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Initial Phylogenetic Analysis on Vervet Monkeys

Yu S. Huang 2011-4-13. Initial Phylogenetic Analysis on Vervet Monkeys. What is vervet monkey? (wikipedia). Rough geographic distribution. Are they still one species?. Relationship between Barbados and the reference (St. Kitts)? Which African subspecies is closest to reference?

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Initial Phylogenetic Analysis on Vervet Monkeys

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  1. Yu S. Huang 2011-4-13 Initial Phylogenetic Analysis on Vervet Monkeys

  2. What is vervet monkey? (wikipedia)

  3. Rough geographic distribution

  4. Are they still one species?

  5. Relationship between Barbados and the reference (St. Kitts)? Which African subspecies is closest to reference? What's the relationship among African subspecies? Main Questions

  6. What NCBI says Disclaimer: The NCBI taxonomy database is not an authoritative source ...

  7. A study based on Mitochondrial 12S rRNA [Kuyl et al. 1995 ]

  8. Capture a few of them (Chris & Trudy) Extract DNA from blood (Chris, Trudy, Katie, Yoon, Ania, Nelson, et al.) Release them (somebody) Sequence the DNA (Warren et al.) Calculate the distance using DNA The game plan

  9. Omit all details of previous 4 stepsCurrent state of genome sequencing.

  10. Not endangered, highly abundant (v.s. rhesus) Model to study high-level phenotypes: novelty-seeking, bipolar disorder (maybe). Model to study primate-specific diseases: SIV-infection, etc. Human curiosity But why do we choose vervet to spend $$$?

  11. The “usual” pipeline for next-gen seq

  12. One caveat in applying “usual” pipeline

  13. Treat “human” as fake monkey

  14. Probably not perfect, let's see the distance first. VRC: Vervet Research Colony (where original ~50 monkeys are from St. Kitts)

  15. Turn it into a picture.

  16. Nelson didn't even want to look at it!

  17. Error rate is a bit, uh, high: ~15.48%

  18. What is causing the high discordance rate between two runs of the reference?

  19. Dist(Het, Homo) = 0.5 The error rate drops to ~8%.

  20. Dropping the error rate further: 0.6%

  21. Turn it into picture

  22. Back to the questions Relationship between Barbados and the reference (St. Kitts)? Which African subspecies is closest to reference? What's the relationship among African subspecies?

  23. Dist(Barbados, vervet ref) = 1.4% Dist(closest African pair) = Dist(pygerythrus, sabaeus) = 2.13% 1. Relationship between Barbados and the reference (St. Kitts)?

  24. 2. Which African subspecies is closest to reference?

  25. 2. Which African subspecies is closest to reference? Dist(vervet ref, sabaeus) = 13.1% Dist(farthest African pair) = Dist(pygerythrus, aethiops) = 5.2%

  26. From sabaeus, but accumulates lots of mutations over time. (killed) More likely from a different subspecies. Even more likely it is a species by itself. (really??) 2. Which African subspecies is closest to reference?

  27. Magnus dropped a comment on the collaboration site:

  28. Select only the ultra-conserved regions of human reference Require the SNPs to be somewhat common among all. My coverage-based variant caller is ad-hoc. No proven track record. ... Now this has something to do with my customization to the “usual” pipeline

  29. 1Mb of vervet reference genome

  30. Data largely concur but need more careful look ...

  31. Katherine Camfield Alden Huang (Geschwind Lab) Anna Jasinska Yoon J. Jung Christopher Schmitt Nam Tran Vasily Ramensky Nelson Freimer Trudy Turner (Univ. of Milwaukee) Wes Warren (WUSTL) Ken Dewar (McGill) Acknowledgement

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