WRITTEN REPORT ON BIOLOGY 2

Limitations on the Classic Model and other Phylogenetic Model

Objectives:

 Identify the limitations to the classic model of phylogenetic trees

 Identify other phylogenetic models

Key Points:

 Horizontal gene transfer is the transfer of genes between unrelated species.

 Gene transfer has provided theories of genome fusion between symbiotic

and endosymbiotic organisms.

 Web of life is a phylogenetic model that resembles a web or a network more

than a tree

 Ring of life is a phylogenetic model where all three domains of life (Archaea,
Bacteria, and Eukarya) evolved from a pool of primitive prokaryotes

Vocabulary words:

Phylogenetic - of, or relating to the evolutionary development of organisms

Prokaryote- an organism whose cells do not contain a distinct nucleus

Eukaryote - cells that have a nucleus enclosed within membranes.

Transformation - horizontal gene transfer mechanism where naked DNA is taken up

by bacterium

Transduction - horizontal gene transfer mechanism in prokaryotes where genes are

transferred using a virus

Conjugation - temporary fusion of organisms, the use of a hollow tube called pilus to
transfer genes

Symbiotic - involving interaction between two different organisms living in close

physical association.
Limitations on the Classic Model

The Prokaryotic Evolution, included in the classic model, is that species evolve
clonally.This view is somewhat complicated in eukaryotes that reproduce sexually.

The Law of Mendelian Genetics explain the variation in offspring, again to be a

result of a mutation within the species. The concept of genes being transferred
between unrelated species was not considered as a possibility until recently.

Vertical Gene Transfer

This is a transfer of genes vertically from parents to offspring. This kind of transfer is
used in sexual reproduction.

Horizontal Gene Transfer

The passing down of genetic material from one species to another species.These
transfers allows even distantly related species to share genes, influencing their
phenotypes.

This transfer mostly happens on prokaryotic cells, however only 2 % of these

genetic materials are acquired or is transfer in this process.These gene transfers
between species are the major mechanism whereby bacteria acquire resistance to
antibiotics. Some bacteria tends to acquire DNA or genetic materials that can give
them the resistance to such antibiotics that makes it hard for doctors or people to fight
diseases.

Horizontal Gene Transfer in Prokaryotes

HGT is very common in prokaryotes compared to eukaryotes. There three different

mechanisms on how a prokaryotic cells transfer genetic material to a distant species.

The first one is transformation, in this mechanism a naked DNA is taken up by a

bacterium. When a cell has been broken there will be a release of its genetic material.
The bacterium then gather this DNA and uses it as its own and if luckily, tends to pass
on these foreign gene when it replicates. Second mechanism is the transduction,
where as DNA is transferred through virus. Lastly, conjugation where as it is known to
be a temporary fusion for it uses hollow tube called a pilus to transfer genes between
organisms.
 There had been a latest discovered type of mechanism called Gene Transfer
Agnets (GTA). This is a small, virus-like particles that transfers random genomic
segments from one species of prokaryote to another.

Horizontal Gene Transfer in Eukaryotes

The gene transfer between multicellular eukaryotes are thought to be difficult.It is

thought that this process is rarer in eukaryotes and has small evolutionary impact than
prokaryotes. Even though its is not really common HGT between distantly related
organisms has been dmonstarted in several eukaryotic species. For example is the red
aphids that got theri color from a pigment called red cartenoid. This kind of genes is
only found in a specific fungi. Scientists thought that when the aphids ate the fungi on
the plant they then acquired this genetic material making their green color turns to red.

Genome Fusion and the Evolution of Eukaryotes

Scientists believe the ultimate in HGT occurs through genome fusion between
different species of prokaryotes when two sybiotic organism become endosymbiotic.
This occurs when one species is taken inside the cytoplasm of another species, which
ultimately results in a genome consisiting of genes from both the endosymbiont and the
host.

This mechanism is an aspect of the endsymbiotic theory, which is accepted by a

majority of bioligists as the mechanism whereby eukaryotic cells obtained their
mitochondria and chlororplast.

“ENDO” latin word that means IN and“SYMBIOTIC” meaning living closely together.
Combining these two words, endosymbiotic then means living closely together inside.
The endosymbiotic theory explains how from a prokaryotic cell evolved into a
eukaryotic cell acquiring mitochondria and chloroplast.

This theory states that there were three kinds of prokaryotes, the aerobic bacteria
(bacteria that produces energy through the use of oxygen), cyanobacteria (bacteria
that produces its own food from sunlight) and a one big prokaryote that is larger than
the two. Then some of the large prokaryotic cells engulf first the aerobic bacteria that
through time then evolved into mitochondria then after some tife the cyanobacteria was
also been engulfed and then evolved into a chloroplast.

The evidences of these theory is that mitochondria and chloroplast has its seperate
kind of DNA and a prokaryotic cell has it’s own genetic material that made the
scientists conclude to this kind of theory.

James lake of the UCLA/NASA Astrobiology Institute proposed that eukaryotic

cells developed from an endosymbiotic gene fusion between two species, one an
archaen and other a bacteria and also that Gram-negative bacteria, which are unique
within their domain contain two lipid bilayer membranes.

Other than Lake’s hypothesis there are three more that explains and uses the
genome fusion and evolution of prokaryotic and eukaryotic cells. First is the
Nucleus-first hypothesis where nucleus is said to be evolved in prokaryotes first,
followed by a later fusion of the new euakaryote with bacteria that became
mitochondria. Second hypothesis is the Mitochondrion-first hypothesis where
mitochondria is said to be first established in a prokaryotic host, which subsequently
acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cells.
And lastly the Eukaryote-first hypothesis which is interesting as it said that
prokaryotes actually evolved from eukaryotes by losing genes and complexity.

Other Phylogenetic Models

Web and Network models

In 1999, a phylogenetic model that resembles a web or a network more than a tree
was proposed. The hypothesis is that eukaryotes evolved not from a single prokaryotic
ancestor, but from a pool of many species that were sharing genes by HGT
mechanisms. Some individual prokaryotes were responsible for transferring the
bacteria that caused mitochondrial development in the new eukaryotes, whereas other
species transferred the bacteria that gave rise to chloroplasts. This model is often
called the “web of life.”

RIng of life models

 This is also porposed by James Lake in accordance to his proposed hypothesis.
This is a phylogenetic model where all the three domains of life evolved from a pool of
primitive prokaryotes.Using the conditioned reconstruction algorithm, it proposes a
ring-like model in which species of all three domains (Archaea, Bacteria, and Eukarya)
evolved from a single pool of gene-swapping prokaryotes.

This structure is proposed as the best fit for data from extensive DNA analyses; the
ring model is the only one that adequately takes HGT and genomic fusion into account.
However, phylogeneticists remain highly skeptical of this model.

In summary, the “tree of life” model proposed by Darwin must be modified to

include HGT. This does not mean a tree, web, or a ring will correlate completely to an
accurate description of phylogenetic relationships of life. A consequence of the new
thinking about phylogenetic models is the idea that Darwin’s original conception of the
phylogenetic tree is too simple, but made sense based on what was known at that time

Submitted by: Submitted to:

Albaira, Arabela S. Mr. Edgar Ubalde

Arandia, Kryzeanne B. Biology Teacher

STEM 11-B