Download Organismal lineages

8392–8396 | PNAS | July 18, 2000 | vol. 97 | no. 15
Interpreting the universal phylogenetic tree
Carl R. Woese*
Department of Microbiology, University of Illinois at Urbana-Champaign,
B103 Chemical and Life Sciences Laboratory, MC-110, 601 South Goodwin Avenue,
Urbana, IL 61801-3709
Archaea | Bacteria | Eucarya | universal ancestor |
horizontal gene transfer
2009/03/06
KORDI, MMG
Jeong, Da Geum
The universal phylogenetic tree
Extant
life
Vertically
derived &
Horizontally
acquired
variation
Ancestor
* The Grand Challenge
•A New Era, a New Perspective
* A Lesson from Some Wanderers.
•Horizontal Gene Transfer
* The Evolutionary Roles of Horizontally Acquired and
Vertically Generated Variation
* How the organization of the Cell Shapes Horizontal Gene
Transfer.
•Organismal History, Genealogy, and the Concept of Organismal Lineage
•What is the Universal Phylogenetic Tree Tell us?
•Cellular Evolution
•Summary and Conclusion
The Grand Challenge
Darwin’s Vision
Molecular Biology (1960s’~)
- Molecular sequencing
⇒ Gene histories + Organismal genealogies
- Genome sequencing
⇒ Full history of cellular life
New molecular approach vs. Old classical ones:
Molecules ancestral to a group, whose phenotypes
are invariant within the group(ex: Plesiomorphies)
Huxley
www.aca2000.com
Darwin
blog.chosun.com
=>Phylogenetic relationships
Comparing the sequence of molecules
 Genealogicla trees for Darwin’s great kingdoms
 Universal phylogenetic tree
(united all of the kingdoms) ”Empire”
Plesiomorphy: An ancestral or primitive character
Apomorphy: A derived or specialized character
The Grand Challenge
http://mic.sgmjournals.org/cgi/content-nw/full/146/5/1045/F1
Ribosomal RNA
•Molecule ubiquitous
•Functional constancy
•Changes slowly
•Tractable
•Highly Complex
<-> Horizontal gene transfer
so, a bona fide organismal trace
* The universal Tree -> Microbiology
Side -> center
Most important impact of the universal phylogenetic tree
A new and powerful perspective
An image that unifies all life (histories and common origin)
Life’s incredible diversity
The Overwhelming importance of the microbial world
A New Era, a New Perspective
1990s
Genomic era.
Sequences of many molecules, whose distriburtions are phylogenetically broad
-> not agree with the rRNA-based universal phylogenetic tree
The cause of this incongruity
•Reticulate Evolution
•Horizontal gene flow
That is what is now beginning to happen.
Confusion of trees
* rRNA tree is not the true organismal tree.
* Archaea and Bacteria are specifically related than with eukaryotes
-> the most basic systems(genome replication, expression system) of the cell
-clearly suggest a specific relationship between the Archaea and the Eukrayotes.
•Horizontal gene transfer as having completely erased any record of the deepest
branchings in the universal phylogenetic tree -> root and earliest branchings of
the tree are not knowable.
I interpret them from a classical biologist’s perspective instead of
asking, tabula rasa, what the rRNA(or any other) tree means,
what it is telling us about the evolutionary process and
about the origin and organization of modern cells.
A Lesson from Some Wanderers
* Aminoacyl-tRNA synthetases (aaRS)
=Subject to extensive horizontal gene transfer(HGT)
From the species level to transfers between organismal domains
=generally be translated independently
journals.prous.com
*From these twenty enzymes => Universal phylogenetic trees
-Unexpected taxonomic juxtaposition.
ex) rickettsias & mycobacteria= ostensible sister relationship (2-I,M aaRS)
-But, same basic branching pattern
-Same major taxonomic grouping within each domain as does the rRNA tree
Consequently, aaRS trees cannot itself be the result of HGT
An organismal gene trace is preserved in certain of the cell’s componentry
-a trace that extends back to the stage of the universal ancestor of all extant lifeis unavoidable
Horizontal Gene Transfer – HGT
Horizontal gene transfer (HGT), also known as lateral
gene transfer, refers to the movement of genetic information
across normal mating barriers, between more
or less distantly related organisms, and thus stands in
distinction to the standard vertical transmission of genes
from parent to offspring.
Ex) plastid, mitochondria
nature reviews | genetics volume 9 | august 2008 | 605-618
Horizontal Gene Transfer – HGT
* Selectively driven
- evolutionary impact
* Selectively neutral
- simpler to interpret
•The universality of the genetic code attests to
the evolutionary importance of the process
mechanisms: exclude, destroy, counteract foreign DNA(deleterious)
none seems to use the strongest defense against alien protein coding genes.
=> Alien genes would be of no value
=>HGT is an avoidable consequence of a universal genetic code
But rather the reverse, HGT selectively maintains
the universality of the genetic code
Horizontal Gene Transfer – HGT
The evolutionary Roles of Horizontally Acquired and
Vertically Generated Variation
The yin and the yang ( - , +)
Without their interplay, evolutions as we know it seems impossible.
Vertically generated variation:
necessarily highly restricted in character
Variations on a lineage’s existing cellular themes
Horizontal transfer:
on the diversity of the entire biosphere, molecules and systems
in a great variety of different cellular environments. => major,
* Evolutionary source of true innovation
Novel enzymatic pathways,
novel membrane transporter capacities,
novel energetics, etc
Horizontal Gene Transfer – HGT
The evolutionary Roles of Horizontally Acquired and
Vertically Generated Variation
What is special about vertically generated variation(VGV)?
VGV may hold the key to the evolution of biological complexity and specificity.
Ex) simple cyclic process, homodimeric molecule -> tandem duplication
Homodimer -> Heterodimer, something potentially more sophisticated functionally
than the original homodimer
A small, simple molecule
Large, functionally complex one
Have a higher biological specificity
Vertically generated variation
The principal way in which biological complexity, specificity,
and cellular integration evolve
True novelty (HGT) + complexity, functional differentiation & integration(VGV)
=> Two forces whose interplay propel the evolution of the cell
Horizontal Gene Transfer – HGT
The evolutionary Roles of Horizontally Acquired and
Vertically Generated Variation
Organism B
Real!
HGT
Organism A
Organism A
Organism B
Organism A
Investigator!
VGV
Organism A
A vs.B
Phylogenetically close enough
Proteins(circle) differ very little in sequence
And not at all in function
Neutral horizontal gene transfers of cellular
Components should predominantly involve
Closely related species
Horizontal Gene Transfer – HGT
How the Organization of the Cell Shapes Horizontal Gene Transfer
Cellular organization in particular strongly affects the quality of HGT
The degree and nature of coupling among the various cellular components
1.Loosely coupled to the cellular fabric.
*Structure: modular component=> independent
*Function: self-defined and minimally connected to other cellular functions
*Ex) The aminoacyl-tRNA synthetases,
*Easy to get HGT, easily involve phylogenetically remote donors.
On the other hand,
2. Tightly coupled into the cellular fabric, strongly integrated with others
*Structurally and/or functionally : make large complexes or complex network
*Tend not to be (fully) functional in their own right.
*ex) Ribosomal proteins
*HGT: relatively small extent, only donors closely related to the recipient.
Organismal History, Geneaology, and the Concept of Organismal Lineage
*Genomics
Evolutionary history of an organismal lineage ≠ Organismal geneaology
A cell’s evolutionary history
From the highly modular to the tightly integrated
*Organismal lineage
Reticular wanderings of modular elements, in which the steady,
predictable vertical descent of the tightly integrated element is lost
*Organismal genealogy
Be central to, integrated into, and so, defining of the fabric of the cell(organism)
Organismal History, Geneaology, and the Concept of Organismal Lineage
Organismal genealogical trace:
The trace of population to which the individuals organism belongs
A subtle but useful change in general and the HGT
1) All sexually reproducing species ->HGT with every generation
-Strictly confined to the gene pool
2)Asexually reproducing species (microorganisms)
-Hard to define a comparable gene pool
*Closely related microoragnisms
Extensive genetic transfer(whole chromosomes, large sections)
* Individuals genes: various vector(phages, plasmids, naked DNA)
-> need not be phylogenetically close, between donar and recipient organisms
ex) transfer of antibiotic resistance
Organismal History, Geneaology, and the Concept of Organismal Lineage
Metaphorically speaking,
Organismal genealogies are fuzzy lines, fuzzier at some junctures than at others.
HGT from closely related donors need not significantly blur
Blurring is a function of taxonomic level
the organismal genealogical trace in the limit becoming indistinguishable
Ex) Proteobacteria : E.coli and Proteus
Same gene transfer would be of no significance
Different taxonomic level-> different degrees of “phylogenetic resolution”
Organismal genealogy: ill-defined, context dependent, not homogeneously mixed
Organismal lineages
HGT is basically confined to a natural taxonomic grouping(gene pool)
Their “fuzziness” does not significantly overlap that of other lineages.
What Is the Universal Phylogenetic Tree Telling Us?
1. The nature of the entity represented by its root
2. How this entity gave rise to the primary organismal lineage
We cannot blithely assume that the universal ancestor is just a typical ancestor,
a modern, fully evolved and complex type of cell.
What the universal ancestor was and how it gave rise to the first lineages
are pivotal biological questions.
What Is the Universal Phylogenetic Tree Telling Us?
1.: The amount of evolutionary change occurring during earlier, > during latter
Different quality of the rate of evolution rapid in the earlier one.
Lack of homology
(aaRA)
Genome replication mechanism
Strongly resemble
3billion yrs
Ancestors of the Bacteria
Universal ancestor stage
1.5
Billion
yrs
1. Relatively short period
Prebiotic chemical stage
What Is the Universal Phylogenetic Tree Telling Us?
Transcription apparatus
-underwent radical change, major refinement
Bacteria vs. Archaea
Archaea vs. Eucarya
Genome replication
mechanism
No resemblance
Resemblance
Transcription apparatus
on the modern cells
Lack of homology
Closely related
Translation apparatus
No counterpart
Closely related
The root and earliest branchings of the universal phylogenetic tree were not modern cells,
but primitive types of cellular entities in the process of becoming modern cells.
The universal phylogenetic tree is not confined to what we can call the
“modern evolutionary era”
The deepest branchings of this tree take us into uncharted evolutionary waters;
Cellular Evolution
Modern cells:
Fully evolved entities,
Be sufficiently complex, integrated, “individualized”
3 distinct celluar design: the bacteria, the archaeal, and the eukaryotic
The stage when cells are simple enough, HGT totally dominates the evolutionary
scene, and all life becomes a single, diverse gene pool;
all of the cell’s componentry can be subject to horizontal gene flow.
-> radical novelty need to progressively boot-strap primitive cellular entities
into modern cells can occur.
At such a stage, evolution was in effect communal: there was a progressive
evolution of the whole, not an evolution of individual organismal lineages per se.
From the universal gene pool (the communal ancestor), there will emerge
“individual” pools, characterized by the fact that HGT continuous to occur in
a more or less, but HGT becomes progressively restricted in character
Cellular Evolution
Primary organimsal
Lineages will be of
“fuzzy” variety
Active HGT
No HGT
Because immunity to displacement
extends to the specific pools
themselves will these subsystems
become fully locked-in
Stable cellular lineage
Vertical inheritance
True organismal geneaology can arise.
The balance between horizontally acquired and vertically generated variation
will continue to change until the evolution of the cell is complete,
until the complex(finalized) modern cell types emerge
Summary and Conclusion
The universal phylogenetic tree based on rRNA is a valid representation
of organismal genealogy,
≠
any other phylogenetic tree.
It transcends the era of modern cells; its deepest branchings extends back in time
to an era when cellular entities were considerably more primitive
than cells are today
The primary bifurcation of the universal phylogenetic tree presents
the first evolutionary stage at which cellular design became sufficiently stable
that horizontal gene transfer could not completely was away a collective
(organismal) trace, and true organismal lineages then gradually began to consolidate
Summary and Conclusion
At the first organismal trace resided in a few molecular species only.
Those that had become sufficiently complex (tightly coupled) and
Woven into the emerging cellular fabric that they were largely refractory
to global horizontal gene displacement
-> RNA component – integrated entities - other functions
Exception: aminoacyl-tRNA synthetases, etc.
: modular components of the translation apparatus
that are subject to widespread HGT…
Summary and Conclusion
The high, pervasive levels of HGT created an evolutionarily communal state
of living systems in the sense that the aboriginal organismal community evolved
With the enevitable emergence of complexity in early cellular entities, a stage
was reached where distinct subpopulations emerged from
the universal ancestral communal state
HGT continued to abate wihin and between these pools- three of which would refine
into the ancestors of the three extant organimsal domains- until the evolution of
the cell (in each) attained a (modern) fully evolved stage.
This stage was probably reached as the major lineages
in each organismal domain emerged