This is not a promising line of argument against UCA. Study of actual mutations yield predictable phylogenetic trees consistent with common ancestry. Furthermore, both mtDNA and Y-chromosome mutation rate studies to date confirm evolutionary timelines. Myself and others have brought several papers to your attention in this regard. If you are not convinced, fine, but rest of the world will have to move along.
4 Likes
HGT is the default state in the biosphere. Whyever would you posit or imagine a time when there was no HGT?
Because the bible says Adam and Eve, not Adam and Eve and Enterococcus faecalis and HIV.
3 Likes
Like?
The LUCA would have existed quite a long time after the biotic chemicals arose in a vent or pond or wherever. It would have been a cell of some complexity, so evolution would already have been going on for quite a while. I canāt be any more specific about how long a while, sorry. Maybe one of the smart guys here you are always torturing knows. 
If I understand correctly, the less HGT that was going on, the more clearly a UCA can be defined. HGT is something creationists often discuss with glee because it contradicts Darwinism and therefore, in their view, evolution.
Go figure.
3 Likes
Thatās right @Faizal_Ali.
HGT ends up being a very important exception to the ātreeā of life, turning into more of a web. It is rare in large animals, like mammals, but it is pervasive in microbes. We observe it all the time in bacteria. They just swap DNA quite a bit.
That makes discerning a tree very difficult, (1) the more HGT there is and (2) the more distant in the past.
4 Likes
Oh dear. 
Thank you for stating succinctly what I didnāt feel like explaining I understood.
HGT doesnāt contradict Darwinism. It only complicates the process of reconstructing evolutionary history.
4 Likes
This article is very pertinent to the discussion about the extent of HGT in early evolution, and how tree-like microbial evolution generally is:
There is a lot of HGT among prokaryotes, but not so much that an overall trend of tree-like evolution can not be extracted from the data.
The concept of āhorizontal genomicsā involves an internal contradiction because the notion of horizontal gene transfer (HGT) inherently implies the existence of a standard of vertical, tree-like evolution, and most of the existing methods for HGT detection are based on the comparison of gene trees to a standard āspecies treeā, in practice often the rRNA tree [16, 17]. If the vertical standard does not exist, the concept of HGT becomes effectively meaningless, so all we can talk about is a network of life, with nodes corresponding to genomes and edges reflecting gene exchange [18]. The stakes here are high because replacement of the TOL with a network graph would change our entire perception of the process of evolution and invalidate all evolutionary reconstruction based on a species tree. However, the tree representation is by no means superfluous to the description of evolution because the very process of the replication of genetic information implies a bifurcating graph - in other words, a tree [19]. Thus, the key question is [1, 20]: in the genome-wide compendium of phylogenetic trees, that we denoted the Forest Of Life (FOL), can we detect any order, any preferred tree topology (branching order) that would reflect a consensus of the topologies of other trees?
We set out to address the above question as objectively as possible, first of all dispensing with any pre-selected standard of tree-like evolution. The analyzed FOL consisted of 6,901 maximum likelihood phylogenetic trees that were built for clusters of orthologous genes from a representative set of 100 diverse bacterial and archaeal genomes [1]. The complete matrix of topological distances between these trees was analyzed using the Inconsistency Score, a measure that we defined specifically for this purpose that reflects the average topological (in)consistency of a given tree with the rest of the trees in the FOL (for the details of the methods employed in this analysis, see [21]). Although the FOL includes very few trees with exactly identical topologies, we found that the topologies of the trees were far more congruent than expected by chance. The 102 Nearly Universal Trees (NUTs; that is, the trees for genes that are represented in all or nearly all archaea and bacteria), which include primarily genes for key protein components of the translation and transcription systems, showed particularly high topological similarity to the other trees in the FOL. Although the topologies of the NUTs are not identical, apparently reflecting multiple HGT events, these transfers appeared to be distributed randomly. In other words, there seem to be no prominent āhighwaysā of HGT that would preferentially connect particular groups of archaea and bacteria. Thus, although the NUTs cannot represent the FOL completely, they appear to reflect a significant central trend, an attractor in the tree space that could be equated with the STOL (Figure 1).
My bolds.
1 Like
It is rare in eukaryotes, though a form of it, allopolyploid speciation, is common-ish in plants, perhaps as much as 5% of new species. I donāt see evidence that itās common in single-celled eukaryotes or other multicellular eukaryotes, and Iām not sure itās common in archaeans either. Eubacteria, thatās where the action is.
3 Likes
So that gives a well controlled test of the hypothesis.
The degree of tree-likeness in different orders (not always the right taxonomic level!) should correlate inversely with the degree of observed HGT in present day, at least to first approximation.
Iām sure it does. Are their any studies that directly or indirectly test this hypothesis?
There are problems. How can you recognize HGT unless there is a tree to compare to? There are studies of reticulation in angiosperms. Itās easy when half the genome goes one way and half the other. Iāve only seen that in talks, though, and I canāt summon up an actual reference. Another problem is that there are other reasons than HGT for departure from apparent treeness: lineage sorting, bad models of evoluton.
Perhaps the consistency of trees varies inversely with HGT?
I hope you arenāt referring to consistency index. Itās fairly useless. I would suggest some measure of tree similarity among loci, or perhaps linkage groups. Mean Robinson-Foulds distance, perhaps? Next hurdle: finding good estimates of present-day HGT in various groups. Also relevant would be the mean taxonomic distance between species involved. If itās only sister species sharing a little introgression here or there, not much effect.
1 Like
This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.