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