Research Topics
Genomes and GenesSpecies | Michael F HammerSummaryAffiliation: University of Arizona Country: USA Publications
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Publications
Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in AfricaMaya 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...- Heterogeneous patterns of variation among multiple human x-linked Loci: the possible role of diversity-reducing selection in non-africansMichael F Hammer
Genomic Analysis and Technology Core, Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
Genetics 167:1841-53. 2004.... - Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomesMichael 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... - Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databasesMichael 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... - Sex-biased evolutionary forces shape genomic patterns of human diversityMichael F Hammer
ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, USA
PLoS Genet 4:e1000202. 2008.... - Genetic structure among 38 populations from the United States based on 11 U.S. core Y chromosome STRsAlan 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... - Major east-west division underlies Y chromosome stratification across IndonesiaTatiana M Karafet
ARL Division of Biotechnology, University of Arizona, AZ, USA
Mol Biol Evol 27:1833-44. 2010.... - 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 coalescentMurray 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... - Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthoodMichael F Hammer
ARL Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
Hum Genet 126:707-17. 2009.... - The extent of linkage disequilibrium caused by selection on G6PD in humansMatthew 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... - Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flowMurray 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... - Reconstructing human origins in the genomic eraDaniel Garrigan
Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
Nat Rev Genet 7:669-80. 2006.... - Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture ratesMurray 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... - Joint match probabilities for Y chromosomal and autosomal markersBruce 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... - Genetic evidence for unequal effective population sizes of human females and malesJason 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... - A Polynesian motif on the Y chromosome: population structure in remote OceaniaMurray 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... - Machine-learning approaches for classifying haplogroup from Y chromosome STR dataJoseph 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... - High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the AmericasStephen 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... - Forensic value of 14 novel STRs on the human Y chromosomeAlan 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... - The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genesMichael 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... - Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian tradersTatiana 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... - Nucleotide variability at G6pd and the signature of malarial selection in humansMatthew A Saunders
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
Genetics 162:1849-61. 2002.... - Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral populationDaniel 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... - Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populationsJ 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... - Increased resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and AfricaFernando 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... - Coevolution of languages and genes on the island of Sumba, eastern IndonesiaJ 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... - New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup treeTatiana 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... - Genetic evidence for archaic admixture in AfricaMichael 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... - Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus malesJason 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... - Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processesElizabeth T Wood
Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
Eur J Hum Genet 13:867-76. 2005.... - Nucleotide variation at Msn and Alas2, two genes flanking the centromere of the X chromosome in humansMichael 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... - An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing dataKrishna 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... - The beta -globin recombinational hotspot reduces the effects of strong selection around HbC, a recently arisen mutation providing resistance to malariaElizabeth 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... - Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populationsMurray 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?.. - Human population structure and its effects on sampling Y chromosome sequence variationMichael 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.... - Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosomeAlan 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... - Recombination-filtered genomic datasets by information maximizationAugust 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... - High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of lifeTatiana M Karafet
Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
Hum Biol 74:761-89. 2002.... - A 122.5-kilobase deletion of the P gene underlies the high prevalence of oculocutaneous albinism type 2 in the Navajo populationZanhua 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... - European ACP1*C allele has recessive deleterious effects on early life viabilityJason 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.... - High levels of Y-chromosome nucleotide diversity in the genus PanAnne C Stone
Department of Anthropology, University of New Mexico, Albuquerque, NM 87131 1086, USA
Proc Natl Acad Sci U S A 99:43-8. 2002.... - A novel multiplex for simultaneous amplification of 20 Y chromosome STR markersJohn M Butler
Biotechnology Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8311, Gaithersburg, MD 20899, USA
Forensic Sci Int 129:10-24. 2002..Haplotype comparisons between the 20plex and a commercially available kit found excellent agreement across the 76 samples in the Y chromosome consortium panel... - Multiple origins of Ashkenazi Levites: Y chromosome evidence for both Near Eastern and European ancestriesDoron M Behar
Bruce Rappaport Faculty of Medicine and Research Institute, Technion and Rambam Medical Center, Haifa, Israel
Am J Hum Genet 73:768-79. 2003.... - Y-chromosomal DNA haplogroups and their implications for the dual origins of the KoreansHan-Jun Jin
Department of Biological Sciences, Dankook University, 330-714 Cheonan, Korea
Hum Genet 114:27-35. 2003.... - Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing dataDaniel Garrigan
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genetics 177:2195-207. 2007..e., from the Bantu-speaking population into other African populations. Conversely, mitochondrial gene flow is more extensive between non-African populations, but appears to be absent between European and Asian populations... - Evidence for archaic Asian ancestry on the human X chromosomeDaniel Garrigan
Mol Biol Evol 22:189-92. 2005..We suggest that this ancient lineage is a remnant of introgressive hybridization between expanding anatomically modern humans emerging from Africa and archaic populations in Eurasia... - Ancient lineages in the genome: a response to Fagundes et alDaniel Garrigan
Proc Natl Acad Sci U S A 105:E3; author reply E4. 2008 - Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populationsDoron M Behar
Bruce Rappaport Faculty of Medicine and Research Institute, Technion and Rambam Medical Center, Haifa, Israel
Hum Genet 114:354-65. 2004..This reduced effective population size may explain the high incidence of founder disease mutations despite overall high levels of NRY diversity... - MtDNA evidence for a genetic bottleneck in the early history of the Ashkenazi Jewish populationDoron M Behar
Bruce Rappaport Faculty of Medicine and Research Institute, Technion and Rambam Medical Center, Haifa, Israel
Eur J Hum Genet 12:355-64. 2004..A genetic bottleneck followed by the recent phenomenon of rapid population growth are likely to have produced the conditions that led to the high frequency of many genetic disease alleles in the Ashkenazi population... - A novel DNA sequence database for analyzing human demographic historyJeffrey D Wall
Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
Genome Res 18:1354-61. 2008.... - From social to genetic structures in central AsiaRaphaelle Chaix
Unité d Eco Anthropologie, Centre National de la Recherche UMR 5145, Universite Paris 7, Musée de l Homme, Paris 75116, France
Curr Biol 17:43-8. 2007..This molecular signature of the pastoral social organization disappears over a few centuries only after conversion to an agricultural way of life... - Archaic admixture in the human genomeJeffrey D Wall
Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
Curr Opin Genet Dev 16:606-10. 2006..Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years...
Research Grants
- Y CHROMOSOME EVOLUTION AND MODERN HUMAN ORIGINSMichael Hammer; Fiscal Year: 2004..abstract_text> ..
- Genomic Patterns of Polymorphism in PrimatesJeffrey D Wall; Fiscal Year: 2010....