Genome Evolution Chapter 24

1. Genome Evolution Chapter 24

2. Introduction • Genomes contain the raw material for evolution • Comparing whole genomes enhances • Our ability to understand evolution • To improve crops • To identify genetic basis of disease

3. Comparative Genomics • Making the connection between a specific change in a gene and a modification in a morphological character is difficult • Genomes carry information on the history of life • Evolutionary differences accumulate over long periods

4. Comparative Genomics • Genomes of viruses and bacteria evolve in a matter of days • Complex eukaryotic species evolve over millions of years • Example: tiger pufferfish (Fugu rubripes), mouse (Mus musculus), and human genomes

5. Comparative Genomics

8. Comparative Genomics • Comparison between human and pufferfish genomes • Last shared common ancestor 450 MYA • 25% human genes no counterparts in Fugu • Extensive genome rearrangements since mammal lineage and teleost fish diverged

9. Comparative Genomics • Human genome is 97% repetitive DNA • Repetitive DNA less than 1/6thFugu genome sequence

10. Comparative Genomics • Human and mouse genomes • Human: 400 million more nucleotides than the mouse • 25,000 genes and they share 99% • Diverged about 75 MYA • 300 genes unique to either organism (1%) • Rearrangements of chromosomal regions large and small

11. Comparative Genomics • Human and chimpanzee genomes • Diverged 35 MYA • 1.06% of the two genomes have fixed differences in single nucleotides • 1.5% difference in insertions and deletions • 53 of human-specific indels lead to loss-of-function changes

12. Comparative Genomics • Smaller ratio in nonsynonymous to synonymous changes • Purifying selection: removal of nonsynonymous genes

13. Comparative Genomics • Genomes evolve at different rates • Mouse DNA has mutated twice as fast as human • Fruit fly and mosquito evolve more rapidly than vertebrates • Difference in generation time accounts for different rates of genome evolution

14. Comparative Genomics • Plant, fungal, and animal genomes have unique and shared genes • Animal genomes are highly conserved • Plant genomes are highly conserved

15. Comparative Genomics • Comparison between two plant genomes • Arabidopsis thaliana (mustard family plant) • 25,948 genes; 125 million base pairs • Rice (Oryza sativa) 430 million base pairs • Share 80% of genes

16. Comparative Genomics Comparison of plants with animals and fungi • 1/3rd genes in Arabidopsis and rice “plant” genes: distinguish plant kingdom from animal kingdom

17. Comparative Genomics • Remaining genes similar to genes found in animal and fungal genomes • Basic intermediary metabolism • Genome replication and repair • RNA transcription & protein synthesis

18. Evolution of Whole Genomes • Polyploidycan result from • Genome duplication in one species • Hybridization of two different species • Autopolyploids: genome of one species is duplicated through a meiotic error • Four copies of each chromosome • Allopolyploids: result from hybridization and duplication of the genomes of two different species

19. Evolution of Whole Genomes

20. Evolution of Whole Genomes Evolutionary history of wheat

21. Evolution of Whole Genomes Ancient and newly created polyploids guide studies of genome evolution • Two avenues of research • Paleopolyploids: comparisons of polyploidy events • Sequence divergence between homologues • Presence or absence of duplicated gene pairs from hybridization

22. Evolution of Whole Genomes • Two avenues of research cont’d • Synthetic polyploids: crossing plants most closely related to ancestral species and chemically inducing chromosome doubling

23. Evolution of Whole Genomes • Plant polyploidy is ubiquitous, with multiple common origins • Comparison of soybean, forage legume, and garden pea shows a huge difference in genome size • Some genomes increased, some decreased in size • Polyploidy induces elimination of duplicated genes

24. Evolution of Whole Genomes Polyploidy has occurred numerous times in the evolution of flowering plants

25. Evolution of Whole Genomes Genome downsizing

26. Evolution of Whole Genomes Polyploidy may be followed by the unequal loss of duplicate genes from the combined genomes

27. Evolution of Whole Genomes Transposons jump around following polyploidization • Barbara McClintock(Nobel Prize) • Controlling elements: jumping DNA regions • Respond to genome shock and jump into a new position • New phenotypes could emerge

28. Evolution of Whole Genomes • New transposon insertions occur because of unusually active transposition • New insertions could cause • Gene mutations • Changes in gene expression • Chromosomal rearrangements

29. Evolution Within Genomes • Aneuploidy: duplication or loss of an individual chromosome • Plants are able to tolerate aneuploidy better than animals • Duplication of segments of DNA is one of the greatest sources of novel traits duplication loss

30. Evolution Within Genomes • Fates of duplicate gene: • Losing function through mutation • Gaining a novel function through mutation • Having total function partitioned into the two duplicates

31. Evolution Within Genomes Segmental duplication on the human Y chromosome

32. Evolution Within Genomes • Gene duplication in humans is most likely to occur in three most gene-rich chromosomes • Growth and development genes • Immune system genes • Cell-surface receptor genes

33. Evolution Within Genomes • 5% of human genome consists of segmental duplications • Duplicated genes have different patterns of gene expression • Rates of duplication vary for different groups of organisms

34. Evolution Within Genomes • Drosophila • 31 new duplicates per genome per million years (0.0023 duplications per gene per million years) • C. elegans 10 times fast rate • Paralogues: two genes within an organism that have arisen from duplication of a single gene in an ancestor • Orthologues: conservation of a single gene from a common ancestor

35. Evolution Within Genomes Genome reorganization • Humans have 1 fewer chromosome than chimpanzees, gorillas, and orangutans • Fusion of two genes into one gene; chromosome 2 in humans • Chromosomal rearrangements in mouse ancestors have occurred at twice the rate seen in humans

36. Evolution Within Genomes Chromosomal rearrangement

37. Evolution Within Genomes Variation in genomes • Conservation of synteny: the preservation over evolutionary time of arrangements of DNA segments in related species • Long segments of chromosomes in mice and humans are the same • Allows researchers to locate a gene in a different species using information about synteny

38. Evolution Within Genomes Synteny and geneidentification Soybean d2 K c2 b2 c1 3 2 M. truncatula

39. Evolution Within Genomes Gene inactivation results in pseudogenes • Loss of gene function: way for genomes to evolve • Olfactory receptor (OR) genes: inactivation best explanation for our reduced sense of smell • Primate genomes: > 1000 copies of OR genes

40. Evolution Within Genomes • Pseudogenes: sequences of DNA that are similar to functional genes but do not function • 70% of human OR genes are inactive pseudogenes • >50% gorilla & chimpanzee OR genes function • >95% New World monkey OR genes work well

41. Active genes Nonolfactory DNA Pseudogenes Human olfactory gene cluster (chromosome 17) Chimpanzee olfactory gene cluster (chromosome 19) Evolution Within Genomes Gene inactivation

42. Evolution Within Genomes • Chimp genome analysis • Indicated both humans and chimps are gradually losing OR genes to pseudogenes • No evidence for positive selection for any OR genes in chimps • Vertical gene transfer (VGT): genes are passed from generation to generation

43. Evolution Within Genomes • Horizontal gene transfer (HGT): genes hitchhike from other species • Can lead to phylogenetic complexity

44. Evolution Within Genomes • HGT continues today • Phylogenies build with rRNA sequences: Archaea more closely related to Eukarya than to Bacteria • Organisms swapped genes • Find organisms with both Archaea and Bacteria genes • Perhaps tree of life is more of a web than a branch

45. Evolution Within Genomes Phylogeny based on a universal common ancestor

46. Evolution Within Genomes • Contribution to the evolution of genomes • Segmental duplication • Genome rearrangement • Loss of gene function • HGT leads to mixing of genes among organisms

47. Gene Function and Expression Patterns • Inferred by comparing genes in different species • Why a mouse develops into a mouse and not a human • Genes are expressed at different times • In different tissues • In different amounts • In different combinations • Example: cystic fibrosis gene

48. Gene Patterns • Chimp DNA: 98.7% identical to human • Chimp protein genes: 99.2% identical • Experiment: human and chimp brain cells • Patterns of gene transcription activity differed • Same genes transcribed • Patterns and levels of transcription varied • Posttranscriptional differences

49. Gene Expression • Speech • FOXP2 gene: single point mutation = impaired speech and grammar but not language comprehension • FOXP2 found in chimps, gorillas, orangutans, rhesus macaques, and mice • FOXP2 protein in mice and humans differs by only 3 AA, 2 AA in other primates • Gene expressed in areas of brain that affect motor function

50. Gene Expression • The difference of only 2 AA sequences for FOXP2 appears to have made it possible for language to arise • Selective pressure for the 2 FOXP2 mutations • Allow brain, larynx and mouth to coordinate to produce speech • Linked to signaling and gene expression • FOXP2 mutation in mice-no squeak !