東南亞水域對蝦科（甲殼亞門：軟甲綱：十足目）之分子親緣關係及多樣性研究

Molecular phylogeny and diversity of Penaeidae (Crustacea: Malacostraca: Decapoda) in South-East Asian waters

胡亞美(Amirah Hurzaid)

指導教授 ： 陳韋仁

共同指導教授 ： 陳天任(Tim-Yam Chan)

國立臺灣大學/理學院/海洋研究所/博士(2020年)

https://doi.org/10.6342/NTU202002900

摘要

十足綱對蝦科包括大多數高經濟價值的海蝦種類，其成員分佈於世界各地，而物種多樣性最高的地區則集中在印度－西太平洋地區。儘管對蝦科具有經濟上的重要性，但由於分子與形態學研究提出的假設並不一致，因此其分類及親緣關係尚無確切的定論。在本研究中，藉由縝密的生物採樣 (特別針對東南亞物種)，旨在 (1) 利用整合性的分類學方法來探勘對蝦科在東南亞水域的物種多樣性；(2) 利用分子親緣關係樹來檢視對蝦科及其目前已知屬是否為單系群；(3) 在穩健的親緣關係下探討對蝦各類群的分化時間; (4) 解決在宗旨 (1) 發現的物種群的分類問題。為探勘其生物多樣性，一個包含371條COI基因序列的基因資料組 (231條在本研究獲得，140條自網路基因資料庫取得) 被編制，隨後使用兩種不同的工具 (ABGD和bPTP) 進行物種界定分析 (species delimitation analysis)。為重建其親緣關係，本研究利用多基因分子標記，包含線粒體基因COI和16S rRNA以及兩個核基因NaK和PEPCK的組合基因資料組 (樣本包括109個內群和6個外群)。物種定界分析結果顯示，在所檢視的71個形態物種中可能存在94個推定物種，這顯示該科的生物多樣性被低估。本研究發現以下的形態物種中可能存在新物種：Kishinouyepenaeopsis cornuta、K. incisa，Mierspenaeopsis sculptilis、M. hardwicki、Parapenaeopsis coromandelica 和草蝦 (Penaeus monodon)。根據研究結果，除了支持對蝦科為非單系群外，單肢蝦科 (Sicyoniidae) 位於糟對蝦系群 (Trachypenaeini)中；而對蝦屬 (Penaeus)、Mierspenaeopsis、仿對蝦屬 (Parapenaeopsis) 均為多系群。分化時間的估計發現，對蝦科的最近共同祖先可能在侏羅紀晚期出現於印度－西太平洋地區的中部。物種多樣化可能於白堊紀晚期至中新世中期爆發。在物種定界分析中檢測到幾種物種群 (species complex)，在此，隨著額外的樣本加入分析，包括所有發佈過的同義種，草蝦種群的分類問題得到了部分的解決。發現自亞齊的新物種在此論文中已描述，而其他兩種潛在物種仍有待描述。這項研究提供了對蝦科的系統分類學的新見解，並為進一步的分類學和演化學研究以及東南亞對蝦漁業管理提供了新的框架。

關鍵字

對蝦科 ； 東南亞 ； 親緣關係 ； 物種界定 ； 整合性的分類學方法 ； 分化時間

並列摘要

The decapod family Penaeidae comprises most of the economically important marine shrimp species. Its members are widespread throughout the world, with its highest species diversity centered in the Indo-West Pacific region. Despite this importance, their taxonomy, classification, and phylogeny are not yet settled due in part to incongruence among hypotheses proposed from molecular versus morphological studies. In the present thesis, using a thorough taxonomic sampling of especially the South-East Asian species, I aim to (1) explore its species diversity in South-East Asian waters using an integrated approach in taxonomy, (2) utilize a reconstructed phylogeny to test the monophyly of the Penaeidae and its currently recognized genera, (3) estimate the divergence times of penaeid under a robust phylogeny, and (4) resolve the taxonomic issue of certain species complex found in (1). To explore its diversity, a dataset that included 371 COI gene sequences (231 newly generated and 140 retrieved from public sources) was compiled and subsequently analyzed with two different tools (ABGD and bPTP) for species delimitation. To infer the phylogeny, a combined gene dataset (including 109 ingroup and six outgroup taxa) of mitochondrial genes, COI and 16S rRNA, and two nuclear genes, NaK and PEPCK, was utilized. The results from species delimitation analysis inferred that 94 putative species actually exist within the 71 morphospecies reviewed, indicating an underestimated biodiversity in this family. Several potential new species within the following morphospecies were found in this study: Kishinouyepenaeopsis cornuta, K. incisa, Mierspenaeopsis sculptilis, M. hardwicki, Parapenaeopsis coromandelica, and Penaeus monodon. The results from phylogenetic inferences based on the combined gene dataset showed that Penaeidae is not monophyletic with Sicyoniidae nested within the penaeid tribe Trachypenaeini. Within the family, the genera Penaeus, Mierspenaeopsis, and Parapenaeopsis were also revealed to be polyphyletic. The divergence time estimation recovered that the most recent common ancestor of the family Penaeidae likely occurred in the central IWP during the Late Jurassic. A burst of species diversification likely took place during the Late Cretaceous to the Middle Miocene. From the species delimitation analyses, several species complexes were detected. Here, with the additional samples including all the synonyms reported for P. monodon, the taxonomic issue within P. monodon complex was partly resolved. One new species from Aceh was described while the other two potential species remain to be described. This study offers an insight into the systematics of the family Penaeidae and provides a framework for further taxonomic and evolutionary studies as well as in fisheries management in SEA shrimp species.

並列關鍵字

Penaeidae ； South-East Asia ； phylogeny ； species delimitation ； integrated approach in taxonomy ； divergence time

參考文獻

References:

Abele, L. G. (1991). Comparison of morphological and molecular phylogeny of the Decapoda. Memoirs of the Queensland Museum, 31, 101-108.

Ahyong, S. T., Lai, J. C., Sharkey, D., Colgan, D. J., Ng, P. K. (2007). Phylogenetics of the brachyuran crabs (Crustacea: Decapoda): the status of Podotremata based on small subunit nuclear ribosomal RNA. Molecular Phylogenetics and Evolution, 45(2), 576-586.

Alafanta, D. (2014). Studi Fenotip Udang Pisang (Penaeus spp.) pada Hasil Budidaya. Aceh, Indonesia: Abulyatama University.

Alam, M. M., Pálsson, S. (2016). Population structure of the giant tiger shrimp Penaeus monodon in Bangladesh based on variation in microsatellites and immune-related genes. Marine Biology Research, 12(7), 706-714.