Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees

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Parallel Patterns of Evolution inthe Genomes and
Transcriptomesof Humans and Chimpanzees

• Philipp Khaitovich, Ines Hellmann, Wolfgang
  Enard, et al
• From Max Planck Institute for
• Evolutionary Anthropology, Germany
• and WE Informatik, Bioinformatik,
• University of Dusseldorf,
• Universitatsstrasse, Germany.
• 1850-1854 VOL 309 SCIENCE
• 16 SEPTEMBER 2005

Presented by Wu Ling-Jia
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Background
Mutations can be divided into 3 groups
deleterious, neutral, and adaptive
mutations Negative selection (Purifying selection
)prevents deleterious mutation from reaching
common frequencies and so should produce an
excess of rare variation. Positive
selection(Darwinian selection) promotes the
emergence of adaptive mutation and so should
produce an excess of variation.
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• Neutral theory postulates that the effects of
  genetic drift predominate over the effects of
  natural selection, at least in the majority of
  the molecular evolutionary changes in DNA
  sequence.
• Nearly neutral theory postulates that the
  majority of spontaneous mutations are slightly
  deleterious, and that both genetic drift and
  natural selection play significant roles in
  determining whether these mutations will become
  fixed in the population.

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abstract

• The determination of the chimpanzee genome
  sequence provides a means to study both
  structural and functional aspects of the
  evolution of the human genome.
• Here the authors compare humans and chimpanzees
  with respect to differences in expression levels
  and protein-coding sequences for genes active in
  brain,heart, liver, kidney, and testis.
• 1. The patterns of differences in gene expression
  and gene sequences are markedly similar.
• (1) In particular, there is a gradation of
  selective constraints among the tissues so that
  the brain shows the least differences between the
  species whereas liver shows the most.
• (2) Furthermore, expression levels as well
  as amino acid sequences of genes active in more
  tissues have diverged less between the species
  than have genes active in fewer tissues.
• In general, these patterns are consistent
  with a model of neutral evolution with negative
  selection.
• 2. However, for X-chromosomal genes
  expressed in testis, patterns suggestive of
  positive selection on sequence changes as well as
  expression changes are seen.
• 3. Furthermore, although genes expressed in
  the brain have changed less than have genes
  expressed in other tissues, in agreement with
  previous work we find that genes active in brain
  have accumulated more changes on the human than
  on the chimpanzee lineage.

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Question 1 What kind of genes violate neutral
expectations and may have been positively
selected ?
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• Data from yeast, fruit flies, humans, and mice
  have been used to argue that regulatory evolution
  and protein evolution act independently of each
  other and thus they are decoupled.
• However,other results seem to contradict this
  assertion.

Question 2 Is the evolution of gene expression
related to the evolution of DNA
sequences(protein sequences)?
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1. Gene expression analysis

• Using probes to target sequences that are
  identical between the human and the chimpanzee,
  in five tissues from six humans and five
  chimpanzees.

(1) Gene expression patterns differ less between
humans and chimpanzees in the brain than in the
other tissues (bootstrap test, P lt 0.0001). (2)
The ratio of expression divergence between
species to diversity within species is higher in
testis than in any other tissue (5.6 versus 1.8
to 2.5, P lt 0.0001)
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• .

The authors analyzed the expression of two groups
of genes tissue-specific genes and ubiquitous
genes.
(1) Both groups of genes show similar patterns of
evolution. In particular, brain shows fewer
differences than other tissues and testis shows
an excess of divergence relative to diversity.
(2) Ubiquitously expressed genes differ less
both among individuals within a species and
between species
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2. DNA sequences analysis

• Ka the number of nonsynonymous(????)
  nucleotide substitutions per nonsynonymous site
• Ki the number of substitutions per site in
  interspersed repeats in a 250-kbp window around
  the center of each gene .

(1)brain-specific genes show lower Ka/Ki ratios
(Mann-Whitney U-test, P lt 10-6) (2)
ubiquitously expressed genes show lower Ka/Ki
ratios (Mann-Whitney U-test, Plt 10-6).
Median protein sequence divergence (Ka/Ki), of
genes expressed in one tissue (lightest color,
left) to five tissues (darkest color, right).
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3. Two factors that influence expression and
protein divergence

• For both sequence and expression divergence,
  brain shows the least differences and liver the
  most, with testis, heart, and kidney at
  intermediate levels.

Median protein sequence divergence (Ka/Ki), of
genes expressed in one tissue (lightest color,
left) to five tissues (darkest color, right).
Median expression divergence of genes expressed
in one tissue (lightest color, left)to five
tissues (darkest color, right).
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• Correlation of expression and protein sequence
  divergences Tissues with a high amino acid
  sequence divergence tend to have a high
  expression divergence (Pearsons r 0.94, P lt
  0.05)

brain
heart
kidney
liver
testis
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• (1) The correlation between expression divergence
  and protein divergence (the higher the expression
  divergence in a tissue, the higher the protein
  divergence)
• (2)Parallel patterns with respect to the
  breadth of expression (ubiquitously expressed
  genes show less divergence both in expression and
  sequence)
• Two factors that influence protein and expression
  divergence are the tissues in which a gene is
  expressed and its expression breadth.
• Both factors influence expression divergence
  (multiway analysis of variance R2 0.075, P lt
  10-6) and protein divergence (R2 0.071, P lt10-6)

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• If we correct for the influence of these factors,
  the relation between expression and protein
  divergence becomes much weaker but remains
  significant (R2 0.00019, P lt 0.05).
• Three possible reasons
• do not consider other factors that may affect
  both expression and sequence divergence, such as
  protein-protein interactions.
• the inherently large measurement errors of
  expression data.
• it may indicate that some evolutionary forces
  affect gene expression and protein divergence
  differentially.

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4. Kp(Kp/Ki) analysis

• Putative core promoters (Kp) a 1500-bp region
  upstream and 500-bp region downstream of the
  transcriptional start.
• Kp and the ratio Kp/Ki are significantly
  correlated with expression divergence (R2
  0.001, P lt 10-6 and R2 0.0004, P lt 10-3,
  respectively).
• Given that genetic differences in promoters
  are more likely to directly cause differences in
  expression levels, these correlations may seem
  surprisingly weak.

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• Problems
• (1)many or most sites in these promoter
  regions are likely not relevant for
  transcriptional activity (median Kp/Ki 0.82
  versus 0.15 for Ka/Ki)
• (2)the relevant transcription start sites
  might not be identified for all tissues.
• Much more work is necessary to elucidate the
  relation between the evolution of promoter
  sequences and expression levels.

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5. The evolution of gene expression largely
conform to a model of neutral evolution with
negative selection.

• Constraints in tissues Each tissue is associated
  with a certain level of evolutionary constraints
  acting on the genes expressed in itfor instance,
  brain imposes more constraints than liver.

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The parallelism between sequence evolution and
expression evolution
Most evolutionary changes in nucleotide sequences
conform to a neutral theory
Most evolutionary changes in gene expression are
similarly selectively neutral or nearly neutral
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Neutral selection
Constraints in tissues
Neutral hypothesis

• The extent of expression differences found
  between species is largely determined by the time
  since they shared a common ancestor and the
  extent of negative selection in a particular
  tissue

• Brain, heart, kidney, and liver have similar
  ratios of expression divergence between species
  to diversity within species is compatible with a
  model in which gene expression changes are a
  function of time.

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• The divergence to diversity ratios are smaller
  than would be expected if time were the sole
  factor influencing gene expression.
• A probable explanation experimental and
  environmental variation contributes
  proportionally more to interindividual
  differences than to divergence.

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6. Genes expressed in testis may have been
positive selected.

• A high ratio of gene expression divergence
  between species to gene expression diversity
  within species may indicate the action of
  positive selection.
• As seen above, testis differs from other organs
  in that the ratio of expression divergence to
  diversity is higher.
• Possibility 1due to a few genetic differences
• However, although human and chimpanzee testicles
  differ in size, there is no evidence that the
  cellular composition of this organ differs
  between the species.

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Possibility 2 gene expression patterns in
testis have a smaller environmental component

• In that case, we would expect genes expressed in
  testis to be subject to as much constraint as
  genes expressed in tissues such as liver or heart
  that have a comparable expression divergence.
• However, we find that among the five tissues,
  expression in testis is associated with the
  highest number of significant reductions in
  diversity in tissues other than testis, whereas
  expression in liver is associated with the
  highest number of significant increases of
  diversity in tissues other than liver.
• This suggests that strong selective constraints
  on genes, rather than low environmental
  influence, account for the low extent of
  expression diversity in testis.

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• Thus, the higher ratio of gene expression
  divergence to diversity in testis as compared
  with the other tissues is indeed indicative of
  positive selection.

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• The authors investigated if genes with expression
  differences between humans and chimpanzees are
  unevenly distributed among chromosomes.

In testis, genes on the X chromosome show a
significant excess of expression differences when
compared to the other chromosomes (binomial test
corrected for multiple testing, Plt10-5), whereas
in the other tissues we find no significant
differences among chromosomes.
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• The authors investigated the DNA sequence
  divergence of genes expressed in different
  tissues with respect to chromosomal location.

(1)For genes expressed in brain, heart, kidney,
and liver, neither the autosomes nor the X differ
from each other with respect to Ka/Ki. (2)In
contrast, among genes expressed in testis, those
located on the X have significantly higher Ka/Ki
ratios than those located on the autosomes
(Mann-Whitney U-test, P lt 0.0005).
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• Thus, genes expressed in testisespecially those
  located on the Xtend to accumulate expression
  changes as well as sequence changes that may have
  been positively selected.
• This is compatible with the observation that
  genes involved in reproduction tend to evolve
  under positive selection. At the organismal
  level, this may correlate with mating strategies
  in different ape species.

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7. More gene expression changes occurred on the
human evolutionary lineage.

• The authors examined whether differences in gene
  expression are equally distributed along the
  human and chimpanzee lineages.
• (1)The distributions are positively and
  significantly skewed(????) for brain, heart,
  liver, and testis. more gene expression changes
  occurred on the human evolutionary lineage than
  on the chimpanzee lineage.
• (2)In magnitude, this acceleration of gene
  expression change is largest in brain, and
  significantly larger than in any of the other
  tissues (P lt 0.05) except heart (P 0.10).

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• This is in agreement with previous work that
  found a larger acceleration of gene expression
  changes on the human relative to the chimpanzee
  lineage in brain than in liver when using an
  orangutan(??) as an outgroup.
• Thus, although gene expression is more
  constrained in brain than in other tissues, it
  has changed relatively more on the human lineage.

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8. More amino acid changes occurred on the human
evolutionary lineage

• The authors investigate if such a pattern is seen
  also at the amino acid sequence level

(1)For genes expressed specifically in heart,
kidney, liver, and testis, the ratios of the
numbers of changes on the human and chimpanzee
lineages vary between 0.79 and 1.04, whereas for
all genes the ratio is 1.12 (2)By contrast, for
genes expressed in brain, the ratio of
human-specific to chimpanzee-specific amino acid
changes is 1.40, higher, though not significantly
(P0.08), than for genes not expressed in brain
and higher than for genes expressed in any other
single tissue (P lt 0.05).
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• This finding is in agreement with recent work
  showing a faster evolution on the human lineage
  for a set of genes involved in brain function and
  development.
• Thus, the acceleration seen for gene expression
  is corroborated on the sequence level for brain
  but not for other tissues.
• Such an acceleration on the human lineage could
  be caused by a relaxation of selective
  constraints on both the structure and expression
  of brain proteins during human evolution. A more
  compelling alternative is that the acceleration
  is caused by positive selection that changed the
  functions of genes expressed in the brains of
  humans more than in the brains of chimpanzees.

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summary

• (1)Evolutionary change in gene expression are
  largely compatible with a neutral model, in which
  different levels of constraints acting in
  different tissues add up for single genes.
• (2) These evolutionary constraints act in a
  similar manner on the coding regions of DNA
  sequences and thus lead to parallel patterns in
  expression and sequence evolution.
• (3)In contrast to the overall picture of
  selective neutrality, two examples of putative
  positive selection stand out.
• First, testis shows an excess of expression
  differences between species and an enrichment of
  both expression and amino acid sequence
  differences on the X chromosome.
• Second, the brain, although under more
  constraints than the other tissues, has an excess
  of gene expression and amino acid changes on the
  human lineage compared to other tissues.

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• This suggests that evolutionary changes at
  both the level of gene regulation and the level
  of protein sequence have played crucial roles in
  the evolution of certain organ systems, such as
  those involved in cognition or male reproduction.
  
• The modest number of sequence differences in
  genes between humans and chimpanzees cannot be
  taken as evidence that regulatory changes would
  necessarily be more important than structural
  protein changes during human evolution Rather,
  both types of changes are likely to have acted in
  concert.

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Thank you!