Data from: Taxon-rich phylogenomic analyses resolve the eukaryotic tree of life and reveal the power of subsampling by sites

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.