The Human Genome and Human Evolution Chris Tyler-Smith The Wellcome Trust Sanger Institute

Outline Information from fossils and archaeology Neutral (or assumed-to-be-neutral) genetic markers Classical markers Y chromosome Demographic changes Genes under selection Balancing selection Positive selection

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

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

Chimpanzee-human divergence 6-8 million years Hominids or hominins Chimpanzees Humans

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

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

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

Additional migrations out of Africa First known Europeans date to ~800 KYA Ascribed to H. heidelbergensis Atapueca 5, Spain, ~300 KYA

Origins of modern humans (1) Anatomically modern humans in Africa ~130 KYA In Israel by ~90 KYA Not enormously successful Omo I, Ethiopia, ~130 KYA

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

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

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

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 Did they leave descendants? 14

Mixing or replacement?

Human genetic diversity is low

Human genetic diversity is evenly distributed Most variation between populations Most variation within populations Templeton (1999) Am. J. Anthropol. 100, 632-650

Phylogenetic trees commonly indicate a recent origin in Africa Y chromosome

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

Classical marker studies Based on 120 protein-coding genes in 1,915 populations Cavalli-Sforza & Feldman (2003) Nature Genet. 33, 266-275

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

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

An African origin

SE Y haplogroups

NW Y haplogroups

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 not independent How much subsequent change?

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

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

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

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

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

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

Demographic changes Population has expanded in range and numbers Genetic impact, e.g. predominantly negative values of Tajima’s D Most data not consistent with simple models e.g. constant size followed by exponential growth

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

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 Departure from Hardy-Weinberg equilibrium for the M129V polymorphism is seen in Fore women over 50 (23/30 heterozygotes, P = 0.01)

Non-neutral evolution at PRNP McDonald-Kreitman test Resequence coding region in ? humans and apes N S Diversity 5 1 Divergence (Gibbon) 2 13 P-value = 0.0055 Mead et al. (2003) Science 300, 640-643 ‘coding’ ‘non-coding’

Balancing selection at PRNP Excess of intermediate-frequency SNPs: e.g. Tajima’s D = +2.98 (Fore), +3.80 (CEPH families) Deep division between the M and V lineages, estimated at 500,000 years (using 5 MY chimp-human split) Observed Expected 24 SNPs in 4.7 kb region, 95 haplotypes

Effect of positive selection Neutral Selection Derived allele of SNP

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

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

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

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

Positive selection at the FOXP2 gene Constant rate of amino-acid replacements? Positive selection in humans? Resequence ~14 kb of DNA adjacent to the amino-acid changes in 20 diverse humans, two chimpanzees and one orang-utan No reduction in diversity Excess of low-frequency alleles (Tajima’s D = -2.20) Excess of high-frequency derived alleles (Fay & Wu’s H =-12.24) Simulations suggest a selective sweep at 0 (0 – 200,000) years replacement (non-synonymous) dN silent (synonymous) dS Orang Gorilla Chimp Human Human-specific increase in dN/dS ratio (P<0.001) Enard et al. (2002) Nature 418, 869-872

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 ASMP gene ASPM-/ASPM- control Bond et al. (2002) Nature Genet. 32, 316-320

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

Evolution of the ASPM gene (2) McDonald-Kreitman test Sequence ASPM coding region from 40 diverse individuals and one chimpanzee N S Diversity 6 10 Divergence 19 7 P-value = 0.025 Evans et al. (2004) Hum. Mol. Genet. 13, 489-494

What changes? FOXP2 is a member of a large family of transcription factors and could therefore influence the expression of a wide variety of genes 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

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

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

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

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

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

Molecular basis of lactase persistence Lactase level is controlled by a cis-acting element Linkage and LD 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

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

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

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 — and that would be my candidate for the top scientific problem solved in the first decade of the new millennium. Nature 427, 208-209 (2004)

Further reading Jobling MA, Hurles ME, Tyler-Smith C (2004) Human Evolutionary Genetics. Garland Science (General textbook) Carroll SB (2003) Genetics and the making of Homo sapiens. Nature, 422, 849-857 (Broad-ranging review) Paabo S (2003) The mosaic that is our genome. Nature 421, 409-412 (Review) Cavalli-Sforza LL, Feldman MW (2003) The application of molecular genetic approaches to the study of human evolution. Nature Genet. 33, 266-275 (Review) Stringer C (2002) Modern human origins. Phil. Trans. R. Soc. Lond. B 357, 563-579 (Fossils and archaeology) Forster P (2004) Ice Ages and the mitochondrial DNA chronology of human dispersals: a review. Phil. Trans. R. Soc. Lond. B 359, 255-264 (mtDNA) Jobling MA, Tyler-Smith C (2003) The human Y chromosome: an evolutionary marker comes of age. Nature Rev. Genet. 4, 589-612 (Y chromosome) Bamshad M, Wooding SP (2003) Signatures of natural selection in the human genome. Nature Rev. Genet. 4, 99-111