The Evolution of the Three Domains
The relationship between the three is so overly complicated because This works between eukaryotes, archaea and bacteria and causes the. Phylogeny refers to the evolutionary relationships between organisms. The three domains are the Archaea, the Bacteria, and the Eukarya. I propose that the ancestors of archaea (and bacteria) escaped Archaea and eukarya clearly share a more complex evolutionary relationship that . A good theory for the origin of archaea and their relationships with.
Skills to Develop Define phylogeny. Name the 3 Domains of the 3 Domain system of classification and recognize a description of each.
Name the four kingdoms of the Domain Eukarya and recognize a description of each. Define horizontal gene transfer. The Earth is 4. Microbial life is still the dominant life form on Earth. It has been estimated that the total number of microbial cells on Earth on the order of 2.
1.3: Classification - The Three Domain System
Phylogeny refers to the evolutionary relationships between organisms. The Three Domain System, proposed by Woese and others, is an evolutionary model of phylogeny based on differences in the sequences of nucleotides in the cell's ribosomal RNAs rRNAas well as the cell's membrane lipid structure and its sensitivity to antibiotics.
Comparing rRNA structure is especially useful. Because rRNA molecules throughout nature carry out the same function, their structure changes very little over time. Therefore similarities and dissimilarities in rRNA nucleotide sequences are a good indication of how related or unrelated different cells and organisms are.
There are various hypotheses as to the origin of prokaryotic and eukaryotic cells. Because all cells are similar in nature, it is generally thought that all cells came from a common ancestor cell termed the last universal common ancestor LUCA.Archaea bacteria Eukarya - three domains of life
These LUCAs eventually evolved into three different cell types, each representing a domain. The three domains are the Archaea, the Bacteria, and the Eukarya. A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryota domains.
The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
More recently various fusion hypotheses have begun to dominate the literature. One proposes that the diploid or 2N nature of the eukaryotic genome occurred after the fusion of two haploid or 1N prokaryotic cells.
Others propose that the domains Archaea and Eukarya emerged from a common archaeal-eukaryotic ancestor that itself emerged from a member of the domain Bacteria. Some of the evidence behind this hypothesis is based on a "superphylum" of bacteria called PVC, members of which share some characteristics with both archaea and eukaryotes.
There is growing evidence that eukaryotes may have originated within a subset of archaea. In any event, it is accepted today that there are three distinct domains of organisms in nature: Bacteria, Archaea, and Eukarya.
This would fit with a provocative scenario in which I suggested that the archaeal and bacterial chromosomes evolved from large DNA plasmids, with divergent replication mechanisms but homologous partition machineries, themselves derived from giant DNA viruses [ 40 ].
Finally, it is striking that archaea and bacteria use homologous defence systems against plasmids and viruses CRISPR, toxin-antitoxin and restriction-modification systems that are very divergent from the siRNA interference defence systems used by eukaryotes [ 4142 ].
Homologues of argonaute proteins, the core component of the eukaryotic interference system, have been detected in archaea and bacteria, but it is not yet known if these proteins are involved in an interference pathway [ 4243 ]. All these observations raise major unresolved questions: Why, on the other hand, so many viruses infecting archaea are unique, having neither bacterial nor eukaryotic counterparts?
A good theory for the origin of archaea and their relationships with eukarya should definitely explain these puzzling observations. Different Scenarios for the Origin of Archaea and Eukarya Several scenarios are in competition to explain the origin of archaea and eukarya [ 20 — 2244 — 52 ]. The most popular presently are the fusion scenarios in which eukarya originated by the intimate association of an archaeon and a bacterium [ 4849 ], reviewed in [ 46 ]; for a more recent hypothesis see [ 21 ].
In these scenarios, the fusion is triggered by the engulfment of one of the two partners the endosymbiont by the other the host. This association is followed by a dramatic reorganization of the structures of the two partners the fusionpromoting the emergence of a completely new type of cell eukaryote instead of prokaryote. Several propositions have been made concerning the origin of the two partners one archaeon and one bacterium involved. The proposed scenarios also differ by the timing of the mitochondrial endosymbiosis.
In some of them, this event takes place after the fusion [ 48 ], in others it corresponds to the fusion itself [ 49 ].
A common point to most fusion scenarios is that they involve two partners that are very similar to some modern archaea and bacteria [ 46 ]. These partners either belong to modern lineages of bacteria and archaea or are derived from an extinct transient archaeal lineage that originated from modern-looking archaea as in the recently proposed phagocytosing archaeon scenario of Martijn and Ettema, [ 21 ]. This led to the common view that eukaryotes ascend from archaea in an evolutionary ladder scala natura leading from LUCA to eukarya via archaea Figure 1 a.
The LECA is the last eukaryotic common ancestor and FME the first eukaryote harbouring mitochondria; the dotted line refers to the hypothesis in which eukaryotes originated by the association of an archaeon with the mitochondrial bacterial ancestor [ 49 ].
Thick arrows indicate the emergence of eukaryotic specific features ESFs.
The fusion scenarios for the origin of eukaryotes are in apparent contrast to the classical tree of life proposed by Woese et al. However, this tree can be reconciled with fusion scenarios if the archaeal-like partner diverged from the branch leading to archaea before the emergence of LACA. The eocyte tree has been rejuvenated because it is apparently validated by phylogenetic analyses of universal proteins in which eukaryotes are nested within archaea [ 5558 — 60 ].
These analyses provided apparent support for a clade grouping eukarya with a candidate archaeal superphylum called TACK, that encompasses Thaumarchaeota, Aigiarchaeota, Crenarchaeota, and Korarchaeota [ 59 ].
Amazingly, if this is true, eukaryotes are members of the archaea as we are apes and should be considered as an archaeal phylum and the TACK superphylum should be renamed TACKE since it also includes eukarya; otherwise, archaea would be paraphyletic, thus not a valid taxon, since the last common ancestor of archaea was also an ancestor of eukarya.
Here, I will first briefly criticize the fusion scenario and argue in favour of the monophyly of archaea so that we do not have to worry about TACKE. I will also try to put viruses in the general picture. Criticism of Fusion Scenarios I have previously proposed my own fusion scenario, as a joke [ 46 ], accompanied by criticisms against my new version of the fusion the association of a thaumarchaeon and a PVC bacterium.
Since this paper is now often cited simply as a new fusion hypothesis! In fusion scenarios, the host cell can be either a bacterium or an archaeon. In both cases, these scenarios first raise major problems for the fate of the ancestral membranes of the host or the endosymbiont, since the putative ancestral archaeal membrane has disappeared in eukaryotes.
In all known real cases of symbiosis, the symbiont keeps its membrane, even in the most extreme cases of reduction e. Membrane conservation throughout evolutionary processes seems to be a major feature of cellular organisms [ 22 ].
This strongly contradicts with fusion hypotheses in which the host is a bacterium, since the archaeal membrane of the endosymbiont has completely disappeared after the fusion the nuclear membrane in eukaryotic cells being derived from the bacterial-like membrane of the endoplasmic reticulum. In fact, disappearance of the membrane of an infectious entity is only known in the case of enveloped viruses, when the membrane of the viral particles virions disappears in the infected cell i.
However, this situation cannot be assimilated to a true endosymbiosis, since the virion is not an organism and should not be confused with the virus itself [ 65 ].
Scenarios with an archaeal host raise other problems, since they involve the transformation of the host archaeal membrane into the bacterial-like membrane of eukaryotes. Indeed, there is no obvious selection pressure that could have favoured this transformation.
As noticed by Lombard and colleagues, such transformation has never been observed in nature [ 22 ]. In particular, acquisition of a bacterial type of membrane never occurred in any archaeal lineage, despite the massive lateral gene transfer LGT of bacterial genes into archaea.
For instance, Nelson-Sathi and co-workers determined recently that about bacterial genes have been transferred, probably in a single event, in the ancestral archaeal lineage from which emerged all modern Haloarchaea [ 66 ]. Fusion scenarios also involve highly unlikely ad hoc hypotheses to explain the emergence of all complex ESFs from the simpler compact and fully integrated molecular machines working in archaea and bacteria for critics, see [ 444650 — 5257 ].
There is no general agreement between proponents of fusion scenarios for most of these ad hoc hypotheses. For instance, several authors proposed different selection pressures to explain the origin of the eukaryotic nucleus [ 2067 — 69 ]. These hypotheses posit that for various reasons some kind of barrier was required between the nucleoid provided by one of the two partners and the cytoplasm provided by the other.
Fundamentally, fusion scenarios posit that modern cells archaea and bacteria were transformed by their association into cells of a completely new domain with an abrupt but transient acceleration of protein evolutionary rates leading to new versions of universal proteins in eukarya.
This possibility was strongly rejected by Woese who wrote that: I fully agree with this statement; the observation of nature tells us indeed that such transformation is not possible. In all known cases of endosymbioses or close association between organisms that belong to different domains, both partners remain members of their respective domains and there is no dramatic acceleration of protein evolutionary rate, especially for universal proteins.
For instance, the association between a cyanobacterium that produced chloroplasts did not transform Viridiplantae into a new domain. Viridiplantae remained eukaryotes with eukaryotic ribosomeswhereas chloroplasts and mitochondria can still be recognized as highly derived bacteria, with highly divergent—but still bacterial—ribosomes.
As already mentioned, the massive invasion of an Haloarchaeal ancestor by more than one thousand bacterial genes had no effect on the archaeal nature of Haloarchaea. Finally, another rarely discussed important argument against fusion scenarios is the uniqueness of eukaryotic viruses and related transposons [ 46 ].
Indeed, fusion scenarios posit that all modern eukaryotes originated from a unique fusion event between one particular archaeon and one particular bacterium.
If the host was an archaeon, all eukaryotic viruses should have originated from those archaeal viruses that were able to specifically recognize the surface of this particular archaeon or of its immediate descendants. Similarly, if the host was a bacterium, eukaryotic viruses should have originated from bacterial viruses that were able to recognize the surface of this particular bacterium or its immediate descendants.
This seems at odds with the present diversity of eukaryotic viral lineages and transposons, especially with the existence of many lineages of eukaryotic DNA and RNA viruses that have no viral counterparts in bacteria and eukarya, such as Baculoviridae, Megavirales, Retroviridae, and many others.
These two possibilities seem unlikely. In summary, fusion scenarios posit a transient but extreme acceleration of protein evolutionary rates and drastic structural changes to take into account the existence of eukaryotic specific versions of universal proteins e.
They should also posit a transient but extreme acceleration of evolution of viral structures and the appearance of many new viral and transposon families in that same period. This does not seem reasonable, even more so if the fusion event is assimilated to the endosymbiosis that produced mitochondria [ 49 ], since in that case, all these dramatic evolutionary changes should have occurred between the appearance of the first mitochondrial eukaryote FME i.
Such scenarios require no less than several miracles for the emergence of eukaryotes, miracles that occurred only once in billion years of coexistence between archaea and bacteria. The Monophyly of Archaea As previously mentioned, it is commonly assumed that the eocyte tree is now validated by phylogenetic analyses in which eukarya emerge from within archaea [ 5558 — 60 ], with the consequence that all eukaryotic ESFs should have originated in a highly divergent archaeal lineage and that archaea are our ancestors.
However, these analyses, concerning very deep phylogenies, are prone to many artefacts for a critical analysis of contradictory results obtained by different authors with more or less the same dataset; see [ 45 ]. In particular, phylogenetic analyses of Embley and colleagues [ 555860 ] include many ribosomal proteins for which there is no significant signal for deep branching because bacterial proteins are too divergent from their archaeal and eukayotic homologues [ 71 ].
Elongation factors, amino-acyl tRNA synthetases, or else V-ATPases are also used in these analyses despite the fact that these proteins are heavily saturated with respect to amino acid substitutions [ 72 ] and cannot even resolve the phylogeny of eukarya, putting microsporidia highly derived fungi at the base of the eukaryotic tree.
Several universal proteins used RNA polymerases, RFC proteins and amino-acyl tRNA synthetases are also encoded by many viruses especially Megavirales and it is unclear if the eukaryotic and archaeal versions are orthologues of if some of them have been independently acquired from viruses [ 407374 ]; see discussion below.
In the analysis of Cox et al. Strikingly, examination one by one of all phylogenies, published by Cox et al. Despite the exhaustive usage of complex alternative models to perform and test them, the phylogenies used in these global analyses cannot provide answer to the question of archaeal monophyly versus paraphyly because, in most cases they lack valid phylogenetic signal.
Moreover, the quality of these phylogenetic analyses itself is also questionable. In the tree of Cox and co-workers the phylogenies of the bacterial and eukaryotic proteins are not resolved, and the archaea are paraphyletic, with eukarya branching with Methanopyrus kandleri and Crenarchaeota!
In striking contrast, the phylogeny of all domains is well resolved in the tree published in Hecker et al. However, the three can be divided in to five groups because an ancient duplication occurred in the bacterial domain leading to two paralogous proteins, YgjD and YeaZ, and mitochondrial proteins, named Qri7, branch within the YgjD tree, in agreement with their bacterial origin Figure 3.
evolution - How do archaea relate to eukaryotes and bacteria? - Biology Stack Exchange
Two contrasting phylogenies of the same universal protein. These simplified phylogenies are adapted from Figure S46 in [ 55 ] left panel and from Figure S1 in [ 56 ] right panel. Squares indicate unresolved nodes, whereas triangles indicate resolve nodes. The tree on the right is congruent with firmly established biological knowledge such as the monophyly of bacteria and eukarya, the bacterial origin of mitochondria.
It favours the classical three-domain tree of Woese and colleagues. This scheme is based on the assumption that the universal tree is rooted in the bacterial branch [ 53 ]. Bacteria experienced independently a similar evolutionary path. The blue arrow indicates the mitochondrial endosymbiosis. In that scenario, the archaeal ancestor should have contained all eukaryotic features that are presently dispersed in modern archaea.
In that case, since LACA was probably more eukaryotic-like than any one of its descendants [ 6 ], the archaeal ancestor should have been LACA itself or a descendant of LACA, which, unlike the others, never lost a single eukaryotic feature.
Why this particular ancestor should have also been the ancestor of eukarya? Another complication for the archaeal ancestor scenario is that LACA was probably a hyperthermophile [ 68081 ].
However, all known mesophilic Thaumarchaeota lack some critical eukaryotic features, such as actin or tubulin [ 6 ]. Again, one should suppose that eukarya originated from a mesophilic descendant of LACA, which has never lost a single eukaryotic feature and left no other descendants itself besides eukarya! This is why the idea that human originated from apes looking like chimps was so prevalent in narratives describing our origin.
However, it seems now that our common ancestor with chimps was possibly already bipedal, looking more like an ancient Homo than a modern chimp [ 83 ]. I will bet here that, as our last common ancestor with chimps neither resembled chimps nor Homo, LAECA was neither an archaeon nor a eukaryote, but a creature endowed with the property to be at the origin of both Figure 3.
It has been clearly shown recently from comparative genomics that a long suspected trend toward simplification indeed occurs in archaea and bacteria. For instance, Wolf and co-workers have shown that gene losses are estimated to outnumber gene gains at least 4 to 1 in these two domains [ 85 ]. Importantly, two independent studies concluded that LACA was an organism of greater complexity than most of the extant archaea [ 8586 ], in agreement with the observation that the ancestral archaeal ribosome contained more proteins than the ribosomes of modern archaea [ 8788 ] and that LACA should have combined all eukaryotic traits presently dispersed in various archaea [ 6 ].
Phylogenomic analyses focusing on protein structures also detected a trend toward proteome reduction in the archaeal and bacterial lineages, suggesting that both lineages originated from ancestors with more complex proteomes [ 89 — 91 ] and references therein.
There are of course some exceptions to this general trend, especially in bacteria, such as the late evolution of giant bacteria in subgroups of proteobacteria [ 93 ], but these are the exceptions that confirm the rule. A nice way to sum it up though not very accurate is "eukaryote in a bacterium's clothing". Their cells look a lot like prokaryotes because they are similar size, have no nucleus, endomembranes or cytoskeleton.
However, some archaeas' DNA is bound by histones and they use similar machinery as eukaryotes for DNA replication, transcription and translation. From the last universal common ancestor, first prokaryotes and archaea diverged.
After this branching, the differences in genetic machinery evolved. Archaea then branched, producing a protoeukaryote line which went on to endosymbiosis with some protobacteria. That would explain the similarities I outlined above: