Data from: Speciation below ground: tempo and mode of diversification in a radiation of endogean ground beetles

Andújar C, Pérez-González S, Arribas P, Zaballos JP, Vogler AP, Ribera I

Date Published: September 18, 2017

DOI: https://doi.org/10.5061/dryad.bk78q

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Title Phylogeny_of_Typhlocharina_RAxML_BestTree
Downloaded 1 time
Description ML trees were obtained using RAxML 7.2.7 (Stamatakis 2006). Data sets were partitioned by gene and the protein-coding genes (cox1-a and cox1-b fragments) were additionally partitioned by separating the third codon positions (Andújar et al. 2012). An independent GTR + G model was applied to each data partition. The best scoring ML tree was selected among 200 searches on the original alignment with different randomized parsimony starting trees. Support values were obtained with 1000 bootstrap replicates (Felsenstein 1985). BI was run in MrBayes 3.2.3 (Huelsenbeck et al. 2001) on the concatenated data, partitioned by gene and codon as before, and for each partition the optimal substitution model was selected using the Akaike information criterion (AIC) in jModelTest 2.1.7 (Darriba et al. 2012).
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Title Phylogeny_of_Typhlocharina_MrBayes_MajorityRuleConsensus
Downloaded 4 times
Description 50% majority rule consensus tree obtained in MrBayes. Bayesian inference consisted of two independent runs, each with three hot and one cold chain, for 10 million generations, whereby trees were sampled every 1000 generations. The standard deviation of split frequencies was checked to assess the convergence of results, as well as the mean and effective sampled size (ESS) of likelihood values computed with TRACER 1.6 (Rambaut et al. 2013). The 50% majority rule trees were calculated excluding 50% of the initial trees as a conservative burn-in, ensuring that the plateau in tree likelihood values had been reached.
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Title Phylogeny_of_Typhlocharis_BEAST_dated_tree_(Rates_ULN_bd)_Complete
Downloaded 2 times
Description Dated phylogenetic tree obtained with BEAST 1.8.1 (Drummond et al. 2012). For the analyses the original concatenated dataset was collapsed to haplotypes and the outgroups were excluded, resulting in a dataset of 330 terminals. We used as calibration prior for each gene an uniform function on the mean substitution rate encompassing the 95% confident interval values obtained for the same DNA fragments (cox1-a, cox1-b, rrnL, LSU and SSU genes) in the confamilial genus Carabus (Andújar et al., 2014, 2012) and the tribe Anillini (Andújar et al., 2016) (Table 1 in original paper). We additionally applied a gamma prior on the root age for the most recent common ancestor (crown group) of Typhlocharina. We used TreeStat 1.6.1 (Rambaut & Drummond 2010) to recover the node age of the ancestor of Typhlocharina from the sample of the MCMC search of the BEAST analysis favoured in Andújar et al. (2016), and we used the “fitdistr” option of the R package MASS to obtain the values of a gamma function adjusting the distribution of sampled ages, thus accounting for the uncertainty associated to the age estimations (Table 1 on the original paper). Analyses were conducted under the model of substitution best fitting to each gene and codon partition as above, and were run for 50 million generations sampling one tree in every 5,000 generations. In the molecular clock settings gene partitions were uncorrelated, and two independent analyses were conducted applying an uncorrelated lognormal (ULN) to all genes. Analyses were conducted under a Birth-Death model (BD) and with the inclusion of the constraint on the age for the ancestor of Typhlocharina (Table 1 on the original paper)
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Title Phylogeny_of_Typhlocharis_BEAST_dated_tree_(Rates_ULN_bd)_Pruned_to_species
Downloaded 1 time
Description Time calibrated tree pruned to keep a single tip branch per species.
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When using this data, please cite the original publication:

Andújar C, Pérez-González S, Arribas P, Zaballos JP, Vogler AP, Ribera I (2017) Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles. Molecular Ecology 26(21): 6053-6070. https://doi.org/10.1111/mec.14358

Additionally, please cite the Dryad data package:

Andújar C, Pérez-González S, Arribas P, Zaballos JP, Vogler AP, Ribera I (2017) Data from: Speciation below ground: tempo and mode of diversification in a radiation of endogean ground beetles. Dryad Digital Repository. https://doi.org/10.5061/dryad.bk78q
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