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Chapter 19

Chapter 19. Comparative Genomics and the Evolution of Animal Diversity. ✣ Author : 倪佩兰 ✣ Number: 200332550042 ✣ 生物科学类 1 ＞ Group8. OUTLINE. Three ways gene expression is changed during evolution. Most animal have essentially the same genes.

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Chapter 19

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  1. Chapter 19 Comparative Genomics and the Evolution of Animal Diversity

  2. ✣Author : 倪佩兰 ✣Number: 200332550042 ✣生物科学类 1 ＞ Group8

  3. OUTLINE • Three ways gene expression is changed during evolution. • Most animal have essentially the same genes. • Experimental manipulations that alter animal morphology. • Morphological changes in crustaceans and insects. • Genome evolution and human origins.

  4. Preface of this chapter • Charles Darwin: all animals arose from a common ancestor. • There are 25 different animal phyla, but where did evolutionary diversity come? • Animal phyla includes :ecdysozoans,. lophotrochozoans, deuterostomes. • Different genomes offer the promise for diversity.

  5. Figure19-1Summery ofphyla

  6. Figure19-2 Phylogeny of assembled genomes

  7. Topic1: Most Animals Have Essentially the Same Genes • A striking factor: different animals have essentially the same genes (human, pufferfish and mice are similar in genome). • The genetic conversion seen among vertebrates extends to Ciona intestinalis . • Increase in gene number in vertebrates is due to the duplication of genes already present in the ecdysozoans rather than the invention of entirely new genes .

  8. Figure19-3 Phylogenetic tree show gene duplication of the fibroblast grouth factor genes

  9. ✰How does gene duplication give rise tobiological diversity? Two models for how duplicated genes can create diersity: ❶Anancestral gene produce multiple genes via duplication ,and the coding regions of the ew genes undergo mutation. ❷The duplicated genes do not take on new functions,but instead acquire new DNA sequences.

  10. Box19-1 The structures of the genes coding the Gsb and Prd proteins

  11. Box19-2 Duplication of β-Globin gene family in the evolution of vertebrates

  12. Topic2:Three Ways Gene Expression Is Changed During Evolution ❶A given pattern determining gene can itself be expressed in a new pattern (this will cause those genes whose expression it controls to aquire new patterns of expression).(Figure19-4a) ❷The regulatory protein encoded by a pattern determining gene can aquire new functions. ).(Figure19-4b) ❸Target pattern of a given pattern determining gene can acquire new regulatory DNA sequences, and thus come under the control of a different regulatory gene. (Figure19-4c)

  13. Figure19-4Summeryof thethree strategies for altering the roles of pattern determininggenes

  14. Topic3:Experimental Manipulations That Alter Animal Morphology • The first pattern determining gene was identified in Drosophila in the Morgan Fly .Lab • During the past 20 years ,a variety of manipulations have document the importance of several pattern determining genes in development.

  15. ⅰChanges in Pax6 expression create ectopic eyes • Pax6 Pax6 is the mostnotorious pattern determining gene. • Normally Pax6 express within developing eyes, but mistake appears, Pax6 causes the development of extra eyes . • Altered expression of Pax6 has been correlated with the formation of eye spot. • Pax6 genes from other animals also produce ectopic eyes when mixexpressed in Drosophila.. ⅱ

  16. Figure19-5 Misexpression of Pax6 and eye formation in Drosophila

  17. ⅱChangesinAntpExpression TransformAntennaeinto Legs • Antpis a secondDrosophila pattern determining gene which contril 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 enbryo. • When misexpressed in the head, Antpcauses astriking change: legs develop instead of antennae.

  18. Figure19-6 A dominant mutation in the Antp geene results in the homeotic transformation of antennae into legs

  19. ⅲImportance of protein transform Antennae into legs • Pattern determining genes need not be expressed in different places to produce changes in morphology. • Example: two relared pattern deternmining genes inDrosophila :ftz and Antp .

  20. Figure19-7Duplicationof ancestralgene leading to Antp and ftz

  21. ⅳSubtle Changesin an enhancer sequence can produce of gene expression • Enhancers with high-affinity sites are expressed in the neurogenic ectoderm . • The enhancer contains two low-affinity Dorsal binging sites,and is activate by high levels of the Dorsal gradient in ventral regions. • Dorsal functions synergisticaly with another transcripton factor Twist to activate gene expression in the neurogenic ectoderm . • So the enhancers can evolve quickly to create new patterns of gene expression .

  22. Figure19-8Regulation oftransgeneexpressionin the earlyDrosophilaembryo

  23. ⅴThemisexpressionof Ubxchanges the morphology of the fruit fly • New patterns of gene expression are produced by changing the Ubx expression pattern, or its target enhancers. • Ubx encodes a homeodomain regulatory protein • In figure 19-9b, Ubx mutants exhibit a spectacular phenotype: fly with four fully developed wings. • In figure 19-10, the Cbx mutation causes Ubx to be misexpressed in the mesothorax; and Ubx now represses the expression of Antp and some other genes. . As a result, in figure 19-10, Cbx mutant flies look like wingless ants.

  24. Figure19-9Ubx mutants cause the transformation of the metathorax into a duplicated mesothorax

  25. Figure19-10 Misexpression of Ubx in the mesothorax results in the loss of wings

  26. ⅵChanges inUbxmodify the morphology of Fruit Fly embryos • Ubx functions as a repressor , and the Ubx protein contains specific sequences that recruit repression complexes. • Transgenic fly embryos have been create that either the Antp or Ubx protein coding sequence under the control of the hsp70 heat shock regulatory DNA. • Ubx normally functions as a repressor.

  27. Figure19-11 Changing the regulatory activities of the Ubx protein

  28. ⅶChanges inUbx target enhancerscan alter patterns of gene expression • Ubx binds DNA as a Ubx-Exd dimer similarly to Antp. • Many homeotic regulatory proteins interact with Exd and binds a composite Exd-Hox recongnition sequence. • Ailering the function or expression of Ubx or its target enhancers changes patterning in the Drosophila embryos and adults .

  29. Figure19-12Interconve-rsion oflabialandUbx bindingsites

  30. Box19-4-1 Orgnization and expression of Hox genes in Drosophilla and in the mouse

  31. Box19-4-2 Conservation of orgnization and expression of homeotic gene complexes in Drosophilla and in the mouse

  32. Box19-4-3 Partial transformation of the first lumbar vertebra in a mutant mouse embryo

  33. Topic4:Morphological Changes InCrustaceansAndInsects • Three strategies for altering the activities of pattern determininggenes. • The first two ,changes in the expression and function of pattern determining genes, explain changes in limb morphology seen in certain ctastaceans and insects. • The third, changes in regulatory sequences, explain different patterns of wing development in fruit flies and butterflies.

  34. ⅰArthropodsare remarkablydiverse • Arthropods embrace five groups: trilobites, hexapods, crustaceans, myriapods, and chelicerates. • The success of the arthropods derives from their modular architecture. • These organisms are com[osed of a series of repeating body segments that can be modified in seemingly limitless ways .

  35. ⅱ Changes in Ubx expressionmodifications in limbs among the crustaceans • Artemia ,a group of crustaceans, is most studied. • Slightly different patterns of Ubx expression are observed in branchiopods and isopods. • Explanation: the Ubx regulatory DNA of isopods acquired mutations .

  36. Figure19-13Changingmophologi-esin twodifferent groupsofcrustaceans

  37. ⅲ Why insects lackabdominal limbs • Theloss of abdominal limbs of insects is due to functional changes in the regulatory protein. • In crustaceans, there are high levers of both Ubx and Dll in all 11 thoracic segment. • The drosophila Ubx protein is functionally distinct from Ubx in crustacean. In contrast with fly, the crustacean protein has a short motif containing 29 amino acid residues that block repression activity. • Both the crustacean and fly proteins contain multiple repression genes. ⅲ

  38. Figure19-14 Evolutionary changes in Ubx protein function

  39. Figure19-15 Comparison of Ubx in crustaceans and insects

  40. ⅳ Modification of flight limbsmight 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 developed. • All members of dipterans contain a sinder pair of wings and a set of halteres. • The two olders diverged from a common ancestor more than 250 million years ago. • Reason for different wing morphologies: changes in the regulatory sequences of several Ubx targrt genes.

  41. Figure19-16 Changes in the regulatory DNA of Ubx targrt genes

  42. Box19-5-1 Distalless expression in various animal embryos

  43. Box19-5-2 The expression of Dll and other pattern determining genes inthe eyespot ofβ.anynana

  44. Topic5:Genome Evolution and Human Origins ⅰHumans contain surprisingly few genes • The human genome contain only 25000---30000 protein coding genes. • The higher vertebrates contain sophisticated mechanisms for gene regulation in order to produce many patterns of gene expression . • Fruit flies is more complex than the worm from an increase in the number of gene expression patterns .

  45. ⅱ The human genome is very similar to themouseand thechimp • Mice and human contain roughly the same number of genes---about 28000 protein coding genes. • The chimp and human genomes are even more highly conserved.

  46. ⅲ The evolutionary origins of human speech • One of the defining features of being human----speech. • Speech depends on the precise coordination of the small muscles in our larynx and mouth • Human’s FOXP2 protein is unique: T to N at position 303 and N to S at position 325. • Changes in the exprssion pattern of or changes in FOXP2 target genes might promote speech in humans . ⅲ

  47. Figure19-17 Summery of amino acid changes in the FOX2 proteins of mice and primates

  48. Figure19-18 Comparison of the FOX2 gene sequences in human, chimp and mouse

  49. ⅳ HowFOXP2fosters speech in humans • Changes in the FOXP2 regulatory DNA might cause the gene to acquire a new pattern of gene expression in the human being. • Perhaps these changes have augmented the levels or timing of gene expression, so critical signals are active in the larynx when effected to language. • It is difficult to estimate the number of “speech regulatory genes” evolved in humans. ⅳ

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