Initial Phylogenetic Analysis on Vervet Monkeys
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Initial Phylogenetic Analysis on Vervet Monkeys
Yu S. Huang 2011-4-13
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What is vervet monkey? (wikipedia)
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Rough geographic distribution
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Are they still one species?
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Main Questions
• Relationship between Barbados and the
reference (St. Kitts)?
• Which African subspecies is closest to
reference?
• What's the relationship among African
subspecies?
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What NCBI says
Disclaimer: The NCBI taxonomy database is not an authoritative source ...
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A study based on Mitochondrial 12S rRNA [Kuyl et al. 1995 ]
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The game plan
•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
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Omit all details of previous 4 stepsCurrent state of genome sequencing.
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But why do we choose vervet to spend $$$?
•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
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The “usual” pipeline for next-gen seq
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One caveat in applying “usual” pipeline
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Treat “human” as fake monkey
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Probably not perfect, let's see the distance first.
VRC: Vervet Research Colony (where original ~50 monkeys are from St. Kitts)
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Turn it into a picture.
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Nelson didn't even want to look at it!
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Error rate is a bit, uh, high: ~15.48%
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What is causing the high discordance rate between two runs
of the reference?
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Dist(Het, Homo) = 0.5
The error rate drops to ~8%.
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Dropping the error rate further: 0.6%
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Turn it into picture
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Back to the questions
1.Relationship between Barbados and the
reference (St. Kitts)?
2.Which African subspecies is closest to
reference?
3.What's the relationship among African
subspecies?
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1. Relationship between Barbados and the reference (St. Kitts)?
Dist(Barbados, vervet ref) = 1.4%
Dist(closest African pair) =Dist(pygerythrus, sabaeus) = 2.13%
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2. Which African subspecies is closest to reference?
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2. Which African subspecies is closest to reference?
Dist(vervet ref, sabaeus) = 13.1%
Dist(farthest African pair) =Dist(pygerythrus, aethiops) = 5.2%
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2. Which African subspecies is closest to reference?
• 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??)
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Magnus dropped a comment on the collaboration site:
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Now this has something to do with my customization to the “usual”
pipeline
• 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.
• ...
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1Mb of vervet reference genome
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Data largely concur but need more careful look ...
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Acknowledgement
Katherine CamfieldAlden Huang (Geschwind Lab)
Anna JasinskaYoon J. Jung
Christopher SchmittNam Tran
Vasily Ramensky
Nelson FreimerTrudy Turner (Univ. of Milwaukee)
Wes Warren (WUSTL)Ken Dewar (McGill)