Data Associated With The Publication "The Origin Of The World'S Smallest Flightless Bird, The Inaccessible Island Rail Atlantisia Rogersi (Aves: Rallidae)"

<strong>DESCRIPTION OF FILES</strong><br> These are files including data and additional results, that support the paper "The origin of the world's smallest flightless bird, the Inaccessible Island Rail Atlantisia rogersi (Aves: Rallidae)", by Stervander et al. 2018, published in Molecular Phylogenetics and Evolution (doi: 10.1016/j.ympev.2018.10.007). The phylogenetic analyses focus on rails (Aves: Rallidae) and outgroups based on (1) a dataset, 'MtProt' comprising the coding sequences (cds) from full mitochondrial genome assemblyes, and (2) a mixed-marker dataset, '2Nc3Mt', comprising the mitochondrial markers cytochrome <em>b</em> (cyt<em>b</em>), cytochrome oxidase subunit I (COI), and 16S ribosomal RNA (16S), and the nuclear markers β-fibrinogen intron 7 (bFib7) and recombination activating gene 1 (RAG1). The latter dataset i largely based on data from Garcia-R et al. (2014), with additions of the Inaccessible Island Rail <em>Atlantisia rogersi</em> and some further sequences (see our paper). Trees mentioned in our paper as "results not shown" can be found below. <br> <strong>This deposition contains five groups of data:</strong><br> 1. Beast input xml files for phylogenetic analyses<br> 2. Beast output: log files<br> 3. Beast output: raw tree files<br> 4. Beast output: Maximum Clade Credibility trees<br> 5. Tree figures (pdf format) <strong>The above are available for the following analyses:</strong><br> A. Mixed-marker dataset ‘2Nc3Mt’, one tree <br> B. Mixed-marker dataset ‘2Nc3Mt’, one tree; Micropygia schomburgkii excluded<br> C. Mixed-marker dataset ‘2Nc3Mt’, separate mitochondrial (‘3Mt’) and nuclear marker trees (RAG1 and bFib7)<br> D. Protein coding dataset ‘MtProt’ from entire mitochondrial genomes The files are thus the following, sorted according to dataset:<br> A1 Beast_input_2Nc3Mt_1tree.xml<br> A2 Beast_output_2Nc3Mt_1tree.log<br> A3 Beast_output_2Nc3Mt_1tree.raw.trees<br> A4 Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees<br> A5 Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf<br> B1 Beast_input_2Nc3Mt_exclMicropygia_1tree.xml<br> B2 Beast_output_2Nc3Mt_exclMicropygia_1tree.log<br> B3 Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees<br> B4 Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees<br> B5 Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf<br> C1 Beast_input_2Nc3Mt_separate_trees.xml<br> C2 Beast_output_2Nc3Mt_separate_trees.log<br> C3 Beast_output_2Nc3Mt_RAG1.raw.trees<br> C3 Beast_output_2Nc3Mt_bFib7.raw.trees<br> C3 Beast_output_2Nc3Mt_mt.raw.trees<br> C4 Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees<br> C4 Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees<br> C4 Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees<br> C5 Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf<br> C5 Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf<br> C5 Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf<br> D1 Beast_input_MtProt_1tree.xml<br> D2 Beast_output_MtProt_1tree.log<br> D3 Beast_output_MtProt_1tree.raw.trees<br> D4 Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees<br> D5 Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf Or, sorted according to file type:<br> 1A Beast_input_2Nc3Mt_1tree.xml<br> 1B Beast_input_2Nc3Mt_exclMicropygia_1tree.xml<br> 1C Beast_input_2Nc3Mt_separate_trees.xml<br> 1D Beast_input_MtProt_1tree.xml<br> 2A Beast_output_2Nc3Mt_1tree.log<br> 2B Beast_output_2Nc3Mt_exclMicropygia_1tree.log<br> 2C Beast_output_2Nc3Mt_separate_trees.log<br> 2D Beast_output_MtProt_1tree.log<br> 3A Beast_output_2Nc3Mt_1tree.raw.trees<br> 3B Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees<br> 3C Beast_output_2Nc3Mt_RAG1.raw.trees<br> 3C Beast_output_2Nc3Mt_bFib7.raw.trees<br> 3C Beast_output_2Nc3Mt_mt.raw.trees<br> 3D Beast_output_MtProt_1tree.raw.trees<br> 4A Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees<br> 4B Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees<br> 4C Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees<br> 4C Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees<br> 4C Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees<br> 4D Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees<br> 5A Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf<br> 5B Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf<br> 5C Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf<br> 5C Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf<br> 5C Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf<br> 5D Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf <strong>Note about the tree figures (pdf format): </strong>Nodes marked with a black circle are supported by a posterior probability (PP) of 1.0, for lower PP the number is given at the node. Blue bars represent the 95% highest posterior density intervals of the node age. MYA = Million years ago. /Martin Stervander ([e-mail])