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Lecture 24 : Human Origins and Signatures of Selection. April 11, 2014. Announcements. Switched labs 11 and 12 Phylogenetics and Coalescence this week (lab 12 in the manual) Signatures of selection next week (lab 11 in the manual). Last Time. Gene trees versus species trees Coalescence

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Presentation Transcript
slide2

Announcements

  • Switched labs 11 and 12
    • Phylogenetics and Coalescence this week (lab 12 in the manual)
    • Signatures of selection next week (lab 11 in the manual)
slide3

Last Time

  • Gene trees versus species trees
  • Coalescence
  • Influence of demographic factors on coalescence times
slide4

Today

  • Human origins: Neanderthals and Denisovans
  • Signatures of selection
evidence for ancient population structure in nuclear but not mitochondrial trees
Evidence for Ancient Population Structure in Nuclear but not Mitochondrial Trees

Garrigan and Hammer 2006 Nature Reviews Genetics 7:669

slide6
Why does mitochondrion show shorter coalescence times than nuclear loci?Why does rate vary much more for nuclear loci?
probability of coalescence
Probability of Coalescence
  • For any two lineages, function of population size
  • Also a function of number of lineages

where k is number of lineages

models of human origin
Models of Human Origin

Origin of modern humans

Garrigan and Hammer 2006 Nature Reviews Genetics 7:669

human evolutionary history
Human Evolutionary History

http://www.cartage.org.lb/en/themes/sciences/paleontology/paleozoology/fossilhominids/ChartHumanEvolution/ChartHumanEvolution.htm

neanderthals
Neanderthals
  • Occurred in Europe and central Asia from 400,000 to 30,000 ybp
  • Morphological features distinguished them from modern humans:
    • strongly-built, stocky frame
    • long, low skull with large cranial capacity
    • Double-arched brow ridges
    • occipital ‘bun’
    • large nose, big front teeth
  • Disappeared from fossil record shortly after Homo sapiens appeared in Europe

Nature 465:148, 2010

http://www.msnbc.msn.com

what happened to the neanderthals
What happened to the Neanderthals?
  • Extinction with no genetic legacy?
  • Do Neanderthals live on within our own genomes?
  • Neanderthal genome sequences are now answering those questions!

http://www.isayev.info

archaic genomics svante p bo march 27 2014 nih
Archaic Genomics - Svante Pääbo March 27, 2014, NIH

https://www.youtube.com/watch?v=M7VdRKQuAa8

neanderthal mitochondrial sequence
Neanderthal Mitochondrial Sequence
  • DNA extracted from bone fragments from 4 locations
  • Sequenced using Next-Gen technology: Roche 454 FLX
  • One individual (from Croatia) sequenced to great depth to give reference genome

Briggs et al. 2009 Science 325:318

neanderthal and human mitochondrial tree
Neanderthal and Human Mitochondrial Tree
  • Neanderthals and humans show no evidence of admixture
  • Most ancient Neanderthals (easternmost) are also most differentiated
  • Very low population structure and low diversity in most recent Neanderthals
  • Low effective population size? Bottleneck? Stay tuned.

https://www.youtube.com/watch?v=M7VdRKQuAa8

neanderthal complete genome sequence
Neanderthal “Complete” Genome Sequence
  • DNA extracted from bone fragments from Vindijia Cave, Croatia
  • 95-99% of DNA was from microbes
  • Cut DNA with restriction enzymes with high CpG recognition sites: eliminate bacterial DNA
  • Sequenced with 454 and Illumina GAII
  • 5.3 Gb of sequence produced

Green et al. 2010 Science 328: 710

human neanderthal hybridization
Human-Neanderthal Hybridization

Distance from Modern Humans

Distance from Neanderthal

  • Segments in European human genome with high identity to Neanderthals are very different from other human sequences
  • Not true for African sequences
  • Evidence for hybridization with Europeans, not Africans

Green et al. 2010 Science 328: 710

human neanderthal hybridization1
Human-Neanderthal Hybridization
  • Four possible scenarios for hybridization
  • Scenario 3 most likely: hybridization with ancestor of all modern Asian and European lineages after splitting from Africa

Green et al. 2010 Science 328: 710

mithochondrial and nuclear stories are different
Mithochondrial and Nuclear Stories are Different

https://www.youtube.com/watch?v=M7VdRKQuAa8

slide19

Why would mitochondrial DNA give a different answer than nuclear DNA?

What other questions could be addressed with ancient, introgressed DNA?

a new human ancestor denisovans1
A new human ancestor: Denisovans
  • Single finger bone and some teeth discovered in cave in Siberia
  • Found in conjunction with human-like artifacts: bracelets and necklaces
  • Sequenced mitochondrion and whole genome (1.9X) using Illumina GAII
  • DNA sequence reveals this is not a human bone!

http://www.time.com/time/health/article/0,8599,1974903,00.html

eurasians probably had continued introgression from other hominids after divergence from africans
Eurasians Probably had continued introgression from other hominids after divergence from Africans
summary
Summary
  • https://www.youtube.com/watch?feature=player_detailpage&v=M7VdRKQuAa8#t=1661
  • \
slide47
The main power of neutral theory is it provides a theoretical expectation for genetic variation in the absence of selection.
slide48
Assume you take a sample of 100 alleles from a large (but finite) population in mutation-drift equilibrium.

What is the expected distribution of allele frequencies in your sample under neutrality and the Infinite Alleles Model?

A.

B.

C.

10

8

6

Number of Alleles

4

2

2

2

2

4

4

4

6

6

6

8

8

8

10

10

10

Number of Observations of Allele