Data

NESP MBH A1 Euryhaline Elasmobranchs genetics outputs

Australian Ocean Data Network
Dr Pierre Feutry ; Dr Peter Kyne
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=http://catalogue-aodn.prod.aodn.org.au/geonetwork/srv/eng/search?uuid=f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339&rft.title=NESP MBH A1 Euryhaline Elasmobranchs genetics outputs&rft.identifier=http://catalogue-aodn.prod.aodn.org.au/geonetwork/srv/eng/search?uuid=f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339&rft.description=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).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.&rft.creator=Dr Pierre Feutry &rft.creator=Dr Peter Kyne &rft.date=2017&rft.coverage=northlimit=-10.6169880271; southlimit=-18.1871908799; westlimit=121.775390625; eastLimit=138.123046875&rft.coverage=northlimit=-10.6169880271; southlimit=-18.1871908799; westlimit=121.775390625; eastLimit=138.123046875&rft_rights=Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0&rft_subject=biota&rft_subject=Close-kin mark-recapture&rft_subject=Population genetics&rft_subject=Euryhaline elasmobranchs&rft_subject=FISH&rft_subject=EARTH SCIENCE&rft_subject=BIOLOGICAL CLASSIFICATION&rft_subject=ANIMALS/VERTEBRATES&rft_subject=SHARKS/RAYS/CHIMAERAS&rft_subject=ENDANGERED SPECIES&rft_subject=BIOSPHERE&rft_subject=ECOLOGICAL DYNAMICS&rft_subject=SPECIES/POPULATION INTERACTIONS&rft_subject=ANIMAL BREEDING AND GENETICS&rft_subject=AGRICULTURE&rft_subject=ANIMAL SCIENCE&rft_subject=SURVIVAL RATES&rft_subject=MIGRATORY RATES/ROUTES&rft_subject=Anoxypristis cuspidata&rft_subject=Carcharhinus leucas&rft_subject=Eusphyra blochii&rft_subject=Glyphis garricki&rft_subject=Glyphis glyphis&rft_subject=Himantura uarnak&rft_subject=Negaprion acutidens&rft_subject=Pateobatis hortlei&rft_subject=Pristis clavata&rft_subject=Pristis pristis&rft_subject=Rhizoprionodon taylori&rft_subject=Urogymnus acanthobothrium&rft_subject=Urogymnus dalyensis&rft_subject=Glaucostegus typus&rft.type=dataset&rft.language=English Access the data

Licence & Rights:

Open Licence view details
CC-BY

Creative Commons Attribution 4.0 International License
http://creativecommons.org/licenses/by/4.0

Access:

Open

Brief description

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).

Lineage

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.

Notes

Credit
National Environmental Science Program (NESP) Marine Biodiversity Hub
Credit
Charles Darwin University
Credit
Commonwealth Scientific and Industrial Research Organisation (CSIRO)

Created: 2017-01-20

Data time period: 2010-10-01

138.123046875,-10.6169880271 138.123046875,-18.1871908799 121.775390625,-18.1871908799 121.775390625,-10.6169880271 138.123046875,-10.6169880271

129.94921875,-14.4020894535

text: northlimit=-10.6169880271; southlimit=-18.1871908799; westlimit=121.775390625; eastLimit=138.123046875

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Euryhaline_elasmo_genetics_sequence_index.csv

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Chen_etal_Anoxypristis_cuspidata_complete_mitochondrial_genome_early_online.pdf

(ASSOCIATED DATA ACCESS - KP233202 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KP233202

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Chen_etal_Pristis_pectinata_complete_mitochondrial_genome_early_online.pdf

(ASSOCIATED DATA ACCESS - KP400584 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KP400584

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Chen_etal_Glyphis_glyphis_complete_mitochondrial_genome__2014.pdf

(ASSOCIATED DATA ACCESS - KF006312 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KF006312

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Pristis_clavata_complete_mitogenome_2015.pdf

(ASSOCIATED DATA ACCESS - KF381507 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KF381507

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Carcharhinus_amblyrhynchoides_complete_mitogenome_2016.pdf

(ASSOCIATED DATA ACCESS - KF956523 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KF956523

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Glyphis_garricki_complete_mitogenome_2015.pdf

(ASSOCIATED DATA ACCESS - KF646786 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KF646786

(PUBLICATION: Complete mitochondrial genome of the Freshwater Whipray Himantura dalyensis)

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Himantura_dalyensis_complete_mitogenome_2016.pdf

(ASSOCIATED DATA ACCESS - KM244769 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KM244769

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Carcharhinus_amboinensis_complete_mitogenome_2016.pdf

(ASSOCIATED DATA ACCESS - KM921745 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KM921745

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

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Eusphyra_blochii_phylogenomic_position_2016.pdf

(ASSOCIATED DATA ACCESS - KU892590 (Genbank))

uri : https://www.ncbi.nlm.nih.gov/nuccore/KU892590

(PUBLICATION: Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing)

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Mitogenomics_speartooth_shark_challenges_2014.pdf

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

uri : https://www.ncbi.nlm.nih.gov/nuccore

URI : 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(PUBLICATION: Inferring contemporary and historical genetic connectivity from juveniles)

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Inferring_contemporary_historical_connectivity_juveniles_2017.pdf

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

uri : https://www.ncbi.nlm.nih.gov/nuccore

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

uri : https://onlinelibrary.wiley.com/action/downloadSupplement

URI : https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fmec.13929&file=mec13929-sup-0003-AppendixS4.xlsx

(PUBLICATION: Whole mitogenome sequencing refines population structure of the Critically Endangered sawfish Pristis pristis)

uri : https://data.imas.utas.edu.au/attachments/f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339/Feutry_etal_Pristis_pristis_mitogenomicspopulation_structure_2015.pdf

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

uri : https://www.ncbi.nlm.nih.gov/sra

URI : https://www.ncbi.nlm.nih.gov/sra?term=((%22srr1732112%22%20OR%20%22srr1732113%22%20OR%20%22srr1732114%22%20OR%20%22srr1732115%22%20OR%20%22srr1732116%22%20OR%20%22srr1732117%22%20OR%20%22srr1732118%22%20OR%20%22srr1732119%22%20OR%20%22srr1732120%22%20OR%20%22srr1732121%22%20OR%20%22srr1732122%22%20OR%20%22srr1732123%22%20OR%20%22srr1732124%22%20OR%20%22srr1732125%22%20OR%20%22srr1732126%22%20OR%20%22srr1732127%22%20OR%20%22srr1732128%22%20OR%20%22srr1732129%22%20OR%20%22srr1732130%22%20OR%20%22srr1732131%22%20OR%20%22srr1732132%22%20OR%20%22srr1732133%22%20OR%20%22srr1732134%22%20OR%20%22srr1732135%22%20OR%20%22srr1732136%22%20OR%20%22srr1732137%22%20OR%20%22srr1732138%22%20OR%20%22srr1732139%22%20OR%20%22srr1732140%22%20OR%20%22srr1732141%22%20OR%20%22srr1732142%22%20OR%20%22srr1732143%22%20OR%20%22srr1732144%22%20OR%20%22srr1732145%22%20OR%20%22srr1732146%22%20OR%20%22srr1732147%22%20OR%20%22srr1732148%22%20OR%20%22srr1732149%22%20OR%20%22srr1732150%22%20OR%20%22srr1732151%22%20OR%20%22srr1732152%22%20OR%20%22srr1732153%22%20OR%20%22srr1732154%22%20OR%20%22srr1732155%22%20OR%20%22srr1732156%22%20OR%20%22srr1732157%22%20OR%20%22srr1732158%22%20OR%20%22srr1732159%22%20OR%20%22srr1732160%22%20OR%20%22srr1732161%22%20OR%20%22srr1732162%22%20OR%20%22srr1732163%22%20OR%20%22srr1732164%22%20OR%20%22srr1732165%22%20OR%20%22srr1732166%22%20OR%20%22srr1732167%22%20OR%20%22srr1732168%22%20OR%20%22srr1732169%22%20OR%20%22srr1732170%22%20OR%20%22srr1732171%22%20OR%20%22srr1732172%22%20OR%20%22srr1732173%22%20OR%20%22srr1732174%22%20OR%20%22srr1732175%22%20OR%20%22srr1732176%22%20OR%20%22srr1732177%22%20OR%20%22srr1732178%22%20OR%20%22srr1732179%22%20OR%20%22srr1732180%22%20OR%20%22srr1732181%22%20OR%20%22srr1732182%22%20OR%20%22srr1732183%22%20OR%20%22srr1732184%22%20OR%20%22srr1732185%22%20OR%20%22srr1732186%22%20OR%20%22srr1732187%22%20OR%20%22srr1732188%22%20OR%20%22srr1732189%22%20OR%20%22srr1732190%22%20OR%20%22srr1732191%22%20OR%20%22srr1732192%22%20OR%20%22srr1732193%22%20OR%20%22srr1732194%22%20OR%20%22srr1732195%22%20OR%20%22srr1732196%22%20OR%20%22srr1732197%22%20OR%20%22srr1732198%22%20OR%20%22srr1732199%22%20OR%20%22srr1732200%22%20OR%20%22srr1732201%22%20OR%20%22srr1732202%22%20OR%20%22srr1732203%22))

(NESP Project A1 [ANDS RDA record])

purl : http://purl.org/au-research/grants/nesp/mb/a1

Identifiers
  • global : f7d3a11e-bd2b-4d8d-af3d-d2fc3a058339