Population Genetics 3

• We can learn a lot about the origins and movements of populations from genetics

• Did all modern humans come from Africa?

• Are we derived from Neanderthals?

• Are dogs really a type of wolf?

DNA Polymorphisms

• Many DNA sequences are polymorphic (have different alleles)

• A common type of polymorphism is SNPs (single nucleotide polymorphisms, e.g. C/T)

• Another type is microsatellite repeats, e.g…...(CA)n...…where n, the number of repeats, is variable, and mutates more quickly than SNPs do

Microsatellite DNA polymorphisms

....CACACACACACA....

chromosome

PCR

No. of CAs varies (alleles)

DNA fragments

Electrophoresis1 2 3 4 5

large

small

Deducing the haplotype• The combination of alleles for two or more linked

markers, on a single individual chromosome, is called a haplotype

• In a haploid organism (one of each chromosome) it is obvious what the haplotype is

• In a diploid, it is not always obvious• Example: 2 markers on human X chromosome,

female with genotype a/a for 1st marker and c/c for 2nd - haplotypes are both a - c

• But if genotypes are a/c and a/c, haplotypes could be a - a and c - c, or a - c and c - a

Haplotypes and recombination

• In a diploid organism reproducing sexually, new haplotypes can be formed by recombination

a

ag

g g

g

a

a

g

g

Mum and Dad’s X chromosomes

Daughter’s X chromosome haplotypesshow there must have been recombination in Mum

Haplotypes and mutation

• New haplotypes can also be formed by mutation

ac

t

gct

g

at

g

aa

Non-recombining regions of genome

• To make a phylogeny from haplotypes it is best to use regions of genome that don’t recombine, because then only have to consider effects of mutation

• In mammals, these regions include the Y chromosome and the mitochondrial chromosome

• Both systems are routinely used for population studies

The human Y chromosome

• The mammalian X and Y chromosomes evolved from a pair of autosomes

• The human Y has a block of material that transposed (moved) from the X since the divergence of chimps and humans

The mitochondrial chromosome

• About 15kb of DNA

• Mutates quite rapidly

• In eggs but not sperm, so shows maternal inheritance

Human origins• The “multi-regional hypothesis” says that modern

humans evolved from Homo erectus independently on different continents starting about 1,000,000 years ago

• The “out-of-Africa” hypothesis is that all modern humans are derived from immigrants of African origin that displaced the indigenous types (such as Neanderthals)

• The variation in modern human mitochondrial DNA suggests common ancestor lived about 200,000 years ago

Phylogeny based on haplotypes• If there has been no recombination, we can deduce

the phylogeny of the haplotypes by parsimony

acgt tgcaagcaaccaacgt acgaOutgroupe.g. chimp Modern humans

Mutation

Y chromosomes and human origins

• Are all modern humans of African origin?

AfricaEurope, Asia

Time ofmigration

African mutations Non-African mutations

Common ancestor

Are modern humans descended from Neanderthals?

• Neanderthal and Cro-Magnon mitochondrial isolated from fossils

• Modern humans are very similar to Cro-Magnon (who lived about 24,000 years ago), much less similar to Neanderthal (common ancestor 600,000 years ago)

• Ancestors of modern humans (e.g. Cro-Magnon) believed to have displaced indigenous Neanderthal types in Europe and other regions of world about 30,000 years ago

Dogs and wolves

• Mitochondrial DNA from modern dogs ( - ) and wolves ( )�

• Domestic dogs and wolves are on same branches, coyote (wild dog) on a different branch