure or levels of gene flow. We used the polymerase chain reaction (PCR) and direct sequence analysis of a 440 bp portion of the mitochondrial DNA (mtDNA) control region to address these issues and to compare haplotype diversity with population size. Twenty-nine mtDNA nucleotide-substitution haplotypes were revealed among 275 specimens from 11 rivers and estuaries. Additionally, mtDNA length variation (6 haplotypes) and heteroplasmy (2-5 haplotypes for some individuals) were found. Significant genetic differentiation (P < 0.05) of mtDNA nucleotide-substitution haplotypes and length-variant haplotypes was observed among populations from all rivers and estuaries surveyed with the exception of the Delaware River and Chesapeake Bay collections. Significant haplotype differentiation was even observed between samples from two rivers (Kennebec and Androscoggin) within the Kennebec River drainage. The absence of haplotype frequency differences between samples from the Delaware River and Chesapeake Bay reflects a probable current absence of spawning within the Chesapeake Bay system and immigration of fish from the adjoining Delaware River. Haplotypic diversity indices ranged between 0.817 and 0.641; no relationship (P > 0.05) was found between haplotype diversity and census size. Gene flow estimates among populations were often low (< 2.0), but were generally higher at the latitudinal extremes of their distribution. A moderate level of haplotype diversity and a high percentage (37.9%) of haplotypes unique to the northern, once-glaciated region suggests that northern populations survived the Pleistocene in a northern refugium. Analysis of molecular variance best supported a five-region hierarchical grouping of populations, but our results indicate that in almost all cases populations of shortnose sturgeon should be managed as separate units.
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Affiliation(s)
- C Grunwald
- Nelson Institute of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
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