DOI: 10.5061/dryad.db78g
title: Data from: Taxon-rich phylogenomic analyses resolve the eukaryotic tree of life and reveal the power of subsampling by sites

description: Most eukaryotic lineages are microbial, and many have only recently been
 sampled for phylogenetic studies or remain in the ‘dark area’ of the tree
 of life where there are no molecular data. To assess relationships among
 eukaryotic lineages, we perform a taxon-rich phylogenomic analysis
 including 232 eukaryotes selected to maximize taxonomic diversity and up
 to 1554 genes chosen as vertically inherited based on their broad
 distribution among eukaryotes. We also include sequences from 486 bacteria
 and 84 archaea to assess the impact of endosymbiotic gene transfer (EGT)
 from plastids and to detect contamination. Overall, our analyses are
 consistent with other less taxon-rich estimates of the eukaryotic tree of
 life and we recover strong support for five major clades: Amoebozoa,
 Excavata (without the genus Malawimonas), Opisthokonta, Archaeplastida and
 SAR (Stramenopila, Alveolata and Rhizaria). Our analyses also highlight
 the existence of ‘orphan’ lineages, lineages that lack robust placement in
 the eukaryotic tree of life and indicate the possibility of as yet
 undiscovered diversity. In analyses including bacteria and archaea, we
 find that ~10% of the 1554 genes, which we choose because they are found
 in four or five of the five major eukaryotic clades and hence may be more
 likely to be inherited vertically, appear to have been acquired from
 cyanobacteria through EGT in photosynthetic lineages. Removing these EGT
 genes places the green algae as sister to the glaucophytes instead of the
 red algae, suggesting that unknowingly including of genes of plastid
 origin, and combining them with genes of nuclear origin, may mislead
 phylogenetic estimates. Finally, the large size of our dataset allows
 comparative analyses of subsets of data; alignments built from randomly
 sampled sites provide greater support, particularly for deep
 relationships, than do equivalent sized datasets built from randomly
 sampled genes.
description: Supplemental_DataIncludes Table S3:Monophyly of subclades, S4:Subsampling results and tree data as newick stringsTable_S1Table_S1.xlsx: Taxon source and code Taxa are listed by major clade, and information is given about the source of the data (e.g. OrthoMCL, Genbank, Moore Transcriptome Project). Codes used throughout the study are given. Taxa in red are in Phylobayes analysis but removed from other analysesTable_S2Table_S2.xlsx: Presence/Absence of genes x taxa Genes present by taxon. 1 = present; 0 = absent. Genes are given by OG name (OrthoMCL) and are marked with an * if a member of the 150 most even gene dataset and with a ^ if identified as a gene affected by EGTAll_1554Alignment file; 1554 genes; eukaryotes, bacteria and archaea.Katz_Grant_README.docxEuk_1554Alignment file; 1554 genes; eukaryotesKatz_Grant_README.docxAll_150Alignment file; 150 genes; eukaryotes, bacteria and archaeaKatz_Grant_README.docxEuk_150Alignment file; 150 genes; eukaryotes.Katz_Grant_README.docxAll_1554_noEGTAlignment file; 1554 genes minus egt genes; eukaryotes, bacteria and archaeaKatz_Grant_README.docxEuk_1554_noEGTAlignment file; 1554 genes minus egt genes; eukaryotesKatz_Grant_README.docxAll_150_noEGTAlignment file; 150 genes minus egt genes; eukaryotes, bacteria and archaeaKatz_Grant_README.docxEuk_150_noEGTAlignment file; 150 genes minus egt genes; eukaryotes.Katz_Grant_README.docx1554_Single_gene_alignments_AllAll 1554 single gene alignments with all taxa. Data were concatenated and columns with &gt; 50% missing data in eukaryotic taxa were removed to make the large matrices analyzed in this study.Katz_Grant_README.docx1554_Single_gene_alignments_Euk_onlyAll 1554 single gene alignments with only eukaryotic taxa. Data were concatenated and columns with &gt; 50% missing data were removed to make the large matrices analyzed in this study.Katz_Grant_README.docx