The Vint genes are present in many eukaryotic groups, but must have been lost multiple times, in particular in multicellular eukaryotes.
The CTD is missing or degenerate in many eukaryotic groups, but is conserved across the broad diversity of animals and fungi, as well as their putative protistan ancestors [ 4].
For example, whole-genome duplications are a major evolutionary force in many eukaryotic groups (Kellis et al. 2004; Adams and Wendel 2005; Dehal and Boore 2005; Aury et al. 2006), and alternatively, in prokaryotes, large-scale deletions have been detected in both experimental and comparative analyses (Moran and Mira 2001; Nilsson et al. 2005).
Importantly, the large numbers of proteobacterial and cyanobacterial genes in eukaryotes are also consistent with the observation that proteobacteria and cyanobacteria are the most common endosymbionts in many eukaryotic groups (e.g. amoebae 23, 66, fungi, 67, plants 68, insects, nematodes, and other animals 69, 70).
Genes for small and large rRNA (12 S and 16 S in Mammals, for example) are found universally; indeed, genes for tRNA vary greatly in terms of numbers, although a set of 22 27 tRNAs is common in many eukaryotic groups.
Second, the genomic sequence of VPS25 in many major eukaryotic groups contain introns, which enables analyses of intron evolution.
The general presence of PDI proteins in the ER in representatives of many different eukaryotic groups strongly supports such a localization in a common eukaryotic ancestor, and suggests that homologs of plastid PDIs originally also were targeted to this compartment.
Given that we recovered good support for many major eukaryotic groups despite this issue, it seems unlikely that compositional biases are a major contributor toward the low support values for the Archaeplastida clade.
The analysis of our data reveals the presence of many common eukaryotic groups, including ciliates, cercozoans, chlorophytes, diatoms, and fungi, which are expected to be present in a freshwater environment like the small river, the Seymaz.
For example, metazoa and fungi share a eukaryotic ancestor to the exclusion of many other eukaryotic groups [ 18], but only gdh2 genes are found in the complete metazoan genome sequences, while gdh1 and gdh3 genes are found in fungi (Table 1 and Figs. 1, 2, 3).
Those reports lead to a wealth of representatives from many of the same groups shown in Figure 2 being uncovered: ciliates, fungi and chromalveolates, in addition to representatives of many other eukaryotic groups, including the choanoflagellates [ 3], which are regarded as the unicellular sisters to the metazoan clade.
