Tracing the dispersal of human populations By analysis of polymorphisms in the

1. Tracing the dispersal of human populations By analysis of polymorphisms in the Non-recombining region of the Human Y Chromosome Underhill et al 2000 Nature Genetics 26: 358-361 Underhill et al 2001 Annals of Human Genetics 65: 43-62

4. Traditional paleoanthropological studies look at where things that look and act like us first appeared and when. Underhill, Cavalli-Sforza and colleagues have used various DNA polymorphisms to follow human evolution. Phylogeography analyzes genetic diversity to predict time to a most recent common ancestor. In addition, the location of populations with diverse alleles is used to predict the location of first appearance of common ancestral genes. Phylogeography assumes a correspondence between overall distribution of polymorphisms and past human movements.

5. Underhill et al 2001 Sampled polymorphic loci on the Y chromosome to follow human evolution. Sampled DNA from 1062 men. Represent 52 indigenous populations distributed around the world. In preliminary studies, they identified 218 Y-linked polymorphic loci. Most loci were biallelic – either an ancestral or derived allele.

6. After scoring each man’s DNA for all 218 loci, they found 131 different haplotypes. A haplotype represents a group of genes that do not separate by recombination. Each haplotype is the collection of alleles for that non-recombining group of genes in an individual. Examples include the human MHC locus, The non-recombining region of the mammalian Y chromosome. One approximately every 200-500 kb in the human genome.

7. NRY haplotypes from Jefferson family members

8. The differences between haplotypes is used to estimate the time to the most recent common ancestor to be 60,000 years. Using maximum parsimony analysis, they grouped the haplotypes into 10 haplogroups Great ape DNA used to make a root in the tree. The geographic distribution of the haplogroups indicates how people migrated to colonize the whole world.

9. Maximum Parsimony Analysis: Fewest changes to establish relationships between all individuals. Sample population with 4 biallelic loci: ABCD AB’CD A’BCD AB’C’D AB’CD’ A’B’C’D A’B’CD ABCD _____________________ AB’CD A’BCD _________ __________ AB’C’D AB’CD’ A’BC’D A’B’CD Each step is one mutation from progenitor – estimate time based on uniform mutation rate.

10. Maximum parsimony analysis of polymorphisms in human Y chromosomes

12. Distribution model assumes that genotypes of modern indigenous people reflects early migration routes Caveots Continuous gene flow Selection effects Effects of recent events such as migrations

13. Estimated time to most recent common ancestor is based on the number of differences that distinguish the haplotypes, an assumed mutation rate and an assumed model of population evolution Caveots Stable mutation rate Selection Unpredicted population bottlenecks

14. Predicted time to common ancestor is 59,000 years. 95% confidence interval is 40,000 – 140,000 years. Paleological evidence indicates modern humans spread throughout Africa 90,0000-130,000 years ago. Estimates based on mitochondrial DNA also indicate common ancestor 100,000-200,000 years ago.

16. 91, 42; 140,000-40,000 years ago 59,000 Yap, RPSY, 89; 50,000-45,000 35, 02; <18,000 201, 09; 45,000-30,000 30,000 172; 30,000-20,0000

17. 60,000 45,000 30,000 18,000 30,000

18. 60,000 45,000 30,000 18,000 30,000

19. 60,000 45,000 30,000 18,000 30,000

20. 60,000 45,000 30,000 18,000 30,000

25. Earlier studies with Mitochondrial DNA monitor the female lineage of modern humans Human genome sequence allowed identification of stable haplotypes of autosomal genes. These have recently also been used to trace the lineage of modern humans The time line is harder to determine and generally the Estimated time to common ancestor is longer Distribution patterns are harder to follow but are Generally consistent with data from the NRY analysis.

26. Y chromosome analysis fits with roughly with paleological and mitochondrial DNA evidence. Reveals more migration events than paleological record. Estimates a fairly recent date to our most recent common ancestor. Did our family replace other humans that existed earlier? Y vs. Mitochondrial time to most recent common ancestor. Reasons for the expansion of our single hominid family are still being examined.

27. 100,000 years ago Homo sapiens filled Africa according to the fossil record 300,000 years ago Homo erectus had migrated all over Europe and Asia Neanderthal man and Java man Why did modern humans spread out and take over all available niches? One suggestion is FOXP2 mutation

28. FOXP2 is a transcription factor that affects speech Family with a known dominant mutation – Problems with motor aspects of speech but also Cognitive aspects Molecular studies of variation at FOXP2 locus Shows FOXP2 has significantly high rate of evolution in hominid lineage – rapid substitutions comparing Humans to chimps and other mammals This analysis concludes that the Human FOXP2 allele may have evolved less than 100,000 years ago.