Evolution of Genomes

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Evolution of Genomes

• Evolution of the eukaryotic cell
• Human evolution

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Endosymbiotic Events

• Mitochondria originated from Proteobacteria
• Chloroplasts originated from Cyanobacteria
• Where did the nucleus originate from?

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Genomic Study of Endosymbiosis

• Takao Shinozawas 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 gt 1.771 indicates Archaeal origin,
  while a value of lt -1.771 indicates Eubacteria.

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Mitochondrial Genes Originated from Eubacteria
t-stats are lt -1.771 for most E-values
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Nuclear Genes Originated from Archaebacteria
t-stats are gt 1.771 for most E-values
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Cytoplasmic Genes Show No Distinct Origin
t-stats are sometimes gt 1.771 and sometimes lt
-1.117
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t-statistics

• In the mitochondrial example, the values at an
  E-value 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 lt -1.771 (Eubacterial origin)

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Existing organisms may provide information on
missing-links between bacteria and eukaryotes
Buchnera
M. leprae
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Buchnera

• 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

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The Buchnera Genome

• 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

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Types of genes which Buchnera lack

• DNA repair enzymes
• cell wall synthesizing enzymes
• enzymes involved in phospholipid synthesis
• components of signaling pathways

Types of genes which Buchnera have

• certain amino acid synthesis
• certain vitamin synthesis
• ATP synthase
• ETC

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Buchnera acts as if it is evolving into a new
organelle

• 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

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Mycobacterium leprae

• The causative agent of leprosy
• Lives inside macrophages and myelin-producing
  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

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The M. leprae Genome

• 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

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Pseudogenes in M. leprae
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M. leprae vs. M. tuberculosis
Genes lacking in M. leprae

• certain membrane lipids
• genes involved in TCA and glycolysis
• malic enzyme
• methionine synthesis

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Slow-growing organisms which have lost many genes
but can still live independently represent one
more step in the production of an organelle
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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.

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Bootstrap Analysis

• How do we know that a tree is right?
• use different methods to create the tree
  distance-based, 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 gt 70 is considered reliable

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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.

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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