DOCSLIB.ORG

Philosophy and the Tree of Life

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Philosophy and the Tree of Life PHILOSOPHY AND THE TREE OF LIFE THE METAPHYSICS AND EPISTEMOLOGY OF PHYLOGENETIC SYSTEMATICS Joel D. Velasco PHILOSOPHY AND THE TREE OF LIFE: THE METAPHYSICS AND EPISTEMOLOGY OF PHYLOGENETIC SYSTEMATICS by Joel D. Velasco A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Philosophy) at the UNIVERSITY OF WISCONSIN-MADISON 2008 © Copyright by Joel Velasco 2008 All Rights Reserved i Abstract: This dissertation examines the foundations of phylogenetic systematics which involves both the construction of phylogenetic trees to represent evolutionary history and the use of those trees to study various aspects of that history. I begin by defending a genealogy-based view of biological taxonomy: the view that all taxa—the formal groups in our classification system—must be monophyletic, i.e., they must consist of an ancestor and all of its descendants. Furthermore, I argue that, contrary to current practice, these taxa should not be assigned ranks (such as genus, family, and order). I then proceed by applying these principles to the debate about species. I argue that non- genealogically based species concepts (such as the popular “biological species concept”) are unacceptable. Instead, a species concept must delimit species so that they form genealogically exclusive groups – groups of organisms more closely related to each other than to any organisms outside the group. With this in mind, I develop two distinct phylogenetic species concepts. Each treats a species as a genealogically exclusive group of organisms. The first determines genealogical relatedness in terms of recency of common ancestry; the second understands genealogy as a composite of gene histories. Finally, I argue that there can be no objective ranking criteria for species and therefore biologists can either keep the species rank, while acknowledging that which taxa are ranked as species is arbitrary, or alternatively, can simply get rid of the rank of species. Having carefully described what phylogenies represent, I move to the epistemological problem of inferring phylogenetic trees and argue that a Bayesian methodology is appropriate. I then focus on one common objection to Bayesian inference – “the problem of prior probabilities.” I argue that this problem has been misunderstood in some cases, which leads to the failure of a variety of objections in the literature. I then develop the beginnings of a solution to this problem within phylogenetics, describe just what has been achieved, and acknowledge what has yet to be accomplished. ii Acknowledgements Thanks to my committee members Elliott Sober, Malcolm Forster, Dan Hausman, Ken Sytsma, Bret Larget and unofficial member David Baum who read the entire manuscript. Elliott and David in particular provided detailed comments on multiple drafts of the entire dissertation making the final version far better than it would have otherwise been. Thanks also to Matt Barker, Marc Ereshefsky, Matt Haber, Joe LaPorte, and Greg Novack who read portions of the thesis in article form again leading to a far better final version. As of the completion of this dissertation (May, 2008), it incorporated text from three journal articles and a number of referees helped improve those articles and therefore this thesis. These include anonymous referees from the British Journal of the Philosophy of Science and Studies in the History and Philosophy of Science who have helped improve portions of Chapters 1 and 2. These include Mike Alfaro on behalf of Molecular Phylogenetics and Evolution, as well as Kim Sterelny and an anonymous referee from Biology and Philosophy who made very helpful suggestions for Chapter 5. iii Contents Abstract i Acknowledgements ii 1 Two Principles of Phylogenetic Systematics 1 The Tree of Life 1 Phylogenetic trees 8 Why paraphyletic groups are bad 17 Ranking 22 Are ranks even consistent? 29 Why sister groups must have the same rank 31 Rank as age 35 Why classification is not important 40 Back to the Tree of Life 44 2 The Need for a Phylogenetic Species Concept 46 Introduction 46 The Biological Species Concept 48 How the BSC distorts history 50 Responses to the paraphyly problem 55 The second kind of misrepresentation 58 Species and the Tree of Life 63 iv 3 Developing a Phylogenetic Species Concept 72 A Phylogenetic Species Concept 72 Monophyletic groups of organisms 76 Epistemological issues 77 The real problem with non-nested groups 80 From monophyly to exclusivity 82 From organism pedigrees to gene genealogies 89 Gene genealogies 92 Exclusivity as recentness of genetic coalescence 98 From 100% to less 100 Criticisms of the genealogical species concept 104 Organisms or genes? 112 4 Species as a Rank 114 Species as a Rank 114 Species as basal taxa 119 Species as individuals 123 Category vs. taxon 127 Sidestepping more metaphysics 129 An ambiguous debate 135 Species as evolutionary units 140 Species as a grade 142 v Getting rid of Species 147 Phylogenetics without species 150 5 Inferring Phylogenetic Trees 155 1 Introduction 155 2 Bayesian phylogenetics 157 Priors on clades 164 Possible Priors and the Principle of Indifference 172 The Yule Process 174 The Base-Rate Fallacy 181 References 185 1 ONE TWO PRINCIPLES OF PHYLOGENETIC SYSTEMATICS 1. The Tree of Life It was, of course, Darwin who revolutionized our understanding of the diversity of life with his On the Origin of Species (Darwin 1859). It is in the Origin that we first see the importance of genealogy on a grand scale where Darwin convincingly argues that common ancestry explains both the striking similarities between different species and the groups within groups hierarchy of traits. As he says, “All the foregoing rules and aids and difficulties in classification are explained, if I do not greatly deceive myself, on the view that the natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical; that community of descent is the hidden bond which naturalists have been unconsciously seeking, and not some unknown plan of creation, or the enunciation of general propositions, and the mere putting together and separating objects more or less alike” (420). Earlier, Darwin had introduced the metaphor of the Tree of Life which connects all life through genealogy. 2 “The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth….…The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species….….the great Tree of Life…covers the earth with ever-branching and beautiful ramifications.” (129-30.) To help us understand the Tree, Darwin gives us a figure – the only figure in the entire Origin – which he then repeatedly refers back to (116). Figure 1.1 Darwin's "Tree-Thinking". The only figure in On the Origin of Species, it represents "decent with modification". 3 Key to understanding the diagram is that this represents real genealogical history – and not simply a subordination of groups within groups such as the diagrams previously given by Linnaeus, among others. It is also important that Darwin did not label the Tree more specifically than he did – for example, by saying that this is how various groups of mammals are related to each other. Rather, the idea is that this same pattern is seen throughout all life. In addition, the Tree is not meant to be just a depiction of how species are related but rather, how taxa are related. A "taxon", (plural "taxa") refers to any formally named group, such as Homo sapiens, in our system of biological classification. Darwin refers to this same diagram in discussing the relationship of higher taxa like genera (123) (where "higher taxa" simply means any taxa more inclusive than a species) and subspecific groups like varieties (117) as well as species (120). In this manner, the figure is rather like a fractal – the same pattern emerges when we “zoom in” or “zoom out” on some particular aspect of the Tree. Although Darwin believed that genealogy was important for classification, he did not believe that it was sufficient for providing a full classification. But for now, ignore classification and focus just on the concept of genealogy and the Tree of Life. This idea of the Tree which connects all life was prevalent in the literature for the next 100 years, but mainly served as a metaphor for evolution or even for progress. Famously, Ernst Haeckel depicted various versions of the Tree in many different works. One of his more famous figures is first seen in his 1874 work Antrhopogenie. Figure 1.2 is from the 1876 translation of this work into English called The Evolution of Man. 4 Figure 1.2 A depiction of the Tree of Life from Ernst Haeckel (1874 and 1876) Plate XV. Although there is certainly some branching depicting common ancestry, the diagram is clearly still influenced by ladder thinking. Notice that humans stand at the top of the Tree while more “primitive” forms are at the base giving the impression that mammals, primates, and humans actually arose from these more primitive groups. However, these 5 primitive groups are not direct ancestors. Rather, they are currently existing groups! Instead of the groups sharing an ancestor/descendant relationship, currently existing groups must share common ancestry – that is, they are all the descendants of some common ancestor. The tree is obviously anthropocentric as well with humans at the top. This smacks of a kind of progressivism – certainly popular historically (Ruse 2005) but which is unpopular today. Not only is it progressively leading to humans at the top, but there is clearly a “main” line of evolution and then various branches split off from the main line.
Load more

Recommended publications
  • Introgression and Hybridization in Animal Parasites
    Genes 2010, 1, 102-123; doi:10.3390/genes1010102 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Review An Infectious Topic in Reticulate Evolution: Introgression and Hybridization in Animal Parasites Jillian T. Detwiler * and Charles D. Criscione Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-979-845-0925; Fax: +1-979-845-2891. Received: 29 April 2010; in revised form: 7 June 2010 / Accepted: 7 June 2010 / Published: 9 June 2010 Abstract: Little attention has been given to the role that introgression and hybridization have played in the evolution of parasites. Most studies are host-centric and ask if the hybrid of a free-living species is more or less susceptible to parasite infection. Here we focus on what is known about how introgression and hybridization have influenced the evolution of protozoan and helminth parasites of animals. There are reports of genome or gene introgression from distantly related taxa into apicomplexans and filarial nematodes. Most common are genetic based reports of potential hybridization among congeneric taxa, but in several cases, more work is needed to definitively conclude current hybridization. In the medically important Trypanosoma it is clear that some clonal lineages are the product of past hybridization events. Similarly, strong evidence exists for current hybridization in human helminths such as Schistosoma and Ascaris. There remain topics that warrant further examination such as the potential hybrid origin of polyploid platyhelminths.
    [Show full text]
  • Pronunciation Guide to Microorganisms
    Pronunciation Guide to Microorganisms This pronunciation guide is provided to aid each student in acquiring a greater ease in discussing, describing, and using specific microorganisms. Please note that genus and species names are italicized. If they cannot be italicized, then they should be underlined (example: a lab notebook). Prokaryotic Species Correct Pronunciation Acetobacter aceti a-se-toh-BAK-ter a-SET-i Acetobacter pasteurianus a-se-toh-BAK-ter PAS-ter-iann-us Acintobacter calcoacetius a-sin-ee-toe-BAK-ter kal-koh-a-SEE-tee-kus Aerococcus viridans (air-o)-KOK-kus vi-ree-DANS Agrobacterium tumefaciens ag-roh-bak-TEAR-ium too-me-FAY-she-ens Alcaligenes denitrificans al-KAHL-li-jen-eez dee-ni-TREE-fee-cans Alcaligenes faecalis al-KAHL-li-jen-eez fee-KAL-is Anabaena an-na-BEE-na Azotobacter vinelandii a-zoe-toe-BAK-ter vin-lan-DEE-i Bacillus anthracis bah-SIL-lus AN-thray-sis Bacillus lactosporus bah-SIL-lus LAK-toe-spore-us Bacillus megaterium bah-SIL-lus Meg-a-TEER-ee-um Bacillus subtilis bah-SIL-lus SA-til-us Borrelia recurrentis bore-RELL-ee-a re-kur-EN-tis Branhamella catarrhalis bran-hem-EL-ah cat-arr-RAH-lis Citrobacter freundii sit-roe-BACK-ter FROND-ee-i Clostridium perfringens klos-TREH-dee-um per-FRINGE-enz Clostridium sporogenes klos-TREH-dee-um spore-AH-gen-ease Clostridium tetani klos-TREH-dee-um TET-ann-ee Corynebacterium diphtheriae koh-RYNE-nee-back-teer-ee-um dif-THEE-ry-ee Corynebacterium hofmanni koh-RYNE-nee-back-teer-ee-um hoff-MAN-eye Corynebacterium xerosis koh-RYNE-nee-back-teer-ee-um zer-OH-sis Enterobacter
    [Show full text]
  • Big Creek Lepidoptera Checklist
    Big Creek Lepidoptera Checklist Prepared by J.A. Powell, Essig Museum of Entomology, UC Berkeley. For a description of the Big Creek Lepidoptera Survey, see Powell, J.A. Big Creek Reserve Lepidoptera Survey: Recovery of Populations after the 1985 Rat Creek Fire. In Views of a Coastal Wilderness: 20 Years of Research at Big Creek Reserve. (copies available at the reserve). family genus species subspecies author Acrolepiidae Acrolepiopsis californica Gaedicke Adelidae Adela flammeusella Chambers Adelidae Adela punctiferella Walsingham Adelidae Adela septentrionella Walsingham Adelidae Adela trigrapha Zeller Alucitidae Alucita hexadactyla Linnaeus Arctiidae Apantesis ornata (Packard) Arctiidae Apantesis proxima (Guerin-Meneville) Arctiidae Arachnis picta Packard Arctiidae Cisthene deserta (Felder) Arctiidae Cisthene faustinula (Boisduval) Arctiidae Cisthene liberomacula (Dyar) Arctiidae Gnophaela latipennis (Boisduval) Arctiidae Hemihyalea edwardsii (Packard) Arctiidae Lophocampa maculata Harris Arctiidae Lycomorpha grotei (Packard) Arctiidae Spilosoma vagans (Boisduval) Arctiidae Spilosoma vestalis Packard Argyresthiidae Argyresthia cupressella Walsingham Argyresthiidae Argyresthia franciscella Busck Argyresthiidae Argyresthia sp. (gray) Blastobasidae ?genus Blastobasidae Blastobasis ?glandulella (Riley) Blastobasidae Holcocera (sp.1) Blastobasidae Holcocera (sp.2) Blastobasidae Holcocera (sp.3) Blastobasidae Holcocera (sp.4) Blastobasidae Holcocera (sp.5) Blastobasidae Holcocera (sp.6) Blastobasidae Holcocera gigantella (Chambers) Blastobasidae
    [Show full text]
  • Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa
    Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
    [Show full text]
  • Generalized Olfactory Detection of Floral Volatiles in the Highly Specialized Greya-Lithophragma Nursery Pollination System
    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2021 Generalized olfactory detection of floral volatiles in the highly specialized Greya-Lithophragma nursery pollination system Schiestl, Florian P ; Wallin, Erika A ; Beck, John J ; Friberg, Magne ; Thompson, John N Abstract: Volatiles are of key importance for host-plant recognition in insects. In the pollination system of Lithophragma flowers and Greya moths, moths are highly specialized on Lithophragma, in whichthey oviposit and thereby pollinate the flowers. Floral volatiles in Lithophragma are highly variable between species and populations, and moths prefer to oviposit into Lithophragma flowers from populations of the local host species. Here we used gas chromatography coupled with electroantennographic detection (GC-EAD) to test whether Greya moths detect specific key volatiles or respond broadly to many volatiles of Lithophragma flowers. We also addressed whether olfactory detection in Greya moths varies across populations, consistent with a co-evolutionary scenario. We analyzed flower volatile samples from three different species and five populations of Lithophragma occurring across a 1400 km range intheWestern USA, and their sympatric female Greya politella moths. We showed that Greya politella detect a broad range of Lithophragma volatiles, with a total of 23 compounds being EAD active. We chemically identified 15 of these, including the chiral 6, 10, 14-trimethylpentadecan-2-one (hexahydrofarnesyl acetone), which was not previously detected in Lithophragma. All investigated Lithophragma species produced the (6R, 10R)-enantiomer of this compound. We showed that Greya moths detected not only volatiles of their local Lithophragma plants, but also those from allopatric populations/species that they not encounter in local populations.
    [Show full text]
  • Slide Show Coevolution of Prodoxid Moths
    One of the Classic Examples of Coevolution Prodoxid Moths and Their Host Plants Yucca Greya moths moths G. variabilis Some unknown G. subalbaancestor G. enchrysa G. obscura G. mitellae G. politella G. piperella Moderately Highly Antagonist Commensal/ Inefficient Efficient Efficient Obligate Antagonist Mutualist Mutualist Mutualist, mutualist (What we knew in 1979) Sometimes Exclusive Thompson, Pellmyr, Segraves, Althoff, Brown,… What We Now Know: Diversification of Traits and Ecological Outcomes Prodoxid Moths and Their Host Plants Yucca Greya moths moths G. variabilis G. subalba G. enchrysa G. obscura G. mitellae G. politella T. maculata G. piperella Antagonist Commensal/ Inefficient Moderately Highly Obligate Antagonist Mutualist Efficient Efficient mutualist Mutualist Mutualist, Sometimes Exclusive Thompson, Pellmyr, Harrison, Brown, Segraves, Althoff, Cunningham, Nuismer, Merg, Cuautle, Rich, Laine, Schwind, Friberg, Raguso,… Diversification of Derived Taxa in Drier Habitats Basal Prodoxidae Basal Greya Derived Greya Yucca moths Wahlberg et al. 2013 for Prodoxidae Pellmyr et al. (various) for Yucca moths Thompson et al. and Pellmyr et al (various) for Greya Pollination Mutualisms Evolved More than Once In Prodoxid Moths Pollinators 18 5 Monocot-feeders 5-6+ Eudicot-feeders Thompson 2014 in Grant and Grant, eds., In Search of the Causes of Evolution, Princeton Univ. Press These Mutualisms Involve Two Plant Families Agavaceae Agavaceae Saxifragaceae Thompson 2014 in Grant and Grant, eds., In Search of the Causes of Evolution, Princeton Univ. Press The Moths Ensure Developing Seeds for Their Offspring: Actively in Yucca Moths Apiaceae Agavaceae Passively in Greya moths: Greya politella on Woodland Stars (Lithophragma) Photos: John N Thompson Lithophragma (Woodland star) Traits Coevolved Unique traits in With Greya Moths Lithophragma parviflorum Variable stigma & style and height, shape, etc.
    [Show full text]
  • Identification of the Meiotic Life Cycle Stage of Trypanosoma Brucei in The
    Identification of the meiotic life cycle stage of Trypanosoma brucei in the tsetse fly Lori Peacocka,b, Vanessa Ferrisa,b, Reuben Sharmac,1, Jack Sunterc, Mick Baileyb, Mark Carringtonc, and Wendy Gibsona,2 aSchool of Biological Sciences, University of Bristol, Bristol BS8 1UG, United Kingdom; bDepartment of Clinical Veterinary Science, University of Bristol, Bristol BS40 7DU, United Kingdom; and cDepartment of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom Edited by Francisco J. Ayala, University of California, Irvine, CA, and approved January 27, 2011 (received for review December 23, 2010) Elucidating the mechanism of genetic exchange is fundamental for genetic exchange in T. brucei involves mixing of mitochondrial understanding how genes for such traits as virulence, disease (kinetoplast) and nuclear genomes, because hybrid progeny have phenotype, and drug resistance are transferred between pathogen hybrid kinetoplast DNA (kDNA) networks with mini-circles de- strains. Genetic exchange occurs in the parasitic protists Trypano- rived from both parents (14, 15). Plausible models for the gen- soma brucei, T. cruzi, and Leishmania major, but the precise cellular eration of hybrid kDNA networks are limited by the complex mechanisms are unknown, because the process has not been ob- structure and highly ordered replication of this concatenated served directly. Here we exploit the identification of homologs of mass of small DNA circles (16). Finally, trypanosomes belong to meiotic genes in the T. brucei genome and demonstrate that three the Euglenozoa, a deep branch within the excavate eukaryote su- functionally distinct, meiosis-specific proteins are expressed in the pergroup (17, 18). The production of four haploid gametes and nucleus of a single specific cell type, defining a previously unde- subsequent fusion to reform the diploid occurring in trypanosomes scribed developmental stage occurring within the tsetse flysalivary would strongly suggest the presence of a typical meiosis in the last gland.
    [Show full text]
  • 23.3 Groups of Protists
    Chapter 23 | Protists 639 cysts that are a protective, resting stage. Depending on habitat of the species, the cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy allows certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried (such as by wind, water, or transport on a larger organism) to a different environment, because cysts exhibit virtually no cellular metabolism. Protist life cycles range from simple to extremely elaborate. Certain parasitic protists have complicated life cycles and must infect different host species at different developmental stages to complete their life cycle. Some protists are unicellular in the haploid form and multicellular in the diploid form, a strategy employed by animals. Other protists have multicellular stages in both haploid and diploid forms, a strategy called alternation of generations, analogous to that used by plants. Habitats Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and even snow. Several protist species are parasites that infect animals or plants. A few protist species live on dead organisms or their wastes, and contribute to their decay. 23.3 | Groups of Protists By the end of this section, you will be able to do the following: • Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes • Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes • Identify defining features of protists in each of the six supergroups of eukaryotes. In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes.
    [Show full text]
  • Trichonympha Cf
    MOLECULAR PHYLOGENETICS OF TRICHONYMPHA CF. COLLARIS AND A PUTATIVE PYRSONYMPHID: THE RELEVANCE TO THE ORIGIN OF SEX by JOEL BRYAN DACKS B.Sc. The University of Alberta, 1995 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER'S OF SCIENCE in THE FACULTY OF GRADUATE STUDIES (Department of Zoology) We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA April 1998 © Joel Bryan Dacks, 1998 In presenting this thesis in partial fulfilment of the requirements for an advanced degree at the University of British Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarly purposes may be granted by the head of my department or by his or her representatives. It is understood that copying or publication of this thesis for financial gain shall not be allowed without my written permission. Department of ~2—oc)^Oa^ The University of British Columbia Vancouver, Canada Date {X^ZY Z- V. /^P DE-6 (2/88) Abstract Why sex evolved is one of the central questions in evolutionary genetics. To address this question I have undertaken a molecular phylogenetic study of two candidate lineages to determine the first sexual line. In my thesis the hypermastigotes are confirmed as closely related to the trichomonads in the phylum Parabasalia and found to be more deeply divergent than a putative pyrsonymphid. This means that the Parabasalia are the first sexual lineage. From this I go on to infer that the ancestral sexual cycle included facultative sex.
    [Show full text]
  • Novel Pellicle Surface Patterns on Euglena Obtusa (Euglenophyta) from the Marine Benthic Environment: Implications for Pellicle Development and Evolution1
    J. Phycol. 44, 132–141 (2008) Ó 2008 Phycological Society of America DOI: 10.1111/j.1529-8817.2007.00447.x NOVEL PELLICLE SURFACE PATTERNS ON EUGLENA OBTUSA (EUGLENOPHYTA) FROM THE MARINE BENTHIC ENVIRONMENT: IMPLICATIONS FOR PELLICLE DEVELOPMENT AND EVOLUTION1 Heather J. Esson2 Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada and Brian S. Leander Departments of Botany and Zoology, University of British Columbia, Vancouver, British Columbia, Canada Euglena obtusa F. Schmitz possesses novel pellicle the cell; Wp, thenumberofwhorlsofexponential surface patterns, including the greatest number of strip reduction strips (120) and the most posterior subwhorls of strip reduction in any euglenid described so far. Although the subwhorls form a mathematically lin- A number of phylogenetic relationships within ear pattern of strip reduction, the pattern observed the Euglenophyta have been resolved in recent here differs from the linear pattern described for years due to the utilization of molecular and mor- Euglena mutabilis F. Schmitz in that it contains seven phological data. For example, extensive taxon sam- linear subwhorls, rather than three, and is develop- pling and phylogenetic analyses using ribosomal mentally equivalent to three whorls of exponential DNA have resulted in the resurrection of the genus reduction, rather than two. These properties imply Monomorphina (Marin et al. 2003) and the designa- that the seven-subwhorled linear pattern observed in tion of a novel genus, Discoplastis (Triemer et al. E. obtusa is evolutionarily derived from an ancestral 2006). Moreover, morphological studies of the bilinear pattern, rather than from a linear pattern, euglenid cytoskeleton, or pellicle, have confirmed of strip reduction.
    [Show full text]
  • Protozoan Parasites
    Welcome to “PARA-SITE: an interactive multimedia electronic resource dedicated to parasitology”, developed as an educational initiative of the ASP (Australian Society of Parasitology Inc.) and the ARC/NHMRC (Australian Research Council/National Health and Medical Research Council) Research Network for Parasitology. PARA-SITE was designed to provide basic information about parasites causing disease in animals and people. It covers information on: parasite morphology (fundamental to taxonomy); host range (species specificity); site of infection (tissue/organ tropism); parasite pathogenicity (disease potential); modes of transmission (spread of infections); differential diagnosis (detection of infections); and treatment and control (cure and prevention). This website uses the following devices to access information in an interactive multimedia format: PARA-SIGHT life-cycle diagrams and photographs illustrating: > developmental stages > host range > sites of infection > modes of transmission > clinical consequences PARA-CITE textual description presenting: > general overviews for each parasite assemblage > detailed summaries for specific parasite taxa > host-parasite checklists Developed by Professor Peter O’Donoghue, Artwork & design by Lynn Pryor School of Chemistry & Molecular Biosciences The School of Biological Sciences Published by: Faculty of Science, The University of Queensland, Brisbane 4072 Australia [July, 2010] ISBN 978-1-8649999-1-4 http://parasite.org.au/ 1 Foreword In developing this resource, we considered it essential that
    [Show full text]
  • Supporting Information Tibayrenc and Ayala 10.1073/Pnas.1212452109
    Supporting Information Tibayrenc and Ayala 10.1073/pnas.1212452109 Table S1. Species surveyed and their references Species References Bacteria Bacillus sp (1, 2) Bacillus anthracis (3, 4) Bacillus cereus (5–7) Bacillus subtilis (8) Bartonella bacilliformis (9) Bartonella henselae (10) Bartonella quintana (11) Borrelia sp (12) Burkholderia sp (2) Burckholderia mallei (13) Burckholderia oklahomensis (13) Burkholderia pseudomallei (6, 7, 13, 14) Burckholderia thailandensis (13) Campylobacter coli (15) Campylobacter jejuni (7, 15) Enterococcus feacalis (16, 17) Enterococcus faecium (7, 16, 17) Escherichia coli (7, 8, 18–28) Francisella tularensis (22) Haemophilus influenzae (7) Helicobacter pylori (6, 7, 24, 29) Legionella pneumophila (30–33) Listeria sp (34) Listeria monocytogenes (35) Moraxella catarrhalis (7) Mycobacterium bovis (36) Mycobacterium tuberculosis (3, 36–42) Neisseria gonorrheae (7, 18, 43–45) Neisseria lactamica (2, 18, 43–45) Neisseria meningitidis (2, 6, 7, 18, 40, 41, 43–56) Pseudomonas aeruginosa (57–59) Pseudomonas syringae (60) Salmonella enterica (61) Salmonella enterica ser typhi (3, 37, 62) Staphylococcus aureus (6, 7, 17, 24, 29, 41, 55, 62–64) Staphylococcus epidermidis (7, 64) Streptococcus agalactiae (7, 65) Streptococcus mitis (66, 67) Streptococcus oralis (66, 67) Streptococcus pneumoniae (6, 7, 17, 41, 65–72) Streptococcus pseudopneumoniae (66, 67) Streptococcus pyogenes (6, 7, 17, 22, 65, 73) Vibrio cholerae (74) Vibrio parahaemolyticus (74) Vibrio vulnificus (7, 74) Xanthomonas campestris (75) Yersinia pestis (3, 18, 37) Yersinia pseudotuberculosis (76) Fungi Aspergillus fumigatus (77) Candida albicans (77–80) Candida dubliniensis (81) Cryptococcus gattiii (82) Cryptococcus neoformans (77, 83, 84) Fusarium oxysporum (85) Tibayrenc and Ayala www.pnas.org/cgi/content/short/1212452109 1of5 Table S1.
    [Show full text]