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Sequencing extinct human ancestors Credits to Vanessa Patel for some of the slides
Sequencing extinct human ancestors
Credits to Vanessa Patel for some of the slides
The Hominid Lineage
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
Archaeology
From bones, compared genomes of three different Neanderthals with five genomes from modern humans from different areas of the world
The Neanderthal Genome
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
Neanderthal Genome
Neanderthal Genome
Model-based analyses
Stoneking, Krause, Nature Reviews Genetics 2011
Neanderthal Genome
Neanderthal Genome
Denisovan – Another human relative
Denisovan – Another human relative
Out of Africa Refined
Stoneking, Krause, Nature Reviews Genetics 2011
Denisovan
Denisovan Admixture
Denisovan Admixture
Aboriginal Australian
Aboriginal Australian
Archaic African Admixtures
Archaic African Admixture
Fixation, Positive & Negative Selection
Neutral Drift Positive SelectionNegative Selection
How can we detect negative
selection?
How can we detect positive
selection?
How can we detect positive selection?
Ka/Ks ratio:Ratio of nonsynonymous tosynonymous substitutions
Very old, persistent, strong positive selection for a protein that keeps adapting
Examples: immune response, spermatogenesis
How can we detect positive selection?
Long Haplotypes –iHS test
Less time:• Fewer mutations• Fewer recombinations
Neanderthal Immune System
Neanderthal Immune System
