Supplementary Data and Code: A subterranean adaptive radiation of amphipods in Europe

Supplementary Data, R code, alignments and settings for phylogenetic analyses for manuscript entitled <em>A subterranean adaptive radiation of amphipods in Europe.</em> <strong>The dataset contains</strong> <strong>Alignments and settings for phylogenetic analyses</strong><br> <em>BEAST2_subset_alignment.nex</em>→ BEAST2 analysis on a subset of MOTUs with at least two markers<br> <em>BEAST2_subset_settings.xml</em>→ BEAST2 analysis on a subset of MOTUs with at least two markers <em>BEAST2_whole_alignment.nex </em>→ BEAST2 analysis on a whole dataset of 377 Niphargus MOTUs (+ outgroup <em>Niphargellus</em>)<br> <em>BEAST2_whole_settings.xml </em>→ BEAST2 analysis on a whole dataset of 377 Niphargus MOTUs (+ outgroup <em>Niphargellus</em>) <em>IQ-TREE_alignment.phy </em>→ IQ-TREE analysis<br> <em>IQ-TREE_settings.nex </em>→ IQ-TREE analysis <em>MrBayes.nex</em> → MrBayes analysis <em>analyses.R </em>→ code for analyses on whole dataset<br> <em>analyses_small.R</em>→ code for repeated LTT, DTT, CTT analyses on subset <em>beast.trees</em> → data for import into R: all BEAST2 trees<br> <em>beast_meanH.tre</em> → data for import into R: maximum credibility tree<br> <em>beast_meanH_small.tre</em> → data for import into R: small maximum credibility tree<br> <em>beast_small.trees</em> → data for import into R: all small BEAST2 trees<br> <em>ecology.xlsx</em> → data for import into R: ecological data<br> <em>morphology.xlsx</em> → data for import into R: morphometric data