Data from: One tree to link them all: a phylogenetic dataset for the European Tetrapoda

Since the ever-increasing availability of phylogenetic informative data,
the last decade has seen an upsurge of ecological studies incorporating
information on evolutionary relationships among species. However, detailed
species-level phylogenies are still lacking for many large groups and
regions, which are necessary for comprehensive large-scale
eco-phylogenetic analyses. Here, we provide a dataset of 100 dated
phylogenetic trees for all European tetrapods based on a mixture of
supermatrix and supertree approaches. Phylogenetic inference was performed
separately for each of the main Tetrapoda groups of Europe except mammals
(i.e. amphibians, birds, squamates and turtles) by means of maximum
likelihood (ML) analyses of supermatrix applying a tree constraint at the
family (amphibians and squamates) or order (birds and turtles) levels
based on consensus knowledge. For each group, we inferred 100 ML trees to
be able to provide a phylogenetic dataset that accounts for phylogenetic
uncertainty, and assessed node support with bootstrap analyses. Each tree
was dated using penalized-likelihood and fossil calibration. The trees
obtained were well-supported by existing knowledge and previous
phylogenetic studies. For mammals, we modified the most complete supertree
dataset available on the literature to include a recent update of the
Carnivora clade. As a final step, we merged the phylogenetic trees of all
groups to obtain a set of 100 phylogenetic trees for all European
Tetrapoda species for which data was available (91%). We provide this
phylogenetic dataset (100 chronograms) for the purpose of comparative
analyses, macro-ecological or community ecology studies aiming to
incorporate phylogenetic information while accounting for phylogenetic
uncertainty.