Montpellier 2 University, France University of the Aegean, Greece Master 2 Ecology & Biodiversity - Research project Specialty : Biodiversity & Evolution Focus : BIODIV “Biodiversity conservation” 2011-2012 First steps in a project integrating phylogeny, climate, geological history and dispersion dynamics, to explain the phylogeography of the genus Batrachoseps . Julian WITTISCHE Internship supervisor: Pr. em. David B. Wake Museum of Vertebrate Zoology Department of Integrative Biology University of California, Berkeley First steps in a project integrating phylogeny, climate, geological history and dispersion dynamics, to explain the phylogeography of the genus Batrachoseps . Julian Wittische University of California, Berkeley, Departement of Integrative Biology, Museum of Vertebrate Zoology, Berkeley CA, USA [email protected] 2 ABSTRACT The slender salamanders genus, Batrachoseps (Plethodontidae), is the most speciose group of caudate amphibians in the western nearctic zone. All clades and even species within these groups show a marked phylogeographic structure, although there is often a discrepancy between mtDNA and nDNA (allozymes) datasets. Batrachoseps species are morphologically cryptic and ecologically very similar. Slender salamander species do not merge when a parapatry occurs and sympatry is limited especially within clades, so that they seem to replace each other spatially. Several elements give insight about the diversification processes of this genus and the non-adaptive radiation hypothesis, where non-ecological speciation occurs, seems likely. To all appearances isolation periods following fragmentation could have have been amply long to create a divergence, great enough to prevent populations from merging and efficiently hybridizing. However the non-adaptive hypothesis has not been studied yet from an environmental niche point of view. Methods from invasive species niche studies are adapted and ordination techniques are used in order to compare and illustrate the environmental niches of slender salamanders based on several climatic variables. Through these comparisons, predictions made by the non-adaptive hypothesis are tested with an increasing complexity and rigor in the methodology. The biological significance of these environmental niche metrics and tests is discussed within a conceptual context and hypotheses about the reasons why our first hypothesis could be true while leading to our results are formulated. Finally an experimental ecology perspective is given and the integration of this study in a wider project is highlighted. Key words: southwestern North America, lungless salamanders, biogeography, niche, species formation, ordination statistics 3 CONTENTS Introduction..........................................................................................................................................5 Materials and Methods.........................................................................................................................7 1. Phylogeny: sister species and their divergence time......................................................................7 2. Georeferences and climatic data.....................................................................................................8 3. First method to calculate climatic overlap of the species temperature regime and associated statistical analyses................................................................................................................................8 4. Second method: addition of precipitation variables and associated multivariate analyses............9 5. Third method: adaptation of Broennimann et al, 2012 to the comparison of the niches of two species.................................................................................................................................................10 Results................................................................................................................................................10 1. Thermal regime analysis on 12 months........................................................................................10 2. Convex hulls and BCA.................................................................................................................11 2. Broennimann et al. Framework....................................................................................................11 Discussion..........................................................................................................................................12 References..........................................................................................................................................17 List of figures.....................................................................................................................................21 Tables.................................................................................................................................................22 Figures................................................................................................................................................25 Appendix............................................................................................................................................33 Acknowledgements............................................................................................................................77 4 INTRODUCTION Patterns in species formation bring a lot of conceptual issues (Williams, 1992; Wake, 2009). The arbitrary level of genetic or morphological divergence used to delimit species is one of them. Biologists always had trouble writing a stable and robust definition of what a species is, although some elements of the concept are shared by most of them (Mayden, 1997; de Queiroz, 1999, 2005, 2007). The main issue is not defining the properties of taxonomic categories but rather to find and describe divergence and eventually split local evolutionary lineages (Vences and Wake, 2007). One can notice numerous examples of diversification bursts in the animal kingdom: they can be produced by physical separation creating divergence by isolation or by adaptive speciation while maintaining opportunity for genetic interaction. Non-adaptive radiations are common and there is a possibility that current ecologically differentiated sympatric species have been the result of such radiation. Also radiations may include elements from both types of speciation (Rundell and Price, 2009). Phylogeographical analysis by its integration of population genetics and historical biogeography is a great tool to identify population-level evolutionary units which can then be used to sort out hypotheses about the formation of species. Both the richness in phylogenetic data and the increasing knowledge of the distribution of species give phylogeography a great power to explain patterns of biological diversity. A lot of the species formation history can be inferred from studying geographic variation both within and between species (Irwin, 2012). All phylogeographical hypotheses one may develop, should respect a few key rules: the vast majority of species have geographic populations with a sometimes great genetic structure and are very likely to show an intraspecific phylogenetic tree (Avise, 1987), dispersal ability (intrinsic and extrinsic) is a major element to understand phylogeography and much of the variance in monophyletic groups with great genetic gaps or lack of phylogeographical structure in a species can be explained by their dispersal history (Fumihito et al., 1996). In bygone days, individuals were diagnosed as belonging to a species by their morphology. However since the discovery of DNA and the ever-increasing use of genetic data, many phenotypically cryptic lineages have been discovered. Previously misapprehended biodiversity was here, defying science and holding back a lot of information. The first to describe one Batrachoseps species, Batrachoseps attenuatus, was Johann Friedrich von Eschscholtz, famous for his two expeditions and for being the first to describe Enteropneusta (Eschscholtz, 1833). Even after a detailed morphological analysis from Hendrickson in 1954, there was still only one species recognized in a huge part of California. Studies have regularly added species in the genus by discovery or splitting of older taxa (Cope, 1865; Cope, 1869; Camp, 1915; Bishop, 1937,Brame and Murray, 1968; Marlow et al., 1979; Wake, 1996; Jockusch et al., 1998; Jockusch et al, 2001; Wake et al., 2002; Jockusch et al., 2012). Each new taxonomy enabled scientists to have a better understanding of the biodiversity in the genus Batrachoseps , which is now the most species-rich salamander clade in western north America. Slender salamanders can be found along the Pacific coast of North America (Fig.2) from the Cascade Mountains of Oregon (USA) to the Sierra San Pedro Mártir in Baja California (Mexico). There are some disjoint interior ranges from the Cascade Mountains of northern Oregon through the Sierra Nevada and Inyo mountain systems in California to the Sierra San Pedro Mártir near the southern end of its range in Baja California. Coastal populations of the subgenus Batrachoseps are very diverse taxonomically and include at least partially three of the four groups of the subgenus Batrachoseps , the relictus group being only in the Sierra Nevada system. The radiation of Batrachoseps is likely to result from the complicated geological history of