|Fig. 1. Phylogeny of Eukaryota based on recent phylogenetic analyses (Hampl et al. 2009; Katz et al. 2011; Burki et al. 2012; Laurin-Lemay et al. 2012; Price et al. 2012; Timme et al. 2012; Zhao etal. 2012, 2013; Brown et al. 2013; Paps et al. 2013; Seenivasan et al. 2013; Yabuki et al. 2010; 2013). Amoeboid intracellular algal parasite group Aphelidea, which were thought to belong to Holozoa (Adl et al. 2012), were actually found to group with Fungi (Karpovet al. 2013). An intracellular parasite of oysters, Mikrocytos, has been confirmed to be a rhizarian (Burki et al. 2013). Consulted classifications: Adl et al. 2012; Cavalier-Smith (2013). Cavalier-Smith's classifications are quite idiosyncratic, super complicated, and change rather often (he's a very prolific author). At least this is the impression I'm getting. He also uses many (often novel) paraphyletic taxa.|
The other interesting development is the rooting of the eukaryote tree, which is a difficult problem to solve because of the lack of a close out-group (all the prokaryotes are too distant) and rapid radiation of lineages at the base of extant eukaryotic tree of life (it is more like a bush than a tree in this case) (Brinkmann & Philippe 2007). Derelle & Lang (2012) have compiled an interesting dataset of 42 mitochondrial proteins (encoded by mitochondrial or nuclear genome) of alpha-proteobacterial origin to root the eukaryote tree. All known eukaryotes have mitochondria or their derivatives (mitosomes or hydrogenosomes; Hjort etal. 2010; Shiflett & Johnson 2010) and thanks to this, genes of mitochondrial origin can be used to reconstruct eukaryote phylogeny (Brinkmann & Philippe 2007). And the other good news is that there is a relatively close outgroup available - Alphaproteobacteria. Previous analyses relying heavily on nuclear informational genes (replication, transcription, translation) of archaeal origin (closest prokaryotic group to eukaryote nuclear lineage) were plagued by long-branch attraction (LBA) artefacts. LBA is an artefact of phylogenetic analyses where long branches (measured in the amount of estimated character change, e.g. nucleotide or amino acid substitutions) tend to group together regardless of evolutionary relationships, if the model or method used is not adequate to correct for multiple substitutions at the same site. For example, the fast evolving lineages (evident as long branches in the phylogenetic trees) of eukaryotes (often parasites) tend to be attracted towards the outgroup represented by long branch leading to Archaea, and in consequence distorting true relationships between eukaryotes. Derelle & Lang (2012) and now also Zhao et al. (2013) found that the root of the eukaryote tree falls between bikonts and unikonts, as suggested about 10 years ago (Stechmann & Cavalier-Smith 2002, 2003; Richards & Cavalier-Smith 2005), with the caveat that some bikonts, like Apusomonadida and Diphyllatea, are 'unikonts'. Standard phylogenomic analyses of eukaryotes (based on usually 100–200 highly expressed genes; e.g. many references in the caption of Fig. 1) without prokaryote outgroups are consistent with this kind of rooting (it is possible to root the resulting unrooted trees so that unikonts and bikonts are monophyletic). It is remarkable, apart from the rooting, that most of the well supported clades found in standard phylogenomic analyses are upheld by Derelle & Lang (2012) and Zhao et al. (2013), because most of the 42 proteins used in the mitochondrial dataset are different from the other analyses. For example, only 3 genes are in common with a dataset of 143 genes used by Hampl et al. (2009) (Derelle & Lang 2012). This gives some confidence that we are not completely lost in deciphering these ancient phylogenies.
Another fascinating aspect of eukaryote evolution is how they came to be in the first place. A straw man of a traditional view is that eukaryote gradually evolved from prokaryotic ancestor, acquiring cytoskeleton, phagocytosis, internal membranes (nuclear envelope, endoplasmic reticulum, golgi apparatus) and then engulfing bacteria which later became mitochondria and plastids. But now, more and more viable alternative seems to be that the origin of mitochondria marks the origin of eukaryotes. Martin & Müller (1998) proposed the hydrogen hypothesis for the first eukaryote, where symbiotic association between an Archaea and Alphaproteobacteria finally lead to Alphaproteobacteria living inside the Archaea.