Montgomery Slatkin's Home Page

Montgomery Slatkin


Research Interests

My research is currently directed to analyzing genetic data within and between species in the context of population genetic models. The overall goal is to show how variation among individuals in DNA sequence can be used to understand population genetic processes including recombination, selection, migration, and past population growth. At present my research is focused on (1) linkage disequilibrium and the generation of haplotype blocks, (2) the spectrum of frequencies of alleles associated with genetic diseases in humans, (3) the inference of allele age and (4) selection on alleles associated with disease resistance in human populations. I retain an interest in quantitative genetics, epistasis, and population structure.

Department of Integrative Biology
University of California
3060 Valley Life Science Building
Berkeley, CA 94720-3140

(510) 643-6300 (office)
(510) 643-6264 (fax)

Selected publications 1998-2007

1998a L. Excoffier and M. Slatkin, Incorporating genotypes of relatives into a test of linkage disequilibrium. American Journal of Human Genetics 62: 171-180. pdf file

------b B. Rannala and M. Slatkin, Likelihood analysis of disequilibrium mapping, and related problems. American Journal of Human Genetics 62: 459-473. pdf file

------c R. Nielsen, J. L. Mountain, J. P. Heulsenbeck and M. Slatkin, Maximum-likelihood estimation of population divergence times and populations phylogeny in models without mutation. Evolution 52: 669-677.

------d M. Slatkin and T. Wiehe, Genetic hitchhiking in a subdivided population. Genetical Research 71:155-160. pdf file

------e B. Rannala and M. Slatkin, Linkage disequilibrium mapping and Parkinson's disease. Science (Technical Comment) 280:175a. pdf file

1999a M. Slatkin, Disequilibrium mapping of a quantitative trait locus in an expanding population. American Journal of Human Genetics 64: 1765-1773. pdf file

------b M. Slatkin and C. A. Muirhead, Overdominant alleles in a population of variable size. Genetics 152: 775-781. pdf file

------c E. G. Williamson and M. Slatkin, Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152:755-761. pdf file

2000a T. Wiehe, J. Mountain, P. Parham, and M. Slatkin, Inference of the relative roles of recombination and intragenic gene conversion in the generation of HLA class I diversity. Genetical Research 75: 61-73. pdf file

------b M. Slatkin, Balancing selection at closely linked, overdominant loci in a finite population. Genetics 54: 1367-1378. pdf file

------c R. Nielsen and M. Slatkin, Likelihood analysis of ongoing gene flow and historical association. Evolution 54: 44-50. pdf file

------d M. Slatkin and B. Rannala, Estimating allele age. Annual Reviews of Genomics and Human Genetics 1: 225-249. pdf file

------e M. Slatkin and C. A. Muirhead, A method of estimating the intensity of overdominant selection from the distribution of allele frequencies. Genetics156: 2119-2126. pdf file

------f M. Slatkin, Allele age and a test for selection on rare alleles. Phil. Trans. Roy. Soc. London, B 355: 1663-1668. pdf file

2001a P. Schliekelman, C. P. Garner and M. Slatkin, Natural selection and resistance to HIV. Nature (Scientific Correspondence) 411: 545-546. pdf file

------b M. Slatkin and G. Bertorelle, The use of intra-allelic variability for testing neutrality and estimating population growth rate. Genetics 158: 865-874. pdf file

------c M. Slatkin, Simulating genealogies of selected alleles in a population of variable size. Genetical Research 78: 49-57. pdf file

2002a C. P. Garner and M. Slatkin, Likelihood-based disequilibrium mapping for two-marker haplotype data. Theoretical Population Biology 61: 153-161. pdf file

------b C. A. Muirhead, N. L. Glass and M. Slatkin, Multilocus self-recognition systems in fungi as a cause of trans-species polymorphism. Genetics: 633-641. pdf file

------c M. Slatkin, A vectorized method of importance sampling with applications to models of mutation and migration. Theoretical Population Biology 62: 339-348. pdf file

------d P._Schliekelman and M._Slatkin, Multiplex relative risk and estimation of the number of loci underlying an inherited disease. American Journal of Human Genetics 71:1369-1385. pdf file

2003a M. O_Hely and M. Slatkin, The loss of statistical power to distinguish populations when certain samples are ambiguous. Theoretical Population Biology 64: 177-192. pdf file

------b E. C. Anderson and M. Slatkin, Orr_s QTL sign test under conditions of trait ascertainment. Genetics 165: 445_446. pdf file

------c M. Slatkin and J. Novembre, Appendix to paper by Wall and Herbeck, Journal of Molecular Evolution 56: 689-690. pdf file

------d A. P. Galvani and M. Slatkin, Evaluating plague and smallpox as historical selective pressures for the CCR5-Delta-32 HIV-resistance allele. Proceedings of the National Academy of Sciences, USA, 100: 15276-15279. pdf file

2004a E. C. Anderson and M. Slatkin, Population genetic basis of haplotype blocks in the 5q31 region. American Journal of Human Genetics, 74: 40-49. pdf file

------b A. P. Galvani and M. Slatkin, Intense selection in an age-structured population. Proceedings of the Royal Society of London, B. 271: 171-176. pdf file

------c M. Slatkin, A population-genetic test of founder effects and implications for Ashkenazi Jewish diseases. American Journal of Human Genetics 75: 282-293. pdf file

------d     M. W. Neff, K. R. Robertson, A. Wong, N. Safra, K. W. Broman, M. Slatkin, K. L. Mealey, and N. C. Pedersen, Breed distribution and history of canine mdr1-1∆, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage. Proceedings of the National Academy of Science, USA 101: 11725-11730. pdf file

2005a    M. Slatkin, Seeing ghosts:  the effect of unsampled populations on migration rates estimated between sampled populations.  Molecular Ecology 14: 67-73. pdf file

------b  Wood, E. T., D. A. Stover,  M. Slatkin, M. W. Nachman, and M. F. Hammer. The b-globin recombinational hotspot reduces the effects of strong selection around HbC, a recently arisen mutation providing resistance to malaria. American Journal of Human Genetics 77: 637-642. pdf file

------c     J. Novembre, A. P. Galvani, M. Slatkin,  The geographic spread of the CCR5 Δ32 HIV-resistance allele.  Public Library of Science, Biology 3:  1954-1962. pdf file

------d     M. A. Saunders, M. Slatkin, C. Garner, M. F. Hammer and M. W. Nachman The span of linkage disequilibrium caused by selection on G6PD in humans.  Genetics 171: 1219-1229. pdf file

2006a    M. Slatkin and J. L. Pollack, The concordance of gene trees and species trees at two linked loci.  Genetics 172 1979-1984. pdf file

------b    J. Krause, P. H. Dear, J. Pollack, M. Slatkin, H. Spriggs, I. Barnes, A. Lister, S. Pääbo and M. Hofreiter, Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae.  Nature 439: 724-727. pdf file

2007 S. N. Evans, Y. Shvets and M. Slatkin, Non-equilibrium theory of the allele frequency spectrum. Theoretical Population Biology 71: 109-119. pdf file

------ Y. S. Song and M. Slatkin A graphical approach to multi-locus match probability computation: revisiting the product rule. Theoretical Population Biology 72: 96-110. pdf file

------ E. C. Anderson and M. Slatkin, Estimation of the number of individuals founding colonized populations. Evolution 61: 927-983. pdf file

------ R. Leblois and M. Slatkin, Estimating the number of founder lineages from haplotypes of closely linked SNPs. Molecular Ecology 16: 2237-2245. pdf file

------ M. Hofreiter, S. Münzel, N. Conard, J. Pollack, M. Slatkin, G. Weiss and S. Pääbo, Sudden replacement of cave bear mitochondrial DNA in the late Pleistocene. Current Biology 19: R122-R123. pdf file

------ N. Rohland, A. S. Malaspinas, J. L. Pollack, M. Slatkin, P. Matheus, et al. (2007). Proboscidean mitogenomics: Analysis of chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol 5(8): e207. doi:10.1371/journal.pbio.0050207 pdf file

------ H.Chen, R. E.Green, S. Paabo, M. Slatkin, The joint allele-frequency spectrum in closely related species. Genetics 177: 387-398. pdf file

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