TemperateReefBase Geonetwork Catalogue
Resilience of Antarctic marine benthic invertebrates and the ecological consequences of environmental change - Amphipod Genetic Data
Overview
The aim of this project was to investigate the genetic connectivity and diversity of Antarctic benthic amphipods over fine (100's of m's), intermediate (10's of km's) and large (1000's of km's) scales, using highly variable molecular markers. To achieve this, we developed seven microsatellite markers specific to the common Antarctic amphipod species Orchomenella franklini. A total of 718 specimens of O. franklini were collected from East Antarctica. Approximately 30 specimens were collected from each site, and sites were spatially hierarchically nested - i.e. sites (separated by 100m) were nested within locations (separated by 1-30km), which were nested within 2 broad regions (separated by approx. 1400km). Each amphipod sample was genotyped for all seven microsatellite loci (although occasionally a locus would not amplify in a given sample). This dataset provides all the resultant genetic data - that is, the size of the two alleles that were amplified for each microsatellite locus, in each of 718 amphipod specimens.
Data collection and analysis
Please refer to the associated publication (see below) for all relevant methodology.
Explanation of worksheet
Sample ID- a unique code given to identify each amphipod sample (the code itself has no actual meaning).
Region- the broad region of the Antarctic coast from which each sample was collected. The two regions (Casey and Davis station) are separated by approx. 1400km.
Location- the locations (within a region) from which each sample was collected. The names of each location reflect actual names registered by the Australian Antarctic Division and therefore their coordinates can be pinpointed on maps held by the Australian Antarctic Division Data Centre. Locations (and corresponding sites) written in italicised typeface are considered polluted (see publication for more information on this classification).
Site- the sites sampled within each location. Sites are named simply by a two -letter abbreviation of the location they are from, followed by a lowercase 'a', 'b', 'c' or 'd' representing site 1, 2, 3 etc.
Microsatellite data - this provides all the microsatellite genetic data generated for each amphipod specimen. Data are presented as the allele sizes (in number of base pairs) recorded for each of the seven microsatellite loci amplified. The seven microsatellite loci are called Orcfra3, Orcfra4, Orcfra5, Orcfra6, Orcfra12, Orcfra13, Orcfra26. As O. franklini is a diploid organism, each microsatellite locus has two allele sizes (hence why there are two columns underneath each locus). A '0' signifies that a particular locus did not amplify successfully in the corresponding organism (after at least two attempts).
Samples were collected from Casey station between January 2009 and March 2009, and from Davis station between November 2009 and April 2010. Genetic data was generated and analysed between April 2009 and November 2009, and between May 2010 and April 2011.
Genetic data obtained from the common Antarctic amphipod species Orchomenella franklini - Genetic data obtained from the common Antarctic amphipod species Orchomenella franklini. A total of 718 specimens were collected from sites within 20 km of Casey station or Davis station. Collection dates ranged from 2009 to 2010. Each amphipod sample was genotyped for seven microsatellite loci (although occasionally a locus would not amplify in a given sample).
Simple
Identification info
- Alternate title
- Resilience of Antarctic marine benthic invertebrates and the ecological consequences of environmental change - Amphipod Genetic Data
- Date (Publication)
- 2012-04-19
- Edition
- 1
Originator
Publisher
Principal investigator
Principal investigator
Principal investigator
Collaborator
- Name
- CAASM Metadata
- Status
- Completed
Custodian
- Topic category
-
- Biota
- Oceans
Extent
))
))
Extent
- Description
- Temporal Coverage
Temporal extent
- TimePeriod
- 2009-01-01 2009-03-31
Extent
- Description
- Temporal Coverage
Temporal extent
- TimePeriod
- 2009-11-01 2010-04-30
- Title
- Genetic Population Structure in the Antarctic Benthos: Insights from the Widespread Amphipod, Orchomenella franklini.
- Date (Publication)
- 2012
- Citation identifier
- 7
- Citation identifier
- doi: 10.1371/journal.pone.0034363.
Author
- Name
- PLoS ONE
- Issue identification
- 3
- Page
- e34363
- NASA/GCMD Earth Science Keywords
-
- EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > AMPHIPODS
- Keywords
-
- Amphipods
- NASA/GCMD Earth Science Keywords
-
- AMD/AU
- CEOS
- AMD
- NASA/GCMD Earth Science Keywords
-
- OCEAN > SOUTHERN OCEAN
- CONTINENT > ANTARCTICA
- GEOGRAPHIC REGION > POLAR
Resource constraints
- Use limitation
- This metadata record is publicly available.
Resource constraints
- Access constraints
- licence
- Other constraints
- These data are publicly available for download from the provided URL.
Resource constraints
- File type
- Portable Network Graphic
- Title
- Attribution 4.0 International (CC BY 4.0)
- Website
-
https://creativecommons.org/licenses/by/4.0/legalcode
Legal code for Creative Commons by Attribution 4.0 International license
- Use constraints
- licence
- Other constraints
- This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/). Please follow instructions listed in the citation reference provided at http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_3051_amphipod_genetics when using these data.
- Language
- English
- Character encoding
- UTF8
Distribution Information
Distributor
Distributor
Distributor
- Fees
- Free
- Planned available datetime
- 2012-04-19T00:00:00
- Units of distribution
- kb
- Transfer size
- 34
- Distribution format
-
- Excel, Text
- OnLine resource
-
GET DATA
Download point for the data
- OnLine resource
-
PROJECT HOME PAGE
Public information for ASAC project 3051
- OnLine resource
-
VIEW RELATED INFORMATION
Citation reference for this metadata record and dataset
- Maintenance and update frequency
- As needed
- Maintenance note
- 2012-04-19 - record created by Dave Connell from a metadata template provided by Helena Baird. 2012-10-16 - record updated by Dave Connell to add a parent DIF. 2017-05-11 - record updated by Dave Connell to correct contact information for Karen Miller.
Metadata
- Metadata identifier
- string/AAS_3051_amphipod_genetics
- Language
- English
- Character encoding
- UTF8
Author
Sponsor
Owner
- Title
- Parent Metadata Record
- Citation identifier
- ASAC_3051
Type of resource
- Resource scope
- Dataset
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Citation identifier
- 764328b8-c30c-4911-87b8-8d486a0511eb
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Date (Last Revision)
- 2015-04-08T11:29:35
Identifier
- Description
- metadata.extraction_date
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Citation identifier
- 8.6
- Metadata linkage
-
http://data.aad.gov.au/metadata/records/AAS_3051_amphipod_genetics
Point of truth for the metadata record
- Date info (Creation)
- 2012-04-19T00:00:00
- Date info (Last Update)
- 2017-05-11
Metadata standard
- Title
- ISO 19115-3
- Edition
- 2014
- Other citation details
- Version 1
- Title
- DIF to ISO 19115-1 Profile
Overviews
Spatial extent
Provided by
