Last universal ancestor
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The last universal ancestor (LUA), also called the last universal common ancestor (LUCA), cenancestor, or progenote, is the most recent organism from which all organisms now living on Earth have common descent. Thus it is the most recent common ancestor (MRCA) of all current life on Earth. The LUA is estimated to have lived some 3.5 to 3.8 billion years ago (sometime in the Paleoarchean era). The earliest evidences for life on Earth are graphite found to be biogenic in 3.7 billion-year-old metasedimentary rocks discovered in Western Greenland and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia.
Charles Darwin proposed the theory of universal common descent through an evolutionary process in his book On the Origin of Species in 1859, saying, "Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed."
Considering what we know of the offspring groups (see phylogenetic bracketing), the LUA was a small, single-cell organism. It probably had a ring-shaped coil of DNA floating freely within the cell, like modern bacteria. It would probably not have been exceptional among a collection of generalized small-size bacteria of the present day.
While the gross anatomy of the LUA must be reconstructed with some uncertainty, its internal mechanisms can be described in some detail, based on the properties currently shared by all independently living organisms on Earth:
- The genetic code was based on DNA. Note, however, that some studies suggest that LUCA may have lacked DNA and been defined wholly through RNA.
- The DNA was composed of four nucleotides (deoxyadenosine, deoxycytidine, deoxythymidine, and deoxyguanosine), to the exclusion of other possible deoxynucleotides.
- The genetic code was composed of three-nucleotide codons, thus producing 64 different codons. Since only 20 amino acids were used, multiple codons code for the same amino acids.
- The DNA was kept double-stranded by a template-dependent DNA polymerase.
- The integrity of the DNA was maintained by a group of maintenance enzymes, including DNA topoisomerase, DNA ligase and other DNA repair enzymes. The DNA was also protected by DNA-binding proteins such as histones.
- The genetic code was expressed via RNA intermediates, which were single-strand.
- The genetic code was expressed into proteins.
- Proteins were assembled from free amino acids by translation of an mRNA by ribosomes, tRNA and a group of related proteins.
- Ribosomes were composed of two subunits, one big 50S and one small 30S.
- Each ribosomal subunit was composed of a core of ribosomal RNA surrounded by ribosomal proteins.
- The RNA molecules (rRNA and tRNA) played an important role in the catalytic activity of the ribosomes.
- Only 20 amino acids were used, to the exclusion of countless other amino acids.
- Only the L-isomers of the amino acids were used.
- ATP was used as an energy intermediate.
- There were several hundred protein enzymes that catalyzed chemical reactions that extract energy from fats, sugars, and amino acids, and that synthesize fats, sugars, amino acids, and nucleic acid bases using arbitrary chemical pathways.
- The cell contained a water-based cytoplasm that was surrounded and effectively enclosed by a lipid bilayer membrane.
- Inside the cell, the concentration of sodium was lower, and potassium was higher, than outside. This gradient was maintained by specific ion transporters (also referred to as ion pumps).
- The cell multiplied by duplicating all its contents followed by cellular division.
- The cell used chemiosmosis to produce energy. It also reduced CO2 and oxidized H2 (methanogenesis or acetogenesis) via acetyl-thioesters 
In 1859, Charles Darwin published The Origin of Species in which he twice stated the hypothesis that there was only one progenitor for all life forms. In the summation he states, "Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed." The very last sentence is a restatement of the hypothesis: "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one."
When LUA was hypothesized, cladograms based on genetic distance between living cells indicated that Archaea split early from the rest of life. This was inferred from the fact that all known archaeans were highly resistant to environmental extremes such as high salinity, temperature or acidity, and led some scientists to suggest that LUA evolved in areas like the deep ocean vents, where such extremes prevail today. Archaea, however, were discovered in less hostile environments and are now believed to be more closely related to eukaryotes than bacteria, although many details are still unknown.
In 2010, based on "the vast array of molecular sequences now available from all domains of life," a formal test of universal common ancestry was published. The formal test favored the existence of a universal common ancestor over a wide class of alternative hypotheses that included horizontal gene transfer. While the formal test overwhelmingly favored the existence of a single LUA, this does not imply that LUA was ever alone. Instead, it was a member of the early microbial community. Given that many other nucleotides are possible besides adenine (A), thymine (T, DNA only), guanine (G), cytosine (C), and uracil (U, RNA only), it is extremely unlikely that organisms descendent from separate abiogenesis events (that is to say separate incidents where organic molecules initially came together to form cell-like structures) would be able to complete a horizontal gene transfer without garbling each other's genes, converting them into noncoding segments. Also, many more amino acids are chemically possible than the twenty found in modern protein molecules. These lines of chemical evidence, taken into account for the formal statistical test by Theobald (2010), point to a single cell's having been LUA in that, although it was a member of the early microbial community, only its descendents survived beyond the Paleoarchean Era. With a common framework in the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have been feasible and may have been very common later on among the progeny of that single cell.
In 1998, Carl Woese proposed (1) that no individual organism can be considered a LUA, and (2) that the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms. While the results described by the later papers Theobald (2010) and Saey (2010) demonstrate the existence of a single LUCA, the argument in Woese (1998) can still be applied to Ur-organisms. At the beginnings of life, ancestry was not as linear as it is today because the genetic code took time to evolve. Before high fidelity replication, organisms could not be easily mapped on a phylogenetic tree. Not to be confused with the Ur-organism, however, LUCA lived after the genetic code and at least some rudimentary early form of molecular proofreading had already evolved. It was not the very first cell, but rather, the one whose descendents survived beyond the very early stages of microbial evolution.
Location of the root
The most commonly accepted location of the root of the tree of life is between a monophyletic domain Bacteria and a clade formed by Archaea and Eukaryota of what is referred to as the "traditional tree of life" based on several molecular studies starting with C. Woese. A very small minority of studies have concluded differently, namely that the root is in the Domain Bacteria, either in the phylum Firmicutes or that the phylum Chloroflexi is basal to a clade with Archaea+Eukaryotes and the rest of Bacteria as proposed by Thomas Cavalier-Smith.
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