Osmundales diverstity through time: stacking networks

2017-07-31T14:01:34Z (GMT) by Guido Grimm
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.html

The 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.