小帽螺生物多樣性探勘及親緣關係研究

Abstract

「小帽螺」泛指居住在深海有機基質 (biogenic substrate) 上的笠型螺類，是一個人為界定的一分類單元, 因這個類群在演化上並非單一起源。牠們分屬兩個總科，小帽螺總科 (Cocculinoidea) 及深海笠螺總科 (Lepetelloidea)，前者屬於小帽螺亞綱 (Cocculiniformia)；後者則被置入於原始腹足亞綱 (Vetigastropoda)。在腹足綱 (Gastropoda) 中，這兩個總科和其他腹足類的親緣關係及其自身的分類尚未被完全解決。因此，本研究的目的為探討小帽螺總科、深海笠螺總科與其他腹足類之親緣關係與釐清其分類，進而了解它們在腹足類演化中所扮演的角色, 尤其是與其棲地利用之間的關聯性。為了探討上述問題，我利用傳統桑格定序 (Sanger sequencing) 以及次世代定序 (Next-Generation Sequencing) 從包含三個小帽螺亞綱、一個蜑形 (Neritimorpha) 亞綱、一個Neomphalina亞綱及十個原始腹足亞綱物種之樣本取得粒線體基因組 (mitogenome) 之DNA序列，並在分析數據中加入從其它從基因庫 (NCBI GenBank) 中下載之腹足綱粒線體基因組，以此建構分子親緣關係樹。結果顯示，小帽螺亞綱與Neomphalina亞綱互為姊妹群，而深海笠螺總科與Lepetodriloidea總科亦互為姊妹群。依此結果推論在腹足類演化史中，曾經出現兩次主要的由淺海轉移至深海棲地的事件：一為發生在小帽螺亞綱與Neomphalina亞綱之最近共同祖先；另一為在深海笠螺總科與Lepetodriloidea總科的最近共同祖先。 在小帽螺總科中，小帽螺科 (Cocculinidae) 的成員主要為生活在沉木上的小型白色外殼笠螺。由於牠們的個體非常小且稀少，且因其生活環境特殊難以取樣，導致小帽螺科成為腹足綱內最少被研究的科之一。因此, 其系統分類 (systematics) 上仍有許多問題，包括物種分布、多樣性、生態環境以及演化關係，都未被解答。因此，在此論文中，我透過「熱帶深海底棲生物探勘」計畫 (Tropical Deep-Sea Benthos) 取得研究用樣本, 並對生存於印度－西太平洋地區的小帽螺進行了全面性的多樣性探勘。我從182個採樣點中選取489個小帽螺科樣本進行分子與形態分析。選用三個不同的基因片段進行物種界定 (species delimitation) (cox1與28S) 以及親緣關係分析 (cox1、28S與H3)；為了進一步進行分類學的檢定，我利用六個形態特徵 (殼形、外殼構造、生殖器、胎殼構造、觸角、齒舌形態) 來鑑定小帽螺的屬與種。根據本研究之分子、形態、生態、地理分布等資訊之整合證據顯示，在印度－西太平洋地區存在有85個小帽螺物種，這與目前該區域所認知的24個已知種相較，有著額外的隱蔽多樣性 (cryptic diversity) 與存在有待描述的新種。此外，經由親緣關係分析與形態檢驗之結果發現小帽螺可分為九個主要系群 (clade)，其中五個可與現生屬相對應，另外四個類群則為待描述之新屬。

'Cocculiniformes' is an artificial taxonomic assemblage that comprises marine and mainly limpet-shaped gastropods that live primarily on biogenic substrates at bathyal or hadal depths. They are currently classified in two different superfamilies, Cocculinoidea and Lepetelloidea that belong to two separate subclasses, Cocculiniformia and Vetigastropoda, respectively. However, their phylogenetic relationships to other gastropods and thus their classification are not fully resolved. The objectives of this dissertation are to elucidate their phylogenetic position(s) within the gastropods, to revise their classification, and to better understand their evolution, especially concerning the evolution of habitat use. To investigate their phylogeny, the analyses were conducted based on the mitogenomic data newly constructed and those from public genomic databases (NCBI Genbank). I reconstructed new mitogenomes from one neritimorph, three cocculinoids, one neomphalinoid, and ten vetigastropods that were obtained by using Sanger sequencing and Next Generation Sequencing (NGS) technologies. The phylogenetic results resolved the sister-group relationship between Cocculiniformia and Neomphalina, and also suggested that the Lepetelloidea is sister to the Lepetodriloidea. According to this result, two major events of habitat switch from shallow water to deep-sea during the evolutionary history of gastropods were inferred: one in common ancestor of Cocculiniformia and Neomphalina; the other in common ancestor of Lepetelloidea and Lepetodriloidea. Among the families of the Cocculinoidea, the Cocculinidae is the family consisting of small, white bathyal gastropods that live primarily on sunken woods. Due to their limited size, rareness, and sampling difficulties, this family is one of the least-studied families of the Gastropoda. Many questions on the systematics of the family Cocculinidae, including their species diversity, geographical and ecological distributions, and evolutionary relationships, remain largely unanswered. Herein, I conducted a comprehensive investigation to explore the diversity and to infer the phylogeny of cocculinids in the Indo-West Pacific (IWP). 489 cocculinid samples were collected from 182 IWP localities during several expeditions under the Tropical Deep-Sea Benthos program. The collected samples were examined using both molecular and morphological methods. Three gene markers were used for species delimitation (cox1, and 28S) and phylogeny reconstruction (cox1, 28S, and H3); six key morphological characters (shell shape, teleoconch structure, copulatory organ, protoconch, epipodial tentacle, and radula) were further explored for the purposes of taxonomic practices including identification of species and genus. In the present thesis, 85 putative IWP species were identified based on the combination of molecular, morphological, and ecological evidences whereas the number of currently recognized IWP species is only 24. My result reveals an exceptional cryptic diversity and the existence of many undescribed species within the Cocculinidae. At higher taxonomic level, the result from phylogenetic analyses and morphological examinations allowed me to identify nine main clades within the Cocculinidae. Five of them may be attributed to existing genera; the others should be assigned to new genera that remain to be described.