Welcome to the Malhi Lab

Founded in 2006, the lab conducts a variety of genetic research. Projects are headed by Dr Ripan Malhi, based at the University of Illinois at Urbana-Champaign.

For up-to-date list please visit https://orcid.org/0000-0002-1484-0292

 

 

IN PRESS Dong Y, Li C, Luan F, Li Z, Li H, Cui Y, Zhou H, Malhi RS. Low mitochondrial DNA diversity in an ancient population from China: Insight into social organization at the Fujia site. Human Biology.

IN PRESS Malhi RS, Bader A. Vital Topics: Engaging Native Americans in genomics research and diversifying science. American Anthropologist. 

IN PRESS Eerkens JW, Carlson T, Malhi RS, Blake J, Bartelink EJ, Barfod GH, Estes A, Garibay R, Glessner J, Greenwald AM, Lentz K, Li H, Marshall CK. Isotopic and genetic analyses of a mass grave in central California: Implications for precontact hunter-gatherer warfare. American Journal of Physical Anthropology.

2015 Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, Damgaard PB, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CP, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science Epub ahead of print.

2015 Rasmussen M, Sikora M, Albrechtsen A, Komeliussen TS, Moreno-Mayar JV, Poznik GD, Zollikofer CP, Ponce de Leon MS, Allentoft ME, Moltke I, Jonsson H, Valdiosera C, Malhi RS, Orlando L, Bustamante CD, Stafford TW Jr, Meltzer DJ, Nielsen R, Willerslev E. The ancestry and affiliations of Kennewick Man. Nature 523(7561): 455-8.

2015 Witt KE, Judd K, Kitchen A, Grier C, Kohler TA, Ortman SG, Kemp BM, Malhi RS. DNA analysis of ancient dogs of the Americas: Identifying possible founding haplotypes and reconstructing population histories. Journal of Human Evolution 79: 105-118.

2015 Kistler L, Ratan A, Godfrey LR, Crowley BE, Hughes CE, Lei R, Cui Y, Wood ML, Muldoon KM, Andriamialison H, McGraw JJ, Tomsho LP, Schuster SC, Miller W, Louis EE Yoder AD, Malhi RS, Perry GH. Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs. Journal of Human Evolution 79: 45-54.

2014 Malhi RS, Kemp BM. Providing a venue for influential research in anthropological genomics.  Human Biology 86(1): 5-6.

2014 Shattuck MR, Satkoski-Trask J, Deinard A, Tito RY, Smith DG, Melnick DJ, Malhi RS. Patterns of genetic variation and the role of selection in HTR1A and HTR1B in macaques (Macaca).  BMC Genetics 15(1): 116.

2014 Mallot EK, Malhi RS, Garber PA. High-throughput sequencing of fecal DNA to identify insects consumed by wild Weddell's saddleback tamarins (Saguinus weddelli, Cebidae, Primates) in Bolivia.  American Journal of Physical Anthropology IN PRESS.

2014 Verdu P, Pemberton TJ, Laurent R, Kemp BM, Gonzalez-Oliver A, Gorodezky C, Hughes CE, Shattuck MR, Petzelt B, Mitchell J, Harry H, William T, Worl R, Cybulski JS, Rosenberg NA, Malhi RS. Patterns of admixture and population structure in native populations of northwest North America 10(8): e1004530.

2014 Kennett DJ, Asmerom Y, Kemp BM, Polyak V, Bolnick DA, Malhi RS, Culleton BJ. Early Americans: misstated results. Science 345(6195): 390.

2014 Chatters JC, Kennett DJ, Asmerom Y, Kemp BM, Polyak V, Blank AN, Beddows PA, Reinhardt E, Arroyo-Cabrales J, Bolnick DA, Malhi RS, Culleton BJ, Erreguerena PL, Rissolo D, Morell-Hart S, Stafford TW Jr.  Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans.  Science 344(6185): 750-4.

2014 Shattuck MR, Satkoski-Trask J, Deinard A, Tito RY, Smith DG, Malhi RS. The evolutionary history of SLC6A4 and the role of plasticity in macaca.  American Journal of Physical Anthropology 153:605-16.

2014 Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav, Malaspinas S, White SS, Allentoft ME, Cornejo OE, Tamberts K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orland L, Balloux F, Manica A, Gupta R, Metspaul M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E.  The genome of a Late Pleistocene human from a Clovis burial site in western Montana.  Nature 506: 225-229.

2013 Achilli A, Perego UA, Lancioni H, Olivieri A, Gandini F, Hooshiar Kashani B, Battaglia V, Grugni V, Angerhofer N, Rogers MP, Herrera RJ, Woodward SR, Labuda D, Smith DG, Cybulski JS, Semino O, Malhi RS, Torroni A. Reconciling migration models to the Americas with the variation of North American native mitogenomes.  Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14308-13.

2013 Cui Y, Lindo J, Hughes CE, Johnson JW, Hernandez AG, Kemp BM, Ma J, Cunningham R, Petzelt B, Mitchell J, Archer D, Cybulski JS, Malhi RS. Ancient DNA analysis of Mid-Holocene individuals from the Northwest Cost of North America reveals different evolutionary paths for mitogenomes.  PLoS ONE 8(7): e66948

2012 Yan C, Shattuck MR, Thimmapuram J, Vullaganti D, Malhi RS. Developing SNPs and STR DNA markers for snub-nosed monkeys (Rhinopithecus roxellana) using next-generation sequencing technology. Conservation Genetics Resources 4: 451-453.

2011 Schroeder KB, Villa Jr G, Malhi RS, Rode AR, Smith DG.  Biological Continuity in the Central Valley:  Evidence from Ancient and Modern Mitochondrial DNA.  Journal of California and Great Basin Anthropology 31(1): 37-56.

2011 Trask JS, Garnica WT, Kanthaswamy S, Malhi RS, Smith DG.  4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta).  Genomics 98(5): 352-8.

2011 Wilson BJ, Crockford SJ, Johnson JW, Malhi RS, Kemp BM. Genetic and archaeological evidence for a former breeding population of Aleutian Cackling Goose (Branta hutchinsii leucopareia) on Adak Island, central Aleutians, Alaska. Canadian Journal of Zoology 89(8): 732-743.

2011 Satkoski Trask J, Garnica WT, Malhi RS, Kanthaswamy S, Smith DG.  High-throughput single-nucleotide polymorphism discovery and the search for candidate genes for long-term SIVmac nonprogression in Chinese rhesus macaques (Macaca mulatta).  Journal of Medical Primatology 40(4): 224-32.

2011 Malhi RS, Trask JS, Shattuck M, Johnson J, Chakraborty D, Kanthaswamy S, Ramakrishnan U, Smith DG. Genotyping single nucleotide polymorphisms (SNPs) across species in Old World Monkeys.  American Journal of Primatology 73(10):1031-40

2011 Trask JA, Malhi RS, Kanthaswamy S, Johnson J, Garnica WT, Malladi VS, Smith DG. The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta). Primates. 2011 Jan 5. [Epub ahead of print]

2010 Kemp BM, Gonzalez-Oliver A, Malhi RS, Monroe C, Schroeder KB, McDonough J, Rhett G, Resendez A, Pealoza-Espinosa RI, Buentello-Malo L, Gorodesky C, Smith DG. Evaluating the Farming/Language Dispersal Hypothesis with genetic variation exhibited by populations in the Southwest and Mesoamerica. Proc Natl Acad Sci U.S.A. 107:6759-64.

2010 Malhi RS, Cybulski JS, Tito RY, Johnson J, Harry H, Dan C. Brief communication: mitochondrial haplotype C4c confirmed as a founding genome in the Americas. American Journal of Physical Anthropology 141: 494-7.

2010 Luetkemeier ES, Sodhi M, Schook LB, Malhi RS. Multiple Asian pig origins revealed through genomic analyses. Molecular Phylogenetics and Evolution 54: 680-6.

2009 Malhi RS, Schroeder KB, Kemp BM. Uses and limitations of genetic data relating to Athapskan migrations: a reply to Seymour. American Journal of Physical Anthropology 140: 203-4.

2009 Schroeder KB, Jakobsson M, Crawford MH, Schurr TG, Boca SM, Conrad DF, Tito RY, Osipova LP, Taraskaia LA, Zhadanov SI, Wall JD, Pritchard JK, Malhi RS, Smith DG, Rosenberg NA. Haplotypic background of a private allele at high frequency in the Americas. Molecular Biology and Evolution 26: 995-1016.

2009 Luetkemeier ES, Malhi RS, Beever JE, Schook LB. Diversification of porcine MHC class II genes: evidence for selective advantage. Immunogenetics 61: 119-29.

2008 Malhi RS, Gonzalez-Oliver A, Schroeder KB, Kemp BM, Greenberg JA, Dobrowski SZ, Smith DG, Resendez A, Karafet T, Hammer M, Zegura S, Brovko T. Distribution of Y chromosomes among native North Americans: a study of Athapaskan population history. American Journal of Physical Anthropology 137: 412-24.

2008 Satkoski JA, Malhi RS, Kanthaswamy S, Tito R, Malladi V, Smith DG. Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta). BMC Genomics 9: 256.

2007 Malhi RS. Book Review: The First Americans Race, Evolution, and the Origins of Native Americans. American Journal of Physical Anthropology 135: 492-493.

2007 Cybulski JS, McMillan AD, Malhi RS, Kemp BM, Harry H, Cousins S. The Big Bar Lake Burial: Middle Period Human Remains from the Canadian Plateau. Canadian Journal of Archaeology 31: 55-78.

2007 Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Mulligan CJ, Bravi CM, Rickards O, Martinez-Labarga C, Khusnutdinova EK, Fedorova SA, Golubenko MV, Stepanov VA, Gubina MA, Zhanadov SL, Ossipova LP, Damba L, Voevoda MI, Dipierra JE, Villems R, Malhi RS. Beringian Standstill and spread of Native American founders. PLoS ONE 2: e829.

2007 Malhi RS, Sickler B, Lin D, Satkoski J, Tito RY, George D, Kanthaswamy S, Smith DG. MamuSNP: a resource for Rhesus Macaque (Macaca mulatta) genomics. PLoS ONE 2: e438.

2007 Kemp BM, Malhi RS, McDonough J, Bolnick DA, Eshleman JA, Rickards O, Martinez-Labarga C, Johnson JR, Lorenz JG, Dixon J, Fifield TE, Heaton T, Worl R, and Smith DG. Timing of the peopling of the Americas: genetic analysis of an early Holocene skeleton. American Journal of Physical Anthropology 132: 605-621.

2007 Malhi RS, Kemp BM, Eshleman JA, Cybluski J, Smith DG, Cousins S, Harry H. Haplogroup M Discovered in Prehistoric North America. Journal of Archaeological Science 34: 642-648.

2006 Malhi RS, Rhett G, Bell AM. Mitochondrial DNA evidence of an early Holocene population expansion of threespine sticklebacks from Scotland. Molecular Phylogenetics and Evolution 40: 148-154.

2006 Schroeder KB, Malhi RS, Smith DG. Opinion: Native American Participation in Genetic Research. Evolutionary Anthropology 13(3) 88-92.

2005 Malhi RS and Schilling AJ. Discovering your Native American heritage using genetic ancestry testing. New Mexico Genealogist. December 2005.

2005 Smith DG, Malhi RS, Eshleman JA, Kaestle FA, Kemp BM. Mitochondrial DNA Haplogroups of Paleoamericans in North America. Paleoamerican Origins: Beyond Clovis. Texas A&M University Press.

2005 Kemp BM, Resendez A, Berrelleza JAR, Malhi RS, and Smith DG. An analysis of ancient Aztec mtDNA from Tlatelolco: Pre-Columbian relations and the spread of Uto-Aztecan. Biomolecular Archaeology: Genetic Approaches to the Past. Carbondale University Press.

2005 Malhi RS, Van Tuinen M, Mountain J, Hadley L. Pilot project: Catalhoyuk ancient DNA project. Catalhoyuk Research Project 4, McDonald Institute for Archaeological Research 2005. British Institute at Ankara Monograph 38.

2004 Eshleman JA, Malhi RS, Johnson JR, Kaestle FA, Lorenz JG, and Smith DG. Mitochondrial DNA and prehistoric settlements: Native migrations on the Western edge of North America. Human Biology 76: 55-75.

2004 Malhi RS, Breece KE, Shook BAS, Kaestle FA, Chatters JC, Hackenberger S, and Smith DG. Patterns of mtDNA diversity in Northwestern North America. Human Biology 76: 33-54.

2003 Eshleman JA, Malhi RS, and Smith DG. Mitochondrial DNA studies of Native Americans: Conceptions and misconceptions of the population prehistory of the Americas. Evolutionary Anthropology 12: 7-18.

2003 Malhi RS, Mortensen HM, Eshleman JA, Lorenz JG, Kaestle FA, Johnson JR, Gorodesky C, and Smith DG. Native American mtDNA prehistory in the American Southwest. American Journal of Physical Anthropology 120: 108-124.
(Abstract)

2002 Malhi RS and Smith DG. Brief Communication: Haplogroup X confirmed in Prehistoric North America. American Journal of Physical Anthropology 119: 84-88.

2002 Malhi RS, Eshleman JA, Greenberg JA, Weiss DA, Schultz BA, Kemp BM, Kaestle FA, Lorenz JG, Johnson JR, and Smith DG. The structure and diversity within New World mtDNA haplogroups: Implications for the prehistory of North America. American Journal of Human Genetics 70: 905-919.

2002 Smith DG, Malhi RS, Eshleman JA, and Kaestle FA. Mitochondrial DNA haplogroups of Paleoamericans in North America. In Bonnichsen R, Gruhn R, Steele DG, Stanford D, Lepper B, and Warren CN, (eds.) Beyond Clovis: Where We Have Been, Where We Are, and Where We Are Going. College Station, TX: Texas A&M University Press.

2002 Smith DG, Rolfs BK, Kaestle FA, Malhi RS, and Doran GH. Serum albumin phenotypes and a preliminary study of the mtDNA haplogroups of the prehistoric population of Windover. In: G.H. Doran (ed.) Multidisciplinary Investigations at Windover. University of Florida Press.

2001 Malhi RS, Schultz BA, and Smith DG. Distribution of mitochondrial DNA lineages among Native American tribes of Northeastern North America. Human Biology 73 23-51.

2000 Smith DG, Lorenz JG, Rolfs BK, Bettinger RL, Green B, Eshleman JA, Schultz BA, and Malhi RS. Implications of the distribution of Albumin Naskapi and Albumin Mexico for New World Prehistory. American Journal of Physical Anthropology 111: 557-572.

1999 Smith DG, Malhi RS, Eshleman JA, Lorenz JG, and Kaestle FA. Disribution of mtDNA Haplogroup X among Native North Americans. American Journal of Physical Anthropology 110: 271-284.

1997 Bettinger RL, Malhi RS, and McCarthy H. Central place models of acorn and mussel processing. Journal of Archaeological Science 24: 887-899.

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