Anne Stone

(selected)

• Vågene, ÅJ, Honap TP, Harkins KM, Rosenberg MS, Griffen K, Cárdenas-Arroyo F, Leguizamón LP, Arnett J, Buikstra JE, Herbig A, Krause J, Stone AC, and Bos KI, Geographically dispersed zoonotic tuberculosis in pre-contact New World human populations. Nature Communications 13: 1195 doi.org/10.1038/s41467-022-28562-8 (2022)

• Emery MV, Bolhofner K, Ghafoor S, Winingear S, Buikstra JE, Fulginiti LC, and Stone AC. Whole mitochondrial genomes assembled from thermally altered forensic bones and teeth. Forensic Science International: Genetics 102610, doi: 10.1016/j.fsigen.2021.102610 (2022)

• Orlando L, Allaby R, Skoglund P, Der Sarkissian C, Stockhammer PW, Avila-Arcos MC, Fu Q, Krause J, Willerslev E, Stone AC, Warinner C. Ancient DNA Analyses, Nature Reviews Methods Primers 1:14 doi.org/10.1038/s43586-020-00011 (2021)

• Perri AR, Mitchell KJ, Mouton A, Alvarez Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Bover P, Brace S, Carmagnini A, Caroe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heinger H, Helgen K, Kapp J,  Linderholm A, Ozga AT, Presslee S, Salis A, Saremi NF, Shew C, Skerry K, Thompson M, Collins MJ, Sinding M-HS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A and Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature 591(7848):87-91 doi: 10.1038/s41586-020-03082-x (2021)

• Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Li Y, Hahn BH, and Stone AC. Urine as a high-quality source of host genomic DNA from wild Populations. Molecular Ecology Resources Jan;21(1):170-182. doi: 10.1111/1755-0998 (2021)

• Morales-Arce AY, Sabin SJ, Stone AC, and Jensen JD. Population genomics of within-host Mycobacterium tuberculois. Heredity 126(1):1-9. doi: 10.1038/s41437-020-00377-7 (2021)

• Stone AC, Lewis CM, and Schuenemann VJ. Insights into health and disease from ancient biomolecules. Philosophical Transactions of the Royal Society, series B, 375(1812):20190568. doi: 10.1098/rstb.2019.0568.(2020)

• Blevins KE, Crane A, Lum C, Furuta K, Fox K, and Stone AC. Evolutionary history of Mycobacterium leprae in the Pacific Islands. Philosophical Transactions of the Royal Society, series B, 375(1812):20190582 c (2020)

• Wagner JK, Colwell C, Claw KG, Stone AC, Bolnick DA, Hawks J, Brothers KB and Garrison NA. ASHG Guidance: Fostering responsible research on ancient DNA. American Journal of Human Genetics 107:183-195, doi: 10.1016/j.ajhg.2020.06.017 (2020)

• Baker BJ, Crane-Kramer G, Dee MW, Gregoricka LA, Henneberg M, Lee C, Lukehart SA, Mabey DC, Roberts CA, Stodder AL, Stone AC and Winingear S Advancing the Understanding of Treponemal Disease in the Past and Present. Yearbook of Physical Anthropology 1-37, doi: 10.1002/ajpa.23988 (2020)

• Nieves-Colón, MA, Pestle WJ, Reynolds AW, Llamas B, de la Fuente C, Fowler K, Skerry K, Crespo-Torres E, Bustamante CD and Stone AC, Reconstructing the diversity and genetic legacies of pre-contact communities in Puerto Rico through ancient DNA analysis. Molecular Biology and Evolution 37:(3) 611-626 doi:10.1093/molbev/msz267 (2020)

• Ozga AT, Gilby I, Nockerts RS, Wilson MA, Pusey A, and Stone AC. Oral microbiome diversity in chimpanzees from Gombe National Park. Scientific Reports 9:17354 doi.org/10.1038/s41598-019-53802-1 (2019)

• Crane A, Goebel M, Kraberger, Stone AC, and Varsani A. Novel anelloviruses identified in buccal swab samples of Antarctic fur seals. Virus Genes doi: 10.1007/s11262-018-1585-9 (2018)

• Mann AE, Sabin S, Ziesemer K, Vågene AJ, Schroeder H, Ozga AT, Sankaranarayanan K, Hofman CA, Fellows Yates J, Salazar Garcia D, Frohlich B, Aldenderfer M, Hoogland M, Read C, Milner G, Stone AC, Lewis CM, Krause J, Hofman C, Bos K, and Warinner C. Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports 8(1):9822. doi: 10.1038/s41598-018-28091-9 (2018)

• Nieves-Colón MA, Ozga AT, Pestle WJ, Cucina A, Tiesler V, Stanton TW, and Stone AC. Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments. American Journal of Physical Anthropology. doi: 10.1002/ajpa.23472 (2018)

• Housman G, Havill LM, Quillen EE, Comuzzie, AG and Stone AC. Assessment of DNA methylation patterns in the bone and cartilage of a nonhuman primate model of osteoarthritis. Cartilage Feb 1:1947603518759173. doi: 10.1177/1947603518759173 (2018)

• Honap TP, Pfister L-A, Housman G, Mills S, Tarara RP, Suzuki K, Cuozzo FP, Sauther ML, Rosenberg MS, and Stone AC. Mycobacterium leprae genomes from naturally infected nonhuman primates. PLoS Neglected Tropical Diseases Jan 30; 12(1):e0006190. doi: 10.1371/journal.pntd.0006190. (2018)

• Benjak A, Honap TP, Avanzi C, Becerril-Villanueva LE, Rojas-Espinosa O, Stone AC and Cole ST. Insights from the genome sequence of Mycobacterium lepraemurium: massive gene decay and reductive evolution. mBio Oct 17;8(5). doi: 10.1128/mBio.01283-17.(2017)

• Ritzman TB, Banovich N, Buss KP, Guida J, Rubel M, Pinney J, Khang B, Ravosa MJ, and Stone AC. Facing the facts: Changes in the Runx2 gene modulates facial morphology in primates. Journal of Human Evolution 111:139-151 (2017).

• Malukiewicz J, Grativol A, Ruiz-Miranda CR, and Stone AC Application of PE-RADSeq Genome Scans to the Study of Genomic Diversity and Divergence in two Brazilian marmoset species (Callithrix jacchus and C. penicillata). American Journal of Primatology 79(2):1-12. doi: 10.1002/ajp.22587 (2017)

• Malukiewicz J, Hepp CM, Guschanski K, and Stone AC. Complete mitochondrial genomes resolve the phylogeny of the jacchus group of Callithrix marmosets. American Journal of Physical Anthropology. Jan;162(1):157-169. doi: 10.1002/ajpa.23105. (2017)

• 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. doi: 10.1002/ajpa.22960 (2016)

• Harkins KM, Schwartz RS, Cartwright RA and Stone AC, Phylogenomic reconstruction supports supercontinent origins for Leishmania. Infection, Genetics and Evolution 38:101-109. (2016)

• 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. (2015)

• Housman G, Boere V, Gravitol AD, Malukiewicz J, Pereira LC 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 (2015)

• 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 (2015)

• Harkins K and Stone AC. Ancient pathogen genomics: insights into timing and adaptation. Journal of Human Evolution 79:137-149 (2015)

• 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. (2015)

• 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 (2014)

• 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 (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. Stone, and Krause J. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature (2014).

• 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 (2014).
• Benn Torres J, Stone AC, and Kittles R. An Anthropological Genetic Perspective on Creolization in the Anglophone Caribbean. The American Journal of Physical Anthropology (2013).
• 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 (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 (2012).
• 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 (2010).
• 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 (2010).
• Stone AC, Battistuzzi F, Kubatko LS, Perry GH, Trudeau E, Lin H, and Kumar S. Analysis of complete mtDNA sequences in Pan. Proceedings of the Royal Society, Series B (2010).
• 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 (2008).
• Verrelli BC, Stone AC, and Lewis CM. Different Selective Pressures Shape the Molecular Evolution of Color Vision in Human and Chimpanzee Populations. Molecular Biology and Evolution (2008).
• A. Wilbur, L. Kubatko, J. Feurstein, Ana Hurtado, Kim Hill, Anne Stone. Vitamin D receptor gene polymorphisms and susceptibility M. tuberculosis in Native Paraguayans. Tuberculosis (2007).
• C. Becquet, N. Patterson, Anne Stone, M. Przeworski, D. Reich. Elucidating the population structure of chimpanzees. PLOS Genetics (2007).
• C. Lewis, A. Cáceres, Anne Stone, B. Lizarraga, R. Tito, P. Lopez, G. Iannacone, A. Medina, R. Marinez, S. Polo, F. de la Cruz. Mitochondrial DNA and the peopling of South America. Human Biology (2007).
• C. Lewis, Jane Buikstra, Anne Stone. Ancient DNA and genetic continuity in the south central Andes. Latin American Antiquity (2007).
• G. Perry, Anne Stone, N. Dominy, K. Claw, A. Lee, J. Werner, F. Villanea, Rajeev Misra, R. Misra, C. Lee. Diet and the evolution of amylase gene copy number variation among human populations. Nature Genetics (2007).
• J. Benn Torres, R. Kittles, Anne Stone. Mitochondrial and Y chromosome diversity in the English-speaking Caribbean. Annals of Human Genetics (2007).
• G Perry, Brian Verrelli, Anne Stone. Molecular evolution of the primate developmental genes MSX1 and PAX9. Molecular Biology and Evolution (2006).
• G Perry, C Lee, Anne Stone, J Tchinda, S McGrath, J Zhang, S Picker, A Cáceres, A Iafrate, S Scherer, E Eichler. Hotspots for copy number variation in chimpanzees and humans. Proceedings of the National Academy of Sciences, USA (2006).
• S Wooding, M Bamshad, B Bufe, C Grassi, M Howard, Anne Stone, M Vazquez, D Dunn, W Meyerhof, R Weiss. Convergent evolution of bitter taste sensitivity in humans and chimpanzees. Nature (2006).
• C Lewis, R Tito, B Lizarraga, Anne Stone. Land, Language, and Loci: MtDNA in Native Americans and the Genetic History of Perú. American Journal of Physical Anthropology (2005).
• G Perry, Brian Verrelli, Anne Stone. Comparative analyses reveal a complex history of molecular evolution for human MYH16. Molecular Biology and Evolution (2005).
• S Wooding, Anne Stone, D Dunn, S Mummidi, L Jorde, R Weiss, S Ahuja, M Bamshad. A selective sweep in chimpanzee CCR5 and resistance to AIDS. American Journal of Human Genetics (2005).
• A Ramenofsky, A Wilbur, Anne Stone. Native American disease history: past, present, future directions. World Archaeology (2003).
• B Hofkin, A Wright, J Brown, R Miller, K Rassmann, H Snell, Anne Stone, H Snell. Ancient DNA gives green light to repatriation of Galápagos Iguanas. Conservation Genetics (2003).
• Anne Stone, R Griffiths, S Zegura, M Hammer. High levels of Y-chromosome nucleotide diversity in the genus Pan troglodytes. Proceedings of the National Academy of Sciences, USA (2002).
• M Bamshad, S Mummidi, E Gonzalez, S Ahuja, D Dunn, Anne Stone, L Jorde, S Ahuja, R Weiss. Evidence of balancing selection in the 5' cis-regulatory region of CCR5. Proceedings of the National Academy of Sciences, USA (2002).

• 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 (1998).

• 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.

• 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 (1994).