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A Thesis Presented to The Facuity of Graduate Studies of The University of Guelph in partial fuifilment of requirements for the degree of Doctor of Philosophy Apni, 1998 Q André-Denis Girard Wright, 1998 Acquisitions and Acquisitions et Bibliographie Services servkes bibliographiques 395 weüirgm Street 395. nie walingtori OttawaON K1AW OGEawa ON K1A ON4 Canada; canada The author has granted a non- L'auteur a accordé une licence non exclusive licence allowing the exclusive permettant a la National Lhmy of Canada to Bibliothèque nationale du Canada de reproduce, loan, distri-bute or sell reproduire, prêter, distriiuer ou copies of this thesis in microform, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/flh, de reproduction sur papier ou sur format électronique. The author retains ownershrp of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantid extracts fiom it Ni la thése ni des extraits substantiels may be printed or otherwise de celle-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. MOLECUUR PHYLOGENY OF TEE ENDOSYMBIOTIC CXLIATES (LITOSTOMATEA: TRICHOSTOMATIA) OF VERTEBRATE ANIMAIS INFERRED FROM 18s rRNA GENE SEQUIENCES An-Denis Girard Wright Univeasity of Guelph, 1998 Complete 18s rRNA sequences were elucidated f?om (1) six entodiniomorphid ruma c*ates7 Diphdnirrrn. En~ocirniurn, Qidinim, Eurlpfodinium, OphyoscoIer, ad Polplasaon, (2) three vestibuliferid rumen ciliates, BaCantidiaum. Daytricha, koû-icha iniestnalis? and /. prosroma. (3) two manupiai ciliates, Cyclopusthium and MUWQ@*. and (4) the fie-living ciliates, Diaïinna, Dilepius, and Enche&&n7 iikely the dosest relatives to these endosynbionts. Phylogenetic analysis of these 15 new sequences revealed that ophryoscolecids are a rnonophyletic group that is divided into three iineages corresponding to the subwal divisions of the Op~oscolecidae,with Entdnium branching first. The menciliates are the siaer group to Cirfoposhium consistent with their placement into the order Entodùiiomorphida. iblacr~pdniumdoes not group with the other entodiniomorphids, but basai to the vestibuliferid-entodiniornorphid clade. Together, the endosymbionts are the sister group to the free-living haptorians, together constituting the class Litostomatea. The rate of nucleotide substitution for ciliates was calibrated to be 1% divergence per 72 to 80 million years (My). nie origin of ciliates (i.e. crown eukaryotes) is caldated to be much older than previously speculated, dahg back to the Paleoproterozoic, 1,980 ta 2,200 million years ago. It was ais0 detennùied that the rate of nucleotide s~bstitution for menciliates is aimost a magnitude faster (1% per 8-1 1 My) than that for fkee-living diates. This faster dock rnight be explaineci by intense seledon on su~vabilityas they invaded the rumen, or by the rdatively high ambient temperature (39" C) of the rumen environment, as such high temperatures are known to decrease the efnciency of DNA repair mechanisms leading to higher mutation rates. Intraspecific sequence variation among diEerent hosts and geographical locations was examineci using the ITS-l/S. 8S/TTS-2 region And* of thk @on fkom I. prastoma fiom Canadian, American, and Australian cattie and sheep, showed that there is no sequence variation within this region. This suggests that populations of l. prostoma on two continents are very recendy diverged, consistent with human colonisation and migration of domestic anirnals in the 18' and 19& centuries. Fiy,secondary mucture of these sequences reveai that mernbers of the ciass Litostomatea have "Ioa" hek E23-5, indicating a new mo1ecuiar diagnostic featrre for this class of ciliates. ACKNO'WLEDGIEMENTS It is dBicuit to single out everybody who has contriiuted, big or srnaIl, to the completion of this degree, so to ail of you my sincere thanks and gratitude are extended. To my advisor and mentor, Dr. Denis H Lynn, thank you for your support, patience, and fiiendship. You have influenceci me in many ways and 1 am very grata to you - Thanks for &hg me a chance. To the memben of rny adMsory cornmittee, Drs. Paul Hebert, John Barta, Cecil Forsberg, and Burk Dehority (Ohio State University, USA), thank you for your tirne, advice, and criticai comments on this thesis. To Dr. Tadeusz Michalowski (ünivenity of Warsaw, Poland), thank you for your gift of ked ceUs of Eud@Idnium moggrï. To Dr. Burk Dehonty, thank you for allowing me to work in your laboratory in Wwster, Ohio. To Dr. Michael Ivan (Agridture Canada), thank you for ailowing me to work in your laboratory in ûttawa. To Dr. Andrew Knoll (Harvard University), thank you for your citicai comments on one the chapters (chapter 4) in this dissertation. To Dr. C. Graham Clark (London School of Hygiene and Tropical Medicine, London, ENGLAND), thank you for your gift of genomic and 18s DNA fiom Bahntidium. To Stephen Cameron (University of Qumland, Brisbane, Australia), thank you for your gift of genomic DNA fiom Mricropociiunz and CycIoposrhium. To Linda Neill (Agriculture Canada), thank you for colecting rumen fluid and assisting me while I was in Ottawa, and to Angela Holliss, thank you for generating sequences using the AB1 Automaîed DNA Sequencer. To my "academic brother and sister", Scott Gransden and Cheryl Jerome. thank you for your fiendship, support, and scholastic advice. Also, thank you to Scott Gransden for the eventfid times - AGAIN (e.g. Alabama! !). To Dr. Michaela Strüder-Kypke and Reinhard 1 Kypke, thank you for your niendship and warmth, we WU dways keep in touch. To the 'Yâmdy", Pat Cooke, Dave O'Hare, Steve Marshall, and John Fox, thank you for the rnany good times we shared (e-g birthday immunity), you guys are great. To the staff of the Shakespeare's Ams, thank you for quenching my thirst and filiïng my appetite, and to the guys and gds on my rnany sof&baUteams, thank you for your support and evening philosophicals. To my good %end Jonita Sornede, thank you for your understanding, fiiendship, and support during the final stretch of my research and writing, and for being there to nurse me back to hedth. To my long rime house-mate and "brother", Dr. Donald Martin, thank you for everything you have taught me7 you have a big heart and 1 will aiways remanber what you have done for me. To my '%ig brother and sister", Dedd and Donna Caldwell, thank you for always behg there for me - you will always be a part of my kdy. To my best Wend Connie Krawqlq thank you for your unconditional love and support - you mean a lot to me and wiii always be my "Sparky" (good luck with your Ph-D!). To my aunt Susan and uncle Stan Wright (cousins Shannon and Jason), thank you for ail that you have done for me while 1 have been away fiom home, this is what f is ail about - 1love each of you. Finally, to my mother and fàther (Jean and Kenneth McG. Dick) - 1DID ïï!! Thank you for aii the sacdices you made, aiI the prayers you said, and for the love, encouragement, and support you gave me to make this degree possible. 1 wdd never repay you for al1 that you have done and given me. 1LOVE YOU BOTH. 1DEDICATE TEDS THESIS TO YOU, MOM AND DAD. This research was supported by an NSERC research grant awarded to Dr. D.H. Lynn CaAPTER ONE General Introduction And Literature IReview INTRODUCCïION... ..................................................................................0.1 Hstorid Background......................................................................... 1 Characteristics Of The Riosoma1 DNA Genes ............................................-4 The Impact Of MoIecular Data On Phylogeneîic Analysis................................ -9 The Paraphyletic Protias ......................................................................16 The Alveolates. .................................................................................21 The Chate Protozoa .........................................................................25 The Rumen Ciliates.......................................................................... -26 RESEARCH OBJECTIVES .........................................................................30 Molecular Phylogeny Of The Endosymbiotic Ciliates Of Vertebrate Anirnals Inferred From Small Subunit Ribosomal RNA Sequences. INTRODUCTION.. .36 . ................................................................................... The Entodmornorphids...................................................................... -39 The Vestibuliferids........................................................................... -49 Monophyly Or Paraphyly Of The Rumen Ciliates......................................... 51 MATERIALS AND METHODS .................................................................... 55 Source Of Sampies And Culture Conditions ..............................................-55 DNAExtraction And Sequencing........................................................... 59 Squence Availability And Phylogenetic Anaiysis ........................................61 RESULTS ..*.....................................................................................-..... 66 Molecular Phylogenies ....................................................................... 82 ... 111 DISCUSSION... ......e...............e..........eee.......e....e.......ee..................*........ ..91 Phylogeny Within The Phylum Ciliophom.. .................................................. 98 Phylogeny ûf The Litostome
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    Chapter 9 Carnivora (Mammalia, Felidae, Canidae, and Mustelidae) From the Earliest Hemphillian Screw Bean Local Fauna, Big Bend National Park, Brewster County, Texas MARGARET SKEELS STEVENS1 AND JAMES BOWIE STEVENS2 ABSTRACT The Screw Bean Local Fauna is the earliest Hemphillian fauna of the southwestern United States. The fossil remains occur in all parts of the informal Banta Shut-in formation, nowhere very fossiliferous. The formation is informally subdivided on the basis of stepwise ®ning and slowing deposition into Lower (least fossiliferous), Middle, and Red clay members, succeeded by the valley-®lling, Bench member (most fossiliferous). Identi®ed Carnivora include: cf. Pseudaelurus sp. and cf. Nimravides catocopis, medium and large extinct cats; Epicyon haydeni, large borophagine dog; Vulpes sp., small fox; cf. Eucyon sp., extinct primitive canine; Buisnictis chisoensis, n. sp., extinct skunk; and Martes sp., marten. B. chisoensis may be allied with Spilogale on the basis of mastoid specialization. Some of the Screw Bean taxa are late survivors of the Clarendonian Chronofauna, which extended through most or all of the early Hemphillian. The early early Hemphillian, late Miocene age attributed to the fauna is based on the Screw Bean assemblage postdating or- eodont and predating North American edentate occurrences, on lack of de®ning Hemphillian taxa, and on stage of evolution. INTRODUCTION southwestern North America, and ®ll a pa- leobiogeographic gap. In Trans-Pecos Texas NAMING AND IMPORTANCE OF THE SCREW and adjacent Chihuahua and Coahuila, Mex- BEAN LOCAL FAUNA: The name ``Screw Bean ico, they provide an age determination for Local Fauna,'' Banta Shut-in formation, postvolcanic (,18±20 Ma; Henry et al., Trans-Pecos Texas (®g.
  • An Integrative Approach Sheds New Light Onto the Systematics

    An Integrative Approach Sheds New Light Onto the Systematics

    www.nature.com/scientificreports OPEN An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea) Thomas Pröschold1*, Daniel Rieser1, Tatyana Darienko2, Laura Nachbaur1, Barbara Kammerlander1, Kuimei Qian1,3, Gianna Pitsch4, Estelle Patricia Bruni4,5, Zhishuai Qu6, Dominik Forster6, Cecilia Rad‑Menendez7, Thomas Posch4, Thorsten Stoeck6 & Bettina Sonntag1 Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of diferent Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable culture medium, (ii) screening of the morphological variability including the presence/absence of algal endosymbionts of living cells by light microscopy, (iii) sequencing of the SSU and ITS rDNA including secondary structures, (iv) assessment of their seasonal and spatial occurrence in two lakes over a one‑year cycle both from morphospecies counts and high‑ throughput sequencing (HTS), and, (v) proof of the co‑occurrence of Coleps and their endosymbiotic algae from HTS‑based network analyses in the two lakes. The Coleps strains showed a high phenotypic plasticity and low genetic variability. The algal endosymbiont in all studied strains was Micractinium conductrix and the mutualistic relationship turned out as facultative. Coleps is common in both lakes over the whole year in diferent depths and HTS has revealed that only one genotype respectively one species, C. viridis, was present in both lakes despite the diferent lifestyles (mixotrophic with green algal endosymbionts or heterotrophic without algae).