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Liu Y, Dietrich CH, Wei C. The impact of geographic isolation and host shifts on population divergence of the rare cicada Subpsaltria yangi. Mol Phylogenet Evol 2024; 199:108146. [PMID: 38986756 DOI: 10.1016/j.ympev.2024.108146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 07/01/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
The contributions of divergent selection and spatial isolation to population divergence are among the main focuses of evolutionary biology. Here we employed integrated methods to explore genomic divergence, demographic history and calling-song differentiation in the cicada Subpsaltria yangi, and compared the genotype and calling-song phenotype of different populations occurring in distinct habitats. Our results indicate that this species comprises four main lineages with unique sets of haplotypes and calling-song structure, which are distinctly associated with geographic isolation and habitats. The populations occurring on the Loess Plateau underwent substantial expansion at ∼0.130-0.115 Ma during the Last Interglacial. Geographic distance and host shift between pairs of populations predict genomic divergence, with geographic distance and acoustical signal together explaining > 60% of the divergence among populations. Differences in calling songs could reflect adaptation of populations to novel environments with different host plants, habitats and predators, which may have resulted from neutral divergence at the molecular level followed by natural selection. Geomorphic barriers and climate oscillations associated with Pleistocene glaciation may have been primary factors in shaping the population genetic structure of this species. Ultimately this may couple with a host shift in leading toward allopatric speciation in S. yangi, i.e., isolation by distance. Our findings improve understanding of divergence in allopatry of herbivorous insects, and may inform future studies on the molecular mechanisms underlying the association between genetic/phenotypic changes and adaptation of insects to novel niches and host plants.
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Affiliation(s)
- Yunxiang Liu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China; State Key Laboratory of Plateau Ecology and Agriculture, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, Qinghai, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Cong Wei
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwest Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
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2
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Backenstose NJC, MacGuigan DJ, Osborne CA, Bernal MA, Thomas EK, Normandeau E, Yule DL, Stott W, Ackiss AS, Albert VA, Bernatchez L, Krabbenhoft TJ. Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum. Commun Biol 2024; 7:978. [PMID: 39134631 PMCID: PMC11319351 DOI: 10.1038/s42003-024-06503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 06/25/2024] [Indexed: 08/15/2024] Open
Abstract
The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex ("ciscoes") radiated rapidly prior to the Last Glacial Maximum (80-90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr (Salvelinus namaycush), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.
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Affiliation(s)
| | - Daniel J MacGuigan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | | | - Moisés A Bernal
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | | | - Eric Normandeau
- Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, G1V 0A6, Canada
| | - Daniel L Yule
- US Geological Survey, Lake Superior Biological Station, Great Lakes Science Center, Ashland, WI, USA
| | - Wendylee Stott
- Freshwater Institute, Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, MB, R3T 2N6, Canada
| | - Amanda S Ackiss
- US Geological Survey, Great Lakes Science Center, Ann Arbor, MI, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Trevor J Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
- RENEW Institute, University at Buffalo, Buffalo, NY, USA.
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3
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Peñafiel Loaiza N, Chafe AH, Moraes R M, Oleas NH, Roncal J. Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products. Evol Appl 2024; 17:e13765. [PMID: 39091352 PMCID: PMC11291087 DOI: 10.1111/eva.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.
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Affiliation(s)
- Nicolás Peñafiel Loaiza
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Present address:
Chone y BabahoyoLojaEcuador
| | - Abigail H. Chafe
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Mónica Moraes R
- Herbario Nacional de Bolivia, Instituto de EcologíaUniversidad Mayor de San AndrésLa PazBolivia
| | - Nora H. Oleas
- Centro de Investigación de la Biodiversidad y Cambio Climático – BioCamb e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio AmbienteUniversidad IndoaméricaQuitoEcuador
| | - Julissa Roncal
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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Pedrazzini C, Rehner SA, Strasser H, Zemp N, Holderegger R, Widmer F, Enkerli J. Clonal genomic population structure of Beauveria brongniartii and Beauveria pseudobassiana: Pathogens of the common European cockchafer (Melolontha melolontha L.). Environ Microbiol 2024; 26:e16612. [PMID: 38622804 DOI: 10.1111/1462-2920.16612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
Beauveria brongniartii is a fungal pathogen that infects the beetle Melolontha melolontha, a significant agricultural pest in Europe. While research has primarily focused on the use of B. brongniartii for controlling M. melolontha, the genomic structure of the B. brongniartii population remains unknown. This includes whether its structure is influenced by its interaction with M. melolontha, the timing of beetle-swarming flights, geographical factors, or reproductive mode. To address this, we analysed genome-wide SNPs to infer the population genomics of Beauveria spp., which were isolated from infected M. melolontha adults in an Alpine region. Surprisingly, only one-third of the isolates were identified as B. brongniartii, while two-thirds were distributed among cryptic taxa within B. pseudobassiana, a fungal species not previously recognized as a pathogen of M. melolontha. Given the prevalence of B. pseudobassiana, we conducted analyses on both species. We found no spatial or temporal genomic patterns within either species and no correlation with the population structure of M. melolontha, suggesting that the dispersal of the fungi is independent of the beetle. Both species exhibited clonal population structures, with B. brongniartii fixed for one mating type and B. pseudobassiana displaying both mating types. This implies that factors other than mating compatibility limit sexual reproduction. We conclude that the population genomic structure of Beauveria spp. is primarily influenced by predominant asexual reproduction and dispersal.
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Affiliation(s)
- Chiara Pedrazzini
- Molecular Ecology, Agroscope, Zürich, Switzerland
- Institute of Environmental Systems Science, ETH, Zürich, Switzerland
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture USDA, Beltsville, Maryland, USA
| | - Hermann Strasser
- Institute of Microbiology, Leopold-Franzens University Innsbruck, Innsbruck, Austria
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH, Zürich, Switzerland
| | - Rolf Holderegger
- Institute of Environmental Systems Science, ETH, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Jürg Enkerli
- Molecular Ecology, Agroscope, Zürich, Switzerland
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Van Nynatten A, Duncan AT, Lauzon R, Sheldon TA, Chen SK, Lovejoy NR, Mandrak NE, Chang BSW. Adaptive Evolution of Nearctic Deepwater Fish Vision: Implications for Assessing Functional Variation for Conservation. Mol Biol Evol 2024; 41:msae024. [PMID: 38314890 PMCID: PMC10896662 DOI: 10.1093/molbev/msae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/15/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Intraspecific functional variation is critical for adaptation to rapidly changing environments. For visual opsins, functional variation can be characterized in vitro and often reflects a species' ecological niche but is rarely considered in the context of intraspecific variation or the impact of recent environmental changes on species of cultural or commercial significance. Investigation of adaptation in postglacial lakes can provide key insight into how rapid environmental changes impact functional evolution. Here, we report evidence for molecular adaptation in vision in 2 lineages of Nearctic fishes that are deep lake specialists: ciscoes and deepwater sculpin. We found depth-related variation in the dim-light visual pigment rhodopsin that evolved convergently in these 2 lineages. In vitro characterization of spectral sensitivity of the convergent deepwater rhodopsin alleles revealed blue-shifts compared with other more widely distributed alleles. These blue-shifted rhodopsin alleles were only observed in deep clear postglacial lakes with underwater visual environments enriched in blue light. This provides evidence of remarkably rapid and convergent visual adaptation and intraspecific functional variation in rhodopsin. Intraspecific functional variation has important implications for conservation, and these fishes are of conservation concern and great cultural, commercial, and nutritional importance to Indigenous communities. We collaborated with the Saugeen Ojibway Nation to develop and test a metabarcoding approach that we show is efficient and accurate in recovering the ecological distribution of functionally relevant variation in rhodopsin. Our approach bridges experimental analyses of protein function and genetics-based tools used in large-scale surveys to better understand the ecological extent of adaptive functional variation.
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Affiliation(s)
- Alexander Van Nynatten
- Department of Biological Science, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Alexander T Duncan
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, Ontario, Canada
- Fisheries Assessment Program, Chippewas of Nawash Unceded First Nation, Neyaashiinigmiing, Ontario, Canada
| | - Ryan Lauzon
- Fisheries Assessment Program, Chippewas of Nawash Unceded First Nation, Neyaashiinigmiing, Ontario, Canada
| | | | - Steven K Chen
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nathan R Lovejoy
- Department of Biological Science, University of Toronto Scarborough, Scarborough, Ontario, Canada
- Department of Ecological and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas E Mandrak
- Department of Biological Science, University of Toronto Scarborough, Scarborough, Ontario, Canada
- Department of Ecological and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Ecological and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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6
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Haltiner L, Spaak P, Dennis SR, Feulner PGD. Population genetic insights into establishment, adaptation, and dispersal of the invasive quagga mussel across perialpine lakes. Evol Appl 2024; 17:e13620. [PMID: 38283608 PMCID: PMC10809192 DOI: 10.1111/eva.13620] [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: 04/25/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 01/30/2024] Open
Abstract
Human activities have facilitated the invasion of freshwater ecosystems by various organisms. Especially, invasive bivalves such as the quagga mussels, Dreissena bugensis, have the potential to alter ecosystem function as they heavily affect the food web. Quagga mussels occur in high abundance, have a high filtration rate, quickly spread within and between waterbodies via pelagic larvae, and colonize various substrates. They have invaded various waterbodies across the Northern Hemisphere. In Central Europe, they have invaded multiple large and deep perialpine lakes with first recordings in Lake Geneva in 2015 and 2016 in Lake Constance. In the deep perialpine lakes, quagga mussels quickly colonized the littoral zone but are also abundant deeper (>80 m), where they are often thinner and brighter shelled. We analysed 675 quagga mussels using ddRAD sequencing to gain in-depth insights into the genetic population structure of quagga mussels across Central European lakes and across various sites and depth habitats in Lake Constance. We revealed substantial genetic differentiation amongst quagga mussel populations from three unconnected lakes, and all populations showed high genetic diversity and effective population size. In Lake Constance, we detected no genetic differentiation amongst quagga mussels sampled across different sites and depth habitats. We also did not identify any convincing candidate loci evidential for adaptation along a depth gradient and a transplant experiment showed no indications of local adaptation to living in the deep based on investigating growth and survival. Hence, the shallow-water and the deep-water morphotypes seem to be a result of phenotypic plasticity rather than local adaptation to depth. In conclusion, our ddRAD approach revealed insight into the establishment of genetically distinct quagga mussel populations in three perialpine lakes and suggests that phenotypic plasticity and life history traits (broadcast spawner with high fecundity and dispersing pelagic larvae) facilitate the fast spread and colonization of various depth habitats by the quagga mussel.
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Affiliation(s)
- Linda Haltiner
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Environmental Systems SciencesETH ZürichZürichSwitzerland
| | - Piet Spaak
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Environmental Systems SciencesETH ZürichZürichSwitzerland
| | - Stuart R. Dennis
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Present address:
Department IT servicesSwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
| | - Philine G. D. Feulner
- Fish Ecology and Evolution, Center for Ecology, Evolution and BiogeochemistrySwiss Federal Institute of Aquatic Science and Technology (Eawag)KastanienbaumSwitzerland
- Aquatic Ecology, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
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Shi Y, Homola JJ, Euclide PT, Isermann DA, Caroffino D, McPhee MV, Larson WA. High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish ( Coregonus clupeaformis) from Lake Michigan. Evol Appl 2022; 15:1776-1791. [PMID: 36426119 PMCID: PMC9679245 DOI: 10.1111/eva.13475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 09/08/2024] Open
Abstract
Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform the management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management.
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Affiliation(s)
- Yue Shi
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
- Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Jared J. Homola
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Daniel A. Isermann
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - David C. Caroffino
- Michigan Department of Natural ResourcesCharlevoix Research StationCharlevoixMichiganUSA
| | - Megan V. McPhee
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
| | - Wesley A. Larson
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
- National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay LaboratoriesNational Oceanic and Atmospheric AdministrationJuneauAlaskaUSA
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Canales‐Aguirre CB, Larson WA, McKinney GJ, Claure CE, Rocha JD, Ceballos SG, Cádiz MI, Yáñez JM, Gomez‐Uchida D. Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from north Patagonia. Ecol Evol 2022; 12:e9343. [PMID: 36225825 PMCID: PMC9530513 DOI: 10.1002/ece3.9343] [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: 08/19/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor an important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. Eleginops maclovinus is a protandrous hermaphrodite species with economic importance for local communities that are currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of E. maclovinus. We used restriction site-associated DNA (RAD) sequencing and outlier tests to obtain neutral and adaptive loci, using FST and GEA approaches. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 (Chepu) to 14,454 (Chaitén) and were influenced more by locality than by salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in E. maclovinus populations. These results suggest a complex interaction between genetic drift, gene flow, and natural selection in this area. Our findings also suggest several evolutionary significant units in this area, and the information should be integrated into the management of this species. We discussed the significance of these results for fishery management and suggest future directions to improve our understanding of how E. maclovinus has adapted to the dynamic waters of Northern Patagonia.
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Affiliation(s)
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science CenterAuke Bay LaboratoriesJuneauAlaskaUSA
| | | | - C. Eliza Claure
- Centro i~mar, Universidad de Los LagosPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
| | - J. Dellis Rocha
- Centro i~mar, Universidad de Los LagosPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
| | - Santiago G. Ceballos
- Centro Austral de Investigaciones Científicas (CADIC‐CONICET)UshuaiaTierra del FuegoArgentina
- Universidad Nacional de Tierra del Fuego (ICPA‐UNTDF)UshuaiaArgentina
| | - María I. Cádiz
- Núcleo Milenio INVASALConcepciónChile
- Department of BiologyAarhus UniversityAarhus CDenmark
| | - José M. Yáñez
- Núcleo Milenio INVASALConcepciónChile
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileLa PintanaSantiagoChile
| | - Daniel Gomez‐Uchida
- Núcleo Milenio INVASALConcepciónChile
- Genomics in Ecology, Evolution & Conservation Lab (GEECLAB), Departamento de Zoología. Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
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Bernal MA, Yule DL, Stott W, Evrard L, Dowling TE, Krabbenhoft TJ. Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae: Coregonus spp.). Mol Ecol 2022; 31:4495-4509. [PMID: 35785504 DOI: 10.1111/mec.16596] [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: 12/16/2020] [Revised: 04/11/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the latter was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as C. hoyi and C. zenithicus, which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent datasets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.
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Affiliation(s)
- Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, Alabama 36849, United States of America.,Department of Biological Sciences and RENEW Institute, University at Buffalo, Buffalo, NY 14260, United States of America
| | - Daniel L Yule
- U.S. Geological Survey, Great Lakes Science Center - Lake Superior Biological Station, 2800 Lake Shore Drive E., Ashland, WI 54806, United States of America
| | - Wendylee Stott
- Michigan State University CESU working for U.S. Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105-2807, United States of America
| | - Lori Evrard
- U.S. Geological Survey, Great Lakes Science Center - Lake Superior Biological Station, 2800 Lake Shore Drive E., Ashland, WI 54806, United States of America
| | - Thomas E Dowling
- Wayne State University, Department of Biological Sciences, Detroit, Michigan, 48202, United States of America
| | - Trevor J Krabbenhoft
- Department of Biological Sciences and RENEW Institute, University at Buffalo, Buffalo, NY 14260, United States of America
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10
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Kim D, Taylor AT, Near TJ. Phylogenomics and species delimitation of the economically important Black Basses (Micropterus). Sci Rep 2022; 12:9113. [PMID: 35668124 PMCID: PMC9170712 DOI: 10.1038/s41598-022-11743-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/28/2022] [Indexed: 01/25/2023] Open
Abstract
Informed management and conservation efforts are vital to sustainable recreational fishing and biodiversity conservation. Because the taxonomic rank of species is important in conservation and management strategies, success of these efforts depends on accurate species delimitation. The Black Basses (Micropterus) are an iconic lineage of freshwater fishes that include some of the world’s most popular species for recreational fishing and world's most invasive species. Despite their popularity, previous studies to delimit species and lineages in Micropterus suffer from insufficient geographic coverage and uninformative molecular markers. Our phylogenomic analyses of ddRAD data result in the delimitation of 19 species of Micropterus, which includes 14 described species, the undescribed but well-known Altamaha, Bartram’s, and Choctaw basses, and two additional undescribed species currently classified as Smallmouth Bass (M. dolomieu). We provide a revised delimitation of species in the Largemouth Bass complex that necessitates a change in scientific nomenclature: Micropterus salmoides is retained for the Florida Bass and Micropterus nigricans is elevated from synonymy for the Largemouth Bass. The new understanding of diversity, distribution, and systematics of Black Basses will serve as important basis for the management and conservation of this charismatic and economically important clade of fishes.
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Affiliation(s)
- Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, 06511, USA.
| | - Andrew T Taylor
- Department of Biology, University of Central Oklahoma, Edmond, OK, 73034, USA.,Department of Biology, University of North Georgia, Dahlonega, GA, 30597, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, 06511, USA.,Peabody Museum, Yale University, New Haven, CT, 06511, USA
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11
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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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12
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Principe NG, Ash KT, Davis MA, Egly RM, Larson ER. A Molecular and Morphological Guide to the Pilose Crayfishes of Western North America. WEST N AM NATURALIST 2021. [DOI: 10.3398/064.081.0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - Kurt T. Ash
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996
| | - Mark A. Davis
- Illinois Natural History Survey, Champaign, IL 61820
| | - Rachel M. Egly
- Institute of Environmental Sustainability, Loyola University, Chicago, IL 60660
| | - Eric R. Larson
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801
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13
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Mehner T, Palm S, Delling B, Karjalainen J, Kiełpińska J, Vogt A, Freyhof J. Genetic relationships between sympatric and allopatric Coregonus ciscoes in North and Central Europe. BMC Ecol Evol 2021; 21:186. [PMID: 34615463 PMCID: PMC8496053 DOI: 10.1186/s12862-021-01920-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Sympatric speciation along ecological gradients has been studied repeatedly, in particular in freshwater fishes. Rapid post-glacial ecological divergence has resulted in numerous endemic species or ecologically distinct populations in lakes of the temperate zones. Here, we focus on the Baltic cisco (Coregonus albula) complex, to study the genetic similarity among two pairs of sympatric autumn- and spring-spawning populations from post-glacial German Lakes Stechlin and Breiter Luzin. For comparison, we included a similar pair of sympatric populations from the Swedish Lake Fegen. We wanted to explore potential genetic similarities between the three sympatric cisco population pairs in the three lakes, to evaluate whether the pairs may have emerged independently in the three lakes, or whether two different species may have colonized all three lakes independently. Furthermore, we considered allopatric C. albula populations from three Polish, three Finnish, and four Swedish locations, added one Siberian population of the sister species C. sardinella and a Swedish C. maraena (whitefish) population. By genotyping nine microsatellite markers in 655 individuals from these 18 populations, we wanted to elucidate how strongly the cisco populations differ across a larger geographical area within Europe. Finally, we compared the genetic differences between the spring- and autumn-spawning populations of ciscoes in the two German lakes to infer the potentially deteriorating effect of strong anthropogenic pressure on the lakes. RESULTS Dendrogram, Principal Coordinate Analysis and admixture analysis all indicated strong correspondence between population differentiation and geographical location for most cisco populations in Europe, including the Siberian population of C. sardinella. However, populations from some Swedish lakes deviated from this general pattern, by showing a distinct genetic structure. We found evidence for independent evolution of the three sympatric population pairs, because the populations co-occurring in the same lake were always most closely related. However, genetic differentiation was weak in the two German population pairs, but strong in the Swedish Lake Fegen, indicating that the weak differentiation in the German pairs reported earlier has eroded further. CONCLUSIONS Our results suggest that the genetic differentiation at neutral genetic markers among populations of the Baltic cisco complex has evolved (and is maintained) by random genetic drift in isolated populations. However, earlier studies on the Swedish populations combining mitochondrial DNA and microsatellite data indicate that also post-glacial immigration from separate glacial refugia has shaped the present genetic population structure. The low neutral differentiation of the German sympatric pairs in contrast to the Swedish pair suggests that recent anthropogenic effects on the lakes in Germany may put the endemic spring-spawners at risk to extinction.
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Affiliation(s)
- Thomas Mehner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany.
| | - Stefan Palm
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - Bo Delling
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Juha Karjalainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Jolanta Kiełpińska
- Department of Aquatic Bioengineering and Aquaculture, Faculty of Food Science and Fisheries, West Pomeranian University of Technology in Szczecin, Szczecin, Poland
| | - Asja Vogt
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Jörg Freyhof
- Museum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
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14
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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15
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Gehri RR, Gruenthal K, Larson WA. It's complicated: Heterogeneous patterns of genetic structure in five fish species from a fragmented river suggest multiple processes can drive differentiation. Evol Appl 2021; 14:2079-2097. [PMID: 34429750 PMCID: PMC8372089 DOI: 10.1111/eva.13268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
Fragmentation of river systems by dams can have substantial genetic impacts on fish populations. However, genetic structure can exist naturally at small scales through processes other than isolation by physical barriers. We sampled individuals from five native fish species with varying life histories above and below a dam in the lower Boardman River, Michigan, USA, and used RADseq to investigate processes influencing genetic structure in this system. Species assessed were white sucker Catostomus commersonii, yellow perch Perca flavescens, walleye Sander vitreus, smallmouth bass Micropterus dolomieu, and rock bass Ambloplites rupestris. We detected significant differentiation within each species, but patterns of population structure varied substantially. Interestingly, genetic structure did not appear to be solely the result of fragmentation by the dam. While genetic structure in yellow perch and walleye generally coincided with "above dam" and "below dam" sampling locations, samples from our other three species did not. Specifically, samples from rock bass, smallmouth bass, and, to a much lesser extent, white sucker, aligned with a putative Great Lakes (GL) group that contained mostly individuals sampled below the dam and a putative Boardman River (BR) group that contained individuals sampled both above and below the dam, with some evidence of admixture among groups. We hypothesize that the GL and BR groups formed prior to dam construction and our samples largely represent a mixed stock that was sampled sympatrically outside of the spawning season. Support for this hypothesis is especially strong in smallmouth bass, where GL fish were 151 mm smaller than BR fish on average, suggesting a potential ontogenetic habitat shift of young GL fish into the lower river for feeding and/or refuge. Our study illuminates the complex dynamics shaping genetic structure in fragmented river systems and indicates that conclusions drawn for a single species cannot be generalized.
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Affiliation(s)
- Rebecca R. Gehri
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Kristen Gruenthal
- Office of Applied ScienceWisconsin Department of Natural ResourcesCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Alaska Department of Fish and GameGene Conservation LaboratoryJuneauAKUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- National Oceanographic and Atmospheric AdministrationNational Marine Fisheries ServiceAlaska Fisheries Science CenterAuke Bay LaboratoriesJuneauAKUSA
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16
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Euclide PT, MacDougall T, Robinson JM, Faust MD, Wilson CC, Chen K, Marschall EA, Larson W, Ludsin S. Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure. Evol Appl 2021; 14:1403-1420. [PMID: 34025775 PMCID: PMC8127713 DOI: 10.1111/eva.13209] [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: 11/03/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/31/2022] Open
Abstract
Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple, weakly differentiated stocks. Freshwater fisheries exemplify this problem, with many populations supported by multiple stocks of young evolutionary age and isolated across small spatial scales. Consequently, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing offer the ability to discriminate among populations with weak population structure, providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We used genomic data to conduct a mixed-stock analysis of eastern Lake Erie's commercial and recreational walleye (Sander vitreus) fisheries and estimate the relative harvest of weakly differentiated stocks (pairwise F ST < 0.01). Using RAD-capture (Rapture), we sequenced and genotyped individuals from western and eastern basin local spawning stocks at 12,081 loci with 95% reassignment accuracy, which was not possible in the past using microsatellite markers. A baseline assessment of 395 walleye from 11 spawning stocks identified three reporting groups and refined previous assessments of gene flow among walleye stocks. Genetic assignment of 1,075 walleye harvested in eastern Lake Erie's recreational and commercial fisheries indicated that western basin stocks constituted the majority of harvest during the peak walleye fishing season (July-September), whereas eastern basin individuals comprised much of the early season harvest (May-June). Clear spatial structure in harvest composition existed; catches in more easterly sites contained more individuals of eastern basin origin than did more westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the utility of genomic data to facilitate mixed-stock analysis in exploited fish populations having weak population structure or limited existing genetic resources.
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Affiliation(s)
- Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Tom MacDougall
- Lake Erie Management UnitOntario Ministry of Natural Resources and ForestryPort DoverONCanada
| | - Jason M. Robinson
- Lake Erie Fisheries Research UnitNew York State Department of Environmental ConservationDunkirkNYUSA
| | - Matthew D. Faust
- Division of Wildlife, Sandusky Fisheries Research StationOhio Department of Natural ResourcesSanduskyOHUSA
| | - Chris C. Wilson
- Aquatic Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryPeterboroughONCanada
| | - Kuan‐Yu Chen
- Aquatic Ecology Laboratory, Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOHUSA
| | - Elizabeth A. Marschall
- Aquatic Ecology Laboratory, Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOHUSA
| | - Wesley Larson
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Present address:
National Oceanic and Atmospheric AdministrationTed Stevens Marine Research InstituteJuneauAKUSA
| | - Stuart Ludsin
- Aquatic Ecology Laboratory, Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityColumbusOHUSA
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17
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Schweizer RM, Saarman N, Ramstad KM, Forester BR, Kelley JL, Hand BK, Malison RL, Ackiss AS, Watsa M, Nelson TC, Beja-Pereira A, Waples RS, Funk WC, Luikart G. Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field. J Hered 2021; 112:313-327. [PMID: 33860294 DOI: 10.1093/jhered/esab019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Norah Saarman
- Department of Biology, Utah State University, Logan, UT
| | - Kristina M Ramstad
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | | | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Brian K Hand
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Rachel L Malison
- Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Amanda S Ackiss
- Wisconsin Cooperative Fishery Research Unit, University of Wisconsin Stevens Point, Stevens Point, WI
| | | | | | - Albano Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Vairão, Portugal.,DGAOT, Faculty of Sciences, University of Porto, Porto, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Faculty of Sciences, University of Porto, Porto, Portugal
| | - Robin S Waples
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
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18
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Bootsma ML, Miller L, Sass GG, Euclide PT, Larson WA. The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye ( Sander vitreus). Evol Appl 2021; 14:1124-1144. [PMID: 33897825 PMCID: PMC8061267 DOI: 10.1111/eva.13186] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Stocking of fish is an important tool for maintaining fisheries but can also significantly alter population genetic structure and erode the portfolio of within-species diversity that is important for promoting resilience and adaptability. Walleye (Sander vitreus) are a highly valued sportfish in the midwestern United States, a region characterized by postglacial recolonization from multiple lineages and an extensive history of stocking. We leveraged genomic data and recently developed analytical approaches to explore the population structure of walleye from two midwestern states, Minnesota and Wisconsin. We genotyped 954 walleye from 23 populations at ~20,000 loci using genotyping by sequencing and tested for patterns of population structure with single-SNP and microhaplotype data. Populations from Minnesota and Wisconsin were highly differentiated from each other, with additional substructure found in each state. Population structure did not consistently adhere to drainage boundaries, as cases of high intra-drainage and low inter-drainage differentiation were observed. Low genetic structure was observed between populations from the upper Wisconsin and upper Chippewa river watersheds, which are found as few as 50 km apart and were likely homogenized through historical stocking. Nevertheless, we were able to differentiate these populations using microhaplotype-based co-ancestry analysis, providing increased resolution over previous microsatellite studies and our other single SNP-based analyses. Although our results illustrate that walleye population structure has been influenced by past stocking practices, native ancestry still exists in most populations and walleye populations may be able to purge non-native alleles and haplotypes in the absence of stocking. Our study is one of the first to use genomic tools to investigate the influence of stocking on population structure in a nonsalmonid fish and outlines a workflow leveraging recently developed analytical methods to improve resolution of complex population structure that will be highly applicable in many species and systems.
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Affiliation(s)
- Matthew L. Bootsma
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Loren Miller
- Minnesota Department of Natural ResourcesUniversity of MinnesotaSt. PaulMNUSA
| | - Greg G. Sass
- Office of Applied ScienceWisconsin Department of Natural ResourcesEscanaba Lake Research StationBoulder JunctionWIUSA
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Present address:
Ted Stevens Marine Research InstituteAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationJuneauAKUSA
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19
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Graham CF, Eberts RL, Goncin U, Somers CM. Spontaneous hybridization and introgression between walleye ( Sander vitreus) and sauger ( Sander canadensis) in two large reservoirs: Insights from genotyping by sequencing. Evol Appl 2021; 14:965-982. [PMID: 33897814 PMCID: PMC8061268 DOI: 10.1111/eva.13174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/22/2022] Open
Abstract
Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. Walleye (Sander vitreus) and sauger (Sander canadensis) are economically valuable freshwater species that can spontaneously hybridize in areas of sympatry. Levels of genomic introgression between walleye and sauger may be increased by modifications to waterbodies (e.g., reservoir development) and inadvertent propagation of hybrids in stocking programs. We used genotyping by sequencing (GBS) to examine 217 fish from two large reservoirs with mixed populations of walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake). Analyses with 20,038 (r90) and 478 (r100) single nucleotide polymorphisms clearly resolved walleye and sauger, and classified hybrids with high confidence. F1, F2, and multigeneration hybrids were detected in Lake Diefenbaker, indicating potentially high levels of genomic introgression. In contrast, only F1 hybrids were detected in Tobin Lake. Field classification of fish was unreliable; 7% of fish were misidentified based on broad species categories. Important for activities such as brood stock selection, 12 of 173 (7%) fish field identified as pure walleye, and one of 24 (4%) identified as pure sauger were actually hybrids. In addition, two of 15 (13%) field-identified hybrids were actually pure walleye or sauger. We conclude that hybridization and introgression are occurring in Saskatchewan reservoirs and that caution is warranted when using these populations in stocking programs. GBS offers a powerful and flexible tool for examining hybridization without preidentification of informative loci, eliminating some of the key challenges associated with other marker types.
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Affiliation(s)
| | - Rebecca L. Eberts
- Fish, Wildlife, and Lands Branch, Ministry of EnvironmentGovernment of SaskatchewanPrince AlbertSKCanada
| | - Una Goncin
- Department of BiologyUniversity of ReginaReginaSKCanada
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20
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Eaton KM, Bernal MA, Backenstose NJC, Yule DL, Krabbenhoft TJ. Nanopore Amplicon Sequencing Reveals Molecular Convergence and Local Adaptation of Rhodopsin in Great Lakes Salmonids. Genome Biol Evol 2021; 13:evaa237. [PMID: 33247716 PMCID: PMC7874997 DOI: 10.1093/gbe/evaa237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2020] [Indexed: 11/13/2022] Open
Abstract
Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle and MinION. We sequenced five visual opsin genes for individuals of Coregonus artedi, Coregonus hoyi, Coregonus kiyi, and Coregonus zenithicus. Comparisons revealed species-specific differences in a key spectral tuning amino acid in rhodopsin (Tyr261Phe substitution), suggesting local adaptation of C. kiyi to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and "toggling" at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.
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Affiliation(s)
- Katherine M Eaton
- Department of Biological Sciences, University at Buffalo, New York, USA
| | - Moisés A Bernal
- Department of Biological Sciences, University at Buffalo, New York, USA
| | | | - Daniel L Yule
- U.S. Geological Survey, Great Lakes Science Center – Lake Superior Biological Station, Ashland, Wisconsin, USA
| | - Trevor J Krabbenhoft
- Department of Biological Sciences, University at Buffalo, New York, USA
- RENEW Institute, University at Buffalo, New York, USA
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21
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Comparison of Specimen- and Image-Based Morphometrics for Cisco. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2020. [DOI: 10.3996/jfwm-20-029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Morphometric data from fish are typically generated using one of two methods: direct measurements made on a specimen or extraction of distances from a digital picture. We compared data on 12 morphometrics collected with these two methods on the same collection of Cisco Coregonus artedi from Lake Ontario, North America, to assess the degree of bias in measurements made directly on a specimen- vs. an image-based method. We also assessed the degree of reproducibility within the image-based method by evaluating the amount of variation between different analysts for each morphometric method. Our results indicate specific morphometrics may be more prone to bias across the two methods and between analysts. Four of 12 morphometrics evaluated showed significant deviation from a 1:1 relationship that would be expected if the imaged-based method produced accurate specimen-based measurements. Pelvic fin length and pelvic–anal fin distance had the highest between-analyst variation for image-based landmarks, indicating low reproducibility for these metrics, compared with pectoral fin or total length, which had lower between-analyst variation. Although some morphometric measurements can be accurately obtained with either method, and therefore potentially used interchangeably in studies on Cisco morphology, our findings highlight the importance of considering method bias in morphometric studies that use data collected by different methods.
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22
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Bootsma ML, Gruenthal KM, McKinney GJ, Simmons L, Miller L, Sass GG, Larson WA. A GT-seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non-model organisms. Mol Ecol Resour 2020; 20:1706-1722. [PMID: 32668508 DOI: 10.1111/1755-0998.13226] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/21/2020] [Accepted: 07/02/2020] [Indexed: 12/27/2022]
Abstract
Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT-seq panels is nontrivial, but studies describing trade-offs associated with different steps of GT-seq panel development are rare. Here, we construct a dual-purpose GT-seq panel for walleye (Sander vitreus), discuss trade-offs associated with different development and genotyping approaches, and provide suggestions for researchers constructing their own GT-seq panels. Our GT-seq panel was developed using an ascertainment set consisting of restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We conducted simulations to test the utility of all loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We then performed three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (i) inexpensive Chelex extractions performed well for genotyping; (ii) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was probably unnecessary; and (iii) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings and suggestions should aid in their construction in myriad taxa.
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Affiliation(s)
- Matthew L Bootsma
- Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI, USA
| | - Kristen M Gruenthal
- Office of Applied Science, Wisconsin Department of Natural Resources, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, USA
| | - Garrett J McKinney
- NRC Research Associateship Program, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Levi Simmons
- Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI, USA
| | - Loren Miller
- Minnesota Department of Natural Resources, University of Minnesota, St. Paul, MN, USA
| | - Greg G Sass
- Wisconsin Department of Natural Resources, Escanaba Lake Research Station, Office of Applied Science, WI, USA
| | - Wesley A Larson
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI, USA.,Ted Stevens Marine Research Institute, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, USA
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