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Jiménez‐Mena B, Flávio H, Henriques R, Manuzzi A, Ramos M, Meldrup D, Edson J, Pálsson S, Ásta Ólafsdóttir G, Ovenden JR, Nielsen EE. Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits. Mol Ecol Resour 2022; 22:2105-2119. [PMID: 35178874 PMCID: PMC9313901 DOI: 10.1111/1755-0998.13598] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 11/27/2022]
Abstract
Targeted sequencing is an increasingly popular next-generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.
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Affiliation(s)
- Belén Jiménez‐Mena
- Section for Marine Living Resources, National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Hugo Flávio
- Section for Marine Living Resources, National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Romina Henriques
- Section for Marine Living Resources, National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Alice Manuzzi
- Section for Marine Living Resources, National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Dorte Meldrup
- Section for Marine Living Resources, National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Janette Edson
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental SciencesUniversity of IcelandReykjavíkIceland
| | | | - Jennifer R. Ovenden
- Molecular Fisheries Laboratory, School of Biomedical SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - Einar Eg Nielsen
- Section for Marine Living Resources, National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
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2
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Taboun ZS, Walter RP, Ovenden JR, Heath DD. Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure. Evol Appl 2021; 14:1286-1300. [PMID: 34025768 PMCID: PMC8127707 DOI: 10.1111/eva.13198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/01/2022] Open
Abstract
Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3-5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only 1 year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects population genetics. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment-related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.
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Affiliation(s)
- Zahra S. Taboun
- Great Lakes Institute for Environmental Research (GLIER)University of WindsorWindsorOntarioCanada
| | - Ryan P. Walter
- Department of Biological ScienceCalifornia State University, FullertonFullertonCAUSA
| | - Jennifer R. Ovenden
- Molecular Fisheries LaboratorySchool of Biomedical SciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research (GLIER)University of WindsorWindsorOntarioCanada
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
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3
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Krueck NC, Treml EA, Innes DJ, Ovenden JR. Ocean currents and the population genetic signature of fish migrations. Ecology 2020; 101:e02967. [PMID: 31925790 DOI: 10.1002/ecy.2967] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 10/04/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022]
Abstract
Animal migrations are a fascinating and global phenomenon, yet they are often difficult to study and sometimes poorly understood. Here, we build on classic ecological theory by hypothesizing that some enigmatic spawning migrations across coastal marine habitats can be inferred from the population genetic signature of larval dispersal by ocean currents. We test this assumption by integrating spatially realistic simulations of alternative spawning migration routes, associated patterns of larval dispersal, and associated variation in the population genetic structure of eastern Australian sea mullet (Mugil cephalus). We then use simulation results to assess the implications of alternative spawning destinations for larval replenishment, and we contrast simulated against measured population genetic variation. Both analyses suggest that the spawning migrations of M. cephalus in eastern Australia are likely to be localized (approximately 100 km along the shore), and that spawning is likely to occur in inshore waters. Our conclusions are supported by multiple lines of evidence available through independent studies, but they challenge the more traditional assumption of a single, long-distance migration event with subsequent offshore spawning in the East Australian Current. More generally, our study operationalizes classic theory on the relationship between fish migrations, ocean currents, and reproductive success. However, rather than confirming the traditionally assumed adaptation of migratory behavior to dominant ocean current flow, our findings support the concept of a genetically measurable link between fish migrations and local oceanographic conditions, specifically water temperature and coastal retention of larvae. We believe that future studies using similar approaches for high resolution and spatially realistic ecological-genetic scenario testing can help rapidly advance our understanding of key ecological processes in many other marine species.
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Affiliation(s)
- Nils C Krueck
- School of Biological Sciences, University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia.,Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Eric A Treml
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, 3216, Australia
| | - David J Innes
- Department of Agriculture and Fisheries, Queensland Government, P.O. Box 6097, Brisbane, Queensland, 4072, Australia
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
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4
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Armstrong AJ, Dudgeon CL, Bustamante C, Bennett MB, Ovenden JR. Development and characterization of 17 polymorphic microsatellite markers for the reef manta ray (Mobula alfredi). BMC Res Notes 2019; 12:233. [PMID: 31010433 PMCID: PMC6477734 DOI: 10.1186/s13104-019-4270-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/15/2019] [Indexed: 11/30/2022] Open
Abstract
Objective Limited sample sizes are often a problem for species of conservation concern when using genetic tools to make population assessments. Lack of analytical power from small sample sizes can be compensated for by use of a large marker set. Here we report on development and characterization of 17 novel microsatellite markers for the reef manta ray (Mobula alfredi). Results Loci were screened on 60 reef manta rays (M. alfredi) sampled from the east coast of Australia. The number of alleles per locus varied from 2 to 13 with observed heterozygosities ranging between 0.300 and 0.917. The development of these 17 additional markers increases the total number of microsatellite markers available for this species to 27.
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Affiliation(s)
- Amelia J Armstrong
- School of Biomedical Science, The University of Queensland, Brisbane, Australia.
| | - Christine L Dudgeon
- School of Biomedical Science, The University of Queensland, Brisbane, Australia
| | - Carlos Bustamante
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
| | - Michael B Bennett
- School of Biomedical Science, The University of Queensland, Brisbane, Australia
| | - Jennifer R Ovenden
- School of Biomedical Science, The University of Queensland, Brisbane, Australia
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5
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Blower DC, Riginos C, Ovenden JR. neogen: A tool to predict genetic effective population size (N e ) for species with generational overlap and to assist empirical N e study design. Mol Ecol Resour 2018; 19:260-271. [PMID: 30194750 DOI: 10.1111/1755-0998.12941] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 12/14/2017] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 12/17/2022]
Abstract
Molecular genetic estimates of population effective size (Ne ) lose accuracy and precision when insufficient numbers of samples or loci are used. Ideally, researchers would like to forecast the necessary power when planning their project. neogen (genetic Ne for Overlapping Generations) enables estimates of precision and accuracy in advance of empirical investigation and allows exploration of the power available in different user-specified age-structured sampling schemes. neogen provides a population simulation and genetic power analysis framework that simulates the demographics, genetic composition, and Ne , from species-specific life history, mortality, population size, and genetic priors. neogen guides the user to establish a tractable sampling regime and to determine the numbers of samples and microsatellite or SNP loci required for accurate and precise genetic Ne estimates when sampling a natural population. neogen is useful at multiple stages of a study's life cycle: when budgeting, as sampling and locus development progresses, and for corroboration when empirical Ne estimates are available. The underlying model is applicable to a wide variety of iteroparous species with overlapping generations (e.g., mammals, birds, reptiles, long-lived fishes). In this paper, we describe the neogen model, detail the workflow for the point-and-click software, and explain the graphical results. We demonstrate the use of neogen with empirical Australian east coast zebra shark (Stegostoma fasciatum) data. For researchers wishing to make accurate and precise genetic Ne estimates for overlapping generations species, neogen facilitates planning for sample and locus acquisition, and with existing empirical genetic Ne estimates neogen can corroborate population demographic and life history properties.
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Affiliation(s)
- Dean C Blower
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,Molecular Fisheries Laboratory, The University of Queensland, St. Lucia, Queensland, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, The University of Queensland, St. Lucia, Queensland, Australia.,School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia
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6
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Williams SM, Pepperell JG, Bennett M, Ovenden JR. Misidentification of istiophorid billfishes by fisheries observers raises uncertainty over stock status. J Fish Biol 2018; 93:415-419. [PMID: 29978473 DOI: 10.1111/jfb.13738] [Citation(s) in RCA: 1] [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: 02/09/2018] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
We investigated whether commercially landed black marlin Istiompax indica were being misidentified by fisheries observers operating throughout the Pacific Ocean. Of 83 samples reported by observers as I. indica, 77% were genetically identified to be blue marlin Makaira nigricans and 2% to be striped marlin Kajikia audax. The high rate of misidentification by observers places considerable uncertainty over historic catch ratios of Indo-Pacific marlin and stock assessments relying on the validity of these data.
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Affiliation(s)
- Samuel M Williams
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Julian G Pepperell
- Pepperell Research and Consulting Pty Ltd, Noosaville DC, Queensland, Australia
| | - Michael Bennett
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland, Australia
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7
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Holmes BJ, Pope LC, Williams SM, Tibbetts IR, Bennett MB, Ovenden JR. Lack of multiple paternity in the oceanodromous tiger shark ( Galeocerdo cuvier). R Soc Open Sci 2018; 5:171385. [PMID: 29410842 PMCID: PMC5792919 DOI: 10.1098/rsos.171385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/01/2017] [Indexed: 06/08/2023]
Abstract
Multiple paternity has been documented as a reproductive strategy in both viviparous and ovoviviparous elasmobranchs, leading to the assumption that multiple mating may be ubiquitous in these fishes. However, with the majority of studies conducted on coastal and nearshore elasmobranchs that often form mating aggregations, parallel studies on pelagic, semi-solitary species are lacking. The tiger shark (Galeocerdo cuvier) is a large pelagic shark that has an aplacental viviparous reproductive mode which is unique among the carcharhinids. A total of 112 pups from four pregnant sharks were genotyped at nine microsatellite loci to assess the possibility of multiple paternity or polyandrous behaviour by female tiger sharks. Only a single pup provided evidence of possible multiple paternity, but with only seven of the nine loci amplifying for this individual, results were inconclusive. In summary, it appears that the tiger sharks sampled in this study were genetically monogamous. These findings may have implications for the genetic diversity and future sustainability of this population.
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Affiliation(s)
- Bonnie J. Holmes
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
- Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
| | - Lisa C. Pope
- Institute for Social Science Research, The University of Queensland, Long Pocket Precinct, Queensland 4072, Australia
| | - Samuel M. Williams
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
- Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
| | - Ian R. Tibbetts
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mike B. Bennett
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jennifer R. Ovenden
- School of Biomedical Sciencesy, The University of Queensland, St Lucia, Queensland 4072, Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia
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8
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Bernatchez L, Wellenreuther M, Araneda C, Ashton DT, Barth JMI, Beacham TD, Maes GE, Martinsohn JT, Miller KM, Naish KA, Ovenden JR, Primmer CR, Young Suk H, Therkildsen NO, Withler RE. Harnessing the Power of Genomics to Secure the Future of Seafood. Trends Ecol Evol 2017; 32:665-680. [PMID: 28818341 DOI: 10.1016/j.tree.2017.06.010] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 11/15/2022]
Abstract
Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration. We conclude that the value of genomic information towards securing the future of seafood does not need to be further demonstrated. Instead, we need immediate efforts to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices. We propose solutions to pave the way forward.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Limited, Port Nelson, Nelson 7043, New Zealand; Department of Biology, Lund University, Lund, Sweden
| | - Cristián Araneda
- Universidad de Chile, Facultad de Ciencias Agronómicas Departamento de Producción Animal, Avda. Santa Rosa 11315, La Pintana 8820808, Santiago, Chile
| | - David T Ashton
- The New Zealand Institute for Plant & Food Research Limited, Port Nelson, Nelson 7043, New Zealand
| | - Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, 4811 QLD, Australia; Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), B-3000 Leuven, Belgium; Genomics Core, UZ Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jann T Martinsohn
- European Commission, Joint Research Centre (JRC), Directorate D - Sustainable Resources, Unit D2 - Water and Marine Resources, Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Kristina M Miller
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Craig R Primmer
- Department of Biosciences, Institute of Biotechnology, 00014, University of Helsinki, Finland
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do 38541, South Korea
| | | | - Ruth E Withler
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
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9
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Taillebois L, Barton DP, Crook DA, Saunders T, Taylor J, Hearnden M, Saunders RJ, Newman SJ, Travers MJ, Welch DJ, Greig A, Dudgeon C, Maher S, Ovenden JR. Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localized fishery collapse in a large Sciaenid fish, Protonibea diacanthus. Evol Appl 2017; 10:978-993. [PMID: 29151854 PMCID: PMC5680636 DOI: 10.1111/eva.12499] [Citation(s) in RCA: 27] [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: 10/21/2016] [Accepted: 05/30/2017] [Indexed: 11/29/2022] Open
Abstract
As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black‐spotted croaker, Protonibea diacanthus, is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due to its food value and predictable aggregating behaviour. Localized declines in the abundance of this species have been observed, highlighting the urgent requirement by managers for information on fine‐ and broad‐scale population connectivity. This study examined the population structure of P. diacanthus across north‐western Australia using three complementary methods: genetic variation in microsatellite markers, otolith elemental composition and parasite assemblage composition. The genetic analyses demonstrated that there were at least five genetically distinct populations across the study region, with gene flow most likely restricted by inshore biogeographic barriers such as the Dampier Peninsula. The otolith chemistry and parasite analyses also revealed strong spatial variation among locations within broad‐scale regions, suggesting fine‐scale location fidelity within the lifetimes of individual fish. The complementarity of the three techniques elucidated patterns of connectivity over a range of spatial and temporal scales. We conclude that fisheries stock assessments and management are required at fine scales (100 s of km) to account for the restricted exchange among populations (stocks) and to prevent localized extirpations of this species. Realistic management arrangements may involve the successive closure and opening of fishing areas to reduce fishing pressure.
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Affiliation(s)
- Laura Taillebois
- Research Institute for the Environment and Livelihoods Charles Darwin University Darwin NT Australia.,North Australia Marine Research Alliance Arafura Timor Research Facility Brinkin NT Australia
| | - Diane P Barton
- Research Institute for the Environment and Livelihoods Charles Darwin University Darwin NT Australia.,Department of Primary Industry and Resources Northern Territory Government Berrimah NT Australia
| | - David A Crook
- Research Institute for the Environment and Livelihoods Charles Darwin University Darwin NT Australia
| | - Thor Saunders
- Department of Primary Industry and Resources Northern Territory Government Berrimah NT Australia
| | - Jonathan Taylor
- Department of Primary Industry and Resources Northern Territory Government Berrimah NT Australia
| | - Mark Hearnden
- Department of Primary Industry and Resources Northern Territory Government Berrimah NT Australia
| | - Richard J Saunders
- Centre for Sustainable Tropical Fisheries and AquacultureJames Cook University Douglas QLD Australia.,Animal Science Queensland Department of Agriculture and Fisheries Brisbane QLD Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Government of Western Australia North Beach WA Australia
| | - Michael J Travers
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Government of Western Australia North Beach WA Australia
| | | | - Alan Greig
- School of Earth Sciences The University of Melbourne Melbourne VIC Australia
| | - Christine Dudgeon
- Molecular Fisheries Laboratory School of Biomedical Sciences The University of Queensland St. Lucia QLD Australia
| | - Safia Maher
- Molecular Fisheries Laboratory School of Biomedical Sciences The University of Queensland St. Lucia QLD Australia
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory School of Biomedical Sciences The University of Queensland St. Lucia QLD Australia
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10
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Holmes BJ, Williams SM, Otway NM, Nielsen EE, Maher SL, Bennett MB, Ovenden JR. Population structure and connectivity of tiger sharks ( Galeocerdo cuvier) across the Indo-Pacific Ocean basin. R Soc Open Sci 2017; 4:170309. [PMID: 28791159 PMCID: PMC5541554 DOI: 10.1098/rsos.170309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/25/2017] [Indexed: 05/15/2023]
Abstract
Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark (Galeocerdo cuvier) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring (FST > 0.14, p < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier.
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Affiliation(s)
- Bonnie J. Holmes
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072Australia
| | - Samuel M. Williams
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072Australia
| | - Nicholas M. Otway
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Einar E. Nielsen
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072Australia
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - Safia L. Maher
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072Australia
| | - Mike B. Bennett
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072Australia
| | - Jennifer R. Ovenden
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072Australia
- Molecular Fisheries Laboratory, The University of Queensland, St Lucia, Queensland 4072Australia
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11
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Dudgeon CL, Coulton L, Bone R, Ovenden JR, Thomas S. Corrigendum: Switch from sexual to parthenogenetic reproduction in a zebra shark. Sci Rep 2017; 7:45881. [PMID: 28387231 PMCID: PMC5383932 DOI: 10.1038/srep45881] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Johnson GJ, Buckworth RC, Lee H, Morgan JAT, Ovenden JR, McMahon CR. A novel field method to distinguish between cryptic carcharhinid sharks, Australian blacktip shark Carcharhinus tilstoni and common blacktip shark C. limbatus, despite the presence of hybrids. J Fish Biol 2017; 90:39-60. [PMID: 27774596 DOI: 10.1111/jfb.13102] [Citation(s) in RCA: 6] [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: 06/11/2015] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Multivariate and machine-learning methods were used to develop field identification techniques for two species of cryptic blacktip shark. From 112 specimens, precaudal vertebrae (PCV) counts and molecular analysis identified 95 Australian blacktip sharks Carcharhinus tilstoni and 17 common blacktip sharks Carcharhinus limbatus. Molecular analysis also revealed 27 of the 112 were C. tilstoni × C. limbatus hybrids, of which 23 had C. tilstoni PCV counts and four had C. limbatus PCV counts. In the absence of further information about hybrid phenotypes, hybrids were assigned as either C. limbatus or C. tilstoni based on PCV counts. Discriminant analysis achieved 80% successful identification, but machine-learning models were better, achieving 100% successful identification, using six key measurements (fork length, caudal-fin peduncle height, interdorsal space, second dorsal-fin height, pelvic-fin length and pelvic-fin midpoint to first dorsal-fin insertion). Furthermore, pelvic-fin markings could be used for identification: C. limbatus has a distinct black mark >3% of the total pelvic-fin area, while C. tilstoni has markings with diffuse edges, or has smaller or no markings. Machine learning and pelvic-fin marking identification methods were field tested achieving 87 and 90% successful identification, respectively. With further refinement, the techniques developed here will form an important part of a multi-faceted approach to identification of C. tilstoni and C. limbatus and have a clear management and conservation application to these commercially important sharks. The methods developed here are broadly applicable and can be used to resolve species identities in many fisheries where cryptic species exist.
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Affiliation(s)
- G J Johnson
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, G. P. O Box 3000, Darwin, NT, 0801, Australia
| | - R C Buckworth
- CSIRO Oceans and Atmosphere Flagship, PMB 44 Winnellie, Darwin, NT, 0822, Australia
| | - H Lee
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, G. P. O Box 3000, Darwin, NT, 0801, Australia
| | - J A T Morgan
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, P. O. Box 6097, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - J R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - C R McMahon
- Sydney Institute of Marine Science, 19 Chowder Bay Road, Mosman, NSW, 2088, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 2001, Australia
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Ovenden JR, Leigh GM, Blower DC, Jones AT, Moore A, Bustamante C, Buckworth RC, Bennett MB, Dudgeon CL. Can estimates of genetic effective population size contribute to fisheries stock assessments? J Fish Biol 2016; 89:2505-2518. [PMID: 27730623 DOI: 10.1111/jfb.13129] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 03/15/2016] [Accepted: 07/28/2016] [Indexed: 06/06/2023]
Abstract
Sustainable exploitation of fisheries populations is challenging to achieve when the size of the population prior to exploitation and the actual numbers removed over time and across fishing zones are not clearly known. Quantitative fisheries' modeling is able to address this problem, but accurate and reliable model outcomes depend on high quality input data. Much of this information is obtained through the operation of the fishery under consideration, but while this seems appropriate, biases may occur. For example, poorly quantified changes in fishing methods that increase catch rates can erroneously suggest that the overall population size is increasing. Hence, the incorporation of estimates of abundance derived from independent data sources is preferable. We review and evaluate a fisheries-independent method of indexing population size; inferring adult abundance from estimates of the genetic effective size of a population (Ne ). Recent studies of elasmobranch species have shown correspondence between Ne and ecologically determined estimates of the population size (N). Simulation studies have flagged the possibility that the range of Ne /N ratios across species may be more restricted than previously thought, and also show that declines in Ne track declines in the abundance of model fisheries species. These key developments bring this new technology closer to implementation in fisheries science, particularly for data-poor fisheries or species of conservation interest.
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Affiliation(s)
- J R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - G M Leigh
- Agri-Science Queensland, Department of Agriculture & Fisheries, St Lucia, QLD, 4072, Australia
| | - D C Blower
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- School of Biological Sciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - A T Jones
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- Centre for Applications in Natural Resource Mathematics, School of Mathematics and Physics, University of Queensland, St Lucia, QLD, 4072, Australia
| | - A Moore
- Fisheries, Forestry & Land, Australian Bureau of Agricultural & Resource Economics and Sciences, Department of Agriculture & Water Resources, Canberra, ACT, 2601, Australia
| | - C Bustamante
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- Shark & Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - R C Buckworth
- Tropical Ecosystems Research Centre, Oceans & Atmosphere, CSIRO, Berrimah, NT, 0820, Australia
| | - M B Bennett
- Shark & Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - C L Dudgeon
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- Shark & Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
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Nielsen EE, Morgan JAT, Maher SL, Edson J, Gauthier M, Pepperell J, Holmes BJ, Bennett MB, Ovenden JR. Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material. Mol Ecol Resour 2016; 17:431-442. [PMID: 27508520 DOI: 10.1111/1755-0998.12580] [Citation(s) in RCA: 10] [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: 03/16/2016] [Revised: 06/10/2016] [Accepted: 06/23/2016] [Indexed: 11/30/2022]
Abstract
Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.
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Affiliation(s)
- E E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark.,School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - J A T Morgan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - S L Maher
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - J Edson
- Queensland Brain Institute, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - M Gauthier
- QFAB Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - J Pepperell
- Pepperell Research and Consulting Pty Ltd, Noosaville, Qld., 4566, Australia
| | - B J Holmes
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - M B Bennett
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - J R Ovenden
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
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Taillebois L, Crook DA, Saunders T, Williams SM, Ovenden JR. The complete mitochondrial genome of the grass emperor, Lethrinus laticaudis (Perciformes: Lethrinidae). Mitochondrial DNA B Resour 2016; 1:277-279. [PMID: 33644359 PMCID: PMC7871818 DOI: 10.1080/23802359.2016.1166076] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/04/2016] [Accepted: 03/11/2016] [Indexed: 11/09/2022] Open
Abstract
The grass emperor Lethrinus laticaudis is a coral reef fish that has high value to fisheries and is vulnerable to overharvesting. The complete mitochondrial genome was assembled from approximately 5.5 million reads produced by Illumina MiSeq. The 16,758 bp consisted of 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes (12S and 16S). The genes and RNAs order and orientation on as well as the A + T base content (50.7%) was similar to what is found in other Teleosts. A phylogenetic tree with the most closely related species available in GenBank was built to validate L. laticaudis mitogenome.
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Affiliation(s)
- Laura Taillebois
- North Australia Marine Research Alliance, Charles Darwin University, Darwin, NT, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - David A. Crook
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Thor Saunders
- Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Samuel M. Williams
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Jennifer R. Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
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16
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Bustamante C, Bennett MB, Ovenden JR. Genetype and phylogenomic position of the frilled shark Chlamydoselachus anguineus inferred from the mitochondrial genome. Mitochondrial DNA B Resour 2016; 1:18-20. [PMID: 33473392 PMCID: PMC7799599 DOI: 10.1080/23802359.2015.1137801] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The genetype of Chlamydoselachus anguineus from Australian waters is described using the whole mitochondrial genome obtained from Illumina NGS technology. Total length of the mitogenome is 17 313 bp, consisting of 2 rRNAs, 13 protein-coding genes, 22 tRNA genes and 2 non-coding regions thus updating the previously available mitogenome for this species. The phylogenomic reconstruction comprising all available species of Superorder Squalomorphi supports the inclusion of C. anguineus in a divergent clade inside Order Hexanchiformes. Phyletic relationships inferred from the whole mitochondrial genomes are in agreement with traditional taxonomy. The low divergence between C. anguineus genomes (>99.9% genetic identity) is consistent with a widespread population in the west Pacific Ocean.
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Affiliation(s)
- Carlos Bustamante
- Shark and Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia.,Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Michael B Bennett
- Shark and Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Jennifer R Ovenden
- Shark and Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
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17
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Bowden DL, Vargas-Caro C, Ovenden JR, Bennett MB, Bustamante C. The phylogenomic position of the grey nurse shark Carcharias taurus Rafinesque, 1810 (Lamniformes, Odontaspididae) inferred from the mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4328-4330. [PMID: 26462847 DOI: 10.3109/19401736.2015.1089486] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 11/13/2022]
Abstract
The complete mitochondrial genome of the grey nurse shark Carcharias taurus is described from 25 963 828 sequences obtained using Illumina NGS technology. Total length of the mitogenome is 16 715 bp, consisting of 2 rRNAs, 13 protein-coding regions, 22 tRNA and 2 non-coding regions thus updating the previously published mitogenome for this species. The phylogenomic reconstruction inferred from the mitogenome of 15 species of Lamniform and Carcharhiniform sharks supports the inclusion of C. taurus in a clade with the Lamnidae and Cetorhinidae. This complete mitogenome contributes to ongoing investigation into the monophyly of the Family Odontaspididae.
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Affiliation(s)
- Deborah L Bowden
- a Shark and Ray Research Group and.,b Molecular Fisheries Laboratory, School of Biomedical Sciences, the University of Queensland , Queensland , St Lucia , Australia
| | - Carolina Vargas-Caro
- a Shark and Ray Research Group and.,b Molecular Fisheries Laboratory, School of Biomedical Sciences, the University of Queensland , Queensland , St Lucia , Australia
| | - Jennifer R Ovenden
- a Shark and Ray Research Group and.,b Molecular Fisheries Laboratory, School of Biomedical Sciences, the University of Queensland , Queensland , St Lucia , Australia
| | | | - Carlos Bustamante
- a Shark and Ray Research Group and.,b Molecular Fisheries Laboratory, School of Biomedical Sciences, the University of Queensland , Queensland , St Lucia , Australia
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18
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Bustamante C, Barría C, Vargas-Caro C, Ovenden JR, Bennett MB. The phylogenetic position of the giant devil ray Mobula mobular (Bonnaterre, 1788) (Myliobatiformes, Myliobatidae) inferred from the mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3540-1. [PMID: 26260171 DOI: 10.3109/19401736.2015.1074208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 11/13/2022]
Abstract
The giant devil ray, Mobula mobular, is a member of one of the most distinct groups of cartilaginous fishes, the Mobulidae (manta and devil rays), and is the only mobulid assessed as Endangered due its restricted distribution, high bycatch mortality and suspected population decline. The complete mitochondrial genome is 18 913 base pairs in length and comprises 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Comparison with the partial mitogenome of M. japanica suggests a sister-cryptic species complex and two different taxonomic units. However, the limited divergence within the species (>99.9% genetic identity) may be the result of a geographically and numerically restricted population of M. mobular within the Mediterranean Sea.
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Affiliation(s)
- Carlos Bustamante
- a School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia .,b Molecular Fisheries Laboratory, The University of Queensland , St Lucia , Queensland , Australia , and
| | - Claudio Barría
- c Institut de Ciències del Mar (ICM-CSIC) , Barcelona , Spain
| | - Carolina Vargas-Caro
- a School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia .,b Molecular Fisheries Laboratory, The University of Queensland , St Lucia , Queensland , Australia , and
| | - Jennifer R Ovenden
- b Molecular Fisheries Laboratory, The University of Queensland , St Lucia , Queensland , Australia , and
| | - Michael B Bennett
- a School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia
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Vargas-Caro C, Bustamante C, Lamilla J, Bennett MB, Ovenden JR. The phylogenetic position of the roughskin skate Dipturus trachyderma (Krefft & Stehmann, 1975) (Rajiformes, Rajidae) inferred from the mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2965-6. [PMID: 26122334 DOI: 10.3109/19401736.2015.1060462] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 11/13/2022]
Abstract
The complete mitochondrial genome of the roughskin skate Dipturus trachyderma is described from 1 455 724 sequences obtained using Illumina NGS technology. Total length of the mitogenome was 16 909 base pairs, comprising 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Phylogenetic analysis based on mtDNA revealed low genetic divergence among longnose skates, in particular, those dwelling the continental shelf and slope off the coasts of Chile and Argentina.
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Affiliation(s)
- Carolina Vargas-Caro
- a Molecular Fisheries Laboratory , School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia and
| | - Carlos Bustamante
- a Molecular Fisheries Laboratory , School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia and
| | - Julio Lamilla
- b Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile , Valdivia , Chile
| | - Michael B Bennett
- a Molecular Fisheries Laboratory , School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia and
| | - Jennifer R Ovenden
- a Molecular Fisheries Laboratory , School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia and
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Vargas-Caro C, Bustamante C, Bennett MB, Ovenden JR. The complete validated mitochondrial genome of the yellownose skateZearaja chilensis(Guichenot 1848) (Rajiformes, Rajidae). ACTA ACUST UNITED AC 2014; 27:1227-8. [DOI: 10.3109/19401736.2014.945530] [Citation(s) in RCA: 6] [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]
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Abstract
The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one individual were assembled into a 16,706 bp mitogenome with 33× average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA's, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure.
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Affiliation(s)
- Dean C Blower
- a School of Biological Sciences, The University of Queensland , St. Lucia , Australia and
| | - Jennifer R Ovenden
- a School of Biological Sciences, The University of Queensland , St. Lucia , Australia and.,b Molecular Fisheries Laboratory , The University of Queensland , St. Lucia , Australia
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Geraghty PT, Williamson JE, Macbeth WG, Blower DC, Morgan JAT, Johnson G, Ovenden JR, Gillings MR. Genetic structure and diversity of two highly vulnerable carcharhinids in Australian waters. ENDANGER SPECIES RES 2014. [DOI: 10.3354/esr00580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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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Williams SM, Morgan JAT, Ovenden JR. The complete validated mitochondrial genome of the black marlin Istiompax indica (Cuvier, 1832). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:418-9. [PMID: 24660926 DOI: 10.3109/19401736.2014.898285] [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] [Indexed: 11/13/2022]
Abstract
Two complete mitochondrial genomes of the black marlin Istiompax indica were assembled from approximately 3.5 and 2.5 million reads produced by Ion Torrent next generation sequencing. The complete genomes were 16,531 bp and 16,532 bp in length consisting of 2 rRNA, 13 protein-coding genes, 22tRNA and 2 coding regions. They demonstrated a similar A + T base (52.6%) to other teleosts. Intraspecific sequence variation was 99.5% for three I. indica mitogenomes and 99.7% for X. gladius. A lower value (85%) was found for the I. platypterus mitogenomes from genbank and accredited to inadvertent inclusion of gene regions from a con-familial species in one record, highlighting the need for cautious downstream use of genbank data.
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Affiliation(s)
- Samuel M Williams
- a Molecular Fisheries Laboratory , University of Queensland , St Lucia , Queensland , Australia and
| | - Jess A T Morgan
- b Queensland Alliance for Agriculture and Food Innovation, The University of Queensland , St Lucia , Australia
| | - Jennifer R Ovenden
- a Molecular Fisheries Laboratory , University of Queensland , St Lucia , Queensland , Australia and
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Bustamante C, Ovenden JR. The complete validated mitochondrial genome of the silver gemfish Rexea solandri (Cuvier, 1832) (Perciformes, Gempylidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:405-6. [PMID: 24621221 DOI: 10.3109/19401736.2014.898279] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The silver gemfish Rexea solandri is an important economic resource but Vulnerable to overfishing in Australian waters. The complete mitochondrial genome sequence is described from 1.6 million reads obtained via next generation sequencing. The total length of the mitogenome is 16,350 bp comprising 2 rRNA, 13 protein-coding genes, 22 tRNA and 2 non-coding regions. The mitogenome sequence was validated against sequences of PCR fragments and BLAST queries of Genbank. Gene order was equivalent to that found in marine fishes.
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Affiliation(s)
- Carlos Bustamante
- a Molecular Fisheries Laboratory , School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia
| | - Jennifer R Ovenden
- a Molecular Fisheries Laboratory , School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia
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25
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Taillebois L, Castelin M, Ovenden JR, Bonillo C, Keith P. Contrasting genetic structure among populations of two amphidromous fish species (Sicydiinae) in the Central West Pacific. PLoS One 2013; 8:e75465. [PMID: 24130714 PMCID: PMC3794023 DOI: 10.1371/journal.pone.0075465] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 08/15/2013] [Indexed: 11/18/2022] Open
Abstract
Both present-day and past processes can shape connectivity of populations. Pleistocene vicariant events and dispersal have shaped the present distribution and connectivity patterns of aquatic species in the Indo-Pacific region. In particular, the processes that have shaped distribution of amphidromous goby species still remain unknown. Previous studies show that phylogeographic breaks are observed between populations in the Indian and Pacific Oceans where the shallow Sunda shelf constituted a geographical barrier to dispersal, or that the large spans of open ocean that isolate the Hawaiian or Polynesian Islands are also barriers for amphidromous species even though they have great dispersal capacity. Here we assess past and present genetic structure of populations of two amphidromous fish (gobies of the Sicydiinae) that are widely distributed in the Central West Pacific and which have similar pelagic larval durations. We analysed sections of mitochondrial COI, Cytb and nuclear Rhodospine genes in individuals sampled from different locations across their entire known range. Similar to other Sicydiinae fish, intraspecific mtDNA genetic diversity was high for all species (haplotype diversity between 0.9–0.96). Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. There was a clear genetic break between the northwestern and the southwestern clusters in Si. zosterophorum (φST = 0.67502 for COI) and coalescent analyses revealed that the two populations split at 306 Kyr BP (95% HPD 79–625 Kyr BP), which is consistent with a Pleistocene separation caused by the Torres Strait barrier. However, this geographical barrier did not seem to affect Sm. fehlmanni. Historical and demographic hypotheses are raised to explain the different patterns of population structure and distribution between these species. Strategies aiming to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion.
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Affiliation(s)
- Laura Taillebois
- Milieux et Peuplements Aquatiques - UMR 7208 (MNHN, CNRS, IRD, UPMC), Muséum national d'Histoire naturelle, Paris, France ; Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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Geraghty PT, Williamson JE, Macbeth WG, Wintner SP, Harry AV, Ovenden JR, Gillings MR. Population expansion and genetic structure in Carcharhinus brevipinna in the southern Indo-Pacific. PLoS One 2013; 8:e75169. [PMID: 24086462 PMCID: PMC3783459 DOI: 10.1371/journal.pone.0075169] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [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: 03/05/2013] [Accepted: 08/12/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Quantifying genetic diversity and metapopulation structure provides insights into the evolutionary history of a species and helps develop appropriate management strategies. We provide the first assessment of genetic structure in spinner sharks (Carcharhinus brevipinna), a large cosmopolitan carcharhinid, sampled from eastern and northern Australia and South Africa. METHODS AND FINDINGS Sequencing of the mitochondrial DNA NADH dehydrogenase subunit 4 gene for 430 individuals revealed 37 haplotypes and moderately high haplotype diversity (h = 0.6770 ±0.025). While two metrics of genetic divergence (ΦST and F ST) revealed somewhat different results, subdivision was detected between South Africa and all Australian locations (pairwise ΦST, range 0.02717-0.03508, p values ≤ 0.0013; pairwise F ST South Africa vs New South Wales = 0.04056, p = 0.0008). Evidence for fine-scale genetic structuring was also detected along Australia's east coast (pairwise ΦST = 0.01328, p < 0.015), and between south-eastern and northern locations (pairwise ΦST = 0.00669, p < 0.04). CONCLUSIONS The Indian Ocean represents a robust barrier to contemporary gene flow in C. brevipinna between Australia and South Africa. Gene flow also appears restricted along a continuous continental margin in this species, with data tentatively suggesting the delineation of two management units within Australian waters. Further sampling, however, is required for a more robust evaluation of the latter finding. Evidence indicates that all sampled populations were shaped by a substantial demographic expansion event, with the resultant high genetic diversity being cause for optimism when considering conservation of this commercially-targeted species in the southern Indo-Pacific.
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Affiliation(s)
- Pascal T. Geraghty
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
- Cronulla Fisheries Research Centre of Excellence, New South Wales Department of Primary Industries, Sydney, New South Wales, Australia
| | - Jane E. Williamson
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - William G. Macbeth
- Cronulla Fisheries Research Centre of Excellence, New South Wales Department of Primary Industries, Sydney, New South Wales, Australia
| | - Sabine P. Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, KwaZulu-Natal, South Africa
| | - Alastair V. Harry
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Jennifer R. Ovenden
- Molecular Fisheries Laboratory, the University of Queensland, St. Lucia, Queensland, Australia
| | - Michael R. Gillings
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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27
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McHale M, Broderick D, Ovenden JR, Lanyon JM. A PCR assay for gender assignment in dugong (Dugong dugon) and West Indian manatee (Trichechus manatus). Mol Ecol Resour 2013; 8:669-70. [PMID: 21585866 DOI: 10.1111/j.1471-8286.2007.02041.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gender assignment for some aquatic mammals in the field is difficult. Molecular sexing from tissue biopsies is possible as males are heterogametic. Here we describe a multiplex PCR assay that amplifies the male specific SRY gene and differentiates ZFX and ZFY gametologues in two sirenian species, dugong (Dugong dugon) and West Indian manatee (Trichechus manatus). The assay was validated with animals of known gender and proved accurate and robust to experimental failure.
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Affiliation(s)
- M McHale
- Molecular Fisheries Laboratory, Queensland Department of Primary Industries and Fisheries, Queensland Biosciences Precinct, University of Queensland, Level 6 North Tower, 306 Carmody Road, St Lucia, Qld 4072, Australia, School of Integrative Biology, University of Queensland, St Lucia, Qld 4072, Australia
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28
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Morgan JAT, Macbeth M, Broderick D, Whatmore P, Street R, Welch DJ, Ovenden JR. Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae). Mitochondrion 2013; 13:852-61. [PMID: 23774068 DOI: 10.1016/j.mito.2013.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 11/16/2022]
Abstract
Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies.
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Affiliation(s)
- Jess A T Morgan
- Molecular Fisheries Laboratory, University of Queensland, PO Box 6097, St Lucia, Queensland 4072, Australia; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, 306 Carmody Rd, St Lucia, Queensland 4072, Australia.
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29
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Krück NC, Innes DI, Ovenden JR. New
SNP
s for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (
Mugil cephalus
). Mol Ecol Resour 2013; 13:715-25. [DOI: 10.1111/1755-0998.12112] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 03/27/2013] [Accepted: 03/29/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Nils C. Krück
- School of Biological Sciences The University of Queensland St Lucia Campus Brisbane Qld 4072 Australia
- Molecular Fisheries Laboratory Queensland Government PO Box 6097 Brisbane Qld 4072 Australia
| | - David I. Innes
- Molecular Fisheries Laboratory Queensland Government PO Box 6097 Brisbane Qld 4072 Australia
| | - Jennifer R. Ovenden
- School of Biological Sciences The University of Queensland St Lucia Campus Brisbane Qld 4072 Australia
- Molecular Fisheries Laboratory Queensland Government PO Box 6097 Brisbane Qld 4072 Australia
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30
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31
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Feutry P, Castelin M, Ovenden JR, Dettaï A, Robinet T, Cruaud C, Keith P. Evolution of diadromy in fish: insights from a tropical genus (Kuhlia species). Am Nat 2012; 181:52-63. [PMID: 23234845 DOI: 10.1086/668593] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Diadromous species undergo regular migration between fresh and marine waters. This behavior is found in many species, including fish, mollusks, and crustaceans, some of which are commercially valuable species. Several attempts to trace the evolution of this behavior have been made in Salmonidae and Galaxiidae, but ambiguous phylogenies and multiple character state changes prevented unequivocal conclusions. The Kuhliidae family consists of 12 fish species that inhabit tropical islands in the Indo-Pacific region. The species have marine, partially catadromous, or fully catadromous life histories (i.e., they migrate from rivers to the sea to reproduce). The evolution of migratory behavior was traced on a well-resolved phylogeny. Catadromous Kuhlia species were basal, and partially catadromous and marine species formed derived monophyletic groups. This is, to our knowledge, the first time that a clear origin and polarity for the diadromous character has been demonstrated. We propose that the relative lack of resources in tropical, inshore, marine habitats and the ephemeral and isolated nature of freshwater environments of tropical islands, combined with phenotypic plasticity of migratory traits, play key roles in driving the evolution of diadromy in the Kuhliidae and probably in other groups. This work is an important starting point to understand the role of diadromy in speciation and adaptation in unstable habitats.
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Affiliation(s)
- Pierre Feutry
- Muséum National d'Histoire Naturelle, Milieux et Peuplements Aquatiques, Unité de Mixte de Recherche (UMR) 7208, Ichtyologie, 57 rue Cuvier, CP026, Paris 75231, France.
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32
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Harry AV, Morgan JAT, Ovenden JR, Tobin AJ, Welch DJ, Simpfendorfer CA. Comparison of the reproductive ecology of two sympatric blacktip sharks (Carcharhinus limbatus and Carcharhinus tilstoni) off north-eastern Australia with species identification inferred from vertebral counts. J Fish Biol 2012; 81:1225-1233. [PMID: 22957866 DOI: 10.1111/j.1095-8649.2012.03400.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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
Precaudal vertebral counts were used to distinguish between 237 morphologically similar Carcharhinus limbatus and Carcharhinus tilstoni and were congruent with differences in reproductive ecology between the species. In addition to differing lengths at maturity and adult body size, the two species had asynchronous parturition, were born at different sizes and the relative frequencies of neonates differed in two coastal nursery areas. Despite evidence that hybridization can occur, these differences suggest the species are largely reproductively isolated.
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Affiliation(s)
- A V Harry
- Centre for Sustainable Tropical Fisheries and Aquaculture & School of Earth and Environmental Sciences, James Cook University, Townsville, Qld 4811, Australia.
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33
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Abstract
Reproductive philopatry in bull sharks Carcharhinus leucas was investigated by comparing mitochondrial (NADH dehydrogenase subunit 4, 797 base pairs and control region genes 837 base pairs) and nuclear (three microsatellite loci) DNA of juveniles sampled from 13 river systems across northern Australia. High mitochondrial and low microsatellite genetic diversity among juveniles sampled from different rivers (mitochondrial φ(ST) = 0·0767, P < 0·05; microsatellite F(ST) = -0·0022, P > 0·05) supported female reproductive philopatry. Genetic structure was not further influenced by geographic distance (P > 0·05) or long-shore barriers to movement (P > 0·05). Additionally, results suggest that C. leucas in northern Australia has a long-term effective population size of 11 000-13 000 females and has undergone population bottlenecks and expansions that coincide with the timing of the last ice-ages.
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Affiliation(s)
- B J Tillett
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT 0810, Australia.
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34
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Kashiwagi T, Marshall AD, Bennett MB, Ovenden JR. The genetic signature of recent speciation in manta rays (Manta alfredi and M. birostris). Mol Phylogenet Evol 2012; 64:212-8. [PMID: 22503670 DOI: 10.1016/j.ympev.2012.03.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 03/22/2012] [Accepted: 03/30/2012] [Indexed: 11/30/2022]
Abstract
Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondrial CO1 (574 bp) and ND5 genes (1188 bp). The assay with CO1 sequences, widely used in DNA barcoding, failed to distinguish the two species. The two species were clearly distinguishable, however, with no shared RAG1 or ND5 haplotypes. The species were reciprocally monophyletic for RAG1, but paraphyletic for ND5 sequences. Qualitative evidence and statistical inferences using the 'Isolation-with-Migration models' indicated that these results were better explained with post-divergence gene flow in the recent past rather than incomplete lineage sorting with zero gene flow since speciation. An estimate of divergence time was less than 0.5 Ma with an upper confidence limit of within 1 Ma. Recent speciation of highly mobile species in the marine environment is of great interest, as it suggests that speciation may have occurred in the absence of long-term physical barriers to gene flow. We propose that the ecologically driven forces such as habitat choice played a significant role in speciation in manta rays.
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Affiliation(s)
- Tom Kashiwagi
- School of Biomedical Sciences, University of Queensland, St. Lucia, QLD 4072, Australia.
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35
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Dudgeon CL, Blower DC, Broderick D, Giles JL, Holmes BJ, Kashiwagi T, Krück NC, Morgan JAT, Tillett BJ, Ovenden JR. A review of the application of molecular genetics for fisheries management and conservation of sharks and rays. J Fish Biol 2012; 80:1789-1843. [PMID: 22497408 DOI: 10.1111/j.1095-8649.2012.03265.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.
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Affiliation(s)
- C L Dudgeon
- The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
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36
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Broderick D, Ovenden JR, Buckworth RC, Newman SJ, Lester RJG, Welch DJ. Genetic population structure of grey mackerel Scomberomorus semifasciatus in northern Australia. J Fish Biol 2011; 79:633-661. [PMID: 21884105 DOI: 10.1111/j.1095-8649.2011.03055.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This study used mtDNA sequence and microsatellite markers to elucidate the population structure of Scomberomorus semifasciatus collected from 12 widespread sampling locations in Australia. Samples (n = 544) were genotyped with nine microsatellite loci, and 353 were sequenced for the control (384 bp) and ATPase (800 bp) mtDNA gene regions. Combined interpretation of microsatellite and mtDNA data identified four genetic stocks of S. semifasciatus: Western Australia, north-west coast of the Northern Territory, Gulf of Carpentaria and the eastern coast of Queensland. Connectivity among stocks across northern Australia from the Northern Territory to the eastern coast of Queensland was high (mean F(ST) = 0·003 for the microsatellite data and Φ(ST) = 0·033 and 0·009 for control region and ATPase, respectively) leading to some uncertainty about stock boundaries. In contrast, there was a clear genetic break between the stock in Western Australia compared to the rest of northern Australia (mean F(ST) = 0·132 for the microsatellite data and Φ(ST) = 0·135 and 0·188 for control region and ATPase, respectively). This indicates a restriction to gene flow possibly associated with suboptimal habitat along the Kimberley coast (north Western Australia). The appropriate scale of management for this species corresponds to the jurisdictions of the three Australian states, except that authorities in Queensland and Northern Territory should co-ordinate the management of the Gulf of Carpentaria stock.
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Affiliation(s)
- D Broderick
- Molecular Fisheries Laboratory, Queensland Department of Employment, Economic Development and Innovation, P O Box 6097, St Lucia, 4069 Queensland, Australia
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37
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Macbeth GM, Broderick D, Ovenden JR, Buckworth RC. Likelihood-based genetic mark-recapture estimates when genotype samples are incomplete and contain typing errors. Theor Popul Biol 2011; 80:185-96. [PMID: 21763337 DOI: 10.1016/j.tpb.2011.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 06/07/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
Abstract
Genotypes produced from samples collected non-invasively in harsh field conditions often lack the full complement of data from the selected microsatellite loci. The application to genetic mark-recapture methodology in wildlife species can therefore be prone to misidentifications leading to both 'true non-recaptures' being falsely accepted as recaptures (Type I errors) and 'true recaptures' being undetected (Type II errors). Here we present a new likelihood method that allows every pairwise genotype comparison to be evaluated independently. We apply this method to determine the total number of recaptures by estimating and optimising the balance between Type I errors and Type II errors. We show through simulation that the standard error of recapture estimates can be minimised through our algorithms. Interestingly, the precision of our recapture estimates actually improved when we included individuals with missing genotypes, as this increased the number of pairwise comparisons potentially uncovering more recaptures. Simulations suggest that the method is tolerant to per locus error rates of up to 5% per locus and can theoretically work in datasets with as little as 60% of loci genotyped. Our methods can be implemented in datasets where standard mismatch analyses fail to distinguish recaptures. Finally, we show that by assigning a low Type I error rate to our matching algorithms we can generate a dataset of individuals of known capture histories that is suitable for the downstream analysis with traditional mark-recapture methods.
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Affiliation(s)
- Gilbert M Macbeth
- Molecular Fisheries Laboratory, Queensland Primary Industries and Fisheries, Ritchie Building No. 64A, Research Road, University of Queensland, PO Box 6097, St Lucia, Queensland, 4072, Australia.
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38
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Morgan JAT, Welch DJ, Harry AV, Street R, Broderick D, Ovenden JR. A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis. Mol Ecol Resour 2011; 11:813-9. [PMID: 21565127 DOI: 10.1111/j.1755-0998.2011.03023.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.
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Affiliation(s)
- Jess A T Morgan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Qld 4069, Australia
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39
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Nock CJ, Ovenden JR, Butler GL, Wooden I, Moore A, Baverstock PR. Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei. J Fish Biol 2011; 78:303-321. [PMID: 21235562 DOI: 10.1111/j.1095-8649.2010.02865.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (F(ST) = 0·09 - 0·49; P < 0·05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.
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Affiliation(s)
- C J Nock
- Centres for Animal and Plant Conservation Genetics, Southern Cross University, P. O. Box 157 Lismore, NSW, Australia.
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40
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Abstract
We developed and optimized 15 polymorphic microsatellite loci in the jungle perch, Kuhlia rupestris. Loci were screened in a single population (n = 24) from Fraser Island, Queensland, Australia. Number of alleles per locus ranged from 3 to 19 and observed heterozygosity from 0.25 to 1. No significant linkage disequilibrium was detected between any pair of loci. Genotype proportions for these loci in the population sampled were in Hardy-Weinberg equilibrium.
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Affiliation(s)
- Maureen B Peters
- Savannah River Ecology Lab, University of Georgia, Drawer E, Aiken, SC 29802, USA Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA Molecular Fisheries Laboratory, Queensland Department of Primary Industries and Fisheries, PO Box 6097, St Lucia, Qld 4067, Australia
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41
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Dudgeon CL, Broderick D, Ovenden JR. IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo-West Pacific. Mol Ecol 2009; 18:248-61. [PMID: 19192179 DOI: 10.1111/j.1365-294x.2008.04025.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Indo-West Pacific (IWP), from South Africa in the western Indian Ocean to the western Pacific Ocean, contains some of the most biologically diverse marine habitats on earth, including the greatest biodiversity of chondrichthyan fishes. The region encompasses various densities of human habitation leading to contrasts in the levels of exploitation experienced by chondrichthyans, which are targeted for local consumption and export. The demersal chondrichthyan, the zebra shark, Stegostoma fasciatum, is endemic to the IWP and has two current regional International Union for the Conservation of Nature (IUCN) Red List classifications that reflect differing levels of exploitation: 'Least Concern' and 'Vulnerable'. In this study, we employed mitochondrial ND4 sequence data and 13 microsatellite loci to investigate the population genetic structure of 180 zebra sharks from 13 locations throughout the IWP to test the concordance of IUCN zones with demographic units that have conservation value. Mitochondrial and microsatellite data sets from samples collected throughout northern Australia and Southeast Asia concord with the regional IUCN classifications. However, we found evidence of genetic subdivision within these regions, including subdivision between locations connected by habitat suitable for migration. Furthermore, parametric F(ST) analyses and Bayesian clustering analyses indicated that the primary genetic break within the IWP is not represented by the IUCN classifications but rather is congruent with the Indonesian throughflow current. Our findings indicate that recruitment to areas of high exploitation from nearby healthy populations in zebra sharks is likely to be minimal, and that severe localized depletions are predicted to occur in zebra shark populations throughout the IWP region.
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Affiliation(s)
- C L Dudgeon
- School of Integrative Biology, University of Queensland, Qld 4072, Australia.
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42
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Ovenden JR, Peel D, Street R, Courtney AJ, Hoyle SD, Peel SL, Podlich H. The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus). Mol Ecol 2007; 16:127-38. [PMID: 17181726 DOI: 10.1111/j.1365-294x.2006.03132.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.
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Affiliation(s)
- Jennifer R Ovenden
- Molecular Fisheries Laboratory, Queensland Department of Primary Industries and Fisheries, Floor 6, North Tower, Queensland Biosciences Precinct, University of Queensland, St Lucia, Queensland 4072 Australia.
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43
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Ovenden JR, Salini J, O'Connor S, Street R. Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle. Mol Ecol 2005; 13:1991-9. [PMID: 15189219 DOI: 10.1111/j.1365-294x.2004.02210.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The East Indies triangle, bordered by the Phillipines, Malay Peninsula and New Guinea, has a high level of tropical marine species biodiversity. Pristipomoides multidens is a large, long-lived, fecund snapper species that is distributed throughout the East Indies and Indo-Pacific. Samples were analysed from central and eastern Indonesia and northern Australia to test for genetic discontinuities in population structure. Fish (n = 377) were collected from the Indonesian islands of Bali, Sumbawa, Flores, West Timor, Tanimbar and Tual along with 131 fish from two northern Australian locations (Arafura and Timor Seas) from a previous study. Genetic variation in the control region of the mitochondrial genome was assayed using restriction fragment length polymorphism and direct sequencing. Haplotype diversity was high (0.67-0.82), as was intraspecific sequence divergence (range 0-5.8%). F(ST) between pairs of populations ranged from 0 to 0.2753. Genetic subdivision was apparent on a small spatial scale; F(ST) was 0.16 over 191 km (Bali/Sumbawa) and 0.17 over 491 km (Bali/Flores). Constraints to dispersal that contribute to, and maintain, the observed degree of genetic subdivision are experienced presumably by all life history stages of this tropical marine finfish. The constraints may include (1) little or no movement of eggs or larvae, (2) little or no home range or migratory movement of adults and (3) loss of larval cohorts due to transport of larvae away from suitable habitat by prevailing currents.
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Affiliation(s)
- Jennifer R Ovenden
- Molecular Fisheries Laboratory, Southern Fisheries Centre, Queensland Department of Primary Industries and Fisheries, 13 Beach Road (PO Box 76), Deception Bay, Queensland, 4508 Australia.
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44
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Ovenden JR, Bywater R, White RW. A Program for the Estimation of Restriction Endonuclease Site Positions from Restriction Fragment Size and Number: An Aid for Mitochondrial DNA Analysis. J Hered 1992; 83:240-1. [PMID: 1352524 DOI: 10.1093/oxfordjournals.jhered.a111206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J R Ovenden
- Department of Zoology, University of Tasmania, Australia
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Ovenden JR, White RW. Mitochondrial and allozyme genetics of incipient speciation in a landlocked population of Galaxias truttaceus (Pisces: Galaxiidae). Genetics 1990; 124:701-16. [PMID: 2155855 PMCID: PMC1203962 DOI: 10.1093/genetics/124.3.701] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Galaxias truttaceus is found in coastal rivers and streams in south-eastern Australia. It spawns at the head of estuaries in autumn and the larvae spend 3 months of winter at sea before returning to fresh water. In Tasmania there are landlocked populations of G. truttaceus in a cluster of geologically young lakes on the recently glaciated Central Plateau. These populations have no marine larval stage and spawn in the lakes in spring. Speciation due to land locking is thought to be a frequent occurrence within Galaxias. To investigate the nature of the speciation event which may be occurring within lake populations of G. truttaceus we studied the mitochondrial DNA (mtDNA) and allozyme diversity of both lake and stream populations. Using the presence or absence of restriction sites recognized by 13 six-base restriction endonucleases, we found 58 mtDNA haplotypes among 150 fish collected from 13 Tasmanian and one south-east Australian mainland stream populations. The most parsimonious network relating the haplotypes by site loss or gain was starlike in shape. We argue that this arrangement is best explained by selection upon slightly beneficial mutations within the mitochondrial genome. Gene diversity analysis under Wright's island model showed that the populations in each drainage were not genetically subdivided. Only two of these stream haplotypes were found among the 66 fish analyzed from four lake populations. Despite the extreme lack of mtDNA diversity in lake populations, the observed nuclear DNA heterozygosity of 40 lake fish (0.10355) was only slightly less than that of 82 stream fish (0.11635). In the short time (3000-7000 years) that the lake fish have been landlocked, random genetic drift in a finite, stable-sized population was probably not responsible for the lack of mtDNA diversity in the lake populations. We infer the lake populations have probably experienced at least one, severe, but transitory bottleneck possibly induced by natural selection for life-history characters essential for survival in the lacustrine habitat. If speciation is occurring in the landlocked populations of G. truttaceus, then it may be driven by genetic transilience.
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Affiliation(s)
- J R Ovenden
- Department of Zoology, University of Tasmania, Hobart, Australia
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Ovenden JR, Mahon RJ. Venereal transmission of Sindbis virus between individuals of Aedes australis (Diptera: Culicidae). J Med Entomol 1984; 21:292-295. [PMID: 6748004 DOI: 10.1093/jmedent/21.3.292] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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