Siphonophore Phylogeny 2005
This repository contains files for the analyses presented in:
Dunn, CW, PR Pugh, and SHD Haddock (2005) Molecular phylogenetics of the Siphonophora (Cnidaria), with implications for the evolution of functional specialization. Systematic Biology 54:916-935. doi:10.1080/10635150500354837
Figure 6 from doi:10.1080/10635150500354837.
The files include:
Dunn_10Mar05.nexThe nexus file submitted to treebase. Sequence matrix data include the aligned sequence data, taxon sets, and character partitions. It includes newick trees, without branch lengths, for figures 5 and 6.
figure_5a.treNewick tree for figure 5a. (Note to self: made by converting nexus tree in
siph\ phylogeny\ 2005/runs/18Jul04ml/branches.LSU.replacenames.treto newick format with Mesquite, then renaming "Prayine_2" as "Gymnopraia_lapislazula", and "Prayine_1" as "Clausophyid_sp_1")
figure_5b.treNewick tree for figure 5b. (Note to self: made as above, but starting from
siph\ phylogeny\ 2005/runs/18Jul04ml/branches.SSU.replacenames.tre)
There have been several updates on taxon names since the publication of the manuscript.
The species listed as Apolemia sp 4 has since been described as Apolemia lanosa by Siebert et al. 2013.
The species listed as Erenna sp has since been described as Erenna sirena by Pugh and Haddock 2016.
The specimen collected during dive T594 was identified as Clausophyes ovata in this manuscript. Subsequently, the species has been moved into a new genus, Kephyes Pugh, 2006. This taxon should now be referred to as Kephyes ovata.
The species listed as Sphaeronectes gracilis is Sphaeronectes koellikeri, Pugh 2009
The species listed as Cordagalma cordiforme is Cordagalma ordinatum, Pugh 2016
Per Article 33.4 of the ICZN, species names that were originally described with ii at the end but subsequently changed to i should now be changed back to ii. This affects the following species in this study: Rhizophysa eysenhardtii, Agalma okenii, and Forskalia edwardsii.