Evolve 4


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Evolve 4

  1. 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
  2. 2. Homo erectus The first example of Homo erectus, known as "Java Man," was discovered in Indonesia in 1893. Fossil remains of Homo erectus have since been found throughout Africa and Asia, making it the first wide-ranging hominid. Despite the primitive appearance of its skull, the erectus skeleton is very similar to that of modern humans, although more robust (thicker and heavier). Homo erectus was probably the first hominid to use fire. 1.8 mya - 300,000 years ago first fossil found in 1893
  3. 3. Homo sapiens (modern) Modern Homo sapiens, also known as Homo sapiens sapiens, have been around for the past 120,000 years. Homo sapiens living about 40,000 years ago made elaborate tools out of bone, antler, ivory, stone, and wood, and produced fine artwork in the form of carvings and cave paintings. 120,000 years ago - present Homo sapiens neanderthalensis Averaging five and a half feet in height and possessing short limbs, Neanderthals were well-adapted to living in a cold climate. Attached to their robust (thick and heavy) bones were powerful muscles. The Neanderthal's brain was larger than the brain of living humans, although its shape was longer from front to back and not as rounded in the front. 230,000 - 30,000 years ago first fossil found in 1856 Homo sapiens (archaic) Also known as Homo heidelbergensis, this species has a brain that was larger than H. erectus' and smaller than that of a modern human. The brain was enclosed in a skull that was more rounded than H. erectus'. Fossil remains of archaic Homo sapiens have been found in Africa and Europe. 500,000 - 200,000 years ago first fossil found in 1921
  4. 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. 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. 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. 7. NRY haplotypes from Jefferson family members
  8. 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. 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. 10. Maximum parsimony analysis of polymorphisms in human Y chromosomes
  11. 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
  12. 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
  13. 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.
  14. 16. 91, 42; 140,000-40,000 years ago 59,000 Yap, RPSY, 89; 50,000-45,000 201, 09; 45,000-30,000 172; 30,000-20,0000 30,000 35, 02; <18,000
  15. 17. 60,000 45,000 18,000 30,000 30,000
  16. 18. 60,000 45,000 18,000 30,000 30,000
  17. 19. 60,000 45,000 18,000 30,000 30,000
  18. 20. 60,000 45,000 18,000 30,000 30,000
  19. 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.
  20. 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.
  21. 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
  22. 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.