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Lecture 23 : Introduction to Coalescence

Lecture 23 : Introduction to Coalescence. April 7, 2014. Last Time. Introduction to phylogenetics Phylogeography Limitations of phylogenetic analysis. Today. Gene trees versus species trees Coalescence Influence of demographic factors on coalescence times Coalescence and human origins.

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Lecture 23 : Introduction to Coalescence

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  1. Lecture 23 : Introduction to Coalescence April 7, 2014

  2. Last Time • Introduction to phylogenetics • Phylogeography • Limitations of phylogenetic analysis

  3. Today • Gene trees versus species trees • Coalescence • Influence of demographic factors on coalescence times • Coalescence and human origins

  4. Gene Trees vs Species Trees Gene Tree B C A • Genes (or loci) evolve at different rates • Why? • Topology derived by a single gene may not match topology based on whole genome, or morphological traits

  5. Coalescence • Retrospective tracing of existing alleles to a common ancestral allele • A reverse reconstruction of the evolution of modern variation • Allows explicit simulation of sequence evolution • Incorporation of factors that cause deviation from neutrality: selection, drift, and gene flow

  6. 9 generations in the history of a population of 14 gene copies Time present Individual alleles Slide courtesy of Yoav Gilad

  7. Gene Trees vs Species Trees Failure to coalesce within species lineages drives divergence of relationships between gene and species trees Divergent Gene Tree: b is closer to c than to a Concordant Gene Tree b is closer to a than to c a b c a b c

  8. How to model this process?

  9. Modeling from Theoretical Ancestors: Forward Evolution • Can model populations in a forward direction, starting with theoretical past • Fisher-Wright model of neutral evolution • Very computationally intensive for large populations

  10. Alternative: Start at the end and work your way back Most recent common ancestor (MRCA) Time present Individual alleles Slide courtesy of Yoav Gilad

  11. The genealogy of a sample of 5 gene copies Most recent common ancestor (MRCA) Time present individuals Slide courtesy of Yoav Gilad

  12. The genealogy of a sample of 5 gene copies Most recent common ancestor (MRCA) Time present Individual alleles Slide courtesy of Yoav Gilad

  13. Examples of coalescent trees for a sample of 6 Time Individual alleles Slide courtesy of Yoav Gilad

  14. Coalescence Advantages • Don’t have to model dead ends • Only consider lineages that survive to modern day: computationally efficient • Based on actual observations • Can simulate different evolutionary scenarios to see what best fits the observed data

  15. Coalescent Tree Example • Coalescence: Merging of two lineages in the Most Recent Common Ancestor (MRCA) • Waiting Time: time to coalescence for two lineages • Increases with each coalescent event

  16. Probability of Coalescence • For any two lineages, function of population size • Also a function of number of lineages where k is number of lineages

  17. Probability of Coalescence • Probability declines over time • Lineages decrease in number • Can be estimated based on negative exponential where k is number of lineages

  18. Time to Coalescence Affected by Population History Bottleneck

  19. Time to Coalescence Affected by Population History Population Growth

  20. How will population structure affect coalescence times?

  21. Time to Coalescence Affected by Population Structure

  22. Applications of the Coalescent Approach • Framework for efficiently testing alternative models for evolution • Inferences about effective population size • Detection of population structure • Signatures of selection (coming attraction) • Reconstructing history of populations

  23. Origins of Modern Humans • Most fossil evidence points to origins in Africa and subsequent migrations Skulls found in Omo Valley, Ethiopia Dated at ~195K Omo 1 Modern http://www-v1.amnh.org/exhibitions/permanent/humanorigins/history/origin.php http://www.dhushara.com/book/unraveltree/unravel.htm

  24. Human Phylogeography: mtDNA • Most ancient and diverse haplotypes in Africa (dots) • Migration and admixture is evident from presence of African haplotypes in other clades

  25. Complexities to Human Phylogeography • Some genes show evidence of Asian origin • Sequence of X-linked ribonucleotidereductase M2 pseudogene 4 (RRM2P4) Garrigan 2007 Nature Reviews Genetics 7:669

  26. Why might some X-linked genes show a human origin in Africa (e.g., PDHA1), while others suggest an Asian origin e.g., (RRM2P4)?

  27. Evidence of Population Structure in Ancient Humans Garrigan and Hammer 2006 Nature Reviews Genetics 7:669

  28. Time to Coalescence Affected by Population Structure

  29. Evidence for Ancient Population Structure in Nuclear but not Mitochondrial Trees Garrigan and Hammer 2006 Nature Reviews Genetics 7:669

  30. Why does mitochondrion show shorter coalescence times than nuclear loci?Why does rate vary much more for nuclear loci?

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