Supplementary material for manuscript submission at Ecology and Evolution

Supplementary data for the manuscript submission at Ecology and Evolution entitled: "<i>Gaps and data ambiguities in DNA reference libraries: A limiting factor for molecular-based biodiversity assessments using annelids as a case study</i>"<b>Checklists:</b>OBIS Arabian Checklist (CL-MTAP)OBIS Mediterranean Checklist (CL-MTMS)Wehe &amp; Fiege (2002) Polychaeta Checklist from the Arabian Peninsula (CL-MTAWF)<b>FASTA datasets</b>BOLD Annelida at species level-only COI dataset (DS-MTWA): https://dx.doi.org/10.5883/DS-MTWA ARMS Annelida Metabarcoding ASV dataset<b> (</b>DS-ARMS)MZGdb Annelida Indian Ocean (MZGDB)MZGdb Annelida Indian Ocean + ARMS Annelida Metabarcoding ASV dataset (MZGdb_+_DS-ARMS)ARMS Species level IDs-only + complexes in the database (ASV-complex)<b>Supplementary Tables and Figures:</b><b>Table S1</b><b>:</b> Obtained ASVs and respective number of reads per ARMS and taxonomic identification based on RDP method.<b>Table S2</b><b>:</b> Database COI accession numbers and respective references used in Fig. 5<b>Table S3: </b>Detailed list of the obtained Genera and Families from DS-ARMS. All belonging to Polychaeta, unless stated otherwise.<b>Fig. S1</b><b>:</b> Neighbour-Joining phylogenetic Tree using Kimura 2-parameters model for DS-ARMS. All 5375 ASVs are individually shown with the respective taxonomic assignment (RDP). Discordant clades (based on ASAP methodology) highlighted in red. The largest MOTU, identified as “Dorvilleidae”, is highlighted in green and match COI sequences of <i>Dorvillea cf. similis</i> from our custom library in development. A section corresponding to the “high taxonomic ambiguity” suspected of being pseudogenes is also displayed.Public DOIs for specific BOLD related datasets will be available upon paper acceptance.

本数据为投稿至《Ecology and Evolution》（《生态与进化》）手稿的补充材料，手稿标题为：《DNA参考库中的缺口与数据歧义：以环节动物为案例的基于分子技术的生物多样性评估限制因素》
**清单列表**：海洋生物普查数据库（Ocean Biogeographic Information System, OBIS）阿拉伯海清单（CL-MTAP）、OBIS地中海清单（CL-MTMS）、Wehe与Fiege（2002）阿拉伯半岛多毛纲（Polychaeta）动物清单（CL-MTAWF）
**FASTA格式数据集**：
生命条形码数据系统（Barcode of Life Data Systems, BOLD）物种级环节动物仅细胞色素c氧化酶亚基I（Cytochrome c Oxidase subunit I, COI）序列数据集（DS-MTWA）：https://dx.doi.org/10.5883/DS-MTWA
ARMS环节动物元条形码（Metabarcoding）扩增子序列变异体（Amplicon Sequence Variant, ASV）数据集（DS-ARMS）
MZGdb印度洋环节动物数据集（MZGDB）
MZGdb印度洋环节动物数据集 + ARMS环节动物元条形码ASV数据集（MZGdb_+_DS-ARMS）
ARMS仅物种水平鉴定+数据库内复合类群数据集（ASV-complex）
**补充表格与附图**：
**表S1**：基于核糖体数据库项目（Ribosomal Database Project, RDP）方法得到的ASV序列、各ARMS样本的对应读长数量及物种分类鉴定结果。
**表S2**：图5中使用的数据库COI序列登录号及对应参考文献。
**表S3**：DS-ARMS数据集得到的属与科详细列表，除特别标注外均属于多毛纲。
**附图S1**：基于DS-ARMS数据集构建的邻接（Neighbour-Joining）系统发育树，采用Kimura双参数模型。所有5375个ASV序列均单独展示并标注对应的RDP分类鉴定结果；基于ASAP方法判定的不一致演化支以红色高亮；被鉴定为“多尔维尔科（Dorvilleidae）”的最大分子操作分类单元（Molecular Operational Taxonomic Unit, MOTU）以绿色高亮，其序列与本研究正在开发的自定义参考库中的<i>Dorvillea cf. similis</i>（相似多尔维尔虫（近似种））的COI序列匹配；同时展示了被推测为假基因的“高分类学歧义”区域。
特定BOLD相关数据集的公开DOI将在论文录用后发布。