Computational protocol: Evaluating the Significance of Paleophylogeographic Species Distribution Models in Reconstructing Quaternary Range Shifts of Nearctic Chelonians

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Protocol publication

[…] We constructed a time-calibrated molecular phylogeny for the 59 chelonian species using a supermatrix approach. Data from four mitochondrial genes (COI, control region, cytb, ND4) and three nuclear genes (R35, RAG-1, TB29) were downloaded from GenBank. The number of loci varied across the taxa, but even with missing data the concatenated data are still expected to provide a reasonable estimate of the phylogeny . GenBank accession numbers for the sequences are reported in Appendix S1 in . Each gene was aligned separately using the MUSCLE algorithm (MUSCLE version 3.6, ) and checked manually. Ambiguously aligned or randomly similar sequence sections were detected with ALISCORE and removed. The final, concatenated data set contained 5742 bp (including gaps). Parameters for the substitution model (GTR+G) were estimated separately for each gene by partitioning the data set during subsequent analyses. A Yule speciation process was used to estimate the prior probability of the tree. Divergence times were estimated with BEAST 1.6.2 with a relaxed molecular clock model with rates with an uncorrelated lognormal distribution –. Two fossil Trachemys species, T. idahoensis (4 Ma) and T. inflata (7 Ma) were used as calibration points for the most recent common ancestors (MRCA) of T. scripta/T. gaigeae and of the North American clade/Tropical clade of Trachemys, respectively . Glyptemys valentinensis (14.5 Ma) was used to calibrate the MRCA of the genus Glyptemys; , and Kinosternon pojoaque (13.3 Ma) was used to calibrate the MRCA of K. arizonense, K. durangoense and K. hirtipes; ) For T. idahoensis, a uniform prior distribution with the lower bound at 4 Ma and the upper bound at 7 Ma (i.e. the lower bound of the older fossil species T. inflata) was used (cf. ). We used single-sided hard bounds for the minimum age of divergence and an exponential distribution as a soft bounds for the maximum age. Every 1000th trees were sampled from three independent runs with 107 generations. The initial 5% of each run was discarded as burn-in, resulting in a total of 28,500 trees. Maximum likelihood bootstrap values (1,000 replicates) were calculated using RAxML v.7.2.X . […]

Pipeline specifications

Software tools MUSCLE, Aliscore, BEAST, RAxML