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Lesturgie P, Braun CD, Clua E, Mourier J, Thorrold SR, Vignaud T, Planes S, Mona S. Like a rolling stone: Colonization and migration dynamics of the gray reef shark ( Carcharhinus amblyrhynchos). Ecol Evol 2023; 13:e9746. [PMID: 36644707 PMCID: PMC9831972 DOI: 10.1002/ece3.9746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here, we investigated the evolutionary history of the endangered gray reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RADseq loci in 173 individuals in the Indo-Pacific (IP). We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo-Australian Archipelago (IAA) where two stepping-stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm ~ 10 per generation) throughout the range, and isolation by distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long-distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (F ST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the gray reef shark should be designed on a range-wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon-associated Carcharhinus melanopterus, known for its restricted dispersal ability. Carcharhinus melanopterus exhibits a similar RE dynamic but is characterized by a stronger genetic structure and a nonhomogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as source of biodiversity and of life-history traits in shaping the extent of genetic structure and diversity.
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Affiliation(s)
- Pierre Lesturgie
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE‐PSLUniversité PSL, CNRS, SU, UAParisFrance
| | - Camrin D. Braun
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Eric Clua
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- EPHE, PSL Research UniversityParisFrance
| | - Johann Mourier
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- Université de Corse Pasquale Paoli, UMS 3514 Plateforme Marine Stella MareBigugliaFrance
| | - Simon R. Thorrold
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | | | - Serge Planes
- Laboratoire d'Excellence CORAILPapetoaiFrench Polynesia
- EPHE, PSL Research UniversityParisFrance
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE‐PSLUniversité PSL, CNRS, SU, UAParisFrance
- EPHE, PSL Research UniversityParisFrance
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2
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Genomic insights into the historical and contemporary demographics of the grey reef shark. Heredity (Edinb) 2022; 128:225-235. [PMID: 35296830 PMCID: PMC8987070 DOI: 10.1038/s41437-022-00514-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/08/2022] Open
Abstract
Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (Ne) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in Ne were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in Ne were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient Ne observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary Ne, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.
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3
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Lesturgie P, Planes S, Mona S. Coalescence times, life history traits and conservation concerns: An example from four coastal shark species from the Indo-Pacific. Mol Ecol Resour 2021; 22:554-566. [PMID: 34407294 DOI: 10.1111/1755-0998.13487] [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: 04/16/2021] [Revised: 07/27/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographical ranges and less mobile ones organized in metapopulations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne ) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (metapopulation) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.
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Affiliation(s)
- Pierre Lesturgie
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia.,EPHE, PSL Research University, Paris, France
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4
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Morin PA, Forester BR, Forney KA, Crossman CA, Hancock-Hanser BL, Robertson KM, Barrett-Lennard LG, Baird RW, Calambokidis J, Gearin P, Hanson MB, Schumacher C, Harkins T, Fontaine MC, Taylor BL, Parsons KM. Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples. Mol Ecol 2021; 30:1457-1476. [PMID: 33544423 DOI: 10.1111/mec.15827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 12/24/2022]
Abstract
Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes (N = 271 samples) in addition to mitochondrial (mtDNA) sequence data (N = 413 samples) to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We confirmed an overall pattern of strong isolation-by-distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (FST = 0.02 [microhaplotypes]; 0.31 [mtDNA]), with both reduced genetic variability and high frequency of an otherwise rare mtDNA haplotype. At the northern end of our study range, we found significant genetic differentiation of samples from the Strait of Georgia, previously identified as a potential biogeographical boundary or secondary contact zone between harbor porpoise populations. Association of microhaplotypes with remotely sensed environmental variables indicated potential local adaptation, especially at the southern end of the species' range. These results inform conservation and management for this nearshore species, illustrate the value of genomic methods for detecting patterns of genetic structure within a continuously distributed marine species, and highlight the power of microhaplotype genotyping for detecting genetic structure in harbor porpoises despite reliance on poor-quality samples.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Karin A Forney
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Moss Landing, CA, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, USA
| | - Carla A Crossman
- Biology Department, Saint Mary's University, Halifax, NS, Canada.,Cetacean Research Program, Vancouver Aquarium, Vancouver, BC, Canada
| | | | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | | | | | | | - Pat Gearin
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | - M Bradley Hanson
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | | | | | - Michael C Fontaine
- MIVEGEC Research Unit (Université de Montpellier, CNRS, IRD) & Centre for Research on the Ecology and Evolution of Diseases (CREES), Centre IRD de Montpellier, Montpellier, France.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Kim M Parsons
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA.,Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
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5
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Feutry P, Devloo-Delva F, Tran Lu Y A, Mona S, Gunasekera RM, Johnson G, Pillans RD, Jaccoud D, Kilian A, Morgan DL, Saunders T, Bax NJ, Kyne PM. One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark. Mol Ecol Resour 2020; 20:1470-1485. [PMID: 32492756 DOI: 10.1111/1755-0998.13204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 01/25/2023]
Abstract
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
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Affiliation(s)
| | - Floriaan Devloo-Delva
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,School of Natural Sciences - Quantitative Marine Science, University of Tasmania, Hobart, TAS, Australia
| | - Adrien Tran Lu Y
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,EPHE, PSL University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | | | - Grant Johnson
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | | | - Damian Jaccoud
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - David L Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Thor Saunders
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, Darwin, NT, Australia
| | - Nicholas J Bax
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.,Institute for Marine and Antarctic Science, University of Tasmania, Hobart, TAS, Australia
| | - Peter M Kyne
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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6
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Delrieu-Trottin E, Hubert N, Giles EC, Chifflet-Belle P, Suwalski A, Neglia V, Rapu-Edmunds C, Mona S, Saenz-Agudelo P. Coping with Pleistocene climatic fluctuations: Demographic responses in remote endemic reef fishes. Mol Ecol 2020; 29:2218-2233. [PMID: 32428327 DOI: 10.1111/mec.15478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Elucidating demographic history during the settlement of ecological communities is crucial for properly inferring the mechanisms that shape patterns of species diversity and their persistence through time. Here, we used genomic data and coalescent-based approaches to elucidate for the first time the demographic dynamics associated with the settlement by endemic reef fish fauna of one of the most remote peripheral islands of the Pacific Ocean, Rapa Nui (Easter Island). We compared the demographic history of nine endemic species in order to explore their demographic responses to Pleistocene climatic fluctuations. We found that species endemic to Rapa Nui share a common demographic history, as signatures of population expansions were retrieved for almost all of the species studied here, and synchronous demographic expansions initiated during the last glacial period were recovered for more than half of the studied species. These results suggest that eustatic fluctuations associated with Milankovitch cycles have played a central role in species demographic histories and in the final stage of the community assembly of many Rapa Nui reef fishes. Specifically, sea level lowstands resulted in the maximum reef habitat extension for Rapa Nui endemic species; we discuss the potential role of seamounts in allowing endemic species to cope with Pleistocene climatic fluctuations, and we highlight the importance of local historical processes over regional ones. Overall, our results shed light on the mechanisms by which endemism arises and is maintained in peripheral reef fish fauna.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France
| | - Emily C Giles
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pascaline Chifflet-Belle
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Arnaud Suwalski
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Valentina Neglia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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7
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Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus). Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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8
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Khimoun A, Doums C, Molet M, Kaufmann B, Peronnet R, Eyer PA, Mona S. Urbanization without isolation: the absence of genetic structure among cities and forests in the tiny acorn ant Temnothorax nylanderi. Biol Lett 2020; 16:20190741. [PMID: 31992150 DOI: 10.1098/rsbl.2019.0741] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Urban alteration of neutral and adaptive evolutionary processes is still underexplored. Using a genome-wide SNP dataset, we investigated (i) urban-induced modifications of population demography, genetic diversity and population structure and (ii) signature of divergent selection between urban and forest populations in the ant species, Temnothorax nylanderi. Our results did not reveal an impact of urbanization on neutral processes since we observed: (i) analogous genetic diversity among paired urban/forest sites and two control populations; (ii) weak population genetic structure explained neither by habitat (urban versus forest) nor by geography; (iii) a remarkably similar demographic history across populations with an ancestral growth followed by a recent decline, regardless of their current habitat or geographical location. The micro-geographical home range of ants may explain their resilience to urbanization. Finally, we detected 19 candidate loci discriminating urban/forest populations and associated with core cellular components, molecular function or biological process. Two of these loci were associated with a gene ontology term that was previously found to belong to a module of co-expressed genes related to caste phenotype. These results call for transcriptomics analyses to identify genes associated with ant social traits and to infer their potential role in urban adaptation.
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Affiliation(s)
- A Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - C Doums
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, 75005 Paris, France.,EPHE, PSL University, 75005 Paris, France
| | - M Molet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), UMR 7618, Sorbonne Université, Université Paris Est Créteil, Université Paris Diderot, CNRS, INRA, IRD, 75005 Paris, France
| | - B Kaufmann
- Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, ENTPE, CNRS, Villeurbanne 69622, France
| | - R Peronnet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), UMR 7618, Sorbonne Université, Université Paris Est Créteil, Université Paris Diderot, CNRS, INRA, IRD, 75005 Paris, France
| | - P A Eyer
- Department of Entomology, Texas A&M University, 2143 TAMU, College Station, TX 77843-2143, USA
| | - S Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, 75005 Paris, France.,EPHE, PSL University, 75005 Paris, France
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9
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Choo LQ, Bal TMP, Choquet M, Smolina I, Ramos-Silva P, Marlétaz F, Kopp M, Hoarau G, Peijnenburg KTCA. Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance. BMC Genomics 2020; 21:11. [PMID: 31900119 PMCID: PMC6942316 DOI: 10.1186/s12864-019-6372-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species. RESULTS We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genome-wide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species. CONCLUSION The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.
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Affiliation(s)
- Le Qin Choo
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
| | - Thijs M P Bal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Paula Ramos-Silva
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ferdinand Marlétaz
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
| | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Katja T C A Peijnenburg
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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10
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Same species, different prerequisites: investigating body condition and foraging success in young reef sharks between an atoll and an island system. Sci Rep 2019; 9:13447. [PMID: 31530846 PMCID: PMC6748967 DOI: 10.1038/s41598-019-49761-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/27/2019] [Indexed: 11/08/2022] Open
Abstract
Acquiring and storing energy is vital to sharks of all age-classes. Viviparous shark embryos receive endogenous maternal energy reserves to sustain the first weeks after birth. Then, in order to maintain body condition, sharks must start foraging. Our goal was to understand whether maternal energy investments vary between blacktip reef sharks (Carcharhinus melanopterus) from two populations and to what extent body condition and the initiation of foraging might be affected by presumably variable maternal investments. A total of 546 young sharks were captured at St. Joseph atoll (Seychelles) and Moorea (French Polynesia) between 2014 and 2018, and indices of body condition and percentage of stomachs containing prey were measured. Maternal investment was found to be site-specific, with significantly larger, heavier, and better conditioned individuals in Moorea. Despite these advantages, as time progressed, Moorea sharks exhibited significant decreases in body condition and were slower to initiate foraging. We suggest that the young sharks' foraging success is independent of the quality of maternal energy resources, and that other factors, such as prey availability, prey quality, and/or anthropogenic stressors are likely responsible for the observed differences across sites. Insights into intraspecific variations in early life-stages may further support site-specific management strategies for young sharks from nearshore habitats.
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11
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Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11040049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations.
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12
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Demographic inferences after a range expansion can be biased: the test case of the blacktip reef shark (Carcharhinus melanopterus). Heredity (Edinb) 2018; 122:759-769. [PMID: 30459340 DOI: 10.1038/s41437-018-0164-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
The evolutionary history of species is a dynamic process as they modify, expand, and contract their spatial distributions over time. Range expansions (REs) occur through a series of founder events that are followed by migration among neighboring demes. The process usually results in structured metapopulations and leaves a distinct signature in the genetic variability of species. Explicitly modeling the consequences of complex demographic events such as REs is computationally very intensive. Here we propose an an alternative approach that requires less computational effort than a comprehensive RE model, but that can recover the demography of species undergoing a RE, by combining spatially explicit modelling with simplified but realistic metapopulation models. We examine the demographic and colonization history of Carcharhinus melanopterus, an abundant reef-associated shark, as a test case. We first used a population genomics approach to statistically confirm the occurrence of a RE in C. melanopterus, and identify its origin in the Indo-Australian Archipelago. Spatial genetic modelling identified two waves of stepping-stone colonization: an eastward wave moving through the Pacific and a westward one moving through the Indian Ocean. We show that metapopulation models best describe the demographic history of this species and that not accounting for this may lead to incorrectly interpreting the observed genetic variation as signals of widespread population bottlenecks. Our study highlights insights that can be gained about demography by coupling metapopulation models with spatial modeling and underscores the need for cautious interpretation of population genetic data when advancing conservation priorities.
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Almojil D, Cliff G, Spaet JLY. Weak population structure of the Spot-tail shark Carcharhinus sorrah and the Blacktip shark C. limbatus along the coasts of the Arabian Peninsula, Pakistan, and South Africa. Ecol Evol 2018; 8:9536-9549. [PMID: 30377521 PMCID: PMC6194305 DOI: 10.1002/ece3.4468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 07/22/2018] [Accepted: 07/23/2018] [Indexed: 11/24/2022] Open
Abstract
The increase in demand for shark meat and fins has placed shark populations worldwide under high fishing pressure. In the Arabian region, the spot-tail shark Carcharhinus sorrah and the Blacktip shark Carcharhinus limbatus are among the most exploited species. In this study, we investigated the population genetic structure of C. sorrah (n = 327) along the coasts of the Arabian Peninsula and of C. limbatus (n = 525) along the Arabian coasts, Pakistan, and KwaZulu-Natal, South Africa, using microsatellite markers (15 and 11 loci, respectively). Our findings support weak population structure in both species. Carcharhinus sorrah exhibited a fine structure, subdividing the area into three groups. The first group comprises all samples from Bahrain, the second from the UAE and Yemen, and the third from Oman. Similarly, C. limbatus exhibited population subdivision into three groups. The first group, comprising samples from Bahrain and Kuwait, was highly differentiated from the second and third groups, comprising samples from Oman, Pakistan, the UAE, and Yemen; and South Africa and the Saudi Arabian Red Sea, respectively. Population divisions were supported by pairwise F ST values and discriminant analysis of principal components (DAPC), but not by STRUCTURE. We suggest that the mostly low but significant pairwise F ST values in our study are suggestive of fine population structure, which is possibly attributable to behavioral traits such as residency in C. sorrah and site fidelity and philopatry in C. limbatus. However, for all samples obtained from the northern parts of the Gulf (Bahrain and/or Kuwait) in both species, the higher but significant pairwise F ST values could possibly be a result of founder effects during the Tethys Sea closure. Based on DAPC and F ST results, we suggest each population to be treated as independent management unit, as conservation concerns emerge.
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Affiliation(s)
| | - Geremy Cliff
- KwaZulu‐Natal Shark BoardUmhlanga, South Africa and School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Julia L. Y. Spaet
- Department of ZoologyUniversity of CambridgeCambridgeUK
- Red Sea Research CenterDivision of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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Lalis A, Mona S, Stoetzel E, Bonhomme F, Souttou K, Ouarour A, Aulagnier S, Denys C, Nicolas V. Out of Africa: demographic and colonization history of the Algerian mouse (Mus spretus Lataste). Heredity (Edinb) 2018; 122:150-171. [PMID: 29795180 DOI: 10.1038/s41437-018-0089-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 11/09/2022] Open
Abstract
North Africa is now recognized as a major area for the emergence and dispersal of anatomically modern humans from at least 315 kya. The Mediterranean Basin is thus particularly suited to study the role of climate versus human-mediated changes on the evolutionary history of species. The Algerian mouse (Mus spretus Lataste) is an endemic species from this basin, with its distribution restricted to North Africa (from Libya to Morocco), Iberian Peninsula and South of France. A rich paleontological record of M. spretus exists in North Africa, suggesting hypotheses concerning colonization pathways, and the demographic and morphologic history of this species. Here we combined genetic (3 mitochondrial DNA loci and 18 microsatellites) and climatic niche modeling data to infer the evolutionary history of the Algerian mouse. We collected 646 new individuals in 51 localities. Our results are consistent with an anthropogenic translocation of the Algerian mouse from North Africa to the Iberian Peninsula via Neolithic navigators, probably from the Tingitane Peninsula. Once arrived in Spain, suitable climatic conditions would then have favored the dispersion of the Algerian mice to France. The morphological differentiation observed between Spanish, French and North African populations could be explained by a founder effect and possibly local adaptation. This article helps to better understand the role of climate versus human-mediated changes on the evolutionary history of mammal species in the Mediterranean Basin.
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Affiliation(s)
- Aude Lalis
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Emmanuelle Stoetzel
- Histoire Naturelle de l'Homme Préhistorique, HNHP-UMR 7194-CNRS, MNHN, UPVD, Sorbonne Universités, Paris, France
| | - François Bonhomme
- Institut des Sciences de l'Evolution, ISEM-UMR 4554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Karim Souttou
- Department of Agronomy, Faculty of Natural Science and Life, University Ziane Achour, Djelfa, Algeria
| | - Ali Ouarour
- Laboratoire de Biologie et Santé, Faculté des Sciences, Université Abdelmalek Essâadi, Tétouan, Morocco
| | - Stéphane Aulagnier
- Institut National de la Recherche Agronomique, UR35 Comportement et Ecologie de la Faune Sauvage, Caytanet-Tolosan, France
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Paris, France.
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16
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Zhu KC, Liang YY, Wu N, Guo HY, Zhang N, Jiang SG, Zhang DC. Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile). Sci Rep 2017; 7:15299. [PMID: 29127415 PMCID: PMC5681689 DOI: 10.1038/s41598-017-15702-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022] Open
Abstract
To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.
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Affiliation(s)
- Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
- Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Yin-Yin Liang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
| | - Na Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, Guangdong Province, The People's Republic of China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China.
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China.
- Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China.
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Benazzo A, Trucchi E, Cahill JA, Maisano Delser P, Mona S, Fumagalli M, Bunnefeld L, Cornetti L, Ghirotto S, Girardi M, Ometto L, Panziera A, Rota-Stabelli O, Zanetti E, Karamanlidis A, Groff C, Paule L, Gentile L, Vilà C, Vicario S, Boitani L, Orlando L, Fuselli S, Vernesi C, Shapiro B, Ciucci P, Bertorelle G. Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers. Proc Natl Acad Sci U S A 2017; 114:E9589-E9597. [PMID: 29078308 PMCID: PMC5692547 DOI: 10.1073/pnas.1707279114] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes.
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Affiliation(s)
- Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 1066, Norway
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pierpaolo Maisano Delser
- Institute de Systematics, Evolution, Biodiversite, UMR 7205-CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, École Pratique des Hautes Études (EPHE), CP39, 75005 Paris, France
- EPHE, Paris Sciences & Lettres Research University, 75005 Paris, France
- Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Stefano Mona
- Institute de Systematics, Evolution, Biodiversite, UMR 7205-CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, École Pratique des Hautes Études (EPHE), CP39, 75005 Paris, France
- EPHE, Paris Sciences & Lettres Research University, 75005 Paris, France
| | - Matteo Fumagalli
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
| | - Lynsey Bunnefeld
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
- Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
| | - Luca Cornetti
- Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Matteo Girardi
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Lino Ometto
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
- Independent Researcher, 38016 Mezzocorona, Italy
| | - Alex Panziera
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Enrico Zanetti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Alexandros Karamanlidis
- Protection and Management of Wildlife and the Natural Environment, ARCTUROS, 53075 Aetos, Florina, Greece
| | - Claudio Groff
- Forest and Wildlife Service, Provincia Autonoma di Trento, 38100 Trento, Italy
| | - Ladislav Paule
- Department of Phytology, Faculty of Forestry, Technical University, 96053 Zvolen, Slovakia
| | - Leonardo Gentile
- Veterinary Service, National Park of Abruzzo Lazio and Molise, 67032 Pescasseroli, Italy
| | - Carles Vilà
- Department of Integrative Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas, 4102 Seville, Spain
| | - Saverio Vicario
- Institute of Atmospheric Pollution Research and Technologies, National Research Council, 70126 Bari, Italy
| | - Luigi Boitani
- Department of Biology and Biotechnologies "Charles Darwin," University of Rome La Sapienza, 00185 Rome, Italy
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 K Copenhagen, Denmark
| | - Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 San Michele all'Adige, Italy
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin," University of Rome La Sapienza, 00185 Rome, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
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Corrigan S, Maisano Delser P, Eddy C, Duffy C, Yang L, Li C, Bazinet AL, Mona S, Naylor GJ. Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks. Mol Phylogenet Evol 2017; 110:122-126. [DOI: 10.1016/j.ympev.2017.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 02/16/2017] [Accepted: 03/08/2017] [Indexed: 11/26/2022]
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