The Hammer Lab | Select Publications

2011

Mendez FL, Karafet TM, Krahn T, Ostrer H, Soodyall H, Hammer MF.
Increased resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa.

Hum Biol. 2011 Feb;83(1):39-53. | View Article

2010

Hammer MF, Woerner AE, Mendez FL, Watkins JC, Cox MP, Wall JD.
The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes.

Nat Genet. 2010 Oct;42(10):830-1. Epub 2010 Aug 29. | View Article

Cox MP, Hammer MF.
A question of scale: Human migrations writ large and small.

BMC Biol. 2010 Jul 21;8:98. | View Article

Behar DM, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, Parik J, Rootsi S, Chaubey G, Kutuev I, Yudkovsky G, Khusnutdinova EK, Balanovsky O, Semino O, Pereira L, Comas D, Gurwitz D, Bonne-Tamir B, Parfitt T, Hammer MF, Skorecki K, Villems R.
The genome-wide structure of the Jewish people.

Nature. 2010 Jul 8;466(7303):238-42. Epub 2010 Jun 9. | View Article

Karafet TM, Hallmark B, Cox MP, Sudoyo H, Downey S, Lansing JS, Hammer MF
Major east-west division underlies Y chromosome stratification across Indonesia.

Mol Biol Evol. 2010 Aug;27(8):1833-44. Epub 2010 Mar 5. | View Article

Cox MP, Karafet TM, Lansing JS, Sudoyo H, Hammer MF.
Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates.

Proc Biol Sci. 2010 May 22;277(1687):1589-96. Epub 2010 Jan 27. | View Article

2009

Cox MP, Morales DA, Woerner AE, Sozanski J, Wall JD, Hammer MF
Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populations.

PLoS One. 2009 Jul 29;4(7):e6366 | View Article

Hammer MF, Behar DM, Karafet TM, Mendez FL, Hallmark B, Erez T, Zhivotovsky LA, Rosset S, Skorecki K.
Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood.

Hum Genet. 2009 Aug 8 | View Article

Lansing, J.S., M.P. Cox, S.S. Downey, M.A. Janssen and J.W. Schoenfelder.
A Robust Budding Model of Balinese Water Temple Networks.

World Archaeology 41:112-133. | View .pdf

2008

Cox, M.P., F.L. Mendez, T.M. Karafet, M. Metni Pilkington, S.B. Kingan, G. Destro-Bisol, B.I. Strassmann and M.F. Hammer.
Testing for Archaic Hominin Admixture on the X-Chromosome: Model Likelihoods for the Modern Human RRM2P4 Region from Summaries of Genealogical Topology under the Structured Coalescent.

Genetics 178:427-437. | View as .pdf | Supplemental Materials

Cox, M.P., A.E. Woerner, J.D. Wall and M.F. Hammer.
Intergenic DNA Sequences from the Human X Chromosome Reveal High Rates of Global Gene Flow.

BMC Genet. 2008 Nov 27;9:76 | View Article

Cox, M.P.
The Genetic Environment of Melanesia: Clines, Clusters and Contact.

In V.T. Koven (ed.), Population Genetics Research Progress, Chapter 2. Nova Science Publishers: New York. pp. 45-83. | View as .pdf.

Cox, M.P.
Accuracy of Molecular Dating with the Rho Statistic: Deviations from Coalescent Expectations under a Range of Demographic Models.

Human Biology 80:335-357 | View .pdf

Downey, S.S., B. Hallmark, M.P. Cox, P. Norquest and J.S. Lansing.
Computational Feature-Sensitive Reconstruction of Language Relationships: Developing the ALINE Distance for Comparative Historical Linguistic Reconstruction.

Journal of Quantitative Linguistics 15:340-369. | View as .pdf.

Garrigan D, Hammer MF.
Ancient lineages in the genome: a response to Fagundes et al.

Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):E3; author reply E4. Epub 2008 Jan 10 | View Article

Hagelberg, E., M.P. Cox, W. Schiefenhövel and I. Frame.
A Genetic Perspective on the Origins and Dispersal of the Austronesians: Mitochondrial DNA Variation from Madagascar to Easter Island.

In A. Sanchez-Mazas, R. Blench, M.D. Ross, I. Peiros and M. Lin (eds.), Past Human Migrations in East Asia: Matching Archaeology, Linguistics and Genetics, Chapter 16. Routledge: London. pp. 356-375. | View as .pdf.

Hammer, M.F., F.L. Mendez, M.P. Cox, A.E. Woerner and J.D. Wall.
Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity.

PLoS Genetics 4:e1000202. | View as .pdf.| Supplemental Materials

Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF
New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

Genome Res. 2008 May;18(5):830-8. Epub 2008 Apr 2 | View Article

Lansing, J.S., J.C. Watkins, B. Hallmark, M.P. Cox, T.M. Karafet, H. Sudoyo and M.F. Hammer.
Male Dominance Rarely Skews the Frequency Distribution of Y Chromosome Haplotypes in Human Populations.

Proceedings of the National Academy of Sciences U.S.A. 105:11645-11650. | View as .pdf | Supplemental Materials

Metni Pilkington, M., J.A. Wilder, F.L. Mendez, M.P. Cox, A. Woerner, T. Angui, S. Kingan, Z. Mobasher, C. Batini, G. Destro-Bisol, H. Soodyall, B.I. Strassmann and M.F. Hammer.
Contrasting Signatures of Population Growth for Mitochondrial DNA and Y Chromosomes among Human Populations in Africa.

Molecular Biology and Evolution 25:517-525. | View as .pdf | mtDNA data | NRY data

Russell, A.L., S.M. Goodman and M.P. Cox.
Coalescent Analyses Support Multiple Mainland-to-Island Dispersals in the Evolution of Malagasy Triaenops Bats (Chiroptera: Hipposideridae).

Journal of Biogeography 35:995-1003. | View as .pdf.

Schlecht J, Kaplan ME, Barnard K, Karafet T, Hammer MF, Merchant NC
Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

PLoS Comput Biol. 2008 Jun 13;4(6):e1000093 | View Article.

Wall, J.D., M.P. Cox, F.L. Mendez, A. Woerner, T. Severson and M.F. Hammer.
A Novel DNA Sequence Database for Analyzing Human Demographic History.

Genome Research 18:1354-1361. | View as .pdf | Supplemental Materials

2007

Woerner, A.E., M.P. Cox and M.F. Hammer.
Recombination-Filtered Genomic Datasets by Information Maximization.

Bioinformatics 23:1851-1853. | View as .pdf

Garrigan, D., S.B. Kingan, M. Metni Pilkington, J.A. Wilder, M.P. Cox, H. Soodyall, B. Strassmann, G. Destro-Bisol, P. de Knijff, A. Novelletto, J. Friedlaender and M.F. Hammer.
Inferring Human Population Sizes, Divergence Times and Rates of Gene Flow from Mitochondrial, X and Y Chromosome Resequencing Data.

Genetics 177:2195-2207. | View as .pdf | Supplemental Data. | Supplemental Figures | Supplemental Tables

Walsh JB, AJ Redd, MF Hammer
Joint match probabilities for Y chromosomal and autosomal markers.

For. Sci. Internat.: in press | View as .pdf.

Chaix R, Quintana-Murci L, Hegay T, Hammer MF, Mobasher Z, Austerlitz F, Heyer E
From social to genetic structures in central Asia.

Curr Biol 17: 43-48 | View as .pdf.

Lansing, J.S., M.P. Cox, S.S. Downey, B.M. Gabler, B. Hallmark, T.M. Karafet, P. Norquest, J.W. Schoenfelder, H. Sudoyo, J.C. Watkins and M.F. Hammer.
Coevolution of Languages and Genes on the Island of Sumba, Eastern Indonesia.

Proceedings of the National Academy of Sciences U.S.A. 104:16022-16026. | View as .pdf.

Pilkington MM, Angui T, Cox MP, Kingan S, Mobasher Z, Batini C, Destro-Bisol G, Soodyall H, Strassmann BI, Hammer MF
Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa.

Mol. Biol. Evol.: in press | Not yet available as .pdf.

Cox, M.P., A.J. Redd, T.M. Karafet, C.A. Ponder, J.S. Lansing, H. Sudoyo and M.F. Hammer.
A Polynesian Motif on the Y Chromosome: Population Structure in Remote Oceania.

Human Biology 79:525-535. | View as .pdf.

Wilder JA, Hammer MF
Extraordinary population structure among the Baining of New Britain.

Genes, Language and Culture History in the Southwest Pacific, Friedlaender JS (ed).
Oxford University Press, Oxford, pp 199-207. | Not yet available as .pdf.

Scheinfeldt L, Friedlaender F, Friedlaender J, Latham Krista, Koki G, Karafet T, Hammer MF, Lorenz J
Unexpected NRY chromosome variation in Northern Island Melanesia.

Genes, Language and Culture History in the Southwest Pacific, Friedlaender JS (ed).
Oxford University Press, Oxford, pp 81-95. | View as .pdf.

Karafet TM, LP Osipova, and MF Hammer
The effect of history and life-style on genetic structure of North Asian populations.

Sagart L, R Blench, and A Sanchez-Mazas (eds).
London and New York: Routledge Curzon: in press | Not yet available as .pdf.

2006

Cox, M.P.
Minimal Hierarchical Analysis of Global Human Y-Chromosome SNP Diversity by PCR-RFLP.

Anthropological Science 114:69-74. | View as .pdf

Redd AJ, VA Contreras, VA Kearney, D Stover, T Karafet, and MF Hammer
Genetic structure among 38 populations from the United States based on 11 U.S. core Y chromosome STRs.

J Foren Sci 51:580-585. | Not yet available as .pdf.

Cox, M.P., and M. Mirazón Lahr.
Y-Chromosome Diversity Is Inversely Associated with Language Affiliation in Paired Austronesian- and Papuan-Speaking Communities from Solomon Islands.

American Journal of Human Biology 18:35-50. | View as .pdf

Wall JD, Hammer MF
Archaic admixture in the human genome.

Curr. Opin. Genet. Devel. 16: 606-610. | Not yet available as .pdf.

Cox, M.P.
Extreme Patterns of Variance in Small Populations: Placing Limits on Human Y-Chromosome Diversity through Time in the Vanuatu Archipelago.

Annals of Human Genetics 71:390-406. | View as .pdf

Scheinfeldt L, Friedlaender F, Friedlaender J, Latham Krista, Koki G, Karafet T, Hammer MF, Lorenz J
Unexpected NRY chromosome variation in Northern Island Melanesia.

Mol Biol Evol 23: 1628-1641. | Not yet available as .pdf.

Karafet TM, SL Zegura, and MF Hammer
Historical peopling of new lands: an ancient link between Asia and Americas.

Vestnik VOGIS (Russian language). | Not yet available as .pdf.

Karafet TM, SL Zegura, and MF Hammer
Y Chromosome Variation.

Handbook of North American Indians, vol. 3, Environment, Origins, and Population. E Szathmary (ed).
Smithsonian Institute, Washington, pp 831-839. | Not yet available as .pdf.

Lansing JS, TM Karafet, J Schoenfelder, and MF Hammer
A DNA signature for the expansion of irrigation in Bali.

Sagart L, R Blench, and A Sanchez-Mazas (eds).
London and New York: Routledge Curzon.: in press. | Not yet available as .pdf.

Garrigan DW, Hammer MF.
Reconstructing human origins in the genomic era.

Nature Rev Genet. 2006 Sep; 7 (9): in press | Supplementary Data.| Not yet available as .pdf

2005

Cox, M.P.
Indonesian Mitochondrial DNA and Its Opposition to a Pleistocene Era Origin of Proto-Polynesians in Island Southeast Asia.

Human Biology 77:179-188. | View as .pdf

Osipova LP, TM Karafet, LE Tabikhanova, OV Andreenkov, OV Ilina, and MF Hammer
Genetic structure of indigenous peoples in Shuryshkarskiy District of Yamal-Nenets Autonomous Region:
classical blood groups and Y-chromosome markers.

Osipova L.P (ed). Native Peoples in Shuryshkarskiy District of Yamal-Nenets Autonomous Region: demographic, genetic and medical aspects.
Novosibirsk. P 77-107 (in Russian). | Not yet available as .pdf

Garrigan D, Mobasher Z, Kingan SB, Wilder JA, Hammer MF.
Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population.

Genetics. 2005 Aug;170(4):1849-56. 2005 Jun 3. | View as .pdf

Garrigan D, Mobasher Z, Severson T, Wilder JA, Hammer MF.
Evidence for archaic Asian ancestry on the human X chromosome

Mol Biol Evol. 2005 Feb;22(2):189-92. | View as .pdf.

Hammer M.F., Karafet TM, Park H, Omoto K, Harihara S, Stoneking M, Horai S.
Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes.

J Hum Genet. 2005 Nov 18. | Not yet available as .pdf

Hammer M.F., Chamberlain V.F., Kearney V.F., Stover D., Zhang G., Karafet T., Walsh B., Redd A.
Population Structure of Y Chromosome SNP Haplogroups in the United States and Forensic Implications for Constructing Y Chromosome STR Databases

For. Sci. Intl. 2005. | View as .pdf

Karafet TM, Lansing JS, Redd AJ, Reznikova S, Watkins JC, Surata SP, Arthawiguna WA, Mayer L, Bamshad M, Jorde LB, Hammer MF. Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders.

Hum Biol. 2005 Feb;77(1):93-114. | View as .pdf.

Saunders MA, Slatkin M, Garner C, Hammer MF, Nachman MW.
The span of linkage disequilibrium caused by selection on G6PD in humans.

Genetics. 2005 171:1219-1229. | View as .pdf.

Wood ET, Stover DA, Slatkin M, Nachman MW, Hammer MF.
The beta -globin recombinational hotspot reduces the effects of strong selection around HbC, a recently arisen mutation providing resistance to malaria.

Am J Hum Genet. 2005 Oct;77(4):637-42. 2005 Aug 29. | View as .pdf

Wood ET, Stover DA, Ehret C, Destro-Bisol G, Spedini G, McLeod H, Louie L, Bamshad M, Strassmann BI, Soodyall H, Hammer MF.
Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes.

Eur J Hum Genet. 2005 Jul;13(7):867-76. | View as .pdf

2004

Behar DM, Garrigan D, Kaplan ME, Mobasher Z, Rosengarten D, Karafet TM, Quintana-Murci L, Ostrer H, Skorecki K, Hammer MF.
Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations.

Hum Genet. 2004 Mar;114(4):354-65. | Not yet available as .pdf

Behar DM, Hammer MF, Garrigan D, Villems R, Bonne-Tamir B, Richards M, Gurwitz D, Rosengarten D, Kaplan M, Della Pergola S, Quintana-Murci L, Skorecki K.
MtDNA evidence for a genetic bottleneck in the early history of the Ashkenazi Jewish population.

Eur J Hum Genet. 2004 May;12(5):355-64. | View as .pdf

Chaix R, Austerlitz F, Khegay T, Jacquesson S, Hammer MF, Heyer E, Quintana-Murci L.
The genetic or mythical ancestry of descent groups: lessons from the Y chromosome.

Am J Hum Genet. 2004 Dec;75(6):1113-6. | View as .pdf

Hammer MF, Garrigan D, Wood E, Wilder JA, Mobasher Z, Bigham A, Krenz JG, Nachman MW. Heterogeneous patterns of variation among multiple human x-linked Loci: the possible role of diversity-reducing selection in non-Africans.

Genetics. 2004 Aug;167(4):1841-53. | View as .pdf

Nachman MW, D'Agostino SL, Tillquist CR, Mobasher Z, Hammer MF.
Nucleotide variation at Msn and Alas2, two genes flanking the centromere of the X chromosome in humans.

Genetics. 2004 May;167(1):423-37. | View as .pdf

Wilder JA, Kingan SB, Mobasher Z, Pilkington MM, Hammer MF.
Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus males.

Nat Genet. 2004 Oct;36(10):1122-5. | View as .pdf

Wilder JA, Mobasher Z, Hammer MF.
Genetic evidence for unequal effective population sizes of human females and males.

Mol Biol Evol. 2004 Nov;21(11):2047-57. | View as .pdf

Wilder JA, Hammer MF.
European ACP1*C allele has recessive deleterious effects on early life viability.

Hum Biol. 2004 Dec;76(6):817-35. | View as .pdf.

Zegura SL, Karafet TM, Zhivotovsky LA, Hammer MF.
High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas.

Mol Biol Evol. 2004 Jan;21(1):164-75. | View as .pdf.

2003

Behar DM, Thomas MG, Skorecki K, Hammer MF, Bulygina E, Rosengarten D, Jones AL, Held K, Moses V, Goldstein D, Bradman N, Weale ME.
Multiple origins of Ashkenazi Levites: Y chromosome evidence for both Near Eastern and European ancestries.

Am J Hum Genet. 2003 Oct;73(4):768-79. 2003 Sep 17. | View as .pdf

Bonne-Tamir B, Korostishevsky M, Redd AJ, Pel-Or Y, Kaplan ME, Hammer MF.
Maternal and paternal lineages of the Samaritan isolate: mutation rates and time to most recent common male ancestor.

Ann Hum Genet. 2003 Mar;67(Pt 2):153-64. | View as .pdf

Jin HJ, Kwak KD, Hammer MF, Nakahori Y, Shinka T, Lee JW, Jin F, Jia X, Tyler-Smith C, Kim W.
Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans.

Hum Genet. 2003 Dec;114(1):27-35. | Not yet available as .pdf

Hammer MF, Blackmer F, Garrigan D, Nachman MW, Wilder JA.
Human population structure and its effects on sampling Y chromosome sequence variation

Genetics. 2003 Aug;164(4):1495-509. | View as .pdf

Yi Z, Garrison N, Cohen-Barak O, Karafet TM, King RA, Erickson RP, Hammer MF, Brilliant MH.
A 122.5-kilobase deletion of the P gene underlies the high prevalence of oculocutaneous albinism type 2 in the Navajo population.

Am J Hum Genet. 2003 Jan;72(1):62-72. 2002 Dec 5. | View as .pdf

2002

Karafet TM, Osipova LP, Gubina MA, Posukh OL, Zegura SL, Hammer MF.
High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life.

Hum Biol. 2002 Dec;74(6):761-89. Review. | View as .pdf

Redd AJ, Agellon AB, Kearney VA, Contreras VA, Karafet T, Park H, de Knijff P, Butler JM, Hammer MF.
Forensic value of 14 novel STRs on the human Y chromosome.

Forensic Sci Int. 2002 Dec 4;130(2-3):97-111. | View as .pdf