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

• Main Author: Stervander, Martin
• Format: Dataset
• Language: English
• Published: Zenodo 2018
• Subjects: phylogeny; Rallidae; bird; phylogeography; taxonomy; Inaccessible Island
• Online Access: https://dx.doi.org/10.5281/zenodo.1193855; https://zenodo.org/record/1193855

DESCRIPTION OF FILES 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 b (cyt b ), 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 Atlantisia rogersi and some further sequences (see our paper). Trees mentioned in our paper as "results not shown" can be found below. This deposition contains five groups of data: 1. Beast input xml files for phylogenetic analyses 2. Beast output: log files 3. Beast output: raw tree files 4. Beast output: Maximum Clade Credibility trees 5. Tree figures (pdf format) The above are available for the following analyses: A. Mixed-marker dataset ‘2Nc3Mt’, one tree B. Mixed-marker dataset ‘2Nc3Mt’, one tree; Micropygia schomburgkii excluded C. Mixed-marker dataset ‘2Nc3Mt’, separate mitochondrial (‘3Mt’) and nuclear marker trees (RAG1 and bFib7) D. Protein coding dataset ‘MtProt’ from entire mitochondrial genomes The files are thus the following, sorted according to dataset: A1 Beast_input_2Nc3Mt_1tree.xml A2 Beast_output_2Nc3Mt_1tree.log A3 Beast_output_2Nc3Mt_1tree.raw.trees A4 Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees A5 Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf B1 Beast_input_2Nc3Mt_exclMicropygia_1tree.xml B2 Beast_output_2Nc3Mt_exclMicropygia_1tree.log B3 Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees B4 Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees B5 Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf C1 Beast_input_2Nc3Mt_separate_trees.xml C2 Beast_output_2Nc3Mt_separate_trees.log C3 Beast_output_2Nc3Mt_RAG1.raw.trees C3 Beast_output_2Nc3Mt_bFib7.raw.trees C3 Beast_output_2Nc3Mt_mt.raw.trees C4 Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees C4 Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees C4 Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees C5 Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf C5 Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf C5 Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf D1 Beast_input_MtProt_1tree.xml D2 Beast_output_MtProt_1tree.log D3 Beast_output_MtProt_1tree.raw.trees D4 Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees D5 Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf Or, sorted according to file type: 1A Beast_input_2Nc3Mt_1tree.xml 1B Beast_input_2Nc3Mt_exclMicropygia_1tree.xml 1C Beast_input_2Nc3Mt_separate_trees.xml 1D Beast_input_MtProt_1tree.xml 2A Beast_output_2Nc3Mt_1tree.log 2B Beast_output_2Nc3Mt_exclMicropygia_1tree.log 2C Beast_output_2Nc3Mt_separate_trees.log 2D Beast_output_MtProt_1tree.log 3A Beast_output_2Nc3Mt_1tree.raw.trees 3B Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees 3C Beast_output_2Nc3Mt_RAG1.raw.trees 3C Beast_output_2Nc3Mt_bFib7.raw.trees 3C Beast_output_2Nc3Mt_mt.raw.trees 3D Beast_output_MtProt_1tree.raw.trees 4A Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees 4B Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees 4C Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees 4C Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees 4C Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees 4D Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees 5A Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf 5B Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf 5C Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf 5C Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf 5C Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf 5D Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf Note about the tree figures (pdf format): 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]) : {"references": ["Garcia-R, J.C., Gibb, G.C., Trewick, S.A., 2014a. Deep global evolutionary radiation in birds: Diversification and trait evolution in the cosmopolitan bird family Rallidae. Molecular Phylogenetics and Evolution 81, 96\u2013108."]}