Comparative Genomics and the Evolution of Animal Diversity

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Chapter 19

• Comparative Genomics and the Evolution of Animal
  Diversity
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Outline

• 1Most animal have essentially the same genes
• 2Three ways expression is changed during
  evolution
• 3Experimental manipulations that alter animal
• Morphology
• 4Morphological changes in crustaceans and
  insects
• 5Genome evolution and human origins

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Topic 1 Most animal have essentially the same
genes

• 1-1 different animals share essentially the same
  genes.
• The genetic conservation seen among vertebrates
  extends to the humble sea squirt.
• The genetic conservation seen among chordates
  appears to extend to other phyla.

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1-2 How does gene duplication give rise to
biological diversity?

• There are two ways this can happen
• 1 The conventional view is that an ancestral gene
  produces multiple genes via duplication ,and the
  new genes undergo mutation.
• 2 Duplication genes can generate diversity has
  been rather neglected until very recently.

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Topic 2 Three ways gene expression is changed
during evolution

• 1. A given pattern determining gene can itself be
  expressed in a new pattern.
• 2.The regulatory protein encoded by a pattern
  determining gene can acquire new functions.
• 3.Target genes of a given pattern determining
  gene can acquire new regulatory DNA sequences,
  and thus come under the control of a different
  regulatory gene.

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Topic 3 Experimental manipulations that alter
animal morphology

• The first pattern determining gene was identified
  in Drosophila in the Morgan fly lab.
• A mutation called bxd causes a partial
  transformation of halteres into wings.

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3-1 Changes in Pax6 expression create Ectopic Eyes

• The most notorious pattern determining gene is
  Pax6, which control s eye development in most or
  all animals .
• Pax6 is normally expressed within developing
  eyes but when misexpressed in the wrong
  tissres,Pax6 causes the development of extra eyes
  in those tissues.
• Evolutionary changes in the regulation of Pax6
  expression have been more important for the
  creation of morphologically diverse eyes than
  have changes in Pax6 protein function.

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3-2 Changes in Antp expression transform Antennae
into Legs

• A second Drosophila pattern determining gene,
  Antp, controls the development of the middle
  segment of the thorax, the mesothorax.
• Antp encodes a homeodomain regulatory protein
  that is normally expressed in the mesothorax of
  the developing embryo .
• But a dominant Antp mutation caused by a
  chromosome inversion brings the Antp protein
  coding sequence under the control of a foreign
  regulatory DNA that mediates gene expression in
  head tissues ,including the antennae.

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3-3 Importance of protein function
interconversion of ftz and Antp

• Pattern determining genes need not be expressed
  in different places to produce changes in
  morphology.
• A second mechanism for evolutionary diversity is
  changes in the sequence and function of the
  regulatory proteins encoded by pattern
  determining genes .

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• The Antp and Ftz proteins recognize distinct
  DNA-binding sites becarse they protein
  interactions are mediated by short peptide motifs
  that map outterapeptide sequence motif, YPWM.

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• Ftz-FtzF1 dimers recognize DNA sequences that are
  distinct from those bound by Antp-Exd dimers. As
  a result, Antp and Ftz regulate different target
  genes.

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3-4 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.

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• The principle that changes in enhancers can
  rapidly evolve new patterns of gene expression
  stems from the experimental manipulation of a 200
  bp tissue specific enhancer that is activated
  only in the mesoderm.

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• Dorsal functions synergistically with another
  transcription factor Twist to activate gene
  expression in the neurogenic ectoderm.
• There are no Twist binding sites in the native
  enhancer.
• A total of eight nucleotide substitutions are
  sufficient to create two Twist binding sites
  (CACATG). When combined with the two nucleotid
  substitutions that produce high-affinity Dorsal
  binding sites,the modified enhancer now directs a
  broad pattern of gene expression in both the
  mesoderm and neurogenic ectoderm.

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• A series of 2, 10, and 14 nucleotide
  substitutions produce a spectrm of Dorsal target
  enhancers which direct expression in the
  mesoderm, the mesoderm and neurogenic ectoderm,
  or just in the urogenic ectoderm. These
  observations suggest that enhancers can evolve
  quickly to create new patterns of gene expression.

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3-5 The misexpression of Ubx changes the
morphology of the fruit fly

• New patterns of gene expression are produced by
  changing the Ubx expression pattern, the encoded
  regulatory protein, or its target enhancers.
• Antp is one of the genes that it regulates Ubx
  represses Antp expression in the metathorax of
  developing embryos.

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• The expression of Ubx in the different tissues of
  the metathorax depends on regulatory sequences
  that encompass more than 80 kb of genomic DNA.
• The consequences of misexpressing a pattern
  determining gene can cause a dramatic change in
  morphology results.

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3-6 Changes in Ubx function modify the morphology
of fruit fly embryos

• Ubx protein can function as a transcriptional
  repressor.
• The Ubx protein contains specific peptide
  sequences that recruit repression complexes.
• Ubx can be converted into an activator by fusing
  the Ubx DNA-binding domain to the potent
  activation domain from the viral VP-16 protein.

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• The protein sequences that mediate
  transcriptional repression map outside the Ubx
  homeodomain and are not present in the Ubx-VP16
  fusion protein .
• The misexpression of the Ubx-VP16 fusion protein
  causes all of the segments to develop as
  mesothoracic segments.
• The Ubx-VP16 fusion protein produces the same
  phenotype as that obtained with Antp.

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3-7 Changes in Ubx target enhancers can alter
patterns of gene expression

• The Ubx protein contains a homeodomain that
  mediates sequence-specific DNA binding, and
• it also contains a tetrapeptide motif (YPWM)
  that mediates interactions with Exd.
• Ubx binds DNA as a Ubx-Exd dimer.

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• Exd binds to a half-site with the core sequence,
  TGAT, Hox proteins such as Ybx bind an adjacent
  half-site with a diferent core consensus
  sequence, A-T-T/G-A/G.
• This obserbation raises the possibility that
  target enhancers regulated by one Hox protein can
  rapidly evolve into a target enhancer for a
  different Hox protein.
• So ,the altering the function or expression of
  the Ubxprotein or its target enhancers profoundly
  changes patterning in the Drosophila embryos and
  adults.

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Topic 4 Morphological changes in crustaceans and
insects

• The first two mechanisms, changes in the
  expression and function of pattern determining
  genes, can account for changes in limb morphology
  seen in certain crustaceans and insects the
  third mechanism, changes in regulatory sequences,
  might provide an explanation for the different
  patterns of wing development in fruit flies and
  butterflies.

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4-1 Arthropods are remarkably diverse

• Arthropods embrace five groups trilobites,
  hexapods, crustaceans, myriapods, and
  chelicerates.
• The success of the arthropods derives 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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4-2 changes in Ubx expression explain
modifications in limbs among the crustaceans

• There are two different groups crustaceans,
  branchiopod and isopod.
• In branchiopods Scr expression is restricter to
  head regions where it helps promote the
  debelopment of feeding appendages,while Ubx is
  expressed in the thorax where it controls the
  development of swinning limbs.

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• In isopods, Scr expression is detected in both
  the head and the first thoracic segment(T1), and
  as a result, the swimming limb in T1 is
  transformed into a feeding appendage.
• This posterior expansion of Scr was made possible
  by the loss of Ubx expression in T1 since Ubx
  normally represses Scr expression.

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• During the divergence of branchiopods and
  isopods, the Ubx regulatory sequence changed in
  isopods. As a result of this change, Ubx
  expression was eliminated in the first thoracic
• segments, and restricted to segments T2-T8.
• In Artemia, these head genes are kept off in all
  11thoracic segments, but in isopods the head
  genes can be expressed in the T1 segment due to
  the loss of the Ubx repressor.

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• Expression of the Scr gene is restricted to head
  regions of branchiopods, but is expressed in T1of
  isopods. The expression of Scr in T1 causes
  maxillipeds to develop in place of normal
  swimming limbs.

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4-3 Why insects lack abdominal limbs?

• The loss of abdominal limbs in insects is due to
  functional changes in the Ubx regulatory protein.
• In insects, Ubx and abd-A repress the expression
  of a critical gene that is required for the
  development of limbs, call Dll.
• Although Ubx is expressed in metathorax, it does
  not interfere with the expression of Dll in that
  segment, because Ubx is not expressed in the
  developing T3 legs until after the time when Dll
  is activated, as a result, Ubx does not interfere
  with limb development in T3.

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• The misexpression of Ubx throughout all of the
  tissues of the presumptive thorax in transgenic
  Drosophila embryos suppresses limb development
  due to the repression of Dll.
• The misexpression of the crustacean Ubx protein
  in transgenic flies does not interfere with Dll
  gene expression and the formation of thoracic
  limbs.

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4-4 modification of flight limbs might arise from
the evolution of regulatory DNA sequences

• Changes in the Ubx expression pattern appear to
  be responsible for the transformation of swimming
  limbs into maxillipeds in crustaceans.

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• Ubx in crustaceans, the C-terminal antirepression
  peptide blocks the activity of the N-terminal
  repression domain.
• Ubxin insects ,the C-terminal antirepression
  peptide was lost throught mutation.

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• Two possibilities
• First, the Ubx protein is functionally distinct
  in flies and butterfiles.
• Second, each of the approximately five to ten
  target genes that are repressed by Ubx in
  Drosophila have evolved changes in their
  regulatory DNAs so that they are no longer
  repredded by Ubx in butterflies.

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• The Ubx repressor is expressed in the halters of
  dipterans and hindwings of lepidopterans.
• Different target fenes contain Ubx repressor
  sites in dipterans. These habe been lost in
  lepidopterans.
• An implication of the preceding arguments is that
  evolutionary changes regulatory DNAs.

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Topic 5 Genome evolution and human origins

• The genomes of mice and humans have been
  sequenced and assembled, and their comparison
  should shed light on our own human origins.

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5-1 Humans contain surprisingly few genes

• The human genome contains only 25000-30000
  protein coding genes. Before the human genome was
  sequenced, there were popular estimates for
  100000 protein coding genes.
• Organismal complexity is not correlated with gene
  number, but instead depends on the number of gene
  expression patterns.

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5-2 The human genome is very similar to that of
the mouse and virtually identical to the chimp

• Mice and humans contain roughly the same number
  of genes, approximately 80 of these genes
  possess a clear and unique one-to-one sequence
  alignment with one another between the two
  species.
• Most of the remaining 20 of the genes in mice
  and humans differ by virtue of lineage-specific
  gene duplication events.

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• The chimp and human genomes are even more highly
  conserved, they vary by an average of just 2
  sequence divergence.
• The regulatory DNA evolve more rapidly than
  proteins.

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5-3 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.
• Changes in the expression pattern or changes in
  FOXP2 target genes might be responsible for the
  ability of FOXP2 to promote speech in humans.

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5-4 How FOXP2 fosters speech in humans

• Changes in the FOXP2 expression pattern, changes
  in its amino acid sequence, and changes in FOXP2
  target fenes might explain its emergence as an
  important mediator of human speech.
• Some might encode neurotransmitters or other
  critical signals that are expressed within the
  developing larynx.
• FOXP2 is just one example of a regulatory fene
  that underlies human speech.

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• A scenario for the evolution of speech in humans.
• A hypothetical regulatory protein is expressed in
  the neocortex of both chimps and humans.
• The human gene is strongly expressed at the
  critical time in the development of the speech
  center and activates all three hypothetical
  target genes in the neocortex, these target gene
  might encode neurotransmitters important for the
  formation of the speech center.

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5-5 The future of comparative genome analysis

• There is a glaring limitation in our ability to
  infer the function of regulatory DNA from simple
  sequence inspection .
• In the future it might also be possible to
  identify changes in the expression profiles of
  homologous genes.

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Summary

• The same concept of differential gene expression
  can explain the evolution of animal diversity.
• Changes in gene expression during evolution
  depend on altering the activities of a special
  class of regulatory genes, called pattern
  determining genes.
• There are three major strategies for altering the
  activities of pattern determining genes.
• We are fast entering a golden era of comparative
  genome analysis.

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The End

• Thank you!