Dataset Open Access

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

Martin Stervander

Researcher(s)
Peter G. Ryan; Martim Melo; Bengt Hansson

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)

Files (337.6 MB)
Name Size
_README_DATA_DESCRIPTION.txt
md5:e9268c42d0de52540f81c78f2da808b8
4.0 kB Download
Beast_input_2Nc3Mt_1tree.xml
md5:ebe9675cc82ba5f3602bc8ae86fc1c23
558.2 kB Download
Beast_input_2Nc3Mt_exclMicropygia_1tree.xml
md5:42d71986cc8b4117486d3e6056de4222
552.6 kB Download
Beast_input_2Nc3Mt_separate_trees.xml
md5:b0b8d5d169503b36b0798f5a261c8c84
503.5 kB Download
Beast_input_MtProt_1tree.xml
md5:5e49b64382bfac9d340c8c2622983dc2
263.2 kB Download
Beast_output_2Nc3Mt_1tree.log.tar.gz
md5:08f6b1af8ff2820d28ab9534265017a4
10.2 MB Download
Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees
md5:40b98c44a5fd859ff1440ae865791c2a
110.6 kB Download
Beast_output_2Nc3Mt_1tree.raw.trees.tar.gz
md5:7ada849cc2233ca33ac2e3e688487385
68.4 MB Download
Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees
md5:ea77cbe6576fee279638f53bc53da313
71.5 kB Download
Beast_output_2Nc3Mt_bFib7.raw.trees.tar.gz
md5:906b59a16b6aac6d4f8e2c96474794e4
43.7 MB Download
Beast_output_2Nc3Mt_exclMicropygia_1tree.log.tar.gz
md5:34f7a4db320bdd68374b01b75109cf37
10.3 MB Download
Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees
md5:413d1461875d393497acf88e1161b55d
109.4 kB Download
Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees.tar.gz
md5:b521557350941d5c22d673d58c5a301a
67.6 MB Download
Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees
md5:2b8d96a44a6494b8cc79a1a2152cf041
110.2 kB Download
Beast_output_2Nc3Mt_mt.raw.trees.tar.gz
md5:f290f457af133b5a992900d04ea1ed19
65.9 MB Download
Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees
md5:a1586fd1b3b3177b6a7946c0c4738bf8
77.3 kB Download
Beast_output_2Nc3Mt_RAG1.raw.trees.tar.gz
md5:d17ea02d5c541e3763ff07d4a28d609b
47.2 MB Download
Beast_output_2Nc3Mt_separate_trees.log.tar.gz
md5:c96e23f7360cdd2e84687349ad4a42d5
12.2 MB Download
Beast_output_MtProt_1tree.log.tar.gz
md5:111dfbd570ad8615c66bf44e5ee5b001
3.5 MB Download
Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees
md5:d76f4dec4d6bd6e2ad8b6a45743da855
21.2 kB Download
Beast_output_MtProt_1tree.raw.trees.tar.gz
md5:17489cd9266fa392ff9aefed82f09a53
6.1 MB Download
Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf
md5:18501e0db25bfe8212ad492067edc042
11.6 kB Download
Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf
md5:6996e17f8659a262fdbd09bf2677c63d
9.3 kB Download
Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf
md5:aac38a99efe30483fac002b2e59eb70c
11.5 kB Download
Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf
md5:4e77f6b0f6e097235af2da1d63996ac2
11.6 kB Download
Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf
md5:a9ecad7f6d24d9fb74112f8e6e90271a
9.6 kB Download
Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf
md5:4e2d4bb48926f3b2334de162083f023f
6.5 kB Download
  • 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, 96–108.
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