Habitat selection, cryptic diversity, phylogeny, and phylogeography of the European Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae) Dissertation for the award of the degree Ph.D. Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen within the doctoral program Biology of the Georg-August University School of Science (GAUSS) submitted by Bing Zhang from Zaoyang, Xiangyang, Hubei province, China Göttingen, November 2018 i Thesis Committee Stefan Scheu, Animal Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology Mark Maraun, Animal Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology Members of the Examination Board Reviewer: Stefan Scheu, Animal Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology Second Reviewer: Christoph Bleidorn, Animal Evolution and Biodiversity, Johann-Friedrich- Blumenbach Institute for Zoology and Anthropology Additional Reviewer (if applicable): Further members of the Examination Board: Elvira Hörandl, Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von- Haller Institute for Plant Sciences Klaus Hövemeyer, Animal Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology Mark Maraun, Animal Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology Marko Rohlfs, Population and Evolutionary Ecology Group, Institute of Ecology, University of Bremen Date of the oral examination: 14th of December, 2018 ii Table of contents Summary ............................................................................................................................................... 1 Chapter I ................................................................................................................................................ 5 General Introduction .......................................................................................................................... 5 1.1 Genetic markers for molecular delimitation, phylogeny, and phylogeography ....................... 6 1.2 “Cryptic” species in Collembola ................................................................................................ 7 1.3 Molecular delimitation criteria in Collembola .......................................................................... 9 1.4 Phylogeny and biogeography of Collembola............................................................................. 9 1.5 The European Lepidocyrtus species and Lepidocyrtus lanuginosus species group ................. 11 1.6 Structure of the thesis ............................................................................................................. 12 References ..................................................................................................................................... 13 Chapter II ............................................................................................................................................. 21 Cryptic species in Lepidocyrtus lanuginosus (Collembola: Entomobryidae) are sorted by habitat type ........................................................................................................................................ 21 Abstract ......................................................................................................................................... 22 2.1 Introduction............................................................................................................................. 22 2.2 Material and methods ............................................................................................................. 24 2.2.1 Sampling of animals and determination ...................................................................... 24 2.2.2 DNA extraction and PCR ............................................................................................... 25 2.2.3 Data analyses ................................................................................................................ 26 2.3 Results ..................................................................................................................................... 27 2.3.1 Habitat sorting of lineages of Lepidocyrtus lanuginosus .............................................. 27 2.3.2 Genetic distances and variances and phylogenetic analysis ........................................ 27 2.4 Discussion ................................................................................................................................ 30 2.4.1 Habitat sorting .............................................................................................................. 30 2.4.2 Genetic distances .......................................................................................................... 33 2.4.3 Systematics ................................................................................................................... 34 2.5 Conclusions.............................................................................................................................. 34 Acknowledgements ....................................................................................................................... 35 References ..................................................................................................................................... 35 Supplementary Materials .............................................................................................................. 40 iii Chapter III ............................................................................................................................................ 45 DNA-based approaches uncover cryptic diversity in the European Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae) ................................................................................ 45 Abstract ......................................................................................................................................... 46 3.1 Introduction ............................................................................................................................. 46 3.2 Material and methods ............................................................................................................. 48 3.2.1 Sampling and DNA extraction ....................................................................................... 48 3.2.2 DNA-based species delimitation ................................................................................... 49 3.2.3 Data analyses ................................................................................................................ 51 3.3 Results ..................................................................................................................................... 51 3.3.1 MOTUs / cryptic species delimitation based on mitochondrial markers ..................... 51 3.3.2 Genetic distances of both nuclear and mitochondrial markers ................................... 52 3.3.3 Phylogenetic analysis .................................................................................................... 54 3.4 Discussion ................................................................................................................................ 55 3.4.1 High cryptic diversity of the Lepidocyrtus lanuginosus species group ......................... 55 3.4.2 Phylogenetic analysis .................................................................................................... 56 3.4.3 DNA-based approaches help discovering species diversity .......................................... 57 3.5 Conclusions .............................................................................................................................. 58 Acknowledgements ....................................................................................................................... 58 References ..................................................................................................................................... 59 Supplementary Materials .............................................................................................................. 64 Chapter IV ........................................................................................................................................... 79 Late Miocene-Pliocene diversification and Pleistocene-Holocene colonization shape phylogeography of the European Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae) ................................................................................................................................. 79 Abstract ......................................................................................................................................... 80 4.1 Introduction ............................................................................................................................. 80 4.2 Material and methods ............................................................................................................. 82 4.2.1 Data collection and lineage assignment ....................................................................... 82 4.2.2 Genetic diversity, population structure and haplotype reconstruction ....................... 83 4.2.3 Phylogenetic analyses and divergence time estimation ............................................... 83 4.3 Results ....................................................................................................................................