Supplementary Data and Code: A subterranean adaptive radiation of amphipods in Europe
Authors/Creators
- 1. SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- 2. Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
Description
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
Files
BEAST2_subset_settings.xml
Files
(685.2 MB)
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Additional details
Related works
- Is supplement to
- Journal article: 10.1038/s41467-021-24023-w (DOI)