Montgomery Slatkin

Montgomery Slatkin

Professor Emeritus

Phone: (510) 643-6300

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Research Description

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) the population genetics of ancient DNA, with particular emphasis on Neanderthals, Denisovans and other archaic hominims, (2) models of range expansion and population subdivision, (3) the genetic basis of complex inherited diseases in humans, and (4) quantitative genetics.

Selected Publications


Cahill, J. A., et al., 2013 Genomic Evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genet 9: e1003345.

Wall, J. D et al. 2013 Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics 194: 199-209.

Rohlfs, R. V., E. E. Murphy, Y. S. Song and M. Slatkin, The influence of relatives on the efficiency and error rate of familial searching. PLoS ONE. 8, e70495.

Peter, B. M. and M. Slatkin, Detecting range expansions from genetic data. Evolution, in press.

Frantz, L. et al., Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome Research, in press.

Slatkin, M. A method for estimating the effective number of loci affecting a quantitative character. Theoretical Population Biology, in press.


Z. Gong, N. J. Matzke, B. Ermentrout, D. Song, J. E. Vandetti, M. Slatkin and G. Oster, Evolution of patterns on Conus shells. PNAS 109:E234-E241.

M. Slatkin and M. Kirkpatrick, Using known QTLs to detect directional epistatic interactions. Genetics Research 94: 39-48.

M. Slatkin and L. Excoffier, Serial founder effects during range expansion: a spatial analog of genetic drift.Genetics 191:171-181.

M. A. Yang, A.-S. Malaspinas, E. Y. Durand, and M. Slatkin, Using the doubly-conditioned site frequency spectrum to distinguish between alternative demographic models. Molecular Biology and Evolution 29: 2987-2995.

M. Meyer et al. [34 coauthors] A high-coverage genome sequence from an archaic Denisovan individual.Science 338:222-226.

Schraiber, J. G., S. Shih, and M. Slatkin. 2012. Genomic tests of variation in inbreeding among individuals and among chromosomes. Genetics 192: 1477-1482.

Wall, J. D., and M. Slatkin. 2012. Paleopopulation genetics. Annual Review of Genetics 46: 635-649.


Durand, E.Y., Patterson, N., Reich, D., and Slatkin, M. Testing for ancient admixture between closely related populations. Mol Biol Evol 28, 2231-2237.

Malaspinas, A.-S., Slatkin, M., and Song, Y.S. Match probabilities in a finite, subdivided population. Theo Popul Biol 79, 55-63.


Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.H.-Y., et al. A Draft Sequence of the Neandertal Genome. Science 328, 710-722.

Reich, D., Green, R.E., Kircher, M., Krause, J., Patterson, N., Durand, E.Y., Viola, B., Briggs, A.W., Stenzel, U., Johnson, P.L.F., et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia.Nature 468, 1053-1060.

Song, Y.S., Wang, F., and Slatkin, M. General epistatic models of the risk of complex diseases. Genetics186, 1467-1473.


Johnson, P.L.F., and Slatkin, M. Inference of microbial recombination rates from metagenomic data. PLoS Genet 5, e1000674.

Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G.A., Castanos, P., Cieslak, M., Lippold, S., Llorente, L., Malaspinas, A.-S., et al. Coat Color Variation at the Beginning of Horse Domestication.Science 324, 485-.

Novembre, J., Slatkin, M., and Posada, D. Likelihood-Based Inference in Isolation-By-Distance Models Using the Spatial Distribution of Low-Frequency Alleles. Evol 63, 2914-2925.

Slatkin, M. Epigenetic inheritance and the missing heritability problem. Genetics 182, 845-850.

Song, Y.S., Patil, A., Murphy, E.E., and Slatkin, M. Average Probability that a "Cold Hit" in a DNA Database Search Results in an Erroneous Attribution. Journal of Forensic Sciences 54, 22-27.


M. Slatkin, A Bayesian method for jointly estimating allele age and selection intensity. Genetics Research90:129-137. pdf

P. L. F. Johnson and M. Slatkin Accounting for bias from sequencing error in population genetic estimates.Molecular Biology and Evolution 25:199-206. pdf

M. Slatkin, Linkage disequilibrium -- understanding the evolutionary past and mapping the medical future.Nature Reviews Genetics 9:477-485. pdf

M. Slatkin, Genotype-specific recurrence risks as indicators of the genetic architecture of complex diseases.American Journal of Human Genetics 83:120-126. pdf