Data associated with the publication "The origin of the world's smallest flightless bird, the Inaccessible Island Rail Atlantisia rogersi (Aves: Rallidae)"

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 (cytb), 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 (martin@stervander.com)