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

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.

### 数据集概述
本项目旨在评估环南极尺度下底栖端足类（甲壳动物）的遗传连通性。本研究选取两种端足类姊妹种作为研究对象：齿真戎（Eusirus perdentatus）与巨真戎（Eusirus giganteus）。两种物种的样本均采集自南极海岸的五大区域（或由其他机构捐赠），详见「样本采集地点信息」工作表。
本数据集包含从上述端足类样本获取的DNA序列信息。每个端足类样本均针对三个基因区域进行测序：细胞色素氧化酶亚基I（cytochrome oxidase subunit I，COI）、内部转录间隔区2（internal transcribed spacer 2，ITS2）以及细胞色素b（cytochrome b，CytB）。所有生成的DNA序列均已提交至公开可访问的基因银行（GenBank）网站（www.ncbi.nlm.nih.gov/genbank/），每条序列均拥有专属的登录号，使用者可通过GenBank搜索栏输入登录号，获取.fasta格式的原始DNA序列。
随附的电子表格提供了各端足类样本的采集地点、水深、采集日期、初步物种鉴定结果*，以及与扩增得到的三个基因区域对应的DNA序列信息（以GenBank登录号形式提供）。

*本项目的研究结果实际表明，齿真戎与巨真戎极可能包含多个额外的隐存种，因此这些物种鉴定结果未来或将被修订。

### 数据采集与分析
本项目中，基因序列在提交至基因银行（GenBank）前的生成与分析完整方法学流程，详见下述关联出版物。
绝大多数端足类样本采集于2007年1月至2010年1月期间；但另有少量样本采集自2002年2月以及2003年12月—2004年1月期间的极星号（Polarstern）科考航次。遗传数据的生成与分析工作开展于2008年6月至2010年5月之间。

本数据集包含采自齿真戎（Eusirus perdentatus）与巨真戎（Eusirus giganteus）两种端足类的环南极DNA序列。两种端足类姊妹种的样本均采集自南极海岸的五大区域：特雷瑟尔浅滩（Tressler Bank）、东海岸、罗斯海、南极半岛以及威德尔海（Weddell Sea），样本采集时间跨度为2002年至2010年，相关采样地点信息已包含于数据集中。

### 电子表格说明
#### 工作表：「样本与遗传数据」
本工作表包含本次研究生成的全部原始数据。相较于直接提供完整基因序列，本工作表通过提供GenBank登录号的形式供使用者在线获取对应序列（详见前文说明）。各列标题说明如下：
- 样本编号（Sample ID）：为每个端足类样本分配的唯一身份编码。
- 形态学鉴定（Morphological ID）：通过形态学方法确定的每个样本的物种鉴定结果（注：后续遗传数据表明此类鉴定结果未来或需修订）。
- 采样位点（Sampling site）：每个端足类样本的具体采样位置编码，相关点位的详细信息请参阅「样本采集地点信息」工作表，该工作表使用相同的编码体系。
- DNA序列（GenBank登录号）：从每个端足类样本获取的DNA序列对应的GenBank登录号。该栏目下包含三列，分别对应本次测序的三个基因区域：COI（细胞色素氧化酶亚基I）、CytB（细胞色素b）以及ITS2（内部转录间隔区2）。部分样本中某一基因区域未能成功扩增，或所得序列存在歧义，因此并非所有样本均能提供三个基因区域的登录号。

#### 工作表：「样本采集地点信息」
本工作表提供端足类标本的实际采集细节信息，各列标题说明如下：
- 采样位点：前文工作表中使用的各采样点位编码。
- 纬度（Latitude）：每个采样位点的坐标信息。
- 经度（Longitude）：每个采样位点的坐标信息。
- 拖网作业水深范围（米）：所有端足类样本均通过科研船开展的底栖拖网采集获得，本列提供各次拖网作业覆盖的海底水深范围。
- 采集日期：各采样位点的采样月份与年份。
- 南极海岸大地理区域：各采样位点所属的南极海岸线大地理分区。
- 科考船：开展底栖拖网作业以采集各点位端足类样本的科研船名称。注：每个大地理区域的所有样本均由单艘科考船负责采集。