Eukaryote Evolution: The Importance of the Stem Group

Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life

“…Phagocytosis by engulfment is indeed a very ancient trait of eukaryotes in general [ 171 , 201 , 202 ], which most likely has taken a long time to evolve in the protoeukaryotic stemline [ 203 , 204 ]. Also, extended evolutionary periods without any feeding predators are quite unlikely [ 205 ].…”

“…Last, not least, the presumably very ancient origins of the protoeukaryotic stemline are reflected in a plethora of functional RNA molecules. Assuming continuity of function in complex RNA-based traits as a potent selective principle, this tentatively links eukaryotes directly to a veritable RNA world when coded protein synthesis was just emerging [ 127 , 128 , 169 , 203 , 210 , 222 , 223 , 224 , 225 , 226 , 227 ]. Among these functional RNAs or RNP complexes, the formidable spliceosomes are considered of particular importance.…”

“…It is widely recognized by now that the last eukaryote common ancestor (LECA) was highly evolved genetically [ 183 , 202 ], combining a modular and interactive core set of eukaryote-specific proteins, maintaining a sophisticated cytoplasmic infrastructure and cytoskeleton organization. This begs paramount questions of how long it took to reach that highly interactive stage and of what happened to all the side shoots to be expected in addition to the solely surviving stemline before the LECA [ 203 ]. Eukaryote-late models resort to an intense period entailing " a dramatic acceleration of evolution " [ 183 ], which would be extended and relaxed quite naturally in eukaryote-early scenarios.…”

A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree

“…Using a clade-based approach, defining eukaryotes is trivial – they are all descendants of the last common ancestor of extant Eukarya, i.e., “crown Eukarya.” All extinct stem lineage members then belong to broader groupings inclusive of crown Eukarya, based on nested subsets of synapomorphies, as is the case with increasingly mammal-like groups nested within the synapsid lineage leading to crown group mammals [although, unlike mammals, we do not have any fossil evidence of these likely extinct stem groups that indicate the order of character acquisition ( Poole, 2010 )]. Alternatively, the definition from a maximally inclusive stem-based approach is equally trivial, including extant Eukarya and all extinct relatives more closely related to Eukarya than any other extant group.…”

“…These characters include the mitochondrion, nuclear envelope, nuclear pores and an endomembrane system, linear chromosomes, spliceosomal machinery and introns, among many others (reviewed in Koonin, 2010 ; Koumandou et al, 2013 ). Many of these traits are associated with genes that appear to be specific to eukaryotes ( Hartman and Fedorov, 2002 ), suggesting that both the traits and the genes underlying them were acquired in the stem lineage separating eukaryotes from Archaea and Bacteria ( Poole, 2010 ). However, recent metagenomics sampling studies from a range of environments have revealed the existence of multiple lineages (dubbed Asgard) which have many archaeal-type genetic and physiological characters but which are most closely related to eukaryotes in molecular phylogenies.…”