DOI: 10.5281/zenodo.1193856
title: Data Associated With The Publication "The Origin Of The World'S Smallest Flightless Bird, The Inaccessible Island Rail Atlantisia Rogersi (Aves: Rallidae)"

description: <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 (martin@stervander.com)
description: {"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."]}