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Open Access Research article

Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders

Leticia Bidegaray-Batista* and Miquel A Arnedo

Author Affiliations

Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Av. Diagonal 643, 08020, Barcelona, Spain

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BMC Evolutionary Biology 2011, 11:317  doi:10.1186/1471-2148-11-317

Published: 31 October 2011

Additional files

Additional file 1:

Specimens and gene sequence information. Specimens and sequence accession numbers included in the study with details of sample codes, voucher number, sex (f: female, m: male, juv.: juvenile), and collection locality. Species names with asterisks were included in lineage age estimation analyses. † sequences obtained from different specimens to complete gene sampling nr: near.

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Additional file 2:

Length of the non-protein coding genes under different alignments. Default, compressed and gappy alignment lengths are indicated for each gene, along with numbers of gaps and informative gaps codified as absence/presence.

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Additional file 3:

Substitution models per gene and partitions selected by AIC. Nucleotide substitution models selected by AIC for a 48 taxon matrix used for phylogenetic analyses, and a 34 taxon matrix under different partitions used for lineage age estimations (see Material and Methods for details).

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Additional file 4:

Bayes factor comparisons for the selection of the clock model, the speciation process and the partition scheme. a) Bayes factor comparisons for selection between Yule and Birth-death speciation models under partition scheme P1. b) Bayes factor comparisons for selection among partition schemes P1, P2, P3 and P1NOINV (see Material and Methods for details). HME: Harmonic mean of the likelihood from the posterior distribution value.

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Additional file 5:

Estimated age of three nodes selected to monitor the effect of alternative methods and parameters. Ages of three selected nodes under different evolutionary models and partition schemes as estimated by R8S, using the best method selected by cross-validation, and BEAST. In R8S analyses, branch lengths were first estimated with RAxML under a fixed topology in Figure 2 and GTR+Γ models, with (INV) or without invariants (NOINV). In BEAST, the best model was selected by jMODELTEST and, for P1 also without invariants (P1NOINV). Partition schemes: by gene (P1, 4412 chars), by gene and mitochondrial protein coding genes 1st + 2nd positions vs. 3rd positions (P2, 4412 chars), by gene and protein coding genes (both mitochondrial and nuclear) 1st + 2nd positions vs. 3rd positions (P3, 4412 chars), by gene with 3rd codon positions removed (P4, 3762 chars) and by gene with mitochondrial 3rd codon positions removed (P5, 3871 chars). NPRS (Non Parametric Rate Smoothing), PL (Penalized Likelihood), log (logarithmic penalty function). S: Smoothing factor in PL. Age: estimated age. Confidence interval obtained by profiling across 100 trees of constrained topology and bootstrapped branch lengths, as estimated with RAxML: max (maximum value observed), min (minimum value observed), mean (average). 95%HPD: upper and lower bound of the 95% highest posterior density interval. †Analyses run removing the opening of the Gibraltar strait as fixed calibration point. *Preliminary cross validation analyses selected PL log as best fit but failed check. **Analyses under PL in partitions and models where cross-validation selected NPRS as best method, but obtained confidence intervals where absurdly large.

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