1
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Smith CD, Payne SE, Morace JL, Nilsen EB. Organohalogenated contaminants in multiple life stages of the Pacific lamprey (Entosphenus tridentatus), Oregon, USA. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122363. [PMID: 37572847 DOI: 10.1016/j.envpol.2023.122363] [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: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
Pacific lamprey (Entosphenus tridentatus) are ecologically and culturally important anadromous animals native to the West Coast of the United States. Pacific lamprey populations are in decline, and contaminants may be a contributing factor. Between 2017 and 2021, three life stages of Pacific lamprey and collocated sediment samples were collected in Oregon (larval lamprey, sediment, and returning adult lamprey) and off the coast of Oregon and Washington (ocean juvenile lamprey). Tissue and sediment samples were analyzed for 56 organohalogenated compounds that included legacy pesticides, current use pesticides, polybrominated diphenyl ether congeners, and polychlorinated biphenyl congeners. Organohalogenated compounds were detected in all three Pacific lamprey life stages. The organohalogenated compounds detected in collocated sediment and larval lamprey samples were generally dissimilar, and compounds detected in larval lamprey indicate potential point sources along the rivers. Ocean-caught juvenile lamprey had significantly higher lipid contents than returning adult lamprey, but lipid content and concentrations of select compounds were not strongly correlated. Concentrations of select compounds detected in both ocean juvenile and returning adult lamprey were either not significantly different or were higher in returning adult lamprey. Concentrations of some compounds in returning adult lamprey-which are consumed by Indigenous peoples-exceeded state and national human health consumption thresholds. Collaboration among Tribes and public-sector agencies helped make this study successful.
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Affiliation(s)
- Cassandra D Smith
- U.S. Geological Survey Oregon Water Science Center, 601 SW 2nd Ave, Suite 1950, Portland, OR, 97204, USA.
| | - Sean E Payne
- U.S. Geological Survey Oregon Water Science Center, 601 SW 2nd Ave, Suite 1950, Portland, OR, 97204, USA
| | - Jennifer L Morace
- U.S. Geological Survey Oregon Water Science Center, 601 SW 2nd Ave, Suite 1950, Portland, OR, 97204, USA
| | - Elena B Nilsen
- U.S. Geological Survey Oregon Water Science Center, 601 SW 2nd Ave, Suite 1950, Portland, OR, 97204, USA
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2
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Baltazar‐Soares M, Britton JR, Pinder A, Harrison AJ, Nunn AD, Quintella BR, Mateus CS, Bolland JD, Dodd JR, Almeida PR, Dominguez Almela V, Andreou D. Seascape genomics reveals limited dispersal and suggests spatially varying selection among European populations of sea lamprey ( Petromyzon marinus). Evol Appl 2023; 16:1169-1183. [PMID: 37360030 PMCID: PMC10286227 DOI: 10.1111/eva.13561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviors. Despite being a freshwater, free-living organism for a large part of their life cycle, its adulthood is spent as a parasite of marine vertebrates. In their native European range, while it is well-established that sea lampreys comprise a single nearly-panmictic population, few studies have further explored the evolutionary history of natural populations. Here, we performed the first genome-wide characterization of sea lamprey's genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase, with the sequencing of 186 individuals from 8 locations spanning the North Eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30,910 bi-allelic SNPs. Population genetic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the North Eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species' dispersal. Seascape genomics suggested a scenario where oxygen concentration and river runoffs impose spatially varying selection across their distribution range. Exploring associations with the abundance of potential hosts further suggested that hake and cod could also impose selective pressures, although the nature of such putative biotic interactions was unresolved. Overall, the identification of adaptive seascapes in a panmictic anadromous species could contribute to conservation practices by providing information for restoration activities to mitigate local extinctions on freshwater sites.
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Affiliation(s)
- Miguel Baltazar‐Soares
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
- MARE – Marine and Environmental Sciences CentreISPA – Instituto UniversitárioLisbonPortugal
- Department of BiologyUniversity of TurkuTurkuFinland
| | - J. Robert Britton
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Adrian Pinder
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Andrew J. Harrison
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Andrew D. Nunn
- University of HullHull International Fisheries InstituteHullUK
| | - Bernardo R. Quintella
- MARE—Marine and Environmental Sciences CentreUniversity of ÉvoraÉvoraPortugal
- Department of Animal BiologyFaculty of Sciences, University of LisbonLisbonPortugal
| | - Catarina S. Mateus
- MARE—Marine and Environmental Sciences CentreUniversity of ÉvoraÉvoraPortugal
| | | | - Jamie R. Dodd
- University of HullHull International Fisheries InstituteHullUK
| | - Pedro R. Almeida
- MARE—Marine and Environmental Sciences CentreUniversity of ÉvoraÉvoraPortugal
- Department of Biology, School of Sciences and TechnologyUniversity of ÉvoraÉvoraPortugal
| | - Victoria Dominguez Almela
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Demetra Andreou
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
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3
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Miller AK, Timoshevskaya N, Smith JJ, Gillum J, Sharif S, Clarke S, Baker C, Kitson J, Gemmell NJ, Alexander A. Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis). J Hered 2022; 113:380-397. [PMID: 35439308 PMCID: PMC9308044 DOI: 10.1093/jhered/esac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/23/2022] [Indexed: 11/12/2022] Open
Abstract
Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft G. australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16 000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n = 186) and sequence data from Cyt-b (766 bp, n = 94) and COI (589 bp, n = 20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.
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Affiliation(s)
- Allison K Miller
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Nataliya Timoshevskaya
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, Kentucky, 40506-0225 USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, Kentucky, 40506-0225 USA
| | - Joanne Gillum
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Saeed Sharif
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Cindy Baker
- National Institute of Water and Atmospheric Research Limited, PO Box 11 115, Hamilton 3251 New Zealand
| | - Jane Kitson
- Ngāi Tahu, Kitson Consulting Ltd, Invercargill/Waihopai, 9879, New Zealand
| | - Neil J Gemmell
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Alana Alexander
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
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4
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Crowley PH, Tentelier C. Polyandry as a Male Strategy? A Game Between Aggressive and Tolerant Males, Arbitrated by Females. Am Nat 2021; 199:345-361. [DOI: 10.1086/718028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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5
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Clemens BJ, Schreck CB. An assessment of terminology for intraspecific diversity in fishes, with a focus on "ecotypes" and "life histories". Ecol Evol 2021; 11:10772-10793. [PMID: 34429881 PMCID: PMC8366897 DOI: 10.1002/ece3.7884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022] Open
Abstract
Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., "PST"), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life-history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life-history traits. Life history is generally used in organismal- and ecology-based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic- and evolution-based journals. "Satellite species" is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life-history components of ISD are not well understood, a conservative approach would be to call them phenotypes.
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Affiliation(s)
| | - Carl B. Schreck
- Department of Fisheries and WildlifeOregon State UniversityCorvallisORUSA
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6
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Zhang Z, Yu D, Liu F, Chen S, Liu H. Gene Flow and Individual Relatedness Suggest Population Spatial Connectivity of Sinogastromyzon sichangensis (Cypriniformes: Balitoridae) in the Chishui River, China. Zoolog Sci 2021; 37:434-443. [PMID: 32972084 DOI: 10.2108/zs190137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/31/2020] [Indexed: 11/17/2022]
Abstract
Sinogastromyzon sichangensis is a hillstream loach endemic to the upper Yangtze River, China. It is unclear whether this fish lives in a very restricted area or may be dispersed over a long distance. In the present study spatial connectivity of populations of S. sichangensis was investigated based on 343 individuals collected from 12 sites of Chishui River and employing 22 microsatellite loci. The results of genetic diversity analysis showed that observed heterozygosity (HO) and polymorphism information content (PIC) ranged from 0.5653 to 0.6999 and 0.8513 to 0.8819, respectively. Population structure analysis suggested that S. sichangensis had an unclear genetic structure. AMOVA showed that 69.36% of genetic variation was attributed to differentiation within individuals and all the pairwise genetic differentiation indices (FST) were low (mean FST = 0.0344), indicating weak differentiation among these populations. Estimation of gene flow showed frequent flow among populations, and contemporary levels (mean contemporary migration rate, mc = 0.0131) were approximately equal to historical levels (mean historical migration rate, mh = 0.0147). Individual relatedness analysis revealed a high level of sibship within and among different populations. The frequent gene flow and widespread sibship were due to S. sichangensis laying drifting eggs which travel for a long distance until hatching, after which the juveniles or adults migrate upstream. The results of unclear geographic structure and frequent exchange also indicate that it is necessary to decrease the negative impacts of anthropogenic activities on the connectivity of rivers to protect the migration routes of S. sichangensis.
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Affiliation(s)
- Zhi Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China.,University of Chinese Academy of Sciences, Beijing 100039, P.R. China
| | - Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Fei Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Sha Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, P.R. China
| | - Huanzhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China,
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7
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Rougemont Q, Dolo V, Oger A, Besnard AL, Huteau D, Coutellec MA, Perrier C, Launey S, Evanno G. Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype. Heredity (Edinb) 2021; 126:235-250. [PMID: 32989279 PMCID: PMC8027852 DOI: 10.1038/s41437-020-00367-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/05/2023] Open
Abstract
Understanding the effect of human-induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident European brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We tested the hypotheses of (i) asymmetric gene flow following water current and (ii) an effect of gene flow with the closely related anadromous river lamprey (L. fluviatilis) ecotype on L. planeri genetic diversity. We genotyped 2472 individuals, including 225 L. fluviatilis, sampled from 81 sites upstream and downstream barriers to migration, in 29 western European rivers. Linear modelling revealed a strong positive relationship between genetic diversity and the distance from the river source, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal mediated by water flow. Downstream L. planeri populations in sympatry with L. fluviatilis displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow drive the genetic make-up of upstream L. planeri populations whereas gene flow between ecotypes maintains higher levels of genetic diversity in L. planeri populations sympatric with L. fluviatilis. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks.
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Affiliation(s)
- Quentin Rougemont
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France.
- Département de biologie, Institut de Biologie Intégrative etsu des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada.
| | - Victoria Dolo
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | - Adrien Oger
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | - Anne-Laure Besnard
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | - Dominique Huteau
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | | | - Charles Perrier
- Centre de Biologie pour la Gestion des Populations UMR CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Sophie Launey
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
| | - Guillaume Evanno
- ESE, Ecology and Ecosystem Health, INRAE, Agrocampus Ouest, 35042, Rennes, France
- OFB, INRAE, Agrocampus Ouest, University Pau Pays Adour, Management of Diadromous Fish in their Environment, Rennes, France
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8
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Hess JE, Smith JJ, Timoshevskaya N, Baker C, Caudill CC, Graves D, Keefer ML, Kinziger AP, Moser ML, Porter LL, Silver G, Whitlock SL, Narum SR. Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey. Mol Ecol 2020; 29:3841-3856. [PMID: 32814354 DOI: 10.1111/mec.15605] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/26/2020] [Accepted: 08/14/2020] [Indexed: 12/26/2022]
Abstract
High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations probably explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent data sets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.
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Affiliation(s)
- Jon E Hess
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | | | - Cyndi Baker
- Oregon Department of Fish and Wildlife, Clackamas, OR, USA
| | | | - David Graves
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | | | | | | | - Laurie L Porter
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | - Greg Silver
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | | | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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9
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Parker KA, Hess JE, Narum SR, Kinziger AP. Evidence for the genetic basis and epistatic interactions underlying ocean‐ and river‐maturing ecotypes of Pacific Lamprey (
Entosphenus tridentatus
) returning to the Klamath River, California. Mol Ecol 2019; 28:3171-3185. [DOI: 10.1111/mec.15136] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Keith A. Parker
- Department of Fisheries Biology Humboldt State University Arcata California
| | - Jon E. Hess
- Columbia River Inter‐Tribal Fish Commission Portland Oregon
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission Hagerman Idaho
| | - Andrew P. Kinziger
- Department of Fisheries Biology Humboldt State University Arcata California
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10
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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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11
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Shink KG, Sutton TM, Murphy JM, López JA. Genetic variation and population structure among larval Lethenteron spp. within the Yukon River drainage, Alaska. JOURNAL OF FISH BIOLOGY 2018; 93:1130-1140. [PMID: 30306562 DOI: 10.1111/jfb.13833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
The absence of information on genetic variation and population structure of lampreys Lethenteron spp. in the eastern part of their distribution limits our understanding of the migration ecology and spatial population genetic structure of the species. We examined genetic variation within and among three aggregations of Lethenteron spp. larvae in the Yukon River drainage, Alaska, using microsatellite genotypes. A total of 120 larval lampreys were genotyped at eight microsatellite loci. Global FST was 0.053 (95% CI 0.021-0.086), while pairwise FST values ranged from 0.048-0.057. Model-based Bayesian clustering analyses with sample locality priors (LOCPRIOR) identified three distinct, but admixed, genetic clusters that corresponded with the three aggregations. Estimates of contemporary gene flow indicate substantial reciprocal migration among sites consistent with no or low-fidelity natal homing. These results are largely in agreement with previous reports of historic and contemporary gene flow among Lethenteron spp. in other parts of their geographic distribution.
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Affiliation(s)
- Katie G Shink
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska
| | - Trent M Sutton
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska
| | - James M Murphy
- Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA Fisheries, Juneau, Alaska
| | - J Andrés López
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska
- University of Alaska Museum of the North, Fairbanks, Alaska
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12
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Hume JB, Recknagel H, Bean CW, Adams CE, Mable BK. RADseq and mate choice assays reveal unidirectional gene flow among three lamprey ecotypes despite weak assortative mating: Insights into the formation and stability of multiple ecotypes in sympatry. Mol Ecol 2018; 27:4572-4590. [PMID: 30252984 DOI: 10.1111/mec.14881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023]
Abstract
Adaptive divergence with gene flow often results in complex patterns of variation within taxa exhibiting substantial ecological differences among populations. One example where this may have occurred is the parallel evolution of freshwater-resident nonparasitic lampreys from anadromous-parasitic ancestors. Previous studies have focused on transitions between these two phenotypic extremes, but here, we considered more complex evolutionary scenarios where an intermediate freshwater form that remains parasitic is found sympatrically with the other two ecotypes. Using population genomic analysis (restriction-associated DNA sequencing), we found that a freshwater-parasitic ecotype was highly distinct from an anadromous-parasitic form (Qlake-P = 96.8%, Fst = 0.154), but that a freshwater-nonparasitic form was almost completely admixed in Loch Lomond, Scotland. Demographic reconstructions indicated that both freshwater populations likely derived from a common freshwater ancestor. However, while the nonparasitic ecotype has experienced high levels of introgression from the anadromous-parasitic ecotype (Qanad-P = 37.7%), there is no evidence of introgression into the freshwater-parasitic ecotype. Paradoxically, mate choice experiments predicted high potential for gene flow: Males from all ecotypes were stimulated to spawn with freshwater-parasitic females, which released gametes in response to all ecotypes. Differentially fixed single nucleotide polymorphisms identified genes associated with growth and development, which could possibly influence the timing of metamorphosis, resulting in significant ecological differences between forms. This suggests that multiple lamprey ecotypes can persist in sympatry following shifts in adaptive peaks, due to environmental change during their repeated colonization of post-glacial regions, followed by periods of extensive gene flow among such diverging populations.
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Affiliation(s)
- John B Hume
- Department of Fisheries and Wildlife, College of Agriculture & Natural Resources, Michigan State University, East Lansing, Michigan.,Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Hans Recknagel
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.,Scottish Natural Heritage, Clydebank, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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13
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Behavioral Responses of Pacific Lamprey to Alarm Cues. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2017. [DOI: 10.3996/042016-jwfm-033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Pacific lamprey (Entosphenus tridentatus), an anadromous ectoparasite, faces several challenges during adult migration to spawning grounds. Developing methods to address these challenges is critical to the success of ongoing conservation efforts. The challenges are diverse, and include anthropogenic alterations to the ecosystem resulting in loss of habitat, impassable barriers such as dams, climate change impacts, and altered predator fields. We conducted a behavioral study to understand how adult migrating Pacific lamprey respond to potential alarm cues: White Sturgeon (Acipenser transmontanus), human saliva, decayed Pacific lamprey, and river otter (Lontra canadensis). Research has shown that some species of lamprey can be guided to a location using odors and similar cues may be useful as a management tool for Pacific lamprey. Experiments were conducted over 2 nights and measured the number of entries (count) and duration of time spent (occupancy) by adult lamprey in each arm of a two-choice maze. During the first night, no odor was added to test for selection bias between arms. During the second night odor was added to one arm of the maze. Contrary to expectations, lamprey were significantly attracted to the river otter odor in both count and occupancy. No significant differences were found in the response of lamprey to the other three odors. Results from this study indicate that Pacific lamprey do respond to some odors; however, additional tests are necessary to better identify the types of odors and concentrations that elicit a repeatable response.
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14
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Kirk MA, Caudill CC. Network analyses reveal intra‐ and interspecific differences in behaviour when passing a complex migration obstacle. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mark A. Kirk
- Department of Fish and Wildlife Sciences College of Natural Resources University of Idaho 875 Perimeter Drive Moscow ID 83844‐1141 USA
| | - Christopher C. Caudill
- Department of Fish and Wildlife Sciences College of Natural Resources University of Idaho 875 Perimeter Drive Moscow ID 83844‐1141 USA
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15
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Rougemont Q, Gagnaire PA, Perrier C, Genthon C, Besnard AL, Launey S, Evanno G. Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes. Mol Ecol 2016; 26:142-162. [PMID: 27105132 DOI: 10.1111/mec.13664] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/22/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022]
Abstract
Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns in geographically connected population pairs were better explained by introgression after secondary contact, whereas disconnected population pairs have retained a signal of ancient migration. In all ecotype pairs, models accounting for differential introgression among loci outperformed homogeneous migration models. Generating neutral predictions from the inferred divergence scenarios to detect highly differentiated markers identified greater proportions of outliers in disconnected population pairs than in connected pairs. However, increased similarity in the most divergent genomic regions was found among connected ecotype pairs, indicating that gene flow was instrumental in generating parallelism at the molecular level. These results suggest that heterogeneous genomic differentiation and parallelism among replicate ecotype pairs have partly emerged through restricted introgression in genomic islands.
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Affiliation(s)
- Quentin Rougemont
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095, Montpellier, France.,Station Méditerranéenne de l'Environnement Littoral, Université de Montpellier, 2 Rue des Chantiers, F-34200, Sète, France
| | - Charles Perrier
- CEFE-CNRS, Centre D'Ecologie Fonctionnelle et Evolutive, Route de Mende, 34090, Montpellier, France
| | - Clémence Genthon
- Plateforme génomique INRA GenoToul Chemin de Borderouge - Auzeville, 31320, Castanet-Tolosan, France
| | - Anne-Laure Besnard
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Sophie Launey
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Guillaume Evanno
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
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16
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Rougemont Q, Roux C, Neuenschwander S, Goudet J, Launey S, Evanno G. Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations. PeerJ 2016; 4:e1910. [PMID: 27077007 PMCID: PMC4830234 DOI: 10.7717/peerj.1910] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/17/2016] [Indexed: 12/19/2022] Open
Abstract
Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey (L. planeri) show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.
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Affiliation(s)
- Quentin Rougemont
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
| | - Camille Roux
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Samuel Neuenschwander
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Vital-IT, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Sophie Launey
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
| | - Guillaume Evanno
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
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17
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Mateus CS, Almeida PR, Mesquita N, Quintella BR, Alves MJ. European Lampreys: New Insights on Postglacial Colonization, Gene Flow and Speciation. PLoS One 2016; 11:e0148107. [PMID: 26871930 PMCID: PMC4752455 DOI: 10.1371/journal.pone.0148107] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 01/13/2016] [Indexed: 01/26/2023] Open
Abstract
Ice ages are known to be the most dominant palaeoclimatic feature occurring on Earth, producing severe climatic oscillations and consequently shaping the distribution and the population structure of several species. Lampreys constitute excellent models to study the colonization of freshwater systems, as they commonly appear in pairs of closely related species of anadromous versus freshwater resident adults, thus having the ability to colonize new habitats, through the anadromous species, and establish freshwater resident derivates. We used 10 microsatellite loci to investigate the spatial structure, patterns of gene flow and migration routes of Lampetra populations in Europe. We sampled 11 populations including the migratory L. fluviatilis and four resident species, L. planeri, L. alavariensis, L. auremensis and L. lusitanica, the last three endemic to the Iberian Peninsula. In this southern glacial refugium almost all sampled populations represent a distinct genetic cluster, showing high levels of allopatric differentiation, reflecting long periods of isolation. As result of their more recent common ancestor, populations from northern Europe are less divergent among them, they are represented by fewer genetic clusters, and there is evidence of strong recent gene flow among populations. These previously glaciated areas from northern Europe may have been colonized from lampreys expanding out of the Iberian refugia. The pair L. fluviatilis/L. planeri is apparently at different stages of speciation in different locations, showing evidences of high reproductive isolation in the southern refugium, and low differentiation in the north.
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Affiliation(s)
- Catarina Sofia Mateus
- MARE – Centro de Ciências do Mar e do Ambiente, Universidade de Évora, Évora, Portugal
- Museu Nacional de História Natural e da Ciência & Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| | - Pedro Raposo Almeida
- MARE – Centro de Ciências do Mar e do Ambiente, Universidade de Évora, Évora, Portugal
- Departamento de Biologia, Escola de Ciências e Tecnologia, Universidade Évora, Évora, Portugal
| | - Natacha Mesquita
- Museu Nacional de História Natural e da Ciência & Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
| | - Bernardo Ruivo Quintella
- MARE – Centro de Ciências do Mar e do Ambiente, Universidade de Évora, Évora, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Maria Judite Alves
- Museu Nacional de História Natural e da Ciência & Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
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18
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Bett NN, Hinch SG. Olfactory navigation during spawning migrations: a review and introduction of the Hierarchical Navigation Hypothesis. Biol Rev Camb Philos Soc 2015; 91:728-59. [PMID: 25923999 DOI: 10.1111/brv.12191] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/31/2022]
Abstract
Migrations are characterized by periods of movement that typically rely on orientation towards directional cues. Anadromous fish undergo several different forms of oriented movement during their spawning migration and provide some of the most well-studied examples of migratory behaviour. During the freshwater phase of the migration, fish locate their spawning grounds via olfactory cues. In this review, we synthesize research that explores the role of olfaction during the spawning migration of anadromous fish, most of which focuses on two families: Salmonidae (salmonids) and Petromyzontidae (lampreys). We draw attention to limitations in this research, and highlight potential areas of investigation that will help fill in current knowledge gaps. We also use the information assembled from our review to formulate a new hypothesis for natal homing in salmonids. Our hypothesis posits that migrating adults rely on three types of cues in a hierarchical fashion: imprinted cues (primary), conspecific cues (secondary), and non-olfactory environmental cues (tertiary). We provide evidence from previous studies that support this hypothesis. We also discuss future directions of research that can test the hypothesis and further our understanding of the spawning migration.
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Affiliation(s)
- Nolan N Bett
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Scott G Hinch
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
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19
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Bracken FSA, Hoelzel AR, Hume JB, Lucas MC. Contrasting population genetic structure among freshwater-resident and anadromous lampreys: the role of demographic history, differential dispersal and anthropogenic barriers to movement. Mol Ecol 2015; 24:1188-204. [PMID: 25689694 PMCID: PMC4413359 DOI: 10.1111/mec.13112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 11/30/2022]
Abstract
The tendency of many species to abandon migration remains a poorly understood aspect of evolutionary biology that may play an important role in promoting species radiation by both allopatric and sympatric mechanisms. Anadromy inherently offers an opportunity for the colonization of freshwater environments, and the shift from an anadromous to a wholly freshwater life history has occurred in many families of fishes. Freshwater-resident forms have arisen repeatedly among lampreys (within the Petromyzontidae and Mordaciidae), and there has been much debate as to whether anadromous lampreys, and their derived freshwater-resident analogues, constitute distinct species or are divergent ecotypes of polymorphic species. Samples of 543 European river lamprey Lampetra fluviatilis (mostly from anadromous populations) and freshwater European brook lamprey Lampetra planeri from across 18 sites, primarily in the British Isles, were investigated for 13 polymorphic microsatellite DNA loci, and 108 samples from six of these sites were sequenced for 829 bp of mitochondrial DNA (mtDNA). We found contrasting patterns of population structure for mtDNA and microsatellite DNA markers, such that low diversity and little structure were seen for all populations for mtDNA (consistent with a recent founder expansion event), while fine-scale structuring was evident for nuclear markers. Strong differentiation for microsatellite DNA loci was seen among freshwater-resident L. planeri populations and between L. fluviatilis and L. planeri in most cases, but little structure was evident among anadromous L. fluviatilis populations. We conclude that postglacial colonization founded multiple freshwater-resident populations with strong habitat fidelity and limited dispersal tendencies that became highly differentiated, a pattern that was likely intensified by anthropogenic barriers.
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Affiliation(s)
- Fiona S A Bracken
- School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK
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20
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Hess JE, Caudill CC, Keefer ML, McIlraith BJ, Moser ML, Narum SR. Genes predict long distance migration and large body size in a migratory fish, Pacific lamprey. Evol Appl 2014; 7:1192-208. [PMID: 25558280 PMCID: PMC4275091 DOI: 10.1111/eva.12203] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/17/2014] [Indexed: 12/20/2022] Open
Abstract
Elucidation of genetic mechanisms underpinning migratory behavior could help predict how changes in genetic diversity may affect future spatiotemporal distribution of a migratory species. This ability would benefit conservation of one such declining species, anadromous Pacific lamprey (Entosphenus tridentatus). Nonphilopatric migration of adult Pacific lamprey has homogenized population-level neutral variation but has maintained adaptive variation that differentiates groups based on geography, run-timing and adult body form. To investigate causes for this adaptive divergence, we examined 647 adult lamprey sampled at a fixed location on the Columbia River and radiotracked during their subsequent upstream migration. We tested whether genetic variation [94 neutral and adaptive single nucleotide polymorphisms (SNPs) previously identified from a genomewide association study] was associated with phenotypes of migration distance, migration timing, or morphology. Three adaptive markers were strongly associated with morphology, and one marker also correlated with upstream migration distance and timing. Genes physically linked with these markers plausibly influence differences in body size, which is also consistently associated with migration distance in Pacific lamprey. Pacific lamprey conservation implications include the potential to predict an individual's upstream destination based on its genotype. More broadly, the results suggest a genetic basis for intrapopulation variation in migration distance in migratory species.
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Affiliation(s)
- Jon E Hess
- Columbia River Inter-Tribal Fish Commission Hagerman, ID, USA
| | - Christopher C Caudill
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho Moscow, ID, USA
| | - Matthew L Keefer
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho Moscow, ID, USA
| | | | - Mary L Moser
- Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration Seattle, WA, USA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission Hagerman, ID, USA
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21
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Lança MJ, Machado M, Mateus CS, Lourenço M, Ferreira AF, Quintella BR, Almeida PR. Investigating population structure of Sea Lamprey (Petromyzon marinus, L.) in Western Iberian Peninsula using morphological characters and heart fatty acid signature analyses. PLoS One 2014; 9:e108110. [PMID: 25259723 PMCID: PMC4178062 DOI: 10.1371/journal.pone.0108110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/20/2014] [Indexed: 11/21/2022] Open
Abstract
This study hypothesizes the existence of three groups of sea lamprey Petromyzon marinus L. in Portugal (North/Central group, Tagus group, and Guadiana group), possibly promoted by seabed topography isolation during the oceanic phase of the life cycle. Within this context, our purpose was to analyze the existence of a stock structure on sea lamprey populations sampled in the major Portuguese river basins using both morphological characters and heart tissue fatty acid signature. In both cases, the multiple discriminant analysis revealed statistically significant differences among groups, and the overall corrected classification rate estimated from cross-validation procedure was particularly high for the cardiac muscle fatty acid profiles (i.e. 83.8%). Morphometric characters were much more useful than meristic ones to discriminate stocks, and the most important variables for group differentiation were eye length, second dorsal fin length and branchial length. Fatty acid analysis showed that all lampreys from the southern Guadiana group were correctly classified and not mixing with individuals from any other group, reflecting a typical heart fatty acid signature. Our results revealed that 89.5% and 72.2% of the individuals from the Tagus and North/Central groups, respectively, were also correctly classified, despite some degree of overlap between individuals from these groups. The fatty acids that contributed to the observed segregation were C16:0; C17:0; C18:1ω9; C20:3ω6 and C22:2ω6. Detected differences are probably related with environmental variables to which lampreys may have been exposed, which leaded to different patterns of gene expression. These results suggest the existence of three different sea lamprey stocks in Portugal, with implication in terms of management and conservation.
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Affiliation(s)
- Maria João Lança
- Escola de Ciências e Tecnologia, Departamento de Zootecnia, Universidade de Évora, Évora, Portugal
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Évora, Portugal
| | - Maria Machado
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Évora, Portugal
| | - Catarina S. Mateus
- Centro de Oceanografia, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Museu Nacional de História Natural e da Ciência & Centro de Biologia Ambiental, Universidade de Lisboa, Lisboa, Portugal
| | - Marta Lourenço
- Centro de Oceanografia, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana F. Ferreira
- Centro de Oceanografia, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Bernardo R. Quintella
- Centro de Oceanografia, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro R. Almeida
- Museu Nacional de História Natural e da Ciência & Centro de Biologia Ambiental, Universidade de Lisboa, Lisboa, Portugal
- Escola de Ciências e Tecnologia, Departamento de Biologia, Universidade de Évora, Évora, Portugal
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22
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Schedina IM, Pfautsch S, Hartmann S, Dolgener N, Polgar A, Bianco PG, Tiedemann R, Ketmaier V. Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data. JOURNAL OF FISH BIOLOGY 2014; 85:960-964. [PMID: 25059996 DOI: 10.1111/jfb.12470] [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: 03/27/2013] [Accepted: 06/12/2014] [Indexed: 06/03/2023]
Abstract
Eight polymorphic microsatellite loci were developed for the brook lamprey Lampetra planeri through 454 sequencing and their usefulness was tested in 45 individuals of both L. planeri and the river lamprey Lampetra fluviatilis. The number of alleles per loci ranged between two and five; the Italian and Irish populations had a mean expected heterozygosity of 0·388 and 0·424 and a mean observed heterozygosity of 0·418 and 0·411, respectively.
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Affiliation(s)
- I M Schedina
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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23
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Paradoxical exploitation of protected fishes as bait for anglers: evaluating the Lamprey bait market in Europe and developing sustainable and ethical solutions. PLoS One 2014; 9:e99617. [PMID: 24936643 PMCID: PMC4061017 DOI: 10.1371/journal.pone.0099617] [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: 12/01/2013] [Accepted: 05/16/2014] [Indexed: 11/19/2022] Open
Abstract
A reoccurring conservation problem is the resolution of consumptive use of threatened wildlife and is especially difficult to defend when it occurs for recreational practices. We explored the commercial capture and supply of threatened European river lamprey (Lampetra fluviatilis) to anglers, to determine the extent of exploitation and seek opportunities for improved conservation. The trade began in 1995 from England, but by 2012 involved sale of lamprey from England, The Netherlands and Estonia, including from protected populations. Lamprey are sold frozen for the capture of predatory fish, mostly in freshwater. In the year 2011/2012 9 tonnes (>90,000 lampreys) of river lamprey were supplied, almost exclusively to British anglers. Although annual catches in the main English lamprey fishery (River Ouse) have varied widely since 1995, catch per unit effort did not decline between 2000 and 2012. Conservation actions since 2011 have included a cap on fishing licenses, catch quotas and restricted fishing seasons. Now, 86% of lamprey bait is imported to Britain. Most bait sellers interviewed would not stock lamprey if they knew they were from threatened populations; many felt their trade would not be impacted if lamprey were not stocked. This facilitates opportunities to enter into dialogue with anglers over alternative baits to threatened lamprey. The study emphasises the need to inform stakeholders about conservation species subjected to market-driven exploitation.
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24
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Hess JE, Campbell NR, Docker MF, Baker C, Jackson A, Lampman R, McIlraith B, Moser ML, Statler DP, Young WP, Wildbill AJ, Narum SR. Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey. Mol Ecol Resour 2014; 15:187-202. [PMID: 24842551 DOI: 10.1111/1755-0998.12283] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 11/29/2022]
Abstract
Next-generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high-throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are FST outliers, and five of these outliers are localized within genes and significantly associated with geography, run-timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species' range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species.
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Affiliation(s)
- Jon E Hess
- Columbia River Inter-Tribal Fish Commission, 3059-F National Fish Hatchery Rd, Hagerman, ID, 83332, USA
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25
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Hess JE, Campbell NR, Close DA, Docker MF, Narum SR. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species. Mol Ecol 2012. [DOI: 10.1111/mec.12150] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jon E. Hess
- Columbia River Inter-Tribal Fish Commission; 3059-F National Fish Hatchery Road Hagerman ID 83332 USA
| | - Nathan R. Campbell
- Columbia River Inter-Tribal Fish Commission; 3059-F National Fish Hatchery Road Hagerman ID 83332 USA
| | - David A. Close
- University of British Columbia; Fisheries Ctr Vancouver Canada BC V6T 1Z4
- Department of Zoology; University of British Columbia; Vancouver Canada BC V6T 1Z4
| | - Margaret F. Docker
- Department of Biological Sciences; University of Manitoba; Winnipeg Canada MB R3T 2N2
| | - Shawn R. Narum
- Columbia River Inter-Tribal Fish Commission; 3059-F National Fish Hatchery Road Hagerman ID 83332 USA
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26
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Boguski DA, Reid SB, Goodman DH, Docker MF. Genetic diversity, endemism and phylogeny of lampreys within the genus Lampetra sensu stricto (Petromyzontiformes: Petromyzontidae) in western North America. JOURNAL OF FISH BIOLOGY 2012; 81:1891-1914. [PMID: 23130690 DOI: 10.1111/j.1095-8649.2012.03417.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phylogenetic structure of four Lampetra species from the Pacific drainage of North America (western brook lamprey Lampetra richardsoni, Pacific brook lamprey Lampetra pacifica, river lamprey Lampetra ayresii and Kern brook lamprey Lampetra hubbsi) and unidentified Lampetra specimens (referred to as Lampetra sp.) from 36 locations was estimated using the mitochondrial cytochrome b gene. Maximum parsimony and Bayesian inferences did not correspond with any taxonomic scheme proposed to date. Rather, although L. richardsoni (from Alaska to California) and L. ayresii (from British Columbia to California) together constituted a well-supported clade distinct from several genetically divergent Lampetra populations in Oregon and California, these two species were not reciprocally monophyletic. The genetically divergent populations included L. pacifica (from the Columbia River basin) and L. hubbsi (from the Kern River basin) and four Lampetra sp. populations in Oregon (Siuslaw River and Fourmile Creek) and California (Kelsey and Mark West Creeks). These four Lampetra sp. populations showed genetic divergence between 2.3 and 5.7% from any known species (and up to 8.0% from each other), and may represent morphologically cryptic and thus previously undescribed species. A fifth population (from Paynes Creek, California) may represent a range extension of L. hubbsi into the Upper Sacramento River.
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Affiliation(s)
- D A Boguski
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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