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

OverviewThe 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 analysisThe 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 spreadsheetWorksheet: '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.

概述
本项目旨在评估环南极尺度下底栖端足类（甲壳动物，benthic amphipods）的遗传连通性。本研究选取两种姊妹端足类物种（sibling amphipod species）作为研究对象：真亮钩虾（Eusirus perdentatus）与巨真亮钩虾（Eusirus giganteus）。两类物种的样本均采自南极沿岸五个大区域（详见「样本位置信息」工作表），或由其他机构捐赠。本数据集包含我们从这些端足类中获取的DNA序列信息。每只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序列均已上传至公开可访问的基因银行（GenBank）网站（www.ncbi.nlm.nih.gov/genbank/），并拥有专属的登录号（可在GenBank搜索栏输入该编号，获取.fasta格式的原始DNA序列）。随附的电子表格详细记录了每一份端足类样本的采集地点、水深与日期，每只样本的初步物种鉴定结果*，以及对应三个扩增基因区域的DNA序列（以GenBank登录号形式提供）。*本项目的研究结果表明，真亮钩虾与巨真亮钩虾几乎确定包含多个额外的隐存种（cryptic species），因此这些物种鉴定结果未来可能会被修订。

数据收集与分析
将DNA序列上传至GenBank之前，用于生成与分析这些序列的完整方法可参阅相关出版物（详见下文）。
绝大多数端足类样本采集于2007年1月至2010年1月之间。不过，有少量样本采集自2002年2月以及2003年12月—2004年1月的极星号（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月期间。
本数据集包含从真亮钩虾与巨真亮钩虾两种姊妹端足类中获取的环南极DNA序列。两类物种的样本均采自南极沿岸五个大区域：特雷勒浅滩（Tressler Bank）、东海岸、罗斯海（Ross Sea）、南极半岛（Antarctic Peninsula）以及威德尔海（Weddell Sea）。采集日期跨度为2002年至2010年。样本位置信息已包含在随附文件中。

电子表格说明
工作表「样本与遗传数据」
本工作表包含所有实际生成的数据，不过未直接提供完整的遗传序列，而是提供可在线获取序列的GenBank登录号（详见前文说明）。各列标题如下：
样本编号（Sample ID）：为每一份端足类样本分配的唯一识别码。
形态学鉴定（Morphological ID）：通过形态学方法确定的每只样本的物种鉴定结果（注：后续遗传研究表明，这些鉴定结果未来可能需要修订）。
采样点（Sampling site）：每只端足类样本的具体采样位置代码。如需了解这些位置的详细信息，请参阅「样本位置信息」工作表，该工作表使用了相同的代码。
DNA序列（GenBank登录号）：从每只端足类样本中获取的DNA序列对应的GenBank登录号。其中包含三列，分别对应我们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）。偶尔会出现某一基因区域在特定样本中无法扩增，或序列存在歧义的情况，因此并非所有样本都拥有三个基因区域的登录号。
工作表「样本位置信息」
本工作表提供端足类标本的实际采集细节。各列标题如下：
采样点（Sampling site）：每一份采样点的代码，与前一工作表中使用的代码一致。
纬度（Latitude）：每个采样点的坐标。
经度（Longitude）：每个采样点的坐标。
拖网水深范围（m）：由于所有端足类样本均通过科研船搭载的底栖拖网采集，本列记录了每一次拖网作业所覆盖的海底水深范围。
采集日期（Collection date）：每个采样点的采样月份与年份。
南极沿岸区域（Region of Antarctic coast）：每一组采样点所属的南极沿岸大地理区域。
科考船（Research vessel）：在每个采样点部署底栖拖网以采集端足类样本的科研船。请注意，每个大地理区域的所有样本均由单艘科考船负责采集。