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mary statistic Var(
) as a means to tease apart migration
from isolation as suggested in [29,30].
The msBayes software pipeline will increasingly become
an important tool as the field of comparative phylogeog-
raphy progresses to become a more rigorous and statistical
enterprise . The program can obtain hyper-parameter
estimates using hierarchical models in a reasonable
amount of time without having the problems associated
with convergence and mixing found in MCMC methods
(Markov chain Monte Carlo). Because the estimation step
is decoupled from the simulation step, one can quickly
evaluate different ABC acceptance/rejection conditions
and the choice of summary statistics. The method can rea-
sonably distinguish biogeographic congruence from tem-
poral incongruence, even with sparse sampling of
individuals. Given the complex and idiosyncratic nature
of testing multi-species biogeographic hypotheses, we
envision msBayes as a powerful and flexible tool that is
open for modification when faced with particularly diffi-
cult research questions. Finally, due to its flexible and
modular design, msBayes will be a well-suited tool for the
heterogeneous data sets that are emerging and being com-
bined to test complex historical hypotheses.
Availability and requirements
The installation instructions, documentation, source code
and precompiled binary for msBayes are all available for
download at http://msbayes.sourceforge.net/
open source license (GNU Public License). The msBayes
pipeline is comprised of several C and R programs that are
run with a Perl "front-end" and runs on Linux, Mac OS-X,
and most POSIX systems.
List of Abbreviations used
ABC: Approximate Bayesian Computation
TSD: Test of simultaneous divergence
mtDNA: Mitochondrial DNA
MJH developed the idea for using ABC within a hierarchi-
cal model to analyze multiple population pairs simulta-
neously. ES developed the finite sites version of D.
Hudson's classic coalescent simulator (ms). MJH and NT
developed C, R, and Perl routines and modified pre-exist-
ing R and C routines to comprise an ABC algorithm that
makes use of a Hierarchical model. NT extensively devel-
oped the C and Perl routines that comprise the user ver-
sion of msBayes now available. NT and MJH maintains
the msBayes website and NT developed the installation
configurations and precompiled binaries. All authors read
and approved the final version of the manuscript.
We thank A. Lancaster and three anonymous reviewers for making helpful
suggestions and E. Andersson for handling the manuscript. We thank M.
Beaumont for kindly providing R scripts and critically useful discussions. We
thank D. Hudson for permission to use E. Stahl's finite sites version of his
ms coalescent simulator under GNU Public License. We thank J. McGuire
and C. Moritz for use of the linux parallel computing cluster housed at the
Museum of Vertebrate zoology (University of California, Berkeley). We
thank MBI (Mathematical Biosciences Institute) for hosting the workshop
on Phylogenetics and Phylogeography. Support for M. J. Hickerson was pro-
vided by a NSF post-doctoral fellowship in interdisciplinary informatics. N.
Takebayashi was supported by NIH Grant Number 2P20RR16466 from the
INBRE program of the National Center for Research Resources and NSF
DEB-0640520. E. Stahl, was supported by Sloan/DOE Fellowship award DE-
1. Avise JC: Phylogeography: The history and formation of spe-
cies. Cambridge: Harvard University Press; 2000.
2. Wen J: Origin and the evolution of the eastern North Ameri-
can distinct distributions of flowering plants. Annu Rev Ecol Syst
3. Lessios HA: The first stage of speciation as seen in organisms
separated by the Isthmus Panama. In Endless Forms: species and
speciation Edited by: Howard DJ, Berlocher S. Oxford, U.K.: Oxford
University Press; 1998:186-201.
4. Barraclough TG, Nee S: Phylogenetics and speciation. Trends
Ecol Evol 2001, 16(7):391-399.
5. Knowles LL, Maddison WP: Statistical phylogeography. Mol Ecol
6. Edwards SV, Liu L, Pearl DK: High-resolution species trees with-
out concatination. Proc Natl Acad Sci USA 2007, 104:5936-5941.
7. Rannala B, Yang ZH: Bayes Estimation of Species Divergence
Times and Ancestral Population Sizes Using DNA
Sequences From Multiple Loci. Genetics 2003, 164:1645-1656.
8. Hey J, Nielsen R: Integration within the Felsenstein equation
for improved Markov chain Monte Carlo methods in popula-
tion genetics. Proc Natl Acad Sci USA 2007, 104:2785-2790.
9. Edwards SV, Beerli P: Perspective: Gene divergence, population
divergence, and the variance in coalescence time in phyloge-
ographic studies. Evolution 2000, 54(6):1839-1854.
10. Hickerson MJ, Stahl E, Lessios HA: Test for simultaneous diver-
gence using approximate Bayesian computation. Evolution
11. Thornton K, Andolfatto P: Approximate Bayesian inference
reveals evidence for a recent, severe bottleneck in a Nether-
lands population of Drosophila melanogaster. Genetics 2005,
12. Excoffier L, Estoup A, Cornuet J-M: Bayesian analysis of an
admixture model with mutations and arbitrarily linked
markers. Genetics 2005, 169:1727-1738.
13. Estoup A, Beaumont BA, Sennedot F, Moritz C, Cornuet J-M:
Genetic analysis of complex demographic scenarios: spa-
tially expanding populations of the cane toad, Bufo marinus.
Evolution 2004, 58:2021-2036.
14. Tallmon DA, Luikart G, Beaumont BA: Comparative evaluation of
a new effective population size estimator based on approxi-
mate Bayesian computation. Genetics 2004, 167:977-988.
15. Beaumont MA, Zhang W, Balding DJ: Approximate Bayesian
computation in population genetics. Genetics 2002,
16. Weiss G, von Haeseler A: Inference of population history using
a likelihood approach. Genetics 1998, 149:1539-1546.
17. Watterson GA: On the number of segregating sites in genetic
models without recombination. Theor Popul Biol 1975,
18. Nei M, Li W: Mathematical model for studying variation in
terms of restriction endonucleases. Proc Natl Acad Sci USA 1979,
19. Hickerson MJ, Dolman G, Moritz C: Comparative phylogeo-
graphic summary statistics for testing simultaneous vicari-
ance across taxon-pairs. Mol Ecol 2006, 15:209-224.