Ecological Archives E096-015-A1

L. Chalmandrier, T. Münkemüller, S. Lavergne, and W. Thuiller. 2015. Effects of species’ similarity and dominance on the functional and phylogenetic structure of a plant meta-community. Ecology 96:143–153. http://dx.doi.org/10.1890/13-2153.1

Appendix A. Detailed information about the trait database and the phylogeny.

Functional traits

We used the functional trait database ANDROSACE (AlpiNe Database ResOurce for Species And eCosystems fEatures, Thuiller et al., unpublished). The database includes trait information for Alpine plants from individual projects (Albert et al. 2010a, 2010b) and freely available databases such as LEDA (Knevel et al. 2003), BioFlor (Kühn et al. 2004), Ecoflora (Fitter and Peat 1994), CATMINAT (Julve 1998) and Kew Gardens (Royal Botanic Gardens Kew 2008).

Phylogeny

A genus-level phylogeny of alpine plants was extracted from Thuiller et al. (2014). For this phylogeny, the authors followed the workflow proposed in Roquet et al. (2013) with DNA sequences downloaded from Genbank: three conserved chloroplastic regions (rbcL, matK and ndhF) and 8 regions for certain families or orders (atpB, ITS, psbA-trnH, rpl16, rps4, rps4-trnS, rps16, trnL-F) which were aligned separately by taxonomic clustering. All sequences were aligned with 3 methods: MUSCLE (Edgar 2004); MAFFT, (Katoh et al. 2005); Kalign, (Lassmann and Sonnhammer 2005) and checked by eye. The best alignment for each region was selected and depurated with TrimAl (Capella-Gutiérrez et al. 2009). Phylogenetic inference by maximum-likelihood (ML) was conducted with RAxML (Stamatakis 2006) applying a supertree constraint at the family-level based on Davies et al. (2004) and Moore et al. (2010). In order to obtain a phylogenetic tree with branch lengths equal to absolute evolutionary time, we dated the best ML tree with penalized-likelihood using r8s (Sanderson 2003) and 25 fossils constraints (Table A1). Finally, the tips of the phylogenetic tree were resolved with polytomies to obtain a species-level phylogeny.

Table A1. Fossil information and age constraints used to calibrate the branch length in the phylogeny. All the fossils were used as minimum age constraints.

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