Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.

<p>This dataset&nbsp;consists of mitochondrial sequence data and specimen information for two species of copepods, <em>Haloptilus longicornis</em> and <em>Pleuromamma xiphias</em>, collected at an open ocean time series site in the North Pacific Subtropical Gyre (station ALOHA, 22.45N, 158W) during 11 of the routine Hawai'i Ocean Time-series (HOT) research cruises from September of 2012 to October of 2013 (HOT-246 to HOT-256).&nbsp;Data for <em>Haloptilus longicornis</em> include&nbsp;a 546 base-pair fragment of mitochondrial cytochrome <em>c </em>oxidase subunit II for each of 483 individuals (mean of 44 animals per cruise). Data for <em>Pleuromamma xiphias</em> include&nbsp;a 551 base-pair fragment of mitochondrial cytochrome <em>c </em>oxidase subunit I for each of 510 individuals (mean of 46 animals per cruise). Information is also provided on the HOT cruise number, date, and specific tow from which each individual was collected. Life stage and sex of each animal are also noted when identifiable</p>

<p>These data are associated with the forthcoming publication:<br />
Iacchei, M.<u>,</u> E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.&nbsp; <em>Limnology and Oceanography &nbsp;</em></p>

<p>The unique haplotypes in these data are also available under NCBI accession numbers KY560470 - KY560514 [<em>Haloptilus longicornis</em>], KY560515 - KY560565&nbsp;[<em>Pleuromamma xiphias</em>].</p>

<p>The following files have been included in this dataset (note that the sequence IDs in these files differ from the NCBI sequence IDs):<br />
HOT-HALO.fasta: A fasta-formatted text file containing sequences for a portion of the mitochondrial cytochrome <em>c</em> oxidase subunit II gene (COII; 546 bp) for 483 <em>Haloptilus longicornis</em> individuals collected at Station ALOHA.</p>

<p>HOT-PLXI.fasta: A fasta-formatted text file containing sequences for a portion of the mitochondrial cytochrome <em>c</em> oxidase subunit I gene (COI; 551 bp) for 510 <em>Pleuromamma xiphias</em> individuals collected at Station ALOHA.</p>

<p>HALO.csv and PLXI.csv: Converted to csv from an Excel file consisting of one worksheet for <em>Haloptilus longicornis </em>and one worksheet for <em>Pleuromamma xiphias. </em>In each worksheet, column headings designate:<br />
sample_id: the sample ID number associated with the original organism collected, DNA extraction, and PCR amplification.<br />
sequence_id: the sample ID number associated with sequences analysed for the project.<br />
genus: Genus of the collected organism.<br />
species: Species of the collected organism.<br />
cruise: The cruise number for the Hawai'i Ocean Time Series (HOT) cruise on which the specimen was collected.<br />
tow: The net tow number on which the specimen was collected.<br />
collection_date: The date on which the specimen was collected, formatted as yyyy-mm-dd.<br />
stage_sex: The life stage (Copepodite or Adult) of the individual, and the sex (Copepodite, Female, Male).<br />
stage: The life stage (Copepodite or Adult) of the individual. Column added by BCO-DMO&nbsp;from the original stage_sex column for ease of use.<br />
sex: The sex (Copepodite, Female, or Male) of the individual.&nbsp;Column added by BCO-DMO&nbsp;from the original stage_sex column for ease of use.<br />
mtCO*_sequence: The mtDNA sequence (COII for <em>Haloptilus longicornis; </em>COI for <em>Pleuromamma xiphias</em>) associated with that individual. This sequence matches the sequence associated with the Sequence ID number in the respective fasta file.</p>

本数据集包含两类桡足类（copepods）动物——长角海羽猛水蚤（*Haloptilus longicornis*）与剑额宽水蚤（*Pleuromamma xiphias*）的线粒体序列数据与标本信息，采集自北太平洋副热带环流的开放海洋长期观测站点ALOHA站（22.45°N，158°W），覆盖2012年9月至2013年10月间的11次夏威夷海洋时间序列（Hawai'i Ocean Time-series, HOT）常规科考航次（航次编号HOT-246至HOT-256）。

长角海羽猛水蚤的序列数据为483个个体的线粒体细胞色素c氧化酶亚基II（cytochrome c oxidase subunit II, COII）546碱基对片段，单次航次平均采集44个个体；剑额宽水蚤的序列数据为510个个体的线粒体细胞色素c氧化酶亚基I（cytochrome c oxidase subunit I, COI）551碱基对片段，单次航次平均采集46个个体。数据集同时提供每个标本对应的HOT航次编号、采集日期与具体网拖信息，若可识别则同步标注个体的生活史阶段与性别。

本数据集关联一篇即将发表的学术论文：
Iacchei, M., Butcher, E., Portner, E., Goetze, E.（已录用）《时间维度：基于生物多样性指数解析海洋浮游动物的时间遗传模式》，刊载于《Limnology and Oceanography（湖沼学与海洋学）》。

本数据中的独特单倍型已提交至NCBI数据库，登录号分别为KY560470 - KY560514（对应长角海羽猛水蚤）、KY560515 - KY560565（对应剑额宽水蚤）。

本数据集包含以下文件（请注意：文件内的序列ID与NCBI序列ID并不一致）：
1. HOT-HALO.fasta：FASTA格式文本文件，包含483尾在ALOHA站采集的长角海羽猛水蚤的线粒体细胞色素c氧化酶亚基II基因（COII；546 bp）部分序列。
2. HOT-PLXI.fasta：FASTA格式文本文件，包含510尾在ALOHA站采集的剑额宽水蚤的线粒体细胞色素c氧化酶亚基I基因（COI；551 bp）部分序列。
3. HALO.csv与PLXI.csv：由Excel文件转换而来的CSV格式文件，原Excel文件包含两个工作表，分别对应长角海羽猛水蚤与剑额宽水蚤。每个工作表的列标题含义如下：
- sample_id：与原始标本采集、DNA提取及PCR扩增相关的样本编号
- sequence_id：与本项目中分析的序列相关的样本编号
- genus：采集生物的属名
- species：采集生物的种名
- cruise：标本采集所属的夏威夷海洋时间序列（HOT）科考航次编号
- tow：标本采集所用的网拖编号
- collection_date：标本采集日期，格式为yyyy-mm-dd
- stage_sex：个体的生活史阶段（桡足幼体或成体）与性别（桡足幼体、雌性、雄性）
- stage：个体的生活史阶段（桡足幼体或成体），该列为BCO-DMO从原始stage_sex列拆分所得，以提升易用性
- sex：个体的性别（桡足幼体、雌性或雄性），该列为BCO-DMO从原始stage_sex列拆分所得，以提升易用性
- mtCO*_sequence：对应个体的线粒体DNA序列（长角海羽猛水蚤为COII；剑额宽水蚤为COI），该序列与对应FASTA文件中序列ID对应的序列完全一致。