Research

Currently, projects in the Stone lab focus on population history and in understanding how humans and other primates have adapted to their environments, including their disease environments. Current projects include: (a) understanding the evolutionary history of mycobacteria (specifically those causing TB and leprosy) affecting human and non-human primates, (b) primate variation, and (c) human population history (including in Kenya and Peru).

Stone Vitae

Selected Publications:

2016

Malukiewicz J, Hepp CM, Guschanski K, and Stone AC. The phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes. American Journal of Physical Anthropology. DOI 10.1002/ajpa.23105

Kotze A, Dalton DL, Strinden M, Sauther ML, Cuozzo FP, and Stone AC. An evaluation of the oral microbiome and potential zoonoses of the Southern Thick-Tailed or Greater Galago (Otolemur crassicaudatus) African Primates 11(1): 19-26.

Harkins KM, Schwartz RS, Cartwright RA and Stone AC, Phylogenomic reconstruction supports supercontinent origins for Leishmania. Infection, Genetics and Evolution 38:101-109

Ozga AT, Nieves-Colón MA, Honap TP, Sankaranarayanan K, Hofman C, Milner G, Lewis CM, Stone AC, and Warinner C. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. American Journal of Physical Anthropology.

2015

Guichon RA, Buikstra JE, Stone AC, Harkins KM, Suby JA, Massone M, Preito Iglesias A, Wilbur AK, Constantinescu F, and Rodriguez Martin C. Pre-Columbian tuberculosis in Tierra del Fuego? Paleopathologies and molecular evidence for discussion. International Journal of Paleopathology 11: 92-101.

Harkins K, Buikstra JE, Campbell T, Bos KI, Johnson ED, Krause J, and Stone AC. Screening ancient tuberculosis with qPCR: challenges and opportunities. Philosophical Transactions of the Royal Society, London, series B 370:20130622

Harkins K and Stone AC. Ancient pathogen genomics: insights into timing and adaptation. Journal of Human Evolution 79:137-149

Housman G, Boere V, Gravitol AD, Malukiewicz J, Pereira LCM, de Oliverira e Silva I, Ruiz-Miranda CR, Truman R, and Stone AC. Validation of qPCR methods for the detection of Mycobacterium in New World animal reservoirs. Plos Neglected Tropical Diseases Nov 16;9(11):e0004198, doi: 10.1371/journal.pntd.0004198

Malukiewicz J, Boere V, Fuzessy L, Grativol AD, Silva IO, Pereira LCM, Ruiz-Miranda CR, Valenca YM, and Stone AC. Natural and anthropogenic hybridization in two species of eastern Brazilian marmosets (Callithrix jacchus and C. penicillata). PLoS One. Jun 10;10(6):e0127268. doi: 10.1371/journal.pone.0127268

Schwartz RS, Harkins KM, Stone AC and Cartwright RA. A composite genome approach to identify phylogenetically informative data from Next-Generation Sequencing. BMC Bioinformatics 16:193,DOI 10.1186/s12859-015-0632-y

2014

Bos KI*, Harkins KM*, Herbig A*, Coscolla M*, Weber N, Comas I, Forrest SA, Parkhill J, Bryant J, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK, Guichon RA, Wolfe Steadman DL, Cook DC, Niemann S, Behr MA, Zumarraga M, Huson D, Nieselt K, Young D, Buikstra JE, Gagneux S, AC. Stoneⱡ, and Krause Jⱡ, Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514:494-497

Cabana GS, Lewis CM Jr, Tito RY, Covey RA, Cáceres AM, de la Cruz AF, Durand D, Housman G, Hulsey BI, Iannacone GC, López PW, Martínez R, Medina Á, Ortego Dávila O, Osorio Pinto KP, Polo SI, Rojas Domínguez P, Rubel M, Smith HF, Smith SE, Rubín de Celis Massa V, Lizárraga B,, and Stone AC. Population genetic structure of traditional populations in the Peruvian central Andes and implications for South American population history. Human Biology 86(3):147-65

Malukiewicz J, Boere V, Fuzessy L, Grativol AD, French JA, de Oliveira e Silva I, Pereira LCM, Ruiz-Miranda CR, Valenca YM, and Stone AC. Hybridization effects   and genetic diversity of the common and black tufted marmoset (Callithrix jacchus and C. penicillata) Mitochondrial Control Region. American Journal of Physical Anthropology 155:522-36

Lou DI, McBee RM, Uyen QL, Stone AC, Wilkerson GK, Demogines AM, and Sawyer SL, Rapid evolution of the BRCA1 and BRCA2 proteins in humans and other primates. BMC Evolutionary Biology. Jul 11;14:155.

2013

Ferreira Z, Hurle B, Andres A, Kretzschmar W, Mullikin J, Cherukuri P, Cruz P, Gonder MK, Stone AC, Tishkoff S, Swanson W, NISC Comparative Sequencing Program, Clark AG, Green E, and S Seixas. Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biology and Evolution 5:2512-2523.

Benn Torres J, Stone AC, and Kittles R. An Anthropological Genetic Perspective on Creolization in the Anglophone Caribbean. American Journal of Physical Anthropology. 151:135-143.

2012

Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, and Lee C. Regulatory element copy number differences shape primate  expression profiles. Proceedings of the National Academy of Sciences, USA 109:12656-12661.

Ferguson W, Dvora S, Stone AC, and Boissinot S. Long-term balancing selection at the antiviral gene OAS1 in central African chimpanzees. Molecular Biology and Evolution. 29:1093-1103

2010

Stone AC, Battistuzzi F, Kubatko LS, Perry GH, Trudeau E, Lin H, and Kumar S. More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Proceedings of the Royal Society, Series B. 365:3277-3288.

Klaus H, Wilbur AK, Temple D, Buikstra, JE, Stone AC, Fernandez M, Wester C, and Tam M. Tuberculosis on the North Coast of Peru: Skeletal and Molecular Paleopathology of Late Pre-Hispanic and Postcontact Mycobacterial Disease. Journal of Archaeological Science 37:2587-2597.

Claw KG, Tito RY, Stone AC, and Verrelli BC. Haplotype structure and divergence at human and chimpanzee serotonin transporter and receptor genes: implications for behavioral disorder association analyses. Molecular Biology and Evolution 27:1518-1529

2009

Stone AC, Wilbur AK, Buikstra JE, and Roberts CA, Tuberculosis and leprosy in perspective. Yearbook of Physical Anthropology 140 Suppl 49:66-94.

Wilbur AK, Bouwman AS, Stone AC, Roberts CA, Pfister LA, Buikstra JE, and Brown TA, Deficiencies and challenges in the study of ancient tuberculosis DNA. Journal of Archaeological Science 36:1990-1997

2008

Verrelli BC, Lewis CM, Stone AC, and Perry GH. Different selective pressures shape the molecular evolution of color vision in human and chimpanzee populations. Molecular Biology and Evolution 25:2735-2743

Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C,  Smith RS, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, and Redon R. Copy number variation and genome evolution in humans and Chimpanzees. Genome Research 18:1698-1710.

2007

Lewis CM, Buikstra JE, and Stone AC. Ancient DNA and genetic continuity in the south central Andes. Latin American Antiquity 18:145-160.

Lewis CM, Lizarraga B, Tito RY, Lopez P, Iannacone GC, Medina AC, Marinez RE,  Polo SI, de la Cruz F, Cáceres AM, and Stone AC. Mitochondrial DNA and the peopling of South America. Human Biology 79:159-178.

Perry GH, Dominy NJ, Claw KG, Lee AS, Werner J, Villanea FA, Mountain JL, Misra R, Lee C, and Stone AC. Diet and the evolution of amylase gene copy number variation among human populations. Nature Genetics 39:1256-1260.

Benn Torres J, Kittles R, and Stone AC. Mitochondrial and Y chromosome diversity in the English-speaking Caribbean. Annals of Human Genetics 71:782-90

Parker-Katiraee L, Carson AR, Yamada, T, Arnaud P, Feil R, Abu-Amero SN, Moore GE, Kaneda M, Perry GH, Stone AC, Lee C, Meguro-Horike M, Sasaki H, Kobayashi K, Scherer SW. Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution. PLOS Genetics, May 4;3(5):e65

Becquet C, Patterson N, Stone A, Przeworski M, and Reich D. Elucidating the population structure of chimpanzees. PLOS Genetics, Apr 20;3(4):e66.

Wilbur AK, Kubatko LS, Feurstein JR,Hurtado AM,Hill KR,and Stone AC. Vitamin D receptor gene polymorphisms and susceptibility M. tuberculosis in Native Paraguayans. Tuberculosis 87:329-337

Clark VJ, Ptak SE, Tiemann I, Qian Y, Coop G, Stone AC, Przeworski M, Arnheim M, and Di Rienzo A, Combining sperm typing and LD analyses reveals differences in selective pressures or recombination rates across human populations. Genetics 175:795-804

 2006

Stone AC and Verrelli BC. Focusing on comparative ape population genetics in the post-genomic age. Current Opinion in Genetics and Development. 16:586-591

Verrelli BC, Tishkoff SA, Stone AC and Touchman JW. Contrasting histories of G6PD molecular evolution and malarial resistance in humans and chimpanzees. Molecular Biology and Evolution. 23:1592-1601.

Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Cáceres AM, Iafrate AJ, Scherer SW, Eichler EE, Lee C, and Stone AC. Hotspots for copy number variation in chimpanzees and humans. Proceedings of the National Academy of Sciences, USA 103:8006-8011.

Wooding S, Bufe B, Grassi C, Howard MT, Stone AC, Vazquez M, Dunn DM, Meyerhof W, Weiss RK, and Bamshad MJ, Convergent evolution of bitter taste sensitivity in humans and chimpanzees. Nature 440:930-934.

Perry GH, Verrelli B, and Stone AC, Molecular evolution of the primate developmental genes MSX1 and PAX9. Molecular Biology and Evolution 23:644-654.

2005

Lewis CM, Tito R, Lizarraga B, and Stone AC, Land, Language, and Loci: MtDNA in Native Americans and the Genetic History of Perú. American Journal of Physical Anthropology. 127: 351-360.

Perry G, Verrelli B, and Stone AC, Comparative analyses reveal a complex history of molecular evolution for human MYH16. Molecular Biology and Evolution 22:379-382.

Wooding S, Stone AC, Dunn DM, Mummidi S, Jorde LB, Weiss RB, Ahuja SK, and Bamshad MJ, A selective sweep in chimpanzee CCR5 and resistance to AIDS. American Journal of Human Genetics 76:291-301.

2003

Ramenofsky AF, Wilbur AK and Stone AC, Native American disease history: past, present, future directions. World Archaeology 35:241-257.

Pearson OM and Stone AC, On the diffusion-wave model for the spread of modern humans. Current Anthropology 44:559-561

Hofkin BV, Wright A, Brown J, Miller RD, Rassmann K, Snell H, Stone AC and Snell H, Ancient DNA gives green light to repatriation of Galápagos Iguanas. Conservation Genetics 4:105-108.

2002

Monsalve MC, Stone AC, Lewis CM, Rempel A, Richards M, Straathof D, and Devine DV, Molecular analysis of 550 year old human remains found in a glacier in Canada. American Journal of Physical Anthropology. 119:288-291

Bamshad M, Mummidi S, Gonzalez E, Ahuja SS, Dunn DM, Stone AC, Jorde LB, Ahuja SK, Weiss RB, Evidence of balancing selection in the 5’ cis-regulatory region of CCR5. Proceedings of the National Academy of Sciences, USA 99:10539-10544

Stone AC, Griffiths RC, Zegura SL and Hammer M, High levels of Y-chromosome nucleotide diversity in the genus Pan troglodytes. Proceedings of the National Academy of Sciences, USA 99:43-48.

2001

Stone AC, Starrs JE and Stoneking M, Mitochondrial DNA analysis of the presumptive remains of Jesse James. Journal of Forensic Sciences 46:173-176.

1999

Stone AC and Stoneking M, Analysis of ancient DNA from a prehistoric Amerindian cemetery. Philosophical Transactions of the Royal Society, London, series B 354:153-159.

1998

Stone AC and Stoneking M, MtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World. American Journal of Human Genetics 62(5):1153-1170.

1997

Krings M, Stone AC, Schmitz RW, Krainitzki H, Stoneking M and Pääbo S, Neandertal DNA sequences and the origin of modern humans. Cell 90(1):19-30.

1996

Stone AC and Stoneking M, Genetic analyses of an 8000 year-old Native American skeleton. Ancient Biomolecules 1:83-87.

Stone AC, Milner GR, Pääbo S and Stoneking M, Sex determination of ancient human skeletons using DNA. American Journal of Physical Anthropology 99:231-238.

1994

Handt O, Richards M, Trommsdorf M, Kilger C, Simanainen J, Georgiev O, Bauer K, Stone A, Hedges R, Schaffner W, Utermann G, Sykes B, and Pääbo S, Molecular genetic analyses of the Tyrolean Ice Man. Science 264:1775-1778.

1993

Stone AC and Stoneking M, Ancient DNA from a Pre-Columbian Amerindian population. American Journal of Physical Anthropology 92:463-471.