Research Overview
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:
- linkage disequilibrium and the generation of haplotype blocks,
- the spectrum of frequencies of alleles associated with genetic diseases in humans,
- the inference of allele age and
- selection on alleles associated with disease resistance in human populations.
I retain an interest in quantitative genetics, epistasis, and population structure.
Selected Publications
2011
a
Durand, E.Y., Patterson, N., Reich, D., and Slatkin, M. Testing for ancient admixture between closely related populations. Mol Biol Evol 28, 2231-2237.
b
Malaspinas, A.-S., Slatkin, M., and Song, Y.S. Match probabilities in a finite, subdivided population. Theo Popul Biol 79, 55-63.
2010
a
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.
b
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.
c
Song, Y.S., Wang, F., and Slatkin, M. General epistatic models of the risk of complex diseases. Genetics 186, 1467-1473.
2009
a
Johnson, P.L.F., and Slatkin, M. Inference of microbial recombination rates from metagenomic data. PLoS Genet 5, e1000674.
b
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-.
c
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.
d
Slatkin, M. Epigenetic inheritance and the missing heritability problem. Genetics 182, 845-850.
e
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
a
M. Slatkin, A Bayesian method for jointly estimating allele age and selection intensity. Genetics Research 90:129-137. pdf
b
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
c
M. Slatkin, Linkage disequilibrium -- understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics 9:477-485. pdf
d
M. Slatkin, Genotype-specific recurrence risks as indicators of the genetic architecture of complex diseases. American Journal of Human Genetics 83:120-126. pdf
2007
a
S.N. Evans, Y. Shvets and M. Slatkin, Non-equilibrium theory of the allele frequency spectrum. Theoretical Population Biology 71: 109-119. pdf
b
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
c
E.C. Anderson and M. Slatkin, Estimation of the number of individuals founding colonized populations. Evolution 61: 927-983. pdf
d
R. Leblois and M. Slatkin, Estimating the number of founder lineages from haplotypes of closely linked SNPs. Molecular Ecology 16: 2237-2245. pdf
e
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
f
N. Rohland, A.S. Malaspinas, J.L. Pollack, M. Slatkin, P. Matheus, et al., 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
g
H. Chen, R.E.Green, S. Pääbo, M. Slatkin, The joint allele-frequency spectrum in closely related species. Genetics 177: 387-398. pdf
h
W. W. Zhai, M. Slatkin and R. Nielsen, Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: Applications to the influenza virus. Journal of Molecular Evolution 65: 340-348. pdf
2006
a
M. Slatkin and J.L. Pollack, The concordance of gene trees and species trees at two linked loci. Genetics 172 1979-1984. pdf
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
2005
a
M. Slatkin, Seeing ghosts: the effect of unsampled populations on migration rates estimated between sampled populations. Molecular Ecology 14: 67-73. pdf
b
E.T. Wood, 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
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
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
2004
a
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
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
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
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 mdr1-1Δ, 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
2003
a
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
b
E.C. Anderson and M. Slatkin, Orr's QTL sign test under conditions of trait ascertainment. Genetics 165: 445_446. pdf
c
M. Slatkin and J. Novembre, Appendix to paper by Wall and Herbeck, Journal of Molecular Evolution 56: 689-690. pdf
d
A.P. Galvani and M. Slatkin, Evaluating plague and smallpox as historical selective pressures for the CCR5-Δ32 HIV-resistance allele. Proceedings of the National Academy of Sciences, USA 100: 15276-15279. pdf
2002
a
C.P. Garner and M. Slatkin, Likelihood-based disequilibrium mapping for two-marker haplotype data. Theoretical Population Biology 61 153-161. pdf
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
c
M. Slatkin, A vectorized method of importance sampling with applications to models of mutation and migration. Theoretical Population Biology 62: 339-348. pdf
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
2001
a
P. Schliekelman, C.P. Garner and M. Slatkin, Natural selection and resistance to HIV. Nature (Scientific Correspondence) 411: 545-546. pdf
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
c
M. Slatkin, Simulating genealogies of selected alleles in a population of variable size. Genetical Research 78: 49-57. pdf
2000
a
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
b
M. Slatkin, Balancing selection at closely linked, overdominant loci in a finite population. Genetics 54: 1367-1378. pdf
c
R. Nielsen and M. Slatkin, Likelihood analysis of ongoing gene flow and historical association. Evolution 54: 44-50. pdf
d
M. Slatkin and B. Rannala, Estimating allele age. Annual Reviews of Genomics and Human Genetics 1: 225-249. pdf
e
M. Slatkin and C.A. Muirhead, A method of estimating the intensity of overdominant selection from the distribution of allele frequencies. Genetics 156: 2119-2126. pdf
f
M. Slatkin, Allele age and a test for selection on rare alleles. Phil. Trans. Roy. Soc. London B 355: 1663-1668. pdf
1999
a
M. Slatkin, Disequilibrium mapping of a quantitative trait locus in an expanding population. American Journal of Human Genetics 64: 1765-1773. pdf
b
M. Slatkin and C.A. Muirhead, Overdominant alleles in a population of variable size. Genetics 152: 775-781. pdf
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
1998
a
L. Excoffier and M. Slatkin, Incorporating genotypes of relatives into a test of linkage disequilibrium. American Journal of Human Genetics 62: 171-180. pdf
b
B. Rannala and M. Slatkin, Likelihood analysis of disequilibrium mapping, and related problems. American Journal of Human Genetics 62: 459-473. pdf
c
R. Nielsen, J.L. Mountain, J.P. Huelsenbeck and M. Slatkin, Maximum-likelihood estimation of population divergence times and populations phylogeny in models without mutation. Evolution 52: 669-677. pdf
d
M. Slatkin and T. Wiehe, Genetic hitchhiking in a subdivided population. Genetical Research 71:155-160. pdf
e
B. Rannala and M. Slatkin, Linkage disequilibrium mapping and Parkinson's disease. Science (Technical Comment) 280:175a. pdf
Updated August 5, 2011