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Brachionus Calyciflorus Combined Molecular-Morphological Approach to Species Complexes of Brachionid and Lecanid Rotifers (Eurotatoria: Monogononta: Brachionidae and Lecanidae) in Thailand Phannee Sa-ardrit A Thesis Submitted in Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology Prince of Songkla University 2016 Copyright of Prince of Songkla University i Combined Molecular-Morphological Approach to Species Complexes of Brachionid and Lecanid Rotifers (Eurotatoria: Monogononta: Brachionidae and Lecanidae) in Thailand Phannee Sa-ardrit A Thesis Submitted in Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology Prince of Songkla University 2016 Copyright of Prince of Songkla University ii Thesis Title Combined molecular-morphological approach to species complexes of Brachionid and Lecanid rotifers (Eurotatoria: Monogononta: Brachionidae and Lecanidae) in Thailand Author Miss Phannee Sa-ardrit Major Program Biology Major Advisor Examining Committee : ............................................................... .......................................... Chairperson (Assoc. Prof. Dr. Pornsilp Pholpunthin) (Prof. Dr. La-orsri Sanoamuang) .............................................Committee Co-advisor (Assoc. Prof. Dr. Pornsilp Pholpunthin) ............................................................... .............................................Committee (Dr. Hendrik Segers) (Dr. Hendrik Segers) .............................................Committee (Dr. Chitchai Chantangsi) ............................................ Committee (Dr. Singtoe Boonrotpong) The Graduate School, Prince of Songkla University, has approved this thesis as fulfillment of the requirements for the Doctor of Philosophy Degree in Biology. ……………………………………… (Assoc. Prof. Dr.Teerapol Srichana) Dean of Graduate School iii This is to certify that the work here submitted is the result of the candidate’s own investigations. Due acknowledgement has been made of any assistance received. ..………….....…..……………Signature (Assoc. Prof. Dr. Pornsilp Pholpunthin) Major Advisor ..………….....………………Signature (Dr. Hendrik Segers) Co-Advisor .………….....………………Signature (Miss Phannee Sa-ardrit) Candidate iv I hereby certify that this work has not been accepted in substance for any other degree, and is not being currently submitted in candidature for any degree. ………………………………….Signature (Miss Phannee Sa-ardrit) Candidate v ชื่อวิทยานิพนธ์ ชีววิทยาเชิงโมเลกุลและสัณฐานวิทยาของชนิดทับซ้อนของโรติเฟอร์ในวงศ์ Brachionidae และวงศ์ Lecanidae (Eurotatoria: Monogononta: Brachionidae and Lecanidae) ในประเทศไทย ผู้เขียน นางสาวพรรณี สอาดฤทธิ์ สาขาวิชา ชีววิทยา ปีการศึกษา 2559 บทคัดย่อ การศึกษาครั้งนี้มีวัตถุประสงค์เพื่อวิเคราะห์หาโรติเฟอร์ชนิดซ่อนเร้นที่อยู่ภายในโรติเฟอร์ ชนิดทับซ้อนในวงศ์ Brachionidae และวงศ์ Lecanidae ที่พบในประเทศไทย โดยศึกษาความ แตกต่างของนิวคลีโอไทด์ของยีน COI และ ITS1 ด้วยวิธีการทางอนุกรมวิธานชีวโมเลกุล 3 วิธี ได้แก่ ABGD, PTP และ GMYC ในการก าหนดขอบเขตของชนิดและประมาณจ านวนชนิดที่พบในโรติเฟอร์ ชนิดทับซ้อน ความสอดคล้องของจ านวนชนิดที่ประมาณได้จากทุกวิธีการ จะใช้ยืนยันการมีอยู่ของ ชนิดซ่อนเร้นภายในโรติเฟอร์ชนิดทับซ้อน การประมาณจ านวนชนิดที่แท้จริงภายในชนิดทับซ้อน นอกจากจะสามารถน าไปใช้ประมาณความหลากหลายทางชีวภาพของโรติเฟอร์ที่แท้จริงในประเทศ ไทยแล้ว ยังน าไปสู่ความเข้าใจทางนิเวศวิทยา และวิวัฒนาการของโรติเฟอร์ในกลุ่มที่มีความสัมพันธ์ ใกล้ชิดกันมากขึ้น นอกจากนี้การศึกษาความแตกต่างทางพันธุกรรมกับการแพร่กระจายทางภูมิศาสตร์ ของชนิดซ่อนเร้นในประเทศไทย ยังถูกศึกษาโดยวิเคราะห์ด้วยวิธีการทางสถิติ Mantel test ผลการศึกษาโดยอาศัยวิธีการทางอนุกรมวิธานชีวโมเลกุล ชี้ให้เห็นถึงชนิดซ่อนเร้นภายใน โรติเฟอร์ชนิดทับซ้อนทั้งสองวงศ์ที่พบในประเทศไทย โดยพบจ านวนชนิดซ่อนเร้นมากที่สุดในกลุ่ม Lecane bulla โดยพบชนิดซ่อนเร้นอย่างน้อย 20 ชนิด อยู่ภายในชนิดทับซ้อนของ Lecane bulla การศึกษาครั้งนี้ได้น าลักษณะทางสัณฐานวิทยาของ Lecane bulla มาวิเคราะห์ร่วมด้วย พบว่า ลักษณะทางสัณฐานวิทยาสามารถน ามาใช้อธิบายความแตกต่างของบางชนิดได้เพียงเล็กน้อย แต่ไม่ สามารถใช้จ าแนกชนิดซ่อนเร้นทั้งหมดที่อยู่ภายใน Lecane bulla นอกจากนี้ยังพบชนิดซ่อนเร้น ภายในชนิดทับซ้อนอื่น ๆ ได้แก่ Brachionus angularis, Brachionus calyciflorus, Brachionus caudatus, Brachionus quadridentatus, Keratella cochlearis, Keratella tropica, Lecane bulla, Lecane closterocerca, Lecane crenata, Lecane curvicornis, Lecane hamata, Lecane leontina, Lecane ludwigii, Lecane luna, Lecane lunaris, Lecane nitida, vi Lecane quadridentata, Lecane signifera และ Lecane unguitata และจากการวิเคราะห์ด้วย DNA taxonomy พบว่าผลที่ได้จากการวิเคราะห์ล าดับนิวคลีโอไทด์ของยีน COI มีความสอดคล้องกัน ของจ านวนชนิดที่ประมาณได้ในแต่ละวิธี ขณะที่การประมาณจากยีน ITS1 มีความแตกต่างกันในแต่ ละวิธี และจากการวิเคราะห์เปรียบเทียบความแตกต่างทางพันธุกรรมภายในชนิดซ่อนเร้นในแต่ละ พื้นที่ของประเทศไทย พบว่าไม่มีความแตกต่างทางพันธุกรรมระหว่างพื้นที่ทางภูมิศาสตร์ ยกเว้น Lecane curvicornis ชี้ให้เห็นว่าโรติเฟอร์ชนิดซ่อนเร้นที่พบในประเทศไทยมีการกระจายทาง ภูมิศาสตร์ที่ซ้อนทับกันและกระจายตัวได้ในบริเวณกว้างในประเทศไทย vii Thesis Title Combined molecular-morphological approach to species complexes of Brachionid and Lecanid rotifers (Eurotatoria: Monogononta: Brachionidae and Lecanidae) in Thailand Author Miss Phannee Sa-ardrit Major Program Biology Academic Year 2016 ABSTRACT This study aims to analyze potential species complexes of rotifers within the families Brachionidae and Lecanidae, to test the hypothesis whether cryptic diversity is indeed as common as is being put forward. Moreover, this study analyzed the geographic distribution and genetic divergence within species complexes in Thailand. The tests for the presence of cryptic species were applied using three methods on both COI and ITS1 datasets: Automatic Barcode Gap Discovery (ABGD), a Poisson Tree Processes (PTP) model, and the Generalized Mixed Yule Coalescent (GMYC) model. Genetic divergence and geographic distance were analyzed using Mantel test. The results from three DNA taxonomy approaches, ABGD, PTP, and GMYC from COI and ITS1 markers clearly indicated the existence of cryptic species in both families. The highest estimate of species diversity in this study was Lecane bulla with at least 20 species existing in the complex. Morphological characters were examined. However, morphology cannot be used to separate some cryptic species in Lecane bulla complex. Moreover, this study reveals the existence of cryptic species in Brachionus angularis, Brachionus calyciflorus, Brachionus caudatus, Brachionus quadridentatus, Keratella cochlearis, Keratella tropica, Lecane bulla, Lecane closterocerca, Lecane crenata, Lecane curvicornis, Lecane hamata, Lecane leontina, Lecane ludwigii, Lecane luna, Lecane lunaris, Lecane nitida, Lecane quadridentata, Lecane signifera, and Lecane unguitata. The species estimated using COI marker is congruent among different DNA taxonomy methods, while there is incongruence among different methods based on ITS1 marker. Only Lecane curvicornis shows significant correlation between genetic and geographic distances. No correlation occurs between genetic and geographic distances in other species complexes. Thus, there is a geographic overlap in rotifer distribution in Thai waters. viii ACKNOWLEDGEMENTS This thesis would not have been completed without some assistance from many people. I would like to express my gratitude to my major advisor, Assoc. Prof. Dr. Pornsilp Pholpunthin, for taking me on as his student, his time for consulting and guidance, and applying the grant for my PhD Program. Moreover, I would like to appreciate my co-advisor, Dr. Hendrik Segers, from Royal Belgian Institute of Natural Sciences, Belgium for inspiring me to do this research in rotifers, as well as sharping my ideas to develop the research framework. He has not given me only assistance for guidance to solve some problems occurring in my thesis research, but also provided me the opportunity for molecular training with his collaboration aboard. Further, I would like to express my deep gratefulness to Dr. Diego Fontaneto, Institute of Ecosystem Study, Italy, who has helped me in many areas of my thesis research including molecular analysis, geomorphometric analysis, and scientific writing. Moreover, I have learned a great deal of some important matters from his experience and his research involving his valuable suggestions and discussion. Plus, I am very appreciated that the chairperson of the examining committee, Prof. Dr. La-orsri Sanoamuang from Department of Biology, Faculty of Science, Khon Kaen University, Dr. Chitchai Chantangsi from Department of Biology, Faculty of Science, Chulalongkorn University, and Dr. Singtoe Boonrotpong from Department of Biology, Faculty of Science, Prince of Songkla University, provided me a lot of valuable suggestions which led my research to be more reasonable. Importantly, this work was supported by the Graduate School at Prince of Songkla University through a scholarship and grant from the Royal Golden Jubilee (RGJ) (Grant no. PHD/0261/2552; 4.B.PS/52/D.2). Also, I would like to acknowledge Plant Genetic Conservation Project under the Royal Initiation of Her Royal Highness Princess Maha Chakri Sirindhorn, under a plankton research project for giving me the chance to join the field trip in order to collect some samples in the Southern part of Thailand. I would like to express my appreciation to Dr. Manuel Elias Gutierrez from Barcode of Life Laboratory, Chetumal Node, Mexico, for the hospitality and technical ix guidances in his laboratory. I would like to thank Mrs. Arely Martinez-Acre from Barcode of Life Laboratory, Chetumal Node, Mexico, for training and sharing
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