Show simple item record

dc.contributor.author Williams, Tom A.
dc.contributor.author Foster, Peter G.
dc.contributor.author Nye, Tom M. W.
dc.contributor.author Cox, Cymon J.
dc.contributor.author Embley, T. Martin
dc.date.accessioned 2012-11-15T18:48:25Z
dc.date.available 2012-11-15T18:48:25Z
dc.date.issued 2012-10-24
dc.identifier doi:10.5061/dryad.0hd1s
dc.identifier.citation Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM (2012) A congruent phylogenomic signal places eukaryotes within the Archaea. Proceedings of the Royal Society B 279(1749): 4870-4879.
dc.identifier.uri http://hdl.handle.net/10255/dryad.44184
dc.description Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook 'three domains' tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.
dc.relation.ispartofseries 279;1749;2012
dc.relation.haspart doi:10.5061/dryad.0hd1s/1
dc.relation.haspart doi:10.5061/dryad.0hd1s/2
dc.relation.haspart doi:10.5061/dryad.0hd1s/3
dc.relation.haspart doi:10.5061/dryad.0hd1s/4
dc.relation.haspart doi:10.5061/dryad.0hd1s/5
dc.relation.haspart doi:10.5061/dryad.0hd1s/6
dc.relation.haspart doi:10.5061/dryad.0hd1s/7
dc.relation.haspart doi:10.5061/dryad.0hd1s/8
dc.relation.haspart doi:10.5061/dryad.0hd1s/9
dc.relation.isreferencedby doi:10.1098/rspb.2012.1795
dc.relation.isreferencedby PMID:23097517
dc.subject phylogenetics
dc.subject evolution
dc.subject eukaryotes
dc.title Data from: A congruent phylogenomic signal places eukaryotes within the Archaea.
dc.type Article *
dwc.ScientificName Bacteria
dwc.ScientificName Archaea
dwc.ScientificName Eukaryota
dc.contributor.correspondingAuthor Williams, Tom A.
prism.publicationName Proceedings of the Royal Society B

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title 29_aeb
Downloaded 78 times
Description Concatenation of 29 genes conserved in Bacteria, Archaea and eukaryotes.
Download 29_aeb.fa (148.2Kb)
Details View File Details
Title aeb_fasta_files.tar
Downloaded 52 times
Description Single genes conserved between Bacteria, Archaea and eukaryotes. These are the "raw" fasta files, before alignment editing.
Download aeb_fasta_files.tar.gz (303.4Kb)
Details View File Details
Title arch_euk_fasta.tar
Downloaded 43 times
Description Single genes conserved between Archaea and eukaryotes. These are the raw sequence files before editing.
Download arch_euk_fasta.tar.gz (513.9Kb)
Details View File Details
Title 63_genes
Downloaded 71 times
Description 63AE dataset (described in article)
Download 63_genes.phy (255.6Kb)
Details View File Details
Title 64_genes
Downloaded 77 times
Description 64AE dataset (described in article)
Download 64_genes.phy (257.9Kb)
Details View File Details
Title 64_singles.tar
Downloaded 44 times
Description The genes used to make the 64AE dataset, after masking of poorly-aligning and uninformative sites.
Download 64_singles.tar.gz (131.1Kb)
Details View File Details
Title 29_alns_cut.tar
Downloaded 41 times
Description The genes used to make the 29BAE dataset, after masking of poorly-aligning and uninformative sites.
Download 29_alns_cut.tar.gz (70.17Kb)
Details View File Details
Title rrna.tar
Downloaded 109 times
Description LSU and SSU rRNA sequence files (FASTA format) and alignment (PHYLIP format). Used to produce Figure 1 of the article.
Download rrna.tar.gz (594.4Kb)
Details View File Details
Title newick_trees.tar
Downloaded 88 times
Description Newick tree files corresponding to Figures 1 and 2 of the article.
Download newick_trees.tar.gz (14.84Kb)
Details View File Details