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2005-2006 Molecular Medicine M.Sc. Lecture 3

Human Evolutionary Genetics

Dr. A. Ruth Freeman,Molecular Population Genetics.Email: abigail.freeman@tcd.ie

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RECAP 1

• Humans are a member of the primate order, and genetic and other molecular studies have shown that they are most closely related to the chimpanzee.

• Fossils that date to the approximate time of the human/chimp split (5-7 MYA) have been described but remain to be fully evaluated.

• Several hominid were present in Africa from ~4-2 MYA. Most are classified as Australopithecines.

• Homo erectus/ergaster first appeared in Africa ~2MYA and was the first hominid to migrate out of the continent.

• Some later Homo species have been described, but their relationships are still debated.

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RECAP 2

• Anatomically modern humans are first found in Africa about 130KYA, and from 70~50KYA in other parts of the world.

• The Multiregional Theory and the Out-of-Africa theory both sought to explain modern human origins.

• Most genetic diversity is found within African populations and most mtDNA phylogenies have an African root, implying an African origin for our ancestors.

• mtDNA from H. neanderthalensis shows that it is a distinct lineage.

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Part 1A: Evidence from the Y chromosome

The X-Y system: Mammals and certain insects (including fruit flies)

Humans44+XY

44+XXParents

44+XX

44+XY

Zygotes(offspring)

22+X22+YSperm 22+

X Ova

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• Y chromosome has few genes. Mostly genetically inert. <100 genes on the Y chromosome.

• Large central portion of the chromosome does not form chiasmata with the X chromosome. Therefore does not recombine.

• Pseudoautosomal regions do synapse and recombine with the X chromosome.

• The sex determining region Y (SRY) contains a gene that produces a protein (testis-determining factor) provides the primary signal for male development.

• Rich in repeats such as LINES and SINES

The Y chromosome

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Evidence from the Y chromosome

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The Y chromosome

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• Male analogue to mtDNA (passed from fathers to sons only).

• Y-haplotypes can be used to track patriarchal genetic history -paternal founders of human populations.

• May detect genetic introgression from archaic populations that would not be recognisable using mtDNA alone.

• Male-mediated gene flow - ‘dissemination via insemination’.

• High mutation rate due to exclusive passage through male line, which leads to higher sequence divergence between species

• BUT lower within species divergence! – RCA due to drift which outweighs high mutation rate– geographic information

The Y chromosome as a toolfor reconstructing human origins

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Gen.

The behaviour of Y chromosome lineages in populationsis the same as that observed for mtDNA lineages.

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• Three types of genetic markers:

1) Unique Alu insertion polymorphism (after human-chimp divergence) in DYS287 locus on non-recombining portion of Y chromosome: YAP+ or YAP-

2) Slowly-evolving bi-allelic single nucleotide polymorphisms(SNPS) in the non-recombining portion of Y chromosome.

3) Rapidly-evolving microsatellite loci in the non-recombining portion of Y chromosome.

The Y chromosome as a toolfor reconstructing human origins

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1995 Two papers in Nature describe sequence analysis of portions of the Y chromosome. Hammer (1995) and Whitfield et al. (1995). Hammer analysed 2.6 kb fragment surrounding YAP polymorphism in 16 human and four chimpanzee Y chromosomes. MRCA was estimated as 188,000 years (51,000 to 411,000 95% CI). Supports OAR. Whitfield sequenced 18.3 kb from five diverse humans and one common chimp. Only 3 mutations were detected among human sequences (approximately 240 mutations between humans and chimp sequence). MRCA ~ 100,000 years. Also supports OAR.

1997 Hammer et al. (1997) analysed the YAP insertion, four SNPs and two microsatellites in 1500 Y chromosomes from 60 global populations. An African origin for human Y chromosomal variation was apparent.

Important landmarks in the study ofhuman Y chromosome variation

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1998 Hammer et al. (1998) found more Y chromosome haplotypes and found the inferred ancestral haplotype (estimated to be ~ 150,000 years old) limited to African populations. Supports OAR. Seemed to indicate some Asian migration back into Africa (Arabs?).

1999 Seielstad et al. (1999) analysed 10 Y chromosome microsatellite loci typed in 506 males representing 49 populations. Find significantly more diversity in Africa.

1999 Scozzari et al. (1999) analysed 7 bi-allelic and 4 microsatellite markers in ~ 800 Y chromosomes from 25 African populations. The "ancestral" haplotype (haplotype 1A) was observed among Ethiopians, "Khoisan” (San people), and populations from northern Cameroon. The San version of the haplotype was quite different from the other haplotypes and its distribution provides evidence that East Africa may have been the area where AMH arose (assuming San had a wider distribution).

Important landmarks in the study ofhuman Y chromosome variation

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Average linkage tree showing population relationships for variation at 10 Y microsatellite markers (Seielstad et al. 1999).

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2000 Forster et al. (2000) studied a range of bi-allelic and microsatellite markers in 256 Y chromosomes from Africa, Asia, Europe and Australasia. They find the earliest branch in the African San sample.

2000 Shen et al. (2000) and Thomson et al. (2000) identified polymorphisms (SNPs) in three Y chromosome genes (total of 64,120 bp and 98 SNPs). The root of their tree is in Africa (used primate sequence data to root tree) and most of the oldest non-African lineages are Asian. Their estimate for the MRCA is ~ 60,000 years. Again, the most ancestral lineages were represented among the Khoisan. The distribution and relationship of haplotypes 3, 14 and 15 suggested that AMH migrated in at least two waves from Africa into Asia and New Guinea, followed by a later dispersal probably out of Western Asia into Central Asia, Europe and the Americas.

Important landmarks in the study ofhuman Y chromosome variation

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Phylogenetic tree for the three genes

described by Thompson et al.

(2000). 32 lineages were described by 56

SNPs.

Genetic diversity outside Africa is

derived from a small number of African

lineages.

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2000 Underhill et al. (2000) analysed ~ 1,000 globally representative samples using denaturing HPLC and ~ 160 polymorphic sites on the Y chromosome. Estimated that AMH populations left Africa between 35,000 to 89,000 years ago.

Important landmarks in the study ofhuman Y chromosome variation

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2001 Ke et al. (2001) analysed 12,127 Y chromosomes from throughout Asia. They typed three diagnostic mutations known to be derived from an ancestral African haplotype. They found that every single Y chromosome that they examined from Asia could be traced back to Africa. There was no evidence of ancient Asian Y lineages in the modern human population. In other words, archaic human populations that existed in Asia prior to the AMH expansion did not contribute Y chromosomes to the modern gene pool.

Important landmarks in the study ofhuman Y chromosome variation

Modern Asian men carry three Y chromosome markers that arose from African marker

M168

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• The shallowness of mtDNA diversity is mirrored by that observed in Y chromosome variation.

• Most estimates for the Y chromosome MRCA are even lower than those found for mtDNA.

• Y chromosome data support the hypothesis that the San people of Southern Africa are the most divergent human population and retain genetic variants from the oldest split in AMH (100-150,000 years ago?).

• Y chromosome analysis suggests that humans left Africa for West Asia (the Levant) via the Sinai. A second migration followed a coastal route around Arabia and India and into South East Asia and Australasia. The third major wave may have been the migration of people from West Asia into East Asia, Europe and finally the Americas.

Implications of Y chromosome workfor theories of modern human origins

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‘Coasting’ out of Africa

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Negrito people from the Andaman and Nicobar Islands

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• Numerous studies of allele frequencies at genetic markers (allozymes, microsatellites, SNPs) in populations support OAR and sub-Saharan African populations represent the earliest branch (African origin). The timing of this split is usually between 100,000 -200,000 years ago.

• Analyses of haplotypes at individual autosomal genes or sequences reflect much greater African diversity and non-Africans represent a subset of the African variation (same as mtDNA or Y chromosome).

• Genes studied include myotonic dystrophy (DM) locus, CD4 T-cell antigen gene, tissue plasminogen-activator locus (PLAT) (Tiskkoffet al. 1996, 1998, 2000) and dystrophin (Zietkiewicz et al. 1997).

Part 1B: Evidence from autosomal sequences

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Population dendrogram of allele frequencies at 29 protein loci. (Nei and Roychoudhury, 1993).

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Evidence from autosomal sequences

• Harding et al 1997 analysed 326 β-globin sequences.

• They found that the root of the phylogeny was in Africa, and theTMRCA was estimated as 740KYA.

• They also found some lineages that were exclusive to Asia (200KYA)

• The older TMRCA is probably due to the larger effective population size of autosomes, neutrality was also assumed.

• Asian samples could represent introgression from ancient lineages in Asia, but more likely not sampled in Africa, or lost by drift

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• Several studies have confirmed low genetic diversity in humans relatively to other hominoids and mammals.

• The levels of diversity observed correspond to a much smaller ancestral population size than would be required for MRE

• For most loci higher levels of diversity are observed in Africa than in other parts of the world.

• Tishkoff et al 1996 closely examined diversity at the CD4 locus

• 2 markers 9.8kb apart-one microsatellite (15), one deletion.

• Outside Africa the deletion was only associated with the 6 repeat allele; the non-deletion was only associated with 5 and 10 repeats

Part 1C: Genetic Diversity-amount and pattern

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• Within Africa the deletion was associated with any of 9 alleles;the non-deletion with 12 different alleles

• The haplotypes found outside of Africa were a subset of those within the continent.

• The maximum age of the deletion chromosomes outside Africa was estimated as 154 KYA

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Simple presence/absence marker haplotypes for the myotonic dystrophy (DM) gene typed in various human populations. The 3 +/- markers used are shown above.From Tishkoff et al. (1998)

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Implications of autosomal workfor theories of modern human origins

• Many autosomal tests have been based on single markers.

• Takahata (2001) examined 10 loci. It was possible to infer the ancestral root of all but one in Africa.

• The single locus which rooted in Asia was based on a sample of only 10 individuals.

• Population sizes not the same on all continents pre-Neolithic. May have been larger in Africa, but prob. not significant.

• Seielstad et al 1999 – drift has not caused huge differentiation in non-African populations

• It is clear that the vast majority, probably all, of our ancestors share a recent common ancestry in Africa.

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Part 2: What make us human?

HUMAN CHARACTERISTICS WHICH CAN BE FOSSILISED

• Brain cavity and central foreamen magnum

• Thinner enamel and smaller canines and incisors

• Cylindrical chests

• Longer legs

• Bipedalism

• Grasping hands with longer thumb

• Slow development and prolonged childhood

• Complex tools and fire use (art?)

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Tool use

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A genetic approach

• 30-60 million point mutations between human and chimp? 15-30 million on the human lineage?

• Probably many important changes

• Cytogenetic variation, repeats, retroposons (LINE, SINE), enhancers

• Duplications, deletions and mutations affecting the copy number,structure or expression pattern.

• Loss of function mutations?

• Microarray – 18,000 genes – Brain genes (Enard et al, 2002, Science)

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•CMP-Neu5Ac hydroxylase inactivation (Chou et al 2002)

• Language -FOXP2 (Enard et al 2002, Nature)

M

C

H

M

C

H

M

C

H

blood liver brain

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The language gene?

• Families with language impairment studied.

• Disorders tend to be highly heritable (0.45), but not Mendelian.

• Linkage study and translocation used to locate FOXP2.

• 3 aa differences between human and mouse, and two of these 2 since humans diverged from chimp.

• Sequencing of 14kb of the gene in 20 individuals revealed an excess of rare alleles suggesting a selective sweep.

• Individuals with disruption in FOXP2 have difficulties with the expressive and receptive aspects of language and grammar.

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Copyright 1999, Cold Spring Harbour Lab

Part 3: Human Genetic Diversity and Differentiation

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Human evolution and diversity in a medical context

• Evolution is the foundation for biology, biology is the foundation of medicine.

• Increased understanding of genetic history and relationships.

• Medical advances-identifying genes predisposing to disease.

• Accurate paternity tests and forensics.

• Population-wide medical advice and training.

• Interest in our own past.

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Human Genetic Diversity

• The study of human races has been linked to blatant and more subtle racism

• Should we study human genetic diversity, or do the potential downsides outweigh any potential benefits?

• Important benefits in the fields of medicine and forensics

• The information actually refutes racism.

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Historical Study of Human Genetic Diversity

• Linneaus (1707-78) divided humans into 2 groups, diurnus and nocturnus (troglodytes)

• The diurnus group was further subdivided into:

►americanus – red with black hair and scanty beards, obstinate, free, painted with fine red lines, regulated by customs.

►europeus – white, long flowing hair, blue eyes, sanguine, muscular, inventive, tight clothing, governed by laws.

►asiaticus – yellow, melancholy, black hair and brown eyes, severe, haughty, stingy, loose clothing, governed by opinions.

►afer – black, cunning, phlegmatic, black curly hair, women without shame and lactate profusely, anointed with grease, ruled by impulse.

►monstrosus – misc including dwarfs and large lazy Patagonians.

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Historical Study of Human Genetic Diversity

• Francis Galton “Hereditary Genius: an inquiry into its laws and consequences” 1869.

• Established a grading system for different human populations

►Top of hierarchy-Ancient Greeks.

►English- couple of grades below-“the calibre of whose intellect is easily gauged by a glance at the contents of a railway book-stall”.

►Lowland Scots and Northern English slightly higher grade than English

►Negros two grades below English and Australian Aboriginals a further grade below them.

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Modern Attitudes to Studying Human Genetic Diversity

• Research can only be carried out with informed consent.

• Participants must understand the nature, purpose of research andhave access to the information.

• They must be aware of the implications in relation to:-health and health insurance-stigmatisation-commercial applications

• Group informed consent may be necessary (e.g. family members)

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Modern Attitudes to Studying Human Genetic Diversity

• Is informed consent from members of cultures that do not ascribeto Western scientific values truly informed?

• How much information should be retained with the sample?

• Can old samples be used?

• Can samples collected for one study be used in another?

• Can an individual give consent for future studies/unknown futureapplications?

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The Human Genome Diversity Project

• 1991 – “material to record human ethnic and geographic diversity....especially from populations that have been isolated for some time and are likely to be linguistically and culturally distinct”

• 500 key populations chosen, but did not succeed in sampling most.

• Concerns-commercialisation, diversion of funds, racism and biological warfare.

• Definition of humans populations (grid/cultural-linguistic differences)Geographic proximity, common language, shared ethnicity, and culture.

• Ernst Renan “group of people united by a mistaken view of the past and a hatred of their neighbours”

• Self determination?

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Early molecular studies

Lewontin (1972) examined 17 classical markers (including blood groups and serum proteins) in many diverse populations. He defined 7 races based on cultural parameters and examined diversity measures for a) each population

b) each racec) total

Average proportion of variation within populations 85.4%

Ave proportion of variation between populations within races 8.3%

Ave proportion of variation between races 6.3%

Most variation lies within populations and the amount between races show that they have no genetic reality. Biological races are defined when 30% of variation is between groups.

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Early molecular studies

“Human racial classification is of no social value and is positively destructive of social and human relations. Since such racial classification is now seen to be of virtually no genetic or taxonomic significance either, no justification can be offered for its continuance”

Lewontin 1972

~ 90%

~ 10%

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Early molecular studies

Since then many studies have confirmed these findings i.e. that 83-88% of variation is found within populations, and 9-13% between continental groups e.g. Tishkoff et al 1996 – CD4.

When mtDNA and Y-chromosomes are examined less of the variation is within populations – more is found between groups.

This is because the effective population size of these loci is smaller.

The effect is further enhanced in Y-chromosomes by patrilocality

FST – describes the degree to which variation at classical markers within a meta-population is apportioned among sub-populations, i.e. the proportion of total variance in allele frequencies thatoccurs between subpopulations-can also be used as a measure of distance.

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Assigning individuals to populations

Given the similarity of human populations, is it possible to determine the origin of an individual based on their genotype?

If all variation was within populations this would be impossible, if all variation was between populations this would be trivial.

In 1994 Bowcock et al examined 30 microsatellite markers in 14 populations and calculated genetic distances based on the number of shared alleles. They found that 88% of individuals were in continent-specific clusters. 7% were in clusters that did not correspond to their continental origin.

9 of the 14 populations formed clusters that included > 50% of individuals

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Assigning individuals to populations

More recent studies have used the computationally-intensive program STRUCTURE (Pritchard et al 1999). This assumes that populations are characterised by a set of allele frequencies at each locus.

Studies using large numbers of individuals and large numbers of markers have shown very good correspondence.

e.g. Wilson et al 2001 39 msats 354 individuals

Rosenberg et al 2002 377 msats 1056 individuals

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African European Near East Cen/S Asia East Asia Oceania America

20 Alu polymorphisms failed to identify these continental groups

►However, with enough information it is possible to deduce much about the population of origin.

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Assigning individuals to populations

How do we reconcile this with the conclusion that most variationexists within populations?

1. Particular alleles are not usually continent- or population-specific.

2. Large numbers of markers are required.

3. Groups identified do not necessarily correspond to races and differences are too small to classify as such.

4. Drift and ancestry is shared by groups – this can cause related individuals to have similar profiles of allele frequencies.

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Gradients of Human Genetic Diversity

• Serre and Paabo 2004.

• Cultural traits used to define populations are at most a few thousand years old.

• Two contrasting approaches – geographical/cultural?

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Different levels of diversity

Low levels of genetic diversity may reflect- limited immigration- extensive drift (small effective population size)- selective pressures against certain alleles

High levels of genetic diversity may reflect- extensive immigration- limited drift (large effective population size)- selection favouring increased genetic diversity- admixture