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