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BIOLOGY 1M03 Study Guide - Nonsynonymous Substitution, Synonymous Substitution, Neanderthal Genome Project


Department
Biology
Course Code
BIOLOGY 1M03
Professor
Ben Evans

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- 40-30kya record in Europe, Neanderthals disappeared and replaced by modern people. They
have high foreheads, sharp chins, less robust body, use sophisticated tools, trading over long
distance, make art (similar to people on world today). Also found in Australia.
- There is evidence that these people first appeared in Africa before Europe. They migrated in
60kya from Africa and spread throughout the world.
Modern Human feature
Round , less robust back cranium
Vertical, high foreheads
Small and flat face, small teeth
Sharp, pointed chin
Neanderthal feature
Long, flat , low braincase
Low, receding forehead
Strong browridge
Large, wide nose
Small face and small teeth are favored by natural selection because these people did not use their
teether as tools as much as earlier people had.
Long limbs and short trunks : The body proportions of these creatures were similar to those of
people who live in warm climates and may reflect the African origins of these people.
Less robust postcranial skeleton: The skeleton of these people was much less robust than
Neanderthal skeletons. These people had longer limbs with thinner walled bones; longer, more
lightly built hands; shorter , thicker pubic bones; and distinctive shoulder blades. These modern
people relied less on body strength and more on elaborate tools and other technological
innovations to do their work.
Rounded skull: Like modern people, these people had high foreheads, distinctive rounded back
of the cranium, greatly reduced browrides.
Cranial capacity of at least 1350cc: This value is smaller than the value for Neanderthals, but
greater than the value for other hominins in the late Middle Pleistocene.
Genetic feature of Modern Homo Sapiens
1, Human and chimpanzee genomes differ in about 1% of the total nucleotides
2, A majority of protein coding genes differ between humans and chimps
- percentage of DNA that differs is not the same as the percentage of genes that differ.
- If the 1% difference is scattered out along the DNA, even 1% create great difference in terms of
what genes will be produced.
- only 29% of the homologous protein coding genes are same between chimps and humans
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3, Only a small fraction of protein coding genes shows evidence of selection since the divergence
of human and chimpanzee lineage.
Based on knowing that DNA code is redundant
Synonymous substitutions: some nucleotide substitution does not produce any change in the
amino acid sequence of the protein that results from the gene.
Nonsynonymous substitutions : alter that amino acid sequence of proteins
(Does negative selection prevents to have nonsynonymous substitution that will result in a new
phenotype that is not favored by the environment?)
(Are all negatively selected sequences synonymous substitution? since negatively selected
sequences does not favor variants)
With negative selection, more nonsynonymous substitution
With positive selection, more synonymous substitution
Directional selection favors a particular protein that produces a particular
phenotype.
Structural genes that have been subjected to selection are expected to show fewer
nonsynonymous substitutions than synonymous ones.
(because natural selection favors a particular new phenotype)
Nonadaptive process such as genetic drift are expected to affect synonymous and
nonsynoymous substitutions to the same extent.
To determine which of the protein coding genes that differ between humans and chimpanzees have
been subject to positive selection in one of the two lineages……..
Found that there is about 2.7%- 4.4% of the genes that show signs of positive selection, and
only a small fraction of these differences seem to be functional.
Hypothesize that human should have undergone a more rapid evolution than chimpanzees,
however research showed that 60% of the positively selected genes occurred in chimps and only
40% have occurred in humans.
1st reason:
Synonymous and nonsynonymous changes underestimates the amount of change due to selection.
This method assumes that the amount of evolution of a protein coding gene is proportional to the
number of nonsynonymous DNA bases that differ between two species. Sometimes the change of
one or two base pairs in a DNA sequence can strongly affect phenotype.
Eg. FOXP2 this is not even identified as a positively selected gene.
2nd reason:
- most of the evolutionary changes are not the result of changes in protein coding genes, but
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