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Phylogenetic tree linking all major groups of living organisms, namely the Bacteria, Archaea, and Eukarya, as proposed by Woese et al 1990,^[1] with the last universal common ancestor (LUCA) shown at the root

The last universal common ancestor (LUCA) is the hypothesized common ancestral cell from which the three domains of life, the Bacteria, the Archaea, and the Eukarya originated. The cell had a lipid bilayer; it possessed the genetic code and ribosomes which translated from DNA or RNA to proteins. The LUCA probably existed at latest 3.6 billion years ago, and possibly as early as 4.3 billion years ago^[2] or earlier. The nature of this point or stage of divergence remains a topic of research.

All earlier forms of life preceding this divergence and all extant organisms are generally thought to share common ancestry. On the basis of a formal statistical test, this theory of a universal common ancestry (UCA) is supported versus competing multiple-ancestry hypotheses. The first universal common ancestor (FUCA) is a hypothetical non-cellular ancestor to LUCA and other now-extinct sister lineages.

Whether the genesis of viruses falls before or after the LUCA–as well as the diversity of extant viruses and their hosts–remains a subject of investigation.

While no fossil evidence of the LUCA exists, the detailed biochemical similarity of all current life (divided into the three domains) makes its existence widely accepted by biochemists. Its characteristics can be inferred from shared features of modern genomes. These genes describe a complex life form with many co-adapted features, including transcription and translation mechanisms to convert information from DNA to mRNA to proteins.

Historical background

A tree of life, like this one from Charles Darwin's notebooks c. July 1837, implies a single common ancestor at its root (labelled "1").

A phylogenetic tree directly portrays the idea of evolution by descent from a single ancestor.^[3] An early tree of life was sketched by Jean-Baptiste Lamarck in his Philosophie zoologique in 1809.^[4]^[5] Charles Darwin more famously proposed the theory of universal common descent through an evolutionary process in his book On the Origin of Species in 1859: "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."^[6] The last sentence of the book begins with 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 ...
— ^[6]

The term "last universal common ancestor" or "LUCA" was first used in the 1990s for such a primordial organism.^[7]^[8]^[9]

Inferring LUCA's features

An anaerobic thermophile

A direct way to infer LUCA's genome would be to find genes common to all surviving descendants, but little can be learnt by this approach, as there are only about 30 such genes. They are mostly for ribosome proteins, proving that LUCA had the genetic code. Many other LUCA genes have been lost in later lineages over 4 billion years of evolution.^[10]

Three ways to infer genes present in LUCA: universal presence, presence in both the Bacterial and Archaean domains, and presence in two phyla in both domains. The first yields as stated only about 30 genes; the second, some 11,000 with lateral gene transfer (LGT) very likely; the third, 355 genes probably in LUCA, since they were found in at least two phyla in both domains, making LGT an unlikely explanation.^[10]

In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced prokaryotic genomes representing many phylogenetic trees, and identified 355 protein clusters that were probably common to the LUCA. The results of their analysis are highly specific, though debated. They depict LUCA as "anaerobic, CO₂-fixing, H₂-dependent with a Wood–Ljungdahl pathway (the reductive acetyl-coenzyme A pathway), N₂-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms."^[11] The cofactors also reveal "dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent methylations."^[11] They show that methanogenic clostridia were basal, near the root of the phylogenetic tree, in the 355 protein lineages examined, and that the LUCA may therefore have inhabited an anaerobic hydrothermal vent setting in a geochemically active environment rich in H₂, CO₂, and iron, where ocean water interacted with hot magma beneath the ocean floor.^[11] It is even inferred that LUCA also grew from H₂ and CO₂ via the reverse incomplete Krebs cycle.^[12] Other metabolic pathways inferred in LUCA are the pentose phosphate pathway, glycolysis, and gluconeogenesis.^[13] Even if phylogenetic evidence may point to a hydrothermal vent environment for a thermophilic LUCA, this does not constitute evidence that the origin of life took place at a hydrothermal vent since mass extinctions may have removed previously existing branches of life.^[14]

While the gross anatomy of the LUCA can be reconstructed only with much uncertainty, its biochemical mechanisms can be described in some detail, based on the "universal" properties currently shared by all independently living organisms on Earth.^[15]

LUCA systems and environment, including the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon, and most likely DNA complete with the genetic code and enzymes to replicate it, transcribe it to RNA, and translate it to proteins.

The LUCA certainly had genes and a genetic code.^[10] Its genetic material was most likely DNA,^[16] so that it lived after the RNA world.^[a]^[19] The DNA was kept double-stranded by an enzyme, DNA polymerase, which recognises the structure and directionality of DNA.^[20] The integrity of the DNA was maintained by a group of repair enzymes including DNA topoisomerase.^[21] If the genetic code was based on dual-stranded DNA, it was expressed by copying the information to single-stranded RNA. The RNA was produced by a DNA-dependent RNA polymerase using nucleotides similar to those of DNA.^[16] It had multiple DNA-binding proteins, such as histone-fold proteins.^[22] The genetic code was expressed into proteins. These were assembled from 20 free amino acids by translation of a messenger RNA via a mechanism of ribosomes, transfer RNAs, and a group of related proteins.^[16]

LUCA was likely capable of sexual interaction in the sense that adaptive gene functions were present that promoted the transfer of DNA between individuals of the population to facilitate genetic recombination. Homologous gene products that promote genetic recombination are present in bacteria, archaea and eukaryota, such as the RecA protein in bacteria, the RadA protein in archaea, and the Rad51 and Dmc1 proteins in eukaryota.^[23]

The functionality of LUCA as well as evidence for the early evolution membrane-dependent biological systems together suggest that LUCA had cellularity and cell membranes.^[24] As for the cell's gross structure, it contained a water-based cytoplasm effectively enclosed by a lipid bilayer membrane; it was capable of reproducing by cell division.^[25] It tended to exclude sodium and concentrate potassium by means of specific ion transporters (or 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.^[26]^[27]

By phylogenetic bracketing, analysis of the presumed LUCA's offspring groups, LUCA appears to have been a small, single-celled organism. It likely had a ring-shaped coil of DNA floating freely within the cell. Morphologically, it would likely not have stood out within a mixed population of small modern-day bacteria. The originator of the three-domain system, Carl Woese, stated that in its genetic machinery, the LUCA would have been a "simpler, more rudimentary entity than the individual ancestors that spawned the three [domains] (and their descendants)".^[1]

The LUCA used the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon, if it was an autotroph, or to respire anaerobically, if it was a heterotroph.

An alternative to the search for "universal" traits is to use genome analysis to identify phylogenetically ancient genes. This gives a picture of a LUCA that could live in a geochemically harsh environment and is like modern prokaryotes. Analysis of biochemical pathways implies the same sort of chemistry as does phylogenetic analysis. Weiss and colleagues write that "Experiments ... demonstrate that ... acetyl-CoA pathway [chemicals used in anaerobic respiration] formate, methanol, acetyl moieties, and even pyruvate arise spontaneously ... from CO₂, native metals, and water", a combination present in hydrothermal vents.^[28]

An experiment shows that Zn²⁺, Cr³⁺, and Fe can promote 6 of the 11 reactions of an ancient anabolic pathway called the reverse Krebs cycle in acidic conditions which implies that LUCA might have inhabited either hydrothermal vents or acidic metal-rich hydrothermal fields.^[29]

Because both bacteria and archaea have differences in the structure of phospholipids and cell wall, ion pumping, most proteins involved in DNA replication, and glycolysis, it is inferred that LUCA had a permeable membrane without an ion pump. The emergence of Na⁺/H⁺ antiporters likely lead to the evolution of impermeable membranes present in eukaryotes, archaea, and bacteria. It is stated that "The late and independent evolution of glycolysis but not gluconeogenesis is entirely consistent with LUCA being powered by natural proton gradients across leaky membranes. Several discordant traits are likely to be linked to the late evolution of cell membranes, notably the cell wall, whose synthesis depends on the membrane and DNA replication".^[30] Although LUCA likely had DNA, it is unknown if it could replicate DNA and is suggested to "might just have been a chemically stable repository for RNA-based replication".^[31] It is likely that the permeable membrane of LUCA was composed of archaeal lipids (isoprenoids) and bacterial lipids (fatty acids). Isoprenoids would have enhanced stabilization of LUCA's membrane in the surrounding extreme habitat. Nick Lane and coauthors state that "The advantages and disadvantages of incorporating isoprenoids into cell membranes in different microenvironments may have driven membrane divergence, with the later biosynthesis of phospholipids giving rise to the unique G1P and G3P headgroups of archaea and bacteria respectively. If so, the properties conferred by membrane isoprenoids place the lipid divide as early as the origin of life".^[32]

A 2024 study suggests that LUCA's genome was similar in size to that of modern prokaryotes, coding for some 2,600 proteins; that it respired anaerobically, and was an acetogen; and that it had an early CAS-based anti-viral immune system.^[33]

Alternative interpretations

Some other researchers have challenged Weiss et al.'s 2016 conclusions. Sarah Berkemer and Shawn McGlynn argue that Weiss et al. undersampled the families of proteins, so that the phylogenetic trees were not complete and failed to describe the evolution of proteins correctly. There are two risks in attempting to attribute LUCA's environment from near-universal gene distribution (as in Weiss et al. 2016). On the one hand, it risks misattributing convergence or horizontal gene transfer events to vertical descent; on the other hand, it risks misattributing potential LUCA gene families as horizontal gene transfer events. A phylogenomic and geochemical analysis of a set of proteins that probably traced to the LUCA show that it had K⁺-dependent GTPases and the ionic composition and concentration of its intracellular fluid was seemingly high K⁺/Na⁺ ratio, NH⁺
₄, Fe²⁺, CO²⁺, Ni²⁺, Mg²⁺, Mn²⁺, Zn²⁺, pyrophosphate, and PO³⁻
₄ which would imply a terrestrial hot spring habitat. It possibly had a phosphate-based metabolism. Further, these proteins were unrelated to autotrophy (the ability of an organism to create its own organic matter), suggesting that the LUCA had a heterotrophic lifestyle (consuming organic matter) and that its growth was dependent on organic matter produced by the physical environment.^[34] Nick Lane argues that Na⁺/H⁺ antiporters could readily explain the low concentration of Na⁺ in the LUCA and its descendants.

The presence of the energy-handling enzymes CODH/acetyl-coenzyme A synthase in LUCA could be compatible not only with being an autotroph but also with life as a mixotroph or heterotroph.^[35] Weiss et al. 2018 reply that no enzyme defines a trophic lifestyle, and that heterotrophs evolved from autotrophs.^[36]

Evidence that LUCA was mesophilic

Several lines of evidence now suggest that LUCA was non-thermophilic.

The content of G + C nucleotide pairs (compared to the occurrence of A + T pairs) can indicate an organism's thermal optimum as they are more thermally stable due to an additional hydrogen bond. As a result they occur more frequently in the rRNA of thermophiles; however this is not seen in LUCA's reconstructed rRNA.^[37]^[38]^[14]

The identification of thermophilic genes in the LUCA has been criticized,^[39] as they may instead represent genes that evolved later in archaea or bacteria, then migrated between these via horizontal gene transfer, as in Woese's 1998 hypothesis.^[40] LUCA could have been a mesophile that fixed CO₂ and relied on H₂, and lived close to hydrothermal vents.^[41]

Further evidence that LUCA was mesophilic comes from the amino acid composition of its proteins. The abundance of I, V, Y, W, R, E, and L amino acids (denoted IVYWREL) in an organism's proteins is correlated with its optimal growth temperature.^[42] According to phylogentic analysis, the IVYWREL content of LUCA's proteins suggests its ideal temperature was below 50°C.^[14]

Finally, evidence that bacteria and archaea both independently underwent phases of increased and subsequently decreased thermo-tolerance suggests a dramatic post-LUCA climate shift that affected both populations and would explain the seeming genetic pervasiveness of thermo-tolerant genetics.^[43]

Age

Studies from 2000 to 2018 have suggested an increasingly ancient time for the LUCA. In 2000, estimates of the LUCA's age ranged from 3.5 to 3.8 billion years ago in the Paleoarchean,^[44] a few hundred million years before the earliest fossil evidence of life, for which candidates range in age from 3.48 to 4.28 billion years ago.^[45]^[46]^[47]^[48]^[49] This placed the origin of the first forms of life shortly after the Late Heavy Bombardment which was thought to have repeatedly sterilized Earth's surface. However, a 2018 study by Holly Betts and colleagues applied a molecular clock model to the genomic and fossil record (102 species, 29 common protein-coding genes, mostly ribosomal), concluding that LUCA preceded the Late Heavy Bombardment (making the LUCA over 3.9 billion years ago). They assumed that there was no sterilizing event after the Moon-forming event, which they dated as 4.520 billion years ago, and concluded that the most likely date for LUCA was within 50 million years of that.^[50] A 2022 study suggested an age of around 3.6-4.2 billion years for the LUCA.^[51] A 2024 study suggested that the LUCA lived around 4.2 billion years ago (with a confidence interval of 4.09–4.33 billion years ago).^[33]

Root of the tree of life

2005 tree of life showing horizontal gene transfers between branches including (coloured lines) the symbiogenesis of plastids and mitochondria. "Horizontal gene transfer and how it has impacted the evolution of life is presented through a web connecting bifurcating branches that complicate, yet do not erase, the tree of life".^[52]

In 1990, a novel concept of the tree of life was presented, dividing the living world into three stems, classified as the domains Bacteria, Archaea, Eukarya.^[1]^[53]^[54]^[55] It is the first tree founded exclusively on molecular phylogenetics, and which includes the evolution of microorganisms. It has been called a "universal phylogenetic tree in rooted form".^[1] This tree and its rooting became the subject of debate.^[53]^[b]

In the meantime, numerous modifications of this tree, mainly concerning the role and importance of horizontal gene transfer for its rooting and early ramifications have been suggested (e.g.^[57]^[52]). Since heredity occurs both vertically and horizontally, the tree of life may have been more weblike or netlike in its early phase and more treelike when it grew three-stemmed.^[52] Presumably horizontal gene transfer has decreased with growing cell stability.^[58]

A modified version of the tree, based on several molecular studies, has its root between a monophyletic domain Bacteria and a clade formed by Archaea and Eukaryota.^[57] A small minority of studies place the root in the domain bacteria, in the phylum Bacillota,^[59] or state that the phylum Chloroflexota (formerly Chloroflexi) is basal to a clade with Archaea and Eukaryotes and the rest of bacteria (as proposed by Thomas Cavalier-Smith).^[60] Metagenomic analyses recover a two-domain system with the domains Archaea and Bacteria; in this view of the tree of life, Eukaryotes are derived from Archaea.^[61]^[62]^[63] With the later gene pool of LUCA's descendants, sharing a common framework of the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have become feasible and could have been common.^[64]

The nature of LUCA remains disputed. In 1994, on the basis of primordial metabolism (sensu Wächtershäuser), Otto Kandler proposed a successive divergence of the three domains of life^[1] from a multiphenotypical population of pre-cells, reached by gradual evolutionary improvements (cellularization).^[65]^[66]^[67] These phenotypically diverse pre-cells were metabolising, self-reproducing entities exhibiting frequent mutual exchange of genetic information. Thus, in this scenario there was no "first cell". It may explain the unity and, at the same time, the partition into three lines (the three domains) of life. Kandler's pre-cell theory is supported by Wächtershäuser.^[68]^[69] In 1998, Carl Woese, based on the RNA world concept, proposed that no individual organism could be considered a LUCA, and that the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms.^[70] Other authors concur that there was a "complex collective genome"^[71] at the time of the LUCA, and that horizontal gene transfer was important in the evolution of later groups;^[71] Nicolas Glansdorff states that LUCA "was in a metabolically and morphologically heterogeneous community, constantly shuffling around genetic material" and "remained an evolutionary entity, though loosely defined and constantly changing, as long as this promiscuity lasted."^[72]

The theory of a universal common ancestry of life is widely accepted. In 2010, based on "the vast array of molecular sequences now available from all domains of life,"^[73] D. L. Theobald published a "formal test" of universal common ancestry (UCA). This deals with the common descent of all extant terrestrial organisms, each being a genealogical descendant of a single species from the distant past. His formal test favoured the existence of a universal common ancestry over a wide class of alternative hypotheses that included horizontal gene transfer. Basic biochemical principles imply that all organisms do have a common ancestry.^[74]

A proposed, earlier, non-cellular ancestor to LUCA is the First universal common ancestor (FUCA).^[75]^[76] FUCA would therefore be the ancestor to every modern cell as well as ancient, now-extinct cellular lineages not descendant of LUCA. FUCA is assumed to have had other descendants than LUCA, none of which have modern descendants. Some genes of these ancient now-extinct cell lineages are thought to have been horizontally transferred into the genome of early descendants of LUCA.^[64]

LUCA and viruses

The origin of viruses remains disputed. Since viruses need host cells for their replication, it is likely that they emerged after the formation of cells. Viruses may even have multiple origins and different types of viruses may have evolved independently over the history of life.^[55] There are different hypotheses for the origins of viruses, for instance an early viral origin from the RNA world or a later viral origin from selfish DNA.^[55]

Based on how viruses are currently distributed across the bacteria and archaea, the LUCA is suspected of having been prey to multiple viruses, ancestral to those that now have those two domains as their hosts.^[77] Furthermore, extensive virus evolution seems to have preceded the LUCA, since the jelly-roll structure of capsid proteins is shared by RNA and DNA viruses across all three domains of life.^[78]^[79] LUCA's viruses were probably mainly dsDNA viruses in the groups called Duplodnaviria and Varidnaviria. Two other single-stranded DNA virus groups within the Monodnaviria, the Microviridae and the Tubulavirales, likely infected the last bacterial common ancestor. The last archaeal common ancestor was probably host to spindle-shaped viruses. All of these could well have affected the LUCA, in which case each must since have been lost in the host domain where it is no longer extant. By contrast, RNA viruses do not appear to have been important parasites of LUCA, even though straightforward thinking might have envisaged viruses as beginning with RNA viruses directly derived from an RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been out-competed by DNA viruses.^[77]

LUCA might have been the ancestor to some viruses, as it might have had at least two descendants: LUCELLA, the Last Universal Cellular Ancestor, the ancestor to all cells, and the archaic virocell ancestor, the ancestor to large-to-medium-sized DNA viruses.^[80] Viruses might have evolved before LUCA but after the First universal common ancestor (FUCA), according to the reduction hypothesis, where giant viruses evolved from primordial cells that became parasitic.^[64]

Notes

^ Other studies propose that LUCA may have been defined wholly through RNA,^[17] consisted of a RNA-DNA hybrid genome, or possessed a retrovirus-like genetic cycle with DNA serving as a stable genetic repository.^[18]
^ One debate dealt with a former cladistic hypothesis: The tree could not be ascribed a root in the usual algorithmic way, because that would require an outgroup for reference. In the case of the universal tree, no outgroup would exist. The cladistic method was used "to root the purple bacteria, for example. But establishing a root for the universal tree of life, the branching order among the primary urkingdoms, was another matter entirely."^[56]

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@@ Line 5: / Line 5: @@
 [[File:Phylogenetic tree of life 1990 LUCA.svg|thumb|upright=1.75|[[Phylogenetic tree]] linking all major groups of living organisms, namely the [[Bacteria]], [[Archaea]], and [[Eukaryote|Eukarya]], as proposed by Woese et al 1990,<ref name="Woese Kandler Wheelis 1990"/> with the last universal common ancestor (LUCA) shown at the root]]
-The '''last universal common ancestor''' ('''LUCA''') is hypothesized to have been a common ancestral [[Cell (biology)|cell]] from which the [[Domain (biology)|three domains of life]],<!--<ref name="Woese Kandler Wheelis 1990"/>--> the [[Bacteria]], the [[Archaea]], and the [[Eukarya]] originated. It is suggested to have been a "cellular [[organism]] that had a [[lipid bilayer]] and used DNA, RNA, and protein".<ref name="Brock_2022"/> The LUCA has also been defined as "a hypothetical organism ancestral to all three domains".<ref name="Harold_2014"/> The LUCA is the point or stage at which the three domains of life diverged from precursing forms of life (about 3.5 - 3.8 billion years ago). The nature of this point or stage of divergence remains a topic of research.<!--<ref name="Harold_2014"/>-->
+The '''last universal common ancestor''' ('''LUCA''') is the hypothesized common ancestral [[Cell (biology)|cell]] from which the [[Domain (biology)|three domains of life]],<!--<ref name="Woese Kandler Wheelis 1990"/>--> the [[Bacteria]], the [[Archaea]], and the [[Eukarya]] originated. The cell had a [[lipid bilayer]]; it possessed the [[genetic code]] and [[ribosome]]s which translated from [[DNA]] or [[RNA]] to [[protein]]s. The LUCA probably existed at latest 3.6 billion years ago, and possibly as early as 4.3 billion years ago<ref>{{cite journal |last1=Moody |first1=Edmund |last2=Álvarez-Carretero |first2=Sandra |last3=Mahendrarajah |first3=Tara |title=The nature of the last universal common ancestor and its impact on the early Earth system |journal=Nat. Ecol. Evol |date=12 July 2024 |doi=10.1038/s41559-024-02461-1 |url=https://www.nature.com/articles/s41559-024-02461-1 |access-date=26 August 2024|doi-access=free }}</ref> or earlier. The nature of this point or stage of divergence remains a topic of research.<!--<ref name="Harold_2014"/>-->
 <!--refs only for DIRECT QUOTATIONS in lead, all else to article body please-->
-All earlier forms of life precursing this divergence and, of course, all extant terrestrial organisms are generally thought to share [[common ancestry]]. On the basis of a formal statistical test, this theory of a universal common ancestry (UCA) is supported versus competing multiple-ancestry hypotheses.<!--<ref name="Theobald-2010"/>--> The [[first universal common ancestor]] (FUCA) is a hypothetical non-cellular ancestor to LUCA and other now-extinct sister lineages.
+All earlier forms of life preceding this divergence and all extant organisms are generally thought to share [[common ancestry]]. On the basis of a formal statistical test, this theory of a universal common ancestry (UCA) is supported versus competing multiple-ancestry hypotheses.<!--<ref name="Theobald-2010"/>--> The [[first universal common ancestor]] (FUCA) is a hypothetical non-cellular ancestor to LUCA and other now-extinct sister lineages.
 <!--refs only for DIRECT QUOTATIONS in lead, all else to article body please-->
-The genesis of [[Virus|viruses]], before or after the LUCA as well as the diversity of extant viruses and their hosts are subjects of investigation.
+Whether the genesis of [[virus]]es falls before or after the LUCA–as well as the diversity of extant viruses and their hosts–remains a subject of investigation.
 <!--refs only for DIRECT QUOTATIONS in lead, all else to article body please-->
-While no specific fossil evidence of the LUCA exists, the detailed biochemical similarity of all current life (divided into the three domains) makes it plausible. Its characteristics can be inferred from [[phylogenetic bracketing|shared features of modern genomes]]. These genes describe a complex life form with many [[co-adapted]] features, including [[transcription (biology)|transcription]] and [[translation (biology)|translation]] mechanisms to convert information from [[DNA]] to [[mRNA]] to [[protein]]s. The earlier forms of life probably lived in the high-temperature water of [[Hydrothermal vent#Black smokers and white smokers|deep sea vents]] near ocean-floor [[magma]] flows<!--Weiss et al 2016--> around 4&nbsp;billion years ago.
+While no fossil evidence of the LUCA exists, the detailed biochemical similarity of all current life (divided into the three domains) makes its existence widely accepted by biochemists. Its characteristics can be inferred from [[phylogenetic bracketing|shared features of modern genomes]]. These genes describe a complex life form with many [[co-adapted]] features, including [[transcription (biology)|transcription]] and [[translation (biology)|translation]] mechanisms to convert information from [[DNA]] to [[mRNA]] to [[protein]]s.
 <!--refs only for DIRECT QUOTATIONS in lead, all else to article body please-->
@@ Line 23: / Line 23: @@
 [[File:Darwin Tree 1837.png|thumb|upright|A [[Tree of life (biology)|tree of life]], like this one from [[Charles Darwin]]'s notebooks {{circa|July&nbsp;1837}}, implies a single common ancestor at its root (labelled "1").]]
-A [[phylogenetic tree]] directly portrays the idea of [[evolution]] by [[common descent|descent from a single ancestor]]<!-- at the root of the tree-->.<ref name="Gregory 2008">{{cite journal |last=Gregory |first=T. Ryan |year=2008 |title=Understanding evolutionary trees |journal=Evolution: Education and Outreach |volume=1 |issue=2 |pages=121–137 |doi=10.1007/s12052-008-0035-x|s2cid=15488906 |doi-access=free }}</ref><!-- <ref name="Baum Smith Donovan 2005">{{cite journal |last=Baum |first=David A. |last2=Smith |first2=Stacey DeWitt |last3=Donovan |first3=Samuel S. S. |title=The Tree-Thinking Challenge |journal=Science |volume=310 |issue=5750 |date=2005 |doi=10.1126/science.1117727 |pages=979–980}}</ref> --> An early tree of life was sketched by [[Jean-Baptiste Lamarck]] in his ''[[Philosophie zoologique]]'' in 1809.<ref>{{cite book |last=Lamarck |first=Jean Baptiste Pierre Antoine de Monet de |author-link=Jean-Baptiste Lamarck |title=Philosophie zoologique |orig-date=1809 |year=1994 |location=Paris |page=737 <!-- |oclc=31599154 --> |url=https://ia801004.us.archive.org/28/items/LamarckPZ/Lamarck_PZ.pdf }}</ref><ref>{{cite journal |last=Noble |first=Denis |author-link=Denis Noble |date=1 July 2020 |title=Editorial: Charles Darwin, Jean-Baptiste Lamarck, and 21st&nbsp;century arguments on the fundamentals of biology |journal=Progress in Biophysics and Molecular Biology |volume=153 |pages=1–4 |doi=10.1016/j.pbiomolbio.2020.02.005 |pmid=32092299 |s2cid=211475380 |url=https://www.sciencedirect.com/science/article/pii/S0079610720300134 |access-date=2022-12-23}}</ref> [[Charles Darwin]] more famously proposed the theory of universal common descent through an evolutionary process in his book ''[[On the Origin of Species]]'' in 1859: "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."<ref name="Darwin 1859">{{cite book |last=Darwin |first=Charles |author-link=Charles Darwin |year=1859 |title=The Origin of Species by Means of Natural Selection |pages=484, 490<!-- original pages --> |publisher=[[John Murray (publishing house)|John Murray]] |url=http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=F373&pageseq=484}}</ref> The last sentence of the book begins with a restatement of the hypothesis:
+A [[phylogenetic tree]] directly portrays the idea of [[evolution]] by [[common descent|descent from a single ancestor]]<!-- at the root of the tree-->.<ref name="Gregory 2008">{{cite journal |last=Gregory |first=T. Ryan |year=2008 |title=Understanding evolutionary trees |journal=Evolution: Education and Outreach |volume=1 |issue=2 |pages=121–137 |doi=10.1007/s12052-008-0035-x|s2cid=15488906 |doi-access=free }}</ref><!-- <ref name="Baum Smith Donovan 2005">{{cite journal |last=Baum |first=David A. |last2=Smith |first2=Stacey DeWitt |last3=Donovan |first3=Samuel S. S. |title=The Tree-Thinking Challenge |journal=Science |volume=310 |issue=5750 |date=2005 |doi=10.1126/science.1117727 |pages=979–980}}</ref> --> An early tree of life was sketched by [[Jean-Baptiste Lamarck]] in his ''[[Philosophie zoologique]]'' in 1809.<ref>{{cite book |last=Lamarck |first=Jean Baptiste Pierre Antoine de Monet de |author-link=Jean-Baptiste Lamarck |title=Philosophie zoologique |orig-date=1809 |year=1994 |location=Paris |page=737 <!-- |oclc=31599154 --> |url=https://ia801004.us.archive.org/28/items/LamarckPZ/Lamarck_PZ.pdf }}</ref><ref>{{cite journal |last=Noble |first=Denis |author-link=Denis Noble |date=1 July 2020 |title=Editorial: Charles Darwin, Jean-Baptiste Lamarck, and 21st&nbsp;century arguments on the fundamentals of biology |journal=Progress in Biophysics and Molecular Biology |volume=153 |pages=1–4 |doi=10.1016/j.pbiomolbio.2020.02.005 |pmid=32092299 |s2cid=211475380 |url=https://www.sciencedirect.com/science/article/pii/S0079610720300134 |access-date=2022-12-23 |archive-date=1 March 2022 |archive-url=https://web.archive.org/web/20220301193402/https://www.sciencedirect.com/science/article/pii/S0079610720300134 |url-status=live }}</ref> [[Charles Darwin]] more famously proposed the theory of universal common descent through an evolutionary process in his book ''[[On the Origin of Species]]'' in 1859: "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."<ref name="Darwin 1859">{{cite book |last=Darwin |first=Charles |author-link=Charles Darwin |year=1859 |title=The Origin of Species by Means of Natural Selection |pages=484, 490<!-- original pages --> |publisher=[[John Murray (publishing house)|John Murray]] |url=http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=F373&pageseq=484 |access-date=8 October 2022 |archive-date=8 October 2022 |archive-url=https://web.archive.org/web/20221008150204/http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=F373&pageseq=484 |url-status=live }}</ref> The last sentence of the book begins with a restatement of the hypothesis:
 {{blockquote|text=There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one&nbsp;...|source=<ref name="Darwin 1859"/>}}
@@ Line 38: / Line 38: @@
 |total_width       = 850
 |image1            = Inferring LUCA's genome.svg
-|caption1          = A direct way to infer LUCA's [[genome]] would be to find genes common to all surviving descendants. Unfortunately, there are only about 30 such genes, mostly for [[ribosome]] proteins, proving that LUCA had the [[genetic code]]. Many other LUCA genes have been lost in later lineages over 4 billion years of evolution.<ref name="Weiss Preiner Xavier 2018"/>
+|caption1          = A direct way to infer LUCA's [[genome]] would be to find genes common to all surviving descendants, but little can be learnt by this approach, as there are only about 30 such genes. They are mostly for [[ribosome]] proteins, proving that LUCA had the [[genetic code]]. Many other LUCA genes have been lost in later lineages over 4 billion years of evolution.<ref name="Weiss Preiner Xavier 2018"/>
 |image2            = Three ways to infer genes present in LUCA.jpg
 |caption2          = Three ways to infer genes present in LUCA: universal presence, presence in both the [[Bacteria]]l and [[Archaea]]n domains, and presence in two [[Phylum|phyla]] in both domains. The first yields as stated only about 30 genes; the second, some 11,000 with [[Horizontal gene transfer|lateral gene transfer]] (LGT) very likely; the third, 355 genes probably in LUCA, since they were found in at least two phyla in both domains, making LGT an unlikely explanation.<ref name="Weiss Preiner Xavier 2018"/>
 }}
-In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced [[Prokaryote|prokaryotic]] genomes representing many [[Phylogenetic tree|phylogenetic trees]], and identified 355 protein clusters that were probably common to the LUCA. The results of their analysis are highly specific, though debated. They depict LUCA as "[[Anaerobic organism|anaerobic]], [[Carbon dioxide|CO<sub>2</sub>]]-fixing, [[Hydrogen|H<sub>2</sub>]]-dependent with a [[Wood–Ljungdahl pathway]] (the reductive [[Acetyl-CoA|acetyl-coenzyme A]] pathway), [[Nitrogen|N<sub>2</sub>]]-fixing and [[Thermophile|thermophilic]]. LUCA's biochemistry was replete with [[Iron(II) sulfide|FeS]] clusters and [[Radical (chemistry)|radical]] reaction mechanisms."<ref name="Weiss et al 20162">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Sousa |first2=F. L. |last3=Mrnjavac |first3=N. |last4=Neukirchen |first4=S. |last5=Roettger |first5=M. |last6=Nelson-Sathi |first6=S. |last7=Martin |first7=William F. |author7-link=William F. Martin |display-authors=3 |year=2016 |title=The physiology and habitat of the last universal common ancestor |url=http://complexityexplorer.s3.amazonaws.com/supplemental_materials/3.6+Early+Metabolisms/Weiss_et_al_Nat_Microbiol_2016.pdf |journal=Nature Microbiology |volume=1 |issue=9 |page=16116 |doi=10.1038/nmicrobiol.2016.116 |pmid=27562259 |s2cid=2997255}}</ref> The [[Cofactor (biochemistry)|cofactors]] also reveal "dependence upon [[Transition metal|transition metals]], [[Flavin mononucleotide|flavins]], [[S-adenosyl methionine]], [[coenzyme A]], [[ferredoxin]], [[molybdopterin]], [[Corrin|corrins]] and [[selenium]]. Its genetic code required [[nucleoside]] modifications and S-adenosylmethionine-dependent [[Methylation|methylations]]."<ref name="Weiss et al 20162" /> They show that [[Methanogen|methanogenic]] [[Clostridium|clostridia]] was [[Basal (phylogenetics)|basal, near the root of the phylogenetic tree]], in the 355<!--yes, the same 355--> protein lineages examined, and that the LUCA may therefore have inhabited an anaerobic [[hydrothermal vent]] setting in a geochemically active environment rich in H<sub>2</sub>, CO<sub>2</sub>, and iron, where [[ocean]] water interacted with hot [[magma]] beneath the [[Seabed|ocean floor]].<ref name="Weiss et al 20162" /> It's even inferred that LUCA also grew from H<sub>2</sub> and CO<sub>2</sub> via the reverse incomplete Krebs cycle.<ref>{{Cite journal |last1=Harrison |first1=Stuart A. |last2=Palmeira |first2=Raquel Nunes |last3=Halpern |first3=Aaron |last4=Lane |first4=Nick |date=2022-11-01 |title=A biophysical basis for the emergence of the genetic code in protocells |journal=Biochimica et Biophysica Acta (BBA) - Bioenergetics |language=en |volume=1863 |issue=8 |pages=148597 |doi=10.1016/j.bbabio.2022.148597 |issn=0005-2728 |pmid=35868450 |doi-access=free}}</ref> Other metabolic pathways inferred in LUCA are the [[pentose phosphate pathway]], [[glycolysis]], and [[gluconeogenesis]].<ref>{{Cite journal |last1=Harrison |first1=Stuart A. |last2=Lane |first2=Nick |date=2018-12-12 |title=Life as a guide to prebiotic nucleotide synthesis |journal=Nature Communications |language=en |volume=9 |issue=1 |pages=5176 |bibcode=2018NatCo...9.5176H |doi=10.1038/s41467-018-07220-y |issn=2041-1723 |pmc=6289992 |pmid=30538225}}</ref> It should be noted that even if phylogenetic evidence may point to a hydrothermal vent environment for a thermophilic LUCA, this does not constitute evidence that the [[Abiogenesis|origin of life]] took place at a hydrothermal vent since mass extinctions may have removed previously existing branches of life.<ref name=":22" />
+In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced [[Prokaryote|prokaryotic]] genomes representing many [[Phylogenetic tree|phylogenetic trees]], and identified 355 protein clusters that were probably common to the LUCA. The results of their analysis are highly specific, though debated. They depict LUCA as "[[Anaerobic organism|anaerobic]], [[Carbon dioxide|CO<sub>2</sub>]]-fixing, [[Hydrogen|H<sub>2</sub>]]-dependent with a [[Wood–Ljungdahl pathway]] (the reductive [[Acetyl-CoA|acetyl-coenzyme A]] pathway), [[Nitrogen|N<sub>2</sub>]]-fixing and [[Thermophile|thermophilic]]. LUCA's biochemistry was replete with [[Iron(II) sulfide|FeS]] clusters and [[Radical (chemistry)|radical]] reaction mechanisms."<ref name="Weiss et al 20162">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Sousa |first2=F. L. |last3=Mrnjavac |first3=N. |last4=Neukirchen |first4=S. |last5=Roettger |first5=M. |last6=Nelson-Sathi |first6=S. |last7=Martin |first7=William F. |author7-link=William F. Martin |display-authors=3 |year=2016 |title=The physiology and habitat of the last universal common ancestor |url=http://complexityexplorer.s3.amazonaws.com/supplemental_materials/3.6+Early+Metabolisms/Weiss_et_al_Nat_Microbiol_2016.pdf |journal=Nature Microbiology |volume=1 |issue=9 |page=16116 |doi=10.1038/nmicrobiol.2016.116 |pmid=27562259 |s2cid=2997255 |access-date=10 October 2022 |archive-date=18 April 2022 |archive-url=https://web.archive.org/web/20220418220101/https://complexityexplorer.s3.amazonaws.com/supplemental_materials/3.6+Early+Metabolisms/Weiss_et_al_Nat_Microbiol_2016.pdf |url-status=live }}</ref> The [[Cofactor (biochemistry)|cofactors]] also reveal "dependence upon [[Transition metal|transition metals]], [[Flavin mononucleotide|flavins]], [[S-adenosyl methionine]], [[coenzyme A]], [[ferredoxin]], [[molybdopterin]], [[Corrin|corrins]] and [[selenium]]. Its genetic code required [[nucleoside]] modifications and S-adenosylmethionine-dependent [[Methylation|methylations]]."<ref name="Weiss et al 20162" /> They show that [[Methanogen|methanogenic]] [[Clostridium|clostridia]] were [[Basal (phylogenetics)|basal, near the root of the phylogenetic tree]], in the 355<!--yes, the same 355--> protein lineages examined, and that the LUCA may therefore have inhabited an anaerobic [[hydrothermal vent]] setting in a geochemically active environment rich in H<sub>2</sub>, CO<sub>2</sub>, and iron, where [[ocean]] water interacted with hot [[magma]] beneath the [[Seabed|ocean floor]].<ref name="Weiss et al 20162" /> It is even inferred that LUCA also grew from H<sub>2</sub> and CO<sub>2</sub> via the reverse incomplete Krebs cycle.<ref>{{Cite journal |last1=Harrison |first1=Stuart A. |last2=Palmeira |first2=Raquel Nunes |last3=Halpern |first3=Aaron |last4=Lane |first4=Nick |date=2022-11-01 |title=A biophysical basis for the emergence of the genetic code in protocells |journal=Biochimica et Biophysica Acta (BBA) - Bioenergetics |volume=1863 |issue=8 |pages=148597 |doi=10.1016/j.bbabio.2022.148597  |pmid=35868450 |doi-access=free}}</ref> Other metabolic pathways inferred in LUCA are the [[pentose phosphate pathway]], [[glycolysis]], and [[gluconeogenesis]].<ref>{{Cite journal |last1=Harrison |first1=Stuart A. |last2=Lane |first2=Nick |date=2018-12-12 |title=Life as a guide to prebiotic nucleotide synthesis |journal=Nature Communications |language=en |volume=9 |issue=1 |pages=5176 |bibcode=2018NatCo...9.5176H |doi=10.1038/s41467-018-07220-y |issn=2041-1723 |pmc=6289992 |pmid=30538225}}</ref> Even if phylogenetic evidence may point to a hydrothermal vent environment for a thermophilic LUCA, this does not constitute evidence that the [[Abiogenesis|origin of life]] took place at a hydrothermal vent since mass extinctions may have removed previously existing branches of life.<ref name="Cantine-2017" />
-While the gross anatomy of the LUCA can only be reconstructed with much uncertainty, its [[Metabolic pathway|biochemical mechanisms]] can be described in some detail, based on the "universal" properties currently shared by all independently living organisms on Earth.<ref name="W19982">{{cite journal |last=Wächtershäuser |first=Günter |year=1998 |title=Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment |journal=Systematic and Applied Microbiology |volume=21 |issue=4 |pages=473–474, IN1, 475–477 |doi=10.1016/S0723-2020(98)80058-1}}</ref>
+While the gross anatomy of the LUCA can be reconstructed only with much uncertainty, its [[Metabolic pathway|biochemical mechanisms]] can be described in some detail, based on the "universal" properties currently shared by all independently living organisms on Earth.<ref name="W19982">{{cite journal |last=Wächtershäuser |first=Günter |year=1998 |title=Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment |journal=Systematic and Applied Microbiology |volume=21 |issue=4 |pages=473–474, IN1, 475–477 |doi=10.1016/S0723-2020(98)80058-1 |bibcode=1998SyApM..21N1475W }}</ref>
 [[File:LUCA systems and environment.svg|thumb|upright=2|LUCA systems and environment, including the [[Wood–Ljungdahl pathway|Wood–Ljungdahl or reductive acetyl–CoA pathway]] to [[Carbon fixation|fix carbon]], and most likely [[DNA]] complete with the [[genetic code]] and [[enzyme]]s to [[DNA replication|replicate]] it, [[Transcription (biology)|transcribe it to RNA]], and [[Translation (biology)|translate it to proteins]].]]
-The LUCA certainly had [[gene]]s and a [[genetic code]].<ref name="Weiss Preiner Xavier 2018">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Preiner |first2=Martina |last3=Xavier |first3=Joana C. |last4=Zimorski |first4=Verena |last5=Martin |first5=William F. |date=2018-08-16 |title=The last universal common ancestor between ancient Earth chemistry and the onset of genetics |journal=PLOS Genetics |volume=14 |issue=8 |pages=e1007518 |doi=10.1371/journal.pgen.1007518 |pmc=6095482 |pmid=30114187 |s2cid=52019935 |doi-access=free}}</ref> Its genetic material was most likely DNA,<ref name="W1998">{{cite journal |last=Wächtershäuser |first=Günter |year=1998 |title=Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment |journal=Systematic and Applied Microbiology |volume=21 |issue=4 |pages=473–474, IN1, 475–477 |doi=10.1016/S0723-2020(98)80058-1}}</ref> so that it lived after the [[RNA world]].{{efn|Other studies propose that LUCA may have been defined wholly through [[RNA]],<ref>{{cite magazine |url=https://www.newscientist.com/article/mg21228404-300-life-began-with-a-planetary-mega-organism/ |title=Life began with a planetary mega-organism |last=Marshall |first=Michael |magazine=[[New Scientist]] |access-date=31 July 2016 |archive-url=https://web.archive.org/web/20160725170104/https://www.newscientist.com/article/mg21228404-300-life-began-with-a-planetary-mega-organism/ |archive-date=25 July 2016 |df=dmy-all |url-status=live}}</ref> consisted of a RNA-DNA hybrid genome, or possessed a retrovirus-like genetic cycle with DNA serving as a stable genetic repository.<ref>{{cite journal |last1=Koonin |first1=Eugene V. |last2=Martin |first2=William |date=1 December 2005 |df=dmy-all |title=On the origin of genomes and cells within inorganic compartments |journal=Trends in Genetics |volume=21 |issue=12 |pages=647–654 |doi=10.1016/j.tig.2005.09.006 |pmid=16223546 |pmc=7172762 }}</ref>}}<ref name="PiP">{{cite journal |last=Garwood |first=Russell J. |title=Patterns In Palaeontology: The first 3&nbsp;billion years of evolution |year=2012 |journal=Palaeontology Online |volume=2 |issue=11 |pages=1–14 |url=http://www.palaeontologyonline.com/articles/2012/patterns-in-palaeontology-the-first-3-billion-years-of-evolution/ |access-date=June 25, 2015 |archive-url=https://web.archive.org/web/20150626104131/http://www.palaeontologyonline.com/articles/2012/patterns-in-palaeontology-the-first-3-billion-years-of-evolution/ |archive-date=June 26, 2015 |url-status=live }}</ref> The DNA was kept double-stranded by an [[enzyme]], [[DNA polymerase]], which recognises the structure and directionality of DNA.<ref>{{cite journal |last1=Koonin |first1=Eugene V. |author1-link=Eugene V. Koonin |last2=Krupovic |first2=M. |last3=Ishino |first3=S. |last4=Ishino |first4=Y. |title=The replication machinery of LUCA: common origin of DNA replication and transcription. |journal=BMC Biology |date=2020 |volume=18 |issue=1 |pages=61 |doi=10.1186/s12915-020-00800-9 |pmid=32517760 |pmc=7281927 |doi-access=free }}</ref> The integrity of the DNA was maintained by a group of [[DNA repair|repair]] enzymes including [[DNA topoisomerase]].<ref>{{Cite journal |last1=Ahmad |first1=Muzammil |last2=Xu |first2=Dongyi |last3=Wang |first3=Weidong |date=2017-05-23 |df=dmy-all |title=Type IA topoisomerases can be "magicians" for both DNA and RNA in all domains of life |journal=RNA Biology |volume=14 |issue=7 |pages=854–864 |doi=10.1080/15476286.2017.1330741 |pmc=5546716 |pmid=28534707 }}</ref> If the genetic code was based on [[Nucleic acid double helix|dual-stranded DNA]], it was expressed by copying the information to single-stranded RNA. The RNA was produced by a DNA-dependent [[RNA polymerase]] using nucleotides similar to those of DNA<!--, with the exception that the DNA nucleotide [[thymidine]] was replaced by [[uridine]] in RNA-->.<ref name="W1998"/> It had multiple [[DNA-binding protein]]s, such as histone-fold proteins.<ref>{{Cite journal |last1=Lupas |first1=Andrei N. |last2=Alva |first2=Vikram |year=2018 |title=Histones predate the split between bacteria and archaea |journal=Bioinformatics |volume=35 |issue=14 |pages=2349–2353 |doi=10.1093/bioinformatics/bty1000 |pmid=30520969}}</ref> The genetic code was expressed into [[protein]]s. These were assembled from 20 free [[amino acid]]s by [[Translation (biology)|translation]] of a [[messenger RNA]] via a mechanism of [[ribosome]]s, [[transfer RNA]]s, and a group of related proteins.<ref name=W1998/>
+The LUCA certainly had [[gene]]s and a [[genetic code]].<ref name="Weiss Preiner Xavier 2018">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Preiner |first2=Martina |last3=Xavier |first3=Joana C. |last4=Zimorski |first4=Verena |last5=Martin |first5=William F. |date=2018-08-16 |title=The last universal common ancestor between ancient Earth chemistry and the onset of genetics |journal=PLOS Genetics |volume=14 |issue=8 |pages=e1007518 |doi=10.1371/journal.pgen.1007518 |pmc=6095482 |pmid=30114187 |s2cid=52019935 |doi-access=free}}</ref> Its genetic material was most likely DNA,<ref name="W1998">{{cite journal |last=Wächtershäuser |first=Günter |year=1998 |title=Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment |journal=Systematic and Applied Microbiology |volume=21 |issue=4 |pages=473–474, IN1, 475–477 |doi=10.1016/S0723-2020(98)80058-1 |bibcode=1998SyApM..21N1475W }}</ref> so that it lived after the [[RNA world]].{{efn|Other studies propose that LUCA may have been defined wholly through [[RNA]],<ref>{{cite magazine |url=https://www.newscientist.com/article/mg21228404-300-life-began-with-a-planetary-mega-organism/ |title=Life began with a planetary mega-organism |last=Marshall |first=Michael |magazine=[[New Scientist]] |access-date=31 July 2016 |archive-url=https://web.archive.org/web/20160725170104/https://www.newscientist.com/article/mg21228404-300-life-began-with-a-planetary-mega-organism/ |archive-date=25 July 2016 |df=dmy-all |url-status=live}}</ref> consisted of a RNA-DNA hybrid genome, or possessed a retrovirus-like genetic cycle with DNA serving as a stable genetic repository.<ref>{{cite journal |last1=Koonin |first1=Eugene V. |last2=Martin |first2=William |date=1 December 2005 |df=dmy-all |title=On the origin of genomes and cells within inorganic compartments |journal=Trends in Genetics |volume=21 |issue=12 |pages=647–654 |doi=10.1016/j.tig.2005.09.006 |pmid=16223546 |pmc=7172762 }}</ref>}}<ref name="PiP">{{cite journal |last=Garwood |first=Russell J. |title=Patterns In Palaeontology: The first 3 billion years of evolution |year=2012 |journal=Palaeontology Online |volume=2 |issue=11 |pages=1–14 |url=http://www.palaeontologyonline.com/articles/2012/patterns-in-palaeontology-the-first-3-billion-years-of-evolution/ |access-date=June 25, 2015 |archive-url=https://web.archive.org/web/20150626104131/http://www.palaeontologyonline.com/articles/2012/patterns-in-palaeontology-the-first-3-billion-years-of-evolution/ |archive-date=June 26, 2015 |url-status=live }}</ref> The DNA was kept double-stranded by an [[enzyme]], [[DNA polymerase]], which recognises the structure and directionality of DNA.<ref>{{cite journal |last1=Koonin |first1=Eugene V. |author1-link=Eugene V. Koonin |last2=Krupovic |first2=M. |last3=Ishino |first3=S. |last4=Ishino |first4=Y. |title=The replication machinery of LUCA: common origin of DNA replication and transcription. |journal=BMC Biology |date=2020 |volume=18 |issue=1 |pages=61 |doi=10.1186/s12915-020-00800-9 |pmid=32517760 |pmc=7281927 |doi-access=free }}</ref> The integrity of the DNA was maintained by a group of [[DNA repair|repair]] enzymes including [[DNA topoisomerase]].<ref>{{Cite journal |last1=Ahmad |first1=Muzammil |last2=Xu |first2=Dongyi |last3=Wang |first3=Weidong |date=2017-05-23 |df=dmy-all |title=Type IA topoisomerases can be "magicians" for both DNA and RNA in all domains of life |journal=RNA Biology |volume=14 |issue=7 |pages=854–864 |doi=10.1080/15476286.2017.1330741 |pmc=5546716 |pmid=28534707 }}</ref> If the genetic code was based on [[Nucleic acid double helix|dual-stranded DNA]], it was expressed by copying the information to single-stranded RNA. The RNA was produced by a DNA-dependent [[RNA polymerase]] using nucleotides similar to those of DNA<!--, with the exception that the DNA nucleotide [[thymidine]] was replaced by [[uridine]] in RNA-->.<ref name="W1998"/> It had multiple [[DNA-binding protein]]s, such as histone-fold proteins.<ref>{{Cite journal |last1=Lupas |first1=Andrei N. |last2=Alva |first2=Vikram |year=2018 |title=Histones predate the split between bacteria and archaea |journal=Bioinformatics |volume=35 |issue=14 |pages=2349–2353 |doi=10.1093/bioinformatics/bty1000 |pmid=30520969}}</ref> The genetic code was expressed into [[protein]]s. These were assembled from 20 free [[amino acid]]s by [[Translation (biology)|translation]] of a [[messenger RNA]] via a mechanism of [[ribosome]]s, [[transfer RNA]]s, and a group of related proteins.<ref name=W1998/>
-LUCA was likely capable of [[sexual reproduction|sexual interaction]] in the sense that adaptive gene functions were present that promoted the transfer of DNA between individuals of the population to facilitate [[genetic recombination]].  Homologous gene products that promote genetic recombination are present in bacteria, archaea and eukaryota, such as the [[RecA]] protein in bacteria, the RadA protein in archaea, and the [[RAD51|Rad51]] and [[DMC1 (gene)|Dmc1]] proteins in eukaryota.<ref>Bernstein, H., Bernstein, C. (2017). Sexual Communication in Archaea, the Precursor to Eukaryotic Meiosis. In: Witzany, G. (eds) Biocommunication of Archaea. Springer, Cham. https://doi.org/10.1007/978-3-319-65536-9_7</ref>
+LUCA was likely capable of [[sexual reproduction|sexual interaction]] in the sense that adaptive gene functions were present that promoted the transfer of DNA between individuals of the population to facilitate [[genetic recombination]]. Homologous gene products that promote genetic recombination are present in bacteria, archaea and eukaryota, such as the [[RecA]] protein in bacteria, the RadA protein in archaea, and the [[RAD51|Rad51]] and [[DMC1 (gene)|Dmc1]] proteins in eukaryota.<ref>Bernstein, H., Bernstein, C. (2017). Sexual Communication in Archaea, the Precursor to Eukaryotic Meiosis. In: Witzany, G. (eds) Biocommunication of Archaea. Springer, Cham. https://doi.org/10.1007/978-3-319-65536-9_7 {{Webarchive|url=https://web.archive.org/web/20240223213424/https://link.springer.com/chapter/10.1007/978-3-319-65536-9_7 |date=23 February 2024 }}</ref>
-The functionality of LUCA as well as evidence for the early evolution membrane-dependent biological systems together suggest that LUCA had cellularity and cell membranes.<ref>{{Cite journal |last1=Gogarten |first1=Johann Peter |last2=Taiz |first2=Lincoln |date=1992 |title=Evolution of proton pumping ATPases: Rooting the tree of life |url=http://dx.doi.org/10.1007/bf00039176 |journal=Photosynthesis Research |volume=33 |issue=2 |pages=137–146 |doi=10.1007/bf00039176 |issn=0166-8595}}</ref> As for the cell's gross structure, it contained a water-based [[cytoplasm]] effectively enclosed by a [[lipid bilayer]] membrane; it was capable of reproducing by cell division.<ref name="W19984">{{cite journal |last=Wächtershäuser |first=Günter |year=1998 |title=Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment |journal=Systematic and Applied Microbiology |volume=21 |issue=4 |pages=473–474, IN1, 475–477 |doi=10.1016/S0723-2020(98)80058-1}}</ref> It tended to exclude [[sodium]] and concentrate [[potassium]] by means of specific [[Ion transporter|ion transporters]] (or ion pumps). The cell multiplied by duplicating all its contents followed by [[cellular division]]. The cell used [[chemiosmosis]] to produce energy. It also [[Redox|reduced]] CO<sub>2</sub> and oxidized H<sub>2</sub> ([[methanogenesis]] or [[acetogenesis]]) via [[acetyl]]-[[Thioester|thioesters]].<ref>{{cite journal |last1=Martin |first1=W. |last2=Russell |first2=M. J. |date=October 2007 |title=On the origin of biochemistry at an alkaline hydrothermal vent |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=362 |issue=1486 |pages=1887–1925 |doi=10.1098/rstb.2006.1881 |pmc=2442388 |pmid=17255002}}</ref><ref>{{cite journal |last1=Lane |first1=Nick |author1-link=Nick Lane |last2=Allen |first2=J. F. |last3=Martin |first3=William |author3-link=William F. Martin |date=April 2010 |title=How did LUCA make a living? Chemiosmosis in the origin of life |journal=BioEssays |volume=32 |issue=4 |pages=271–280 |doi=10.1002/bies.200900131 |pmid=20108228}}</ref>
+The functionality of LUCA as well as evidence for the early evolution membrane-dependent biological systems together suggest that LUCA had cellularity and cell membranes.<ref>{{Cite journal |last1=Gogarten |first1=Johann Peter |last2=Taiz |first2=Lincoln |date=1992 |title=Evolution of proton pumping ATPases: Rooting the tree of life |url=http://dx.doi.org/10.1007/bf00039176 |journal=Photosynthesis Research |volume=33 |issue=2 |pages=137–146 |doi=10.1007/bf00039176 |pmid=24408574 |bibcode=1992PhoRe..33..137G |s2cid=20013957 |issn=0166-8595 |access-date=4 December 2023 |archive-date=23 February 2024 |archive-url=https://web.archive.org/web/20240223213452/https://link.springer.com/article/10.1007/BF00039176 |url-status=live }}</ref> As for the cell's gross structure, it contained a water-based [[cytoplasm]] effectively enclosed by a [[lipid bilayer]] membrane; it was capable of reproducing by cell division.<ref name="W19984">{{cite journal |last=Wächtershäuser |first=Günter |year=1998 |title=Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment |journal=Systematic and Applied Microbiology |volume=21 |issue=4 |pages=473–474, IN1, 475–477 |doi=10.1016/S0723-2020(98)80058-1|bibcode=1998SyApM..21N1475W }}</ref> It tended to exclude [[sodium]] and concentrate [[potassium]] by means of specific [[Ion transporter|ion transporters]] (or ion pumps). The cell multiplied by duplicating all its contents followed by [[cellular division]]. The cell used [[chemiosmosis]] to produce energy. It also [[Redox|reduced]] CO<sub>2</sub> and oxidized H<sub>2</sub> ([[methanogenesis]] or [[acetogenesis]]) via [[acetyl]]-[[Thioester|thioesters]].<ref>{{cite journal |last1=Martin |first1=W. |last2=Russell |first2=M. J. |date=October 2007 |title=On the origin of biochemistry at an alkaline hydrothermal vent |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=362 |issue=1486 |pages=1887–1925 |doi=10.1098/rstb.2006.1881 |pmc=2442388 |pmid=17255002}}</ref><ref>{{cite journal |last1=Lane |first1=Nick |author1-link=Nick Lane |last2=Allen |first2=J. F. |last3=Martin |first3=William |author3-link=William F. Martin |date=April 2010 |title=How did LUCA make a living? Chemiosmosis in the origin of life |journal=BioEssays |volume=32 |issue=4 |pages=271–280 |doi=10.1002/bies.200900131 |pmid=20108228}}</ref>
 By [[phylogenetic bracketing]], analysis of the presumed LUCA's offspring groups, LUCA appears to have been a small, single-celled organism. It likely had a ring-shaped coil of [[DNA]] floating freely within the cell. Morphologically, it would likely not have stood out within a mixed population of small modern-day bacteria. The originator of the [[three-domain system]], [[Carl Woese]], stated that in its genetic machinery, the LUCA would have been a "simpler, more rudimentary entity than the individual ancestors that spawned the three [domains] (and their descendants)".<ref name="Woese Kandler Wheelis 1990">{{cite journal |last1=Woese |first1=C.R. |author1-link=Carl Woese |last2=Kandler |first2=O. |author-link2=Otto Kandler |last3=Wheelis |first3=M.L. |author-link3=Mark Wheelis |date=June 1990 |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=PNAS |volume=87 |issue=12 |pages=4576–4579 |bibcode=1990PNAS...87.4576W |doi=10.1073/pnas.87.12.4576 |doi-access=free |pmc=54159 |pmid=2112744}}</ref>
@@ Line 61: / Line 61: @@
 An alternative to the search for "universal" traits is to use genome analysis to identify phylogenetically ancient genes. This gives a picture of a LUCA that could live in a geochemically harsh environment and is like modern prokaryotes. Analysis of biochemical pathways implies the same sort of chemistry as does phylogenetic analysis. Weiss and colleagues write that "Experiments ... demonstrate that ... [[Wood–Ljungdahl pathway|acetyl-CoA pathway]] [chemicals used in anaerobic respiration] [[formate]], [[methanol]], [[Acetyl group|acetyl]] moieties, and even [[pyruvate]] arise spontaneously ... from CO<sub>2</sub>, native metals, and water", a combination present in hydrothermal vents.<ref name="Weiss Preiner Xavier 20182">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Preiner |first2=Martina |last3=Xavier |first3=Joana C. |last4=Zimorski |first4=Verena |last5=Martin |first5=William F. |date=2018-08-16 |title=The last universal common ancestor between ancient Earth chemistry and the onset of genetics |journal=PLOS Genetics |volume=14 |issue=8 |pages=e1007518 |doi=10.1371/journal.pgen.1007518 |pmc=6095482 |pmid=30114187 |s2cid=52019935 |doi-access=free}}</ref>
-An experiment shows that Zn<sup>2+</sup>, Cr<sup>3+</sup>, and Fe can promote 6 of the 11 reactions of an ancient anabolic pathway called the [[reverse Krebs cycle]] in acidic conditions which implies that LUCA might have inhabited either hydrothermal vents or acidic metal-rich hydrothermal fields.<ref>{{Cite journal |last1=Muchowska |first1=Kamila B. |last2=Varma |first2=Sreejith J. |last3=Chevallot-Beroux |first3=Elodie |last4=Lethuillier-Karl |first4=Lucas |last5=Li |first5=Guang |last6=Moran |first6=Joseph |date=2 October 2017 |title=Metals promote sequences of the reverse Krebs cycle |url=https://www.researchgate.net/publication/320171263 |journal=Nature Ecology & Evolution |language=en |volume=1 |issue=11 |pages=1716–1721 |doi=10.1038/s41559-017-0311-7 |issn=2397-334X |pmc=5659384 |pmid=28970480}}</ref>
+An experiment shows that Zn<sup>2+</sup>, Cr<sup>3+</sup>, and Fe can promote 6 of the 11 reactions of an ancient anabolic pathway called the [[reverse Krebs cycle]] in acidic conditions which implies that LUCA might have inhabited either hydrothermal vents or acidic metal-rich hydrothermal fields.<ref>{{Cite journal |last1=Muchowska |first1=Kamila B. |last2=Varma |first2=Sreejith J. |last3=Chevallot-Beroux |first3=Elodie |last4=Lethuillier-Karl |first4=Lucas |last5=Li |first5=Guang |last6=Moran |first6=Joseph |date=2 October 2017 |title=Metals promote sequences of the reverse Krebs cycle |url=https://www.researchgate.net/publication/320171263 |journal=Nature Ecology & Evolution |volume=1 |issue=11 |pages=1716–1721 |doi=10.1038/s41559-017-0311-7 |issn=2397-334X |pmc=5659384 |pmid=28970480 |bibcode=2017NatEE...1.1716M }}</ref>
-Because both bacteria and archaea have differences in the structure of phospholipids and cell wall, ion pumping, most proteins involved in DNA replication, and glycolysis, it is inferred that LUCA had a permeable membrane without an ion pump. The emergence of Na<sup>+</sup>/H<sup>+</sup> antiporters likely lead to the evolution of impermeable membranes present in eukaryotes, archaea, and bacteria. It's stated that "The late and independent evolution of glycolysis but not gluconeogenesis is entirely consistent with LUCA being powered by natural proton gradients across leaky membranes. Several discordant traits are likely to be linked to the late evolution of cell membranes, notably the cell wall, whose synthesis depends on the membrane and DNA replication".<ref name="Sojo Pomiankowski Lane 20142">{{Cite journal |last1=Sojo |first1=Víctor |last2=Pomiankowski |first2=Andrew |last3=Lane |first3=Nick |date=2014-08-12 |title=A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria |journal=PLOS Biology |language=en |volume=12 |issue=8 |pages=e1001926 |doi=10.1371/journal.pbio.1001926 |issn=1545-7885 |pmc=4130499 |pmid=25116890 |doi-access=free}}</ref> Although LUCA likely had DNA, it is unknown if it could replicate DNA and is suggested to "might just have been a chemically stable repository for RNA-based replication".<ref name="Weiss Preiner Xavier 20183">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Preiner |first2=Martina |last3=Xavier |first3=Joana C. |last4=Zimorski |first4=Verena |last5=Martin |first5=William F. |date=2018-08-16 |title=The last universal common ancestor between ancient Earth chemistry and the onset of genetics |journal=PLOS Genetics |volume=14 |issue=8 |pages=e1007518 |doi=10.1371/journal.pgen.1007518 |pmc=6095482 |pmid=30114187 |s2cid=52019935 |doi-access=free}}</ref> It is likely that the permeable membrane of LUCA was composed of archaeal lipids ([[isoprenoids]]) and bacterial lipids ([[Fatty acid|fatty acids]]). Isoprenoids would have enhanced stabilization of LUCA's membrane in the surrounding extreme habitat. Nick Lane and coauthors state that "The advantages and disadvantages of incorporating isoprenoids into cell membranes in different microenvironments may have driven membrane divergence, with the later biosynthesis of phospholipids giving rise to the unique G1P and G3P headgroups of archaea and bacteria respectively. If so, the properties conferred by membrane isoprenoids place the lipid divide as early as the [[origin of life]]".<ref name="Jordan Nee Lane 20192">{{Cite journal |last1=Jordan |first1=S. F. |last2=Nee |first2=E. |last3=Lane |first3=Nick |author3-link=Nick Lane |date=18 October 2019 |title=Isoprenoids enhance the stability of fatty acid membranes at the emergence of life potentially leading to an early lipid divide |journal=Interface Focus |volume=9 |issue=6 |doi=10.1098/rsfs.2019.0067 |issn=2042-8901 |pmc=6802135 |pmid=31641436}}{{Creative Commons text attribution notice|cc=by4|from this source=yes}}</ref>
+Because both bacteria and archaea have differences in the structure of phospholipids and cell wall, ion pumping, most proteins involved in DNA replication, and glycolysis, it is inferred that LUCA had a permeable membrane without an ion pump. The emergence of Na<sup>+</sup>/H<sup>+</sup> antiporters likely lead to the evolution of impermeable membranes present in eukaryotes, archaea, and bacteria. It is stated that "The late and independent evolution of glycolysis but not gluconeogenesis is entirely consistent with LUCA being powered by natural proton gradients across leaky membranes. Several discordant traits are likely to be linked to the late evolution of cell membranes, notably the cell wall, whose synthesis depends on the membrane and DNA replication".<ref name="Sojo Pomiankowski Lane 20142">{{Cite journal |last1=Sojo |first1=Víctor |last2=Pomiankowski |first2=Andrew |last3=Lane |first3=Nick |author3-link=Nick Lane |date=2014-08-12 |title=A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria |journal=PLOS Biology |volume=12 |issue=8 |pages=e1001926 |doi=10.1371/journal.pbio.1001926 |pmc=4130499 |pmid=25116890 |doi-access=free}}</ref> Although LUCA likely had DNA, it is unknown if it could replicate DNA and is suggested to "might just have been a chemically stable repository for RNA-based replication".<ref name="Weiss Preiner Xavier 20183">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Preiner |first2=Martina |last3=Xavier |first3=Joana C. |last4=Zimorski |first4=Verena |last5=Martin |first5=William F. |date=2018-08-16 |title=The last universal common ancestor between ancient Earth chemistry and the onset of genetics |journal=PLOS Genetics |volume=14 |issue=8 |pages=e1007518 |doi=10.1371/journal.pgen.1007518 |pmc=6095482 |pmid=30114187 |s2cid=52019935 |doi-access=free}}</ref> It is likely that the permeable membrane of LUCA was composed of archaeal lipids ([[isoprenoids]]) and bacterial lipids ([[Fatty acid|fatty acids]]). Isoprenoids would have enhanced stabilization of LUCA's membrane in the surrounding extreme habitat. Nick Lane and coauthors state that "The advantages and disadvantages of incorporating isoprenoids into cell membranes in different microenvironments may have driven membrane divergence, with the later biosynthesis of phospholipids giving rise to the unique G1P and G3P headgroups of archaea and bacteria respectively. If so, the properties conferred by membrane isoprenoids place the lipid divide as early as the [[origin of life]]".<ref name="Jordan Nee Lane 20192">{{Cite journal |last1=Jordan |first1=S. F. |last2=Nee |first2=E. |last3=Lane |first3=Nick |author3-link=Nick Lane |date=18 October 2019 |title=Isoprenoids enhance the stability of fatty acid membranes at the emergence of life potentially leading to an early lipid divide |journal=Interface Focus |volume=9 |issue=6 |doi=10.1098/rsfs.2019.0067 |pmc=6802135 |pmid=31641436}}{{Creative Commons text attribution notice|cc=by4|from this source=yes}}</ref>
+A 2024 study suggests that LUCA's genome was similar in size to that of modern prokaryotes, coding for some 2,600 proteins; that it respired anaerobically, and was an [[acetogen]]; and that it had an early [[CRISPR|CAS]]-based anti-viral immune system.<ref name="Moody et al 2024"/>
-UV light between 200-280 nm (at the time, unprotected by the ozone layer) would have been damaging to nucleotides at the surface, as it can cause mutations or transcription errors and ultimately damaging consequences for organisms at the cellular level. However, it is likely that LUCA existed in a UV environment because of the prevalence of [[photolyase]] across the tree of life. Photolyase uses UV to drive photoreactivation, a that works to repair damage from radiation, caused by UV.
 === Alternative interpretations ===
-Some other researchers have challenged Weiss et al.'s 2016 conclusions. Sarah Berkemer and Shawn McGlynn argue that Weiss et al. undersampled the families of proteins, so that the phylogenetic trees were not complete and failed to describe the evolution of proteins correctly. There are two risk in attempting to attribute LUCA's environment from near-universal gene distribution (as in Weiss et al. 2016). On the one hand, it risks misattributing [[Convergent evolution|convergence]] or horizontal gene transfer events to vertical descent and, on the other hand, it risks misattributing potential LUCA gene families as horizontal gene transfer events.
+Some other researchers have challenged Weiss et al.'s 2016 conclusions. Sarah Berkemer and Shawn McGlynn argue that Weiss et al. undersampled the families of proteins, so that the phylogenetic trees were not complete and failed to describe the evolution of proteins correctly. There are two risks in attempting to attribute LUCA's environment from near-universal gene distribution (as in Weiss et al. 2016). On the one hand, it risks misattributing [[Convergent evolution|convergence]] or horizontal gene transfer events to vertical descent; on the other hand, it risks misattributing potential LUCA gene families as horizontal gene transfer events. A phylogenomic and geochemical analysis of a set of proteins that probably traced to the LUCA show that it had K<sup>+</sup>-dependent GTPases and the ionic composition and concentration of its intracellular fluid was seemingly high K<sup>+</sup>/Na<sup>+</sup> ratio, {{chem|NH|4|+}}, Fe<sup>2+</sup>, CO<sup>2+</sup>, Ni<sup>2+</sup>, Mg<sup>2+</sup>, Mn<sup>2+</sup>, Zn<sup>2+</sup>, pyrophosphate, and {{chem|PO|3-|4}} which would imply a terrestrial [[hot spring]] habitat. It possibly had a phosphate-based metabolism. Further, these proteins were unrelated to [[Autotroph|autotrophy]] (the ability of an organism to create its own [[organic matter]]), suggesting that the LUCA had a [[Heterotroph|heterotrophic]] lifestyle (consuming organic matter) and that its growth was dependent on organic matter produced by the physical environment.<ref>{{Cite journal |last1=Mulkidjanian |first1=Armen Y. |last2=Bychkov |first2=Andrew Yu |last3=Dibrova |first3=Daria V. |last4=Galperin |first4=Michael Y. |last5=Koonin |first5=Eugene V. |author5-link=Eugene V. Koonin |year=2012 |title=Origin of first cells at terrestrial, anoxic geothermal fields |journal=[[Proceedings of the National Academy of Sciences of the United States of America|Proceedings of the National Academy of Sciences]] |volume=109 |issue=14 |pages=E821-30 |bibcode=2012PNAS..109E.821M |doi=10.1073/pnas.1117774109 |pmc=3325685 |pmid=22331915 |doi-access=free}}</ref> [[Nick Lane]] argues that Na<sup>+</sup>/H<sup>+</sup> antiporters could readily explain the low concentration of Na<sup>+</sup> in the LUCA and its descendants.
-A phylogenomic and geochemical analysis of a set of proteins that probably traced to the LUCA show that it had K<sup>+</sup>-dependent GTPases and the ionic composition and concentration of its intracellular fluid was seemingly high K<sup>+</sup>/Na<sup>+</sup> ratio, {{chem|NH|4|+}}, Fe<sup>2+</sup>, CO<sup>2+</sup>, Ni<sup>2+</sup>, Mg<sup>2+</sup>, Mn<sup>2+</sup>, Zn<sup>2+</sup>, pyrophosphate, and {{chem|PO|3-|4}} which would imply a terrestrial [[hot spring]] habitat. It possibly had a phosphate-based metabolism. Further, these proteins were unrelated to [[Autotroph|autotrophy]] (the ability of an organism to create its own [[organic matter]]), suggesting that the LUCA had a [[Heterotroph|heterotrophic]] lifestyle (consuming organic matter) and that its growth was dependent on organic matter produced by the physical environment.<ref>{{Cite journal |last1=Mulkidjanian |first1=Armen Y. |last2=Bychkov |first2=Andrew Yu |last3=Dibrova |first3=Daria V. |last4=Galperin |first4=Michael Y. |last5=Koonin |first5=Eugene V. |author5-link=Eugene V. Koonin |year=2012 |title=Origin of first cells at terrestrial, anoxic geothermal fields |journal=[[Proceedings of the National Academy of Sciences of the United States of America|Proceedings of the National Academy of Sciences]] |volume=109 |issue=14 |pages=E821-30 |bibcode=2012PNAS..109E.821M |doi=10.1073/pnas.1117774109 |pmc=3325685 |pmid=22331915 |doi-access=free}}</ref> [[Nick Lane]] argues that Na<sup>+</sup>/H<sup>+</sup> antiporters could readily explain the low concentration of Na<sup>+</sup> in the LUCA and its descendants.
 The presence of the energy-handling enzymes [[CODH]]/[[Acetyl-CoA|acetyl-coenzyme A]] synthase in LUCA could be compatible not only with being an [[autotroph]] but also with life as a [[mixotroph]] or [[heterotroph]].<ref>{{cite journal |last1=Adam |first1=Panagiotis S. |last2=Borrel |first2=Guillaume |last3=Gribaldo |first3=Simonetta |date=6 February 2018 |title=Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes |journal=PNAS |volume=115 |issue=6 |pages=E1166–E1173 |bibcode=2018PNAS..115E1166A |doi=10.1073/pnas.1716667115 |pmc=5819426 |pmid=29358391 |doi-access=free}}</ref> Weiss et al. 2018 reply that no enzyme defines a trophic lifestyle, and that heterotrophs evolved from autotrophs.<ref name="Weiss Preiner Xavier 20184">{{cite journal |last1=Weiss |first1=Madeline C. |last2=Preiner |first2=Martina |last3=Xavier |first3=Joana C. |last4=Zimorski |first4=Verena |last5=Martin |first5=William F. |date=2018-08-16 |title=The last universal common ancestor between ancient Earth chemistry and the onset of genetics |journal=PLOS Genetics |volume=14 |issue=8 |pages=e1007518 |doi=10.1371/journal.pgen.1007518 |pmc=6095482 |pmid=30114187 |s2cid=52019935 |doi-access=free}}</ref>
-'''Evidence for a [[Mesophile|mesophilic]] LUCA'''
+==== Evidence that LUCA was mesophilic ====
 Several lines of evidence now suggest that LUCA was non-thermophilic.
-The content of G + C nucleotide pairs (compared to the occurrence of A + T pairs) can indicate an organism's thermal optimum as they are more thermally stable due to an additional hydrogen bond. As a result they occur more frequently in the rRNA of thermophiles; however this is not seen in LUCA's reconstructed rRNA.<ref>{{Cite journal |last1=Galtier |first1=Nicolas |last2=Tourasse |first2=Nicolas |last3=Gouy |first3=Manolo |date=1999-01-08 |title=A Nonhyperthermophilic Common Ancestor to Extant Life Forms |url=http://dx.doi.org/10.1126/science.283.5399.220 |journal=Science |volume=283 |issue=5399 |pages=220–221 |doi=10.1126/science.283.5399.220 |issn=0036-8075}}</ref><ref>{{Cite journal |last1=Groussin |first1=Mathieu |last2=Boussau |first2=Bastien |last3=Charles |first3=Sandrine |last4=Blanquart |first4=Samuel |last5=Gouy |first5=Manolo |date=2013-10-23 |title=The molecular signal for the adaptation to cold temperature during early life on Earth |url=http://dx.doi.org/10.1098/rsbl.2013.0608 |journal=Biology Letters |volume=9 |issue=5 |pages=20130608 |doi=10.1098/rsbl.2013.0608 |issn=1744-9561}}</ref><ref name=":22">{{Cite journal |last1=Cantine |first1=Marjorie D. |last2=Fournier |first2=Gregory P. |date=2017-07-06 |title=Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor |url=http://dx.doi.org/10.1007/s11084-017-9542-5 |journal=Origins of Life and Evolution of Biospheres |volume=48 |issue=1 |pages=35–54 |doi=10.1007/s11084-017-9542-5 |issn=0169-6149}}</ref>
+The content of G + C nucleotide pairs (compared to the occurrence of A + T pairs) can indicate an organism's thermal optimum as they are more thermally stable due to an additional hydrogen bond. As a result they occur more frequently in the rRNA of thermophiles; however this is not seen in LUCA's reconstructed rRNA.<ref>{{Cite journal |last1=Galtier |first1=Nicolas |last2=Tourasse |first2=Nicolas |last3=Gouy |first3=Manolo |date=1999-01-08 |title=A Nonhyperthermophilic Common Ancestor to Extant Life Forms |url=http://dx.doi.org/10.1126/science.283.5399.220 |journal=Science |volume=283 |issue=5399 |pages=220–221 |doi=10.1126/science.283.5399.220 |pmid=9880254 |issn=0036-8075 |access-date=4 December 2023 |archive-date=23 February 2024 |archive-url=https://web.archive.org/web/20240223213446/https://www.science.org/doi/10.1126/science.283.5399.220 |url-status=live }}</ref><ref>{{Cite journal |last1=Groussin |first1=Mathieu |last2=Boussau |first2=Bastien |last3=Charles |first3=Sandrine |last4=Blanquart |first4=Samuel |last5=Gouy |first5=Manolo |date=2013-10-23 |title=The molecular signal for the adaptation to cold temperature during early life on Earth |journal=Biology Letters |volume=9 |issue=5 |pages=20130608 |doi=10.1098/rsbl.2013.0608 |doi-access=free |pmid=24046876 |pmc=3971708 }}</ref><ref name="Cantine-2017">{{Cite journal |last1=Cantine |first1=Marjorie D. |last2=Fournier |first2=Gregory P. |date=2017-07-06 |title=Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor |url=http://dx.doi.org/10.1007/s11084-017-9542-5 |journal=Origins of Life and Evolution of Biospheres |volume=48 |issue=1 |pages=35–54 |doi=10.1007/s11084-017-9542-5 |pmid=28685374 |hdl=1721.1/114219 |s2cid=254888920 |hdl-access=free |access-date=4 December 2023 |archive-date=23 February 2024 |archive-url=https://web.archive.org/web/20240223213446/https://link.springer.com/article/10.1007/s11084-017-9542-5 |url-status=live }}</ref>
-The identification of thermophilic genes in the LUCA has been criticized,<ref name="GogartenDeamer20162">{{cite journal |last1=Gogarten |first1=Johann Peter |last2=Deamer |first2=David |year=2016 |title=Is LUCA a thermophilic progenote? |url=https://zenodo.org/record/895471 |journal=Nature Microbiology |volume=1 |issue=12 |pages=16229 |doi=10.1038/nmicrobiol.2016.229 |pmid=27886195 |s2cid=205428194}}</ref> as they may instead represent genes that evolved later in archaea or bacteria, then migrated between these via [[Horizontal gene transfer|horizontal gene transfers]], as in Woese's 1998 hypothesis.<ref name=":02">{{cite journal |last=Woese |first=Carl |author-link=Carl Woese |date=June 1998 |title=The universal ancestor |journal=PNAS |volume=95 |issue=12 |pages=6854–6859 |bibcode=1998PNAS...95.6854W |doi=10.1073/pnas.95.12.6854 |pmc=22660 |pmid=9618502 |doi-access=free}}</ref> LUCA could have been a mesophile that fixed CO<sub>2</sub> and relied on H<sub>2</sub>, and lived close to hydrothermal vents.<ref>{{Cite journal |last1=Camprubí |first1=E. |last2=de Leeuw |first2=J. W. |last3=House |first3=C. H. |last4=Raulin |first4=F. |last5=Russell |first5=M. J. |last6=Spang |first6=A. |last7=Tirumalai |first7=M. R. |last8=Westall |first8=F. |date=2019-12-12 |title=The Emergence of Life |journal=Space Science Reviews |volume=215 |issue=8 |pages=56 |bibcode=2019SSRv..215...56C |doi=10.1007/s11214-019-0624-8 |issn=1572-9672 |doi-access=free}}</ref>
+The identification of thermophilic genes in the LUCA has been criticized,<ref name="GogartenDeamer20162">{{cite journal |last1=Gogarten |first1=Johann Peter |last2=Deamer |first2=David |year=2016 |title=Is LUCA a thermophilic progenote? |url=https://zenodo.org/record/895471 |journal=Nature Microbiology |volume=1 |issue=12 |pages=16229 |doi=10.1038/nmicrobiol.2016.229 |pmid=27886195 |s2cid=205428194 |access-date=25 June 2019 |archive-date=3 April 2020 |archive-url=https://web.archive.org/web/20200403040656/https://zenodo.org/record/895471 |url-status=live }}</ref> as they may instead represent genes that evolved later in archaea or bacteria, then migrated between these via [[horizontal gene transfer]], as in Woese's 1998 hypothesis.<ref>{{cite journal |last=Woese |first=Carl |author-link=Carl Woese |date=June 1998 |title=The universal ancestor |journal=PNAS |volume=95 |issue=12 |pages=6854–6859 |bibcode=1998PNAS...95.6854W |doi=10.1073/pnas.95.12.6854 |pmc=22660 |pmid=9618502 |doi-access=free}}</ref> LUCA could have been a mesophile that fixed CO<sub>2</sub> and relied on H<sub>2</sub>, and lived close to hydrothermal vents.<ref>{{Cite journal |last1=Camprubí |first1=E. |last2=de Leeuw |first2=J. W. |last3=House |first3=C. H. |last4=Raulin |first4=F. |last5=Russell |first5=M. J. |last6=Spang |first6=A. |last7=Tirumalai |first7=M. R. |last8=Westall |first8=F. |date=2019-12-12 |title=The Emergence of Life |journal=Space Science Reviews |volume=215 |issue=8 |pages=56 |bibcode=2019SSRv..215...56C |doi=10.1007/s11214-019-0624-8 |issn=1572-9672 |doi-access=free}}</ref>
-Further evidence of a mesophilic LUCA comes from the amino acid composition of its proteins. The abundance of I, V, Y, W, R, E, and L amino acids (denoted IVYWREL) in an organism's proteins is correlated with its optimal growth temperature.<ref>{{Cite journal |last1=Zeldovich |first1=Konstantin B |last2=Berezovsky |first2=Igor N |last3=Shakhnovich |first3=Eugene I |date=2007 |title=Protein and DNA Sequence Determinants of Thermophilic Adaptation |journal=PLOS Computational Biology |volume=3 |issue=1 |pages=e5 |doi=10.1371/journal.pcbi.0030005 |issn=1553-7358 |doi-access=free }}</ref> According to phylogentic analysis, the IVYWREL content of LUCA's proteins suggests its ideal temperature was below 50°C.<ref name=":22" />
+Further evidence that LUCA was [[Mesophile|mesophilic]] comes from the amino acid composition of its proteins. The abundance of I, V, Y, W, R, E, and L amino acids (denoted IVYWREL) in an organism's proteins is correlated with its optimal growth temperature.<ref>{{Cite journal |last1=Zeldovich |first1=Konstantin B |last2=Berezovsky |first2=Igor N |last3=Shakhnovich |first3=Eugene I |date=2007 |title=Protein and DNA Sequence Determinants of Thermophilic Adaptation |journal=PLOS Computational Biology |volume=3 |issue=1 |pages=e5 |doi=10.1371/journal.pcbi.0030005 |pmid=17222055 |pmc=1769408 |arxiv=q-bio/0607004 |bibcode=2007PLSCB...3....5Z |issn=1553-7358 |doi-access=free }}</ref> According to phylogentic analysis, the IVYWREL content of LUCA's proteins suggests its ideal temperature was below 50°C.<ref name="Cantine-2017"/>
-Finally, evidence that bacteria and archaea both independently underwent phases of increased and subsequently decreased thermo-tolerance suggests a dramatic post-LUCA climate shift that affected both populations and would explain the seeming genetic pervasiveness of thermo-tolerant genetics.<ref>{{Cite journal |last1=Boussau |first1=Bastien |last2=Blanquart |first2=Samuel |last3=Necsulea |first3=Anamaria |last4=Lartillot |first4=Nicolas |last5=Gouy |first5=Manolo |date=2008-11-26 |title=Parallel adaptations to high temperatures in the Archaean eon |url=http://dx.doi.org/10.1038/nature07393 |journal=Nature |volume=456 |issue=7224 |pages=942–945 |doi=10.1038/nature07393 |issn=0028-0836}}</ref>
+Finally, evidence that bacteria and archaea both independently underwent phases of increased and subsequently decreased thermo-tolerance suggests a dramatic post-LUCA climate shift that affected both populations and would explain the seeming genetic pervasiveness of thermo-tolerant genetics.<ref>{{Cite journal |last1=Boussau |first1=Bastien |last2=Blanquart |first2=Samuel |last3=Necsulea |first3=Anamaria |last4=Lartillot |first4=Nicolas |last5=Gouy |first5=Manolo |date=2008-11-26 |title=Parallel adaptations to high temperatures in the Archaean eon |url=http://dx.doi.org/10.1038/nature07393 |journal=Nature |volume=456 |issue=7224 |pages=942–945 |doi=10.1038/nature07393 |pmid=19037246 |bibcode=2008Natur.456..942B |s2cid=4348746 |access-date=4 December 2023 |archive-date=23 February 2024 |archive-url=https://web.archive.org/web/20240223213509/https://www.nature.com/articles/nature07393 |url-status=live }}</ref>
 == Age ==
@@ Line 91: / Line 89: @@
 {{further|Abiogenesis}}
-Studies from 2000 to 2018 have suggested an increasingly ancient time for the LUCA. In 2000, estimates of the LUCA's age ranged from 3.5 to 3.8 billion years ago in the [[Paleoarchean]],<ref>{{cite journal |last=Doolittle |first=W. F. |date=February 2000 |title=Uprooting the tree of life |journal=[[Scientific American]] |volume=282 |issue=2 |pages=90–95 |bibcode=2000SciAm.282b..90D |pmid=10710791 |doi=10.1038/scientificamerican0200-90|jstor=26058605 }}</ref> a few hundred million years before the [[Earliest known life forms|earliest fossil evidence of life]], for which candidates range in age from 3.48 to 4.28 billion years ago.<ref name="AST-20131108">{{cite journal |last1=Noffke |first1=N. |author1-link=Nora Noffke |last2=Christian |first2=D. |last3=Wacey |first3=D. |last4=Hazen |first4=R. M. |date=December 2013 |title=Microbially induced sedimentary structures recording an ancient ecosystem in the ca. 3.48 billion-year-old Dresser Formation, Pilbara, Western Australia |journal=Astrobiology |volume=13 |issue=12 |pages=1103–1124 |bibcode=2013AsBio..13.1103N |pmc=3870916 |pmid=24205812 |doi=10.1089/ast.2013.1030}}</ref><ref name="NG-20131208">{{cite journal |last1=Ohtomo |first1=Yoko |last2=Kakegawa |first2=Takeshi |last3=Ishida |first3=Akizumi |last4=Nagase |first4=Toshiro |last5=Rosing |first5=Minik T. |year=2013 |title=Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks |journal=Nature Geoscience |volume=7 |issue=1 |pages=25–28 |bibcode=2014NatGe...7...25O |doi=10.1038/ngeo2025}}</ref><ref>{{Cite journal |last1=Hassenkam |first1=T. |last2=Andersson |first2=M. P. |last3=Dalby |first3=K. N. |last4=Mackenzie |first4=D. M. A. |last5=Rosing |first5=M. T. |display-authors=3 |s2cid=205257931 |year=2017 |title=Elements of Eoarchean life trapped in mineral inclusions |journal=Nature |volume=548 |issue=7665 |pages=78–81 |bibcode=2017Natur.548...78H |pmid=28738409 |doi=10.1038/nature23261}}</ref><ref>{{Cite journal |last1=Bell |first1=Elizabeth A. |last2=Boehnke |first2=Patrick |last3=Harrison |first3=T. Mark |last4=Mao |first4=Wendy L. |author-link4=Wendy Mao |date=24 November 2015 |title=Potentially biogenic carbon preserved in a 4.1&nbsp;billion-year-old zircon |journal=PNAS |volume=112 |issue=47 |pages=14518–14521 |bibcode=2015PNAS..11214518B |doi=10.1073/pnas.1517557112 |pmc=4664351 |pmid=26483481|doi-access=free }}</ref><ref>{{cite journal |last1=Dodd |first1=Matthew S. |last2=Papineau |first2=Dominic |last3=Grenne |first3=Tor |author4=Slack, John F. |author5=Rittner, Martin |author6=Pirajno, Franco |author7=O'Neil, Jonathan |author8=Little, Crispin T. S. |display-authors=3 |s2cid=2420384 |date=2 March 2017 |title=Evidence for early life in Earth's oldest hydrothermal vent precipitates |journal=Nature |volume=543 |issue=7643 |pages=60–64 |bibcode=2017Natur.543...60D |doi=10.1038/nature21377 |pmid=28252057 |url=http://eprints.whiterose.ac.uk/112179/1/ppnature21377_Dodd_for%20Symplectic.pdf |access-date=25 June 2019 |archive-url=https://web.archive.org/web/20180723232142/http://eprints.whiterose.ac.uk/112179/1/ppnature21377_Dodd_for%20Symplectic.pdf |archive-date=23 July 2018 |url-status=live|doi-access=free }}</ref> This placed the origin of the first forms of life shortly after the [[Late Heavy Bombardment]] which was thought to have repeatedly sterilized Earth's surface. However, a 2018 study by Holly Betts and colleagues applied a [[molecular clock]] model to the genomic and fossil record (102 species, 29 common protein-coding genes, mostly ribosomal), concluding that LUCA preceded the Late Heavy Bombardment. They assumed that there was no sterilizing event after the [[Giant-impact hypothesis|Moon-forming event]], which they dated as 4.520 billion years ago, and concluded that the most likely date for LUCA was within 50 million years of that.<ref name="Betts Puttick Clark 2018">{{cite journal |last1=Betts |first1=Holly C. |last2=Puttick |first2=Mark N. |last3=Clark |first3=James W. |last4=Williams |first4=Tom A. |last5=Donoghue |first5=Philip C. J. |last6=Pisani |first6=Davide |title=Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin |journal=Nature Ecology & Evolution |year=2018 |volume=2 |issue=10 |pages=1556–1562 |doi=10.1038/s41559-018-0644-x |pmid=30127539 |pmc=6152910}}</ref>
+Studies from 2000 to 2018 have suggested an increasingly ancient time for the LUCA. In 2000, estimates of the LUCA's age ranged from 3.5 to 3.8 billion years ago in the [[Paleoarchean]],<ref>{{cite journal |last=Doolittle |first=W. F. |date=February 2000 |title=Uprooting the tree of life |journal=[[Scientific American]] |volume=282 |issue=2 |pages=90–95 |bibcode=2000SciAm.282b..90D |pmid=10710791 |doi=10.1038/scientificamerican0200-90|jstor=26058605 }}</ref> a few hundred million years before the [[Earliest known life forms|earliest fossil evidence of life]], for which candidates range in age from 3.48 to 4.28 billion years ago.<ref name="AST-20131108">{{cite journal |last1=Noffke |first1=N. |author1-link=Nora Noffke |last2=Christian |first2=D. |last3=Wacey |first3=D. |last4=Hazen |first4=R. M. |date=December 2013 |title=Microbially induced sedimentary structures recording an ancient ecosystem in the ca. 3.48 billion-year-old Dresser Formation, Pilbara, Western Australia |journal=Astrobiology |volume=13 |issue=12 |pages=1103–1124 |bibcode=2013AsBio..13.1103N |pmc=3870916 |pmid=24205812 |doi=10.1089/ast.2013.1030}}</ref><ref name="NG-20131208">{{cite journal |last1=Ohtomo |first1=Yoko |last2=Kakegawa |first2=Takeshi |last3=Ishida |first3=Akizumi |last4=Nagase |first4=Toshiro |last5=Rosing |first5=Minik T. |year=2013 |title=Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks |journal=Nature Geoscience |volume=7 |issue=1 |pages=25–28 |bibcode=2014NatGe...7...25O |doi=10.1038/ngeo2025}}</ref><ref>{{Cite journal |last1=Hassenkam |first1=T. |last2=Andersson |first2=M. P. |last3=Dalby |first3=K. N. |last4=Mackenzie |first4=D. M. A. |last5=Rosing |first5=M. T. |display-authors=3 |s2cid=205257931 |year=2017 |title=Elements of Eoarchean life trapped in mineral inclusions |journal=Nature |volume=548 |issue=7665 |pages=78–81 |bibcode=2017Natur.548...78H |pmid=28738409 |doi=10.1038/nature23261}}</ref><ref>{{Cite journal |last1=Bell |first1=Elizabeth A. |last2=Boehnke |first2=Patrick |last3=Harrison |first3=T. Mark |last4=Mao |first4=Wendy L. |author-link4=Wendy Mao |date=24 November 2015 |title=Potentially biogenic carbon preserved in a 4.1&nbsp;billion-year-old zircon |journal=PNAS |volume=112 |issue=47 |pages=14518–14521 |bibcode=2015PNAS..11214518B |doi=10.1073/pnas.1517557112 |pmc=4664351 |pmid=26483481|doi-access=free }}</ref><ref>{{cite journal |last1=Dodd |first1=Matthew S. |last2=Papineau |first2=Dominic |last3=Grenne |first3=Tor |author4=Slack, John F. |author5=Rittner, Martin |author6=Pirajno, Franco |author7=O'Neil, Jonathan |author8=Little, Crispin T. S. |display-authors=3 |s2cid=2420384 |date=2 March 2017 |title=Evidence for early life in Earth's oldest hydrothermal vent precipitates |journal=Nature |volume=543 |issue=7643 |pages=60–64 |bibcode=2017Natur.543...60D |doi=10.1038/nature21377 |pmid=28252057 |url=http://eprints.whiterose.ac.uk/112179/1/ppnature21377_Dodd_for%20Symplectic.pdf |access-date=25 June 2019 |archive-url=https://web.archive.org/web/20180723232142/http://eprints.whiterose.ac.uk/112179/1/ppnature21377_Dodd_for%20Symplectic.pdf |archive-date=23 July 2018 |url-status=live|doi-access=free }}</ref> This placed the origin of the first forms of life shortly after the [[Late Heavy Bombardment]] which was thought to have repeatedly sterilized Earth's surface. However, a 2018 study by Holly Betts and colleagues applied a [[molecular clock]] model to the genomic and fossil record (102 species, 29 common protein-coding genes, mostly ribosomal), concluding that LUCA preceded the Late Heavy Bombardment (making the LUCA over 3.9 billion years ago). They assumed that there was no sterilizing event after the [[Giant-impact hypothesis|Moon-forming event]], which they dated as 4.520 billion years ago, and concluded that the most likely date for LUCA was within 50 million years of that.<ref name="Betts Puttick Clark 2018">{{cite journal |last1=Betts |first1=Holly C. |last2=Puttick |first2=Mark N. |last3=Clark |first3=James W. |last4=Williams |first4=Tom A. |last5=Donoghue |first5=Philip C. J. |last6=Pisani |first6=Davide |title=Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin |journal=Nature Ecology & Evolution |year=2018 |volume=2 |issue=10 |pages=1556–1562 |doi=10.1038/s41559-018-0644-x |pmid=30127539 |pmc=6152910|bibcode=2018NatEE...2.1556B }}</ref> A 2022 study suggested an age of around 3.6-4.2 billion years for the LUCA.<ref>{{Cite journal |last1=Moody |first1=Edmund RR |last2=Mahendrarajah |first2=Tara A. |last3=Dombrowski |first3=Nina |last4=Clark |first4=James W. |last5=Petitjean |first5=Celine |last6=Offre |first6=Pierre |last7=Szöllősi |first7=Gergely J. |last8=Spang |first8=Anja |last9=Williams |first9=Tom A. |date=2022-02-22 |title=An estimate of the deepest branches of the tree of life from ancient vertically evolving genes |journal=eLife |language=en |volume=11 |doi=10.7554/eLife.66695 |doi-access=free |issn=2050-084X |pmc=8890751 |pmid=35190025}}</ref> A 2024 study suggested that the LUCA lived around 4.2 billion years ago (with a confidence interval of 4.09–4.33 billion years ago).<ref name="Moody et al 2024">{{Cite journal |last1=Moody |first1=Edmund R. R. |last2=Álvarez-Carretero |first2=Sandra |last3=Mahendrarajah |first3=Tara A. |last4=Clark |first4=James W. |last5=Betts |first5=Holly C. |last6=Dombrowski |first6=Nina |last7=Szánthó |first7=Lénárd L. |last8=Boyle |first8=Richard A. |last9=Daines |first9=Stuart |last10=Chen |first10=Xi |last11=Lane |first11=Nick |author11-link=Nick Lane |last12=Yang |first12=Ziheng |last13=Shields |first13=Graham A. |last14=Szöllősi |first14=Gergely J. |last15=Spang |first15=Anja |date=12 July 2024 |title=The nature of the last universal common ancestor and its impact on the early Earth system |url=https://www.nature.com/articles/s41559-024-02461-1 |journal=Nature Ecology & Evolution|pages=1–13 |doi=10.1038/s41559-024-02461-1 |issn=2397-334X|doi-access=free }}</ref>
 == Root of the tree of life ==
@@ Line 99: / Line 97: @@
 {{for|branching of bacteria phyla|Bacterial phyla}}
-In 1990, a novel concept of the [[Tree of life (biology)|tree of life]] was presented, dividing the living world into three stems, classified as the domains [[Bacteria]], [[Archaea]], [[Eukarya]].<ref name="Woese Kandler Wheelis 1990" /><ref name="Sapp2009">{{Cite book |last=Sapp |first=Jan A. |url=https://books.google.com/books?id=d7zOviXnbSYC |title=The new foundations of evolution: on the tree of life |publisher=Oxford University Press |year=2009 |isbn=978-0-199-73438-2 |location=New York |pages=Chapter 19: 257ff (novel concept of the tree of life); Chapters 17-21 plus concluding remarks: 226-318 (discussion of the tree and its rooting); 286ff (LUCA) |author-link=Jan Sapp}}</ref><ref name="Brock_2015">{{Cite book |last1=Madigan |first1=Michael T. |title=Brock Biology of Microorganisms |last2=Martinko |first2=John M. |last3=Bender |first3=Kelly S. |last4=Buckley |first4=Daniel H. |last5=Stahl |first5=David A. |publisher=Pearson Education Limited |year=2015 |isbn=978-1-292-01831-7 |edition=14 |location=Boston |pages=29; 374; 381}}</ref><ref name="Brock_2022">{{Cite book |last1=Madigan |first1=Michael T. |title=Brock Biology of Microorganisms |last2=Aiyer |first2=Jennifer |last3=Buckley |first3=Daniel H. |last4=Sattley |first4=Matthew |last5=Stahl |first5=David A. |publisher=Pearson Education |year=2022 |isbn=978-1-292-40479-0 |edition=16 |location=Harlow |pages=Unit 3, chapter 13: 431 (LUCA); 435 (tree of life); 428, 438, 439 (viruses)}}</ref> It is the first tree founded exclusively on molecular phylogenetics, and which includes the evolution of microorganisms. It has been called a "universal phylogenetic tree in rooted form".<ref name="Woese Kandler Wheelis 1990"/> This tree and its rooting became the subject of debate.<ref name="Sapp2009"/>{{efn|One debate dealt with a former [[Cladistics|cladistic]] hypothesis: The tree could not be ascribed a root in the usual algorithmic way, because that would require an [[Outgroup (cladistics)|outgroup]] for reference. In the case of the universal tree, no outgroup would exist.
+In 1990, a novel concept of the [[Tree of life (biology)|tree of life]] was presented, dividing the living world into three stems, classified as the domains [[Bacteria]], [[Archaea]], [[Eukarya]].<ref name="Woese Kandler Wheelis 1990" /><ref name="Sapp2009">{{Cite book |last=Sapp |first=Jan A. |url=https://books.google.com/books?id=d7zOviXnbSYC |title=The new foundations of evolution: on the tree of life |publisher=Oxford University Press |year=2009 |isbn=978-0-199-73438-2 |location=New York |pages=Chapter 19: 257ff (novel concept of the tree of life); Chapters 17-21 plus concluding remarks: 226-318 (discussion of the tree and its rooting); 286ff (LUCA) |author-link=Jan Sapp |access-date=21 November 2023 |archive-date=6 November 2023 |archive-url=https://web.archive.org/web/20231106185704/https://books.google.com/books?id=d7zOviXnbSYC |url-status=live }}</ref><ref name="Brock_2015">{{Cite book |last1=Madigan |first1=Michael T. |title=Brock Biology of Microorganisms |last2=Martinko |first2=John M. |last3=Bender |first3=Kelly S. |last4=Buckley |first4=Daniel H. |last5=Stahl |first5=David A. |publisher=Pearson Education Limited |year=2015 |isbn=978-1-292-01831-7 |edition=14 |location=Boston |pages=29; 374; 381}}</ref><ref name="Brock_2022">{{Cite book |last1=Madigan |first1=Michael T. |title=Brock Biology of Microorganisms |last2=Aiyer |first2=Jennifer |last3=Buckley |first3=Daniel H. |last4=Sattley |first4=Matthew |last5=Stahl |first5=David A. |publisher=Pearson Education |year=2022 |isbn=978-1-292-40479-0 |edition=16 |location=Harlow |pages=Unit 3, chapter 13: 431 (LUCA); 435 (tree of life); 428, 438, 439 (viruses)}}</ref> It is the first tree founded exclusively on molecular phylogenetics, and which includes the evolution of microorganisms. It has been called a "universal phylogenetic tree in rooted form".<ref name="Woese Kandler Wheelis 1990"/> This tree and its rooting became the subject of debate.<ref name="Sapp2009"/>{{efn|One debate dealt with a former [[Cladistics|cladistic]] hypothesis: The tree could not be ascribed a root in the usual algorithmic way, because that would require an [[Outgroup (cladistics)|outgroup]] for reference. In the case of the universal tree, no outgroup would exist.
 The cladistic method was used "to root the purple bacteria, for example. But establishing a root for the universal tree of life, the branching order among the primary urkingdoms, was another matter entirely."{{sfn|Sapp|2009|p=255}} }}
-In the meantime, numerous modifications of this tree, mainly concerning the role and importance of horizontal gene transfer for its rooting and early ramifications have been suggested (e.g.<ref name="Brown Doolittle 1995" /><ref name="Smets Barkay 2005" />). Since heredity occurs both vertically and horizontally, the tree of life may have been more weblike or netlike in its early phase and more treelike when it grew three-stemmed.<ref name="Smets Barkay 2005" /> Presumably horizontal gene transfer has decreased with growing cell stability.<ref name="Harold_2014">{{Cite book |last=Harold |first=Franklin M. |url=https://books.google.com/books?id=XjOOBAAAQBAJ&q=In+Search+of+Cell+History |title=In Search of Cell History: The Evolution of Life's Building Blocks |publisher=University of Chicago Press |year=2014 |isbn=978-0-226-17428-0 |location=Chicago, London}}</ref>
+In the meantime, numerous modifications of this tree, mainly concerning the role and importance of horizontal gene transfer for its rooting and early ramifications have been suggested (e.g.<ref name="Brown Doolittle 1995" /><ref name="Smets Barkay 2005" />). Since heredity occurs both vertically and horizontally, the tree of life may have been more weblike or netlike in its early phase and more treelike when it grew three-stemmed.<ref name="Smets Barkay 2005" /> Presumably horizontal gene transfer has decreased with growing cell stability.<ref name="Harold_2014">{{Cite book |last=Harold |first=Franklin M. |url=https://books.google.com/books?id=XjOOBAAAQBAJ&q=In+Search+of+Cell+History |title=In Search of Cell History: The Evolution of Life's Building Blocks |publisher=University of Chicago Press |year=2014 |isbn=978-0-226-17428-0 |location=Chicago, London |access-date=12 October 2023 |archive-date=31 October 2023 |archive-url=https://web.archive.org/web/20231031202816/https://books.google.com/books?id=XjOOBAAAQBAJ&q=In+Search+of+Cell+History |url-status=live }}</ref>
-A modified version of the tree, based on several molecular studies, has its root between a [[monophyletic]] [[domain (biology)|domain]] [[Bacteria]] and a [[clade]] formed by [[Archaea]] and [[Eukaryota]].<ref name="Brown Doolittle 1995">{{cite journal |last1=Brown |first1=J. R. |last2=Doolittle |first2=W. F. |year=1995 |title=Root of the Universal Tree of Life Based on Ancient Aminoacyl-tRNA Synthetase Gene Duplications |journal=PNAS |volume=92 |issue=7 |pages=2441–2445 |pmid=7708661 |pmc=42233 |doi=10.1073/pnas.92.7.2441 |bibcode=1995PNAS...92.2441B |doi-access=free }}</ref> A small minority of studies place the root in the domain bacteria, in the phylum [[Bacillota]],<ref>{{cite journal |last1=Valas |first1=R. E. |last2=Bourne |first2=P. E. |title=The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon |journal=Biology Direct |volume=6 |page=16 |year=2011 |pmid=21356104 |pmc=3056875 |doi=10.1186/1745-6150-6-16 |doi-access=free }}</ref> or state that the phylum [[Chloroflexota]] (formerly Chloroflexi) is [[Basal (phylogenetics)|basal]] to a clade with Archaea and Eukaryotes and the rest of bacteria (as proposed by [[Thomas Cavalier-Smith]]).<ref name="CS2">{{cite journal |last=Cavalier-Smith |first=Tom |author-link=Tom Cavalier-Smith |title=Rooting the tree of life by transition analyses |journal=Biology Direct |volume=1 |page=19 |year=2006 |pmid=16834776 |pmc=1586193 |doi=10.1186/1745-6150-1-19 |doi-access=free }}</ref> [[Metagenomics|Metagenomic]] analyses recover a two-domain system with the domains Archaea and Bacteria; in this view of the tree of life, Eukaryotes are derived from Archaea.<ref>{{Cite journal |last1=Raymann |first1=Kasie |last2=Brochier-Armanet |first2=Céline |last3=Gribaldo |first3=Simonetta |date=2015-05-26 |title=The two-domain tree of life is linked to a new root for the Archaea |journal=Proceedings of the National Academy of Sciences |volume=112 |issue=21 |pages=6670–6675 |doi=10.1073/pnas.1420858112 |issn=0027-8424 |pmc=4450401 |pmid=25964353|bibcode=2015PNAS..112.6670R |doi-access=free }}</ref><ref>{{Cite journal |last1=Hug |first1=Laura A. |last2=Baker |first2=Brett J. |last3=Anantharaman |first3=Karthik |last4=Brown |first4=Christopher T. |last5=Probst |first5=Alexander J. |last6=Castelle |first6=Cindy J. |last7=Butterfield |first7=Cristina N. |last8=Hernsdorf |first8=Alex W. |last9=Amano |first9=Yuki |last10=Ise |first10=Kotaro |last11=Suzuki |first11=Yohey |last12=Dudek |first12=Natasha |last13=Relman |first13=David A. |last14=Finstad |first14=Kari M. |last15=Amundson |first15=Ronald |display-authors=3 |date=2016-04-11 |title=A new view of the tree of life |journal=Nature Microbiology |volume=1 |issue=5 |page=16048 |doi=10.1038/nmicrobiol.2016.48 |pmid=27572647 |s2cid=3833474 |issn=2058-5276|doi-access=free }}</ref><ref>{{Cite journal |last1=Williams |first1=Tom A. |last2=Foster |first2=Peter G. |last3=Cox |first3=Cymon J. |last4=Embley |first4=T. Martin |date=December 11, 2013 |title=An archaeal origin of eukaryotes supports only two primary domains of life |url=https://www.nature.com/articles/nature12779 |journal=Nature |volume=504 |issue=7479 |pages=231–236 |doi=10.1038/nature12779 |pmid=24336283 |bibcode=2013Natur.504..231W |s2cid=4461775 |issn=1476-4687}}</ref> With the later gene pool of LUCA's descendants, sharing a common framework of the [[Chargaff's rules|AT/GC rule]] and the standard twenty amino acids, horizontal gene transfer would have become feasible and could have been common.<ref name="Harris Hill 2021"/>
+A modified version of the tree, based on several molecular studies, has its root between a [[monophyletic]] [[domain (biology)|domain]] [[Bacteria]] and a [[clade]] formed by [[Archaea]] and [[Eukaryota]].<ref name="Brown Doolittle 1995">{{cite journal |last1=Brown |first1=J. R. |last2=Doolittle |first2=W. F. |year=1995 |title=Root of the Universal Tree of Life Based on Ancient Aminoacyl-tRNA Synthetase Gene Duplications |journal=PNAS |volume=92 |issue=7 |pages=2441–2445 |pmid=7708661 |pmc=42233 |doi=10.1073/pnas.92.7.2441 |bibcode=1995PNAS...92.2441B |doi-access=free }}</ref> A small minority of studies place the root in the domain bacteria, in the phylum [[Bacillota]],<ref>{{cite journal |last1=Valas |first1=R. E. |last2=Bourne |first2=P. E. |title=The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon |journal=Biology Direct |volume=6 |page=16 |year=2011 |pmid=21356104 |pmc=3056875 |doi=10.1186/1745-6150-6-16 |doi-access=free }}</ref> or state that the phylum [[Chloroflexota]] (formerly Chloroflexi) is [[Basal (phylogenetics)|basal]] to a clade with Archaea and Eukaryotes and the rest of bacteria (as proposed by [[Thomas Cavalier-Smith]]).<ref name="CS2">{{cite journal |last=Cavalier-Smith |first=Tom |author-link=Tom Cavalier-Smith |title=Rooting the tree of life by transition analyses |journal=Biology Direct |volume=1 |page=19 |year=2006 |pmid=16834776 |pmc=1586193 |doi=10.1186/1745-6150-1-19 |doi-access=free }}</ref> [[Metagenomics|Metagenomic]] analyses recover a two-domain system with the domains Archaea and Bacteria; in this view of the tree of life, Eukaryotes are derived from Archaea.<ref>{{Cite journal |last1=Raymann |first1=Kasie |last2=Brochier-Armanet |first2=Céline |last3=Gribaldo |first3=Simonetta |date=2015-05-26 |title=The two-domain tree of life is linked to a new root for the Archaea |journal=Proceedings of the National Academy of Sciences |volume=112 |issue=21 |pages=6670–6675 |doi=10.1073/pnas.1420858112 |issn=0027-8424 |pmc=4450401 |pmid=25964353|bibcode=2015PNAS..112.6670R |doi-access=free }}</ref><ref>{{Cite journal |last1=Hug |first1=Laura A. |last2=Baker |first2=Brett J. |last3=Anantharaman |first3=Karthik |last4=Brown |first4=Christopher T. |last5=Probst |first5=Alexander J. |last6=Castelle |first6=Cindy J. |last7=Butterfield |first7=Cristina N. |last8=Hernsdorf |first8=Alex W. |last9=Amano |first9=Yuki |last10=Ise |first10=Kotaro |last11=Suzuki |first11=Yohey |last12=Dudek |first12=Natasha |last13=Relman |first13=David A. |last14=Finstad |first14=Kari M. |last15=Amundson |first15=Ronald |display-authors=3 |date=2016-04-11 |title=A new view of the tree of life |journal=Nature Microbiology |volume=1 |issue=5 |page=16048 |doi=10.1038/nmicrobiol.2016.48 |pmid=27572647 |s2cid=3833474 |issn=2058-5276|doi-access=free }}</ref><ref>{{Cite journal |last1=Williams |first1=Tom A. |last2=Foster |first2=Peter G. |last3=Cox |first3=Cymon J. |last4=Embley |first4=T. Martin |date=December 11, 2013 |title=An archaeal origin of eukaryotes supports only two primary domains of life |url=https://www.nature.com/articles/nature12779 |journal=Nature |volume=504 |issue=7479 |pages=231–236 |doi=10.1038/nature12779 |pmid=24336283 |bibcode=2013Natur.504..231W |s2cid=4461775 |issn=1476-4687 |access-date=23 September 2022 |archive-date=1 October 2022 |archive-url=https://web.archive.org/web/20221001043017/https://www.nature.com/articles/nature12779 |url-status=live }}</ref> With the later gene pool of LUCA's descendants, sharing a common framework of the [[Chargaff's rules|AT/GC rule]] and the standard twenty amino acids, horizontal gene transfer would have become feasible and could have been common.<ref name="Harris Hill 2021"/>
-The nature of LUCA remains disputed. In 1994, on the basis of primordial metabolism (sensu [[Günter Wächtershäuser|Wächtershäuser]]), [[Otto Kandler]] proposed a successive divergence of the three domains of life<ref name="Woese Kandler Wheelis 1990"/> from a multiphenotypical ''population'' of [[Pre-cell|pre-cells]], reached by gradual evolutionary improvements ([[cellularization]]).<ref name="Kandler_1994">{{Cite book |last=Kandler |first=Otto |title=Early Life on Earth. Nobel Symposium 84 |date=1994 |publisher=Columbia U.P. |editor=Stefan Bengtson |location=New York |pages=152–160 |chapter=The early diversification of life |author-link=Otto Kandler }}</ref><ref name="Kandler_1995">{{cite journal|last=Kandler|first=Otto|title=Cell Wall Biochemistry in Archaea and its Phylogenetic Implications|journal=Journal of Biological Physics|volume=20 |issue=1–4|pages=165–169 |year=1995 |doi=10.1007/BF00700433 |s2cid=83906865 |author-link=Otto Kandler}}</ref><ref name="Kandler_1998">{{Cite book |last=Kandler |first=Otto |title=Thermophiles: The keys to molecular evolution and the origin of life? |publisher=Taylor and Francis Ltd. |year=1998 |isbn=978-0-203-48420-3 |editor1=Jürgen Wiegel |location=London |pages=19–31 |chapter=The early diversification of life and the origin of the three domains: A proposal |author-link=Otto Kandler |editor2=Michael W.W. Adams |chapter-url=https://books.google.com/books?id=FtSzl4iastsC}}</ref> These phenotypically diverse pre-cells were metabolising, self-reproducing entities exhibiting frequent mutual exchange of genetic information. Thus, in this scenario there was no "first cell". It may explain the unity and, at the same time the partition into three lines (the three domains) of life. Kandler’s pre-cell theory is supported by Wächtershäuser.<ref name="Wächtershäuser_2003">{{cite journal |last=Wächtershäuser |first=Günter |author-link=Günter Wächtershäuser |year=2003 |title=From pre-cells to Eukarya – a tale of two lipids |journal=Molecular Microbiology |volume=47 |issue=1 |pages=13–22 |doi=10.1046/j.1365-2958.2003.03267.x |pmid=12492850 |s2cid=37944519 |doi-access=free}}</ref><ref name="Wächtershäuser_2006">{{Cite journal |last=Wächtershäuser |first=Günter |date=October 2006 |title=From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences|volume=361 |issue=1474 |pages=1787–1808 |doi=10.1098/rstb.2006.1904 |pmc=1664677 |pmid=17008219}}</ref> In 1998, [[Carl Woese]], based on the RNA world concept, proposed that no individual organism could be considered a LUCA, and that the genetic heritage of all modern organisms derived through [[horizontal gene transfer]] among an ancient community of organisms.<ref name=":0">{{cite journal |last=Woese |first=Carl |author-link=Carl Woese |title=The universal ancestor |journal=PNAS |volume=95 |issue=12 |pages=6854–6859 |date=June 1998 |pmid=9618502 |bibcode=1998PNAS...95.6854W |pmc=22660 |doi=10.1073/pnas.95.12.6854 |doi-access=free }}</ref> Other authors concur that there was a "complex collective genome"<ref name="Egel 2012">{{cite journal |last=Egel |first=Richard |date=March 2012 |title=Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life |journal=Life |volume=2 |issue=1 |pages=170–212 |bibcode=2012Life....2..170E |doi=10.3390/life2010170 |pmc=4187143 |pmid=25382122 |doi-access=free}}</ref> at the time of the LUCA, and that horizontal gene transfer was important in the evolution of later groups;<ref name="Egel 2012"/> Nicolas Glansdorff states that LUCA "was in a metabolically and morphologically heterogeneous community, constantly shuffling around genetic material" and "remained an evolutionary entity, though loosely defined and constantly changing, as long as this promiscuity lasted."<ref name="Glansdorff Xu Labedan 2008">{{cite journal |last1=Glansdorff |first1=Nicolas |last2=Xu |first2=Ying |last3=Labedan |first3=Bernard |title=The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner |journal=Biology Direct |volume=3 |issue=1 |date=9 July 2008 |page=29 |doi=10.1186/1745-6150-3-29 |pmid=18613974 |pmc=2478661 |s2cid=18250196 |doi-access=free }}</ref>
+The nature of LUCA remains disputed. In 1994, on the basis of primordial metabolism (sensu [[Günter Wächtershäuser|Wächtershäuser]]), [[Otto Kandler]] proposed a successive divergence of the three domains of life<ref name="Woese Kandler Wheelis 1990"/> from a multiphenotypical ''population'' of [[Pre-cell|pre-cells]], reached by gradual evolutionary improvements ([[cellularization]]).<ref name="Kandler_1994">{{Cite book |last=Kandler |first=Otto |title=Early Life on Earth. Nobel Symposium 84 |date=1994 |publisher=Columbia University Press |editor=Stefan Bengtson |location=New York |pages=152–160 |chapter=The early diversification of life |author-link=Otto Kandler }}</ref><ref name="Kandler_1995">{{cite journal |last=Kandler |first=Otto |title=Cell Wall Biochemistry in Archaea and its Phylogenetic Implications |journal=Journal of Biological Physics |volume=20 |issue=1–4 |pages=165–169 |year=1995 |doi=10.1007/BF00700433 |s2cid=83906865 |author-link=Otto Kandler}}</ref><ref name="Kandler_1998">{{Cite book |last=Kandler |first=Otto |title=Thermophiles: The keys to molecular evolution and the origin of life? |publisher=Taylor and Francis Ltd. |year=1998 |isbn=978-0-203-48420-3 |editor1=Jürgen Wiegel |location=London |pages=19–31 |chapter=The early diversification of life and the origin of the three domains: A proposal |author-link=Otto Kandler |editor2=Michael W. W. Adams |chapter-url=https://books.google.com/books?id=FtSzl4iastsC |access-date=21 June 2023 |archive-date=25 February 2023 |archive-url=https://web.archive.org/web/20230225201522/https://books.google.com/books?id=FtSzl4iastsC |url-status=live }}</ref> These phenotypically diverse pre-cells were metabolising, self-reproducing entities exhibiting frequent mutual exchange of genetic information. Thus, in this scenario there was no "first cell". It may explain the unity and, at the same time, the partition into three lines (the three domains) of life. Kandler's pre-cell theory is supported by Wächtershäuser.<ref name="Wächtershäuser_2003">{{cite journal |last=Wächtershäuser |first=Günter |author-link=Günter Wächtershäuser |year=2003 |title=From pre-cells to Eukarya – a tale of two lipids |journal=Molecular Microbiology |volume=47 |issue=1 |pages=13–22 |doi=10.1046/j.1365-2958.2003.03267.x |pmid=12492850 |s2cid=37944519 |doi-access=free}}</ref><ref name="Wächtershäuser_2006">{{Cite journal |last=Wächtershäuser |first=Günter |date=October 2006 |title=From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences|volume=361 |issue=1474 |pages=1787–1808 |doi=10.1098/rstb.2006.1904 |pmc=1664677 |pmid=17008219}}</ref> In 1998, [[Carl Woese]], based on the RNA world concept, proposed that no individual organism could be considered a LUCA, and that the genetic heritage of all modern organisms derived through [[horizontal gene transfer]] among an ancient community of organisms.<ref>{{cite journal |last=Woese |first=Carl |author-link=Carl Woese |title=The universal ancestor |journal=PNAS |volume=95 |issue=12 |pages=6854–6859 |date=June 1998 |pmid=9618502 |bibcode=1998PNAS...95.6854W |pmc=22660 |doi=10.1073/pnas.95.12.6854 |doi-access=free }}</ref> Other authors concur that there was a "complex collective genome"<ref name="Egel 2012">{{cite journal |last=Egel |first=Richard |date=March 2012 |title=Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life |journal=Life |volume=2 |issue=1 |pages=170–212 |bibcode=2012Life....2..170E |doi=10.3390/life2010170 |pmc=4187143 |pmid=25382122 |doi-access=free}}</ref> at the time of the LUCA, and that horizontal gene transfer was important in the evolution of later groups;<ref name="Egel 2012"/> Nicolas Glansdorff states that LUCA "was in a metabolically and morphologically heterogeneous community, constantly shuffling around genetic material" and "remained an evolutionary entity, though loosely defined and constantly changing, as long as this promiscuity lasted."<ref name="Glansdorff Xu Labedan 2008">{{cite journal |last1=Glansdorff |first1=Nicolas |last2=Xu |first2=Ying |last3=Labedan |first3=Bernard |title=The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner |journal=Biology Direct |volume=3 |issue=1 |date=9 July 2008 |page=29 |doi=10.1186/1745-6150-3-29 |pmid=18613974 |pmc=2478661 |s2cid=18250196 |doi-access=free }}</ref>
 The theory of a universal common ancestry of life is widely accepted. In 2010, based on "the vast array of molecular sequences now available from all domains of life,"<ref name="Steel">{{cite journal |last1=Steel |first1=M. |last2=Penny |first2=D. |s2cid=205055573 |title=Origins of life: Common ancestry put to the test |journal=Nature |volume=465 |issue=7295 |pages=168–169 |date=May 2010  |pmid=20463725 |doi=10.1038/465168a |bibcode=2010Natur.465..168S|doi-access=free }}</ref> D. L. Theobald published a "[[statistical hypothesis test|formal test]]" of universal common ancestry (UCA). This deals with the [[common descent]] of all extant terrestrial organisms, each being a genealogical descendant of a single species from the distant past. His formal test favoured the existence of a universal common ancestry over a wide class of alternative hypotheses that included horizontal gene transfer. Basic biochemical principles imply that all organisms do have a common ancestry.<ref name="Theobald-2010">{{cite journal |last=Theobald |first=D. L. |s2cid=4422345 |title=A formal test of the theory of universal common ancestry |journal=Nature |volume=465 |issue=7295 |pages=219–222 |date=May 2010 |pmid=20463738 |doi=10.1038/nature09014 |bibcode=2010Natur.465..219T }}</ref>
-A proposed, earlier, non-cellular ancestor to LUCA is the [[First universal common ancestor]] (FUCA).<ref name="Prosdocimi 2019">{{cite book |last1=Prosdocimi |first1=Francisco |date=2019 |url=https://doi.org/10.1007/978-3-030-30363-1_3 |title=Evolution, Origin of Life, Concepts and Methods |pages=43–54 |editor-last=Pontarotti |editor-first=Pierre |access-date=2023-11-02 |place=Cham |publisher=Springer |doi=10.1007/978-3-030-30363-1_3 |isbn=978-3-030-30363-1 |last2=José |first2=Marco V. |last3=de Farias |first3=Sávio Torres|chapter=The First Universal Common Ancestor (FUCA) as the Earliest Ancestor of LUCA's (Last UCA) Lineage |s2cid=199534387 }}</ref><ref name="Prosdocimi 2023">{{Citation |last1=Prosdocimi |first1=Francisco |last2=José |first2=Marco V. |last3=de Farias |first3=Sávio Torres |chapter=The First Universal Common Ancestor (FUCA) as the Earliest Ancestor of LUCA's (Last UCA) Lineage |date=2019 |url=https://doi.org/10.1007/978-3-030-30363-1_3 |title=Evolution, Origin of Life, Concepts and Methods |pages=43–54 |editor-last=Pontarotti |editor-first=Pierre |access-date=2023-11-02 |place=Cham |publisher=Springer |doi=10.1007/978-3-030-30363-1_3 |isbn=978-3-030-30363-1|s2cid=199534387 }}</ref> FUCA would therefore be the ancestor to every modern cell as well as ancient, now-extinct cellular lineages not descendant of LUCA. FUCA is assumed to have had other descendants than LUCA, none of which have modern descendants. Some genes of these ancient now-extinct cell lineages are thought to have been [[Horizontal gene transfer|horizontally transferred]] into the genome of early descendants of LUCA.<ref name="Harris Hill 2021">{{Cite journal |last1=Harris |first1=Hugh M. B. |last2=Hill |first2=Colin |date=2021 |title=A Place for Viruses on the Tree of Life |journal=Frontiers in Microbiology |volume=11 |doi=10.3389/fmicb.2020.604048 |pmid=33519747 |pmc=7840587 |issn=1664-302X |doi-access=free }}</ref>
+A proposed, earlier, non-cellular ancestor to LUCA is the [[First universal common ancestor]] (FUCA).<ref name="Prosdocimi 2019">{{cite book |last1=Prosdocimi |first1=Francisco |date=2019 |chapter-url=https://doi.org/10.1007/978-3-030-30363-1_3 |title=Evolution, Origin of Life, Concepts and Methods |pages=43–54 |editor-last=Pontarotti |editor-first=Pierre |access-date=2023-11-02 |place=Cham |publisher=Springer |doi=10.1007/978-3-030-30363-1_3 |isbn=978-3-030-30363-1 |last2=José |first2=Marco V. |last3=de Farias |first3=Sávio Torres|chapter=The First Universal Common Ancestor (FUCA) as the Earliest Ancestor of LUCA's (Last UCA) Lineage |s2cid=199534387 }}</ref><ref name="Prosdocimi 2023">{{Citation |last1=Prosdocimi |first1=Francisco |last2=José |first2=Marco V. |last3=de Farias |first3=Sávio Torres |chapter=The First Universal Common Ancestor (FUCA) as the Earliest Ancestor of LUCA's (Last UCA) Lineage |date=2019 |url=https://doi.org/10.1007/978-3-030-30363-1_3 |title=Evolution, Origin of Life, Concepts and Methods |pages=43–54 |editor-last=Pontarotti |editor-first=Pierre |access-date=2023-11-02 |place=Cham |publisher=Springer |doi=10.1007/978-3-030-30363-1_3 |isbn=978-3-030-30363-1 |s2cid=199534387 |archive-date=23 February 2024 |archive-url=https://web.archive.org/web/20240223214032/https://link.springer.com/chapter/10.1007/978-3-030-30363-1_3 |url-status=live }}</ref> FUCA would therefore be the ancestor to every modern cell as well as ancient, now-extinct cellular lineages not descendant of LUCA. FUCA is assumed to have had other descendants than LUCA, none of which have modern descendants. Some genes of these ancient now-extinct cell lineages are thought to have been [[Horizontal gene transfer|horizontally transferred]] into the genome of early descendants of LUCA.<ref name="Harris Hill 2021">{{Cite journal |last1=Harris |first1=Hugh M. B. |last2=Hill |first2=Colin |date=2021 |title=A Place for Viruses on the Tree of Life |journal=Frontiers in Microbiology |volume=11 |doi=10.3389/fmicb.2020.604048 |pmid=33519747 |pmc=7840587 |issn=1664-302X |doi-access=free }}</ref>
 == LUCA and viruses ==
-The [[Viral evolution|origin of viruses]] remains disputed. Since viruses need host cells for their replication, it is likely that they emerged ''after'' the [[Evolution of cells|formation of cells]]. Viruses may even have multiple origins and different types of viruses may have evolved independently over the history of life.<ref name="Brock_2022"/>
+The [[Viral evolution|origin of viruses]] remains disputed. Since viruses need host cells for their replication, it is likely that they emerged ''after'' the [[Evolution of cells|formation of cells]]. Viruses may even have multiple origins and different types of viruses may have evolved independently over the history of life.<ref name="Brock_2022"/> There are different hypotheses for the origins of viruses, for instance an early viral origin from the [[RNA world]] or a later viral origin from [[Selfish dna|selfish DNA]].<ref name="Brock_2022"/>
-There are different hypotheses for the origins of viruses, for instance an early viral origin from the [[RNA world]] or a later viral origin from [[Selfish dna|selfish DNA]].<ref name="Brock_2022"/>
-Based on how viruses are currently distributed across the [[bacteria]] and [[archaea]], the LUCA may well have been prey to multiple viruses, ancestral to those that now have those two domains as their hosts.<ref name="KrupovicLUCA2020">{{cite journal |last1=Krupovic |first1=M. |last2=Dolja |first2=V. V. |last3=Koonin |first3=Eugene V. |author3-link=Eugene V. Koonin |title=The LUCA and its complex virome. |journal=Nature Reviews Microbiology |date=2020 |volume=18 |issue=11 |pages=661–670 |doi=10.1038/s41579-020-0408-x |pmid=32665595|s2cid=220516514 |url=https://hal-pasteur.archives-ouvertes.fr/pasteur-02909671/file/Krupovic_Koonin_edit_1591967607_1_R2_upload.pdf }}</ref> Furthermore, extensive virus evolution seems to have preceded the LUCA, since the [[Jelly roll fold|jelly-roll structure]] of [[capsid]] proteins is shared by RNA and DNA viruses across all three domains of life.<ref name="Forterre Prangishvili 2009">{{cite journal |last1=Forterre |first1=Patrick |last2=Prangishvili |first2=David |title=The origin of viruses |journal=Research in Microbiology |volume=160 |issue=7 |year=2009 |doi=10.1016/j.resmic.2009.07.008 |pages=466–472|pmid=19647075 |s2cid=2767388 }}</ref><ref name="Durzyńska Goździcka-Józefiak 2015">{{cite journal |last1=Durzyńska |first1=Julia |last2=Goździcka-Józefiak |first2=Anna |title=Viruses and cells intertwined since the dawn of evolution |journal=Virology Journal |volume=12 |issue=1 |date=16 October 2015 |page=169 |doi=10.1186/s12985-015-0400-7 |pmid=26475454 |pmc=4609113 |doi-access=free }}</ref> LUCA's viruses were probably mainly dsDNA viruses in the groups called ''[[Duplodnaviria]]'' and ''[[Varidnaviria]]''. Two other [[single-stranded DNA virus]] groups within the ''[[Monodnaviria]]'', the ''[[Microviridae]]'' and the ''[[Tubulavirales]]'', likely infected the last bacterial common ancestor. The last archaeal common ancestor was probably host to spindle-shaped viruses. All of these could well have affected the LUCA, in which case each must since have been lost in the host domain where it is no longer extant. By contrast, RNA viruses do not appear to have been important parasites of LUCA, even though straightforward thinking might have envisaged viruses as beginning with [[RNA viruses]] directly derived from an RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been out-competed by DNA viruses.<ref name="KrupovicLUCA2020"/>
+Based on how viruses are currently distributed across the [[bacteria]] and [[archaea]], the LUCA is suspected of having been prey to multiple viruses, ancestral to those that now have those two domains as their hosts.<ref name="KrupovicLUCA2020">{{cite journal |last1=Krupovic |first1=M. |last2=Dolja |first2=V. V. |last3=Koonin |first3=Eugene V. |author3-link=Eugene V. Koonin |title=The LUCA and its complex virome. |journal=Nature Reviews Microbiology |date=2020 |volume=18 |issue=11 |pages=661–670 |doi=10.1038/s41579-020-0408-x |pmid=32665595 |s2cid=220516514 |url=https://hal-pasteur.archives-ouvertes.fr/pasteur-02909671/file/Krupovic_Koonin_edit_1591967607_1_R2_upload.pdf |access-date=15 August 2021 |archive-date=21 October 2022 |archive-url=https://web.archive.org/web/20221021002511/https://hal-pasteur.archives-ouvertes.fr/pasteur-02909671/file/Krupovic_Koonin_edit_1591967607_1_R2_upload.pdf |url-status=live }}</ref> Furthermore, extensive virus evolution seems to have preceded the LUCA, since the [[Jelly roll fold|jelly-roll structure]] of [[capsid]] proteins is shared by RNA and DNA viruses across all three domains of life.<ref name="Forterre Prangishvili 2009">{{cite journal |last1=Forterre |first1=Patrick |last2=Prangishvili |first2=David |title=The origin of viruses |journal=Research in Microbiology |volume=160 |issue=7 |year=2009 |doi=10.1016/j.resmic.2009.07.008 |pages=466–472|pmid=19647075 |s2cid=2767388 }}</ref><ref name="Durzyńska Goździcka-Józefiak 2015">{{cite journal |last1=Durzyńska |first1=Julia |last2=Goździcka-Józefiak |first2=Anna |title=Viruses and cells intertwined since the dawn of evolution |journal=Virology Journal |volume=12 |issue=1 |date=16 October 2015 |page=169 |doi=10.1186/s12985-015-0400-7 |pmid=26475454 |pmc=4609113 |doi-access=free }}</ref> LUCA's viruses were probably mainly dsDNA viruses in the groups called ''[[Duplodnaviria]]'' and ''[[Varidnaviria]]''. Two other [[single-stranded DNA virus]] groups within the ''[[Monodnaviria]]'', the ''[[Microviridae]]'' and the ''[[Tubulavirales]]'', likely infected the last bacterial common ancestor. The last archaeal common ancestor was probably host to spindle-shaped viruses. All of these could well have affected the LUCA, in which case each must since have been lost in the host domain where it is no longer extant. By contrast, RNA viruses do not appear to have been important parasites of LUCA, even though straightforward thinking might have envisaged viruses as beginning with [[RNA viruses]] directly derived from an RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been out-competed by DNA viruses.<ref name="KrupovicLUCA2020"/>
-LUCA might have been the ancestor to some viruses, as it might have had at least two descendants : LUCELLA, the Last Universal Cellular Ancestor, the ancestor to all cells, and the archaic virocell ancestor, the ancestor to large-to-medium-sized [[DNA virus|DNA viruses]].<ref>{{Cite journal |last1=Nasir |first1=Arshan |last2=Kim |first2=Kyung Mo |last3=Caetano-Anollés |first3=Gustavo |date=2012-09-01 |title=Viral evolution |journal=Mobile Genetic Elements |volume=2 |issue=5 |pages=247–252 |doi=10.4161/mge.22797 |issn=2159-2543 |pmc=3575434 |pmid=23550145}}</ref> Viruses might have evolved before LUCA but after the [[First universal common ancestor]] (FUCA), according to the reduction hypothesis, where [[Giant virus|giant viruses]] evolved from primordial cells that became [[Parasitism|parasitic]].<ref name="Harris Hill 2021"/>
+LUCA might have been the ancestor to some viruses, as it might have had at least two descendants: LUCELLA, the Last Universal Cellular Ancestor, the ancestor to all cells, and the archaic virocell ancestor, the ancestor to large-to-medium-sized [[DNA virus|DNA viruses]].<ref>{{Cite journal |last1=Nasir |first1=Arshan |last2=Kim |first2=Kyung Mo |last3=Caetano-Anollés |first3=Gustavo |date=2012-09-01 |title=Viral evolution |journal=Mobile Genetic Elements |volume=2 |issue=5 |pages=247–252 |doi=10.4161/mge.22797 |issn=2159-2543 |pmc=3575434 |pmid=23550145}}</ref> Viruses might have evolved before LUCA but after the [[First universal common ancestor]] (FUCA), according to the reduction hypothesis, where [[Giant virus|giant viruses]] evolved from primordial cells that became [[Parasitism|parasitic]].<ref name="Harris Hill 2021"/>
 == See also ==
@@ Line 131: / Line 127: @@
 * {{annotated link|Mitochondrial Eve}}
 * {{annotated link|Pre-cell}}
+* {{Annotated link|Proto-metabolism|prefer=explicit}}
 * {{annotated link|Timeline of the evolutionary history of life}}
 * {{annotated link|Urmetazoan}}

v t e Origin of life
History of research	Panspermia (5th century BC) Spontaneous generation (4th century BC) Primordial soup (19th century)
Prebiotic synthesis	Pseudo-panspermia Miller–Urey experiment Formamide-based prebiotic chemistry Alternative abiogenesis scenarios
Protocells	GADV-protein world Clay hypothesis Iron–sulfur world Primordial sandwich PAH world Peptide-RNA world Quasispecies model RNA world
Earliest organisms	Earliest known life forms Last universal common ancestor (LUCA)
Research	Astrobiology Paleobiology

v t e Evolutionary biology
Introduction Outline Timeline of evolution History of life Index
Evolution	Abiogenesis Adaptation Adaptive radiation Altruism Cheating Reciprocal Baldwin effect Cladistics Coevolution Mutualism Common descent Convergence Divergence Earliest known life forms Evidence of evolution Evolutionary arms race Evolutionary pressure Exaptation Extinction Event Homology Last universal common ancestor Macroevolution Microevolution Mismatch Non-adaptive radiation Origin of life Panspermia Parallel evolution Signalling theory Handicap principle Speciation Species Species complex Taxonomy Unit of selection Gene-centered view of evolution
Population genetics	Artificial selection Biodiversity Evolutionarily stable strategy Fisher's principle Fitness Inclusive Gene flow Genetic drift Kin selection Parental investment Parent–offspring conflict Mutation Population Natural selection Sexual dimorphism Sexual selection Flowering plants Fungi Mate choice Social selection Trivers–Willard hypothesis Variation
Development	Canalisation Evolutionary developmental biology Genetic assimilation Inversion Modularity Phenotypic plasticity
Of taxa	Bacteria Birds origin Brachiopods Molluscs Cephalopods Dinosaurs Fish Fungi Insects butterflies Life Mammals cats canids wolves dogs hyenas dolphins and whales horses Kangaroos primates humans lemurs sea cows Plants pollinator-mediated Reptiles Spiders Tetrapods Viruses
Of organs	Cell DNA Flagella Eukaryotes symbiogenesis chromosome endomembrane system mitochondria nucleus plastids In animals eye hair auditory ossicle nervous system brain
Of processes	Aging Death Programmed cell death Avian flight Biological complexity Cooperation Color vision in primates Emotion Empathy Ethics Eusociality Immune system Metabolism Monogamy Morality Mosaic evolution Multicellularity Sexual reproduction Gamete differentiation/sexes Life cycles/nuclear phases Mating types Meiosis Sex-determination Snake venom
Tempo and modes	Gradualism/Punctuated equilibrium/Saltationism Micromutation/Macromutation Uniformitarianism/Catastrophism
Speciation	Allopatric Anagenesis Catagenesis Cladogenesis Cospeciation Ecological Hybrid Non-ecological Parapatric Peripatric Reinforcement Sympatric
History	Renaissance and Enlightenment Transmutation of species David Hume Dialogues Concerning Natural Religion Charles Darwin On the Origin of Species History of paleontology Transitional fossil Blending inheritance Mendelian inheritance The eclipse of Darwinism Neo-Darwinism Modern synthesis History of molecular evolution Extended evolutionary synthesis
Philosophy	Darwinism Alternatives Catastrophism Lamarckism Orthogenesis Mutationism Saltationism Structuralism Spandrel Theistic Vitalism Teleology in biology
Related	Biogeography Ecological genetics Evolutionary medicine Group selection Cultural evolution Cultural group selection Dual inheritance theory Hologenome theory of evolution Missing heritability problem Molecular evolution Astrobiology Phylogenetics Tree Polymorphism Protocell Systematics Transgenerational epigenetic inheritance
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