Abstract: A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum , which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood–Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer
From the paper:
Inferring Ancestral Genome Sizes.
The DTL model provides inferences of ancestral genome size, and, because the reconciliation model explicitly allows for horizontal transfer as well as gene loss, there is no trend toward inferring increasing genome size for earlier nodes on the tree. Thus, the use of this model ameliorates the “genome of Eden” problem, a tendency toward inferring unrealistically large ancestral genomes in the absence of HGT that is so marked that it has been used to set a lower bound on rates of HGT through time. Previous simulation studies and analyses of empirical data have suggested that ancestral gene content inferences under this model are realistic and robust to gene tree uncertainty, and thus the ancestral sizes that we present here have been corrected to account for gene families that have been lost in all sampled species, as described above. Our analyses suggest that there has been an ongoing increase in gene content throughout archaeal history, from ∼1,090 genes in the common ancestor to 537–5,359 (mean, 1,686.4) genes among modern lineages. This trend is not dependent on the basal placement of the DPANN clade in the tree; in the analysis without DPANN, the common ancestor was predicted to encode 1,328 genes, increasing to 1,373–5,359 (mean, 2,081.1) genes among modern genomes. These reconstructions do not support the hypothesis, based on an analysis of phylogenetic presence-absence profiles that a large-genome archaeal common ancestor gave rise to modern lineages by genomic streamlining.
Note this paper was edited and approved by Dr. Ford Doolittle himself.
That would be the last universal common ancestor, not the first life. What you would need to show is that the life preceding LUCA was not simpler.
Also, there is doubt being cast on the transition between prokaryotes and eukaryotes which is well past LUCA. Prokaryotes don’t have intron splicing, while eukaryotes do, so we already know that prokaryotes were simpler in this respect than eukaryotes.
The study lends support to a hypothesis that LUCA may have been more complex even than the simplest organisms alive today, said James Whitfield, a professor of entomology at Illinois and a co-author on the study.
Though you have a point that if scientists are willing to discount many Genes which are prevalent in all three domains of life as LGTs and not as homologues, they can reduce the complexity of LUCA.
This seems a lot like twisting data to fit a theory.
More than a week later, and no specification for the helicase protein has been produced.
There wasn’t even any back-pedalling or special pleading, just the tranquil silence of a field that’s been fled.