Atlantic Puffin Fecal DNA Metabarcoding: 2021-2022, Maine, USA

AbstractThese data include quantifications of prey types identified through metabarcoding using 12S and 18S genes and the DNA present in Atlantic puffin <i>(Fratercula arctica)</i><i> </i>feces<i>.</i> Fecal samples were collected on Matinicus Rock, Maine during the incubation and chick-rearing periods of 2021 and 2022. Fecal samples were stored in DNA/RNA shield and were processed within 12 weeks of collection, with processing performed at the Cornell Lab of Ornithology and sequencing performed on an Illumina Hi-seq 2500 at the University of New Hampshire. Samples have been rarefied to an even read depth (600 reads for 12S, 2500 for 18S) and all bioinformatics work was performed by GVC in Qiime2. Data are presented here in separate csv files for each year and gene region examined, as well as corresponding metadata relating to sample collection (date and age of bird).Subject keywordsBiological sciences, DNA metabarcoding, Fratercula arctica, Gulf of Maine, seabird dietREADME: Atlantic Puffin Fecal DNA Metabarcoding: 2021-2022, Maine, USACSV files included display rows representing unique fecal samples, with ID numbers corresponding to individual fecal samples obtained from breeding Atlantic puffins (<i>Fratercula arctica</i>). Columns represent the DNA sequence reads belonging to each prey type, as identified in the top row. This data structure enables easy calculation of RRA values using the number of taxa-specific DNA sequences within an individual sample or conversion to binary presence/absence for FOO calculations. All samples have been rarefied to equal read depths for each gene region (12S - 600 reads, 18S - 2500 reads). CSVs containing sample information include the data of sample collection, the age of the bird the sample is from, and the position of the samples on the plate during processing. All samples were collected fresh and so the sample collection date is the same as sample deposition date.<br>Code/SoftwareFollowing sequencing, these data were processed in Qiime2 using scripts accessible at:https://github.com/GemmaClucas/Matinicus-Rock-2021-Atlantic-PuffinsStraightforward use of R package 'vegan' allowed for calculation of species diversity metrics and nonparametric tests (ANOSIM, PERMANOVA, and more) examining community similarity. Other packages used with this dataset include 'stats' and 'ggplot2' but the data presented here have only been processed using Qiime2.

摘要 本数据集包含通过12S和18S基因的DNA宏条形码（DNA metabarcoding）技术鉴定得到的大西洋海雀（Atlantic puffin，学名*Fratercula arctica*）粪便DNA中猎物类群的定量数据。粪便样本于2021年和2022年的海雀孵卵期及育雏期，在缅因州马蒂尼库斯岩（Matinicus Rock）采集。样本保存于DNA/RNA保存液（DNA/RNA shield）中，并于采集后12周内完成前处理，前处理工作在康奈尔鸟类学实验室（Cornell Lab of Ornithology）开展，测序工作由新罕布什尔大学使用Illumina Hi-seq 2500测序平台完成。所有样本均经抽平处理至统一测序深度（12S基因区为600条reads，18S基因区为2500条reads），全部生物信息学分析均由GVC在Qiime2环境中完成。本数据集按采集年份及测序基因区分为多个独立CSV文件，同时附带与样本采集相关的元数据（包括采集日期及取样海雀的年龄）。
主题关键词：生物科学、DNA宏条形码（DNA metabarcoding）、*Fratercula arctica*、缅因湾（Gulf of Maine）、海雀食性
README：美国缅因州马蒂尼库斯岩2021-2022年大西洋海雀粪便DNA宏条形码数据集
所附CSV文件中，每一行代表一份独立的粪便样本，其ID编号对应于从繁殖种群大西洋海雀（*Fratercula arctica*）采集的单份粪便样本。每一列代表第一行所鉴定出的某一类猎物的DNA序列读段（reads）。该数据结构可便捷地基于单份样本内类群特异性DNA序列读段数计算相对读段丰度（Relative Read Abundance, RRA），或转换为二元存在/缺失矩阵以用于出现频率（Frequency of Occurrence, FOO）计算。所有样本均已抽平至各基因区的统一测序深度（12S基因区为600条reads，18S基因区为2500条reads）。包含样本信息的CSV文件包括样本采集相关数据、取样海雀的年龄，以及样本在测序前处理平板上的孔位信息。所有样本均为新鲜采集，因此样本采集日期与样本保存日期一致。
代码与软件 测序完成后，本数据集使用Qiime2进行分析，所用脚本可于以下网址获取：https://github.com/GemmaClucas/Matinicus-Rock-2021-Atlantic-Puffins。可直接使用R语言包‘vegan’计算物种多样性指数，并开展非参数检验（如ANOSIM、PERMANOVA等）以分析群落相似性。本数据集分析还用到了‘stats’与‘ggplot2’等R包，但本数据集所呈现的原始数据仅经Qiime2处理。