Initial Phylogenetic Analysis on Vervet Monkeys

Yu S. Huang 2011-4-13

What is vervet monkey? (wikipedia)

Rough geographic distribution

Are they still one species?

Main Questions

• Relationship between Barbados and the

reference (St. Kitts)?

• Which African subspecies is closest to

reference?

• What's the relationship among African

subspecies?

What NCBI says

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

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

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

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

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

The “usual” pipeline for next-gen seq

One caveat in applying “usual” pipeline

Treat “human” as fake monkey

Probably not perfect, let's see the distance first.

VRC: Vervet Research Colony (where original ~50 monkeys are from St. Kitts)

Turn it into a picture.

Nelson didn't even want to look at it!

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

What is causing the high discordance rate between two runs

of the reference?

Dist(Het, Homo) = 0.5

The error rate drops to ~8%.

Dropping the error rate further: 0.6%

Turn it into picture

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?

1. Relationship between Barbados and the reference (St. Kitts)?

Dist(Barbados, vervet ref) = 1.4%

Dist(closest African pair) =Dist(pygerythrus, sabaeus) = 2.13%

2. Which African subspecies is closest to reference?

2. Which African subspecies is closest to reference?

Dist(vervet ref, sabaeus) = 13.1%

Dist(farthest African pair) =Dist(pygerythrus, aethiops) = 5.2%

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??)

Magnus dropped a comment on the collaboration site:

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.

• ...

1Mb of vervet reference genome

Data largely concur but need more careful look ...

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)