Transcript Evolution of Genomes

Evolution of Genomes
Evolution of the eukaryotic cell
Human evolution
Endosymbiotic Events
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Mitochondria originated from Proteobacteria
Chloroplasts originated from Cyanobacteria
Where did the nucleus originate from?
Genomic Study of Endosymbiosis
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Takao Shinozawa’s group in Japan compared
orthologs between yeast an either eubacteria or
archaea.
E-values are represented as -log E (the larger the #
the better E-value).
The bit scores get larger as the E-values decrease,
resulting in a lower # of hits (lines have - slope)
A t-statistic test was performed comparing data from
the two domains.
A t-stat of > 1.771 indicates Archaeal origin, while a
value of < -1.771 indicates Eubacteria.
Mitochondrial Genes
Originated from Eubacteria
t-stats are < -1.771
for most E-values
Nuclear Genes Originated
from Archaebacteria
t-stats are > 1.771
for most E-values
Cytoplasmic Genes Show
No Distinct Origin
t-stats are sometimes
> 1.771 and
sometimes < -1.117
t-statistics
In the mitochondrial example, the values at an Evalue of 10-5 were 12, 15, 19, 21 ,24 & 27 for
Archaea and 65, 66, 68, 73, 75, 80, 81, 82 & 93 for
Eubacteria. We then determine the sample size (n),
the mean (y), and the standard deviation (s) for each.
 The standard deviations are then pooled using:
sp = sq rt [((n1 - 1) s12 + (n2 -1) s22)/(n1 + n2 -2)]
 The t-statistic is then determined by:
t = (y1 - y2)/(sp * sq rt [1/ n1 + 1/ n2]
In this case, t < -1.771 (Eubacterial origin)
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Existing organisms may provide
information on “missing-links”
between bacteria and eukaryotes
Buchnera
M. leprae
Buchnera
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All animals, with the exception of aphids,
excrete toxic nitrogenous waste
Aphids have 60-80 large cells in their
abdomens called bacteriocytes
Bacteria called Buchnera inhabit this organ
Neither organism can reproduce without the
other
Their symbiotic relationship is thought to date
back 225 million years
The Buchnera Genome
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At 640,681 bp, it is the 2nd smallest sequenced
Contains 583 genes
500 are very similar to E. coli, 79 are related to
other bacterial, only 4 are unique to Buchnera
Many genes which are non-essential to the
symbiotic relationship have been lost over time
Buchnera can only synthesize amino acids
which aphids are unable to produce
Types of genes which Buchnera lack
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DNA repair enzymes
cell wall synthesizing enzymes
enzymes involved in phospholipid synthesis
components of signaling pathways
Types of genes which Buchnera have
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certain amino acid synthesis
certain vitamin synthesis
ATP synthase
ETC
Buchnera acts as if it is evolving
into a new organelle
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It uses glutamine as a substrate to make
essential amino acids, hence no nitrogenous
waste is produced
Someday it may be completely engulfed by
cells as an “aminoacid-plast”
Mycobacterium leprae
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The causative agent of leprosy
Lives inside macrophages and myelinproducing Schwann cells
Still infects many people, mostly in 3rd world
countries Unable to be cultured in the
laboratory
Must be grown in the nine-banded armadillo
The bacterium divides once every 14 days
The M. leprae Genome
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Contains 3.3 million bp (compared to the 4.4
million of M. tuberculosis)
Encodes 1,600 proteins (compared to 4,000)
Only 50% of genome codes for proteins
The rest is pseudogenes (1100 in number)
Other genes appear to have been replaced by
orthologs
Pseudogenes in M. leprae
M. leprae vs. M. tuberculosis
Genes lacking in M. leprae
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certain membrane lipids
genes involved in TCA and glycolysis
malic enzyme
methionine synthesis
Slow-growing organisms which
have lost many genes but can still
live independently represent one
more step in the production of an
organelle
Human Evolution
3000 bp of nuclear sequence was used to create
phylogenetic trees.
Humans are closely related to the great apes.
The base of the mammalian tree is a Tree shrew.
Bootstrap Analysis
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How do we know that a tree is right?
use different methods to create the tree: distancebased, maximum parsimony, etc.
use bootstrap analysis
Bootstrapping repeats the tree-building process
thousands of times using different subsequences
The percent of times that a branch point agrees in
the various replicates becomes its bootstrap value
A bootstrap value > 70 is considered reliable
How much diversity is there
among groups of primates?
10,000 bp of non-coding DNA from X
chromosomes of various primates was compared.
The MRCA (Most Recent Common Ancestor) was
determined for each.
 MRCA for humans was 540,000 years ago
 MRCA for gorilla was 1.2 million years ago
 MRCA for chimps was 1.9 m years ago
 MRCA for orangutans was 2.1 m years ago
Humans were seen to have less diversity than any of the
great apes since Neanderthals have become extinct.
Where and when did modern
humans evolve?
One theory: “recent Africa hypothesis” predicts
African origin 100,000-200,000 years ago.
 Another theory: “multiregional hypothesis” predicts a
gradual evolution at sites around the world.
Genomic data from mitochondria (16,500 bp) were
compared between people from diverse locations.
A phylogenetic tree reveals how long it has been since
African and non-African populations converged.
The MRCAs for various populations can be determined
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The origin and dispersal of humans
MRCA for Africans and non-Africans was
52,000 +/- 27,500 years
 MRCA for all modern humans was 171,500
+/- 50,000 years
These data support the recent Africa hypothesis
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