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