Population Genetics 3

1. 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?

2. 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

3. Microsatellite DNA polymorphisms chromosome ....CACACACACACA.... No. of CAs varies (alleles) PCR DNA fragments 1 2 3 4 5 Electrophoresis large small

4. 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

5. a g g g a g a g a g Haplotypes and recombination • In a diploid organism reproducing sexually, new haplotypes can be formed by recombination Mum and Dad’s X chromosomes Daughter’s X chromosome haplotypes show there must have been recombination in Mum

6. a g g g c c a a t t t a Haplotypes and mutation • New haplotypes can also be formed by mutation

7. 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

8. 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

9. The mitochondrial chromosome • About 15kb of DNA • Mutates quite rapidly • In eggs but not sperm, so shows maternal inheritance

11. 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

13. Phylogeny based on haplotypes • If there has been no recombination, we can deduce the phylogeny of the haplotypes by parsimony Mutation acgt acgt acga acca agca tgca Outgroup e.g. chimp Modern humans

14. Common ancestor Time of migration Africa Europe, Asia African mutations Non-African mutations Y chromosomes and human origins • Are all modern humans of African origin?

15. 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

16. 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