Comparative Genomics and the Evolution of Animal Diversity

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Comparative Genomics and the Evolution of Animal
Diversity
Chapter 19
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• There are 25 different animal phylaeach phylum
  represents a basic type of animal (f19-1).Where
  did all this evolutionary diversity come from?The
  systematic comparison of different animal genmes
  offers the promise of identifying the genetic
  basis for diversity.

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TOPIC 1

• MOST ANIMALS HAVE ESSENTIALLY THE SAME GENES

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• Comparion of the currently avaible genomes
  reveals one particularly striking
  featuredifferent animals share essentially the
  same genens. With very few exceptions, just about
  every human gene has a clear counterpart in the
  mouse genime. In other words, no new genes were
  "invented"during the 50 million years of
  evolutionary divergence that separate mice and
  humans from their last share ancestor over
  400million years ago. Yet,the two genomes contain
  the same number of genes, and most of these
  genes-more than three quarters-can be
  unambiguously alignes.

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• The genetic conservation seen among vertebrates
  extends to the humble sea squirt, Ciona
  intestinalis. It contains half the number of
  genes group more than 500 million years ago.
  Nonetheless, nearly twothirds of the protein
  coding genes in sea squirts contain a clear,
  recognizable counterpart in vertebrates. Moreover
  the increase in gene number seen in vertebrates
  is primarily due to the duplicationof genes
  already present in the sea squirt.

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• The genetic conservation seen among chordates
  appears to extend to other phyla. As seen for the
  sea squirt, increase in gene number in
  vertebrates is primarily due to the duplication
  of genes already present ub the ecdyszoans rather
  than the invertion of entirsly new genes.

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How Does Gene Duplication Give Rise to Biological
Diversity?

• The increace in gene number seen in vertebrates
  is largely due to gene duplication.
• There are two ways this can happen.

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• First, the conventional view is that an ancestral
  gene produces nultiple genes via duplication, and
  the coding regions of the new genes undergo
  mutation.
• The second way that duplicated genes can generate
  diversity has been rather neglected until very
  recently. According to this model, the duplicated
  genes do not necessarily take on new functions,
  but instead acquire new regulatory DNA sequences.

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• Thus, we have two models for how duplicated
  genes can create diversity. According to one
  scenario, the function of the gene is modified,
  through mutation of the coding sequence.
  According to the other scenario, the two genes
  are exoressed in different patterns within the
  organism. In some cases both mechanisms operate.

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TOPIC 2

• THREE WAYS GENE EXPRESSION IS CHANGED DURING
  EVOLUTION

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• Regulatory genes encode proteins that control the
  expression of other genes. Most often these
  proteins are transcription factors, but some
  influence other steps of gene expression instead.
  Of particular interest form the perspective of
  the current discussion seem to cause significant
  changes in anmal morphology. The ds\istinguishing
  characteristic of pattern determining genes is
  that they cause the correct structures to
  develop, but in the wrong place,when they are
  misexpressed during development.

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• The major focus of this chapter is to describe
  how changes in the deployment or activities of
  these pattern determining genes produce diversity
  during evolution.
• there are three major strategies for altering the
  activites of pattern determining genes.
• 1.A given pattern detemining gene can itself be
  expressed in a new pattern. This, in turn, will
  cause those genes whose expressed it
  control(so-called target genes)to acquire new
  patterns of expression.

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• 2.The regulatory protein encoded by a pattern
  determining gene can acquire new functions, for
  example, a transcriptinal activation domain can
  be converted into a repression domain. Thus,a
  regulatory protein that was an activator of a set
  of genes might now repress them. note that,
  although this strategy involves a change in
  protein function, the evolutionary consequence is
  a result of changes in expression pattern of
  target genes.

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• 3.Target genes of a given parttern determining
  gene can acquire new regulaory DNA sequences, and
  thus come under the control of a different
  regulatory gene. In this way, their pattern of
  expression is altered.

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TOPIC 3

• EXPERIMENTAL MENIPULATIONS THAT ALTER ANIMAL
  MORPHOLOGY

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• The first pattern determining gene was identified
  in Drosophila in the Morgan fly lab. A mutation
  called bxd cause a partial transformation of
  halteres into wings.
• Abnomal morphologies are obtained through each of
  the three mechanisms descibed above altering the
  expression, function, and target of pattern
  determining genes.

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Changes in Pax6 Expreesion Create Ectopic Eyes

• The most notorious pattern determining gene is
  Pax6, which controls eye development in most or
  all animal.
• Pax6 is normally expressed within developing
  eyes but, when miseyes in the wrong tissues.
• Changes in the Pax6 expressiong pattern during
  evolutuion probably account for differences in
  the positioning of eyes in different animals.

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• Evolutonary charges in the regulation of Pax6
  expression have been more important for the
  creation of morphologically diverse eyes than
  have changes in Pax6 protein function. Thus, Pax6
  genes from other animals also produce ectopic
  eyes when misexpressed in Drosophila.

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• For example, fruit flies were engineered to
  misexpress the squid Pax6 gene. Extra eyes were
  obtained in the wings and legs, similar to those
  obtained when the Drosophila Pax6 was
  misexpressed. The flyand squid Pax6 protein share
  only 30overall amino acid sequence indentity,
  yet they mediate similar activities in transgenic
  flies.

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Changes in Antp Expression Transform Antennae
into legs

• Asecond Drosophila pattern determining gene,
  Antp, controls the development of the middle
  segement of the thorax, the masothorax.
• Antp encodes a homeodomain regulatory protein
  that is nomally expressed in the mesothorax of
  the developing embryo.

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• But, a dominant Antp mutation, cause by a
  chromosome inversion, brings the Antp protein
  coding sequence under the crotrol of a foreign
  regulatory DNA that mediates gene expression in
  head tissues, including the antennae.
• When misexpressed in the head, Antp cause a
  striking change in morphologylegs develop
  instead of antennae.

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Importance of Protein Function Interconversion
of ftz and Antp

• A second mechanism for evolutionary diversity is
  changes in the sequence and functiong of the
  regulator proteins encoded by pattern determining
  genes.
• Consider two related pattern detemining genes in
  Drosophila, the segmentation gene ftz and the
  homeotic gene Antp.

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• These genes are linked and arose from an ancient
  dupication event that predated the divergence of
  crustaceans and insects more than 400million
  years ago.
• The two cnoded proteins are related and contain
  very similar DNA-binding domains(homeodomains).
• Ftz-FtzF1 dimers recognize DNA sequences that are
  distinct from those bound by Antp-Exd dimers.

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Subtle Changes in an Enhancer Sequence Can
Produce New Patterns of Gene Expression

• The third mechanism for evolutionary diversity is
  changes in the target enhancers that are
  regulated by pattern determining genes.In this
  case neither the pcpression pattern nor the
  functiong of the encoded regulatory protein is
  altered.

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• The principle that changes in enchancers can
  rapidlly evolve new patterns of gene expression
  stems from the experimental manipulation of a 200
  bp tissue specific enchancer that is activated
  only in the mesoderm.
• Sigle nucleotide substitutions that convert each
  site into an primal Dorsal binding site cause the
  modified enhancer to be activated in a broader
  pattern.

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• Dorsal functons synergistically with another
  transcription factor Twist to activate gene
  expression in the neurogenic ectoderm.
• The modified enhancer now directs a broad pattern
  of gene expression in both the mesoderm and
  neurogenic ectoderm.
• Afew additional necleotide changes create binding
  siters for a zinc finger repressor,Snail.
• A modified enhancer contains optimal Dorsal
  sites, Twist activator, and Snail repressor
  sites,

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The Misexpression of Ubx Changes the Morphology
of the Fruit Fly

• The analysis of a Drosophila pattern determining
  gene called Ubx illustrates all three principles
  of evolutiongary change new patterns of gene
  expression are produced by changing the Ubx
  expressiong pattern, the encoded regulator
  protein, or its target enhancers.

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• Ubx encodes a homeodomain regulatory protein that
  controls the development of the third thoracic
  segment, the metathorax.
• Ubx specifically represses the expression of
  genes that are requires for the development of
  the second thoracic segement, or mesothorax.
• Indeed, Antp is one of the genes that it
  regulates. This misexpression of Antp causes a
  transformation of the metathorax into a
  duplicated mesothorax.

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• The expression of Ubx in the different tissues of
  the metathorax depends on regulatory sequences
  that encompass more than 80kb of genomic DNA.
• Amutation called Cbx disrupts this Ubx regulatory
  DNA without changing the Ubx protein coding
  region.

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Changes in Ubx Function Modify the Morphology of
Fruit Fly Embryos

• It is not currently known how Ubx functions as a
  repressor. Howover, the Ubx protein contains
  specific peptide squences that recruit repression
  complexes. One such peptide is composed of a
  stretch of alanine residues.

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• Ubx normally functions as a repressor. Ii can be
  converted into an activator by fusing the Ubx DNA
  binding domainto the potent activation domain
  from the viral VP16 protein.
• The misexepression of he mesothoracic segments,
  not metathoracic segments an seen when the normal
  Ubx protein is misexepressed in engineered
  embryos.

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• Thus, rather than behaving like the normal Ubx
  protein, the Ubx-VP16 fusion protein produces the
  same phenotype as that obtained with Antp.

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TOPIC 4

• MORPHOLOGICAL CHANGES IN CRUSTACEANS AND INSECTS

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• We now discuss how the three strtegies for
  altering the activities of pattern detemining
  genes can explain examples of natural
  morphological diversity found among different
  arthropods. The first two machanisms,changes in
  the expression and function of pattern detemining
  genes, can account for changes in limb morphology
  seen in certain crustaceans and insect.The third
  mechanism is changes in regulatory sequences.

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Arthropods Are Remarkably Diverse

• The success of the arthropods derives, in part,
  from their modular architecture.
• These organisms are composed of a series of
  repeating body segments that can be modified in
  seemingly limitless ways.

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Changes in Ubx Expression Explain Modifications
in Limbs among the Crustaceans

• Crustaceans include most, but not all, of the
  arthropods that swim.
• Slightly different patterns of Ubx expression are
  observedin branchiopods and isopods. These
  different expression patterns are correlated with
  the modification of the swimming limbs on the
  first thoracic segment of isopods.

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What is the basis for the different patterns of
Ubx exoression in isopods and branchiopods?

• There are several possible explanations, but the
  most likely one is that the Ubx regilatory DNA of
  isopods acquired mutations.
• In fact, there is a tight correlation between the
  absence of Ubx expression in the throax and the
  developmet of the feeding appendages in the
  different crustaceans.

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Why Insects Lack Abdominal Limbs

• In inscts, Ubx and abd-A repress the expression
  of a critical gene that is required for the
  development of limbs, called Distalless(Dll).

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• IN crustaceans, there are high levels of both Ubx
  and Dll in all 11thoracic segments. The Ubx
  protein has diverged between insects and
  crustaceans. Thus, Ubx represses Dll expression
  in the abdominal sedments of insects, but nut
  crustaceans.

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Modification of Flight Limbs Might Arise from the
Evolution of Regulatory DNA SEquences

• In Drosophila, Ubx is expressed in the developing
  halteres where it functions as a repressor of
  wing development.
• It is likely that Ubx functions as a repressor of
  wing development in all dipteras.

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• For example. In butterflies, the loss of Ubx in
  pacthes of cells in the hindwing causes them to
  be transformed into forewing structures. This
  observation suggests that the butterfly Ubx
  protein functions as a expressor that suppresses
  the development of forewings. Whil not proven, it
  is possible that the regulatory DNAs of the wing
  patterning genes have lost the Ubx binding sites.
  As a result, they are no longer repressed by Ubx
  in the developing hindwing.

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TOPIC 5

• GENOME EVOLUTION AND HUMAN ORIGINS

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Humans Contain Surprisingly Few Genes

• Based on the logic that we have introduces in
  this chapter, we anticipate that higher
  vertebrates, such as humans, contain
  sophisticated mechanisms fir gene regulation in
  order to produce many paterns of gene expression.
  In other words, organismal complexity is not
  correlated with gene number, but instead depends
  in the number of gene expression patterns.

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The Human Genome is very Similar o that of the
Mouse and Virtually Identical to the Chimp

• Mice and humans contain roughly he same number of
  genes-about 28,000 protein coding genes.
• The chimp and human genomes are even more highly
  conserved.

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• Between mice and human, approximately 80of these
  genes possessa clear and unique one-to-one
  sequence alignment with one another between the
  two species.
• Between the chimp and human,they vary by an
  average of just 2squence divergence.

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• By comparison, two sea squirts in the same
  population differ by more than 1sequence
  divergence, while individuals from different
  populations exhibit as much as 2.5 sequence
  variation.
• We have seen that regulatory Dna evolve more
  repidly than proeins. Perhaps the limited
  sequence divergence between chimps and humans is
  sufficient to alter the activities of several key
  regulatory DNAs.

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The Evolutionary Origins of Human Speech

Speech depends on the precise coordination of the
small muscles in our larynx and mouth. Reduced
levels of a regulatory protein called FOXP2 cause
severe defects in speech.
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• The human form of the protein is slightly
  different from those present in mice and the
  primates. In particular, there are two amino acid
  residues at positions 303and 325 that are unique
  to human thr to asn(T to N) at position 303and
  asn to ser (N to S) at possition 325. Perhaps
  these changes have altered the function of the
  human FOXP2 protein.
• Alternatively, changes in the expression
  patternor changes in FOXP2 target genes might br
  responsible for the ability of FOXP2 to promote
  speech in humans.

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How FOXP2 Fosters Speech in Humans

• A combination of all three mechanisms,changes in
  the FOXP2 expression pattern, changes in its
  amino acid sequence, and changes in FOXP2target
  genes micht explain its emergence as an imprtant
  meditor of human speech.

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• FOXP2 is just one example of a regulatory gene
  that underlies human speech. However, we have
  seen that fewer than 100 pattern detemining genes
  are sufficient to account for the morphological
  diversification of different arthropod goups.
  Perhaps a significantly smaller set can account
  for the acquisition of the language.