1. The Human Genome and Human Evolution Y Chromosome Dr Derakhshandeh, PhD

2. 2 Outline Information from fossils and archaeology Neutral (or assumed-to-be-neutral) genetic markers –Classical markers –Y chromosome Genes under selection –Balancing selection: Balancing selection can arise by the heterozygotes having a selective advantage, as in the case of sickle cell anemia It can also arise in cases where rare alleles have a selective advantage –Positive selection

3. 3 Why Y? "Adam passed a copy of his Y chromosome to his sons The Y chromosome is paternally inherited the Y chromosome a father passes to his son is, in large measure, an unchanged copy of his own

4. 4

5. 5 But small changes (called polymorphisms) do occur passed down from generation to generation

6. 6 CHROMOSOME CHANGES indels –insertions into or deletions of the DNA at particular locations on the chromosome YAP –which stands for ”Y chromosome Alu Polymorphism” –Alu is a sequence of approximately 300 letters (base pairs) which has inserted itself into a particular region of the DNA

7. 7 Snips –"single nucleotide polymorphisms“ –Stable indels and snips are relatively rare –so infrequent –they have occurred at any particular position in the genome only once in the course of human evolution –Snips and stable Alus have been termed "unique event polymorphisms" (UEPs)

8. 8 microsatellites –short sequences of nucleotides (such as GATA) –repeated over and over again a variable number of times in tandem –The specific number of repeats in a particular variant (or allele) usually remains unchanged from generation to generation –but changes do sometimes occur and the number of repeats may increase or decrease

9. 9 increases or decreases in the number of repeats take place in single steps for instance from nine repeats to ten whether decreases in number are as common as increases has not been established

10. 10 Changes in microsatellite length occur much more frequently than new UEPs arise ( Snips and stable Alus : "unique event polymorphisms) while we can reasonably assume that a UEP has arisen only once the number of repeat units in a microsatellite may have changed many times along a paternal lineage

11. 11 The microsatellite data can facilitate the estimation of population divergence times which can then be compared (and contrasted) with estimated mutational ages of the polymorphic markers the combination of these two kinds of data: –offers a powerful tool with which to assess patterns of migration, admixture, and ancestry

12. 12 minisatellites –10-60 base pairs long –the number of repeats often extends to several dozen –Changes during the copying process take place more frequently in minisatellites than in microsatellites

13. 13 the evolutionary clock –the UEPs as the hour hand –the microsatellite polymorphisms as the minute hand –the minisatellites as a sweep second hand

14. 14 a further benefit of using “Y chromosome” to study evolution most of the Y chromosome does not exchange DNA with a partner all the markers are joined one to another along its entire length linkage of markers

15. 15 The human Y chromosome can also be used to draw evolutionary trees the relationships of the Y chromosomes of other primates The different polymorphic loci are distinguished from each other by their chain lengths it can be measured using an automatic DNA sequencer

16. 16 Gene scan output of microsatellite DNA analysis from a single individual The microsatellite peaks are sorted by size, the different colors representing different microsatellites. The small red peaks are size markers

17. 17 new UEP arises in a certain man As the new UEP is copied from generation to generation The UEP does not change but, albeit not very often: – increasing –decreasing in length The longer the time since the UEP arose –the greater will be the number of different UEP allele

18. 18 Such a process: – differentiates one population from another – the more closely two populations –display common haplotype frequencies –the more closely related is their biological history likely to be

19. 19 IN ANCIENT TIMES only the analysis of DNA obtained from our contemporaries suggested ways in which we might deduce past history from an interpretation of those data: – DNA can be extracted from ancient remains

20. 20 Amelogenin gene exists in two forms: –the one on the X chromosome being different in length from the one on Y Small portions of: –cranial bones –and teeth were crushed to powder and decalcified

21. 21 The amelogenin gene is a single copy gene homologues of which are located on: –Xp22.1-Xp22.3 –and Yp 11.2

22. 22 Yp 11.2

23. 23 DNA was purified copied by PCR using primers flanking the region the size of the products was measured by agarose gel electrophoresis Since Y chromosomes yield fragments 218 base pairs long while X chromosome products contain 330 base pairs they should be clearly distinguishable: –if the specimen yields the shorter gene, it must come from a Y chromosome fragment and thus from a male.

24. 24 Disadvantages DNA is often degraded so that continuous fragments are no longer present cannot be copied substances may be present: –inhibit both purification and amplification

25. 25 The first two human Y chromosome marker studies appeared in 1985 (Casanova et al. 1985; Lucotte and Ngo 1985)Casanova et al. 1985Lucotte and Ngo 1985 It was not until almost a decade later that Torroni and co-workers (1994a) published the first Y chromosome data on Native Americans Torroni and co-workers (1994a) Numerous surveys of variation on the non- recombining portion of the Y chromosome (NRY)

26. 26 Who are our closest living relatives? Chen FC & Li WH (2001) Am. J. Hum. Genet. 68 444-456

27. 27 selected 53 autosomal / Y Ch intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan.

28. 28 The average sequence divergence was only 1.24% +/- 0.07% for the human-chimpanzee pair 1.62% +/- 0.08% for the human-gorilla Pair and 1.63% +/- 0.08% for the chimpanzee- gorilla pair

29. 29 Taking the orangutan speciation date as 12 to 16 million years ago an estimate of 4.6 to 6.2 million years for the Homo-Pan divergence an estimate of 6.2 to 8.4 million years for the gorilla speciation date gorilla lineage branched off 1.6 to 2.2 million years earlier than did the human- chimpanzee divergence 12 to 16 million 4.6 to 6.2 million 6.2 to 8.4 million 1.6 to 2.2 million

30. 30 Phenotypic differences between humans and other apes *Carroll (2003) Nature 422, 849-857

31. 31 Chimpanzee-human divergence ChimpanzeesHumans 6-8 million years Hominids or hominins

32. 32 Origins of hominids Sahelanthropus tchadensis Chad (Central Africa) Dated to 6 – 7 million years ago Posture uncertain, but slightly later hominids were bipedal ‘Toumai’, Chad, 6-7 MYA Brunet et al. (2002) Nature 418, 145-151

33. 33 Hominid fossil summary Found only in AfricaFound both in Africa and outside, or only outside Africa

34. 34 Origins of the genus Homo Homo erectus/ergaster ~1.9 million years ago in Africa Use of stone tools H. erectus in Java ~1.8 million years ago Nariokatome boy, Kenya, ~1.6 MYA

35. 35 Additional migrations out of Africa First known Europeans date to ~800 KYA Ascribed to H. heidelbergensis

36. 36 Origins of modern humans (1) Anatomically modern humans in Africa ~130 KYA In Israel by ~90 KYA Omo I, Ethiopia, ~130 KYA

37. 37 Origins of modern humans (2) Modern human behaviour starts to develop in Africa after ~80 KYA By ~50 KYA, features such as complex tools and long-distance trading are established in Africa The first art? Inscribed ochre, South Africa, ~77 KYA

38. 38 Expansions of fully modern humans Two expansions: Middle Stone Age technology in Australia ~50 KYA Upper Palaeolithic technology in Israel ~47 KYA Lake Mungo 3, Australia, ~40 KYA

39. 39 the Upper Paleolithic period In the Upper Paleolithic period: – Neanderthal man disappears –and is replaced by a variety of Homo sapiens

40. 40 Routes of migration? archaeological evidence Middle Stone Age Upper Paleolithic ~130 KYA

41. 41 Strengths and weaknesses of the fossil/archaeological records Major source of information for most of the time period Only source for extinct species Dates can be reliable and precise –need suitable material, C calibration required 14

42. 42 Mixing or replacement?

43. 43 Human genetic diversity is low

44. 44 Modern human mtDNA is distinct from Neanderthal mtDNA Krings et al. (1997) Cell 90, 19-30

45. 45 Nature Genetics 33, 266 - 275 (2003) The application of molecular genetic approaches to the study of human evolution L. Luca Cavalli-Sforza1 & Marcus W. Feldman2

46. 46 Haploid markers from mitochondrial DNA and the Y chromosome have proven invaluable for generating a standard model for evolution of modern humans earlier research on protein polymorphisms Co-evolution of genes with language and some slowly evolving cultural traits, together with the genetic evolution

47. 47 Evolutionary events affecting genomic variation (1) All genetic variation is caused by mutations The most common and most useful for many purposes are SNPs which can be detected by DNA sequencing

48. 48 Evolutionary events affecting genomic variation (2) Allelic frequencies change in populations owing to two factors: –natural selection: –population variation among individual genotypes in their probabilities of survival and/or reproduction, random genetic drift –next generation –Both natural selection and genetic drift can ultimately lead to the elimination or fixation of a particular allele In the presence of mutation and in the absence of selection: –neutral conditions: the rate of neutral evolution of a finite population is equal to the mutation rate!

49. 49 Evolutionary events affecting genomic variation (3) The earliest evidence of selection : –heterozygotes of the hemoglobin A/S polymorphism have greater resistance to malaria than do AA or SS homozygotes –G6PD locus: resistance to malaria

50. 50 Evolutionary events affecting genomic variation (4) Strong directional selection : for FOXP2 –a two amino-acid difference between the human protein and in primates –selectively important for the evolution of speech and language in modern humans

51. 51 Evolutionary events affecting genomic variation (5) the agent of selection is not at all obvious: –the CCR5 gene seems : related to HIV resistance – mutations in the BRCA1 gene: produce an increased risk of female breast cancer

52. 52 Migration is another important factor in human evolution that can profoundly affect genomic variation within a population

53. 53 Summary tree of world populations. Phylogenetic tree based on polymorphisms of 120 protein genes in 1,915 populations Cavalli-Sforza & Feldman (2003) Nature Genet. 33, 266-275

54. 54 For populations that are geographically close, genetic and geographic distances are often highly correlated Cavalli-Sforza & Feldman (2003) Nature Genet. 33, 266-275

55. 55 Dating the origin of our species using genetic data (1) The mutation rate of the NRY is comparable to that of nuclear DNA polymorphisms are more difficult to find but genealogies are easier to reconstruct The greater length of DNA on the NRY (perhaps 30 million bases of euchromatic DNA) lower mutation rate Even though the NRY behaves effectively as a single locus usually insufficient for evolutionary analyses it has provided results that are consistent across many studies and in agreement with many archeological findings

56. 56 High resolution history using haploid markers SNPs on the NRY and mtDNA : – higher resolution of population history through the reconstruction of the phylogenetic relationships of extant Y chromosomes and mtDNA the Y Chromosome Consortium: –the first two haplogroups (A and B) are almost completely African and even today represent mostly their descendants

57. 57 NRY Siberia India Eskimo

58. 58 The migration of modern Homo sapiens. begins with a radiation from East Africa to the rest of Africa about 100 kya and from the same area to Asia, southern and northern between 60 and 40 kya. Oceania, Europe and America were settled from Asia in that order. Cavalli-Sforza & Feldman (2003) Nature Genet. 33, 266-275

59. 59 NRY Slow growth is indicated by the accumulation of many mutations within a branch, as in most descendants of haplogroup A and B and in those of the earliest branches of haplogroups C, D, E and F

60. 60 NRY By contrast, when there are many branches (called a starburst) after a specific mutation or group of mutations, we can infer rapid growth The major expansions are those of haplogoup F (seven branches) after an initial lag in population growth, and even more remarkable is the later expansion of haplogroup K (nine branches).

61. 61 haplogroup K (nine branches) These began in the last 40 kya and led to the major settlement of all continents from Africa, first to Asia, and from Asia to the other three continents.

62. 62 mtDNA The tree of mtDNA is more bushy, but there are more haplogroups because of the higher mutation rate!

63. 63 mtDNA

64. 64 mtDNA The earliest branches all remain in Africa in both trees they clearly refer to the slowly growing hunter-gatherers In both trees the major growth in Africa is due to a late branch, taking place in the second part of the last 100,000 years and clearly connected with the expansion to Asia

65. 65 Language families of the world

66. 66 Phylogeographic studies Analysis of the geographical distributions of lineages within a phylogeny Nodes or mutations within the phylogeny may be dated Extensive studies of mtDNA and the Y chromosome

67. 67 Phylogenetic trees commonly indicate a recent origin in Africa Y chromosome

68. 68 Y haplogroup distribution Jobling & Tyler-Smith (2003) Nature Rev. Genet. 4, 598-612

69. 69

70. 70

71. 71

72. 72 An African origin

73. 73 SE Y haplogroups

74. 74 NW Y haplogroups

75. 75 Did both migrations leave descendants? General SE/NW genetic distinction fits two- migration model –Basic genetic pattern established by initial colonisation All humans outside Africa share same subset of African diversity (e.g. Y: M168, mtDNA: L3) –Large-scale replacement, or migrations were dependent How much subsequent change?

76. 76 Fluctuations in climate Ice ages Antarctic ice core data Greenland ice core data

77. 77 Possible reasons for genetic change Adaptation to new environments Food production – new diets Population increase – new diseases

78. 78 Debate about the Paleolithic- Neolithic transition Major changes in food production, lifestyle, technology, population density Were these mainly due to movement of people or movement of ideas? Strong focus on Europe

79. 79 Estimates of the Neolithic Y contribution in Europe ~22% (=Eu4, 9, 10, 11); Semino et al. (2000) Science 290, 1155-1159 >70% (assuming Basques = Paleolithic and Turks/Lebanese/ Syrians = Neolithic populations); Chikhi et al. (2002) Proc. Natl. Acad. Sci. USA 99, 11008-11013

80. 80 The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective (1) It was derived from 22 markers of the nonrecombining Y chromosome (NRY) Ten lineages account for >95% of the 1007 European Y chromosomes Geographic distribution and age estimates of alleles are compatible with two Paleolithic and one Neolithic migratory episode ( Semino et al. (2000)

81. 81 The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective (2) that have contributed to the modern European gene pool A significant correlation between the NRY haplotype data and principal components based on 95 protein markers was observed indicating the effectiveness of NRY polymorphisms in the characterization of human population composition and history ( Semino et al. (2000)

82. 82 More recent reshaping of diversity ‘Star cluster’ Y haplotype originated in/near Mongolia ~1,000 (700-1,300) years ago Now carried by ~8% of men in Central/East Asia, ~0.5% of men worldwide Suggested association with Genghis Khan Zerjal et al. (2003) Am. J. Hum. Genet. 72, 717-721

83. 83 Mongolia (1) (Zerjal et al. (2003) Am. J. Hum. Genet. 72, 717-721) It was found in 16 populations throughout a large region of Asia stretching from the Pacific to the Caspian Sea present at high frequency: – ∼ 8% of the men in this region carry it – ∼ 0.5% of the world total behavior

84. 84 Mongolia (2) (Zerjal et al. (2003) Am. J. Hum. Genet. 72, 717-721) The pattern of variation within the lineage: –it originated in Mongolia ∼ 1,000 years ago Such a rapid spread cannot have occurred by chance it must have been a result of selection The lineage is carried by likely male-line descendants of Genghis Khan propose that it has spread by a novel form of social selection

85. 85 Is the Y a neutral marker? Recurrent partial deletions of a region required for spermatogenesis Possible negative selection on multiple (14/43) lineages Repping et al. (2003) Nature Genet. 35, 247-251

86. 86 1.6-Mb deletion (1) Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between: – recurrent mutation –and haploid selection Repping et al. (2003) Nature Genet. 35, 247-251

87. 87 AZF

88. 88 1.6-Mb deletion (2) Many human Y-chromosomal deletions: –severely impair reproductive fitness –precludes their transmission to the next generation –ensures their rarity in the population Repping et al. (2003) Nature Genet. 35, 247-251

89. 89 1.6-Mb deletion (3) 1.6-Mb deletion that persists over generations It is sufficiently common to be considered a polymorphism They hypothesized that this deletion might affect spermatogenesis because it removes almost half of the Y chromosome's AZFc region (1.6 Mb) a gene-rich segment that is critical for sperm production1

90. 90 gr/gr deletion Y chromosomes lower penetrance with respect to spermatogenic failure than previously characterized Y-chromosomal deletions it is often transmitted from father to son the existence of this deletion: –as a polymorphism –reflects a balance between haploid selection – and homologous recombination –which continues to generate new gr/gr deletions Repping et al. (2003) Nature Genet. 35, 247-251

91. 91 Selection in the human genome time Neutral Negative (Purifying, Background) Balancing Positive (Directional) Bamshad & Wooding (2003) Nature Rev. Genet. 4, 99-111

92. 92 Selection in the human genome (1) Natural selection leaves signatures in our genome that can be used to identify the genes that might underlie variation in disease resistance or drug metabolism Evidence of positive selection acting on genes is beginning to accumulate

93. 93 Selection in the human genome (2) Demographic processes should affect all loci in a similar way, whereas the effects of selection should be restricted to specific loci

94. 94 Demographic changes Population has expanded in range and numbers

95. 95 The Prion protein gene and human disease Prion protein gene PRNP linked to ‘protein- only’ diseases e.g. CJD, kuru A common polymorphism, M129V, influences the course of these diseases the MV heterozygous genotype is protective Kuru acquired from ritual cannibalism was reported (1950s) in the Fore people of Papua New Guinea, where it caused up to 1% annual mortality

96. 96 Creutzfeldt-Jakob Disease (CJD) a neurodegenerative disease called Kuru found in cannibalistic Pacific Islanders a disorder diagnosed in one person per million common symptoms: –gait disorders –jerky movements –dementia that lead to death months after the first appearance of symptoms

97. 97 Balancing selection at PRNP Deep division between the M and V lineages, estimated at 500,000 years Kuru imposed strong balancing selection on the Fore essentially eliminating PRNP 129 homozygotes Worldwide PRNP haplotype diversity and coding allele frequencies : – strong balancing selection at this locus –during the evolution of modern humans

98. 98 NeutralSelection Derived allele of SNP Effect of positive selection

99. 99 What changes do we expect? New genes Changes in amino-acid sequence Changes in gene expression (e.g. level, timing or location) Changes in copy number

100. 100 How do we find such changes? Chance –φhHaA type I hair keratin gene inactivation in humans Identify phenotypic changes, investigate genetic basis Identify genetic changes, investigate functional consequences

101. 101 Human type I hair keratin pseudogene φhHaA This mutant protein is unable to activate hair keratin gene expression the nude phenotype has functional orthologs in the chimpanzee and gorilla: –evidence for recent inactivation of the human gene after the Pan-Homo divergence –5. 5 million years ago

102. 102 Inheritance of a language/speech defect in the KE family Lai et al. (2000) Am. J. Hum. Genet. 67, 357-367 Autosomal dominant inheritance pattern

103. 103 A forkhead-domain gene is mutated in a severe speech and language disorder the gene FOXP2 encodes a putative transcription factor Containing: –a polyglutamine tract –a forkhead DNA-binding domain disrupted by the translocation or point mutation the KE family that alters an invariant amino-acid residue in the forkhead domain

104. 104 Mutation and evolution of the FOXP2 gene Chr 7 7q31 FOXP2 gene Nucleotide substitutions silentreplacement Enard et al. (2002) Nature 418, 869-872

105. 105 Positive selection at the FOXP2 gene Resequence ~14 kb of DNA adjacent to the amino-acid changes in 20 diverse humans, two chimpanzees and one orang-utan OrangGorillaChimpHuman silent (synonymous) dS replacement (non-synonymous) dN Human-specific increase in dN/dS ratio (P<0.001) Constant rate of amino-acid replacements?Positive selection in humans? Enard et al. (2002) Nature 418, 869-872

106. 106 A gene affecting brain size Microcephaly (MCPH) Small (~430 cc v ~1,400 cc) but otherwise ~normal brain, only mild mental retardation MCPH5 shows Mendelian autosomal recessive inheritance Due to loss of activity of the ASPM gene ASPM-/ASPM-control Bond et al. (2002) Nature Genet. 32, 316-320

107. 107 Evolution of the ASPM gene (1) Summary dN/dS values OrangGorillaChimpHuman Human-specific increase in dN/dS ratio (P<0.03) 1.44 0.56 0.53 0.52 0.62 Sliding-window dN/dS analysis Evans et al. (2004) Hum. Mol. Genet. 13, 489-494

108. 108 What changes? The Drosophila homolog of ASPM codes for a microtubule-binding protein that influences spindle orientation and the number of neurons do Carmo Avides and Glover (1999) Science 283, 1773-1735 DNA Microtubules asp Subtle changes to the function of well-conserved genes

109. 109 Genome-wide search for protein sequence evolution 7645 human-chimp-mouse gene compared Most significant categories showing positive selection include: –Olfaction: sense of smell –Development: e.g. skeletal –Hearing: for speech perception –brain size: IQ Clark et al. (2003) Science 302, 1960-1963

110. 110 Gene expression differences in human and chimpanzee cerebral cortex Increased expression Decreased expression Caceres et al. (2003) Proc. Natl. Acad. Sci. USA 100, 13030-13035 Affymetrix oligonuclotide array (~10,000) genes 91 show human-specific changes, ~90% increases

111. 111 Copy number differences between human and chimpanzee genomic DNA Human male reference genomic DNA hybridised with female chimpanzee genomic DNA Locke et al. (2003) Genome Res. 13, 347-357

112. 112 Selection at the CCR5 locus CCR5  32/CCR5  32 homozygotes are resistant to HIV and AIDS The high frequency and wide distribution of the  32 allele suggest past selection by an unknown agent

113. 113 The Role of the Chemokine Receptor Gene CCR5 and Its Allele ( del32 CCR5) Since the late 1970s 8.4 million people worldwide including 1.7 million children, have died of AIDS an estimated 22 million people are infected with human immunodeficiency virus (HIV)

114. 114 CCR5 and Its Allele ( del32 CCR5) T-cell line (Tl ) monocyte/macrophage (M), a circulating T-cell (T)

115. 115 Lactase persistence All infants have high lactase enzyme activity to digest the sugar lactose in milk In most humans, activity declines after weaning, but in some it persists: LCT*P

116. 116 Molecular basis of lactase persistence Lactase level is controlled by a cis-acting element Linkage studies show association of lactase persistence with the T allele of a T/C polymorphism 14 kb upstream of the lactase gene Enattah et al. (2002) Nature Genet. 30, 233-237

117. 117 The lactase-persistence haplotype The persistence- associated T allele occurs on a haplotype (‘A’) showing over > 1 Mb Association of lactase persistence and the A haplotype is less clear outside Europe

118. 118 Selection at the G6PD gene by malaria Reduced G6PD enzyme activity (e.g. A allele) confers some resistance to falciparum malaria Extended haplotype homozygosity at the A allele Sabeti et al. (2002) Nature 419, 832-837

119. 119 Final words Is there a genetic continuum between us and our ancestors and the great apes? If there is, then we can say that: these [i.e. microevolutionary] processes are genetically sufficient to fully account for human uniqueness