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Devloo‐Delva F, Burridge CP, Kyne PM, Brunnschweiler JM, Chapman DD, Charvet P, Chen X, Cliff G, Daly R, Drymon JM, Espinoza M, Fernando D, Barcia LG, Glaus K, González‐Garza BI, Grant MI, Gunasekera RM, Hernandez S, Hyodo S, Jabado RW, Jaquemet S, Johnson G, Ketchum JT, Magalon H, Marthick JR, Mollen FH, Mona S, Naylor GJP, Nevill JEG, Phillips NM, Pillans RD, Postaire BD, Smoothey AF, Tachihara K, Tillet BJ, Valerio‐Vargas JA, Feutry P. From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator. Ecol Evol 2023; 13:e9837. [PMID: 36844667 PMCID: PMC9944188 DOI: 10.1002/ece3.9837] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.
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Affiliation(s)
- Floriaan Devloo‐Delva
- Oceans and Atmosphere, CSIROHobartTasmaniaAustralia
- Quantitative Marine Science, Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Christopher P. Burridge
- Discipline of Biological Sciences, School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Peter M. Kyne
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | | | - Demian D. Chapman
- Department of Biological SciencesFlorida International UniversityNorth MiamiFloridaUSA
| | - Patricia Charvet
- Programa de Pós‐graduação em Sistemática, Uso e Conservação da BiodiversidadeUniversidade Federal do Ceará (PPGSis ‐ UFC)FortalezaBrazil
| | - Xiao Chen
- College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
| | - Geremy Cliff
- KwaZulu‐Natal Sharks Board, Umhlanga 4320, South Africa and School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Ryan Daly
- Oceanographic Research Institute, South African Association for Marine Biological Research, PointDurbanSouth Africa
- South African Institute for Aquatic BiodiversityMkhandaSouth Africa
| | - J. Marcus Drymon
- Coastal Research and Extension CenterMississippi State UniversityBiloxiMississippiUSA
- Mississippi‐Alabama Sea Grant ConsortiumOcean SpringsMississippiUSA
| | - Mario Espinoza
- Centro de Investigación en Ciencias del Mar y Limnología & Escuela de BiologíaUniversidad de Costa Rica, San Pedro de Montes de OcaSan JoséCosta Rica
| | | | - Laura Garcia Barcia
- Department of Biological SciencesFlorida International UniversityNorth MiamiFloridaUSA
| | - Kerstin Glaus
- Faculty of Science, Technology and Environment, School of Marine StudiesThe University of the South PacificSuvaFiji
| | | | - Michael I. Grant
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQueenslandAustralia
| | | | - Sebastian Hernandez
- Biomolecular Laboratory, Center for International ProgramsUniversidad VERITASSan JoséCosta Rica
- Sala de Colecciones, Facultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research InstituteUniversity of TokyoKashiwa, ChibaJapan
| | - Rima W. Jabado
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQueenslandAustralia
- Elasmo ProjectDubaiUnited Arab Emirates
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - Grant Johnson
- Department of Industry, Tourism and Trade, Aquatic Resource Research UnitDarwinNorthern TerritoryAustralia
| | | | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - James R. Marthick
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesParisFrance
- EPHEPSL Research UniversityParisFrance
| | - Gavin J. P. Naylor
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | | | - Nicole M. Phillips
- School of Biological, Environmental and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | | | - Bautisse D. Postaire
- UMR ENTROPIE (Université de La Réunion, Université de Nouvelle‐Calédonie, IRD, CNRS, IFREMER), Faculté des Sciences et TechnologiesUniversité de La RéunionCedex 09, La RéunionFrance
| | - Amy F. Smoothey
- NSW Department of Primary Industries, Fisheries ResearchSydney Institute of Marine ScienceMosmanNew South WalesAustralia
| | - Katsunori Tachihara
- Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of ScienceUniversity of Ryukyus, NishiharaOkinawaJapan
| | - Bree J. Tillet
- Translational Research Institute, University of Queensland Diamantina InstituteBrisbaneQueenslandAustralia
| | - Jorge A. Valerio‐Vargas
- Centro de Investigación en Ciencias del Mar y Limnología & Escuela de BiologíaUniversidad de Costa Rica, San Pedro de Montes de OcaSan JoséCosta Rica
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2
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Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès‐Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Mol Ecol 2022; 31:3888-3902. [PMID: 35638312 PMCID: PMC9546496 DOI: 10.1111/mec.16554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long-standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade-specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
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Affiliation(s)
- Mareike C. Janiak
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Felipe E. Silva
- Research Group on Primate Biology and ConservationMamirauá Institute for Sustainable DevelopmentTeféAMBrazil
- Unit of Evolutionary Biology and Ecology (EBE), Département de Biologie des OrganismesUniversité Libre de BruxellesBrusselsBelgium
| | - Robin M. D. Beck
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Dorien de Vries
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Lukas F. K. Kuderna
- Institute of Evolutionary Biology (UPF‐CSIC)BarcelonaUSA
- Present address:
Illumina Artificial Intelligence LaboratoryIllumina Inc.San DiegoCAUSA
| | - Nicole S. Torosin
- Department of GeneticsHuman Genetics Institute of New JerseyRutgers UniversityPiscatawayNew JerseyUSA
| | - Amanda D. Melin
- Department of Anthropology & Archaeology and Department of Medical GeneticsUniversity of CalgaryCalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteCalgaryAlbertaCanada
| | - Tomàs Marquès‐Bonet
- Institute of Evolutionary Biology (UPF‐CSIC)BarcelonaUSA
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de Barcelona, Edifici ICTA‐ICPCerdanyola del Vallès, BarcelonaSpain
| | - Ian B. Goodhead
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Mariluce Messias
- Department of BiologyUniversidade Federal de RondôniaPorto VelhoROBrazil
| | | | | | - Izeni P. Farias
- Laboratory of Evolution and Animal GeneticsUniversidade Federal do AmazonasManausAMBrazil
| | - Rogerio Rossi
- Instituto de BiociênciasUniversidade Federal do Mato GrossoCuiabáMTBrazil
| | - Fabiano R. de Melo
- Department of Forestry EngineeringUniversidade Federal de ViçosaViçosaMGBrazil
| | - João Valsecchi
- Research Group on Primate Biology and ConservationMamirauá Institute for Sustainable DevelopmentTeféAMBrazil
| | - Tomas Hrbek
- Department of BiologyTrinity UniversitySan AntonioTexasUSA
| | - Jean P. Boubli
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
- Coleção de MamíferosInstituto Nacional de Pesquisas da AmazôniaManausAMBrazil
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3
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Raoult V, Grant MI, Barbosa Martins AP, Feitosa LM, Braccini M, Cardeñosa D, Carlson J, Chin A, Curtis T, Carvalho Costa LF, Rodrigues Filho LF, Giarrizzo T, Nunes JLS, Sales JBL, Williamson JE, Simpfendorfer CA. Assigning shark fin origin using species distribution models needs a reality check. Biol Lett 2021; 17:20200907. [PMID: 34256580 PMCID: PMC8278065 DOI: 10.1098/rsbl.2020.0907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Vincent Raoult
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales 2258, Australia
| | - Michael I Grant
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, 1 James Cook Drive, Townsville, Queensland 4811, Australia
| | | | - Leonardo Manir Feitosa
- Bren School of Environmental Science and Management, University of California, Santa Barbara, CA 931117, USA
| | - Matias Braccini
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, PO Box 20, North Beach, Western Australia 6920, Australia
| | - Diego Cardeñosa
- Department of Biological Sciences, Florida International University, 3000 NE 151st Street, North Miami, FL 33181, USA
| | - John Carlson
- NOAA Fisheries Service, Southeast Fisheries Science Center, Panama City, FL 32408, USA
| | - Andrew Chin
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, 1 James Cook Drive, Townsville, Queensland 4811, Australia
| | - Tobey Curtis
- Atlantic Highly Migratory Species Management Division, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Gloucester, MA 01930, USA
| | - Luís Fernando Carvalho Costa
- Departamento de Biologia, Universidade Federal do Maranhão, Avenida dos Portugueses 1966, CEP 65080-805 São Luís, MA, Brazil
| | - Luís Fernando Rodrigues Filho
- Universidade Federal Rural da Amazônia (UFRA), Campus Universitário de Capanema, Rua João Pessoa 121, CEP 68700-030 Capanema, PA, Brazil
| | - Tommaso Giarrizzo
- Núcleo de Ecologia Aquática e Pesca da Amazônia, Universidade Federal do Pará, Avenida Perimetral 2651, Terra Firme, CEP 66040-170 Belém, PA, Brazil
| | - Jorge Luiz S Nunes
- Departamento de Oceanografia e Limnologia, Universidade Federal do Maranhão, Avenida dos Portugueses 1966, CEP 65080-805 São Luís, MA, Brazil
| | - João Bráullio L Sales
- Grupo de Investigação Biologica Integrada (GIBI), Universidade Federal do Pará, Avenida Perimetral da Ciência, Km01, PCT-Guamá, Terreno 11, CEP 66075-750 Belém, PA, Brazil
| | - Jane E Williamson
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Colin A Simpfendorfer
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, 1 James Cook Drive, Townsville, Queensland 4811, Australia
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