Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia
文献类型：期刊论文
| 作者 | Li, Yi-Xuan2,3; Ip, Jack Chi-Ho4; Chen, Chong5; Xu, Ting3,6; Zhang, Qian7; Sun, Yanan1; Ma, Pei-Zhen8 ; Qiu, Jian-Wen2,3
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| 刊名 | SYSTEMATIC BIOLOGY
 |
| 出版日期 | 2024-10-23 |
| 页码 | 18 |
| 关键词 | Bivalves mollusca phylogenetics phylogeny target capture |
| ISSN号 | 1063-5157 |
| DOI | 10.1093/sysbio/syae052 |
| 通讯作者 | Qiu, Jian-Wen(qiujw@hkbu.edu.hk) |
| 英文摘要 | Despite significant advances in phylogenetics over the past decades, the deep relationships within Bivalvia (phylum Mollusca) remain inconclusive. Previous efforts based on morphology or several genes have failed to resolve many key nodes in the phylogeny of Bivalvia. Advances have been made recently using transcriptome data, but the phylogenetic relationships within Bivalvia historically lacked consensus, especially within Pteriomorphia and Imparidentia. Here, we inferred the relationships of key lineages within Bivalvia using matrices generated from specifically designed ultraconserved elements (UCEs) with 16 available genomic resources and 85 newly sequenced specimens from 55 families. Our new probes (Bivalve UCE 2k v.1) for target sequencing captured an average of 849 UCEs with 1085 bp in mean length from in vitro experiments. Our results introduced novel schemes from 6 major clades (Protobranchina, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata, and Imparidentia), though some inner nodes were poorly resolved, such as paraphyletic Heterodonta in some topologies potentially due to insufficient taxon sampling. The resolution increased when analyzing specific matrices for Pteriomorphia and Imparidentia. We recovered 3 Pteriomorphia topologies different from previously published trees, with the strongest support for ((Ostreida + (Arcida + Mytilida)) + (Pectinida + (Limida + Pectinida))). Limida were nested within Pectinida, warranting further studies. For Imparidentia, our results strongly supported the new hypothesis of (Galeommatida + (Adapedonta + Cardiida)), while the possible non-monophyly of Lucinida was inferred but poorly supported. Overall, our results provide important insights into the phylogeny of Bivalvia and show that target enrichment sequencing of UCEs can be broadly applied to study both deep and shallow phylogenetic relationships. |
| WOS关键词 | 28S RIBOSOMAL-RNA ; PHYLOGENETIC ANALYSIS ; MOLLUSCA-BIVALVIA ; MISSING DATA ; EVOLUTIONARY RELATIONSHIPS ; MOLECULAR PHYLOGENY ; LARGE-SCALE ; TREE ; DEEP ; LIFE |
| 资助项目 | Collaborative Research Fund[C2013-22GF] ; General Research Fund from the University Grants Committee of Hong Kong SAR[12102222] |
| WOS研究方向 | Evolutionary Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:001338777900001 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/199522]  |
| 专题 | 海洋研究所_海洋生物分类与系统演化实验室 |
| 通讯作者 | Qiu, Jian-Wen |
| 作者单位 | 1.Chinese Acad Sci, Qingdao Key Lab Marine Biodivers & Conservat, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, 8 Nanhai Rd, Qingdao 266071, Peoples R China 2.Hong Kong Baptist Univ, Dept Biol, Kowloon Tong, Kowloon, 224 Waterloo Rd, Hong Kong, Peoples R China 3.Southern Marine Sci & Engn Guangdong Lab Guangzhou, 1119 Haibin Rd, Guangzhou 511458, Guangdong, Peoples R China 4.Lingnan Univ, Sci Unit, Tuen Mun, 8 Castle Peak Rd, Hong Kong, Peoples R China 5.Japan Agcy Marine Earth Sci & Technol JAMSTEC, X STAR, 2-15 Natsushima Cho, Yokosuka, Kanagawa 2370061, Japan 6.Hong Kong Univ Sci & Technol, Dept Ocean Sci, Kowloon, Clear Water Bay, Hong Kong, Peoples R China 7.MNR, Inst Oceanog 1, Key Lab Marine Ecoenvironm Sci & Technol, 6 Xianxialing Rd, Qingdao 266100, Peoples R China 8.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, State Key Lab Mariculture Biobreeding & Sustainabl, 106 Nanjing Rd, Qingdao 266071, Peoples R China |
| 推荐引用方式 GB/T 7714 | Li, Yi-Xuan,Ip, Jack Chi-Ho,Chen, Chong,et al. Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia[J]. SYSTEMATIC BIOLOGY,2024:18. |
| APA | Li, Yi-Xuan.,Ip, Jack Chi-Ho.,Chen, Chong.,Xu, Ting.,Zhang, Qian.,...&Qiu, Jian-Wen.(2024).Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia.SYSTEMATIC BIOLOGY,18. |
| MLA | Li, Yi-Xuan,et al."Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia".SYSTEMATIC BIOLOGY (2024):18. |
入库方式： OAI收割
来源：海洋研究所
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