Dear EvolDir Members
I had a few requests to post answers to my recent question about
estimating founder population size. The original post and answers are
at the bottom of this email. Many thanks to all that replied, most
suggestions helpfully directed me to papers and software that have
tackled similar problems.
I hope this helps!
Jacqui
ORIGINAL POSTING
Dear EvolDir members
I am attempting to estimate founder population size for a recently
introduced population (c. seven years/max 10 generations) of Anolis
using microsatellite data. Standard estimates of effective population
size are likely to be inappropriate in this case since mutation rate
cannot be accurately estimated due to the recent nature of the
introduction.
I have come across a paper (Rasner et al 2004, Molecular Ecology) that
attempts to answer the question using the number of alleles (n) within
the most variable locus in the introduced population as an absolute
minimum estimate of the founder population size. (Eight generations
were assumed to have passed between founding and sampling). The paper
then uses simulation to resample a specified number of 'founder
individuals' from the native population 1000 times and calculates the
proportion of times that at least this number (n) of alleles are
captured in the samples. The smallest number of founders consistent
with the data was taken to be the number that gave a probability >
0.05 of capturing n observed alleles (Rasner et al 2004).
My questions are
first, does anyone know of a method for estimating founder population
size using microsatellite data in such a recently founded population?
second, is there a program in the public domain that can handle a
simulation such as that described above? It is presumably relatively
easy to write such a program, unfortunately it is not my expertise!
Many thanks for your anticipated help on this problem,
Jacqui Eales
Doctoral candidate, Bangor University, Wales, UK
ANSWERS:
"Andrew J. Bohonak"
See the following papers (pdfs on my web site), in which I have
simulated founding events similar to that you describe:
Vandergast, A. G., A. J. Bohonak, D. B. Weissman and R. N. Fisher.
2007. Understanding the genetic effects of recent habitat
fragmentation in the context of evolutionary history: phylogeography
and landscape genetics of a southern California endemic Jerusalem
cricket (Orthoptera: Stenopelmatidae: Stenopelmatus). Molecular
Ecology 16: 977-992.
Bohonak, A. J., N. Davies, F. X. Villablanca, and G. K. Roderick.
2001. Invasion genetics of New World medflies: testing alternative
colonization scenarios. Biological Invasions 3: 103-111.
Bohonak, A. J., and G. K. Roderick. 2001. Dispersal of invertebrates
among temporary ponds: are genetic estimates accurate? Israel Journal
of Zoology 47: 367-386. (Special Issue: Ecology of temporary pools)
Hairston, N. G., Jr., L. J. Perry, A. J. Bohonak, M. Q. Fellows, C. M.
Kearns and D. R. Engstrom. 1999. Population biology of a failed
invasion: paleolimnology of Daphnia exilis in upstate New York.
Limnology and Oceanography 44: 477-486.
Dear Jacqui Eales,
have a look at Wang (2005) Estimation of effective population size from data
on genetic markers. Phil Trans R Soc B 360:1395-1409.
and at his software page: http://www.zoo.cam.ac.uk/ioz/software.htm
Maybe this helps,
cheers, Rodolfo Jaffé
Hi Jacqui,
It may be worth looking at some of Mark Beaumont's programs:
http://www.rubic.rdg.ac.uk/~mab/software.html
There is a nice use of such approaches in Goossens et al. 2006 Plos Biol, 4(2)
0285-0291, looking at very recent bottlenecks in Orang-utans.
Good luck,
Mark de Bruyn
Hi Jacqui,
Check out E. C. Anderson and M. Slatkin, Estimation of the number of
individuals
founding colonized populations. 2007. Evolution 61: 927-983, and the
corresponding
software.
Also see
http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000868 - an article of mine where I estimate founder population size for a North American invasive bee species (using
forward
simulations).
Cheers,
Amro
Amro Zayed, PhD
NSERC Postdoctoral Fellow
Department of Entomology University of Illinois at Urbana-Champaign
Hi Jacqui,
Have you tried Rmetasim (Strand 2002)? We used this program to
estimate the number of founders in non-native populations of
bulllfrogs in Europe (Ficetola et al. 2008). We used mDNA data but it
also works with microsatellites. I send you the two papers.I hope this
helps.
Aurélie Bonin, Grenoble
Hi Jacqui,
I wanted to do something similar for a species that had been
introduced for biological
control. I used msVAR, which is freeware. I used it to estimate
current population
sizes based on various reasonable priors, and then argued, that given that the
introduction was so recent, the variation wasn't likely due to
mutation, and so the
estimate of population size was a reasonable estimate of the size of
the founding
population. If you search for msVAR is the attached Molecular Ecology
paper, you should
find what I did pretty quickly.
Best,
Ruth
Ruth A. Hufbauer
Associate Professor
BSPM, GDPE, PRIMES
Colorado State University
Hi Jacqui
you can use MULTSIM as described in
Noor, M. A. F., M. Pascual, and K. R. Smith. 2000. Genetic variation
in the spread of Drosophila subobscura from a nonequilibrium
population. Evolution, 54: 696-703.
Or the methodology described in
Pascual, M.; Chapuis, MP.; Mestres, F.; Balanyà, J.; Huey, RB.;
Gilchrist, GW.; Serra, L.; Estoup, A. 2007. Introduction history of
Drosophila subobscura in the New World: a microsatellite based survey
using ABC methods. Molecular Ecology, 16: 3069-3083.
Arnaud Estoup has carried out done the estimations
cheers
Marta
Marta Pascual Berniola
Departament de Genetica
Facultat de Biologia, Edifici annex
Universitat de Barcelona
Hi,
In a similar case of estimating founder population after recently founded
populations in an ant, I have calculated a crude estimator from the
relatedness among individuals within populations compared to those in other
populations. If all descend from one pair, their average r (queller &
goodnight's program; also implemented in Fstat) across loci should be 0.5
in diploids. More founders will lower r. However this assumes that no
alleles are lost by drift or inbreeding within the population during time,
since this will inflate r. R is thus conversely associated with the number
of founders and this measure will give a conservative maximum of Nf. I
published it in "Conservation Genetics", came out late -07 or early -08.
Best wishes,
Kalevi Trontti, PhD
University of Helsinki
Finland
Finally, Rich Glor (University of Rochester) has an R script
for running simulations that resample from allele frequency
distributions as described in Rasner et al 2004.
Rich can be contacted by email: rglor@mail.rochester.edu
bsp030@bangor.ac.uk