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Acta Oceanologica Sinica 2007，V01．26，No．6，P．83～90 http：／／www．oceanpress．COB．cn E—mail：hyxbe@263．net on the Phylogenetic analysis of Pectinidae(Bivalvia)based ribosomal DNA internal transcribed spacer region Zhenminl+ HUANG Xiaotin91，BI Kel，HU Jingjiel，HU Xiaolil，BAO of of Marine Life of China， 1．Laboratory of Molecular Genetics and Breeding Mollusk，College Science，Ocean University Qingdao 266003，China Received 14 September 2006；accepted 2 1 March 2007 Abstract and The ribOSOmal DNA internal transcribed spacer(ITS)region is auseful genomic region for understanding evolutionary genetic molecular of using relationships．In the current study，the phylogenetie analysis Pectinidae(Mollusca：Bivalvia)was performed nine of this were obtained from the the nucleotide sequences of the nuclear ITS region in species family．The sequences sca]lop and nobilis，and compared with the species Argopecten irradians，Mizuhopecten yessoensis，Amusium pleuronectes Mimachlamys an species published sequences of Aequipecten opercularis，Chlamys知rreri，C．distorta，肛varia，Pecten maximu$，and outgroup &黝viridis．The molecular phylogenetic tree was constructed by the neighbor-joining and maximum parsimony methods·Phylo。 the nor— their combination trees of similar results suppofl genetic analysis based on ITSl，ITS2，or always yielded topology．The with classification of two and Pectininae) Dhological classificatioas of bivalve and are nearly consistent subfamilies(Chlamydinae made of that fbmulated by Waller．However，A．irrad／ans，together with A．opercularis up genera Amusium，evidences they may of Wailer who them in belong to the subfamily Pectinidae．The data are incompatible with the conclusion placed Chlamydinae by and con。 morDhological characteristics．These results provide new insights into the evolutionary relationships among scallop species of classification tribute to the improvement existing systems． Key words：bivalve，Pectinidae，ribosomal DNA，ITS，phylogeny 1 Introduction veniles．He divided the family Pectinidae into three subfamilies，Camptonectinae，Chlamydinae，and Pectininae．He further divided into the The family Pectinidae(Mollusca：Bivalvia)in— Chlamydinae tribes cludes many well．known marine invertebrates that Chlamydini，Crassadomini，Mimachlamydini， and Aequipectinini．and Pectininae into Palliolini， play important roles in aquaculture．The phylogenet— Pectinini．Molecular phyloge— ic relationships among these species are still an issue Decatopectinini，and netic studies of the Pectinidae have of debate．Among the classification systems devised family developed over the last decades(Barucca et a1．，2004； for the family Pectinidae，Waller(1993，1991) rapidly shell Insua et a1．，2003；Canapa et a1．，2000；Matsumo— proposed a system based on microsculptural to and et a1．，1999；Steiner features and the morphological characteristics of ju一 Hayami，2000；Canapa and Mtiller，1996；Littlewood，1994；Gjetvaj et }Corresponding author．E—mail：zmbao@OUC．edu．cn HUANG Xiaoting et a1．Acta Oceanologica Sinica 2007，V01．26，No．6，P．83—90 a1．，1992)． of the systematic and phylogenetic relationships of Ribosomal DNA is a multiple··copy cluster of re·· several groups of bivalves，especially at the genus peat units；each unit contains the 18S，5．8S and level．We cloned and sequenced the ITS region of 28S rRNA genes，and the internal transcribed spacer four scallops(Mimachlamys nobilis，Mizuhopecten between the 18S and 5．8S rRNA genes(ITSl)as yessoensis，Am潞ium pleuronectes and A．irradians) well as between the 5．8S and 28S rRNA genes to obtain the basic characteristics of these se— (ITS2)．ITS sequences are of an appropriate size to quences．Moreover，the ITS sequences，both indi— be amplified easily with a pair of primers designed vidually 7 ITSl or ITS2) and collectively according to the 3 7end of 18S rDNA and the 5 7end of (ITSt+ITS2)were used to determine the phyloge— 28 S rDNA．Furthermore，ITS sequences are more netic relationships among ten Pectinidae species． diverse than ribosomal RNA genes f Hillis and Dix— on，1991)，and they have been employed to resolve 2 Materials and methods phylogenetic classification problems in the lower tax— onomical levels such as genera and species(Morgen 2．1 Sample collection and DNA extraction and Blair，1998；Navajas et a1．，1998；Perera et M．nobilis and were collected a1．．1998)．In bivalve，ITS has been studied in A．pleuronectes from the wild of the East China Sea and several species．The size and restriction pattern of population the South China A．irradin瑚 the ITS region have been employed to distinguish Sea．respectively．The collected in this was introduced from Mytilus mussels(Toro，1998；Heath et a1．， study originally 1996)，Veneridae clams(Ferntindez et a1．，2001)， the USA and reared in the Huanghai Sea，and was from and reared in the Bo— certain pectinid scallops(Wang et a1．，2006； M．yessoensis Japan hai Sea．Only adult specimens were used for DNA L6pez—Pifi6n et a1．，2002)，and populations of the was extracted from the adductor giant clam Tridacna crocea(Yu et a1．，2000)．The preparation．DNA muscle a traditional method complete sequence of ITS l or ITS2 has been used in using phenol／chloroform as described Sambrook and the phylogenetic analysis of freshwater bivalves Las— by Russell(2001)． migona(King et a1．，1999)，Brazilian Biomphalar— 2．2 PCR amplification，cloning and sequencing ia species(Vidigal et a1．，2000)，Mytilus species The ITS was (Riginos et a1．，2002)，and certain Pectinidae region prepared by polymerase chain reaction(PCR)．The forward primer(5’一 scallops(Insua et a1．，2003)． reverse Pectinidae scallops have a wide distribution in GT／TCTGTAGGTGAACCTGC-3’)and primer the world．Waller(1993，1991)produced a de— (5'-CTCGTCTGATCTGAGGTCG一3 7)were designed based on the nucleotide retrieved from tailed morphological taxonomy of Pectinidae．Barue— sequences GenBank(AF245687 and AF245688；Yu et al，， ca(2004)constructed phylogenetic trees of Pectini- was set in a volume dae using 16S and 12S ribosomal rRNA 2001)．PCR up 50／xL containing 10 of of each genes．However，there is a disagreement between ng templates DNA．0．1扯mol／dm3 of each morphological and molecular classifications about the primer，0．2 mmol／dm3 dNTP，with 1．0 U phylogeny of bay scallop，Argopecten irradians(La— 如DNA polymerase(Promega)and 1×buffer． o marck，1819)．In the present study，we focused on The amplification conditions were as follows：94 C， the ribosomal DNA internal transcribed spacer region 60 s(denaturation)；56。c，60 s(anneal)；72。C， because it has proved to be very useful for the study 90 s(elongation)for 30 cycles．Amplified fragments HUANG Xiaoting et a1．Acta Oeeanologica Sinica 2007，V01．26，No．6，P．83～90 85 were checked by electrophoresis with l％agarose gel 2．3 Sequence alignment and phylogenetie analysis and visualized by ethidium bromide． The PCR．．amplified fragments of three individu．． The identity of the sequences obtained was deter- als from each species were ligated into a pMDl8一T mined using the BLAST program(Altschul et a1．， Vector(TaKaRa)and transferred into the competent 1 997)，Beside the sequences of OUF clones from坛 E．col；DI-IS∞The recombinants were identified nobilis，M yessoensis，A．irradians and A．pleuronect— retrieved also those of through blue or white selection(Sambrook and Rus— es，we Chlamys扣rreri，C．dis— sell．2001)．Sequence reactions were carried out with torta，胍varia，Aequipecten opercularis，Pecten maxi— mlA$and Perna viridis from GenBank．The species uti— an ABI PRISM 3730xL DNA sequencer． A1l se— lized in this comparative study are listed in Table 1． quenees were deposited into GenBank with the acces． All were sion number listed in Table 1． sequences aligned using CLUSTALX(Thomp- son et a1．，1997)．The base composition，the ratio of Table used for the 1．Species phylogenetic analysis and transition to transversion and Kimura 2-parameter dis- Genebank accession number tance were calculated using the MEGA version 3，l Accession No． Species (Kumar et a1．，2004)． Chlamys fa册一 AF245687 Phylogenetic trees were produced using the neigh— (Jones et Preston，1904) A蹦5688 bor-joining(NJ)(Saitou and Net，1 987)and maxi— Chlamys distorta A『428409 mum parasimony(MP)methods with MEGA 3．1 pro— (da Costa，t778) gram．Neighbor—joining trees were constructed emplo— Mizuhopecten yessoemis AY690600 ying the Kimura 2-parameter distance．Maximum-par- (Jay，1856) DQnl7585 simony trees were produced using branch·-and--bound DQ417586 search by attributing equal mass to transitions and Mimachlamys nobilis AY690599 transversions．In all analyses，the deletion (Reeve，1852) DQ417587 complete was selected for values DQ444298 option handling gaps．Bootstrap (Felsenstein，1 985)，indicating robustness of nodes in Mimachlamys vart。a AJ428408 (Linnaeus，1758) neighbor．joining and maximum—parsimony trees， refer to 1 000 Argopecten irradianz AY695802 replications， (Lamarek，1819) DQ417588 DQ417589 3 Results Amt“dum plelrronectes DQ417590 (Linnaeus，1758) DQ4t7591 3．1 PCR amplification and data analysis DQ417592 The entire ITS region was amplified from at least Aequipecten opercularis AJ428407 30 individuals of each scallop species．In all cases． (Lamarck，1758) the PCR yielded a single band of approximately 750 bp Pecten maximus Aj428410 in length．Tahle 2 lists the ITS lengths and the nueleo— (Linnaeus，1758) tide composition percentage of three individuals from Perna viridis AF353098 each species．The total length of the ITS region ranged (Linnaeus，1758) from 520 bp(旭nobilis)to 558 bp(A．irradians) and the GC content from 44．4％(舱yessoensis)to 50．1％(A．pleuronectes)． 86 HUANG Xiaoting et a1．Acta Oceanologica Sinica 2007，V01．26，No．6，P．83～90 Table 2．Nucleotide composition(GC)and
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  • Convergent Evolution of Life Habit and Shell Shape in Scallops (Bivalvia: Pectinidae) with a Description of a New Genus Alvin Alejandrino Iowa State University

    Convergent Evolution of Life Habit and Shell Shape in Scallops (Bivalvia: Pectinidae) with a Description of a New Genus Alvin Alejandrino Iowa State University

    Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 Convergent evolution of life habit and shell shape in scallops (Bivalvia: Pectinidae) with a description of a new genus Alvin Alejandrino Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Biology Commons, and the Evolution Commons Recommended Citation Alejandrino, Alvin, "Convergent evolution of life habit and shell shape in scallops (Bivalvia: Pectinidae) with a description of a new genus" (2014). Graduate Theses and Dissertations. 14056. https://lib.dr.iastate.edu/etd/14056 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Convergent evolution of life habit and shell shape in scallops (Bivalvia: Pectinidae) with a description of a new genus by Alvin Alejandrino A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Ecology and Evolutionary Biology i Program of Study Committee: Jeanne M. Serb, Major Professor Dean C. Adams Dennis Lavrov Nicole Valenzuela Kevin J. Roe Iowa State University Ames, Iowa 2014 Copyright © Alvin Alejandrino, 2014. All rights reserved. ii DEDICATION To my brother, Edward Andrew Haffner (May 19, 1986 – December 26, 2011). You showed me that family and happiness are the most important things in life. I miss and love you.