Michael F Hammer

Summary

Affiliation: University of Arizona
Country: USA

Publications

  1. doi request reprint The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes
    Michael F Hammer
    Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USA
    Nat Genet 42:830-1. 2010
  2. pmc Genetic evidence for archaic admixture in Africa
    Michael F Hammer
    Arizona Research Laboratories, Division of Biotechnology, Department of Ecology and Evolutionary Biology, and Mathematics Department, University of Arizona, Tucson, AZ 85721, USA
    Proc Natl Acad Sci U S A 108:15123-8. 2011
  3. ncbi request reprint Genetic structure among 38 populations from the United States based on 11 U.S. core Y chromosome STRs
    Alan J Redd
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    J Forensic Sci 51:580-5. 2006
  4. pmc 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
    Murray P Cox
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, USA
    Genetics 178:427-37. 2008
  5. pmc Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood
    Michael F Hammer
    ARL Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Hum Genet 126:707-17. 2009
  6. doi request reprint Major east-west division underlies Y chromosome stratification across Indonesia
    Tatiana M Karafet
    ARL Division of Biotechnology, University of Arizona, AZ, USA
    Mol Biol Evol 27:1833-44. 2010
  7. doi request reprint The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific
    Meryanne K Tumonggor
    Department of Anthropology, University of Arizona, Tucson, AZ, USA
    J Hum Genet 58:165-73. 2013
  8. pmc The extent of linkage disequilibrium caused by selection on G6PD in humans
    Matthew A Saunders
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 171:1219-29. 2005
  9. pmc Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow
    Murray P Cox
    ARL Division of Biotechnology, University of Arizona, AZ 85721, USA
    BMC Genet 9:76. 2008
  10. ncbi request reprint Reconstructing human origins in the genomic era
    Daniel Garrigan
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Nat Rev Genet 7:669-80. 2006

Collaborators

Detail Information

Publications49

  1. doi request reprint The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes
    Michael F Hammer
    Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USA
    Nat Genet 42:830-1. 2010
    ..This pattern may be explained by stronger locally acting selection on X-linked genes compared with autosomal genes, combined with larger effective population sizes for females than for males...
  2. pmc Genetic evidence for archaic admixture in Africa
    Michael F Hammer
    Arizona Research Laboratories, Division of Biotechnology, Department of Ecology and Evolutionary Biology, and Mathematics Department, University of Arizona, Tucson, AZ 85721, USA
    Proc Natl Acad Sci U S A 108:15123-8. 2011
    ..Taken together our results suggest that polymorphisms present in extant populations introgressed via relatively recent interbreeding with hominin forms that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene...
  3. ncbi request reprint Genetic structure among 38 populations from the United States based on 11 U.S. core Y chromosome STRs
    Alan J Redd
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    J Forensic Sci 51:580-5. 2006
    ..We recommend that separate databases be constructed for different NA groups...
  4. pmc 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
    Murray P Cox
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, USA
    Genetics 178:427-37. 2008
    ..The pmc summary statistic, which has improved power with larger samples of chromosomes, yields values that are significantly unlikely under the RAR model and fit expectations better under a range of archaic admixture scenarios...
  5. pmc Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood
    Michael F Hammer
    ARL Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Hum Genet 126:707-17. 2009
    ....
  6. doi request reprint Major east-west division underlies Y chromosome stratification across Indonesia
    Tatiana M Karafet
    ARL Division of Biotechnology, University of Arizona, AZ, USA
    Mol Biol Evol 27:1833-44. 2010
    ....
  7. doi request reprint The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific
    Meryanne K Tumonggor
    Department of Anthropology, University of Arizona, Tucson, AZ, USA
    J Hum Genet 58:165-73. 2013
    ..This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region's complex history of immigration, transitory migrants and populations that have endured in situ since the region's first settlement...
  8. pmc The extent of linkage disequilibrium caused by selection on G6PD in humans
    Matthew A Saunders
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 171:1219-29. 2005
    ..1 < s < 0.2). These results also show that selection can lead to nonrandom associations among SNPs over great physical and genetic distances, even in African populations...
  9. pmc Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow
    Murray P Cox
    ARL Division of Biotechnology, University of Arizona, AZ 85721, USA
    BMC Genet 9:76. 2008
    ..This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions...
  10. ncbi request reprint Reconstructing human origins in the genomic era
    Daniel Garrigan
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Nat Rev Genet 7:669-80. 2006
    ....
  11. pmc Sex-biased evolutionary forces shape genomic patterns of human diversity
    Michael F Hammer
    ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, USA
    PLoS Genet 4:e1000202. 2008
    ....
  12. pmc Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates
    Murray P Cox
    ARL Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Proc Biol Sci 277:1589-96. 2010
    ..The matrilocal marriage practices that dominated early Austronesian societies may be one factor contributing to this observed sex bias in admixture rates...
  13. ncbi request reprint Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa
    Maya Metni Pilkington
    Department of Anthropology, University of Arizona, USA
    Mol Biol Evol 25:517-25. 2008
    ..We hypothesize that males experienced smaller effective population sizes and/or lower rates of migration during the Bantu expansion, which occurred over the last 5,000 years...
  14. ncbi request reprint Joint match probabilities for Y chromosomal and autosomal markers
    Bruce Walsh
    Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ 85721, USA
    Forensic Sci Int 174:234-8. 2008
    ..For example, if the amount of structure in the population is theta=0.01 or 0.03 (the NRCII range), then the effect of conditioning on the Y results in only a trivial increase in theta to 0.02-0.04, respectively...
  15. pmc Machine-learning approaches for classifying haplogroup from Y chromosome STR data
    Joseph Schlecht
    Computer Science Department, University of Arizona, Tucson, Arizona, USA
    PLoS Comput Biol 4:e1000093. 2008
    ..The result is an integrated high-throughput analysis system that automatically classifies large numbers of samples into haplogroups in a cost-effective and accurate manner...
  16. doi request reprint Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations
    Fernando L Mendez
    Department of Ecology and Evolutionary Biology, University of Arizona, USA
    Mol Biol Evol 29:1513-20. 2012
    ....
  17. pmc An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data
    Krishna R Veeramah
    Arizona Research Laboratories Division of Biotechnology, University of Arizona, Arizona, USA
    Mol Biol Evol 29:617-30. 2012
    ..This approach is likely to prove to be an invaluable tool for demographic inference using genome-wide resequencing data...
  18. ncbi request reprint A Polynesian motif on the Y chromosome: population structure in remote Oceania
    Murray P Cox
    Arizona Research Laboratories, University of Arizona, Tucson, AZ 85721, USA
    Hum Biol 79:525-35. 2007
    ..Such patterning, a product of early regional contact and subsequent isolation, signals the conflicting roles of mobility and seclusion in Polynesian prehistory...
  19. ncbi request reprint Genetic evidence for unequal effective population sizes of human females and males
    Jason A Wilder
    Division of Biotechnology, University of Arizona, Tucson, USA
    Mol Biol Evol 21:2047-57. 2004
    ..7 kya for the NRY and 92.8 kya for mtDNA). Our data do not suggest that differential natural selection is the cause of this difference in TMRCAs. Rather, these results are most consistent with a higher female effective population size...
  20. pmc Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populations
    J Stephen Lansing
    Department of Anthropology, University of Arizona, Tucson, AZ 85721, USA
    Proc Natl Acad Sci U S A 105:11645-50. 2008
    ..We conclude that patrilines seldom are dominant for more than a few generations, and thus traits or behaviors that are strictly paternally inherited are unlikely to be under strong cultural selection...
  21. doi request reprint Increased resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa
    Fernando L Mendez
    ARL Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Hum Biol 83:39-53. 2011
    ..Finally, the moderately high frequency (-18%) of T1b* chromosomes in the Lemba of southern Africa supports the hypothesis of a Near Eastern, but not necessarily a Jewish, origin for their paternal line...
  22. pmc An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree
    Fernando L Mendez
    Division of Biotechnology, Arizona Research Laboratories, University of Arizona, Tucson, AZ 85721, USA
    Am J Hum Genet 92:454-9. 2013
    ....
  23. pmc Coevolution of languages and genes on the island of Sumba, eastern Indonesia
    J Stephen Lansing
    Department of Anthropology, University of Arizona, 1009 East South Campus Drive, Tucson, AZ 85721, USA
    Proc Natl Acad Sci U S A 104:16022-6. 2007
    ..We propose a model to explain linguistic and demographic coevolution at fine spatial and temporal scales...
  24. pmc New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
    Tatiana M Karafet
    ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
    Genome Res 18:830-8. 2008
    ..Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree...
  25. pmc Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population
    Daniel Garrigan
    Genomic Analysis and Technology Core, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 170:1849-56. 2005
    ..This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo...
  26. pmc The beta -globin recombinational hotspot reduces the effects of strong selection around HbC, a recently arisen mutation providing resistance to malaria
    Elizabeth T Wood
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Am J Hum Genet 77:637-42. 2005
    ..The rapid decay in LD upstream of the HbC allele demonstrates the large effect the ss-globin hotspot has in mitigating the effects of positive selection on linked variation...
  27. pmc A haplotype at STAT2 Introgressed from neanderthals and serves as a candidate of positive selection in Papua New Guinea
    Fernando L Mendez
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
    Am J Hum Genet 91:265-74. 2012
    ..Although we are not able to pinpoint the precise target of positive selection, we identify nonsynonymous mutations in ERBB3, ESYT1, and STAT2-all of which are part of the same 250 kb introgressive haplotype-as good candidates...
  28. pmc Heterogeneous patterns of variation among multiple human x-linked Loci: the possible role of diversity-reducing selection in non-africans
    Michael F Hammer
    Genomic Analysis and Technology Core, Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 167:1841-53. 2004
    ....
  29. ncbi request reprint Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus males
    Jason A Wilder
    Division of Biotechnology, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Nat Genet 36:1122-5. 2004
    ..Although patrilocality may be important at the local scale, patterns of genetic structure on the continental and global scales are not shaped by the higher rate of migration among females than among males...
  30. ncbi request reprint Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases
    Michael F Hammer
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Forensic Sci Int 164:45-55. 2006
    ..We infer that both inter-ethnic admixture and population structure in ancestral source populations may contribute to fine scale Y-STR heterogeneity within U.S. ethnic groups...
  31. doi request reprint Multistate structural modeling and voltage-clamp analysis of epilepsy/autism mutation Kv10.2-R327H demonstrate the role of this residue in stabilizing the channel closed state
    Yang Yang
    Department of Neurology and Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, Connecticut 06510, Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut 06516, and Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721
    J Neurosci 33:16586-93. 2013
    ..2 channel mutation associated with neurological disease. ..
  32. ncbi request reprint Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes
    Elizabeth T Wood
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Eur J Hum Genet 13:867-76. 2005
    ....
  33. ncbi request reprint Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders
    Tatiana M Karafet
    Division of Biotechnology, Biosciences West, University of Arizona, Tucson, AZ 85721, USA
    Hum Biol 77:93-114. 2005
    ..These results indicate that the Austronesian expansion had a profound effect on the composition of the Balinese paternal gene pool and that cultural transmission from India to Bali was accompanied by substantial levels of gene flow...
  34. doi request reprint Neandertal origin of genetic variation at the cluster of OAS immunity genes
    Fernando L Mendez
    Department of Ecology and Evolutionary Biology, University of Arizona, Arizona, USA
    Mol Biol Evol 30:798-801. 2013
    ..This is the second locus in the human genome, after STAT2, carrying distinct haplotypes that appear to have introgressed separately from both Neandertals and Denisova...
  35. pmc Nucleotide variation at Msn and Alas2, two genes flanking the centromere of the X chromosome in humans
    Michael W Nachman
    Department of Ecology and Evolutionary Biology, Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 167:423-37. 2004
    ..These observations are difficult to reconcile with a simple demographic model but may be consistent with positive and/or purifying selection acting on loci within this large region of low recombination...
  36. ncbi request reprint Recombination-filtered genomic datasets by information maximization
    August E Woerner
    Arizona Research Laboratories Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Bioinformatics 23:1851-3. 2007
    ..Availability: http://hammerlab.biosci.arizona.edu/software.html...
  37. pmc A 122.5-kilobase deletion of the P gene underlies the high prevalence of oculocutaneous albinism type 2 in the Navajo population
    Zanhua Yi
    Department of Pediatrics, College of Medicine, University of Arizona, Tucson, AZ 85724, USA
    Am J Hum Genet 72:62-72. 2003
    ..5%. The estimated prevalence of OCA2 in Navajos is between approximately 1 per 1,500 and 1 per 2,000. We further estimate that this mutation originated 400-1,000 years ago from a single founder...
  38. ncbi request reprint Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes
    Michael F Hammer
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    J Hum Genet 51:47-58. 2006
    ..The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence...
  39. pmc Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populations
    Murray P Cox
    ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, United States of America
    PLoS ONE 4:e6366. 2009
    ..human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?..
  40. ncbi request reprint Forensic value of 14 novel STRs on the human Y chromosome
    Alan J Redd
    Division of Biotechnology, University of Arizona, Biosciences West room 239, Tucson, AZ 85721, USA
    Forensic Sci Int 130:97-111. 2002
    ..Furthermore, these novel Y-STRs greatly improved the resolution of paternal lineages, above the level obtained with commonly used Y-STRs, in the European-American population...
  41. ncbi request reprint Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome
    Alan J Redd
    Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Curr Biol 12:673-7. 2002
    ..These results provide strong evidence for an influx of Y chromosomes from the Indian subcontinent to Australia that may have occurred during the Holocene...
  42. pmc The KCNJ8-S422L variant previously associated with J-wave syndromes is found at an increased frequency in Ashkenazi Jews
    Krishna R Veeramah
    Division of Biotechnology, Arizona Research Laboratories, University of Arizona, Tucson, AZ, USA
    Eur J Hum Genet 22:94-8. 2014
    ....
  43. pmc European ACP1*C allele has recessive deleterious effects on early life viability
    Jason A Wilder
    Department of Ecology and Evolutionary Biology and Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
    Hum Biol 76:817-35. 2004
    ....
  44. pmc Human population structure and its effects on sampling Y chromosome sequence variation
    Michael F Hammer
    Genomic Analysis and Technology Core, Division of Biotechnology, Biosciences West Building, University of Arizona, Tucson, AZ 85721, USA
    Genetics 164:1495-509. 2003
    ....
  45. ncbi request reprint High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas
    Stephen L Zegura
    Department of Anthropology, University of Arizona, USA
    Mol Biol Evol 21:164-75. 2004
    ..Divergence dates between the Altai plus North Asians versus the Native American population system ranged from 10,100 to 17,200 years for all lineages, precluding a very early entry into the Americas...
  46. ncbi request reprint High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life
    Tatiana M Karafet
    Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
    Hum Biol 74:761-89. 2002
    ....
  47. pmc Exome sequencing reveals new causal mutations in children with epileptic encephalopathies
    Krishna R Veeramah
    ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
    Epilepsia 54:1270-81. 2013
    ..Herein we explore the utility of WES for identifying candidate causal de novo variants in a cohort of children with heterogeneous sporadic epilepsies without etiologic diagnoses...
  48. pmc De novo pathogenic SCN8A mutation identified by whole-genome sequencing of a family quartet affected by infantile epileptic encephalopathy and SUDEP
    Krishna R Veeramah
    Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, 85721, USA
    Am J Hum Genet 90:502-10. 2012
    ..This work identifies SCN8A as the fifth sodium-channel gene to be mutated in epilepsy and demonstrates the value of WGS for the identification of pathogenic mutations causing severe, sporadic neurological disorders...
  49. pmc Nucleotide variability at G6pd and the signature of malarial selection in humans
    Matthew A Saunders
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 162:1849-61. 2002
    ....