Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples

<p>Beast v. 2.6.3 input (<em>.xml</em>) files and output (<em>.log</em> and <em>.trees</em>) files for phylogenetic analyses of rails, used to determined the evolutionary history of the Gal&aacute;pagos Rail <em>Laterallus spilonota</em>. There are two main datasets: coding sequences of the mitochondrial genome (&#39;mtCDS&#39;), partitioned per codon position,&nbsp;and a two mitochondrial/one nuclear marker dataset (&#39;2mt1nc&#39;). For each of the datasets, separate runs have been made in which the fossil calibration of Rallidae is applied to the stem of the present-day family (&#39;calRallidaeStem&#39;) or the crown node (&#39;calRallidaeCrown), and finally all runs have been replicated with three different starting seeds (&#39;seed_NNNNNNNNN&#39;, with the different seeds 123456789, 456789123, and 789123456).</p> <p>We provide raw output&nbsp;(<em>.log</em> and <em>.raw.trees</em>) as well as maximum clade credibility (&#39;mcc&#39;) trees (<em>.mcc.trees</em>), calculated after discarding 10% of the trees as burn-in, using median (&#39;heights_median&#39;) or mean (&#39;heights_mean&#39;) node heights as estimated node age.</p> <p>The runs used for Table 1 (and Figure 2) in the accompanying paper are:</p> <ul> <li>Dataset mtCDS, Rallidae calibration of stem: seed 123456789</li> <li>Dataset mtCDS, Rallidae calibration of crown: seed 456789123&nbsp;</li> <li>Dataset 2mt1nc, Rallidae calibration of stem: seed 789123456</li> <li>Dataset 2mt1nc, Rallidae calibration of crown: seed&nbsp;123456789</li> </ul> <p>This version of the data includes <em>Pellornis mikkelseni</em> among the fossils making up the calibration distribution for crown Gruiformes. In a previous version of this data deposit, that&nbsp;data point was represented by <em>Messelornis cristata </em>(see accompanying paper).</p>