OPP-PRF: Exploration of How Historical Climate Events Impacted Pacific Cod (Gadus macrocephalus) Evolution and Fishery Use (2023)

The main objective of our research is to investigate how two late Holocene climatic events affected Pacific cod populations throughout the last millennium. We combined zooarchaeological, archaeogenomic, and isotopic data from Pacific cod bones excavated from archaeological sites in three locations across the North Pacific: Eleanor Island in Prince William Sound, Mink Island in Amalik Bay near the Kodiak archipelago in the western GOA, and Amchitka Island in the Aleutian Islands. Our research objectives are to 1) characterize the population genetic structure, genetic diversity, and effective population sizes of Pacific cod populations over the last millennium; 2) identify genomic signatures of selection in response to historical climatic events and compare to adaptive regions found in modern Aleutian Islands Pacific cod; 3) determine whether there is evidence for genomic evolution following past climatic events related to a change in trophic level; and 4) compare and contrast the seasonality of fishing on fishing grounds between modern and historical time periods. The archaeological samples described above date to three main time periods: pre-Medieval Warm Period (MWP; ca. 2000-1500 BP (before present)), post-MWP/pre-Little Ice Age (LIA; ca. ~1000 BP), and end of the LIA (ca. ~500-200 BP). These data are whole genome resequencing data from 5 Novaseq X Plus lanes from 96 samples. The dataset includes samples that were resequenced to increase coverage so the number of fastq files is 137 for 96 unique samples.
**Data is submitted to Sequence Read Archive (SRA), but embargoed until 2027.**

本研究的核心目标为探究全新世晚期两次气候事件在过去千年间对太平洋鳕（Pacific cod）种群的影响。
我们整合了北太平洋三个地点考古遗址出土的太平洋鳕骨骼的动物考古学、古基因组学及同位素数据，这三个地点分别为：威廉王子湾的埃莉诺岛（Eleanor Island）、阿拉斯加湾（Gulf of Alaska, GOA）西部科迪亚克群岛附近阿马利克湾的明克岛（Mink Island），以及阿留申群岛的安奇卡岛（Amchitka Island）。
本研究的具体目标包括：1. 刻画过去千年间太平洋鳕种群的群体遗传结构、遗传多样性及有效种群规模；2. 识别响应历史气候事件的选择基因组特征，并与现代阿留申群岛太平洋鳕的适应性基因组区域进行对比；3. 探明是否存在与营养级变化相关的、在过往气候事件后发生基因组演化的证据；4. 对比现代与历史时期渔场的捕捞季节特征。
上述考古样本可划分为三个主要时期：中世纪暖期（Medieval Warm Period, MWP）前（约距今2000-1500年，BP即before present）、中世纪暖期后/小冰期（Little Ice Age, LIA）前（约距今1000年），以及小冰期末期（约距今500-200年）。
本数据集的原始数据为96个样本经NovaSeq X Plus测序仪的5个测序通道产出的全基因组重测序数据。为提升测序覆盖度对部分样本进行了重测序，因此96个唯一样本对应的fastq文件总数为137个。
本数据集已提交至序列读取档案库（Sequence Read Archive, SRA），但处于保密期至2027年。