Here is my original question: Dear EvolDir folks, I have a sample from a single cohort of juvenile frogs and am wondering if I can apply the linkage disequilibrium method (as implemented in the NeEstimator program) to this sample to get an estimate of the effective number of the parents ( *N*b) that produced the juvenile cohort. Can anyone verify or refute this? I have microsatellite genotype data for the juveniles as well as the adults, so I will have an *N*b estimate from the temporal method as well. I am hoping to use the LD method to get an additional estimate of *N*b. Any of your comments on this issue will be greatly appreciated! Thank you, Ivan ----------- And here are the answers I received: Yes, you certainly can get an estimate of parental Nb from your samples of juvenile frogs (you can also get another estimate from your sample of adults). You can get such an estimate from NeEstimator, but you might want to consider as an alternative a program (LDNe) we wrote and have described in a paper in press at Mol. Ecol. Notes. LDNe has a couple of advantages over other methods based on linkage disequilibrium: * it implements the bias correction described in Waples 2006 (Con. Genetics 7:167-184.) * It provides separate estimates based on different user-specified criteria for excluding rare alleles. this facilitates evaluation of potential biases from use of microsat data. it is easy to use and reads standard input files (FSTAT, GenePop). you can access the program, user's manual, and related files at http://fish.washington.edu/xfer/LDNE/ you might also consider using OneSamp (recently described in an online early paper by Tallmon et al. in Mol. Ecol. Notes). this program uses approximate Bayesian computation methods to derive an estimate of effective size based on a single sample. for your temporal estimate, if you have sampled the adults non-lethally you have Plan I samples and you should make sure you use an estimator that accounts for the correlation in allele frequencies between parents and offspring. this requires an estimate of N, the total number of adults your initial sample was (presumably randomly) sampled from. best wishes, and let me know if you have any questions. Robin Waples Regarding your question posted on EvolDir: First of all I suspect you already have the references on this method? Here are some - there may be more: Bartely D, Bagley M, Gall G, Bentley B (1992). Use of linkage disequilibrium data to estimate effective size of hatchery and natural fish populations. Conservation Biology, 6, 365-375. England PR., Cornuet J-M, Berthier P, Tallmon DA, Luikart G (2006). Estimating effective population size from linkage disequilibrium: severe bias in small samples. Conservation Genetics, 7, 303-308. Hill WG (1981). Estimation of effective population size from data on linkage disequilibrium. Genetical Research, Cambridge, 38, 209-216. Waples RS (1991). Genetic methods for estimating the effective size of cetacean populations. Report of the International Whaling Commission (special issue 13), 279-300. Waples RS (2005). Genetic estimates of contemporary effective population size: To what time periods do the estimates apply? Molecular Ecology, 14, 3335-3352. Weir BS, Hill WG (1980). Effect of mating structure on variation in linkage disequilibrium. Genetics, 95, 477-488. I've used Ne estimator to estimate the number of breeders from a single cohort of amphibian progeny as you outline. With my dataset (40 tadpoles per population and 9 microsatellite markers), I definitely received estimates within a plausible range, when applying this method. Not knowing the actual number of breeders in the various populations, I had no way of testing the reliability however. I can only say that in general the results appeared in the range we expected, and that large populations yielded a larger Ne-estimate than small populations. Nonetheless, I think you should be very careful to use any of the Ne methods isolated, and the results should always be interpreted with caution. To employ several methods in combination and use a large number of polymorphic markers would of course be preferable. I would be very keen to see the answers you get, so please post them, if you receive anything useful. Also, I would appreciate to learn your opinion and experiences with the method once/if you chose to apply it to your data. Cheers, Morten Morten E. Allentoft M.Sc., Ph.D. candidate School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch New Zealand ----------- Ivan C. Phillipsen Department of Zoology Oregon State University Corvallis, OR 97331-2914 philliiv@science.oregonstate.edu