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Vol. 95, Issue 12, 6854-6859, June 9, 1998 (progenote / lateral gene transfer / genetic
annealing / evolutionary temperature / communal ancestor)
Department of Microbiology, University of Illinois at
Urbana-Champaign, B103 Chemical and Life Sciences Laboratory, MC-110,
601 South Goodwin Avenue, Urbana, IL 61801
Contributed by Carl R. Woese, April 3, 1998
A genetic annealing model for the universal ancestor of all extant
life is presented; the name of the model derives from its resemblance
to physical annealing. The scenario pictured starts when "genetic
temperatures" were very high, cellular entities (progenotes) were
very simple, and information processing systems were inaccurate.
Initially, both mutation rate and lateral gene transfer levels were
elevated. The latter was pandemic and pervasive to the extent that it,
not vertical inheritance, defined the evolutionary dynamic. As
increasingly complex and precise biological structures and processes
evolved, both the mutation rate and the scope and level of lateral gene
transfer, i.e., evolutionary temperature, dropped, and the evolutionary
dynamic gradually became that characteristic of modern cells. The
various subsystems of the cell "crystallized," i.e., became
refractory to lateral gene transfer, at different stages of
"cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not
exist at these early stages. The universal phylogenetic tree,
therefore, is not an organismal tree at its base but gradually becomes
one as its peripheral branchings emerge. The universal ancestor is not
a discrete entity. It is, rather, a diverse community of cells that
survives and evolves as a biological unit. This communal ancestor has a
physical history but not a genealogical one. Over time, this ancestor
refined into a smaller number of increasingly complex cell types with
the ancestors of the three primary groupings of organisms arising as a
result.
Biologists have long subscribed to the powerful, unifying idea
that all life on Earth arose from a common ancestor (1). Nothing
concrete could be said about the nature of this ancestor initially, but
it was intuitively assumed to be simple, often likened to a prokaryote,
and generally held to have had little or no intermediary metabolism
(2). Only when biology could be defined on the level of molecular
sequences would it become possible to seriously question the nature of
this ancestor.
The unrooted universal phylogenetic tree that emerged from ribosomal
RNA (rRNA) sequence comparisons provided the first glimpse of our
ultimate ancestor, albeit an indirect one (3, 4). Whatever it was, this
cryptic entity had spawned three remarkably different primary groupings
of organisms (domains) When it proved possible to root the tree, by using the
Schwartz-Dayhoff paralogous gene outgroup method (14-16), the
ancestor became a node on the tree, implying that it was a specific
entity. This rooted tree also unexpectedly revealed the Archaea to be specific relatives of the eukaryotes. If prokaryotes (Archaea and
Bacteria) were on both sides of the primary phylogenetic divide, then
"prokaryote" was not a phylogenetically meaningful taxon. In
addition, given the fundamental molecular differences between Archaea
and Bacteria, it made no sense to call the universal ancestor a
"prokaryote." What then was this universal ancestor?
A discrete picture of the ancestor began to emerge only when many more
sequences representing all three phylogenetic domains became available.
These sequences could be seen as putting phenotypic flesh on an
ancestral phylogenetic skeleton. Yet that task has turned out to be
anything but straightforward. Indeed, it would seem to require
disarticulating the skeleton. No consistent organismal phylogeny has
emerged from the many individual protein phylogenies so far
produced.
Phylogenetic incongruities can be seen everywhere in the universal
tree, from its root to the major branchings within and among the
various taxa to the makeup of the primary groupings themselves. Yet
there is no consistent alternative to the rRNA phylogeny, and that
phylogeny is supported by a number of fundamental genes. The
aminoacyl-tRNA synthetases (aaRSs) epitomize this confused situation
(17, 18). For example, it is common to see archaeal versions of some of
the aaRSs scattered throughout the Bacteria (17) (C.W., unpublished
data). The aaRSs can in principle be used to root the universal tree
(because some of them obviously reflect common ancestral gene
duplications). Yet different (related) aaRSs root that tree
differently: the ileRS tree roots (using the valRSs) canonically; i.e.,
the Archaea and eukaryotes are sister groups (19). The valRS tree,
however, roots on the archaeal branch, which makes sister groups of the
Bacteria and eukaryotes (C.W., unpublished data). Exceptions to the
topology of the rRNA tree such as these are sufficiently frequent and
statistically solid that they can be neither overlooked nor trivially
dismissed on methodological grounds. Collectively, these conflicting
gene histories are so convoluted that lateral gene transfer is their only reasonable explanation (18).
A concept of the universal ancestor turns on more than phylogenetic
trees, however. The Archaea and Bacteria share a large number of
metabolic genes that are not found in eukaryotes (18, 20). If these two
"prokaryotic" groups span the primary phylogenetic divide and
their genes are vertically (genealogically) inherited, then the
universal ancestor must have had all of these genes, these many
functions: This distribution of genes would make the ancestor a
prototroph with a complete tricarboxylic acid cycle, polysaccharide
metabolism, both sulfur oxidation and reduction, and nitrogen fixation;
it was motile by means of flagella; it had a regulated cell cycle, and
more. This is not the simple ancestor, limited in metabolic
capabilities, that biologists originally intuited. That ancestor can
explain neither this broad distribution of diverse metabolic functions
nor the early origin of autotrophy implied by this distribution. The
ancestor that this broad spread of metabolic genes demands is
totipotent (21), a genetically rich and complex entity, as rich and
complex as any modern cell Yet the totipotent ancestor also fails: it cannot explain the manner of
the ancestor's evolution, i.e., how it became so miraculously complex
in so short a time and just as rapidly gave rise to the ancestors of
the three primary lines of descent. All of this apparently happened in
far less than 1 billion years, whereas evolution within each of the
three primary lines of descent has been going on for over 3 billion
years now with outcomes that don't even begin to compare with the
spectacular ones associated with the ancestor and its original
offspring (4) The Pivotal Assumption.
Most theories of early evolution
tacitly assume that organismal lineages, organismal genealogies, have
always existed and extend into the stage of the universal ancestor.
Eukaryotes, of course, contain organellar genes, whose heritages are
not those of nuclear genes in general. Laterally transferred genes are
seen in prokaryotes as well. Strictly speaking both eukaryotes and prokaryotes are of mixed heritage. Yet, we still speak of eukaryotic and prokaryotic "lineages" (and for good reason) because in both cases the vast majority of their genes presumably share a common history. If and only if this assumption holds, however, can we speak of
organismal lineages and corresponding phylogenetic trees. But the
assumption automatically makes the universal ancestor an organism that
itself had a lineage, a discrete genealogy.
Evolution
The universal ancestor
ABSTRACT
Top
Abstract
Background
Conclusion
References
BACKGROUND
Top
Abstract
Background
Conclusion
References
the Archaea, the Bacteria, and the Eucarya-and
these necessarily reflected the ancestor's nature. Phylogenies derived
from the few other molecules that then had been sequenced confirmed the
three predicted groupings, and concurrent biochemical characterizations
further developed their uniqueness (5-12). But, from this first
universal tree, one could infer only that the ancestor was some
ill-defined "urstoff" from which three primary lines of descent
somehow arose (3, 13).
seemingly more so.
yet experience teaches that complex, integrated
structures change more slowly than do simple ones. Moreover, the
totipotent ancestor associates physiologies that have not been observed
together in any modern lineage and asks that all of this come about
through vertical inheritance. Thus, we are left with no consistent and
satisfactory picture of the universal ancestor. It is time to question
underlying assumptions.
indeed, the very definition of
"organism" itselfcomes into question. It is time to release this notion of organismal lineages altogether and see where that leaves
us. Let molecular phylogenetic trees represent exactly what they in the
first instance do represent, histories of individual genes or gene
groupings. When do individual gene histories define an organismal
history, an organismal lineage? Did organismal lineages even exist at
the time of the universal ancestor? If not, then what exactly was this
ancestor, and what was the nature of the evolutionary process that
formed it?
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THE GENETIC ANNEALING MODEL |
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A very different picture of the universal ancestor comes to light when the notion of organismal lineages is released, a picture that flows naturally from a consideration of what the evolutionary dynamic might be when cells are very primitive. I have been developing parts of this idea in various publications over the last three decades (4, 22-26). Now, in the context of far greater amounts of molecular sequence data, a synthesis is emerging. The primitive evolutionary dynamic I envision bears a superficial resemblance to the physical annealing process, hence, its name.
First consider the analogy: a physical annealing system starts at a high enough temperature that structures cannot form and then proceeds to slowly cool. In this quasi-stable condition, various combinations of the system's elements form, dissociate, and reform in new ways, with only the most stable and structured of these combinations initially persisting, i.e., "crystallizing." As the temperature continues to drop, less stable structures begin to form, to crystallize, and many of the preexisting ones add new features, becoming more elaborate. In the evolutionary counterpart of physical annealing, the elements of the system are primitive cells, mobile genetic elements, and so on, and physical temperature becomes "evolutionary temperature," the evolutionary tempo. The evolutionary analog of "crystallization" is emergence of new structures, new cellular subsystems that are refractory to major evolutionary change (see below). The analogy between physical cooling and the drop in evolutionary temperature is somewhat inexact, as we shall see. And although the outcomes of a physical annealing process are highly circumscribed if not certain, the evolutionary world is open-ended to an extreme.
Primitive Cells: Progenotes.
The scenario about to unfold
starts at the point when the translation mechanism first came into
being. (How it arose does not concern us here). It is assumed that
cells existed at this time but were very different from modern cells,
different enough that they should not be looked at as organisms (see
below). The properties of the rudimentary translation mechanism
severely limited these cells in both their nature and evolutionary
potential. The rudimentary translation mechanism was far simpler than
the complex modern one and, as a consequence, was far less accurate
(26); codon recognition and reading frame movement (procession) were both so inaccurate that most, if not all, modern types of proteins could not be produced. At this stage, only small proteins could evolvealong with any larger, imprecisely translated ones (called "statistical proteins") that the primitive cell was able to
produce and use (26, 27). Entities in which translation had not yet developed to the point that proteins of the modern type could arise
have been termed "progenotes," and the era during which these
were the most advanced forms of life, the "progenote era" (26).
there is little or
no benefit in inheriting only part of a new metabolic pathway. And
mobile genetic elements are well suited for lateral transfer as well.
Upon cell division, the mini-chromosomes distribute randomly between
the daughter cells. This fact would lessen the mutational burden
imposed by high mutation rates in the sense that the daughter cell with
the better balance of functional copies of important genes has a
selective advantage. If replication errors could be directly detected
(e.g., as mispairings), a more direct way to eliminate them seems
possible, through simple destruction of the mini-chromosome in
question, say, by nuclease cleavage (25).
Small primitive genomes with low genetic capacity and imprecision in
both translation and genome replication imply a primitive cell that was
rudimentary in every respect (26). The progenote probably had no cell
wall (see below) (13). Its subsystems were generally less complex and
hierarchically organized and the cell itself was less integrated than
are cells today. The states of that cell were fewer, simpler, and
imprecisely defined and controlled (26). The progenote was more or less
a bag of semi-autonomous genetic elements (the mini-chromosomes). These
elements would come and go, especially on an evolutionary time scale.
Higher level organization, among the mini-chromosomes and throughout the cell, was minimal.
Evolutionary Temperature. Macroscopic evolutionists recognized long ago a relationship between the "tempo" (rate) of evolution and what they called its "mode" (a measure of the outcomes): the more rapid the former, the more unusual and varied the latter (29, 30). When microbial evolution finally came into the picture, a similar (and seemingly related) phenomenon was encountered on the molecular level (4), suggesting that this tempo/mode relationship was a fundamental manifestation of the evolutionary process. Because of high mutation rates and other factors (below), the progenote era is seen as one of very high evolutionary tempo.
Evolutionary tempo, i.e., "temperature," is defined here as a composite of the two processes critical to evolution: (i) mutation and the fields of variants that result, and (ii) lateral gene transfer, including its frequency and quality. A lineage's field of variants, the anlage for evolutionary change, is a strong function of mutation rate. Multi-site variants, the more useful, creative ones, obviously occur as higher order functions of this rate. These variants will disproportionately increase and become more varied in kind as mutation rate increases, and that increase will, in effect, qualitatively change the field of variants, changing the mode of evolution (4). The field of variants in which progenotes evolve may be even richer than that so far implied. Cell lines are capable of going into error catastrophe, a state in which their mutation rates increase out of control (31, 32), and the line replicates itself into extinction in short order. These short-lived, error-prone cell lines take on special significance in a world of lateral gene transfer (below). In this context, they become "super-mutator" strains for the population as a whole. The variant genes they produce, ones that viable cell lines cannot afford to produce, add great richness to the delocalized field of variants from which all progenotes can draw. The primitive lateral gene transfer envisioned is very unlike that seen today. It effectively involves all entities existing at the time and all of their genes, and transfers, like mutations, occur at very high frequencies. The reason why all cellular entities are potential recipients and all genes potentially transferable is that progenotes in essence comprised what would now be called the "essential functions," and primitive evolution (as measured by its outcomes) was concerned with the development and refinement of these. All functions of this sort and their refinements could be globally exchanged. The high frequencies of lateral transfer reflected the simplicity of the progenote's genetic mechanisms and the lack of barriers to lateral exchangein this primitive context any lineages
evolving barriers to acquisition or expression of foreign genes would
be left behind in the evolutionary progression toward modern life.
Lateral gene transfer of this kind and intensity would not only
contribute significantly to but also would completely dominate the
primitive evolutionary dynamic.
The Communal Ancestor. Progenotes were very unlike modern cells. Their component parts had different ancestries, and the complexion of their componentry changed drastically over time. All possessed the machinery for gene expression and genome replication and at least some rudimentary capacity for cell division. But even these common functions had no genealogical continuity, for they too were subject to the confusion of lateral gene transfer. Progenotes are cell lines without pedigrees, without long-term genetic histories. With no organismal history, no individuality or "self-recognition," progenotes are not "organisms" in any conventional sense.
Their small genomes require progenotes to be metabolically simple, minimal. However, different progenotes could have differed metabolically. The collectively genetic complement of the progenote population could have been far greater than that of any individual cell, indeed totipotent in the above sense (13, 22). The fact that innovations could easily spread through the population by lateral transfer gave the progenote community enormous evolutionary potential; each cell line was the potential recipient of any innovation that occurred within the entire diverse population. There are different ways of looking at such a community of progenotes. On the one hand, it could have been the loose-knit evolutionary (genetic) community just discussed. On the other, it could have been more like a modern bacterial consortium, with cells cross-feeding one another not only genetically but also metabolically. Cell-cell contacts would have facilitated both processes. In both views of the community, the latter in particular, it is not individual cell lines but the community of progenotes as a whole that survives and evolves. It was such a community of progenotes, not any specific organism, any single lineage, that was our universal ancestora genetically rich,
distributed, communal ancestor. It was also this loose-knit biological
unit that ultimately evolved to a stage in which it somehow pulled apart into two, then three communities, isolated by the fact that they
could no longer communicate laterally with one another in an
unrestricted way. Each had become sufficiently complex and idiosyncratic that only some genes, some subsystems, could be usefully
transferred laterally. Each of these three self-defining communities
then further congealed, giving rise to what we perceive as the three
"primary lines of descent."
Translation Improves: Progenotes Become Genotes. At these early stages of life, everything turned upon the evolution of translation. Each slight improvement in that process, each increase in its accuracy, would have permitted a new generation of proteins to emerge (26). These new proteins, in turn, refined and developed the metabolic pathways and generally improved the cell, which then set the stage for a further round of improvement in translation. In this way, wave after wave of innovation occurred, each triggered by a refinement in translation and spread throughout the community by lateral gene transfer. This iterative, bootstrapping evolution continued until the accuracy of translation reached a level where it no longer prevented the evolution of the types of proteins we see today. The evolutionary dynamic then ceased to be constrained by imprecise translation, and progenotes, by definition, became genotes (26). This transition did not mean that translation had stopped evolving, nor did it mean that the initial genotes were modern types of cells. That latter development required many more innovations and refinements.
Cooling. Evolutionary temperature is postulated to drop gradually during the primitive evolutionary process. This cooling, however, does not bring about the crystallization of structures as in physical annealing: evolutionary cooling occurs as a result of crystallization. All structures in the progenote cell, all cellular subsystems, are initially simple, as are their relationships and as is the cell itself. As progenotes evolve (above), structures of increasing complexity emerge, relationships among them become more intricate, and the cell itself becomes more integrated, more highly organized. In the process, individual cells (cell lines) become increasingly dissimilar, increasingly idiosyncratic. In other words, the biological specificity of the system increases in every respect.
The more complex a subsystem becomes, the harder it is to find a foreign part compatible with it, and the few that are tend to come from cells that have related subsystems. The more a subsystem becomes integrated into the fabric of the cell, the harder it becomes to replace it in toto. There comes a stage, then, when the subsystem can no longer change through lateral gene transfer: all changes must come from within the cell line, through gene duplications and mutations. At this point, the subsystem has crystallized, evolving essentially through vertical inheritance.Crystallizing. The annealing scenario predicts that different subsystems of the cell will crystallize (become more or less refractory to lateral transfer) at different evolutionary stages. This point will be reached when (as just stated) foreign parts are no longer compatible with the subsystem, and it becomes firmly integrated into the fabric of the cell.
I would argue that translation was among the first, if not the first, of the cellular subsystems to crystallize: The fact that translation is an RNA-based mechanism suggests antiquity. The fact that it is complex and its key components tend to be universal argues for an early consolidation as well. And, as the leading edge of the early evolutionary waves, translation would have refined at each step before the other cellular systems did. Not all of translation's components are universal in distribution, indicating that the mechanism continued to refine (in yet to be understood ways) after its core had crystallized and the stage of the universal ancestor had passed. These later refinements do not appear to involve lateral gene transfer although subtle forms of that transfer (involving relatively closely related organisms) cannot be ruled out. Immunity to lateral transfer would be expected for a mechanism so complex (idiosyncratic) and tightly integrated, i.e., one that had crystallized. The aaRSs are telling exceptions to the vertical inheritance that characterizes the other translational components. These enzymes are a study in lateral transfer. For example, several different versions of a given synthetase often occur within the Bacteria alone. (Insufficient data prevent assessing this for the Archaea and eukaryotes.) For the different bacterial versions of a given synthetase: (i) more than one of them can be simultaneously present in the same organism; (ii) the taxonomic makeup of these synthetase subgroupings are individually idiosyncratic (none seems to conform to established phylogenetic pattern, or to agree with the others); and (iii) some bacterial versions of a given enzyme are more related to the archaeal and/or eukaryotic versions than they are to the other bacterial versions (17) (C.W., unpublished data). These phenomena are all indicative of lateral transfer of the synthetase genes throughout the evolution of the Bacteria. It is obvious why the aaRSs are so evolutionarily migratory (17, 18). They are "modular": they occur free in the cell, unassociated with the ribosome; each synthetase type interacts with only one or a few tRNAs; and their functions are universal. This all adds up to a capacity to function in a great variety of foreign cellular environments. Lateral movement and diversification should characterize other modular elements as well, and there is mounting evidence to support this: sulfate reduction, for example, appears to have been laterally transferred between Bacteria and Archaea, if not within the bacteria as well (20, 33). Transcription, too, seems to have crystallized at an early stage, although it is not known whether this stage was before or after translation. What can be said is that the first transcription mechanism to achieve genealogical coherence was only a rudimentary one. Substantial differences in the mechanism separate the Bacteria on the one hand from the Archaea and eukaryotes on the other: all versions of the polymerase possess the core subunits, i.e.,
, 
, and ' in
bacterial terminology, but these subunits differ substantially in
sequence, particularly in the case of , in which an obvious deep
structural divergence strongly distinguishes the bacterial and
archaeal/eukaryotic versions (34). The Archaea and eukaryotes have a
number of additional common subunits that are not seen in the bacterial
mechanism (34). As was the case with translation, there is little
evidence to suggest that lateral transfer was involved in the evolution
of transcription; all of the components of the apparatus seem to
provide the same genealogical pattern. Of course, the question of
phylogenetically local transfers remains open.
Genome replication presents a different picture. No genome replication
system is universally distributed; the bacterial mechanism bears no
specific relationship to the one that is basically common between the
Archaea and eukaryotes (21). Such a universal mechanism probably
existed early on (as is suggested by the general homologies among
various types of DNA polymerases spread across the phylogenetic spectrum), but that mechanism must have been too primitive to be simply
refined into those we see today. It stands to reason that the evolution
of (a particular) genome organization goes hand in hand with that of
the corresponding mechanism to replicate it. Therefore, modern genomes
appear to have arisen only after the primary lines of descent were
established (21), and the evolution leading to their replication
mechanisms involved major innovations, innovations that did (could) not
spread globally.
Cellular evolution, the emergence of modern cells, seems a protracted
process with a somewhat ill-defined ending. The evolution of modern
genome structure and genome replication mechanisms appears the last
great innovation in the evolution of the cell, and so, it may have
marked the beginning of the end of that process. For genomes to reach
the size of modern genomes, the mutation rate has to be low, in the
range of one error per 1 billion base pairs read (32). This rate lowers
the evolutionary temperature (at least the mutational aspect thereof)
to modern levels. And the implied complexity and specialization of
cells and their subsystems at this point should restrict lateral
transfer significantly.
The Universal Phylogenetic Tree.
By now, it is obvious that
what we have come to call the universal phylogenetic tree is no
conventional organismal tree. Its primary branchings reflect the common
history of central components of the ribosome, components of the
transcription apparatus, and a few other genes. But that is all. In its
deep branches, this tree is merely a gene tree. Genuine organisms
(self-replicating entities that have true individuality and a history
of their own) did not exist at the time the tree started to form. The
tree arose in a communal universal ancestor, an "entity" that had
a physical history but not a genealogical one. This tree became an
organismal tree only as it grew, only as its more superficial branches
emerged. By the time these formed, many more functions had crystallized and so, had come to have discernible histories; and these histories coincided with those of the ribosomal components and the likebut only
after the point of their crystallization.
The Problem of Shared Metabolic Genes. The genetic annealing model does not (now) account satisfactorily for the large number of metabolic genes that are shared by the Archaea and Bacteria but not found in the eukaryotes. It does, however, suggest a new way of looking at the problem. These genes are shared, not because of vertical inheritance but because of lateral gene transfer. Metabolic functions are among the most modular in the cell, and so, their genes are expected to travel laterally, even today. Many cases now are known in which a bacterial metabolic gene occurs in one or a few Archaea or vice versa. Cases of seemingly lateral transfer within the Bacteria or within the Archaea also occur, even more frequently. However, sporadic lateral transfer of a bacterial or an archaeal metabolic gene is one thing, transfers that result in a broad, if not universal, distribution of a metabolic gene within both the Archaea and the Bacteria may be another. It would help to have many more genomic sequences, so that the distributions of these genes can be defined in some detail and their phylogenetic relationships can be determined. Then we would be in a much better position to interpret their "universal" distribution among the Bacteria and Archaea.
The sequence similarities among the various versions of a given metabolic enzyme may be of some help in understanding their organismal distribution. It would appear that, in most cases, specific archaeal and bacterial versions of the genes in question can be recognized. This means that were lateral transfer responsible for their organismal distribution, the gene transfers effectively ceased before the first branchings occurred within either of the domains. Although the bacterial and archaeal versions of the enzyme are distinguishable, the sequence distinctions between the two versions tend to be relatively minornot like the profound differences that
separate the bacterial and archaeal versions of various components of
the translation or transcription machineries. This lack of genuinely
telling differences between the bacterial and archaeal versions is
exactly what would happen for genes that transferred laterally well
after the ribosome had crystallized but had themselves crystallized
before the initial branchings within each of the primary lines of
descent had occurred. (A tree based on a molecule with these lateral
transfer characteristics would be congruent with the rRNA tree, but,
unlike the rRNA tree, it would be "bushy" at its base.)
However, none of this addresses the absence of these genes in
eukaryotes. Given that metabolic genes tend to be laterally mobile and
that the eukaryotes engage in lateral gene transfers, especially (but
not exclusively) through endosymbioses, it is reasonable to expect that
the eukaryotes had no opportunity to sample the genes in question.
Thus, the lack of these metabolic genes in eukaryotes seems more
related to the nature of the early eukaryotic cell than to any specific
ancestral relationship between Archaea and Bacteria. When the genomes
of some of the deeply branching eukaryotes have been sequenced, the
perspective to resolve this problem may exist.
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CONCLUSION |
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Top
Abstract
Background
Conclusion
References
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The Universal Ancestor. The genetic annealing model is an attempt to develop a consistent general picture of the universal ancestor, and it almost succeeds at this. The ancestor cannot have been a particular organism, a single organismal lineage. It was communal (13, 22), a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn become the three primary lines of descent. The primary lines, however, were not conventional lineages. Each represented a progressive consolidation of the corresponding community into a smaller number of more complex cell types, which ultimately developed into the ancestor(s) of that organismal domain. The universal ancestor is not an entity, not a thing. It is a process characteristic of a particular evolutionary stage.
Lateral Gene Transfer. Lateral gene transfer, which has long been recognized as a secondary evolutionary mechanism, becomes primary in this primitive evolutionary dynamic. It is through lateral transfer, not vertical inheritance, that systems primarily evolve at the progenote stage. As a result of genetic mixing, organismal lineages, consensus histories of an organism's genes, did not exist, although short-term "cell lines" necessarily did. The universal ancestor does have an evolutionary history, but that history is physical, not genealogical.
Evolution in the progenote era can be seen as occurring on the subcellular level, although it actually happens in the context of (primitive) cells. The distinction here is that, in the modern world, evolutionary innovation tends to become established through selection acting on organisms, whereas in a world dominated by lateral gene transfer, an innovation takes over by direct "invasion." The organism (organismal lineage) that carries the innovation also brings with it all its other idiosyncrasies, which are potential determinants of the future evolutionary course. The innovation established through lateral transfer, however, becomes stripped of extraneous genetic baggage by that process. Evolution at the subcellular level can be viewed as a bridge between modern organismal evolution and the much earlier evolution that involved "organic" chemicals in an abiotic world. Allow me one final word about lateral gene transfer: The genetic annealing model sees two aspects to genetic temperature, mutation rate and the level of lateral gene transfer, which loosely covary. The question is whether or not this connection held only in the past, only in a world of progenotes. It is now clear that lateral transfer is far more widespread than had previously been appreciated (28), and that episodes of rapid evolution (high evolutionary temperature) have been common throughout evolution (4). The rRNA signature of this increased evolutionary temperature is unusually long ancestral branches on an rRNA tree (4), branches that are sparsely populated taxonomically (have few side branches). The length of these branches in part reflects unusual variations in the underlying rRNA sequences (4). What is seen in terms of rRNA sequence in these cases is presumably mirrored at the protein sequence level: (vertically inherited) protein genes would be more highly diverged than are their relatives in slowly evolving sister lineages (4). Now we add to this conjecture that the genomes resulting from episodes of rapid evolution will contain an abnormally high proportion of foreign genes. Genome sequences will soon be available in sufficient number to properly test whether the tempo/mode relationship (rapid evolution) invariably links increased mutation rate and increased levels of lateral gene transfer or vice versa.| |
ACKNOWLEDGEMENTS |
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I am indebted to Gary Olsen, Charles Kurland, and Ross Overbeek, for critical suggestions regarding details of the argument, to Norman Pace and David Graham for important suggestions as to making the final manuscript more readable, and to Claudia Reich for editorial suggestions. I am most indebted to Gary Olsen for the amount of time, trenchant analysis, and care he put into helping me present this thesis in an understandable manner. The author is supported in part by a grant from the National Aeronautics and Space Administration.
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FOOTNOTES |
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* To whom reprint requests should be addressed. e-mail: carl{at}ninja.life.uiuc.edu.
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ABBREVIATIONS |
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rRNA, ribosomal RNA; RS, tRNA synthetase; aaRS, aminoacyl-tRNA synthetase.
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REFERENCES |
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Top
Abstract
Background
Conclusion
References
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