Abstract
Over the past 2 decades major advancements in phylogenetics have been made and this in turn
has influenced our understanding of eukaryotic evolution. The use of morphological data
combined with sequence data has been the basis for the recent division of eukaryotes into five
supergroups . This hypothesis is yet to be proven, as a general lack of both taxon and gene
sequences has only led to the resolution of some of the groups. The chromalveolates are
possibly the most contested of these groups, and it remains to be proven if they belong to one
major lineage or several distinct groups. Chromalveolate resolution has been suggested to be
dependent on the sampling of residual lineages. One such phylum, Telonemia, has been
recently inferred with a two-gene phylogeny, indicating an affinity to two groups belonging to
the chromalveolates, the cryptomonads and haptophytes. This placement however was weakly
supported and a more conclusive phylogeny is vital to the further understanding of
chromalveolates and other eukaryotic supergroup relationships. For this purpose an
orthologous multigene phylogeny of 9 nuclear protein coding genes and the small subunit
(SSU) rRNA gene from Telonema and a broad sampling of eukaryotic taxa was used for
phylogenetic inferences. Five of these Telonema protein-coding sequences were amplified for
the purpose this study; the remainder were generated from previous studies. The resulting 10
gene global eukaryotic phylogeny is the largest dataset as yet to include broad sampled taxa
from all five of the hypothesized supergroups. The phylogentic analysis again placed
Telonema as a deep eukaryotic lineage, increased gene and taxon sampling inferred stronger
phylogenetic affinity to the cryptomonads, haptophytes and a third chromalveolate group of
katablepharids. The backbone of the global eukaryotic phylogeny however could not resolve
the monophyly of chromalveolates, alternatively placing the group into three separate clades.
Otherwise, the result demonstrated strong monophyly for thee other supergroups, the
unikonts, Rhizaria and for the first time Excavata. The fifth supergroup of plants only
demonstrated monophyly with two of its three lineages, here identified to be caused by
phylogenetic artifacts. A focus toward the addition of both genes and taxa should be
prioritised for our further understanding of the relationships between the eukaryotic
supergroups.