Euryhaline Elasmobranchs genetics outputs (NESP MBH A1)

This database contains molecular data of elasmobranchs in northern Australian rivers, estuaries and coasts undertaken under the National Environmental Research Program (NERP) Marine Biodiversity Hub Project 2.4 'Supporting Management of Listed and Rare Species'. and the National Environmental Science Program (NESP) Marine Biodiversity Hub Project A1 'Northern Australian Hotspots for the Recovery of Threatened Euryhaline Elasmobranchs'. Surveys using gillnets and rod-and-line were undertaken in the Top End region of the Northern Territory and the Kimberley region of Western Australia. Tissue samples were collected from all elasmobranchs for molecular analyses (population genetics and close-kin mark-recapture).

Simple

Identification info

Date (Creation)
2017-01-20

Point of contact

CSIRO Oceans and Atmosphere – Hobart - Dr Pierre Feutry
GPO Box 1538
Hobart
Tasmania
7001
Australia
ORCID ID >

Principal investigator

Charles Darwin University (CDU) - Dr Peter Kyne
Research Institute for the Environment and Livelihoods
Charles Darwin University
Darwin
Northern Territory
0909
Australia
Credit
National Environmental Science Program (NESP) Marine Biodiversity Hub
Credit
Charles Darwin University
Credit
Commonwealth Scientific and Industrial Research Organisation (CSIRO)
Status
Completed

Point of contact

CSIRO Oceans and Atmosphere – Hobart - Dr Pierre Feutry
GPO Box 1538
Hobart
Tasmania
7001
Australia
ORCID ID >

Principal investigator

Charles Darwin University (CDU) - Dr Peter Kyne
Research Institute for the Environment and Livelihoods
Charles Darwin University
Darwin
Northern Territory
0909
Australia
Topic category
  • Biota

Extent

N
S
E
W


Temporal extent

Time period
2010-10-01 2015-12-01

Vertical element

Minimum value
0
Maximum value
25
Identifier
EPSG::5715
Name
MSL depth
Maintenance and update frequency
Irregular
Keywords (Theme)
  • Close-kin mark-recapture
  • Population genetics
  • Euryhaline elasmobranchs
Global Change Master Directory (GCMD) Earth Science Keywords Version 8.0
Keywords (Taxon)
  • Anoxypristis cuspidata
  • Carcharhinus leucas
  • Eusphyra blochii
  • Glyphis garricki
  • Glyphis glyphis
  • Himantura uarnak
  • Negaprion acutidens
  • Pateobatis hortlei
  • Pristis clavata
  • Pristis pristis
  • Rhizoprionodon taylori
  • Urogymnus acanthobothrium
  • Urogymnus dalyensis
  • Glaucostegus typus

Resource constraints

Classification
Unclassified

Resource constraints

Use limitation
The data described in this record are the intellectual property of CSIRO through Oceans and Atmosphere, and Charles Darwin University through the Research Institute for the Environment and Livelihoods.

Resource constraints

Linkage
http://i.creativecommons.org/l/by/4.0/88x31.png

License Graphic

Title
Creative Commons Attribution 4.0 International License


>

Website
http://creativecommons.org/licenses/by/4.0/

License Text

Other constraints
Data was sourced from the NESP Marine Biodiversity Hub - The Marine Biodiversity Hub is supported through funding from the Australian Government's National Environmental Science Program (NESP), administered by the Department of the Environment (DOE).
Other constraints
This data is hosted by the Institute for Marine and Antarctic Studies, University of Tasmania, on behalf of CSIRO Oceans and Atmosphere, and Charles Darwin University.
Language
English
Character encoding
UTF8
Supplemental Information
Chen, X., Liu, M., Grewe, P. M., Kyne, P. M., & Feutry, P. (2014). Complete mitochondrial genome of the Critically Endangered speartooth shark Glyphis glyphis (Carcharhiniformes: Carcharhinidae). Chen, X., Wiley, T., Kyne, P. M., & Feutry, P. (2016). Complete mitochondrial genome of the Critically Endangered Smalltooth Sawfish Pristis pectinata (Rajiformes: Pristidae). Mitochondrial DNA Part A, 27(5), 3331-3332. Chen, X., Kyne, P. M., Pillans, R. D., & Feutry, P. (2016). Complete mitochondrial genome of the endangered narrow sawfish Anoxypristis cuspidata (Rajiformes: Pristidae). Mitochondrial DNA Part A, 27(6), 4172-4173. Feutry, P., Kyne, P. M., Grewe, P. M., Chen, X., & Liu, M. (2015). Whole mitogenome of the Endangered dwarf sawfish Pristis clavata (Rajiformes: Pristidae). Mitochondrial DNA, 26(2), 329-330. Feutry, P., Pillans, R. D., Kyne, P. M., & Chen, X. (2016). Complete mitogenome of the graceful shark Carcharhinus amblyrhynchoides (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA Part A, 27(1), 314-315. Feutry, P., Grewe, P. M., Kyne, P. M., & Chen, X. (2015). Complete mitogenomic sequence of the Critically Endangered northern river shark Glyphis garricki (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA, 26(6), 855-856. Feutry, P., Kyne, P. M., Peng, Z., Pan, L., & Chen, X. (2016). Complete mitochondrial genome of the Freshwater Whipray Himantura dalyensis. Mitochondrial DNA Part A, 27(3), 1589-1590. Feutry, P., Every, S. L., Kyne, P. M., Sun, R., & Chen, X. (2016). Complete mitochondrial genome of the Pigeye Shark Carcharhinus amboinensis (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA Part A, 27(3), 2129-2130. Feutry, P., Kyne, P. M., & Chen, X. (2016). The phylogenomic position of the Winghead Shark Eusphyra blochii (Carcharhiniformes, Sphyrnidae) inferred from the mitochondrial genome. Mitochondrial DNA Part B, 1(1), 386-387. Feutry, P., Kyne, P. M., Pillans, R. D., Chen, X., Naylor, G. J., & Grewe, P. M. (2014). Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing. BMC evolutionary biology, 14(1), 232. Feutry, P., Berry, O., Kyne, P. M., Pillans, R. D., Hillary, R. M., Grewe, P. M., ... & Bravington, M. (2016). Inferring contemporary and historical genetic connectivity from juveniles. Molecular Ecology. Feutry, P., Kyne, P. M., Pillans, R. D., Chen, X., Marthick, J., Morgan, D. L., & Grewe, P. M. (2015). Whole mitogenome sequencing refines population structure of the Critically Endangered sawfish Pristis pristis. Marine Ecology Progress Series, 533, 237-244.

Distribution Information

Distribution format
  • online sequence database

OnLine resource
DATA ACCESS - Euryhaline elasmobranch genetics sequence index accession/run numbers (for search in Genbank, Sequence Read Archive)

OnLine resource
PUBLICATION: Complete mitochondrial genome of the endangered narrow sawfish Anoxypristis cuspidata (Rajiformes: Pristidae)

OnLine resource
ASSOCIATED DATA ACCESS - KP233202 (Genbank)

OnLine resource
PUBLICATION: Complete mitochondrial genome of the Critically Endangered Smalltooth Sawfish Pristis pectinata (Rajiformes: Pristidae)

OnLine resource
ASSOCIATED DATA ACCESS - KP400584 (Genbank)

OnLine resource
PUBLICATION: Complete mitochondrial genome of the Critically Endangered speartooth shark Glyphis glyphis (Carcharhiniformes: Carcharhinidae)

OnLine resource
ASSOCIATED DATA ACCESS - KF006312 (Genbank)

OnLine resource
PUBLICATION: Whole mitogenome of the Endangered dwarf sawfish Pristis clavata (Rajiformes: Pristidae)

OnLine resource
ASSOCIATED DATA ACCESS - KF381507 (Genbank)

OnLine resource
PUBLICATION: Complete mitogenome of the graceful shark Carcharhinus amblyrhynchoides (Carcharhiniformes: Carcharhinidae)

OnLine resource
ASSOCIATED DATA ACCESS - KF956523 (Genbank)

OnLine resource
PUBLICATION: Complete mitogenomic sequence of the Critically Endangered northern river shark Glyphis garricki (Carcharhiniformes: Carcharhinidae)

OnLine resource
ASSOCIATED DATA ACCESS - KF646786 (Genbank)

OnLine resource
PUBLICATION: Complete mitochondrial genome of the Freshwater Whipray Himantura dalyensis

OnLine resource
ASSOCIATED DATA ACCESS - KM244769 (Genbank)

OnLine resource
PUBLICATION: Complete mitochondrial genome of the Pigeye Shark Carcharhinus amboinensis (Carcharhiniformes: Carcharhinidae)

OnLine resource
ASSOCIATED DATA ACCESS - KM921745 (Genbank)

OnLine resource
PUBLICATION: The phylogenomic position of the Winghead Shark Eusphyra blochii (Carcharhiniformes, Sphyrnidae) inferred from the mitochondrial genome

OnLine resource
ASSOCIATED DATA ACCESS - KU892590 (Genbank)

OnLine resource
PUBLICATION: Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing

OnLine resource
ASSOCIATED DATA ACCESS - KM100613 to KM100704 (Genbank)

OnLine resource
PUBLICATION: Inferring contemporary and historical genetic connectivity from juveniles

OnLine resource
ASSOCIATED DATA ACCESS - KY039188 to KY039268 (Genbank)

OnLine resource
ASSOCIATED DATA ACCESS - SNP Geontypes (Appendix S4 from /10.1111/mec.13929)

OnLine resource
PUBLICATION: Whole mitogenome sequencing refines population structure of the Critically Endangered sawfish Pristis pristis

OnLine resource
ASSOCIATED DATA ACCESS - SRR1732112 to SRR1732203 (Sequence Read Archive)

OnLine resource
NESP Project A1 [ANDS RDA record]

Resource lineage

Statement
Genomic DNA was extracted from fin clips prior to sequencing. Reference mitogenomes were sequenced using Sanger sequencing whereas mitogenomes resequencing for population analyses were carried out with an Illumina Miseq sequencer. SNP genotyping was done using the DArTseq proprietary method.
Hierarchy level
Dataset

Metadata

Metadata identifier
urn:uuid/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339

Language
English
Character encoding
UTF8

Point of contact

Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS) - Emma Flukes (NESP Marine Biodiversity Hub Data Manager)
Parent metadata

Type of resource

Resource scope
Dataset
Metadata linkage
https://metadata.imas.utas.edu.au/geonetwork/srv/eng/catalog.search#/metadata/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339

Point of truth URL of this metadata record

Date info (Creation)
2018-12-14T19:02:12
Date info (Revision)
2024-06-17T16:06:56

Metadata standard

Title
ISO 19115-3:2018
 
 

Overviews

Spatial extent

N
S
E
W


Keywords

Close-kin mark-recapture Euryhaline elasmobranchs Population genetics
Global Change Master Directory (GCMD) Earth Science Keywords Version 8.0
EARTH SCIENCE | AGRICULTURE | ANIMAL SCIENCE | ANIMAL BREEDING AND GENETICS EARTH SCIENCE | BIOLOGICAL CLASSIFICATION | ANIMALS/VERTEBRATES | FISH EARTH SCIENCE | BIOLOGICAL CLASSIFICATION | ANIMALS/VERTEBRATES | FISH | SHARKS/RAYS/CHIMAERAS EARTH SCIENCE | BIOSPHERE | ECOLOGICAL DYNAMICS | SPECIES/POPULATION INTERACTIONS | ENDANGERED SPECIES EARTH SCIENCE | BIOSPHERE | ECOLOGICAL DYNAMICS | SPECIES/POPULATION INTERACTIONS | MIGRATORY RATES/ROUTES EARTH SCIENCE | BIOSPHERE | ECOLOGICAL DYNAMICS | SPECIES/POPULATION INTERACTIONS | SURVIVAL RATES

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Not available