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 Figure 6 from doi:10.1080/10635150500354837.


The files include:

  • Dunn_10Mar05.nex The 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.tre Newick tree for figure 5a. (Note to self: made by converting nexus tree in siph\ phylogeny\ 2005/runs/18Jul04ml/branches.LSU.replacenames.tre to newick format with Mesquite, then renaming "Prayine_2" as "Gymnopraia_lapislazula", and "Prayine_1" as "Clausophyid_sp_1")

  • figure_5b.tre Newick tree for figure 5b. (Note to self: made as above, but starting from siph\ phylogeny\ 2005/runs/18Jul04ml/branches.SSU.replacenames.tre)

Taxon names

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.