1
|
Euclide PT, Larson WA, Bootsma M, Miller LM, Scribner KT, Stott W, Wilson CC, Latch EK. A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus. Ecol Evol 2022; 12:e9591. [PMID: 36532137 PMCID: PMC9750844 DOI: 10.1002/ece3.9591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research, which relies on data about specific markers in an organism's genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for nonmodel organisms. Here, we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen, which were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false-positive rates of parent-offspring and full-sibling kinship identification were found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region.
Collapse
Affiliation(s)
- Peter T. Euclide
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteIndianaUSA
| | - Wesley A. Larson
- College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA,National Marine Fisheries Service, Alaska Fisheries Science CenterNational Oceanographic and Atmospheric AdministrationJuneauAlaskaUSA
| | - Matthew Bootsma
- College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Loren M. Miller
- Minnesota Department of Natural ResourcesSt. PaulMinnesotaUSA
| | - Kim T. Scribner
- Department of Fish and WildlifeDepartment of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Wendylee Stott
- Department of Fisheries and Oceans, Artic and Aquatic Research DivisionWinnipegManitobaCanada
| | - Chris C. Wilson
- Ontario Ministry of Natural Resources and ForestryTrent UniversityPeterboroughOntarioCanada
| | - Emily K. Latch
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWisconsinUSA
| |
Collapse
|
2
|
Olivares‐Zambrano D, Daane J, Hyde J, Sandel MW, Aguilar A. Speciation genomics and the role of depth in the divergence of rockfishes (
Sebastes
) revealed through Pool‐seq analysis of enriched sequences. Ecol Evol 2022; 12:e9341. [PMID: 36188524 PMCID: PMC9502067 DOI: 10.1002/ece3.9341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ecological divergence in fishes, and yet it is unclear how adaptation along these gradients' shapes genomic divergence. The genus Sebastes contains numerous species pairs that are depth‐segregated and can provide a better understanding of the mode and tempo of genomic diversification. Here, we present exome data on two species pairs of rockfishes that are depth‐segregated and have different degrees of divergence: S. chlorostictus–S. rosenblatti and S. crocotulus–S. miniatus. We were able to reliably identify “islands of divergence” in the species pair with more recent divergence (S. chlorostictus–S. rosenblatti) and discovered a number of genes associated with neurosensory function, suggesting a role for this pathway in the early speciation process. We also reconstructed demographic histories of divergence and found the best supported model was isolation followed by asymmetric secondary contact for both species pairs. These results suggest past ecological/geographic isolation followed by asymmetric secondary contact of deep to shallow species. Our results provide another example of using rockfish as a model for studying speciation and support the role of depth as an important mechanism for diversification in the marine environment.
Collapse
Affiliation(s)
- Daniel Olivares‐Zambrano
- Department of Biological SciencesCalifornia State University Los AngelesLos AngelesCaliforniaUSA
- Present address:
Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jacob Daane
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
| | - John Hyde
- National Oceanic and Atmospheric Administration, National Marine Fisheries ServiceNational Marine Fisheries ServiceSouthwest Fisheries Science CenterLa JollaCaliforniaUSA
| | - Michael W. Sandel
- Biological and Environmental SciencesUniversity of West AlabamaLivingstonAlabamaUSA
- Department of WIldlifeFisheries, and Aquaculture, Mississippi State UniversityMississippi StateMississippiUSA
| | - Andres Aguilar
- Department of Biological SciencesCalifornia State University Los AngelesLos AngelesCaliforniaUSA
| |
Collapse
|
3
|
Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
Collapse
Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
| | | |
Collapse
|
4
|
Johannesson K, Le Moan A, Perini S, André C. A Darwinian Laboratory of Multiple Contact Zones. Trends Ecol Evol 2020; 35:1021-1036. [DOI: 10.1016/j.tree.2020.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
|
5
|
Wenne R, Bernaś R, Kijewska A, Poćwierz-Kotus A, Strand J, Petereit C, Plauška K, Sics I, Árnyasi M, Kent MP. SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea. Sci Rep 2020; 10:9738. [PMID: 32546719 PMCID: PMC7298039 DOI: 10.1038/s41598-020-66518-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/11/2020] [Indexed: 01/02/2023] Open
Abstract
Atlantic cod (Gadus morhua) is one of the most important fish species in northern Europe for several reasons including its predator status in marine ecosystems, its historical role in fisheries, its potential in aquaculture and its strong public profile. However, due to over-exploitation in the North Atlantic and changes in the ecosystem, many cod populations have been reduced in size and genetic diversity. Cod populations in the Baltic Proper, Kattegat and North Sea have been analyzed using a species specific single nucleotide polymorphism (SNP) array. Using a subset of 8,706 SNPs, moderate genetic differences were found between subdivisions in three traditionally delineated cod management stocks: Kattegat, western and eastern Baltic. However, an FST measure of population differentiation based on allele frequencies from 588 outlier loci for 2 population groups, one including 5 western and the other 4 eastern Baltic populations, indicated high genetic differentiation. In this paper, differentiation has been demonstrated not only between, but also within western and eastern Baltic cod stocks for the first time, with salinity appearing to be the most important environmental factor influencing the maintenance of cod population divergence between the western and eastern Baltic Sea.
Collapse
Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland.
| | - Rafał Bernaś
- Department of Migratory Fishes in Rutki, Inland Fisheries Institute, Olsztyn, 10-719, Poland
| | - Agnieszka Kijewska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Anita Poćwierz-Kotus
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Jakob Strand
- Arctic Research Centre, Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Christoph Petereit
- GEOMAR, Helmholtz Centre for Ocean Research Kiel, Research Division 3: Marine Ecology, Research Unit: Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany
- Bruno-Lorenzen-Schule Schleswig, Spielkoppel 6, 24837, Schleswig, Germany
| | - Kęstas Plauška
- Fisheries Service under the Ministry of Agriculture Division of Fisheries Research & Science, Smiltynes 1, 91001, Klaipeda, Lithuania
| | - Ivo Sics
- Institute of Food Safety, Animal Health and Environment "BIOR", Riga, Latvia
| | - Mariann Árnyasi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), PO Box, 5003, Aas, Norway
| | - Matthew P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), PO Box, 5003, Aas, Norway
| |
Collapse
|