Exploring the signals in the data used by Solovyeva et al. (2018)

2018-04-01T10:40:55Z (GMT) by Guido Grimm
This is a fileset generated following the suggestion of one of the authors of the paper to do consensus networks based on these data by myself in response to two questions I had on the paper (https://peerj.com/questions/3501-what-to-the-hyphens-stand-for-low-amplitude-signal/#annotation-3508)<br><br>It shows the typical issues of non-trivial data sets: decreased support either relates to low amplitude signal or two (rarer three) competing topological alternatives found in the bootstrap samples that can be inferred from each gene region. The best-known trees are not necessarily showing the best-supported alternative. In some cases the (including weak) signals from each gene region are additive (high support in the combined tree, see original paper), in others not (low support in the combined tree).<br><br>Update to v2 — Added distance-based neighbour-nets (uncorrected <i>p</i>-distances) for each gene region and artwork for an (upcoming: 2/4/2018) #GWoN (http://phylonetworks.blogspot.com) post entitled: Things you can learn in a blink about your data <br><br>Update to v3 — Added the two missing annotated (optimised for Mesquite) all-inclusive matrices to the archive.<br><br>The fileset includes<br><br>Graphically enhanced neighbour-nets related to the #GWoN post for <br>— one mitochondrial gene region (<i>coxI</i>): <b>NeighbourNetUncPCoxI.png</b><br>— one nuclear gene region (<i>AKAP9</i>): <b>NeighbourNetUncPAKAP9.png</b><br><br>A 7z archive (<b>Lizard.7z</b>) with <br>(i) NEXUS-reformatted matrices based on the FASTA-files provided in the supplementary information to the original paper.<br>(ii) The results of an unpartitioned maximum likelihood analysis of the provided single-gene data (four mitochondrial + four nuclear gene regions).<br>(iii) Corresponding distance matrices and neighbour-nets in Splits-NEXUS-format. <br>(iv) Two annotated, Mesquite-optimised NEXUS-files: <b>combined.nex </b>includes all gene partitions as seperate alignment blocks; <b>all.conc.nex </b>is a ready-to-use (tentatively) concatenated matrix of the data provided in the original FASTA-files. Files can be opened with any NEXUS-compatible programme, annotations require the use of the (open software) Mesquite: http://mesquiteproject.wikispaces.com/<br>For further details (archive structure, labelling conventions, software; see <b>ReadMe.txt</b> in the archive).<br><br>When re-using these data make sure to also reference the original publication:<br>Solovyeva​ EN, Lebedev VS, Dunayev EA, Nazarov RA, Bannikova AA, Che J, Murphy RW, Poyarkov​ NA. 2018. Cenozoic aridization in Central Eurasia shaped diversification of toad-headed agamas (Phrynocephalus; Agamidae, Reptilia). PeerJ 6:e4543. https://doi.org/10.7717/peerj.4543<br>