Professor Emeritus
Email: slatkin@berkeley.edu
Phone: (510) 643-6300
Research Description
My current research is concerned with the population genetics of the HLA region of the human genome. I am studying the effects of balancing selection and epistatic interactions among loci on haplotype frequencies of Class I and Class II loci.
Selected Publications
2022
Slatkin, M. Joint estimation of selection intensity and mutation rate under balancing selection with applications to HLA. Genetics 221: iyac058.
2021
Mualim, K, C. Theunert and M. Slatkin Estimation of coalescence probabilities and population divergence times from SNP data. Heredity 127: 1-9.
2019
Del Vecchyo, D. and M. Slatkin FST between archaic and present-day samples. Heredity 122: 711-718.
Lee, Y. et al, Genome-wide divergence among invasive populations of Aedes aegypti in California. BMC Genomics 20: 204.
Schmidt, H., et al, Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events. Communications Biology 2: 473.
2018
Hajdinjak, M. et al, Reconstructing the genetic history of late Neanderthals. Nature 555:652-656.
Barlow, A. et al, Partial genomic survival of cave bears in living brown bears. Nature Ecology and Evolution 2: 1563-1570.
2017
Rogers, R. L., and M. Slatkin, Excess of genomic defects in a woolly mammoth on Wrangel island. PLoS Genetics 13: e1006601.
Theunert, C., and M. Slatkin, Distinguishing recent admixture from ancestral population structure. Genome Biology and Evolution 9: 427-437.
Theunert, C., F. Racimo and M. Slatkin, Joint estimation of relatedness coefficients and allele frequencies from ancient samples. Genetics 206: 1025-1035.
Martin, M. D., F. Jay, S. Castellano and M. Slatkin, Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations. Molecular Ecology 26: 4145-4157.
Prüfer, K. et al, A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358: 655-658.
Yang, M. A., et al, 40,000-Year-Old Individual from Asia Provides insight into early population structure in Eurasia. Current Biology 27: 3202-3208.
2013
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.
2012
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.
2011
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.
2010
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.
2009
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.
2008
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