Brook Milligan
Title: Professor
Research area: Population genetics, Conservation
biology, Molecular sequence evolution, Population demography,
Statistical modeling, Scientific software engineering
Office location: FH 306
Laboratory Location: FH 308 and
FH 316
Email Address: brook@nmsu.edu
Office Phone: 575-646-7980
Lab Phone: 575-646-1150
Lab Webpage: ---
Research Interests:
Research in my laboratory focuses on the interface between
population genetics, ecology, and evolutionary biology.
Specifically, we are interested in quantifying the rates at which
evolution proceeds and in elucidating the rules governing evolutionary
change of ecological and molecular traits. Ongoing population
studies address such questions as 1) at what rate does neutral
evolutionary change proceed and how does that determine the balances
between genetic drift, migration, and natural selection, and 2) how do
population size, mating system, and the demographic characteristics of
populations interact to determine the rate of evolution? At a
larger evolutionary scale we are concerned with such questions as 1) at
what rate do large-scale evolutionary changes occur, and 2) are changes
in one trait influenced by changes in others? One common theme in
our research is the interest in quantifying the demographic properties
of natural populations-population size, mating system, and migration
rate, for example-that determine the rate of evolutionary change.
A second major theme is the interest in using quantitative models of
evolution to test alternative evolutionary or biogeographic
hypotheses. Finally, we are interested in applying our research
to practical concerns such as those arising in conservation biology.
Our approach to answering these
questions combines both empirical and theoretical aspects.
Genetic information from both nuclear and chloroplast DNA is collected
from natural populations using modern molecular techniques including
DNA sequencing and the polymerase chain reaction. Concurrently,
we develop enhanced means of analyzing the genetic data, often
relying on genealogical information for genes in natural
populations. The genealogical approach to studying demographic
properties of populations articulates directly with our studies of
broader scale evolutionary patterns using phylogenies. Models of
genetics, mating systems, and evolution coupled with demographic
ecological models are central to our analysis of populations, while at
broader evolutionary scales explicit models of character evolution play
a central role. Finally, we are using populations of
bacteriophage to simulate the processes we study in natural populations
as a means of testing empirically the models used in our data analysis.
While much of our research is
directed toward developing a fundamental understanding of the processes
occurring in natural populations, we are specifically interested in the
role our genetic data and models can play in conservation
biology. As a result, we are currently studying a group of plants
in the genus Aquilegia that occur in small, isolated populations and
therefore model the situation encountered with many rare plants.
We are also expanding our research focus to apply the techniques
developed for Aquilegia to other rare plant species. In this way
we hope to integrate our studies of basic evolutionary and ecological
processes with the immediate need for information concerning the
demographic properties of rare or endangered populations.
Selected Publications:
- Chris Stubben and Brook Milligan. Estimating and analyzing
demographic models using the popbio package in R. Journal of
Statistical Software, 22(11), September 2007.
http://www.jstatsoft.org/v22/i11.
- Brook Milligan. Probability: a C++ library for probabilities and
likelihoods. http://biology.nmsu.edu/software/probability/, October
2007. Version 0.4.
- Colleen B. Jonsson, Brook G. Milligan, and Jeffrey B. Arterburn.
Potential importance of error catastrophe to the development of
antiviral strategies for hantaviruses. Virus Research, 107:195–205,
2005.
- Brook G. Milligan. Maximum likelihood estimation of relatedness.
Genetics, 163:1153–1167, 2003.
- E. Pontelli, D. Ranjan, G. Gupta, and Brook Milligan. Design and
implementation of a domain specific language for phylogenetic
inference. Journal of Bioinformatics and Computational Biology,
1:201–230, 2003.
- E. Pontelli, D. Ranjan, B. Milligan, and G. Gupta. ΦLOG: A domain
specific language for solving phylogenetic inference problems. In IEEE
Computer Society Bioinformatics Conference, pages 9–20. IEEE Computer
Society, Institute of Electrical and Electronics Engineers, 2002.
- Juan Raymundo Iglesias, Gopal Gupta, Enrico Pontelli, Desh
Ranjan, and Brook Milligan. Interoperability between bioinformatics
tools: A logic programming approach. In I. V. Ramakrishnan, editor,
Practical Aspects of Declarative Languages: Third International
Symposium, volume 1990 of Lecture Notes in Computer Science, pages
153–168. Springer-Velag, 2001.
- Brook G. Milligan. Estimating long-term mating systems using DNA
sequences. Genetics, 142:619–627, 1996.
- Allan E. Strand, Brook G. Milligan, and Casey M. Pruitt. Are
populations islands? Analysis of chloroplast DNA variation in
Aquilegia. Evolution, 50:1822–1829, 1996.
- Brook G. Milligan, James Leebens-Mack, and Allan E. Strand.
Conservation genetics: beyond the maintenance of marker diversity.
Molecular Ecology, 3:423–435, 1994.
- Brook G. Milligan. Estimating evolutionary rates for discrete
characters. In Robert W. Scotland, Darrell J. Siebert, and David M.
Williams, editors, Models in Phylogeny Reconstruction, chapter 16,
pages 299–311. Clarendon Press, Oxford, England, 1994.
- Michael Lynch and Brook G. Milligan. Analysis of population genetic structure with RAPD markers. Molecular Ecology, 3:91–99, 1994.