Resilience of Antarctic marine benthic invertebrates and the ecological consequences of environmental change - Amphipod Data 2002/10

Occurrence
Versão mais recente published by Australian Antarctic Data Centre on set. 19, 2018 Australian Antarctic Data Centre
Publication date:
19 de setembro de 2018
Licença:
CC-BY 4.0

Baixe a última versão do recurso de dados, como um Darwin Core Archive (DwC-A) ou recurso de metadados, como EML ou RTF:

Dados como um arquivo DwC-A download 125 registros em English (9 KB) - Frequência de atualização: desconhecido
Metadados como um arquivo EML download em English (23 KB)
Metadados como um arquivo RTF download em English (20 KB)

Descrição

Overview The aim of the project was to assess the genetic connectivity of benthic amphipods (crustaceans) on a circumantarctic scale. Two sibling amphipod species were chosen as the subjects for this study: Eusirus perdentatus and Eusirus giganteus. Samples of both species were collected (or donated by other institutions) from five broad regions of the Antarctic coast (see 'Sample location information' worksheet). The dataset we generated represents DNA sequences we obtained from these amphipods. Each amphipod was sequenced for three gene regions - these were cytochrome oxidase subunit I (COI), internal transcribed spacer 2 (ITS2) and cytochrome b (CytB). Each DNA sequence generated has been deposited on the publicly-accessible GenBank website (www.ncbi.nlm.nih.gov/genbank/) and therefore has its own accession number (which can be typed into the GenBank search bar to access the actual DNA sequence in .fasta format). The attached spreadsheet provides details on the location, depth and date of each amphipod sample collected, the preliminary species ID for each amphipod*, and the resultant DNA sequences corresponding to each of the three gene regions amplified (these are provided as Genbank accession numbers). *Results of this project have actually highlighted that Eusirus perdentatus and Eusirus giganteus almost certainly contain several extra cryptic species, therefore these ID's are likely to be revised in the future. Data collection and analysis The full methodology used to generate and analyse the DNA sequences prior to their deposition on Genbank can be found in the associated publication (see below). Most amphipod samples were collected between January 2007 and January 2010. However, a small proportion of the samples were collected on Polarstern voyages that took place in February 2002 and December 2003-January 2004. Genetic data was generated and analysed between June 2008 and May 2010. Circumantarctic DNA sequences obtained from two amphipod species, Eusirus perdentatus and Eusirus giganteus - DNA sequences obtained from two sibling amphipod species, Eusirus perdentatus and Eusirus giganteus. Samples of both species were collected (or donated by other institutions) from five broad regions of the Antarctic coast: Tressler Bank, East Coast, Ross Sea, Antarctic Peninsula and Weddell Sea. Collection dates ranged from 2002 to 2010. Sample location information is included. Explanation of spreadsheet Worksheet: 'Samples and genetic data' This worksheet contains all of the actual data generated, although rather than providing entire genetic sequences, we provide the Genbank accession number which can be used to access the sequence online (as explained above). The column headings are as follows: Sample ID- a unique code given to each amphipod sample as a form of identity. Morphological ID- the species identification for each amphipod, as determined morphologically (i.e. the genetic data has since illuminated that these IDs may need revision in the future). Sampling site- a code for the exact location from which each amphipod was sampled. For details on these locations, refer to 'Sample location information' worksheet, which uses the same codes. DNA sequence (Genbank accession number)- Genbank accession numbers for the DNA sequences obtained from each amphipod. The three columns within this represent the three gene regions we sequenced: COI (cytochrome oxidase subunit I), CytB (cytochrome b) and ITS2 (internal transcribed spacer 2). Occasionally one of these gene regions would fail to amplify in a particular sample, or the sequence was ambiguous, therefore not all amphipod samples have an accession number for all three gene regions. Worksheet: 'Sample location information' This worksheet provides the details on the actual collection of the amphipod specimens. Column headings are as follows: Sampling site- the code for each site from which amphipods were sampled, as used in the previous worksheet. Latitude- coordinates for each sampling site. Longitude- coordinates for each sampling site. Depth range of trawl (m)- As all amphipod samples were collected in benthic trawls deployed from research vessels, this column provides the depth range of the seabed over which each trawl was dragged. Collection date- the month and year in which each site was sampled. Region of Antarctic coast- the broad geographic region of the Antarctic coastline into which each set of sampling sites is grouped. Research vessel- the research vessel from which benthic trawls were deployed to collect the amphipods at each site. Note that for each broad geographic region, a single vessel was responsible for collecting all samples.

Registros de Dados

Os dados deste recurso de ocorrência foram publicados como um Darwin Core Archive (DwC-A), que é o formato padronizado para compartilhamento de dados de biodiversidade como um conjunto de uma ou mais tabelas de dados. A tabela de dados do núcleo contém 125 registros.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

Baird, H., Miller, K., Stark, J.S. (2012, updated 2017) Resilience of Antarctic marine benthic invertebrates and the ecological consequences of environmental change - Amphipod Data Australian Antarctic Data Centre - CAASM Metadata.

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é Australian Antarctic Data Centre. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 53334055-d64e-48cd-8c83-2295d3891782.  Australian Antarctic Data Centre publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Atlas of Living Australia.

Palavras-chave

Occurrence; Amphipods

Contatos

Helena Baird
  • Originador ●
  • Ponto De Contato
  • Technical contact
University of Tasmania
Hobart
AU
Dave Connell
  • Provedor Dos Metadados
Australia Antarctic Division
  • 203 Channel Highway
7050 Hobart
Tasmania
AU
Karen Miller
  • Ponto De Contato
  • Investigator
Australian Institute of Marine Science
AU
Jonathan Stark
  • Ponto De Contato
  • Investigator
Australia Antarctic Division
  • 203 Channel Highway
7050 Hobart
Tasmania
AU

Cobertura Geográfica

Southern Ocean, Antarctica, Polar

Coordenadas delimitadoras Sul Oeste [-77, -143], Norte Leste [-61, -61]

Cobertura Taxonômica

The aim of the project was to assess the genetic connectivity of benthic amphipods (crustaceans) on a circumantarctic scale. Two sibling amphipod species were chosen as the subjects for this study: Eusirus perdentatus and Eusirus giganteus. Samples of both species were collected (or donated by other institutions) from five broad regions of the Antarctic coast (see 'Sample location information' worksheet). The dataset we generated represents DNA sequences we obtained from these amphipods. Each amphipod was sequenced for three gene regions - these were cytochrome oxidase subunit I (COI), internal transcribed spacer 2 (ITS2) and cytochrome b (CytB). Each DNA sequence generated has been deposited on the publicly-accessible GenBank website (www.ncbi.nlm.nih.gov/genbank/) and therefore has its own accession number (which can be typed into the GenBank search bar to access the actual DNA sequence in .fasta format). *Results of this project have actually highlighted that Eusirus perdentatus and Eusirus giganteus almost certainly contain several extra cryptic species, therefore these ID's are likely to be revised in the future.

Espécie Eusirus perdentatus, Eusirus giganteus

Cobertura Temporal

Data Inicial / Data final 2002-01-01 / 2010-01-01

Dados Sobre o Projeto

Overview The aim of the project was to assess the genetic connectivity of benthic amphipods (crustaceans) on a circumantarctic scale. Two sibling amphipod species were chosen as the subjects for this study: Eusirus perdentatus and Eusirus giganteus. Samples of both species were collected (or donated by other institutions) from five broad regions of the Antarctic coast (see 'Sample location information' worksheet). The dataset we generated represents DNA sequences we obtained from these amphipods. Each amphipod was sequenced for three gene regions - these were cytochrome oxidase subunit I (COI), internal transcribed spacer 2 (ITS2) and cytochrome b (CytB). Each DNA sequence generated has been deposited on the publicly-accessible GenBank website (www.ncbi.nlm.nih.gov/genbank/) and therefore has its own accession number (which can be typed into the GenBank search bar to access the actual DNA sequence in .fasta format). The attached spreadsheet provides details on the location, depth and date of each amphipod sample collected, the preliminary species ID for each amphipod*, and the resultant DNA sequences corresponding to each of the three gene regions amplified (these are provided as Genbank accession numbers). *Results of this project have actually highlighted that Eusirus perdentatus and Eusirus giganteus almost certainly contain several extra cryptic species, therefore these ID's are likely to be revised in the future. Data collection and analysis The full methodology used to generate and analyse the DNA sequences prior to their deposition on Genbank can be found in the associated publication (see below). Most amphipod samples were collected between January 2007 and January 2010. However, a small proportion of the samples were collected on Polarstern voyages that took place in February 2002 and December 2003-January 2004. Genetic data was generated and analysed between June 2008 and May 2010. Circumantarctic DNA sequences obtained from two amphipod species, Eusirus perdentatus and Eusirus giganteus - DNA sequences obtained from two sibling amphipod species, Eusirus perdentatus and Eusirus giganteus. Samples of both species were collected (or donated by other institutions) from five broad regions of the Antarctic coast: Tressler Bank, East Coast, Ross Sea, Antarctic Peninsula and Weddell Sea. Collection dates ranged from 2002 to 2010. Sample location information is included.

Título Resilience of Antarctic marine benthic invertebrates and the ecological consequences of environmental change - Amphipod Data
Identificador ASAC_3051
Descrição da Área de Estudo Sampling site- the code for each site from which amphipods were sampled, as used in the previous worksheet. Latitude- coordinates for each sampling site. Longitude- coordinates for each sampling site. Depth range of trawl (m)- As all amphipod samples were collected in benthic trawls deployed from research vessels, this column provides the depth range of the seabed over which each trawl was dragged. Collection date- the month and year in which each site was sampled. Region of Antarctic coast- the broad geographic region of the Antarctic coastline into which each set of sampling sites is grouped. Research vessel- the research vessel from which benthic trawls were deployed to collect the amphipods at each site. Note that for each broad geographic region, a single vessel was responsible for collecting all samples.
Descrição do Design This worksheet contains all of the actual data generated, although rather than providing entire genetic sequences, we provide the Genbank accession number which can be used to access the sequence online (as explained above). The column headings are as follows: Sample ID- a unique code given to each amphipod sample as a form of identity. Morphological ID- the species identification for each amphipod, as determined morphologically (i.e. the genetic data has since illuminated that these IDs may need revision in the future). Sampling site- a code for the exact location from which each amphipod was sampled. For details on these locations, refer to 'Sample location information' worksheet, which uses the same codes. DNA sequence (Genbank accession number)- Genbank accession numbers for the DNA sequences obtained from each amphipod. The three columns within this represent the three gene regions we sequenced: COI (cytochrome oxidase subunit I), CytB (cytochrome b) and ITS2 (internal transcribed spacer 2). Occasionally one of these gene regions would fail to amplify in a particular sample, or the sequence was ambiguous, therefore not all amphipod samples have an accession number for all three gene regions.

O pessoal envolvido no projeto:

Karen Miller
  • Pesquisador Principal

Métodos de Amostragem

Worksheet: 'Samples and genetic data' This worksheet contains all of the actual data generated, although rather than providing entire genetic sequences, we provide the Genbank accession number which can be used to access the sequence online (as explained above). The column headings are as follows: Sample ID- a unique code given to each amphipod sample as a form of identity. Morphological ID- the species identification for each amphipod, as determined morphologically (i.e. the genetic data has since illuminated that these IDs may need revision in the future). Sampling site- a code for the exact location from which each amphipod was sampled. For details on these locations, refer to 'Sample location information' worksheet, which uses the same codes. DNA sequence (Genbank accession number)- Genbank accession numbers for the DNA sequences obtained from each amphipod. The three columns within this represent the three gene regions we sequenced: COI (cytochrome oxidase subunit I), CytB (cytochrome b) and ITS2 (internal transcribed spacer 2). Occasionally one of these gene regions would fail to amplify in a particular sample, or the sequence was ambiguous, therefore not all amphipod samples have an accession number for all three gene regions. This worksheet provides the details on the actual collection of the amphipod specimens. Column headings are as follows: Sampling site- the code for each site from which amphipods were sampled, as used in the previous worksheet. Latitude- coordinates for each sampling site. Longitude- coordinates for each sampling site. Depth range of trawl (m)- As all amphipod samples were collected in benthic trawls deployed from research vessels, this column provides the depth range of the seabed over which each trawl was dragged. Collection date- the month and year in which each site was sampled. Region of Antarctic coast- the broad geographic region of the Antarctic coastline into which each set of sampling sites is grouped. Research vessel- the research vessel from which benthic trawls were deployed to collect the amphipods at each site. Note that for each broad geographic region, a single vessel was responsible for collecting all samples.

Área de Estudo Overview The aim of the project was to assess the genetic connectivity of benthic amphipods (crustaceans) on a circumantarctic scale. Two sibling amphipod species were chosen as the subjects for this study: Eusirus perdentatus and Eusirus giganteus. Samples of both species were collected (or donated by other institutions) from five broad regions of the Antarctic coast (see 'Sample location information' worksheet). The dataset we generated represents DNA sequences we obtained from these amphipods. Each amphipod was sequenced for three gene regions - these were cytochrome oxidase subunit I (COI), internal transcribed spacer 2 (ITS2) and cytochrome b (CytB). Each DNA sequence generated has been deposited on the publicly-accessible GenBank website (www.ncbi.nlm.nih.gov/genbank/) and therefore has its own accession number (which can be typed into the GenBank search bar to access the actual DNA sequence in .fasta format). The attached spreadsheet provides details on the location, depth and date of each amphipod sample collected, the preliminary species ID for each amphipod*, and the resultant DNA sequences corresponding to each of the three gene regions amplified (these are provided as Genbank accession numbers). *Results of this project have actually highlighted that Eusirus perdentatus and Eusirus giganteus almost certainly contain several extra cryptic species, therefore these ID's are likely to be revised in the future.
Controle de Qualidade Some problems with the quality of sequences obtained for the ITS2 gene region: this is explained in the associated publication.

Descrição dos passos do método:

  1. Original datasheets were reformatted to fit IPT Biodiversity.AQ standard. The new datasheet "amphipods.csv" provides the dataset ID, verbatim latitude and verbatim longitude that were converted to decimal latitude and longitude, also provided. Taxonomical organisation to the lowest taxonomical rank that could be determined, after matched in WoRMS (World Register of Marine Species). The associated sequences for identified species and the associated reference.

Citações bibliográficas

  1. Baird,H.P., Miller,K.J. and Stark,J.S. 2011 Evidence of hidden biodiversity, ongoing speciation and diverse patterns of genetic structure in giant Antarctic amphipods. Marine Ecology 20 (16): 3439-54. https://doi.org/10.1111/j.1365-294X.2011.05173.x

Metadados Adicionais