This submission includes the data for the following post on the Genealogical World of Phylogenetic Networks entitled:Want to place a fossil in a minute? Just use neighbour-netshttps://phylonetworks.blogspot.com/2018/06/want-to-place-fossil-in-minute-just-use.htmlIt includes the graphics shown in the post and a 7z-archive with the following content: Splits-NEXUS-formatted raw neighbour-net files, which include the used distance matrices (*.dist).DE18.mean.dist — the all-inclusive graph (and distance matrix)DE18.FG.VS.dist — a graph reduced to the focus group (fossils + Chloranthales + Ceratophyllum + Amborella) and using a distance matrix as input generated by excluding all invariable ("constant") characters within the focus groupReady-to-use NEXUS-formatted versions of Doyle & Endress' 2010 and 2018 matrices – files labelled as DE10.simple.nex and DE18.simple.nex.Important citation note: Make sure that when you re-use these data to cite not only this figshare fileset but also the original papersDoyle JA, Endress PK. 2010. Integrating Early Cretaceous fossils into the phylogeny of living angiosperms: Magnoliidae and eudicots. Journal of Systematics and Evolution 48:1–35.Doyle JA, Endress PK. 2018. Phylogenetic analyses of Cretaceous fossils related to Chloranthaceae and their evolutionary implications. Botanical Review DOI:10.1007/s12229-018-9197-6.

This package provides source code and data for the two blog post on animal names ("Man gave names to all those animals..."), which were published in the blog "The genealogical world of phylogenetic networks" (http://phylonetworks.blogspot.de/2017/10/man-gave-names-to-all-those-animals.html). This upload also contains the data from Gerhard Jäger's paper titled "Support for linguistic macrofamilies from weighted sequence alignment" (PNAS, DOI: 10.1073/pnas.1500331112), generously provided by the author.

These files provide the data used for the following post on Genealogical World of Networks (http:///phylonetworks.blogspot.com/) Grimm GW. Posted 5/3/2018. Visualizing U.S. gun laws. The Genealogical World of Phylogenetic Networks (ed. by D. Morrison). http://phylonetworks.blogspot.fr/2018/03/visualizing-us-gun-laws.htmlThe data matrix scores GunsToCarry's breakdown of U.S. gun legislation as a set of 17 binary and ternary characters, which is then used to infer inter-state pairwise (mean/Hamming) distances. I provide the data matrix in two formats:*.nex — A fully annotated version (character states labelled) generated with (and optimised for) Mesquite (https://mesquiteproject.wikispaces.com/)*.simple.nex — Version in (old) NEXUS format (data block) showing the set-up for the distance analysis such as the used weighting schemeResults are provided raw and graphically enhanced*.dst — the resultant pairwise distance matrix in (extended) PHYLIP format*.dist — the resultant neighbour-net, Splits-NEXUS-formatted (can be opened and visualised with SplitsTree, www.splitstree.org, and R/phangorn, https://github.com/KlausVigo/phangorn)*.png – graphically enhanced versions of the resultant neighbour-net as shown in the original post and the related long-read at Res.I.P. (http:///phylonetworks.blogspot.com/)Listed programmes are free-to-use software, *.simple.nex and .dst files can also be viewed with any text-editor (.nex and *.dist can be viewed but include complex additional code-lines)

This fileset includes stacked neighbour-net splits graphs (planar meta-phylogenetic networks) illustrating the taxic diversity change within the royal fern lineage (Osmundales) from the Permian to now. The networks are based on taxon subsets of the matrix compiled by Bomfleur et al., PeerJ 5: e3433, 2017, https://peerj.com/articles/3433/Figures 1 and 2 show time-slice-wise networks, each network includes only species of one geological period. Permian, Triassic and Jurassic (Fig. 1); Cretaceous, Paleogene+Neogene, and modern-day (Fig. 2). Species names are abbreviated/contracted by three-letter codes. Higher taxa and according colouring of species (dot) follow Bomfleur et al. (2017). Refer to this study for basic inference methodology and information on the data.Figures 3 to 6 show connected neighbour-nets, each including the species of two subsequent time-slices (older at bottom): Permian + Triassic and Triassic + Jurassic (Fig. 3); Triassic + Jurassic and Jurassic + Cretaceous (Fig. 4); Cretaceous + Paleogene and Paleogene + Neogene (Fig. 5); Paleogene + Neogene and Neogene + modern-day (Fig. 6). For the motivation to stack networks see Grimm, GW. Posted 18/7/2017.Stacking neighbour-nets: ancestors and descendants. The Genealogical World of Phylogenetic Networks (ed. by D. Morrison). http://phylonetworks.blogspot.fr/2017/07/stacking-neighbour-nets-ancestors-and.htmlThe XLSX-file includes the basic distance matrix including the full taxon names; cells are coloured as heat-map: green = low pairwise morphological distances; red = high pairwise morphological distances.All primary data files including the NEXUS-file used to generate the distance matrices for network inference can be found in the ZIP-archive. The *.DIST files are Split-NEXUS-formatted files and are partly colour-coded using in-built functions of SplitsTree. See Readme.txt for archive content and contact details.

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)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).Update to v2 — Added distance-based neighbour-nets (uncorrected p-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 Update to v3 — Added the two missing annotated (optimised for Mesquite) all-inclusive matrices to the archive.The fileset includesGraphically enhanced neighbour-nets related to the #GWoN post for — one mitochondrial gene region (coxI): NeighbourNetUncPCoxI.png— one nuclear gene region (AKAP9): NeighbourNetUncPAKAP9.pngA 7z archive (Lizard.7z) with (i) NEXUS-reformatted matrices based on the FASTA-files provided in the supplementary information to the original paper.(ii) The results of an unpartitioned maximum likelihood analysis of the provided single-gene data (four mitochondrial + four nuclear gene regions).(iii) Corresponding distance matrices and neighbour-nets in Splits-NEXUS-format. (iv) Two annotated, Mesquite-optimised NEXUS-files: combined.nex includes all gene partitions as seperate alignment blocks; all.conc.nex 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/For further details (archive structure, labelling conventions, software; see ReadMe.txt in the archive).When re-using these data make sure to also reference the original publication: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