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Postdoctoral position -- Coalescent methods

Allen Rodrigo a.rodrigo at auckland.ac.nz
Sun Nov 7 12:25:56 EST 1999

Coalescent Methods for Measurably Evolving Populations

Funding is presently being organized for a 2-year postdoctoral appointment
at the School of Biological Sciences, University of Auckland, to work with
Dr. Allen Rodrigo on coalescent methods for measurably evolving populations
(MEPs).  Investigators on the project include Drs. J. Mullins and J.
Felsenstein at the University of Washington.

Research Description and Scope

A population is a MEP if the expected number of substitutions between a
descendant sequence (obtained at some later time)  and its ancestor
(present in the populatiion at an earlier sampling occasion) is much
greater than 1/L where L is the length of the sequences.  The concept of a
measurably evolving population has emerged jointly from research on rapidly
evolving populations (e.g., viral populations) and recent biotechnological
developments. These developments enhance our ability to obtain longer
molecular sequences from many invididuals in a population, and are
sensitive enough so that ancient DNA sequences from sub-fossils and fossils
are accumulating.  There are two implications of this. 

*  There is the potential to obtain samples of short or moderately-sized
molecular sequences from populations that are separated far apart in time,
e.g., those from fossil organisms.

*  Longer sequences from samples that are separated by only a moderate
number of generations may be acquired. 

Even with low rates of mutation, it is possible, even likely, that these
samples of sequences will be genetically distinguishable. 

Our research anticipates the inevitable demand for new population genetic
methods to analyze MEP genetic data, particularly when such data are
available from samples drawn serially in time. In particular, we focus on
the development of new coalescent-likelihood methods for estimating the
intensity of historical population processes including migration,
recombination, and growth, based on serial samples of molecular sequences
drawn from MEPs.  The following papers outline the ideas and types of
samples that will form the focus of this research program:

Rodrigo, A. G. and Felsenstein, J. (1999).  Coalescent Approaches to HIV-1
Population Genetics. In The Molecular Evolution of HIV (ed. Crandall,
K.A.).  Johns Hopkins University Press. 

Rodrigo, A. G., Shpaer, E. G., Delwart, E. L., Iversen, A. K. N., Gallo, M.
V., Jurgen Brojatsch, J., Hirsch, M. S., Walker, B. D., and Mullins, J. I.
(1999). Coalescent estimates of HIV-1 generation time in vivo. Proceedings
of the National Academy of Science, USA.96:2187-2191.

Subject to final funding confirmation, the postdoctoral position will be
available at the start of the new year, or shortly thereafter.  We
anticipate that the appointee will be conversant with recent theoretical
developments in population genetics and molecular evolution, have
programming experience in one or more high-level languages,  preferably
including JAVA, and be well-grounded in mathematics/statistics.
Individuals who are presently completing their doctoral research are
encouraged to apply.  Individuals interested in the position should contact
Allen Rodrigo to discuss details and application procedures (email:
a.rodrigo at auckland.ac.nz  ; phone: 64-9-3737599 Ext 7296; fax: 64-9-3737
414; eFax (US) 1-413-826 5970).

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