1
|
Ekimova IA, Schepetov DM, Green B, Stanovova MV, Antokhina TI, Gosliner T, Malaquias MAE, Valdés Á. Scaling the high latitudes: evolution, diversification, and dispersal of Coryphella nudibranchs across the Northern Hemisphere. Mol Phylogenet Evol 2024; 201:108214. [PMID: 39369862 DOI: 10.1016/j.ympev.2024.108214] [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: 04/19/2024] [Revised: 09/05/2024] [Accepted: 10/03/2024] [Indexed: 10/08/2024]
Abstract
Nudibranch molluscs Coryphella are widely distributed and species-rich gastropod group lacking fossil record and displaying a complex distribution across both Southern and Northern hemispheres. In this paper we provide a detailed review of the morphology, ecology, and distribution of Coryphella, estimation of divergence times between species, an ancestral area reconstruction, and a population analysis of widely distributed trans-Arctic species Coryphella verrucosa to investigate the evolution, phylogeographic patterns and reconstruct possible historical routes of oceanic dispersal. The inclusion of a larger sample size and five molecular markers has revealed a complex evolutionary history of Coryphella, shaped by transgression, vicariance, and dietary shifts, and overall driven by the pervasive effect of glacial cycles. We also revealed the presence of additional cryptic diversity, which suggests that further sampling may produce additional species in this group of nudibranchs. Tree calibration indicates the genus Coryphella originates in the middle Miocene in the Pacific Ocean and the early divergence within this group also occurred in the Pacific, specifically in different regions of the North Pacific. The ancestral area reconstruction inferred five independent instances of transgression from the Pacific Ocean to the Atlantic via different migration routes, including the Panamanian seaway and the Bering Strait. Among them, we identified three cases of successful transition to the Arctic waters from the North Pacific via the Bering Strait, associated with interglacial conditions of middle Pleistocene. Consequently, Pleistocene glacial cycles likely prompted pulses of boreal faunal elements to disperse southwards followed by range disjunction and temporary isolation of distant populations and resulting in allopatric speciation. Evidence from the population structure of contemporary trans-Arctic species suggests an occurrence of independent recolonization pathways of Arctic waters from both southernly and northernly refugia after the Last Glacial Maximum.
Collapse
Affiliation(s)
- Irina A Ekimova
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia.
| | | | - Brenna Green
- Department of Invertebrate Zoology, California Academy of Sciences, San Francisco, CA, USA
| | - Maria V Stanovova
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Terrence Gosliner
- Department of Invertebrate Zoology, California Academy of Sciences, San Francisco, CA, USA
| | | | - Ángel Valdés
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, USA
| |
Collapse
|
2
|
Venney CJ, Cayuela H, Rougeux C, Laporte M, Mérot C, Normandeau E, Leitwein M, Dorant Y, Præbel K, Kenchington E, Clément M, Sirois P, Bernatchez L. Genome-wide DNA methylation predicts environmentally driven life history variation in a marine fish. Evolution 2023; 77:186-198. [PMID: 36622671 DOI: 10.1093/evolut/qpac028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/21/2022] [Accepted: 11/16/2022] [Indexed: 01/10/2023]
Abstract
Epigenetic modifications are thought to be one of the molecular mechanisms involved in plastic adaptive responses to environmental variation. However, studies reporting associations between genome-wide epigenetic changes and habitat-specific variations in life history traits (e.g., lifespan, reproduction) are still scarce, likely due to the recent application of methylome resequencing methods to non-model species. In this study, we examined associations between whole genome DNA methylation and environmentally driven life history variation in 2 lineages of a marine fish, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbor 2 contrasting life history tactics (demersal vs. beach-spawning). Performing whole genome and methylome sequencing, we showed that life history tactics are associated with epigenetic changes in both lineages, though the effect was stronger in European capelin. Genetic differentiation between the capelin harboring different life history tactics was negligible, but we found genome-wide methylation changes in both lineages. We identified 9,125 European and 199 North American differentially methylated regions (DMRs) due to life history. Gene ontology (GO) enrichment analysis for both lineages revealed an excess of terms related to neural function. Our results suggest that environmental variation causes important epigenetic changes that are associated with contrasting life history tactics in lineages with divergent genetic backgrounds, with variable importance of genetic variation in driving epigenetic variation. Our study emphasizes the potential role of genome-wide epigenetic variation in adaptation to environmental variation.
Collapse
Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,University of Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Clément Rougeux
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Maëva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Kim Præbel
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ellen Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial University of Newfoundland, St. John's, NL, Canada.,Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Pascal Sirois
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| |
Collapse
|
3
|
Kolbasova G, Schmidt-Rhaesa A, Syomin V, Bredikhin D, Morozov T, Neretina T. Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816. ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
4
|
Santín A, Uriz MJ, Cristobo J, Xavier JR, Ríos P. Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea. PeerJ 2021; 9:e12515. [PMID: 35036117 PMCID: PMC8710052 DOI: 10.7717/peerj.12515] [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: 08/05/2021] [Accepted: 10/27/2021] [Indexed: 11/21/2022] Open
Abstract
Sponges are amongst the most difficult benthic taxa to properly identify, which has led to a prevalence of cryptic species in several sponge genera, especially in those with simple skeletons. This is particularly true for sponges living in remote or hardly accessible environments, such as the deep-sea, as the inaccessibility of their habitat and the lack of accurate descriptions usually leads to misclassifications. However, species can also remain hidden even when they belong to genera that have particularly characteristic features. In these cases, researchers inevitably pay attention to these peculiar features, sometimes disregarding small differences in the other "typical" spicules. The genus Melonanchora Carter, 1874, is among those well suited for a revision, as their representatives possess a unique type of spicule (spherancorae). After a thorough review of the material available for this genus from several institutions, four new species of Melonanchora, M. tumultuosa sp. nov., M. insulsa sp. nov., M. intermedia sp. nov. and M. maeli sp. nov. are formally described from different localities across the Atlanto-Mediterranean region. Additionally, all Melonanchora from the Okhotsk Sea and nearby areas are reassigned to other genera; Melonanchora kobjakovae is transferred to Myxilla (Burtonanchora) while two new genera, Hanstoreia gen. nov. and Arhythmata gen. nov. are created to accommodate Melonanchora globogilva and Melonanchora tetradedritifera, respectively. Hanstoreia gen. nov. is closest to Melonanchora, whereas Arhythmata gen. nov., is closer to Stelodoryx, which is most likely polyphyletic and in need of revision.
Collapse
Affiliation(s)
- Andreu Santín
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - María-Jesús Uriz
- Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Javier Cristobo
- Instituto Español de Oceanografía. Centro Oceanográfico de Gijón., Gijón, Asturias, Spain
- Departamento de Ciencias de la Vida, EU‑US Marine Biodiversity Group, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - Joana R. Xavier
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Pilar Ríos
- Instituto Español de Oceanografía. Centro Oceanográfico de Gijón., Gijón, Asturias, Spain
- Departamento de Biología Animal, Universidad de Málaga, Málaga, Spain
| |
Collapse
|
5
|
Semenova AV, Stroganov AN, Ponomareva EV, Afanas’ev KI, Vilkina OV. Large-scale genetic structure and diversity of Arctic rainbow smelt Osmerus dentex Steindachner et Kner, 1870 throughout its distributional range based on microsatellites. Polar Biol 2021. [DOI: 10.1007/s00300-021-02848-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
6
|
Cayuela H, Dorant Y, Mérot C, Laporte M, Normandeau E, Gagnon-Harvey S, Clément M, Sirois P, Bernatchez L. Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. Mol Ecol 2021; 30:1624-1641. [PMID: 33565147 DOI: 10.1111/mec.15835] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs). Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast to that inferred based on SNPs in a previous study. Our findings underline the complementarity of those two types of genomic variation in population genomics studies.
Collapse
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Stéphane Gagnon-Harvey
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Marie Clément
- Center for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial, University of Newfoundland, St. John's, NL, Canada.,Labrador Institute of Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Pascal Sirois
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| |
Collapse
|
7
|
Silva CNS, Murphy NP, Bell JJ, Green BS, Duhamel G, Cockcroft AC, Hernández CE, Strugnell JM. Global drivers of recent diversification in a marine species complex. Mol Ecol 2021; 30:1223-1236. [PMID: 33342039 DOI: 10.1111/mec.15780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 11/03/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Investigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence during speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome-wide divergence, introgression patterns and inferred demographic history between species pairs of all six extant rock lobster species (Jasus spp.), which have a long larval duration of up to two years and have populated continental shelf and seamount habitats around the globe at approximately 40o S. Genetic differentiation patterns reflected geographic isolation and the environment (i.e. habitat structure). Eastern Pacific species (J. caveorum and J. frontalis) were geographically more distant and genetically more differentiated from the remaining four species. Species associated with continental shelf habitats shared a common ancestry, but are geographically distant from one another. Similarly, species associated with island/seamount habitats in the Atlantic and Indian Oceans shared a common ancestry, but are also geographically distant. Benthic temperature was the environmental variable that explained most of the genetic differentiation (FST ), while controlling for the effects of geographic distance. Eastern Pacific species retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa, and seamounts in the Indian and Atlantic oceans, included events of introgression after secondary contact. Our results reveal important effects of habitat and demographic processes on the recent divergence of species within the genus Jasus, providing one of the first empirical studies of genome-wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.
Collapse
Affiliation(s)
- Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Nicholas P Murphy
- Department of Ecology, Environment & Evolution, La Trobe University, Melbourne, Vic, Australia
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Bridget S Green
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Guy Duhamel
- Département Adaptations du Vivant, BOREA, MNHN, Paris, France
| | - Andrew C Cockcroft
- Department of Agriculture, Forestry and Fisheries, Cape Town, South Africa
| | - Cristián E Hernández
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Universidad Católica de Santa María, Arequipa, Perú
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Department of Ecology, Environment & Evolution, La Trobe University, Melbourne, Vic, Australia
| |
Collapse
|
8
|
Tempestini A, Pinchuk AI, Dufresne F. Spatial genetic structure in Themisto libellula (Amphipoda: Hyperiidae) from the coastal Gulf of Alaska, Bering and Chukchi seas. Polar Biol 2020. [DOI: 10.1007/s00300-020-02745-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
9
|
Laakkonen HM, Hardman M, Strelkov P, Väinölä R. Cycles of trans-Arctic dispersal and vicariance, and diversification of the amphi-boreal marine fauna. J Evol Biol 2020; 34:73-96. [PMID: 32671913 DOI: 10.1111/jeb.13674] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 06/05/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
The amphi-boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans-Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent inter-oceanic vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further trans-Arctic dispersal have risen at times, however, and molecular data now expose more complex patterns of inter-oceanic affinities and dispersal histories. For a general view on the trans-Arctic dynamics and of the roles of potential dispersal-vicariance cycles in generating systematic diversity, we produced new phylogeographic data sets for amphi-boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 inter-oceanic comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond to a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene-Pleistocene-Holocene time frame. Repeated inter-oceanic exchange was inferred for 23 taxa, and the latest connection was usually post-glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late- or post-glacial exchange was inferred in 46% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the North Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter-oceanic vicariance scenario underlying amphi-boreal speciation, the data expose complex patterns of reinvasion and reticulation that complicate the interpretation of taxon boundaries in the region.
Collapse
Affiliation(s)
- Hanna M Laakkonen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Michael Hardman
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Petr Strelkov
- Department of Ichthyology and Hydrobiology, Saint Petersburg State University, St. Petersburg, Russia
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| |
Collapse
|
10
|
Cayuela H, Rougemont Q, Laporte M, Mérot C, Normandeau E, Dorant Y, Tørresen OK, Hoff SNK, Jentoft S, Sirois P, Castonguay M, Jansen T, Praebel K, Clément M, Bernatchez L. Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish. Mol Ecol 2020; 29:2379-2398. [DOI: 10.1111/mec.15499] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Siv Nam Khang Hoff
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Pascal Sirois
- Département des sciences fondamentales Université du Québec à Chicoutimi Chicoutimi QC Canada
| | - Martin Castonguay
- Fisheries and Oceans Canada Institut Maurice‐Lamontagne Mont‐Joli QC Canada
| | - Teunis Jansen
- GINR‐Greenland Institute of Natural Resources Nuuk Greenland
- DTU Aqua‐National Institute of Aquatic Resources Technical University of Denmark Charlottenlund Castle, Charlottenlund Denmark
| | - Kim Praebel
- Norwegian College of Fishery Science Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Marie Clément
- Center for Fisheries Ecosystems Research Fisheries and Marine Institute of Memorial University of Newfoundland St. John's NL Canada
- Labrador Institute of Memorial University of Newfoundland Happy Valley‐Goose Bay NL Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| |
Collapse
|
11
|
Skurikhina LA, Oleinik AG, Kukhlevsky AD, Novoselov AP, Sendek DS. Molecular Genetic Analysis of the Relationships and Origin of Smelt (Hypomesus, Osmeridae), a New Component of the Fauna of the Barents Sea. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Fairweather R, Bradbury IR, Helyar SJ, de Bruyn M, Therkildsen NO, Bentzen P, Hemmer‐Hansen J, Carvalho GR. Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod. Ecol Evol 2018; 8:12140-12152. [PMID: 30598806 PMCID: PMC6303715 DOI: 10.1002/ece3.4672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/11/2022] Open
Abstract
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.
Collapse
Affiliation(s)
- Robert Fairweather
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- School of Biological SciencesBangor UniversityBangorUK
| | - Ian R. Bradbury
- Science Branch, Department of FisheriesSt John’s, Newfoundland and LabradorCanada
| | - Sarah J. Helyar
- Institute of Global Food SecurityQueen’s University BelfastBelfastUK
| | - Mark de Bruyn
- School of Biological SciencesBangor UniversityBangorUK
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jakob Hemmer‐Hansen
- Section for Marine Living Resources, National Institute for Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | |
Collapse
|
13
|
Byrne L, Chapleau F, Aris-Brosou S. How the Central American Seaway and an Ancient Northern Passage Affected Flatfish Diversification. Mol Biol Evol 2018; 35:1982-1989. [PMID: 29788493 DOI: 10.1093/molbev/msy104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering > 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range. We show that flatfish diversified in two bouts, as species that are today distributed around the equator diverged during the closure of CAS, whereas those with a northern range diverged after this, hereby suggesting the existence of a postCAS closure dispersal for these northern species, most likely along a trans-Arctic northern route, a hypothesis fully compatible with paleogeographic reconstructions.
Collapse
Affiliation(s)
- Lisa Byrne
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Mathematics & Statistics, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
14
|
Makhrov AA, Lajus DL. Postglacial Colonization of the North European Seas by Pacific Fishes and Lamprey. CONTEMP PROBL ECOL+ 2018. [DOI: 10.1134/s1995425518030071] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
15
|
Tempestini A, Rysgaard S, Dufresne F. Species identification and connectivity of marine amphipods in Canada's three oceans. PLoS One 2018; 13:e0197174. [PMID: 29791459 PMCID: PMC5965885 DOI: 10.1371/journal.pone.0197174] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/27/2018] [Indexed: 11/28/2022] Open
Abstract
Monitoring the distribution of marine biodiversity is a crucial step to better assess the impacts of global changes. Arctic marine fauna is dominated by amphipods in terms of abundance and biomass. These peracarids are an important marine order of crustaceans but the number of species found in the different Canadian oceans is currently unknown. Furthermore, most species are difficult to identify due to poor taxonomic descriptions and morphological convergence. The aim of this study was to assess the species diversity of marine amphipods in the three Canadian oceans using DNA barcoding. To do so, we produced a database of DNA barcodes of amphipods from the three Canadian Oceans publicly available from the BOLD website to which we added 310 new sequences from the Canadian Arctic Archipelago. We first delimited amphipod species based on barcode gap detection techniques and tree based method (bPTP) and then compared the composition of amphipods among the three oceans in order to assess the influence of past transarctic exchanges on Arctic diversity. Our analysis of 2309 sequences which represent more than 250 provisional species revealed a high connectivity between the Atlantic and Arctic Oceans. Our results also suggest that a single threshold to delimitate species is not suitable for amphipods. This study highlights the challenges involved in species delimitation and the need to obtain complete barcoding inventories in marine invertebrates.
Collapse
Affiliation(s)
- Astrid Tempestini
- Département de biologie et Québec Océan, Université du Québec à Rimouski, Rimouski, QC, Canada
- * E-mail:
| | - Søren Rysgaard
- University of Manitoba, Centre for Earth Observation Science, Winnipeg, MB, Canada
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Aarhus University, Arctic Research Centre, Aarhus, Denmark
| | - France Dufresne
- Département de biologie et Centre d’étude Nordique, Université du Québec à Rimouski, Rimouski, QC, Canada
| |
Collapse
|
16
|
Loeza-Quintana T, Adamowicz SJ. Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events. J Mol Evol 2018; 86:118-137. [DOI: 10.1007/s00239-018-9831-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 02/02/2018] [Indexed: 01/04/2023]
|
17
|
Neiva J, Paulino C, Nielsen MM, Krause-Jensen D, Saunders GW, Assis J, Bárbara I, Tamigneaux É, Gouveia L, Aires T, Marbà N, Bruhn A, Pearson GA, Serrão EA. Glacial vicariance drives phylogeographic diversification in the amphi-boreal kelp Saccharina latissima. Sci Rep 2018; 8:1112. [PMID: 29348650 PMCID: PMC5773594 DOI: 10.1038/s41598-018-19620-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/04/2018] [Indexed: 11/08/2022] Open
Abstract
Glacial vicariance is regarded as one of the most prevalent drivers of phylogeographic structure and speciation among high-latitude organisms, but direct links between ice advances and range fragmentation have been more difficult to establish in marine than in terrestrial systems. Here we investigate the evolution of largely disjunct (and potentially reproductively isolated) phylogeographic lineages within the amphi-boreal kelp Saccharina latissima s. l. Using molecular data (COI, microsatellites) we confirm that S. latissima comprises also the NE Pacific S. cichorioides complex and is composed of divergent lineages with limited range overlap and genetic admixture. Only a few genetic hybrids were detected throughout a Canadian Arctic/NW Greenland contact zone. The degree of genetic differentiation and sympatric isolation of phylogroups suggest that S. latissima s. l. represents a complex of incipient species. Phylogroup distributions compared with paleo-environmental reconstructions of the cryosphere further suggest that diversification within S. latissima results from chronic glacial isolation in disjunct persistence areas intercalated with ephemeral interglacial poleward expansions and admixture at high-latitude (Arctic) contact zones. This study thus supports a role for glaciations not just in redistributing pre-existing marine lineages but also as a speciation pump across multi-glacial cycles for marine organisms otherwise exhibiting cosmopolite amphi-boreal distributions.
Collapse
Affiliation(s)
- João Neiva
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal.
| | - Cristina Paulino
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Mette M Nielsen
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
| | - Dorte Krause-Jensen
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Gary W Saunders
- Centre for Environmental and Molecular Algal Research, University of New Brunswick, Fredericton, Canada
| | - Jorge Assis
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Ignacio Bárbara
- Biocost Research Group, Universidade de A Coruña, A Coruña, Spain
| | - Éric Tamigneaux
- NSERC Industrial Research Chair for Colleges in Marine Macroalgae, Cégep de la Gaspésie et des Îles, Grande-Rivière, Québec, Canada
| | - Licínia Gouveia
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Tânia Aires
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Núria Marbà
- Department of Global Change Research, IMEDEA (CSIC-UIB), Esporles, Spain
| | - Annette Bruhn
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
| | - Gareth A Pearson
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Ester A Serrão
- CCMAR- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal.
| |
Collapse
|
18
|
Skurikhina LA, Oleinik AG, Kukhlevsky AD, Kovpak NE, Frolov SV, Sendek DS. Phylogeography and demographic history of the Pacific smelt Osmerus dentex inferred from mitochondrial DNA variation. Polar Biol 2018. [DOI: 10.1007/s00300-018-2250-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
19
|
McNicholl DG, Davoren GK, Reist JD. Life history variation across latitudes: observations between capelin (Mallotus villosus) from Newfoundland and the eastern Canadian Arctic. Polar Biol 2018. [DOI: 10.1007/s00300-017-2225-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
20
|
Layton KKS, Corstorphine EA, Hebert PDN. Exploring Canadian Echinoderm Diversity through DNA Barcodes. PLoS One 2016; 11:e0166118. [PMID: 27870868 PMCID: PMC5117606 DOI: 10.1371/journal.pone.0166118] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.
Collapse
Affiliation(s)
- Kara K. S. Layton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
- * E-mail:
| | - Erin A. Corstorphine
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
21
|
Tu Z, Liu M, Wang Y, Xu S, Song N, Gao T, Han Z. The low mitochondrial diversities in lizardfish Saurida elongate: Recent population expansion and selection. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
22
|
Sukhikh N, Souissi A, Souissi S, Winkler G, Castric V, Holl AC, Alekseev V. Genetic and morphological heterogeneity among populations of Eurytemora affinis (Crustacea: Copepoda: Temoridae) in European waters. C R Biol 2016; 339:197-206. [PMID: 27156447 DOI: 10.1016/j.crvi.2016.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/28/2016] [Indexed: 11/29/2022]
Abstract
Our understanding of the systematics of the Eurytemora affinis complex developed at a fast pace over the last decades. Formerly considered as a complex of cryptic species, it is now believed to include three valid species: E. affinis, Eurytemora carolleeae, and Eurytemora caspica. American and European representatives have been studied in detail with respect to fine-scale geographic distribution, levels of genetic subdivision, evolutionary and demographic histories. Morphological components have been less explored. In this study, an analysis of the phylogeny and morphology of E. affinis was done, with a special focus on European populations. A total of 447 individuals of E. affinis from Europe were analyzed with genetic tools and 170 individuals according to morphological criteria. Common and new morphological and genetic features were analyzed. For this, we used ML and Bayesian methods to analyze the bar coding mt-DNA gene cytochrome c oxidase I subunit. Both genetic and morphological analyses showed high heterogeneities among the E. affinis populations from Europe. As a result, three local populations of E. affinis in Western Europe, including the European part of Russia, were established. Their genetic and morphological heterogeneity corresponded to the subspecies level.
Collapse
Affiliation(s)
| | - Anissa Souissi
- Université de Lille, CNRS, ULCO, UMR 8187, Laboratoire d'océanologie et de géosciences (LOG), 62930 Wimereux, France
| | - Sami Souissi
- Université de Lille, CNRS, ULCO, UMR 8187, Laboratoire d'océanologie et de géosciences (LOG), 62930 Wimereux, France
| | - Gesche Winkler
- Institut des sciences de la mer de Rimouski, Québec-Océan, Université du Québec à Rimouski, 310, allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Vincent Castric
- Université Lille-1 (Sciences et Technologies), UMR CNRS 8016, UFR de biologie, 59655 Villeneuve-d'Ascq cedex, France
| | - Anne-Catherine Holl
- Université Lille-1 (Sciences et Technologies), UMR CNRS 8016, UFR de biologie, 59655 Villeneuve-d'Ascq cedex, France
| | | |
Collapse
|
23
|
Skurikhina LA, Oleinik AG, Kukhlevsky AD, Kovpak NE, Sendek DS, Maznikova OA. Genetic differentiation of Pacific smelt Osmerus mordax dentex inferred from the data of mitochondrial DNA analysis. RUSS J GENET+ 2015. [DOI: 10.1134/s102279541512011x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
Elliott M, Borja Á, McQuatters-Gollop A, Mazik K, Birchenough S, Andersen JH, Painting S, Peck M. Force majeure: Will climate change affect our ability to attain Good Environmental Status for marine biodiversity? MARINE POLLUTION BULLETIN 2015; 95:7-27. [PMID: 25837772 DOI: 10.1016/j.marpolbul.2015.03.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
The EU Marine Strategy Framework Directive (MSFD) requires that Good Environmental Status (GEnS), is achieved for European seas by 2020. These may deviate from GEnS, its 11 Descriptors, targets and baselines, due to endogenic managed pressures (from activities within an area) and externally due to exogenic unmanaged pressures (e.g. climate change). Conceptual models detail the likely or perceived changes expected on marine biodiversity and GEnS Descriptors in the light of climate change. We emphasise that marine management has to accommodate 'shifting baselines' caused by climate change particularly during GEnS monitoring, assessment and management and 'unbounded boundaries' given the migration and dispersal of highly-mobile species. We suggest climate change may prevent GEnS being met, but Member States may rebut legal challenges by claiming that this is outside its control, force majeure or due to 'natural causes' (Article 14 of the MSFD). The analysis is relevant to management of other global seas.
Collapse
Affiliation(s)
- Michael Elliott
- Institute of Estuarine & Coastal Studies, University of Hull, Hull HU6 7RX, UK.
| | - Ángel Borja
- AZTI-Tecnalia, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | | | - Krysia Mazik
- Institute of Estuarine & Coastal Studies, University of Hull, Hull HU6 7RX, UK
| | - Silvana Birchenough
- Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk NR33 OHT, UK
| | - Jesper H Andersen
- NIVA Denmark Water Research, Winghouse, Ørestads Boulevard 73, 2300 Copenhagen S, Denmark
| | - Suzanne Painting
- Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk NR33 OHT, UK
| | - Myron Peck
- Institut für Hydrobiologie und Fischereiwissenschaft, Olbersweg 24, 22767 Hamburg, Germany
| |
Collapse
|
25
|
Kenchington EL, Nakashima BS, Taggart CT, Hamilton LC. Genetic structure of capelin (Mallotus villosus) in the northwest Atlantic Ocean. PLoS One 2015; 10:e0122315. [PMID: 25822621 PMCID: PMC4378951 DOI: 10.1371/journal.pone.0122315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 02/19/2015] [Indexed: 11/19/2022] Open
Abstract
Capelin (Mallotus villosus) is a commercially exploited, key forage-fish species found in the boreal waters of the North Pacific and North Atlantic Oceans. We examined the population structure of capelin throughout their range in the Canadian northwest Atlantic Ocean using genetic-based methods. Capelin collected at ten beach and five demersal spawning locations over the period 2002 through 2008 (N = 3,433 fish) were genotyped using six polymorphic microsatellite loci. Temporally distinct samples were identified at three beach spawning locations: Chance Cove, Little Lawn and Straitsview, Newfoundland. Four capelin stocks are assumed for fisheries management in the northwest Atlantic Ocean based on meristics, morphometrics, tag returns, and seasonal distribution patterns. Our results suggested groupings that were somewhat different than the assumed structure, and indicate at least seven genetically defined populations arising from two ancestral populations. The spatial mosaic of capelin from each of the two basal cluster groups explains much of the observed geographic variability amongst neighbouring samples. The genetic-defined populations were resolved at Jost’s Dest ≥ 0.01 and were composed of fish collected 1) in the Gulf of St. Lawrence, 2) along the south and east coasts of Newfoundland, 3) along coastal northern Newfoundland and southern Labrador, 4) along coastal northern Labrador, 5) near the Saguenay River, and at two nearshore demersal spawning sites, 6) one at Grebes Nest off Bellevue Beach on the east coast of Newfoundland, and 7) one off the coast of Labrador at Domino Run. Moreover, the offshore demersal spawners on the Scotian Shelf and Southeast Shoal appeared to be related to the inshore demersal spawners at Grebes Nest and in Domino Run and to beach spawners from the Gulf of St. Lawrence.
Collapse
Affiliation(s)
- Ellen L. Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
- * E-mail:
| | - Brian S. Nakashima
- Department of Fisheries and Oceans, Northwest Atlantic Fisheries Centre, St. John’s, Newfoundland and Labrador, Canada
| | | | - Lorraine C. Hamilton
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| |
Collapse
|
26
|
Penton PM, McFarlane CT, Spice EK, Docker MF, Davoren GK. Lack of genetic divergence in capelin (Mallotus villosus) spawning at beach versus subtidal habitats in coastal embayments of Newfoundland. CAN J ZOOL 2014. [DOI: 10.1139/cjz-2013-0261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Capelin (Mallotus villosus (Müller, 1776)), a focal forage fish in the north Atlantic, spawn on both beach and demersal (deep-water) sites throughout their circumpolar distribution. Although these habitats rarely occur in close proximity, demersal spawning sites within 4 km of beach spawning sites (subtidal) have recently been discovered in two coastal embayments in Newfoundland, Canada. The physical environment differs considerably between beach and subtidal spawning sites, creating the potential for local adaptation and genetic divergence of capelin from the two habitats, but this has never been investigated on a fine spatial scale. We use eight microsatellite loci to test for genetic divergence between capelin spawning at beach and subtidal sites within these two coastal regions in Newfoundland. We found no genetic differentiation between fish spawning at beach and subtidal sites or between the two regions. The results from this fine-scale study are in agreement with the lack of habitat-based structure reported in other studies examining beach and demersal sites separated by a larger geographic area. We suggest that instead of showing site fidelity and local adaptation, the facultative use of alternate spawning habitats may be a more successful strategy in an unpredictable environment.
Collapse
Affiliation(s)
- Paulette M. Penton
- Department of Biological Sciences, 212B Biological Sciences Building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Craig T. McFarlane
- Department of Biological Sciences, 212B Biological Sciences Building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Erin K. Spice
- Department of Biological Sciences, 212B Biological Sciences Building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Margaret F. Docker
- Department of Biological Sciences, 212B Biological Sciences Building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Gail K. Davoren
- Department of Biological Sciences, 212B Biological Sciences Building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
27
|
Layton KK, Martel AL, Hebert PDN. Patterns of DNA barcode variation in Canadian marine molluscs. PLoS One 2014; 9:e95003. [PMID: 24743320 PMCID: PMC3990619 DOI: 10.1371/journal.pone.0095003] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/21/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. METHODOLOGY/PRINCIPAL FINDINGS This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%), and showed a significant positive correlation with nearest neighbour distances. CONCLUSIONS/SIGNIFICANCE DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.
Collapse
Affiliation(s)
- Kara K.S. Layton
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - André L. Martel
- Research and Collections (Zoology), Canadian Museum of Nature, Gatineau, Quebec, Canada
| | - Paul DN. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
28
|
Laakkonen HM, Lajus DL, Strelkov P, Väinölä R. Phylogeography of amphi-boreal fish: tracing the history of the Pacific herring Clupea pallasii in North-East European seas. BMC Evol Biol 2013; 13:67. [PMID: 23510113 PMCID: PMC3637224 DOI: 10.1186/1471-2148-13-67] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/07/2013] [Indexed: 11/11/2022] Open
Abstract
Background The relationships between North Atlantic and North Pacific faunas through times have been controlled by the variation of hydrographic circumstances in the intervening Arctic Ocean and Bering Strait. We address the history of trans-Arctic connections in a clade of amphi-boreal pelagic fishes using genealogical information from mitochondrial DNA sequence data. The Pacific and Atlantic herrings (Clupea pallasii and C. harengus) have basically vicarious distributions in the two oceans since pre-Pleistocene times. However, remote populations of C. pallasii are also present in the border waters of the North-East Atlantic in Europe. These populations show considerable regional and life history differentiation and have been recognized in subspecies classification. The chronology of the inter-oceanic invasions and genetic basis of the phenotypic structuring however remain unclear. Results The Atlantic and Pacific herrings both feature high mtDNA diversities (large long-term population sizes) in their native basins, but an ocean-wide homogeneity of C. harengus is contrasted by deep east-west Pacific subdivision within Pacific C. pallasii. The outpost populations of C. pallasii in NE Europe are identified as members of the western Pacific C. pallasii clade, with some retained inter-oceanic haplotype sharing. They have lost diversity in colonization bottlenecks, but have also thereafter accumulated abundant new variation. The data delineate three phylogeographic groups within the European C. pallasii: herring from the inner White Sea; herring from the Mezen and Chesha Bays; and a strongly bottlenecked peripheral population in Balsfjord of the Norwegian Sea. Conclusions The NE European outposts of C. pallasii are judged to be early post-glacial colonists from the NW Pacific. A strong regional substructure has evolved since that time, in contrast to the apparent broad-scale uniformity maintained by herrings in their native basins. The structure only partly matches the previous biological concepts based on seasonal breeding stocks or geographical subspecies designations. The trans-Arctic herring phylogeography is notably similar to those of the amphi-boreal mollusk taxa Macoma and Mytilus, suggesting similar histories of inter-oceanic connections. We also considered the time dependency of molecular rates, critical for interpreting timing of relatively recent biogeographical events, by comparing the estimates from coding and non-coding mitochondrial regions of presumably different mutation dynamics.
Collapse
Affiliation(s)
- Hanna M Laakkonen
- Finnish Museum of Natural History, University of Helsinki, POB 17, FI-00014 Helsinki, Finland.
| | | | | | | |
Collapse
|
29
|
Relationships of osmerid fishes (Osmeridae) of Russia: divergence of nucleotide sequences of mitochondrial and nuclear genes. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0099-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
30
|
McCusker MR, Denti D, Guelpen L, Kenchington E, Bentzen P. Barcoding Atlantic Canada's commonly encountered marine fishes. Mol Ecol Resour 2012; 13:177-88. [DOI: 10.1111/1755-0998.12043] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/09/2012] [Accepted: 10/15/2012] [Indexed: 11/29/2022]
Affiliation(s)
- M. R. McCusker
- University of Toronto at Scarborough 1265 Military Trail Toronto Ontario Canada M1C‐A4
| | - D. Denti
- Department of Biology Life Sciences Centre Dalhousie University 1355 Oxford Street PO BOX 15000 Halifax Nova Scotia Canada B3H 4R2
| | - L. Guelpen
- Atlantic Reference Centre Huntsman Marine Science Centre 1 Lower Campus Road St. Andrews New Brunswick Canada E5B 2L7
| | - E. Kenchington
- Department of Fisheries and Oceans Bedford Institute of Oceanography 1 Challenger Drive Dartmouth Nova Scotia Canada B2Y 4A2
| | - P. Bentzen
- Department of Biology Life Sciences Centre Dalhousie University 1355 Oxford Street PO BOX 15000 Halifax Nova Scotia Canada B3H 4R2
| |
Collapse
|
31
|
Skurikhina LA, Kukhlevsky AD, Zheleznova KO, Kovalev MY. Analysis of the mitochondrial DNA variation in pond smelt Hypomesus olidus (Osmeridae). RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412060142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
32
|
Kovpak NE, Skurikhina LA, Kukhlevsky AD, Oleinik AG, Sendek DS. Genetic divergence and relationships among smelts of the genus Osmerus from the Russian waters. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411080102] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
33
|
Carr CM, Hardy SM, Brown TM, Macdonald TA, Hebert PDN. A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes. PLoS One 2011; 6:e22232. [PMID: 21829451 PMCID: PMC3136506 DOI: 10.1371/journal.pone.0022232] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 06/17/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Although polychaetes are one of the dominant taxa in marine communities, their distributions and taxonomic diversity are poorly understood. Recent studies have shown that many species thought to have broad distributions are actually a complex of allied species. In Canada, 12% of polychaete species are thought to occur in Atlantic, Arctic, and Pacific Oceans, but the extent of gene flow among their populations has not been tested. METHODOLOGY/PRINCIPAL FINDINGS Sequence variation in a segment of the mitochondrial cytochrome c oxidase I (COI) gene was employed to compare morphological versus molecular diversity estimates, to examine gene flow among populations of widespread species, and to explore connectivity patterns among Canada's three oceans. Analysis of 1876 specimens, representing 333 provisional species, revealed 40 times more sequence divergence between than within species (16.5% versus 0.38%). Genetic data suggest that one quarter of previously recognized species actually include two or more divergent lineages, indicating that richness in this region is currently underestimated. Few species with a tri-oceanic distribution showed genetic cohesion. Instead, large genetic breaks occur between Pacific and Atlantic-Arctic lineages, suggesting their long-term separation. High connectivity among Arctic and Atlantic regions and low connectivity with the Pacific further supports the conclusion that Canadian polychaetes are partitioned into two distinct faunas. CONCLUSIONS/SIGNIFICANCE Results of this study confirm that COI sequences are an effective tool for species identification in polychaetes, and suggest that DNA barcoding will aid the recognition of species overlooked by the current taxonomic system. The consistent geographic structuring within presumed widespread species suggests that historical range fragmentation during the Pleistocene ultimately increased Canadian polychaete diversity and that the coastal British Columbia fauna played a minor role in Arctic recolonization following deglaciation. This study highlights the value of DNA barcoding for providing rapid insights into species distributions and biogeographic patterns in understudied groups.
Collapse
Affiliation(s)
- Christina M Carr
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.
| | | | | | | | | |
Collapse
|
34
|
COLBECK GABRIELJ, TURGEON JULIE, SIROIS PASCAL, DODSON JULIANJ. Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus). Mol Ecol 2011; 20:1976-87. [DOI: 10.1111/j.1365-294x.2011.05069.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
35
|
Liu M, Lu ZC, Gao TX, Yanagimoto T, Sakurai Y. Remarkably low mtDNA control-region diversity and shallow population structure in Pacific cod Gadus macrocephalus. JOURNAL OF FISH BIOLOGY 2010; 77:1071-1082. [PMID: 21039491 DOI: 10.1111/j.1095-8649.2010.02743.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
To investigate the genetic diversity and describe the population structure in Gadus macrocephalus, a 452 base pair (bp) fragment of the mitochondrial DNA control region was analysed in 259 individuals. The results showed remarkably low nucleotide diversity and a lack of genealogical structure. Small but significant genetic differentiations, however, were detected among north-western Pacific populations, but no large-scale regional differences were detected. These results indicate that populations of G. macrocephalus in the north-western Pacific are genetically subdivided and represent evolutionary lineages that should be managed individually.
Collapse
Affiliation(s)
- M Liu
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China Liaoning Marine Fisheries Research Institute, Dalian, Liaoning 116023, China
| | | | | | | | | |
Collapse
|
36
|
McCUSKER MEGANR, BENTZEN PAUL. Historical influences dominate the population genetic structure of a sedentary marine fish, Atlantic wolffish (Anarhichas lupus), across the North Atlantic Ocean. Mol Ecol 2010; 19:4228-41. [DOI: 10.1111/j.1365-294x.2010.04806.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
37
|
McCusker MR, Bentzen P. Phylogeography of 3 North Atlantic Wolffish species (Anarhichas spp.) with phylogenetic relationships within the family Anarhichadidae. ACTA ACUST UNITED AC 2010; 101:591-601. [PMID: 20511379 DOI: 10.1093/jhered/esq062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Phylogenetic analyses of all 4 wolffish species (Atlantic, Spotted, Northern, and Bering wolffishes) and the Wolfeel were assessed with both mitochondrial (D-loop and ND1) and nuclear (amplified fragment length polymorphism) DNA to resolve relationships within the family Anarhichadidae. Species-specific mitochondrial DNA (mtDNA) mutation rates were estimated based on 2 possible dates of divergence between the Pacific and Atlantic lineages. Phylogeographic patterns within each of the 3 North Atlantic wolffishes were investigated with Markov chain Monte Carlo simulations based on mtDNA to determine whether population size changes occurred following the last glaciation and where wolffishes likely survived glaciation. All 3 species of North Atlantic wolffishes showed evidence of postglacial expansion but did not show evidence of persistence in multiple refugia in both the eastern and western Atlantic Ocean. Rather, the data supported persistence in a single refuge, with postglacial expansion into the rest of the range. Nucleotide diversity, in particular, was low in wolffishes compared with other marine fishes, possibly related to reductions in population sizes during the last glaciation.
Collapse
Affiliation(s)
- Megan R McCusker
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
| | | |
Collapse
|
38
|
Skurikhina LA, Kukhlevsky AD, Oleinik AG, Kovpak NE. Phylogenetic analysis of smelts (Osmeridae) based on the variation of cytochrome b gene. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410010114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
39
|
TSURUDA S, SAKAMOTO T, AKAKI K, HIWAKI H. Detection of Pacific Cod and Capelin Roes in Alaska Pollack Roe Product by Real-Time PCR Assay. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2010; 51:110-4. [DOI: 10.3358/shokueishi.51.110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
40
|
von der Heyden S, Lipinski MR, Matthee CA. Remarkably low mtDNA control region diversity in an abundant demersal fish. Mol Phylogenet Evol 2009; 55:1183-8. [PMID: 19761857 DOI: 10.1016/j.ympev.2009.09.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 09/09/2009] [Indexed: 10/20/2022]
Abstract
Cape hake, Merluccius paradoxus, is a valuable commercially exploited demersal species. Using the 5' mtDNA control region we show that 96% of 1013 fishes sampled over a three-year period share one of two dominant haplotypes; 19 haplotypes were recovered in total, suggesting a genetically homogenous population of fish. Accordingly, haplotype and nucleotide diversities are low (h = 0.53, pi = 0.0014); an asymptotic haplotype accumulation curve suggests that few additional haplotypes exist. Comparing h and pi with other fish species shows that M. paradoxus and other southern African fish species have remarkably low genetic diversity values compared with other global marine fishes. Despite low genetic variability, frequency differences among M. paradoxus haplotypes suggest weakly structured populations between Namibia and South Africa. However, given the remarkably homogeneous mtDNA population genetic structure between fishes sampled along 1800 km, it is clear that faster evolving markers such a microsatellites are also needed before inferences can be made regarding stock identification and management of this species.
Collapse
Affiliation(s)
- Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
| | | | | |
Collapse
|
41
|
Skurikhina LA, Oleinik AG, Kovpak NE. Mitochondrial DNA variation in Pacific capelin (Mallotus villosus catervarius) from the Sea of Okhotsk, inferred from PCR-RFLP analysis. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408070089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|