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Kokarev V, Dufour SC, Raeymaekers JAM, Mailli AA, Reiss H. Thyasirid species composition (Bivalvia: Thyasiridae) and genetic connectivity of Parathyasira equalis (A. E. Verrill & K. J. Bush, 1898) in deep basins of sub-Arctic fjords. BMC Ecol Evol 2024; 24:91. [PMID: 38965473 PMCID: PMC11223403 DOI: 10.1186/s12862-024-02278-3] [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: 04/12/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Thyasirid bivalves are often recorded as a dominant component of macrobenthic infaunal communities in depositional environments such as fjord basins. Fjord basins comprise patchy soft-bottom habitats bounded by steep walls and sills; however, little is known how this semi-isolated nature of fjords affects benthic populations. Accordingly, data on the composition and population connectivity of thyasirids can provide valuable information on the ecology of these ecosystems. RESULTS The species composition of thyasirid bivalves has been studied in the basins of three sub-Arctic fjords (Nordland, Northern Norway). Overall, six thyasirid species were recorded: Parathyasira equalis, Parathyasira dunbari, Mendicula ferruginosa, Genaxinus eumyarius, Thyasira sarsii, and Thyasira obsoleta. The species composition remained stable within the basins during the sampling period (2013-2020) and suggested the importance of local reproduction over advection of individuals for population dynamics. Only one species, Parathyasira equalis, was common in all fjords. We have further investigated the population genetics of this species by combining two types of genetic markers: a 579 bp fragment of the cytochrome c oxidase subunit I (COI) gene and 4043 single-nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing. The latter provided a more in-depth resolution on the population genetics of this species and revealed a weak but significant differentiation of populations within fjords, further indicating limited connectivity between basins. CONCLUSION Based on our findings, we conclude that limited dispersal between the basin communities results in weakly connected populations and might be an important structuring factor for macrobenthic communities.
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Affiliation(s)
- Valentin Kokarev
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway.
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | | | - Amalia A Mailli
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway
| | - Henning Reiss
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway
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2
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Bernard AM, Finnegan KA, Pavinski Bitar P, Stanhope MJ, Shivji MS. Genomic assessment of global population structure in a highly migratory and habitat versatile apex predator, the tiger shark (Galeocerdo cuvier). J Hered 2021; 112:497-507. [PMID: 34374783 DOI: 10.1093/jhered/esab046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022] Open
Abstract
Understanding the population dynamics of highly mobile, widely distributed, oceanic sharks, many of which are overexploited, is necessary to aid their conservation management. We investigated the global population genomics of tiger sharks (Galeocerdo cuvier), a circumglobally distributed, apex predator displaying remarkable behavioral versatility in its diet, habitat use (near coastal, coral reef, pelagic), and individual movement patterns (spatially resident to long-distance migrations). We genotyped 242 tiger sharks from 10 globally distributed locations at more than 2000 single nucleotide polymorphisms. Although this species often conducts massive distance migrations, the data show strong genetic differentiation at both neutral (FST=0.125-0.144) and candidate outlier loci (FST=0.570-0.761) between western Atlantic and Indo-Pacific sharks, suggesting the potential for adaptation to the environments specific to these oceanic regions. Within these regions, there was mixed support for population differentiation between northern and southern hemispheres in the western Atlantic, and none for structure within the Indian Ocean. Notably, the results demonstrate a low level of population differentiation of tiger sharks from the remote Hawaiian archipelago compared to sharks from the Indian Ocean (FST=0.003-0.005, P<0.01). Given concerns about biodiversity loss and marine ecosystem impacts caused by overfishing of oceanic sharks in the midst of rapid environmental change, our results suggest it imperative that international fishery management prioritize conservation of the evolutionary potential of the highly genetically differentiated Atlantic and Indo-Pacific populations of this unique apex predator. Furthermore, we suggest targeted management attention to tiger sharks in the Hawaiian archipelago based on a precautionary biodiversity conservation perspective.
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Affiliation(s)
- Andrea M Bernard
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA
| | - Kimberly A Finnegan
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA.,Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA
| | - Paulina Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Mahmood S Shivji
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA.,Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, Florida, USA
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3
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Álvarez-Varas R, Rojas-Hernández N, Heidemeyer M, Riginos C, Benítez HA, Araya-Donoso R, Reséndiz E, Lara-Uc M, Godoy DA, Muñoz-Pérez JP, Alarcón-Ruales DE, Alfaro-Shigueto J, Ortiz-Alvarez C, Mangel JC, Vianna JA, Véliz D. Green, yellow or black? Genetic differentiation and adaptation signatures in a highly migratory marine turtle. Proc Biol Sci 2021; 288:20210754. [PMID: 34229490 DOI: 10.1098/rspb.2021.0754] [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] [Indexed: 11/12/2022] Open
Abstract
Marine species may exhibit genetic structure accompanied by phenotypic differentiation related to adaptation despite their high mobility. Two shape-based morphotypes have been identified for the green turtle (Chelonia mydas) in the Pacific Ocean: the south-central/western or yellow turtle and north-central/eastern or black turtle. The genetic differentiation between these morphotypes and the adaptation of the black turtle to environmentally contrasting conditions of the eastern Pacific region has remained a mystery for decades. Here we addressed both questions using a reduced-representation genome approach (Dartseq; 9473 neutral SNPs) and identifying candidate outlier loci (67 outlier SNPs) of biological relevance between shape-based morphotypes from eight Pacific foraging grounds (n = 158). Our results support genetic divergence between morphotypes, probably arising from strong natal homing behaviour. Genes and enriched biological functions linked to thermoregulation, hypoxia, melanism, morphogenesis, osmoregulation, diet and reproduction were found to be outliers for differentiation, providing evidence for adaptation of C. mydas to the eastern Pacific region and suggesting independent evolutionary trajectories of the shape-based morphotypes. Our findings support the evolutionary distinctness of the enigmatic black turtle and contribute to the adaptive research and conservation genomics of a long-lived and highly mobile vertebrate.
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Affiliation(s)
- Rocío Álvarez-Varas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile.,Qarapara Tortugas Marinas Chile NGO, Santiago, Chile
| | - Noemi Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Maike Heidemeyer
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, Costa Rica
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Hugo A Benítez
- Laboratorio de Ecología y Morfometría Evolutiva, Centro de Investigación de Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | | | - Eduardo Reséndiz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Mexico
| | - Mónica Lara-Uc
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Mexico
| | - Daniel A Godoy
- Coastal-Marine Research Group, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Juan Pablo Muñoz-Pérez
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galápagos, Ecuador.,University of the Sunshine Coast USC, 90 Sippy Downs Dr, Sippy Downs, Queensland 4556, Australia
| | - Daniela E Alarcón-Ruales
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galápagos, Ecuador
| | - Joanna Alfaro-Shigueto
- ProDelphinus, Lima, Peru.,Facultad de Biología Marina, Universidad Científica del Perú, Lima, Peru
| | | | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - David Véliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
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4
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Goodall J, Westfall KM, Magnúsdóttir H, Pálsson S, Örnólfsdóttir EB, Jónsson ZO. RAD sequencing of common whelk, Buccinum undatum, reveals fine-scale population structuring in Europe and cryptic speciation within the North Atlantic. Ecol Evol 2021; 11:2616-2629. [PMID: 33767824 PMCID: PMC7981227 DOI: 10.1002/ece3.7219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 01/01/2023] Open
Abstract
Buccinum undatum is a subtidal gastropod that exhibits clear spatial variation in several phenotypic shell traits (color, shape, and thickness) across its North Atlantic distribution. Studies of spatial phenotypic variation exist for the species; however, population genetic studies have thus far relied on a limited set of mitochondrial and microsatellite markers. Here, we greatly expand on previous work by characterizing population genetic structure in B. undatum across the North Atlantic from SNP variation obtained by RAD sequencing. There was a high degree of genetic differentiation between Canadian and European populations (Iceland, Faroe Islands, and England) consistent with the divergence of populations in allopatry (F ST > 0.57 for all pairwise comparisons). In addition, B. undatum populations within Iceland, the Faroe Islands, and England are typified by weak but significant genetic structuring following an isolation-by-distance model. Finally, we established a significant correlation between genetic structuring in Iceland and two phenotypic traits: shell shape and color frequency. The works detailed here enhance our understanding of genetic structuring in B. undatum and establish the species as an intriguing model for future genome-wide association studies.
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Affiliation(s)
- Jake Goodall
- Faculty of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókurIceland
| | - Kristen Marie Westfall
- Vör – Marine Research Center in BreiðafjörðurÓlafsvíkIceland
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Hildur Magnúsdóttir
- Faculty of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókurIceland
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
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Mladineo I, Hrabar J, Trumbić Ž, Manousaki T, Tsakogiannis A, Taggart JB, Tsigenopoulos CS. Community Parameters and Genome-Wide RAD-Seq Loci of Ceratothoa oestroides Imply Its Transfer between Farmed European Sea Bass and Wild Farm-Aggregating Fish. Pathogens 2021; 10:pathogens10020100. [PMID: 33494355 PMCID: PMC7912605 DOI: 10.3390/pathogens10020100] [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: 12/07/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 12/28/2022] Open
Abstract
Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed. The double-digest RAD-Seq of 310 C. oestroides specimens collected from farmed European sea bass (138) and different wild farm-aggregating fish (172) identified 313 robust SNPs that evidenced a close genetic relatedness between the “wild” and “farmed” genotypes. ddRAD-Seq proved to be an effective method for detecting the discrete genetic structuring of C. oestroides and genotype intermixing between two populations. The parasite prevalence in the farmed sea bass was 1.02%, with a mean intensity of 2.0 and mean abundance of 0.02, while in the wild fish, the prevalence was 8.1%; the mean intensity, 1.81; and the mean abundance, 0.15. Such differences are likely a consequence of human interventions during the farmed fish’s rearing cycle that, nevertheless, did not affect the transfer of C. oestroides.
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Affiliation(s)
- Ivona Mladineo
- Institute of Oceanography and Fisheries, Laboratory of Aquaculture, 21000 Split, Croatia;
- Institute of Parasitology, Biology Centre of Czech Academy of Science, 37005 Ceske Budejovice, Czech Republic
- Correspondence: or
| | - Jerko Hrabar
- Institute of Oceanography and Fisheries, Laboratory of Aquaculture, 21000 Split, Croatia;
| | - Željka Trumbić
- University Department of Marine Studies, University of Split, 21000 Split, Croatia;
| | - Tereza Manousaki
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71003 Heraklion, Greece; (T.M.); (A.T.); (C.S.T.)
| | - Alexandros Tsakogiannis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71003 Heraklion, Greece; (T.M.); (A.T.); (C.S.T.)
| | - John B. Taggart
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK;
| | - Costas S. Tsigenopoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71003 Heraklion, Greece; (T.M.); (A.T.); (C.S.T.)
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6
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Maroso F, Gkagkavouzis K, De Innocentiis S, Hillen J, do Prado F, Karaiskou N, Taggart JB, Carr A, Nielsen E, Triantafyllidis A, Bargelloni L. Genome-wide analysis clarifies the population genetic structure of wild gilthead sea bream (Sparus aurata). PLoS One 2021; 16:e0236230. [PMID: 33428622 PMCID: PMC7799848 DOI: 10.1371/journal.pone.0236230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/22/2020] [Indexed: 11/30/2022] Open
Abstract
Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. Its distribution ranges from the Mediterranean to the African and European coasts of the North-East Atlantic. Until now, the population genetic structure of this species in the wild has largely been studied using microsatellite DNA markers, with minimal genetic differentiation being detected. In this geographically widespread study, 958 wild gilthead sea bream from 23 locations within the Mediterranean Sea and Atlantic Ocean were genotyped at 1159 genome-wide SNP markers by RAD sequencing. Outlier analyses identified 18 loci potentially under selection. Neutral marker analyses identified weak subdivision into three genetic clusters: Atlantic, West, and East Mediterranean. The latter group could be further subdivided into an Ionian/Adriatic and an Aegean group using the outlier markers alone. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, this being also supported by preliminary genomic functional analysis. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry.
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Affiliation(s)
- Francesco Maroso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro (PD), Italy
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | | | - Jasmien Hillen
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Leuven, Belgium
| | - Fernanda do Prado
- Department of Biological Sciences, São Paulo State University, Bauru, Brazil
| | - Nikoleta Karaiskou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | | | - Adrian Carr
- Fios Genomics Ltd, Edinburgh, United Kingdom
| | - Einar Nielsen
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro (PD), Italy
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Levis NA, Pfennig DW. Plasticity‐led evolution: A survey of developmental mechanisms and empirical tests. Evol Dev 2019; 22:71-87. [DOI: 10.1111/ede.12309] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Nicholas A. Levis
- Department of Biology University of North Carolina Chapel Hill North Carolina
| | - David W. Pfennig
- Department of Biology University of North Carolina Chapel Hill North Carolina
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Evolutionary Toxicogenomics of the Striped Killifish ( Fundulus majalis) in the New Bedford Harbor (Massachusetts, USA). Int J Mol Sci 2019; 20:ijms20051129. [PMID: 30841640 PMCID: PMC6429206 DOI: 10.3390/ijms20051129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 12/27/2022] Open
Abstract
In this paper, we used a Genotyping-by-Sequencing (GBS) approach to find and genotype more than 4000 genome-wide SNPs (Single Nucleotide Polymorphisms) from striped killifish exposed to a variety of polychlorinated biphenyls (PCBs) and other aromatic pollutants in New Bedford Harbor (NBH, Massachusetts, USA). The aims of this study were to identify the genetic consequences of exposure to aquatic pollutants and detect genes that may be under selection. Low genetic diversity (HE and π) was found in the site exposed to the highest pollution level, but the pattern of genetic diversity did not match the pollution levels. Extensive connectivity was detected among sampling sites, which suggests that balanced gene flow may explain the lack of genetic variation in response to pollution levels. Tests for selection identified 539 candidate outliers, but many of the candidate outliers were not shared among tests. Differences among test results likely reflect different test assumptions and the complex pollutant mixture. Potentially, selectively important loci are associated with 151 SNPs, and enrichment analysis suggests a likely involvement of these genes with pollutants that occur in NBH. This result suggests that selective processes at genes targeted by pollutants may be occurring, even at a small geographical scale, and may allow the local striped killifish to resist the high pollution levels.
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Choquet M, Smolina I, Dhanasiri AKS, Blanco-Bercial L, Kopp M, Jueterbock A, Sundaram AYM, Hoarau G. Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton Calanus finmarchicus. ROYAL SOCIETY OPEN SCIENCE 2019; 6:180608. [PMID: 30891252 PMCID: PMC6408391 DOI: 10.1098/rsos.180608] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 01/07/2019] [Indexed: 05/09/2023]
Abstract
Advances in next-generation sequencing technologies and the development of genome-reduced representation protocols have opened the way to genome-wide population studies in non-model species. However, species with large genomes remain challenging, hampering the development of genomic resources for a number of taxa including marine arthropods. Here, we developed a genome-reduced representation method for the ecologically important marine copepod Calanus finmarchicus (haploid genome size of 6.34 Gbp). We optimized a capture enrichment-based protocol based on 2656 single-copy genes, yielding a total of 154 087 high-quality SNPs in C. finmarchicus including 62 372 in common among the three locations tested. The set of capture probes was also successfully applied to the congeneric C. glacialis. Preliminary analyses of these markers revealed similar levels of genetic diversity between the two Calanus species, while populations of C. glacialis showed stronger genetic structure compared to C. finmarchicus. Using this powerful set of markers, we did not detect any evidence of hybridization between C. finmarchicus and C. glacialis. Finally, we propose a shortened version of our protocol, offering a promising solution for population genomics studies in non-model species with large genomes.
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Affiliation(s)
- Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Author for correspondence: Marvin Choquet e-mail:
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | | | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Arvind Y. M. Sundaram
- Norwegian Sequencing Centre, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Nunez JCB, Biancani LM, Flight PA, Nacci DE, Rand DM, Crawford DL, Oleksiak MF. Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171532. [PMID: 29892357 PMCID: PMC5990737 DOI: 10.1098/rsos.171532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/02/2018] [Indexed: 05/15/2023]
Abstract
Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in Ne and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade.
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Affiliation(s)
- Joaquin C. B. Nunez
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI 02912, USA
| | - Leann M. Biancani
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI 02912, USA
| | - Patrick A. Flight
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI 02912, USA
| | - Diane E. Nacci
- Population Ecology Branch, Atlantic Ecology Division, Office of Research and Development, US Environmental Protection Agency, 27 Tarzwell Drive, Narragansett, RI 02882, USA
| | - David M. Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI 02912, USA
| | - Douglas L. Crawford
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Marjorie F. Oleksiak
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
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Adaptation Without Boundaries: Population Genomics in Marine Systems. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Nunez JCB, Elyanow RG, Ferranti DA, Rand DM. Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_58] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensis. Sci Rep 2017; 7:44559. [PMID: 28300177 PMCID: PMC5353582 DOI: 10.1038/srep44559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/09/2017] [Indexed: 12/15/2022] Open
Abstract
Marine benthic organisms inhabit a heterogeneous environment in which connectivity between populations occurs mainly through dispersive larval stages, while local selective pressures acting on early life history stages lead to non-random mortality, shaping adaptive genetic structure. In order to test the influence of local adaptation and neutral processes in a marine benthic species with low dispersal, in this study we used Genotyping by Sequencing technology to compare the neutral and putatively selected signals (neutral and outlier loci, respectively) in SNPs scattered throughout the genome in six local populations of the commercially exploited ascidian Pyura chilensis along the southeast Pacific coast (24°–42°S). This species is sessile as an adult, has a short-lived larval stage, and may also be dispersed by artificial transport as biofouling. We found that the main signal in neutral loci was a highly divergent lineage present at 39°S, and a subjacent signal that indicated a separation at 30°S (north/south), widely reported in the area. North/south separation was the main signal in outlier loci, and the linage divergence at 39°S was subjacent. We conclude that the geographic structure of the genetic diversity of outlier and neutral loci was established by different strengths of environmental, historical and anthropogenic factors.
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Fine-scale genetic structure due to adaptive divergence among microhabitats. Heredity (Edinb) 2017; 118:594-604. [PMID: 28295034 DOI: 10.1038/hdy.2017.6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/20/2016] [Accepted: 01/22/2017] [Indexed: 02/03/2023] Open
Abstract
It has been suggested that adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation is polygenic-does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation (for example, microhabitats) is not resolved. Here we analyze the genetic divergence of the teleost fish, Fundulus heteroclitus, among microhabitats that are <200 m apart in three separate saltmarshes using 4741 single-nucleotide polymorphisms (SNPs). Among these SNPs, 1.3-2.3% have large and highly significant differences among microhabitats (mean FST=0.15; false discovery rate ⩽1%). The divergence among microhabitats for these outlier SNPs is larger than that among populations, exceeds neutral expectation and indicates surprising population structure among microhabitats. Thus, we suggest that polygenic selection is surprisingly effective in altering allele frequencies among many different SNPs that share similar biological functions in response to environmental and ecological differences over very small geographic distances. We acknowledge the evolutionary difficulty of large genetic divergence among well-connected habitats. Therefore, these studies are only the first step to discern whether natural selection is responsible and capable of effecting genetic divergence on such a fine scale.
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