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Jarva TM, Phillips NM, Von Eiff C, Poulakis GR, Naylor G, Feldheim KA, Flynt AS. Gene expression, evolution, and the genetics of electrosensing in the smalltooth sawfish, Pristis pectinata. Ecol Evol 2024; 14:e11260. [PMID: 38694751 PMCID: PMC11057056 DOI: 10.1002/ece3.11260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 03/14/2024] [Accepted: 03/28/2024] [Indexed: 05/04/2024] Open
Abstract
Sawfishes (Pristidae) are large, highly threatened rays named for their tooth-studded rostrum, which is used for prey sensing and capture. Of all five species, the smalltooth sawfish, Pristis pectinata, has experienced the greatest decline in range, currently found in only ~20% of its historic range. To better understand the genetic underpinnings of these taxonomically and morphologically unique animals, we collected transcriptomic data from several tissue types, mapped them to the recently completed reference genome, and contrasted the patterns observed with comparable data from other elasmobranchs. Evidence of positive selection was detected in 79 genes in P. pectinata, several of which are involved in growth factor/receptor tyrosine kinase signaling and body symmetry and may be related to the unique morphology of sawfishes. Changes in these genes may impact cellular responses to environmental conditions such as temperature, dissolved oxygen, and salinity. Data acquired also allow for examination of the molecular components of P. pectinata electrosensory systems, which are highly developed in sawfishes and have likely been influential in their evolutionary success.
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Affiliation(s)
- Taiya M. Jarva
- School of Biological, Environmental, and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | - Nicole M. Phillips
- School of Biological, Environmental, and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | - Cory Von Eiff
- School of Biological, Environmental, and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | - Gregg R. Poulakis
- Charlotte Harbor Field LaboratoryFish and Wildlife Research Institute, Florida Fish and Wildlife Conservation CommissionPort CharlotteFloridaUSA
| | - Gavin Naylor
- Florida Program for Shark ResearchUniversity of FloridaGainesvilleFloridaUSA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, the Field MuseumChicagoIllinoisUSA
| | - Alex S. Flynt
- School of Biological, Environmental, and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
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2
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Baeza JA, Stephens NC, Baker A, Lyons A, Franks B, Pirro S, Feldheim KA. Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement. Gene 2024; 894:147939. [PMID: 38572145 PMCID: PMC10990291 DOI: 10.1016/j.gene.2023.147939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.
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Affiliation(s)
- J. Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA
- Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, Chile
| | | | - Alyssa Baker
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Andrew Lyons
- Marine Science Research Institute, Jacksonville University, Florida, USA
| | - Bryan Franks
- Marine Science Research Institute, Jacksonville University, Florida, USA
| | | | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, Chicago, IL, USA
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3
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Swenson JD, Brooks EN, Kacev D, Boyd C, Kinney MJ, Marcy‐Quay B, Sévêque A, Feldheim KA, Komoroske LM. Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments. Ecol Evol 2024; 14:e10854. [PMID: 38327683 PMCID: PMC10847890 DOI: 10.1002/ece3.10854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 01/01/2024] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve the monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding the application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.
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Affiliation(s)
- John D. Swenson
- Department of Environmental ConservationThe University of Massachusetts AmherstAmherstMassachusettsUSA
| | - Elizabeth N. Brooks
- Population Dynamics Branch, Northeast Fisheries Science Center, National Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationWoods HoleMassachusettsUSA
| | - Dovi Kacev
- Marine Biology Research DivisionScripps Institution of OceanographySan DiegoCaliforniaUSA
| | - Charlotte Boyd
- International Union for Conservation of NatureNorth America OfficeWashington DCMarylandUSA
| | - Michael J. Kinney
- NOAA FisheriesPacific Island Fisheries Science CenterHonoluluHawaiiUSA
| | - Benjamin Marcy‐Quay
- Rubenstein Ecosystem Science LaboratoryUniversity of VermontBurlingtonVermontUSA
| | - Anthony Sévêque
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and EvolutionThe Field MuseumChicagoIllinoisUSA
| | - Lisa M. Komoroske
- Department of Environmental ConservationThe University of Massachusetts AmherstAmherstMassachusettsUSA
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4
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Feldheim KA, Dubach J, Watson L. Parthenogenesis in an elasmobranch in the presence of conspecific males. J Fish Biol 2023; 102:525-527. [PMID: 36369968 DOI: 10.1111/jfb.15268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Parthenogenesis has been observed in several elasmobranch species, primarily in public aquaria. The majority of cases of parthenogenesis have occurred either when females were held without males or once a male was removed from a female's habitat. Here we report a second instance of parthenogenesis in a zebra shark female that was housed with conspecific mature males. This study calls into question the conditions under which elasmobranch females undergo parthenogenesis.
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Affiliation(s)
- Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, Chicago, Illinois, USA
| | - Jean Dubach
- Loyola University, Chicago, Health Science Center, Comparative Medicine Facility, Maywood, Illinois, USA
| | - Lise Watson
- John G. Shedd Aquarium, Chicago, Illinois, USA
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5
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Harned SP, Bernard AM, Salinas‐de‐León P, Mehlrose MR, Suarez J, Robles Y, Bessudo S, Ladino F, López Garo A, Zanella I, Feldheim KA, Shivji MS. Genetic population dynamics of the critically endangered scalloped hammerhead shark ( Sphyrna lewini) in the Eastern Tropical Pacific. Ecol Evol 2022; 12:e9642. [PMID: 36619714 PMCID: PMC9797937 DOI: 10.1002/ece3.9642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/17/2022] [Accepted: 11/30/2022] [Indexed: 12/30/2022] Open
Abstract
The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young-of-year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure suggesting that scalloped hammerheads in this ETP region comprise a single genetic stock. Galápagos aggregations of adults were not comprised of related individuals, suggesting that kinship does not play a role in the formation of the repeated, annual gatherings at these remote offshore locations. Despite high levels of fisheries exploitation of this species in the ETP, the adult scalloped hammerheads here showed greater genetic diversity compared with adult conspecifics from other parts of the species' global distribution. A phylogeographic analysis of available, globally sourced, mitochondrial control region sequence data (n = 1818 sequences) revealed that scalloped hammerheads comprise three distinct matrilines corresponding to the three major world ocean basins, highlighting the need for conservation of these evolutionarily unique lineages. This study provides the first view of the genetic properties of a scalloped hammerhead aggregation, and the largest sample size-based investigation of population structure and phylogeography of this species in the ETP to date.
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Affiliation(s)
- Sydney P. Harned
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA
| | - Andrea M. Bernard
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA
| | - Pelayo Salinas‐de‐León
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA,Charles Darwin Research StationCharles Darwin FoundationGalápagos IslandsEcuador
| | - Marissa R. Mehlrose
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA
| | - Jenifer Suarez
- Direccion Parque Nacional GalápagosDepartamento de Ecosistemas MarinosIslas GalápagosEcuador
| | - Yolani Robles
- Universidad de Panamá, Centro Regional Universitario de VeraguasSan Martín de PorresPanama
| | - Sandra Bessudo
- Fundacion Malpelo y Otros Ecosistemas MarinosBogotáColombia
| | - Felipe Ladino
- Fundacion Malpelo y Otros Ecosistemas MarinosBogotáColombia
| | - Andrés López Garo
- Asociación Conservacionista Misión Tiburon, Playas del CocoCarrilloGuanacasteCosta Rica
| | - Ilena Zanella
- Asociación Conservacionista Misión Tiburon, Playas del CocoCarrilloGuanacasteCosta Rica
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and EvolutionField Museum of Natural HistoryChicagoIllinoisUSA
| | - Mahmood S. Shivji
- Save Our Seas Foundation Shark Research Center and Guy Harvey Research InstituteNova Southeastern UniversityDania BeachFloridaUSA
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6
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Cicero C, Mason NA, Oong Z, Title PO, Morales ME, Feldheim KA, Koo MS, Bowie RCK. Deep ecomorphological and genetic divergence in Steller's Jays ( Cyanocitta stelleri, Aves: Corvidae). Ecol Evol 2022; 12:e9517. [PMCID: PMC9712489 DOI: 10.1002/ece3.9517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 12/05/2022] Open
Abstract
The relationship between ecology and morphology is a cornerstone of evolutionary biology, and quantifying variation across environments can shed light on processes that give rise to biodiversity. Three morphotypes of the Steller's Jay (Cyanocitta stelleri) occupy different ecoregions in western North America, which vary in climate and landcover. These morphotypes (Coastal, Interior, Rocky Mountain) differ in size, plumage coloration, and head pattern. We sampled 1080 Steller's Jays from 68 populations (plus 11 outgroups) to address three main questions using data on morphology, plumage, genetics (mtDNA, microsatellites), and ecological niches: (1) How do phenotypic and genetic traits vary within and among populations, morphotypes, and ecoregions? (2) How do population‐level differences in Steller's Jays compare with other sister species pairs of North American birds? (3) What can we infer about the population history of Steller's Jays in relation to past climates, paleoecology, and niche evolution? We found substantial morphological, genetic, and ecological differentiation among morphotypes. The greatest genetic divergence separated Coastal and Interior morphotypes from the Rocky Mountain morphotype, which was associated with warmer, drier, and more open habitats. Microsatellites revealed additional structure between Coastal and Interior groups. The deep mtDNA split between Coastal/Interior and Rocky Mountain lineages of Steller's Jay (ND2 ~ 7.8%) is older than most North American avian sister species and dates to approximately 4.3 mya. Interior and Rocky Mountain morphotypes contact across a narrow zone with steep clines in traits and reduced gene flow. The distribution of the three morphotypes coincides with divergent varieties of ponderosa pine and Douglas fir. Species distribution models support multiple glacial refugia for Steller's Jays. Our integrative dataset combined with extensive geographic sampling provides compelling evidence for recognizing at least two species of Steller's Jay.
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Affiliation(s)
- Carla Cicero
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Nicholas A. Mason
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA,Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisianaUSA
| | - Zheng Oong
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA,Bell Museum of Natural History and Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Pascal O. Title
- Environmental Resilience InstituteIndiana UniversityBloomingtonIndianaUSA,Department of Ecology & EvolutionStony Brook UniversityStony BrookNew YorkUSA
| | - Melissa E. Morales
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Michelle S. Koo
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Rauri C. K. Bowie
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA,Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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7
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Gonzalez C, Postaire B, Domingues RR, Feldheim KA, Caballero S, Chapman D. Phylogeography and population genetics of the cryptic bonnethead shark Sphyrna aff. tiburo in Brazil and the Caribbean inferred from mtDNA markers. J Fish Biol 2021; 99:1899-1911. [PMID: 34476811 DOI: 10.1111/jfb.14896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Resolving the identity, phylogeny and distribution of cryptic species within species complexes is an essential precursor to management. The bonnethead shark, Sphyrna tiburo, is a small coastal shark distributed in the Western Atlantic from North Carolina (U.S.A.) to southern Brazil. Genetic analyses based on mitochondrial markers revealed that bonnethead sharks comprise a species complex with at least two lineages in the Northwestern Atlantic and the Caribbean (S. tiburo and Sphyrna aff. tiburo, respectively). The phylogeographic and phylogenetic analysis of two mitochondrial markers [control region (mtCR) and cytochrome oxidase I (COI)] showed that bonnethead sharks from southeastern Brazil correspond to S. aff. tiburo, extending the distribution of this cryptic species >5000 km. Bonnethead shark populations are only managed in the U.S.A. and in the 2000s were considered to be regionally extinct or collapsed in southeast Brazil. The results indicate that there is significant genetic differentiation between S. aff. tiburo from Brazil and other populations from the Caribbean (ΦST = 0.9053, P < 0.000), which means that collapsed populations in the former are unlikely to be replenished from Caribbean immigration. The species identity of bonnethead sharks in the Southwest Atlantic and their relationship to North Atlantic and Caribbean populations still remains unresolved. Taxonomic revision and further sampling are required to reevaluate the status of the bonnethead shark complex through its distribution range.
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Affiliation(s)
- Cindy Gonzalez
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
| | - Bautisse Postaire
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
| | - Rodrigo R Domingues
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Instituto do Mar, São Paulo, Brazil
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, Chicago, Illinois, USA
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Demian Chapman
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
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8
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Cardeñosa D, Fields AT, Babcock E, Shea SKH, Feldheim KA, Kraft DW, Hutchinson M, Herrera MA, Caballero S, Chapman DD. Indo‐Pacific origins of silky shark fins in major shark fin markets highlights supply chains and management bodies key for conservation. Conserv Lett 2020. [DOI: 10.1111/conl.12780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Diego Cardeñosa
- School of Marine and Atmospheric Science Stony Brook University New York USA
- Fundación Colombia Azul Bogotá Colombia
- Department of Biological Sciences Florida International University North Miami Florida USA
| | - Andrew T. Fields
- School of Marine and Atmospheric Science Stony Brook University New York USA
| | - Elizabeth Babcock
- Rosenstiel School of Marine and Atmospheric Science, Department of Marine Biology and Ecology University of Miami Miami Florida USA
| | | | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution The Field Museum Chicago Illinois USA
| | - Derek W. Kraft
- Hawai‘i Institute of Marine Biology University of Hawai‘i Kane‘ohe Hawaii USA
| | - Melanie Hutchinson
- Hawai‘i Institute of Marine Biology University of Hawai‘i Kane‘ohe Hawaii USA
- Joint Institute for Marine and Atmospheric Research, Pacific Islands Fisheries Science Center, NOAA University of Hawaii Honolulu Hawaii USA
| | - Maria A. Herrera
- Departamento de Ciencias Naturales y Matemáticas Pontificia Universidad Javeriana Cali Colombia
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos – LEMVA Departamento de Ciencias Biológicas Universidad de Los Andes Bogotá Colombia
| | - Demian D. Chapman
- Department of Biological Sciences Florida International University North Miami Florida USA
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9
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Flowers KI, Chapman DD, Kemp T, Wert D, Feldheim KA. Annual breeding in a captive smalltooth sawfish, Pristis pectinata. J Fish Biol 2020; 97:1586-1589. [PMID: 32888190 DOI: 10.1111/jfb.14523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
The critically endangered smalltooth sawfish Pristis pectinata reproduces biennially in central west Florida, U.S.A. Here we demonstrate that smalltooth sawfish are physiologically capable of reproducing annually in a captive environment. The smalltooth sawfish are held in an open system, with abiotic conditions that vary naturally with the surrounding environment in The Bahamas. This suggests wild smalltooth sawfish may also be capable of annual reproduction provided there are adequate prey resources, limited competition and mate availability.
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Affiliation(s)
- Kathryn I Flowers
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Demian D Chapman
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Todd Kemp
- Marine and Aquarium Operations, Atlantis Paradise Island, Paradise Island, The Bahamas
| | - Dave Wert
- Marine and Aquarium Operations, Atlantis Paradise Island, Paradise Island, The Bahamas
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum, Chicago, Illinois, USA
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10
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Cardeñosa D, Fields AT, Babcock EA, Shea SKH, Feldheim KA, Chapman DD. Species composition of the largest shark fin retail-market in mainland China. Sci Rep 2020; 10:12914. [PMID: 32737392 PMCID: PMC7395743 DOI: 10.1038/s41598-020-69555-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/14/2020] [Indexed: 11/30/2022] Open
Abstract
Species-specific monitoring through large shark fin market surveys has been a valuable data source to estimate global catches and international shark fin trade dynamics. Hong Kong and Guangzhou, mainland China, are the largest shark fin markets and consumption centers in the world. We used molecular identification protocols on randomly collected processed fin trimmings (n = 2000) and non-parametric species estimators to investigate the species composition of the Guangzhou retail market and compare the species diversity between the Guangzhou and Hong Kong shark fin retail markets. Species diversity was similar between both trade hubs with a small subset of species dominating the composition. The blue shark (Prionace glauca) was the most common species overall followed by the CITES-listed silky shark (Carcharhinus falciformis), scalloped hammerhead shark (Sphyrna lewini), smooth hammerhead shark (S. zygaena) and shortfin mako shark (Isurus oxyrinchus). Our results support previous indications of high connectivity between the shark fin markets of Hong Kong and mainland China and suggest that systematic studies of other fin trade hubs within Mainland China and stronger law-enforcement protocols and capacity building are needed.
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Affiliation(s)
- Diego Cardeñosa
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY, 11794, USA. .,Fundación Colombia Azul, Bogotá, Colombia.
| | - Andrew T Fields
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Elizabeth A Babcock
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA
| | - Stanley K H Shea
- BLOOM Association, c/o, ADMCF, Suite 2405, Queen's Road Central, Hong Kong, China
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL, 60605, USA
| | - Demian D Chapman
- Department of Biological Sciences, Florida International University, 3000 NE 151st Street, North Miami, FL, 33181, USA
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11
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Castro JC, Maddox JD, Rodríguez HN, Orbe RB, Grandez GE, Feldheim KA, Cobos M, Paredes JD, Castro CG, Marapara JL, Adrianzén PM, Braga J. Metagenomic 16S rDNA amplicon data on bacterial diversity profiling and its predicted metabolic functions of varillales in Allpahuayo-Mishana National Reserve. Data Brief 2020; 30:105625. [PMID: 32382622 PMCID: PMC7201190 DOI: 10.1016/j.dib.2020.105625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 02/01/2023] Open
Abstract
The white-sands forests or varillales of the Peruvian Amazon are characterized by their distinct physical characteristics, patchy distribution, and endemism [1, 2]. Much research has been conducted on the specialized plant and animal communities that inhabit these ecosystems, yet their soil microbiomes have yet to be studied. Here we provide metagenomic 16S rDNA amplicon data of soil microbiomes from three types of varillales in Allpahuayo-Mishana National Reserve near Iquitos, Peru. Composite soil samples were collected from very low varillal, high-dry varillal, and high-wet varillal. Purified metagenomic DNA was used to prepare and sequence 16S rDNA metagenomic libraries on the Illumina MiqSeq platform. Raw paired-endsequences were analyzed using the Metagenomics RAST server (MG-RAST) and Parallel-Meta3 software and revealed the existence of a high percentage of undiscovered sequences, potentially indicating specialized bacterial communities in these forests. Also, were predicted several metabolic functions in this dataset. The raw sequence data in fastq format is available in the public repository Discover Mendeley Data (https://data.mendeley.com/datasets/syktzxcnp6/2). Also, is available at NCBI's Sequence Read Archive (SRA) with accession numbers SRX7891206 (very low varillal), SRX7891207 (high-dry varillal), and SRX7891208 (high-wet varillal).
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Affiliation(s)
- Juan C Castro
- Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Perú
| | - J Dylan Maddox
- Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, Perú.,Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.,Environmental Sciences, American Public University System, Charles Town, WV 25414, USA
| | - Hicler N Rodríguez
- Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Perú.,Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, Perú
| | - Richard B Orbe
- Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Perú
| | - Gad E Grandez
- Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Perú.,Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, Perú
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Marianela Cobos
- Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, Perú
| | - Jae D Paredes
- Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, Perú
| | - Carlos G Castro
- Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Perú.,Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, Perú
| | - Jorge L Marapara
- Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Perú
| | - Pedro M Adrianzén
- Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Perú
| | - Janeth Braga
- Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Perú
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12
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Smukall MJ, Kessel ST, Franks BR, Feldheim KA, Guttridge TL, Gruber SH. No apparent negative tagging effects after 13 years at liberty for lemon shark, Negaprion brevirostris implanted with acoustic transmitter. J Fish Biol 2019; 94:173-177. [PMID: 30393865 DOI: 10.1111/jfb.13856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/25/2018] [Indexed: 06/08/2023]
Abstract
An intact and uncompromised internal acoustic transmitter was non-lethally recovered from a lemon shark Negaprion brevirostris, after 13 years at liberty. The shark, first tagged at an estimated age of 2 years old near South Bimini, Bahamas in 2004, was recaptured in 2017 with a total length of 264 cm. The tagged shark displayed typical growth rate, pregnancy, natal homing and pupping behaviour of other individuals in this population. This observation provides important evidence regarding the effects from long-term retention of implanted acoustic transmitters in a carcharhinid shark.
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Affiliation(s)
- Matthew J Smukall
- Department of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Bimini Biological Field Station Foundation, Bimini, Bahamas
| | - Steven T Kessel
- Bimini Biological Field Station Foundation, Bimini, Bahamas
- Daniel P. Haerther Center for Conservation and Research, Chicago, Illinois, USA
| | - Bryan R Franks
- Bimini Biological Field Station Foundation, Bimini, Bahamas
- Department of Biology and Marine Science, Marine Science Research Institute, Jacksonville University, Jacksonville, Florida, USA
| | - Kevin A Feldheim
- Bimini Biological Field Station Foundation, Bimini, Bahamas
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, Illinois, USA
| | | | - Samuel H Gruber
- Bimini Biological Field Station Foundation, Bimini, Bahamas
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida, USA
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13
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Fields AT, Fischer GA, Shea SKH, Zhang H, Abercrombie DL, Feldheim KA, Babcock EA, Chapman DD. Species composition of the international shark fin trade assessed through a retail-market survey in Hong Kong. Conserv Biol 2018; 32:376-389. [PMID: 29077226 DOI: 10.1111/cobi.13043] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 08/02/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
The shark fin trade is a major driver of shark exploitation in fisheries all over the world, most of which are not managed on a species-specific basis. Species-specific trade information highlights taxa of particular concern and can be used to assess the efficacy of management measures and anticipate emerging threats. The species composition of the Hong Kong Special Administrative Region of China, one of the world's largest fin trading hubs, was partially assessed in 1999-2001. We randomly selected and genetically identified fin trimmings (n = 4800), produced during fin processing, from the retail market of Hong Kong in 2014-2015 to assess contemporary species composition of the fin trade. We used nonparametric species estimators to determine that at least 76 species of sharks, batoids, and chimaeras supplied the fin trade and a Bayesian model to determine their relative proportion in the market. The diversity of traded species suggests species substitution could mask depletion of vulnerable species; one-third of identified species are threatened with extinction. The Bayesian model suggested that 8 species each comprised >1% of the fin trimmings (34.1-64.2% for blue [Prionace glauca], 0.2-1.2% for bull [Carcharhinus leucas] and shortfin mako [Isurus oxyrinchus]); thus, trade was skewed to a few globally distributed species. Several other coastal sharks, batoids, and chimaeras are in the trade but poorly managed. Fewer than 10 of the species we modeled have sustainably managed fisheries anywhere in their range, and the most common species in trade, the blue shark, was not among them. Our study and approach serve as a baseline to track changes in composition of species in the fin trade over time to better understand patterns of exploitation and assess the effects of emerging management actions for these animals.
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Affiliation(s)
| | | | - Stanley K H Shea
- BLOOM Association Hong Kong, Suite 2405, 9 Queens Road, Central, Hong Kong
| | | | - Debra L Abercrombie
- Abercrombie and Fish, 14 Dayton Avenue, Port Jefferson Station, NY 11776, U.S.A
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, U.S.A
| | - Elizabeth A Babcock
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, U.S.A
| | - Demian D Chapman
- Stony Brook University, Stony Brook, NY 11794, U.S.A
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, Miami, FL 33199, U.S.A
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14
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Feldheim KA, Fields AT, Chapman DD, Scharer RM, Poulakis GR. Insights into reproduction and behavior of the smalltooth sawfish Pristis pectinata. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00868] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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da Silva JM, Feldheim KA, Measey GJ, Doucette-Riise S, Daniels RJ, Chauke LF, Tolley KA. Genetic diversity and differentiation of the Western Leopard Toad (Sclerophrys pantherina) based on mitochondrial and microsatellite markers. AFR J HERPETOL 2017. [DOI: 10.1080/21564574.2017.1294115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jessica M. da Silva
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
- Department of Botany & Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - G. John Measey
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Natural Sciences Building, Matieland, Stellenbosch, South Africa
| | - Stephen Doucette-Riise
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 770, Cape Town, South Africa
| | - Ryan J. Daniels
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
| | - Lucas F. Chauke
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
| | - Krystal A. Tolley
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa
- Department of Botany & Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
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16
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Hussey NE, DiBattista JD, Moore JW, Ward EJ, Fisk AT, Kessel S, Guttridge TL, Feldheim KA, Franks BR, Gruber SH, Weideli OC, Chapman DD. Risky business for a juvenile marine predator? Testing the influence of foraging strategies on size and growth rate under natural conditions. Proc Biol Sci 2017; 284:rspb.2017.0166. [PMID: 28381626 DOI: 10.1098/rspb.2017.0166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/09/2017] [Indexed: 11/12/2022] Open
Abstract
Mechanisms driving selection of body size and growth rate in wild marine vertebrates are poorly understood, thus limiting knowledge of their fitness costs at ecological, physiological and genetic scales. Here, we indirectly tested whether selection for size-related traits of juvenile sharks that inhabit a nursery hosting two dichotomous habitats, protected mangroves (low predation risk) and exposed seagrass beds (high predation risk), is influenced by their foraging behaviour. Juvenile sharks displayed a continuum of foraging strategies between mangrove and seagrass areas, with some individuals preferentially feeding in one habitat over another. Foraging habitat was correlated with growth rate, whereby slower growing, smaller individuals fed predominantly in sheltered mangroves, whereas larger, faster growing animals fed over exposed seagrass. Concomitantly, tracked juveniles undertook variable movement behaviours across both the low and high predation risk habitat. These data provide supporting evidence for the hypothesis that directional selection favouring smaller size and slower growth rate, both heritable traits in this shark population, may be driven by variability in foraging behaviour and predation risk. Such evolutionary pathways may be critical to adaptation within predator-driven marine ecosystems.
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Affiliation(s)
- Nigel E Hussey
- University of Windsor - Biological Sciences, Windsor, Ontario, N9B 3P4, Canada
| | - Joseph D DiBattista
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6845, PO Box U1987, Australia
| | - Jonathan W Moore
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Eric J Ward
- Northwest Fisheries Science Center, 2725 Montlake Blvd East, Seattle, WA 98112, USA
| | - Aaron T Fisk
- Great Lakes Institute for Environmental Science, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Steven Kessel
- University of Windsor - Biological Sciences, Windsor, Ontario, N9B 3P4, Canada
| | - Tristan L Guttridge
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, Bahamas
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Bryan R Franks
- Department of Biology, Florida Southern College, Lakeland, FL, USA
| | - Samuel H Gruber
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, Bahamas
| | - Ornella C Weideli
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Universite de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France
| | - Demian D Chapman
- Institute for Ocean Conservation Science/School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
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17
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Feldheim KA, Clews A, Henningsen A, Todorov L, McDermott C, Meyers M, Bradley J, Pulver A, Anderson E, Marshall A. Multiple births by a captive swellshark Cephaloscyllium ventriosum via facultative parthenogenesis. J Fish Biol 2017; 90:1047-1053. [PMID: 27861877 DOI: 10.1111/jfb.13202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
Using a novel set of 12 microsatellites, a captive, adult female swellshark Cephaloscyllium ventriosum that produced five pups via parthenogenesis is described; naturally occurring parthenogenesis has been observed in every vertebrate class with the exception of mammals. As demonstrated in this study, a captive environment is ideal for long-term monitoring of animals under controlled conditions, and easily allows the detection of particular facets of their biology.
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Affiliation(s)
- K A Feldheim
- Field Museum of Natural History, Pritzker Laboratory for Molecular Systematics and Evolution, 1400 S. Lake Shore Drive, Chicago, IL, 60605, U.S.A
| | - A Clews
- National Aquarium, Animal Science and Welfare, Pier 3, 501 E. Pratt Street, Baltimore, MD, 21202, U.S.A
| | - A Henningsen
- National Aquarium, Animal Science and Welfare, Pier 3, 501 E. Pratt Street, Baltimore, MD, 21202, U.S.A
| | - L Todorov
- Field Museum of Natural History, Pritzker Laboratory for Molecular Systematics and Evolution, 1400 S. Lake Shore Drive, Chicago, IL, 60605, U.S.A
| | - C McDermott
- National Aquarium, Animal Science and Welfare, Pier 3, 501 E. Pratt Street, Baltimore, MD, 21202, U.S.A
| | - M Meyers
- National Aquarium, Animal Science and Welfare, Pier 3, 501 E. Pratt Street, Baltimore, MD, 21202, U.S.A
| | - J Bradley
- National Aquarium, Animal Science and Welfare, Pier 3, 501 E. Pratt Street, Baltimore, MD, 21202, U.S.A
| | - A Pulver
- National Aquarium, Animal Science and Welfare, Pier 3, 501 E. Pratt Street, Baltimore, MD, 21202, U.S.A
| | - E Anderson
- National Aquarium, Animal Science and Welfare, Pier 3, 501 E. Pratt Street, Baltimore, MD, 21202, U.S.A
| | - A Marshall
- America's Wildlife Museum & Aquarium, 500 West Sunshine Street, Springfield, MO, 65807, U.S.A
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18
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Fields AT, Feldheim KA, Gelsleichter J, Pfoertner C, Chapman DD. Population structure and cryptic speciation in bonnethead sharks Sphyrna tiburo in the south-eastern U.S.A. and Caribbean. J Fish Biol 2016; 89:2219-2233. [PMID: 27600497 DOI: 10.1111/jfb.13025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/11/2016] [Indexed: 06/06/2023]
Abstract
Population structure and lineage diversification within a small, non-dispersive hammerhead shark species, the bonnethead shark Sphyrna tiburo, was assessed. Sphyrna tiburo is currently described as one continuously distributed species along the Atlantic continental margins of North, Central and South America, but recent genetic analysis of an insular population (Trinidad) suggests the possibility of cryptic speciation. To address this issue S. tiburo were sampled at six sites along c. 6200 km of continuous, continental coastline and from one island location (Grand Bahama) across a discontinuity in their distribution (the Straits of Florida), in order to test if they constitute a single lineage over this distribution. A total of 1030 bp of the mitochondrial control region (CR) was obtained for 239 S. tiburo, revealing 73 distinct haplotypes, high nucleotide diversity (0·01089) and a pair of highly divergent lineages estimated to have separated 3·61-5·62 million years ago. Mitochondrial cytochrome oxidase I and nuclear internal transcribed spacer loci show the same pattern. Divergence is similar within S. tiburo to that observed between established elasmobranch sister species, providing further evidence of cryptic speciation. A global AMOVA based on CR confirms that genetic diversity is primarily partitioned among populations (ΦST = 0·828, P < 0·001) because the divergent lineages are almost perfectly segregated between Belize and North America-The Bahamas. An AMOVA consisting solely of the North American and Bahamian samples is also significantly different from zero (ΦST = 0·088, P < 0·001) and pairwise FST is significantly different between all sites. These findings suggest that S. tiburo comprises a species complex and supports previous research indicating fine population structure, which has implications for fisheries management and biodiversity conservation.
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Affiliation(s)
- A T Fields
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY, 11794, U.S.A..
| | - K A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, U.S.A
| | - J Gelsleichter
- Department of Biology, University of North Florida, 1 UNF Drive, Jacksonville, FL, 32224, U.S.A
| | - C Pfoertner
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY, 11794, U.S.A
| | - D D Chapman
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY, 11794, U.S.A
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19
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da Silva JM, Feldheim KA, Daniels RJ, Edwards S, Tolley KA. Analysis of genetic diversity in Rose’s mountain toadlet (Capensibufo rosei) using novel microsatellite markers. AFR J HERPETOL 2016. [DOI: 10.1080/21564574.2016.1234511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jessica M. da Silva
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Claremont, South Africa
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL, USA
| | - Ryan J. Daniels
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Claremont, South Africa
| | - Shelley Edwards
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Claremont, South Africa
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Krystal A. Tolley
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Claremont, South Africa
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
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20
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Bernard AM, Feldheim KA, Heithaus MR, Wintner SP, Wetherbee BM, Shivji MS. Global population genetic dynamics of a highly migratory, apex predator shark. Mol Ecol 2016; 25:5312-5329. [DOI: 10.1111/mec.13845] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea M. Bernard
- Save Our Seas Shark Research Center Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
| | - Kevin A. Feldheim
- The Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Michael R. Heithaus
- School of Environment and Society Florida International University Miami FL USA
| | - Sabine P. Wintner
- KwaZulu‐Natal Sharks Board Private Bag 2 Umhlanga Rocks 4320 South Africa
- Biomedical Resource Unit University of KwaZulu‐Natal Durban 4000 South Africa
| | - Bradley M. Wetherbee
- Department of Biological Sciences University of Rhode Island Kingston RI USA
- Guy Harvey Research Institute Dania Beach, FL 33004 USA
| | - Mahmood S. Shivji
- Save Our Seas Shark Research Center and Guy Harvey Research Institute Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
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21
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DiBattista JD, Whitney J, Craig MT, Hobbs JPA, Rocha LA, Feldheim KA, Berumen ML, Bowen BW. Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes. Mol Phylogenet Evol 2016; 101:203-215. [DOI: 10.1016/j.ympev.2016.04.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/12/2016] [Accepted: 04/29/2016] [Indexed: 11/27/2022]
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22
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Brooks JL, Guttridge TL, Franks BR, Grubbs RD, Chapman DD, Gruber SH, Dibattista JD, Feldheim KA. Using genetic inference to re-evaluate the minimum longevity of the lemon shark Negaprion brevirostris. J Fish Biol 2016; 88:2067-2074. [PMID: 27060882 DOI: 10.1111/jfb.12943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
A combination of mark-recapture and genetic sampling was used to extend the minimum longevity of an elasmobranch species and the life span estimate of the lemon shark Negaprion brevirostris was increased conservatively from 20·2 to 37 years. This increase in longevity means higher vulnerability and a longer recovery time from exploitation.
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Affiliation(s)
- J L Brooks
- Bimini Biological Field Station Foundation, South Bimini, Bahamas
- Fish Ecology and Conservation Physiology Lab., Carleton Technology and Training Centre, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - T L Guttridge
- Bimini Biological Field Station Foundation, South Bimini, Bahamas
| | - B R Franks
- Department of Biology, Florida Southern College, Lakeland, FL, 33801, U.S.A
| | - R D Grubbs
- FSU Coastal and Marine Laboratory, 3618 Coastal Highway 98, St Teresa, FL, 32358-2702, U.S.A
| | - D D Chapman
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, U.S.A
| | - S H Gruber
- Bimini Biological Field Station Foundation, South Bimini, Bahamas
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, U.S.A
| | - J D Dibattista
- Department of Environment and Agriculture, Curtin University, P. O. Box U1987, Perth, WA 6845, Australia
| | - K A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, U.S.A
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23
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Wogan GO, Feldheim KA, Tsai AS, Brown AA, Kapelke J, Galinato M, Tung JN, Bates JM, Kaliba P, Voelker G, Bowie RC. New genetic resources and a preliminary multi-locus assessment of species boundaries in the Batis capensis species complex (Passeriformes: Platysteridae). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Abstract
Facultative parthenogenesis - the ability of sexually reproducing species to sometimes produce offspring asexually - is known from a wide range of ordinarily sexually reproducing vertebrates in captivity, including some birds, reptiles and sharks [1-3]. Despite this, free-living parthenogens have never been observed in any of these taxa in the wild, although two free-living snakes were recently discovered each gestating a single parthenogen - one copperhead (Agkistrodon contortrix) and one cottonmouth (Agkistrodon piscivorus) [1]. Vertebrate parthenogens are characterized as being of the homogametic sex (e.g., females in sharks, males in birds) and by having elevated homozygosity compared to their mother [1-3], which may reduce their viability [4]. Although it is unknown if either of the parthenogenetic snakes would have been carried to term or survived in the wild, facultative parthenogenesis might have adaptive significance [1]. If this is true, it is reasonable to hypothesize that parthenogenesis would be found most often at low population density, when females risk reproductive failure because finding mates is difficult [5]. Here, we document the first examples of viable parthenogens living in a normally sexually reproducing wild vertebrate, the smalltooth sawfish (Pristis pectinata). We also provide a simple approach to screen any microsatellite DNA database for parthenogens, which will enable hypothesis-driven research on the significance of vertebrate parthenogenesis in the wild.
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Affiliation(s)
- Andrew T Fields
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Gregg R Poulakis
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Charlotte Harbor Field Laboratory, 585 Prineville Street, Port Charlotte, FL 33954, USA
| | - Demian D Chapman
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11794, USA.
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25
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Gledhill KS, Kessel ST, Guttridge TL, Hansell AC, Bester-van der Merwe AE, Feldheim KA, Gruber SH, Chapman DD. Genetic structure, population demography and seasonal occurrence of blacktip shark Carcharhinus limbatus in Bimini, the Bahamas. J Fish Biol 2015; 87:1371-1388. [PMID: 26709212 DOI: 10.1111/jfb.12821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 09/18/2015] [Indexed: 06/05/2023]
Abstract
A longline survey was conducted from 2004 to 2014 to investigate the demographic population structure and seasonal abundance of the blacktip shark Carcharhinus limbatus in the Bimini Islands, the Bahamas. All individuals sampled (n = 242) were sub-adult or adults [70·1-145·1 cm pre-caudal length (LPC) range] with no neonates or YOY recorded in Bimini. Carcharhinus limbatus abundance peaked in September, coincident with the largest ratio of female to male sharks and a peak in fresh mating wounds on females. Mitochondrial control region (mtCR) DNA sequences were obtained from C. limbatus at Bimini to test whether Bimini C. limbatus are most closely related to geographically proximate populations sampled on the south-eastern coast of the U.S.A., the closest known nursery areas for this species. Nine mtCR haplotypes were observed in 32 individuals sampled at Bimini [haplotype diversity (h) = 0·821, nucleotide diversity (π) = 0·0015]. Four haplotypes observed from Bimini matched those previously found in the northern Yucatan (Mexico)-Belize and two matched a haplotype previously found in the U.S.A. Four haplotypes were novel but were closely related to the northern Yucatan-Belizean haplotypes. Pair-wise ΦST analysis showed that Bimini was significantly differentiated from all of the populations previously sampled (U.S.A. Atlantic, U.S.A. Gulf of Mexico, northern Yucatan, Belize and Brazil). This indicates that C. limbatus sampled from Bimini are unlikely from the described, proximate U.S.A. nurseries.
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Affiliation(s)
- K S Gledhill
- South African Shark Conservancy, Old Harbour Museum, Hermanus 7200, South Africa
| | - S T Kessel
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - T L Guttridge
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, Bahamas
| | - A C Hansell
- Department of Fisheries Oceanography, School for Marine Science and Technology, University of Massachusetts - Dartmouth, Fairhaven, MA 02719, U.S.A
| | - A E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - K A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, U.S.A
| | - S H Gruber
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, Bahamas
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL 33124, U.S.A
| | - D D Chapman
- Institute for Ocean Conservation Science/School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, U.S.A
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Wogan GO, Kapelke J, Feldheim KA, Papenfuss TJ, Bowie RC. Isolation and characterization of nine tetranucleoide microsatellite loci for the secretive limbless lizards of the genus Anniella (Anguidae). BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Khan NF, Murdoch KC, Feldheim KA, Marks BD, Cordeiro NJ. Isolation and development of microsatellite loci in an African Woodpecker (Campethera nivosa) using polymerase chain reaction and DNA sequencing. BMC Res Notes 2015; 8:201. [PMID: 26025432 PMCID: PMC4449581 DOI: 10.1186/s13104-015-1165-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Buff-spotted Woodpecker (Campethera nivosa) is a resident bird species that is distributed in lowland rainforest habitats from western to eastern Africa. We developed species-specific microsatellite markers to examine the population genetics of this species. FINDINGS Twenty-one microsatellite loci were isolated from C. nivosa. Of these, 15 were found to amplify consistently. These loci were then tested for variability in 15 individuals from different lowland forest localities. The number of alleles ranged from 3 to 13 per locus, with observed and expected heterozygosity ranging from 0.100 to 0.917 and 0.485 to 0.901, respectively. Four loci exhibited significant heterozygote deficiency while one had an excess of heterozygotes. None of the loci exhibited linkage disequilibrium. CONCLUSION These polymorphic microsatellite markers will be used to study genetic variability in populations of C. nivosa across either sides of the Congo River to evaluate the effect of the river as a barrier to gene flow.
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Affiliation(s)
- Nausheen F Khan
- Department of Biological and Chemical Sciences, Roosevelt University, 430S Michigan Ave, Chicago, USA.
| | - Kellie C Murdoch
- Pritzker Laboratory for Molecular Systematics and Evolution, Integrative Research Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA. .,Gantz Family Collections Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA.
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Integrative Research Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA.
| | - Ben D Marks
- Gantz Family Collections Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA.
| | - Norbert J Cordeiro
- Department of Biological and Chemical Sciences, Roosevelt University, 430S Michigan Ave, Chicago, USA. .,Pritzker Laboratory for Molecular Systematics and Evolution, Integrative Research Center, Field Museum, 1400 S Lake Shore Dr, Chicago, USA.
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Chaves-Fonnegra A, Feldheim KA, Secord J, Lopez JV. Population structure and dispersal of the coral-excavating spongeCliona delitrix. Mol Ecol 2015; 24:1447-66. [DOI: 10.1111/mec.13134] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 02/13/2015] [Accepted: 02/20/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Andia Chaves-Fonnegra
- Nova Southeastern University; Oceanographic Center; 8000 North Ocean Drive Dania Beach FL 33004 USA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution; Field Museum of Natural History; 1400 S Lake Shore Drive Chicago IL 60605 USA
| | - Jesse Secord
- Nova Southeastern University; Oceanographic Center; 8000 North Ocean Drive Dania Beach FL 33004 USA
| | - Jose V. Lopez
- Nova Southeastern University; Oceanographic Center; 8000 North Ocean Drive Dania Beach FL 33004 USA
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O'Leary SJ, Feldheim KA, Fields AT, Natanson LJ, Wintner S, Hussey N, Shivji MS, Chapman DD. Genetic Diversity of White Sharks, Carcharodon carcharias, in the Northwest Atlantic and Southern Africa. J Hered 2015; 106:258-65. [PMID: 25762777 DOI: 10.1093/jhered/esv001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 01/16/2015] [Indexed: 11/12/2022] Open
Abstract
The white shark, Carcharodon carcharias, is both one of the largest apex predators in the world and among the most heavily protected marine fish. Population genetic diversity is in part shaped by recent demographic history and can thus provide information complementary to more traditional population assessments, which are difficult to obtain for white sharks and have at times been controversial. Here, we use the mitochondrial control region and 14 nuclear-encoded microsatellite loci to assess white shark genetic diversity in 2 regions: the Northwest Atlantic (NWA, N = 35) and southern Africa (SA, N = 131). We find that these 2 regions harbor genetically distinct white shark populations (Φ ST = 0.10, P < 0.00001; microsatellite F ST = 0.1057, P < 0.021). M-ratios were low and indicative of a genetic bottleneck in the NWA (M-ratio = 0.71, P < 0.004) but not SA (M-ratio = 0.85, P = 0.39). This is consistent with other evidence showing a steep population decline occurring in the mid to late 20th century in the NWA, whereas the SA population appears to have been relatively stable. Estimates of effective population size ranged from 22.6 to 66.3 (NWA) and 188 to 1998.3 (SA) and evidence of inbreeding was found (primarily in NWA). Overall, our findings indicate that white population dynamics within NWA and SA are determined more by intrinsic reproduction than immigration and there is genetic evidence of a population decline in the NWA, further justifying the strong domestic protective measures that have been taken for this species in this region. Our study also highlights how assessment of genetic diversity can complement other sources of information to better understand the status of threatened marine fish populations.
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Affiliation(s)
- Shannon J O'Leary
- From the School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11394 (O'Leary, Fields, and Chapman); the Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605 (Feldheim); the National Marine Fisheries Service, Apex Predators Program, Narragansett, RI 02882 (Natanson); the KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban 4000, South Africa (Wintner); the Great Lakes Institute for Environmental Research University of Windsor, Windsor, Ontario N9B3P4, Canada (Hussey); the Save our Seas Shark Center and Guy Harvey Research Institute, Nova Southeastern University, FL 33004 (Shivji); and the Institute of Ocean Conservation Science, Stony Brook, NY 11794 (Chapman). shannon.O'
| | - Kevin A Feldheim
- From the School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11394 (O'Leary, Fields, and Chapman); the Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605 (Feldheim); the National Marine Fisheries Service, Apex Predators Program, Narragansett, RI 02882 (Natanson); the KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban 4000, South Africa (Wintner); the Great Lakes Institute for Environmental Research University of Windsor, Windsor, Ontario N9B3P4, Canada (Hussey); the Save our Seas Shark Center and Guy Harvey Research Institute, Nova Southeastern University, FL 33004 (Shivji); and the Institute of Ocean Conservation Science, Stony Brook, NY 11794 (Chapman)
| | - Andrew T Fields
- From the School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11394 (O'Leary, Fields, and Chapman); the Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605 (Feldheim); the National Marine Fisheries Service, Apex Predators Program, Narragansett, RI 02882 (Natanson); the KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban 4000, South Africa (Wintner); the Great Lakes Institute for Environmental Research University of Windsor, Windsor, Ontario N9B3P4, Canada (Hussey); the Save our Seas Shark Center and Guy Harvey Research Institute, Nova Southeastern University, FL 33004 (Shivji); and the Institute of Ocean Conservation Science, Stony Brook, NY 11794 (Chapman)
| | - Lisa J Natanson
- From the School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11394 (O'Leary, Fields, and Chapman); the Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605 (Feldheim); the National Marine Fisheries Service, Apex Predators Program, Narragansett, RI 02882 (Natanson); the KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban 4000, South Africa (Wintner); the Great Lakes Institute for Environmental Research University of Windsor, Windsor, Ontario N9B3P4, Canada (Hussey); the Save our Seas Shark Center and Guy Harvey Research Institute, Nova Southeastern University, FL 33004 (Shivji); and the Institute of Ocean Conservation Science, Stony Brook, NY 11794 (Chapman)
| | - Sabine Wintner
- From the School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11394 (O'Leary, Fields, and Chapman); the Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605 (Feldheim); the National Marine Fisheries Service, Apex Predators Program, Narragansett, RI 02882 (Natanson); the KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban 4000, South Africa (Wintner); the Great Lakes Institute for Environmental Research University of Windsor, Windsor, Ontario N9B3P4, Canada (Hussey); the Save our Seas Shark Center and Guy Harvey Research Institute, Nova Southeastern University, FL 33004 (Shivji); and the Institute of Ocean Conservation Science, Stony Brook, NY 11794 (Chapman)
| | - Nigel Hussey
- From the School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11394 (O'Leary, Fields, and Chapman); the Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605 (Feldheim); the National Marine Fisheries Service, Apex Predators Program, Narragansett, RI 02882 (Natanson); the KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban 4000, South Africa (Wintner); the Great Lakes Institute for Environmental Research University of Windsor, Windsor, Ontario N9B3P4, Canada (Hussey); the Save our Seas Shark Center and Guy Harvey Research Institute, Nova Southeastern University, FL 33004 (Shivji); and the Institute of Ocean Conservation Science, Stony Brook, NY 11794 (Chapman)
| | - Mahmood S Shivji
- From the School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11394 (O'Leary, Fields, and Chapman); the Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605 (Feldheim); the National Marine Fisheries Service, Apex Predators Program, Narragansett, RI 02882 (Natanson); the KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban 4000, South Africa (Wintner); the Great Lakes Institute for Environmental Research University of Windsor, Windsor, Ontario N9B3P4, Canada (Hussey); the Save our Seas Shark Center and Guy Harvey Research Institute, Nova Southeastern University, FL 33004 (Shivji); and the Institute of Ocean Conservation Science, Stony Brook, NY 11794 (Chapman)
| | - Demian D Chapman
- From the School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11394 (O'Leary, Fields, and Chapman); the Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL 60605 (Feldheim); the National Marine Fisheries Service, Apex Predators Program, Narragansett, RI 02882 (Natanson); the KwaZulu-Natal Sharks Board and Biomedical Resource Unit, University of KwaZulu-Natal, Durban 4000, South Africa (Wintner); the Great Lakes Institute for Environmental Research University of Windsor, Windsor, Ontario N9B3P4, Canada (Hussey); the Save our Seas Shark Center and Guy Harvey Research Institute, Nova Southeastern University, FL 33004 (Shivji); and the Institute of Ocean Conservation Science, Stony Brook, NY 11794 (Chapman)
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Malvezzi AJ, Murray CS, Feldheim KA, DiBattista JD, Garant D, Gobler CJ, Chapman DD, Baumann H. A quantitative genetic approach to assess the evolutionary potential of a coastal marine fish to ocean acidification. Evol Appl 2015; 8:352-62. [PMID: 25926880 PMCID: PMC4408146 DOI: 10.1111/eva.12248] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/15/2015] [Indexed: 12/24/2022] Open
Abstract
Assessing the potential of marine organisms to adapt genetically to increasing oceanic CO2 levels requires proxies such as heritability of fitness-related traits under ocean acidification (OA). We applied a quantitative genetic method to derive the first heritability estimate of survival under elevated CO2 conditions in a metazoan. Specifically, we reared offspring, selected from a wild coastal fish population (Atlantic silverside, Menidia menidia), at high CO2 conditions (∼2300 μatm) from fertilization to 15 days posthatch, which significantly reduced survival compared to controls. Perished and surviving offspring were quantitatively sampled and genotyped along with their parents, using eight polymorphic microsatellite loci, to reconstruct a parent–offspring pedigree and estimate variance components. Genetically related individuals were phenotypically more similar (i.e., survived similarly long at elevated CO2 conditions) than unrelated individuals, which translated into a significantly nonzero heritability (0.20 ± 0.07). The contribution of maternal effects was surprisingly small (0.05 ± 0.04) and nonsignificant. Survival among replicates was positively correlated with genetic diversity, particularly with observed heterozygosity. We conclude that early life survival of M. menidia under high CO2 levels has a significant additive genetic component that could elicit an evolutionary response to OA, depending on the strength and direction of future selection.
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Affiliation(s)
- Alex J Malvezzi
- School of Marine and Atmospheric Sciences, Stony Brook University Stony Brook, NY, USA
| | | | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History Chicago, IL, USA
| | - Joseph D DiBattista
- Red Sea Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Dany Garant
- Département de Biologie, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University Stony Brook, NY, USA
| | - Demian D Chapman
- School of Marine and Atmospheric Sciences, Stony Brook University Stony Brook, NY, USA
| | - Hannes Baumann
- Department of Marine Sciences, University of Connecticut Groton, CT, USA
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Chapman DD, Feldheim KA, Papastamatiou YP, Hueter RE. There and back again: a review of residency and return migrations in sharks, with implications for population structure and management. Ann Rev Mar Sci 2015; 7:547-70. [PMID: 25251267 DOI: 10.1146/annurev-marine-010814-015730] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The overexploitation of sharks has become a global environmental issue in need of a comprehensive and multifaceted management response. Tracking studies are beginning to elucidate how shark movements shape the internal dynamics and structure of populations, which determine the most appropriate scale of these management efforts. Tracked sharks frequently either remain in a restricted geographic area for an extended period of time (residency) or return to a previously resided-in area after making long-distance movements (site fidelity). Genetic studies have shown that some individuals of certain species preferentially return to their exact birthplaces (natal philopatry) or birth regions (regional philopatry) for either parturition or mating, even though they make long-distance movements that would allow them to breed elsewhere. More than 80 peer-reviewed articles, constituting the majority of published shark tracking and population genetic studies, provide evidence of at least one of these behaviors in a combined 31 shark species from six of the eight extant orders. Residency, site fidelity, and philopatry can alone or in combination structure many coastal shark populations on finer geographic scales than expected based on their potential for dispersal. This information should therefore be used to scale and inform assessment, management, and conservation activities intended to restore depleted shark populations.
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Affiliation(s)
- Demian D Chapman
- Institute for Ocean Conservation Science and School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000;
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Bernard AM, Shivji MS, Prince ED, Hazin FHV, Arocha F, Domingo A, Feldheim KA. Comparative population genetics and evolutionary history of two commonly misidentified billfishes of management and conservation concern. BMC Genet 2014; 15:141. [PMID: 25494814 PMCID: PMC4278234 DOI: 10.1186/s12863-014-0141-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/01/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Misidentifications between exploited species may lead to inaccuracies in population assessments, with potentially irreversible conservation ramifications if overexploitation of either species is occurring. A notable showcase is provided by the realization that the roundscale spearfish (Tetrapturus georgii), a recently validated species, has been historically misidentified as the morphologically very similar and severely overfished white marlin (Kajikia albida) (IUCN listing: Vulnerable). In effect, no information exists on the population status and evolutionary history of the enigmatic roundscale spearfish, a large, highly vagile and broadly distributed pelagic species. We provide the first population genetic evaluation of the roundscale spearfish, utilizing nuclear microsatellite and mitochondrial DNA sequence markers. Furthermore, we re-evaluated existing white marlin mitochondrial genetic data and present our findings in a comparative context to the roundscale spearfish. RESULTS Microsatellite and mitochondrial (control region) DNA markers provided mixed evidence for roundscale spearfish population differentiation between the western north and south Atlantic regions, depending on marker-statistical analysis combination used. Mitochondrial DNA analyses provided strong signals of historical population growth for both white marlin and roundscale spearfish, but higher genetic diversity and effective female population size (1.5-1.9X) for white marlin. CONCLUSIONS The equivocal indications of roundscale spearfish population structure, combined with a smaller effective female population size compared to the white marlin, already a species of concern, suggests that a species-specific and precautionary management strategy recognizing two management units is prudent for this newly validated billfish.
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Affiliation(s)
- Andrea M Bernard
- The Guy Harvey Research Institute, Oceanographic Center, Nova Southeastern University, 8000 N. Ocean Drive, Dania Beach, FL, 33004, USA.
| | - Mahmood S Shivji
- The Guy Harvey Research Institute, Oceanographic Center, Nova Southeastern University, 8000 N. Ocean Drive, Dania Beach, FL, 33004, USA.
| | - Eric D Prince
- National Marine Fisheries Service, Southeast Fisheries Science Center, 75 Virginia Beach Drive, Miami, FL, 33149, USA.
| | - Fabio H V Hazin
- Departamento de Pesca e Aquicultura, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-032, Brazil.
| | - Freddy Arocha
- Instituto Oceanográfico de Venezuela, Universidad de Oriente, Apartado de Correos, 204, Cumaná, 6101, Venezuela.
| | - Andres Domingo
- Laboratorio de Recursos Pelágicos, Dirección Nacional de Recursos Acuáticos, Constituyente 1497, Montevideo, CP, 11200, Uruguay.
| | - Kevin A Feldheim
- The Field Museum of Natural History, Pritzker Laboratory for Molecular Systematics and Evolution, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.
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Feldheim KA, Kreiser BR, Schmidt B, Duvernell DD, Schaefer JF. Isolation and characterization of microsatellite loci for the blackstripe topminnow Fundulus notatus and their variability in two closely related species. J Fish Biol 2014; 85:1726-1732. [PMID: 25123486 DOI: 10.1111/jfb.12469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 06/05/2014] [Indexed: 06/03/2023]
Abstract
A total of 17 polymorphic microsatellite loci were isolated from the blackstripe topminnow Fundulus notatus. In a sample of 29 individuals, these loci were found to possess two to 19 alleles with expected heterozygosity values ranging from 0.212 to 0.919 and all but one of the loci conformed to Hardy-Weinberg equilibrium expectations. Many of these loci were polymorphic in the closely related species Fundulus olivaceus and Fundulus euryzonus providing a set of markers that should prove useful in future ecological and evolutionary studies of members of this species complex.
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Affiliation(s)
- K A Feldheim
- The Field Museum of Natural History, Pritzker Laboratory for Molecular Systematics and Evolution, 1400 S. Lake Shore Drive, Chicago, IL 60605, U.S.A
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Tolley KA, Daniels RJ, Feldheim KA. Characterisation of microsatellite markers in the Spotted Sand Lizard (Pedioplanis lineoocellata) shows low levels of inbreeding and moderate genetic diversity on a small spatial scale. AFR J HERPETOL 2014. [DOI: 10.1080/21564574.2014.893927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Harrison HB, Feldheim KA, Jones GP, Ma K, Mansour H, Perumal S, Williamson DH, Berumen ML. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae). Ecol Evol 2014; 4:2046-57. [PMID: 25360247 PMCID: PMC4201420 DOI: 10.1002/ece3.1002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 11/29/2022] Open
Abstract
Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent–offspring relationships in natural populations, with over 99.6% accuracy in parent–offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28–96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.
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Affiliation(s)
- Hugo B Harrison
- Centre of Excellence for Coral Reef Studies, James Cook University Townsville, Queensland, 4811, Australia
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum 1400 S. Lake Shore Drive, Chicago, 60605, Illinois
| | - Geoffrey P Jones
- Centre of Excellence for Coral Reef Studies, James Cook University Townsville, Queensland, 4811, Australia ; School of Marine and Tropical Biology, James Cook University Townsville, Queensland, 4811, Australia
| | - Kayan Ma
- School of Marine and Tropical Biology, James Cook University Townsville, Queensland, 4811, Australia
| | - Hicham Mansour
- Biosciences Core Laboratory, King Abdullah University of Science and Technology 23955-6900, Thuwal, Saudi Arabia
| | - Sadhasivam Perumal
- Biosciences Core Laboratory, King Abdullah University of Science and Technology 23955-6900, Thuwal, Saudi Arabia
| | - David H Williamson
- Centre of Excellence for Coral Reef Studies, James Cook University Townsville, Queensland, 4811, Australia
| | - Michael L Berumen
- Red Sea Research Center, King Abdullah University of Science and Technology 23955-6900, Thuwal, Saudi Arabia
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Affiliation(s)
- Krystal A. Tolley
- Applied Biodiversity Research Division, South African National Biodiversity Institute, Cape Town, South Africa
- Department of Botany & Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Lucas F. Chauke
- Applied Biodiversity Research Division, South African National Biodiversity Institute, Cape Town, South Africa
| | - Jennifer C. Jackson
- Department of Botany & Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, IL, USA
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Wirshing HH, Feldheim KA, Baker AC. Vectored dispersal of Symbiodinium by larvae of a Caribbean gorgonian octocoral. Mol Ecol 2014; 22:4413-32. [PMID: 23980762 DOI: 10.1111/mec.12405] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 11/28/2022]
Abstract
The ability of coral reefs to recover from natural and anthropogenic disturbance is difficult to predict, in part due to uncertainty regarding the dispersal capabilities and connectivity of their reef inhabitants. We developed microsatellite markers for the broadcast spawning gorgonian octocoral Eunicea (Plexaura) flexuosa (four markers) and its dinoflagellate symbiont, Symbiodinium B1 (five markers), and used them to assess genetic connectivity, specificity and directionality of gene flow among sites in Florida, Panama, Saba and the Dominican Republic. Bayesian analyses found that most E. flexuosa from the Florida reef tract, Saba and the Dominican Republic were strongly differentiated from many E. flexuosa in Panama, with the exception of five colonies from Key West that clustered with colonies from Panama. In contrast, Symbiodinium B1 was more highly structured. At least seven populations were detected that showed patterns of isolation by distance. The symbionts in the five unusual Key West colonies also clustered with symbionts from Panama, suggesting these colonies are the result of long-distance dispersal. Migration rate tests indicated a weak signal of northward immigration from the Panama population into the lower Florida Keys. As E. flexuosa clonemates only rarely associated with the same Symbiodinium B1 genotype (and vice versa), these data suggest a dynamic host-symbiont relationship in which E. flexuosa is relatively well dispersed but likely acquires Symbiodinium B1 from highly structured natal areas prior to dispersal. Once vectored by host larvae, these symbionts may then spread through the local population, and/or host colonies may acquire different local symbiont genotypes over time.
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Affiliation(s)
- Herman H Wirshing
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbaker Causeway, Miami, FL 33149, USA.
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Feldheim KA, Gruber SH, DiBattista JD, Babcock EA, Kessel ST, Hendry AP, Pikitch EK, Ashley MV, Chapman DD. Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks. Mol Ecol 2013; 23:110-7. [DOI: 10.1111/mec.12583] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/25/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution; Field Museum of Natural History; 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Samuel H. Gruber
- Division of Marine Biology and Fisheries; Rosenstiel School of Marine and Atmospheric Science; 4600 Rickenbacker Causeway Miami FL 33149 USA
- Bimini Biological Field Station Foundation; Miami FL 33176 USA
| | - Joseph D. DiBattista
- Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Saudi Arabia
| | - Elizabeth A. Babcock
- Division of Marine Biology and Fisheries; Rosenstiel School of Marine and Atmospheric Science; 4600 Rickenbacker Causeway Miami FL 33149 USA
| | - Steven T. Kessel
- Great Lakes Institute for Environmental Research; 401 Sunset Avenue Windsor ON N9B 3P4 Canada
| | - Andrew P. Hendry
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke Street West Montréal QC H3A 2K6 Canada
| | - Ellen K. Pikitch
- Institute for Ocean Conservation Science/School of Marine and Atmospheric Sciences; Stony Brook University; Stony Brook NY 11794-5000 USA
| | - Mary V. Ashley
- Department of Biological Sciences; University of Illinois at Chicago; 845 West Taylor Street Chicago IL 60608 USA
| | - Demian D. Chapman
- Institute for Ocean Conservation Science/School of Marine and Atmospheric Sciences; Stony Brook University; Stony Brook NY 11794-5000 USA
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O'Leary SJ, Hice LA, Feldheim KA, Frisk MG, McElroy AE, Fast MD, Chapman DD. Severe inbreeding and small effective number of breeders in a formerly abundant marine fish. PLoS One 2013; 8:e66126. [PMID: 23762473 PMCID: PMC3676343 DOI: 10.1371/journal.pone.0066126] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/01/2013] [Indexed: 12/04/2022] Open
Abstract
In contrast to freshwater fish it is presumed that marine fish are unlikely to spawn with close relatives due to the dilution effect of large breeding populations and their propensity for movement and reproductive mixing. Inbreeding is therefore not typically a focal concern of marine fish management. We measured the effective number of breeders in 6 New York estuaries for winter flounder (Pseudopleuronectes americanus), a formerly abundant fish, using 11 microsatellite markers (6–56 alleles per locus). The effective number of breeders for 1–2 years was remarkably small, with point estimates ranging from 65–289 individuals. Excess homozygosity was detected at 10 loci in all bays (FIS = 0.169–0.283) and individuals exhibited high average internal relatedness (IR; mean = 0.226). These both indicate that inbreeding is very common in all bays, after testing for and ruling out alternative explanations such as technical and sampling artifacts. This study demonstrates that even historically common marine fish can be prone to inbreeding, a factor that should be considered in fisheries management and conservation plans.
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Affiliation(s)
- Shannon J O'Leary
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, New York, United States of America.
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O’Leary SJ, Feldheim KA, Chapman DD. Novel microsatellite loci for winter flounder (Pseudopleuronectus americanus). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-012-9854-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Oatley G, Feldheim KA, Voelker G, Bowie RCK. Development of twelve tetranucleotide microsatellite loci for White-eyes (Zosterops spp.) for use in phylogeographic and hybridization studies. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9947-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Chapman DD, Wintner SP, Abercrombie DL, Ashe J, Bernard AM, Shivji MS, Feldheim KA. The behavioural and genetic mating system of the sand tiger shark, Carcharias taurus, an intrauterine cannibal. Biol Lett 2013; 9:20130003. [PMID: 23637391 DOI: 10.1098/rsbl.2013.0003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sand tiger sharks (Carcharias taurus) have an unusual mode of reproduction, whereby the first embryos in each of the paired uteri to reach a certain size ('hatchlings') consume all of their smaller siblings during gestation ('embryonic cannibalism' or EC). If females commonly mate with multiple males ('behavioural polyandry') then litters could initially have multiple sires. It is possible, however, that EC could exclude of all but one of these sires from producing offspring thus influencing the species genetic mating system ('genetic monogamy'). Here, we use microsatellite DNA profiling of mothers and their litters (n = 15, from two to nine embryos per litter) to quantify the frequency of behavioural and genetic polyandry in this system. We conservatively estimate that nine of the females we examined (60%) were behaviourally polyandrous. The genetic mating system was characterized by assessing sibling relationships between hatchlings and revealed only 40 per cent genetic polyandry (i.e. hatchlings were full siblings in 60% of litters). The discrepancy stemmed from three females that were initially fertilized by multiple males but only produced hatchlings with one of them. This reveals that males can be excluded even after fertilizing ova and that some instances of genetic monogamy in this population arise from the reduction in litter size by EC. More research is needed on how cryptic post-copulatory and post-zygotic processes contribute to determining paternity and bridging the behavioural and genetic mating systems of viviparous species.
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Affiliation(s)
- Demian D Chapman
- School of Marine and Atmospheric Science, Institute for Ocean Conservation Science, Stony Brook University, Stony Brook, NY 11794, USA.
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Chapman DD, Frisk MG, Abercrombie DL, Safina C, Gruber SH, Babcock EA, Feldheim KA, Pikitch EK, Ward-Paige C, Davis B, Kessel S, Heithaus M, Worm B. Give shark sanctuaries a chance. Science 2013; 339:757. [PMID: 23413336 DOI: 10.1126/science.339.6121.757-a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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O’Leary SJ, Feldheim KA, Chapman DD. Novel microsatellite loci for white, Carcharodon carcharias and sandtiger sharks, Carcharias taurus (order Lamniformes). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9866-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bernard AM, Feldheim KA, Shivji MS. Development and characterization of 11 novel microsatellite loci for the roundscale spearfish Tetrapturus georgii and their cross-species amplification among other istiophorid species. J Fish Biol 2012; 81:1781-1786. [PMID: 23020576 DOI: 10.1111/j.1095-8649.2012.03442.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Eleven novel polymorphic microsatellite loci were developed and characterized for the recently validated roundscale spearfish Tetrapturus georgii. Characterization of these markers, based on 35 roundscale spearfish from the western North Atlantic, revealed two to 21 alleles per locus with an average expected heterozygosity (H(E) ) of 0·09-0·94, and all loci conformed to Hardy-Weinberg expectations. Cross-amplification of these 11 loci against all other eight known istiophorid species indicates promising prospects for the utility of these markers for istiophorids in general.
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Affiliation(s)
- A M Bernard
- Guy Harvey Research Institute, Oceanographic Center, Nova Southeastern University, Dania Beach, FL 33004, USA
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DiBattista JD, Rocha LA, Craig MT, Feldheim KA, Bowen BW. Phylogeography of two closely related Indo-Pacific butterflyfishes reveals divergent evolutionary histories and discordant results from mtDNA and microsatellites. ACTA ACUST UNITED AC 2012; 103:617-29. [PMID: 22888133 DOI: 10.1093/jhered/ess056] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Marine biogeographic barriers can have unpredictable consequences, even among closely related species. To resolve phylogeographic patterns for Indo-Pacific reef fauna, we conducted range-wide surveys of sister species, the scrawled butterflyfish (Chaetodon meyeri; N = 134) and the ornate butterflyfish (Chaetodon ornatissimus; N = 296), using mitochondrial DNA cytochrome b sequences and 10 microsatellite loci. The former is distributed primarily in the Indian Ocean but also extends to the Line Islands in the Central Pacific, whereas the latter is distributed primarily in the Central-West Pacific (including Hawaii and French Polynesia) but extends to the eastern margin of the Indian Ocean. Analyses of molecular variance and Bayesian STRUCTURE results revealed 1 range-wide group for C. meyeri and 3 groups for C. ornatissimus: 1) eastern Indian Ocean and western Pacific, 2) Central Pacific, and 3) Hawaii. Estimates of the last population expansion were much more recent for C. meyeri (61 500 to 95 000 years) versus C. ornatissimus (184 700 to 286 300 years). Despite similarities in ecology, morphology, life history, and a broadly overlapping distribution, these sister species have divergent patterns of dispersal and corresponding evolutionary history. The mtDNA and microsatellite markers did not provide concordant results within 1 of our study species (C. meyeri), or in 7 out of 12 other cases of marine fishes in the published literature. This discordance renews caution in relying on one or a few markers for reconstructing historical demography.
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Harrison HB, Williamson DH, Evans RD, Almany GR, Thorrold SR, Russ GR, Feldheim KA, van Herwerden L, Planes S, Srinivasan M, Berumen ML, Jones GP. Larval Export from Marine Reserves and the Recruitment Benefit for Fish and Fisheries. Curr Biol 2012; 22:1023-8. [PMID: 22633811 DOI: 10.1016/j.cub.2012.04.008] [Citation(s) in RCA: 363] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/04/2012] [Accepted: 04/04/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Hugo B Harrison
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia.
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Chapman DD, Simpfendorfer CA, Wiley TR, Poulakis GR, Curtis C, Tringali M, Carlson JK, Feldheim KA. Genetic diversity despite population collapse in a critically endangered marine fish: the smalltooth sawfish (Pristis pectinata). ACTA ACUST UNITED AC 2011; 102:643-52. [PMID: 21926063 DOI: 10.1093/jhered/esr098] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sawfish (family Pristidae) are among the most critically endangered marine fish in the world, yet very little is known about how genetic bottlenecks, genetic drift, and inbreeding depression may be affecting these elasmobranchs. In the US Atlantic, the smalltooth sawfish (Pristis pectinata) has declined to 1-5% of its abundance in the 1900s, and its core distribution has contracted to southwest Florida. We used 8 polymorphic microsatellite markers to show that this remnant population still exhibits high genetic diversity in terms of average allelic richness (18.23), average alleles per locus (18.75, standard deviation [SD] 6.6) and observed heterozygosity (0.43-0.98). Inbreeding is rare (mean individual internal relatedness = -0.02, SD 0.14; F(IS) = -0.011, 95% confidence interval [CI] = -0.039 to 0.011), even though the estimated effective population size (N(e)) is modest (250-350, 95% CI = 142-955). Simulations suggest that the remnant smalltooth sawfish population will probably retain >90% of its current genetic diversity over the next century even at the lower estimate of N(e). There is no evidence of a genetic bottleneck accompanying last century's demographic bottleneck, and we discuss hypotheses that could explain this. We also discuss features of elasmobranch life history and population biology that could make them less vulnerable than other large marine vertebrates to genetic change associated with reduced population size.
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Affiliation(s)
- Demian D Chapman
- Institute for Ocean Conservation Science & School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY 11794, USA.
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Keirle MR, Avis PG, Feldheim KA, Hemmes DE, Mueller GM. Investigating the Allelic Evolution of an Imperfect Microsatellite Locus in the Hawaiian Mushroom Rhodocollybia laulaha. J Hered 2011; 102:727-34. [DOI: 10.1093/jhered/esr099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ribeiro AM, Lloyd P, Feldheim KA, Bowie RCK. Microgeographic socio-genetic structure of an African cooperative breeding passerine revealed: integrating behavioural and genetic data. Mol Ecol 2011; 21:662-72. [PMID: 21883586 DOI: 10.1111/j.1365-294x.2011.05236.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Dispersal can be motivated by multiple factors including sociality. Dispersal behaviour affects population genetic structure that in turn reinforces social organization. We combined observational information with individual-based genetic data in the Karoo scrub-robin, a facultative cooperatively breeding bird, to understand how social bonds within familial groups affect mating patterns, cause sex asymmetry in dispersal behaviour and ultimately influence the evolution of dispersal. Our results revealed that males and females do not have symmetrical roles in structuring the population. Males are extremely philopatric and tend to delay dispersal until they gain a breeding position within a radius of two territories around the natal site. By contrast, females dispersed over larger distances, as soon as they reach independence. This resulted in male neighbourhoods characterized by high genetic relatedness. The long-distance dispersal strategy of females ensured that Karoo scrub-robins do not pair with relatives thereby compensating for male philopatry caused by cooperation. The observed female-biased strategy seems to be the most prominent mechanism to reduce the risk of inbreeding that characterizes social breeding system. This study demonstrates that tying together ecological data, such as breeding status, determining social relationships with genetic data, such as kinship, provides valuable insights into the proximate causes of dispersal, which are central to any evolutionary interpretation.
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Affiliation(s)
- A M Ribeiro
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.
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