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Mutations As Molecular Tools: the Metabolic-Rate Dependent Molecular Clock and DNA Barcoding of Allied Species

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Mutations As Molecular Tools: the Metabolic-Rate Dependent Molecular Clock and DNA Barcoding of Allied Species Mutations as molecular tools: The metabolic-rate dependent molecular clock and DNA barcoding of allied species Lena Alena Brüstle Zoological Museum Finnish Museum of Natural History University of Helsinki Finland Department of Biological and Environmental Sciences Faculty of Biosciences University of Helsinki Finland Academic dissertation To be presented, with the permission of the Faculty of Biosciences of the University of Helsinki, for public criticism in Auditorium 2, Viikin Infokeskus Korona, Viikinkaari 11 on 26th September 2009, at 10 a.m. Helsinki 2009 © Lena Alena Brüstle (Summary, Chapter IV) © Pearson Education Inc, Benjamin Cummings (Figure 1) © University of Helsinki (Appendix I) © Entomological Society of Finland (Chapter I) © Wiley-Blackwell, John Wiley & Sons (Chapter II) © Willi Hennig Society (Chapter III) Author’s address: Finnish Museum of Natural History P.O. Box 17 (P. Rautatiekatu 13) FIN-00014 University of Helsinki Finland Author’s email: [email protected] [email protected] ISBN 978-952-92-6040-9 (paperback) ISBN 978-952-10-5700-7 (PDF) http://ethesis.helsinki.fi Yliopistopaino Helsinki 2009 2 Die Kultur hat in Verbindung mit einer ewigen Evolution, in Jahrmillionen, aus dem Tier den Menschen geformt. Die Zivilisation macht in wenigen Jahren mit Hilfe der Technik und Kriegsmaschinen aus dem Menschen wieder ein Tier. Wilhelm Brüstle (1965) 3 Mutations as molecular tools: The metabolic-rate dependent molecular clock and DNA barcoding of allied species Lena Alena Brüstle List of original articles This thesis is based on the following articles, which are referred to in the text by their Roman numerals: I. Muona, J., and Brüstle, L. (2008) Observations on the biology of Hylochares cruentatus (Gyllenhal) (Coleoptera: Eucnemidae). Entomol. Fennica 19: 151-158. II. Brüstle, L., and Muona, J. Life-history studies versus genetic markers - the case of Hylochares cruentatus (Coleoptera, Eucnemidae). J. Zool. Syst. Evol. Res. (in press). III. Brüstle, L., Alaruikka, D., Muona, J., and Teräväinen, M. The phylogeny of the Pantropical genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae). Cladistics (in press). IV. Brüstle, L., Muona, J., and Salamin, N. Influence of temperature on invertebrate mutation rates: do different approaches tell the same story? (manuscript). 4 Table of contributions The following table highlights the major contributions of authors to the presented articles and manuscripts listed below I II III IV Original Idea JM LB, JM LB, JM LB Data Collection LB, JM LB, JM JM LB, JM Molecular Data - LB LB, MT LB Morphology JM JM JM, DA - Analysis LB, JM LB, JM LB, JM LB, NS Manuscript preparation LB, JM LB, JM LB, JM LB LB= Lena Brüstle, JM= Jyrki Muona, NS= Nicolas Salamin, MT= Marianna Teräväinen, DA= Diane Alaruikka Supervised by: Dr. Jyrki Muona Finnish Museum of Natural History Helsinki, Finland Reviewed by: Prof. Jaakko Hyvönen University of Helsinki Helsinki, Finland Dr. Ilari Sääksjärvi University of Turku Turku, Finland Examined by: Prefekt Mari Källersjö Göteborgs botaniska trädgård Göteborg, Sweden 5 Contents Abstract ..................................................................................................................................... 8 I. Introduction .................................................................................................................. 9 DNA the Building Block of Life ............................................................................. 9 The Molecular Clock ............................................................................................. 10 Concept and Application of the Molecular Clock ....................................... 10 Problems with the Concept of the Molecular Clock .................................... 10 “Relaxing” the Molecular Clock .................................................................. 11 The Metabolic-Rate Dependent Molecular Clock ....................................... 12 DNA Barcoding ..................................................................................................... 13 The Concept of DNA Barcoding ................................................................. 13 Criticism of DNA Barcoding ....................................................................... 13 DNA Barcoding and Conservation .............................................................. 14 The Molecular Clock and DNA Barcoding ........................................................... 15 Different Purpose, similar Problem ............................................................. 15 II. Aim of the Thesis ........................................................................................................ 15 III. Study Organisms ........................................................................................................ 16 Molecular Clock Study .......................................................................................... 16 False-click beetles (Coleoptera: Eucnemidae) ............................................. 16 Tribe Syrphini (Diptera: Syrphidae) ............................................................ 17 Barcoding Study .................................................................................................... 17 Hylochares (Coleoptera: Eucnemidae) ........................................................ 17 IV. Materials and Methods .............................................................................................. 18 Molecular Clock Study .......................................................................................... 18 Molecular and Morphological Data ............................................................. 18 Phylogenetic Inference................................................................................. 18 Dating, Molecular Clock Models and Temperature Estimates .................... 19 Methods applied to test the Metabolic-Rate Dependent Molecular Clock .. 22 Barcoding Study .................................................................................................... 23 Molecular, Morphological and Life-History Data ....................................... 23 V. Results .......................................................................................................................... 23 Molecular Clock Study .......................................................................................... 23 Phylogeny of the Pantropical Genus Arrhipis ............................................. 23 Temperature Effect on the Metabolic-Rate Dependent Molecular Clock ... 24 6 Barcoding Study .................................................................................................... 26 Biology of the Finnish Hylochares cruentatus (Coleoptera: Eucnemidae) . 26 Hylochares cruentatus: Life-History versus Genetic Markers ................... 27 VI. Discussion and Conclusion......................................................................................... 28 Discussion ............................................................................................................ 28 Molecular Clock Study ............................................................................... 28 Barcoding Study .......................................................................................... 30 Conclusion ............................................................................................................ 31 Appendix I .............................................................................................................................. 33 Appendix II ............................................................................................................................ 34 Acknowledgements ................................................................................................................ 35 References .............................................................................................................................. 37 7 Abstract Mutation and recombination are the fundamental processes leading to genetic variation in natural populations. This variation forms the raw material for evolution through natural selection and drift. Therefore, studying mutation rates may reveal information about evolutionary histories as well as phylogenetic interrelationships of organisms. In this thesis two molecular tools, DNA barcoding and the molecular clock were examined. In the first part, the efficiency of mutations to delineate closely related species was tested and the implications for conservation practices were assessed. The second part investigated the proposition that a constant mutation rate exists within invertebrates, in form of a metabolic-rate dependent molecular clock, which can be applied to accurately date speciation events. DNA barcoding aspires to be an efficient technique to not only distinguish between species but also reveal population-level variation solely relying on mutations found on a short stretch of a single gene. In this thesis barcoding was applied to discriminate between Hylochares populations from Russian Karelia and new Hylochares findings from the greater Helsinki region in Finland. Although barcoding failed to delineate the two reproductively isolated groups, their distinct morphological features and differing life-history traits led to their classification as two closely related, although separate species. The lack of genetic differentiation appears to be due to a recent divergence event not yet reflected in the beetles’ molecular make-up. Thus,
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