Re: Las universal common ancestor

On 7/14/2024 7:51 AM, RonO wrote:

On 7/13/2024 11:01 AM, erik simpson wrote:

The nature of the last universal common ancestor and its impact on the early Earth system
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Abstract
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.
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https://www.nature.com/articles/s41559-024-02461-1
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 It has been a long time since I published in this field, and they use terminology that wasn't being used back then.  I do not know why, but they call genes "markers" and do not use gene names, but marker designations that are in the NCBI database and give you a protein sequence comparision and superfamily designation.  TIGR01032 is a member of superfamily cl00d393.  You have to use the protein alignment names to get the name of the gene.  I clicked on P47440 in the protein sequence alignment and found out that it was 50s ribosomal protein L20.
 They identified 59 single copy markers in their 700 reference genomes, and used 57 of them in their analysis.  They created a phylogeny of their 700 reference genomes by doing phylogenetic analysis on the 57 concatenated gene sequences.
 They claim to use duplicated genes whose duplication preceded LUCA. They did an analysis to identify all the gene families in their 700 reference genomes. They identified the genes and did a comparative analysis and grouped them into families.  They ended up with 5 groups of related genes whose duplication may have occurred before LUCA existed. They used analysis of these groups of related genes to estimate when LUCA may have existed.
 I do not know how accurate any estimate could be.  They do have phylogeny of their 700 reference genomes, and they do have the duplicated sequence families.  I do not know if they have enough nodes to estimate how the protein sequences have evolved over the last 4 billion years.  They have the extant sequence and are trying to recreate the sequence of the original protein gene in order to make their clock estimates.  They are trying to infer how many substitutions have occurred in 4 billion years for 700 reference genomes when it is likely that a high percentage of the amino acid positions have been substituted many times within each of their 700 lineages.
 Their estimate of 4.2 Ga for the LUCA would mean that the genetic code had evolved within 300 million years of their 4.5 Ga estimate for when the earth's surface was essentially molten.
 They reject the late heavy bombardment episode that was supposed to have occurred around 3.8 Ga that would have sterilized the planet and note that it has come into question as ever happening.
 Ron Okimoto
 

I've looked at this paper again, and they do not discuss the fact that their model indicates that all lineages derived from LUCA went to extinction except for two (Archaea and bacteria).  The last common Archaea and independent last common ancestor of bacteria existed over a billion years after LUCA.  The paper doesn't discuss the point, but it looks like there was some event that reduced the surviving lineages derived from LUCA to just two around a billion years after the LUCA of those two surviving lineages existed.
They dismiss the late heavy bombardment episode that would have sterilized the earth between 4.1 and 3.8 billion years ago, but it could explain the lack of diversification for the billion years after LUCA existed.  Both Archaea and bacteria inherited reverse gyrase from LUCA and that seems to indicate that the lineages that survived this period of lineage extinctions were thermophilic probably living around hydrothermal vents in volcanically active areas that may have been spawned by the late heavy bombardment if it wasn't as bad as they think that it was.  Their analysis indicates that somehow only two thermophilic lineages survived to coalesce a billion years after LUCA existed.
They think that LUCA may have been a heterotrophe and may have relied on chemotrophes to fix carbon, but LUCA had ATPase (evolved in chemotrophes) and they admit that LUCA could have been chemotrophic. They think that LUCA existed in an ecology of diverse lifeforms, but this ecology would have needed to be decimated in order for only two lineages derived from LUCA to represent all extant life on earth.
It would seem that life nearly went extinct within a billion years after LUCA existed.  Something happened to all the lifeforms that shared the planet with LUCA and all the lineages that were spawned from LUCA within a billion year period after LUCA existed.  Somehow only two lineages survived and both independent lineages coalesce into two single lineages around a billion years after LUCA existed.
Ron Okimoto