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

OverviewThe 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 analysisPlease refer to the associated publication (see below) for all relevant methodology.Explanation of worksheetSample 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).

# 数据集概述
本项目旨在利用高变异分子标记，探究南极底栖端足类在精细（数百米）、中等（数十公里）及大尺度（数千公里）下的遗传连通性与多样性。为此，我们针对常见南极端足类物种**富兰克林尔钩虾（Orchomenella franklini）**开发了7个特异性微卫星（microsatellite）标记。本研究共从东南极海域采集到718份O. franklini标本，每个采样位点约采集30份标本，且采样位点在空间上呈层级嵌套结构：即间距100米的位点嵌套于间距1-30公里的区域内，而这些区域又嵌套于2个大尺度区域（间距约1400公里）中。所有端足类标本均针对7个微卫星位点进行了基因分型（尽管部分标本中部分位点无法成功扩增）。本数据集包含所有获得的遗传数据：即718份端足类标本中，每个成功扩增的微卫星位点的两个等位基因片段长度。

# 数据收集与分析
请参阅相关已发表文献（见下文）以获取完整的实验方法细节。

# 工作表说明
1. **样本编号（Sample ID）**：用于识别每份端足类标本的唯一编码，编码本身无实际生物学意义。
2. **区域（Region）**：每份标本的采集海域所属大尺度区域，本次研究的两个区域为凯西站（Casey Station）与戴维斯站（Davis Station），二者间距约1400公里。
3. **采样区域（Location）**：单一大区域内的具体采样点，其名称为澳大利亚南极署（Australian Antarctic Division）登记的官方名称，因此可通过澳大利亚南极署数据中心的地图获取精确坐标。以斜体标注的采样区域（及对应采样位点）被归类为受污染区域，详细分类标准请参阅相关文献。
4. **采样位点（Site）**：每个采样区域内的具体采样点，命名规则为所属采样区域的两位字母缩写，后接小写字母a、b、c或d，分别代表第1、2、3、4号位点。
5. **微卫星数据（Microsatellite data）**：包含所有为每份端足类标本获得的微卫星遗传数据。数据以每个成功扩增的7个微卫星位点的等位基因片段长度（单位：碱基对）形式呈现，7个位点分别命名为Orcfra3、Orcfra4、Orcfra5、Orcfra6、Orcfra12、Orcfra13、Orcfra26。由于O. franklini为二倍体（diploid）生物，每个微卫星位点对应两个等位基因片段（因此每个位点下设两列数据）。若某份标本的某一位点经至少两次尝试后仍无法成功扩增，则以‘0’表示。

本研究于2009年1月至3月在凯西站采集标本，2009年11月至2010年4月在戴维斯站采集标本。遗传数据的生成与分析工作分别于2009年4月至11月，以及2010年5月至2011年4月完成。

本数据集来源于常见南极端足类物种富兰克林尔钩虾（Orchomenella franklini）的遗传数据：共采集718份标本，采样点均位于凯西站或戴维斯站周边20公里范围内，采集时间为2009年至2010年。所有标本均针对7个微卫星位点进行基因分型（部分标本中个别位点无法成功扩增）。