Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1097 Diversity Underfoot Systematics and Biogeography of the Dictyostelid Social Amoebae ALLISON L PERRIGO ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-554-8804-856 UPPSALA urn:nbn:se:uu:diva-210074 2013 Dissertation presented at Uppsala University to be publicly examined in Lindahlsalen, Norbyvägen 18D, Uppsala, Friday, 13 December 2013 at 10:00 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Prof David Bass (Natural History Museum, London). Abstract Perrigo, A. L. 2013. Diversity Underfoot. Systematics and Biogeography of the Dictyostelid Social Amoebae. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1097. 56 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-8804-856. Dictyostelids (Amoebozoa) are a group of social amoebae consisting of approximately 150 species, which are found in terrestrial habitats worldwide. They are divided into eight major clades based on molecular phylogeny, and within these clades are many species complexes. Some species are seemingly cosmopolitan in distribution, while others are geographically restricted. In this thesis dictyostelids were recovered from high latitude habitats (soils in Sweden and Iceland) as well as from the soles of shoes. Morphological characters and DNA sequence analyses were used to identify isolates that were recovered and delimit new species, as well as to investigate the monophyly of Dictyostelium aureostipes. Nine species were reported from Northern Sweden and four from Iceland. Among the isolates recorded in Sweden were two new species, described as D. barbibulus and Polysphondylium fuscans. P. fuscans was among the four species recovered from footwear, contributing evidence for anthropogenic transport of dictyostelids. Ecological patterns were assessed using linear regression and generalized linear models. The ecological analyses of dictyostelids recovered from Iceland indicate that these organisms are most frequently found in soils of near-neutral pH, but also exhibit a species richness peak in moderately acidic soils. These analyses indicate that in Iceland dictyostelid species richness decreases with altitude, and in the northern hemisphere the species richness increases with decreasing latitude. A three-region analysis of the D. aureostipes species complex indicated that this species is in fact made up of at least five phylogenetically distinct clades, and in light of this the group is in need of taxonomic revision. These results indicate that the dictyostelid species richness is higher than previously known, especially in high- latitude regions, and that even seemingly well-defined species may harbour cryptic diversity. Presently, species ranges may be expanding via anthropogenic dispersal but despite this, the dictyostelids are found to exhibit biogeographic trends well known from macroorganisms, such as a latitudinal gradient of species richness. Keywords: Amoeba, biogeography, cryptic species, dictyostelid, latitudinal gradient, multicellularity, protist, social amoeba, phylogenetics, systematics, new species Allison L Perrigo, Department of Organismal Biology, Systematic Biology, Norbyv. 18 D, Uppsala University, SE-75236 Uppsala, Sweden. © Allison L Perrigo 2013 ISSN 1651-6214 ISBN 978-91-554-8804-856 urn:nbn:se:uu:diva-210074 (http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-210074) For Dad List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals: I Perrigo, A.L., Romeralo, M., Baldauf, S.L. (2012) What’s on your boots: an investigation into the role we play in protist dispersal. Journal of Biogeography, 39(5):998–1003 II Perrigo, A.L., Baldauf, S.L., Romeralo, M. (2013) Diversity of dic- tyostelid social amoebae in high latitude habitats of Northern Swe- den. Fungal Diversity, 57(1):185–198 III Perrigo, A.L., Moya-Larano, J., Baldauf, S.L., Romeralo, M. (Sub- mitted) Everything is not everywhere: a latitudinal gradient of pro- tist diversity. Submitted IV Perrigo, A.L., Romeralo, M., Baldauf, S.L. (Submitted) The yellow slime mold is a red herring: hidden genetic diversity in one protist morphospecies. Submitted Reprints of published papers were made with permission from the respective publishers. Allison Perrigo conceived the ideas, collected and analyzed the data, and was primarily responsible for the writing in Papers I and IV. In Paper II she contributed to data analysis and writing the paper. In Paper III, she collected the data, did the linear regression analysis for the latitudinal gradi- ent and was primarily responsible for the writing. Contents Introduction .................................................................................................... 9 Protists ....................................................................................................... 9 Amoebozoa .............................................................................................. 13 Dictyostelids ............................................................................................ 13 Biogeography ........................................................................................... 18 If everything is everywhere, where is everybody? .................................. 19 The taxonomic dilemma .......................................................................... 20 Aims ......................................................................................................... 21 Materials and Methods ................................................................................. 22 Collections ............................................................................................... 22 Culture, isolation and DNA extraction .................................................... 23 Morphological diagnoses ......................................................................... 24 Genetic markers ....................................................................................... 27 Phylogenetic Analyses ............................................................................. 28 Summary of Papers ...................................................................................... 29 Paper I: The boots study .......................................................................... 29 Paper II: Northern Sweden and new species ........................................... 31 Paper III: Iceland and the latitudinal gradient ......................................... 33 Paper IV: Dictyostelium aureostipes species complex ............................ 34 Conclusions .................................................................................................. 37 Svensk Sammanfattning ............................................................................... 38 Acknowledgements ...................................................................................... 41 References .................................................................................................... 46 Abbreviations AMP Adenosine monophosphate BS Bootstrap ca. Circa cf. Confer DNA Deoxyribonucleic acid GPS Global positioning system HI Hay infusion agar ITS Internal transcribed spacer mm Millimeter ml Milliliter MYA Million years ago NNA Non-nutrient agar OTU Operational Taxonomic Unit PCR Polymerase chain reaction PP Posterior probability RAxML Randomized Accelerated Maximum Likelihood rRNA Ribosomal ribonucleic acid s.l. Sensu lato SM Standard media agar sp. Species sp. nov. Species novum SSU Small subunit µm Micrometer UU Uppsala University var. Variety Introduction “When a biologist studies a group of species, ranging anywhere from, say, elephants with three living species to ants with fourteen thousand species, he or she typically aims to learn everything possible over a large range of bio- logical phenomena. Most researchers working this way… are properly called scientific naturalists. … They will tell you, correctly, that there is infinite de- tail and beauty even in those that people at first find least attractive – slime molds, for example, dung beetles, cobweb spiders, and pit vipers. Their joy is in finding something new, the more surprising the better. They are the ecol- ogists, taxonomists, and biogeographers.” E.O. Wilson in Letters to a Young Scientist This thesis is the compilation of four papers and manuscripts that broadly aim to increase the collective knowledge about something many of us didn’t even know existed: dictyostelid social amoebae, or cellular slime molds. Over the course of these studies I have heard these amoebae likened to aliens (or, ‘moon snot’), a microscopic forest, the mood slime from Ghost Busters, an inverse fountain and many other strange and variously accurate images. For now, I will not offer further comparisons. Instead I will focus on famil- iarizing you, my audience, with these creatures, such that you can develop your own understanding and, possibly, analogies. So put up your feet, pour a cup of coffee, and take a few minutes to enjoy the intricacies of these organ- isms that I have spent the last five years sometimes hating but more often loving, and always in awe of. Protists The Earth is home to many extraordinary and wonderful creatures. We are all familiar with animals, plants and fungi. Bacteria and viruses are 9 also in our repertoire. However, there is a massive diversity of organisms that are eukaryotic