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Sequencing extinct human ancestors. Credits to Vanessa Patel for some of the slides. The Hominid Lineage. Archaeology. Archaeology – “the scientific study of material remains (as fossil relics, artifacts, and monuments) of past human life and activities ”
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Sequencing extinct human ancestors Credits to Vanessa Patel for some of the slides
Archaeology • Archaeology – “the scientific study of material remains (as fossil relics, artifacts, and monuments) of past human life and activities” • Studies the time period starting at the Paleolithic time until the advent of literacy
The Neanderthal Genome • From bones, compared genomes of three different Neanderthals with five genomes from modern humans from different areas of the world • Figure 1- R. E. Green et al., Science 328, 710-722 (2010)
Genomic Analysis Stoneking, Krause, Nature Reviews Genetics 2011
Genomic Analysis Stoneking, Krause, Nature Reviews Genetics 2011
Model-based analyses Stoneking, Krause, Nature Reviews Genetics 2011
Out of Africa Refined Stoneking, Krause, Nature Reviews Genetics 2011
Fixation, Positive & Negative Selection How can we detect negative selection? How can we detect positive selection? Negative Selection Neutral Drift Positive Selection
How can we detect positive selection? Ka/Ks ratio: Ratio of nonsynonymous to synonymous substitutions Very old, persistent, strong positive selection for a protein that keeps adapting Examples: immune response, spermatogenesis
Long Haplotypes –iHS test • Less time: • Fewer mutations • Fewer recombinations