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Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia.

Brucato N, Fernandes V, Kusuma P, Černý V, Mulligan CJ, Soares P, Rito T, Besse C, Boland A, Deleuze JF, Cox MP, Sudoyo H, Stoneking M, Pereira L, Ricaut FX.

Genome Biol Evol. 2019 Mar 1;11(3):748-758. doi: 10.1093/gbe/evz028.


Confinement of Positrons Exceeding 1 s in a Supported Magnetic Dipole Trap.

Horn-Stanja J, Nißl S, Hergenhahn U, Sunn Pedersen T, Saitoh H, Stenson EV, Dickmann M, Hugenschmidt C, Singer M, Stoneking MR, Danielson JR.

Phys Rev Lett. 2018 Dec 7;121(23):235003. doi: 10.1103/PhysRevLett.121.235003.


Lossless Positron Injection into a Magnetic Dipole Trap.

Stenson EV, Nißl S, Hergenhahn U, Horn-Stanja J, Singer M, Saitoh H, Pedersen TS, Danielson JR, Stoneking MR, Dickmann M, Hugenschmidt C.

Phys Rev Lett. 2018 Dec 7;121(23):235005. doi: 10.1103/PhysRevLett.121.235005.


The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola.

Oliveira S, Hübner A, Fehn AM, Aço T, Lages F, Pakendorf B, Stoneking M, Rocha J.

Eur J Hum Genet. 2019 Mar;27(3):475-483. doi: 10.1038/s41431-018-0304-2. Epub 2018 Nov 22.


Genetic structure and sex-biased gene flow in the history of southern African populations.

Bajić V, Barbieri C, Hübner A, Güldemann T, Naumann C, Gerlach L, Berthold F, Nakagawa H, Mpoloka SW, Roewer L, Purps J, Stoneking M, Pakendorf B.

Am J Phys Anthropol. 2018 Nov;167(3):656-671. doi: 10.1002/ajpa.23694. Epub 2018 Sep 7.


Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia.

Arias L, Schröder R, Hübner A, Barreto G, Stoneking M, Pakendorf B.

Mol Biol Evol. 2018 Nov 1;35(11):2719-2735. doi: 10.1093/molbev/msy169.


Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia.

Duong NT, Macholdt E, Ton ND, Arias L, Schröder R, Van Phong N, Thi Bich Thuy V, Ha NH, Thi Thu Hue H, Thi Xuan N, Thi Phuong Oanh K, Hien LTT, Hoang NH, Pakendorf B, Stoneking M, Van Hai N.

Sci Rep. 2018 Aug 3;8(1):11651. doi: 10.1038/s41598-018-29989-0.


Sex-specific differences in the occurrence of Fusobacterium nucleatum subspecies and Fusobacterium periodonticum in the oral cavity.

Henne K, Schilling H, Stoneking M, Conrads G, Horz HP.

Oncotarget. 2018 Apr 17;9(29):20631-20639. doi: 10.18632/oncotarget.25042. eCollection 2018 Apr 17.


Positron-Induced Luminescence.

Stenson EV, Hergenhahn U, Stoneking MR, Pedersen TS.

Phys Rev Lett. 2018 Apr 6;120(14):147401. doi: 10.1103/PhysRevLett.120.147401.


Strong selection during the last millennium for African ancestry in the admixed population of Madagascar.

Pierron D, Heiske M, Razafindrazaka H, Pereda-Loth V, Sanchez J, Alva O, Arachiche A, Boland A, Olaso R, Deleuze JF, Ricaut FX, Rakotoarisoa JA, Radimilahy C, Stoneking M, Letellier T.

Nat Commun. 2018 Mar 2;9(1):932. doi: 10.1038/s41467-018-03342-5.


New insights from Thailand into the maternal genetic history of Mainland Southeast Asia.

Kutanan W, Kampuansai J, Brunelli A, Ghirotto S, Pittayaporn P, Ruangchai S, Schröder R, Macholdt E, Srikummool M, Kangwanpong D, Hübner A, Arias L, Stoneking M.

Eur J Hum Genet. 2018 Jun;26(6):898-911. doi: 10.1038/s41431-018-0113-7. Epub 2018 Feb 26.


Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand.

Kutanan W, Kampuansai J, Changmai P, Flegontov P, Schröder R, Macholdt E, Hübner A, Kangwanpong D, Stoneking M.

Sci Rep. 2018 Jan 24;8(1):1536. doi: 10.1038/s41598-018-20020-0.


Matriclans shape populations: Insights from the Angolan Namib Desert into the maternal genetic history of southern Africa.

Oliveira S, Fehn AM, Aço T, Lages F, Gayà-Vidal M, Pakendorf B, Stoneking M, Rocha J.

Am J Phys Anthropol. 2018 Mar;165(3):518-535. doi: 10.1002/ajpa.23378. Epub 2018 Jan 3.


The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor.

Brucato N, Fernandes V, Mazières S, Kusuma P, Cox MP, Ng'ang'a JW, Omar M, Simeone-Senelle MC, Frassati C, Alshamali F, Fin B, Boland A, Deleuze JF, Stoneking M, Adelaar A, Crowther A, Boivin N, Pereira L, Bailly P, Chiaroni J, Ricaut FX.

Am J Hum Genet. 2018 Jan 4;102(1):58-68. doi: 10.1016/j.ajhg.2017.11.011.


The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data.

Pugach I, Duggan AT, Merriwether DA, Friedlaender FR, Friedlaender JS, Stoneking M.

Mol Biol Evol. 2018 Apr 1;35(4):871-886. doi: 10.1093/molbev/msx333.


Enclaves of genetic diversity resisted Inca impacts on population history.

Barbieri C, Sandoval JR, Valqui J, Shimelman A, Ziemendorff S, Schröder R, Geppert M, Roewer L, Gray R, Stoneking M, Fujita R, Heggarty P.

Sci Rep. 2017 Dec 12;7(1):17411. doi: 10.1038/s41598-017-17728-w.


High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia.

Arias L, Barbieri C, Barreto G, Stoneking M, Pakendorf B.

Am J Phys Anthropol. 2018 Feb;165(2):238-255. doi: 10.1002/ajpa.23345. Epub 2017 Oct 27.


Unraveling the human salivary microbiome diversity in Indian populations.

Sarkar A, Stoneking M, Nandineni MR.

PLoS One. 2017 Sep 8;12(9):e0184515. doi: 10.1371/journal.pone.0184515. eCollection 2017.


Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture.

Jinam TA, Phipps ME, Aghakhanian F, Majumder PP, Datar F, Stoneking M, Sawai H, Nishida N, Tokunaga K, Kawamura S, Omoto K, Saitou N.

Genome Biol Evol. 2017 Aug 1;9(8):2013-2022. doi: 10.1093/gbe/evx118.


Genomic landscape of human diversity across Madagascar.

Pierron D, Heiske M, Razafindrazaka H, Rakoto I, Rabetokotany N, Ravololomanga B, Rakotozafy LM, Rakotomalala MM, Razafiarivony M, Rasoarifetra B, Raharijesy MA, Razafindralambo L, Ramilisonina, Fanony F, Lejamble S, Thomas O, Mohamed Abdallah A, Rocher C, Arachiche A, Tonaso L, Pereda-Loth V, Schiavinato S, Brucato N, Ricaut FX, Kusuma P, Sudoyo H, Ni S, Boland A, Deleuze JF, Beaujard P, Grange P, Adelaar S, Stoneking M, Rakotoarisoa JA, Radimilahy C, Letellier T.

Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):E6498-E6506. doi: 10.1073/pnas.1704906114. Epub 2017 Jul 17.


Erratum to: Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages.

Kutanan W, Kampuansai J, Srikummool M, Kangwanpong D, Ghirotto S, Brunelli A, Stoneking M.

Hum Genet. 2017 Jun;136(6):803. doi: 10.1007/s00439-017-1780-0. No abstract available.


Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages.

Kutanan W, Kampuansai J, Srikummool M, Kangwanpong D, Ghirotto S, Brunelli A, Stoneking M.

Hum Genet. 2017 Jan;136(1):85-98. doi: 10.1007/s00439-016-1742-y. Epub 2016 Nov 11. Erratum in: Hum Genet. 2017 Jun;136(6):803.


A genomic history of Aboriginal Australia.

Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peischl S, Rasmussen S, Schiffels S, Subramanian S, Wright JL, Albrechtsen A, Barbieri C, Dupanloup I, Eriksson A, Margaryan A, Moltke I, Pugach I, Korneliussen TS, Levkivskyi IP, Moreno-Mayar JV, Ni S, Racimo F, Sikora M, Xue Y, Aghakhanian FA, Brucato N, Brunak S, Campos PF, Clark W, Ellingvåg S, Fourmile G, Gerbault P, Injie D, Koki G, Leavesley M, Logan B, Lynch A, Matisoo-Smith EA, McAllister PJ, Mentzer AJ, Metspalu M, Migliano AB, Murgha L, Phipps ME, Pomat W, Reynolds D, Ricaut FX, Siba P, Thomas MG, Wales T, Wall CM, Oppenheimer SJ, Tyler-Smith C, Durbin R, Dortch J, Manica A, Schierup MH, Foley RA, Lahr MM, Bowern C, Wall JD, Mailund T, Stoneking M, Nielsen R, Sandhu MS, Excoffier L, Lambert DM, Willerslev E.

Nature. 2016 Oct 13;538(7624):207-214. doi: 10.1038/nature18299. Epub 2016 Sep 21.


Refining the Y chromosome phylogeny with southern African sequences.

Barbieri C, Hübner A, Macholdt E, Ni S, Lippold S, Schröder R, Mpoloka SW, Purps J, Roewer L, Stoneking M, Pakendorf B.

Hum Genet. 2016 May;135(5):541-553. doi: 10.1007/s00439-016-1651-0. Epub 2016 Apr 4.


The Complex Admixture History and Recent Southern Origins of Siberian Populations.

Pugach I, Matveev R, Spitsyn V, Makarov S, Novgorodov I, Osakovsky V, Stoneking M, Pakendorf B.

Mol Biol Evol. 2016 Jul;33(7):1777-95. doi: 10.1093/molbev/msw055. Epub 2016 Mar 18.


Age-Related and Heteroplasmy-Related Variation in Human mtDNA Copy Number.

Wachsmuth M, Hübner A, Li M, Madea B, Stoneking M.

PLoS Genet. 2016 Mar 15;12(3):e1005939. doi: 10.1371/journal.pgen.1005939. eCollection 2016 Mar.


Improvement in detection of minor alleles in next generation sequencing by base quality recalibration.

Ni S, Stoneking M.

BMC Genomics. 2016 Feb 27;17:139. doi: 10.1186/s12864-016-2463-2.


Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck.

Li M, Rothwell R, Vermaat M, Wachsmuth M, Schröder R, Laros JF, van Oven M, de Bakker PI, Bovenberg JA, van Duijn CM, van Ommen GJ, Slagboom PE, Swertz MA, Wijmenga C; Genome of Netherlands Consortium, Kayser M, Boomsma DI, Zöllner S, de Knijff P, Stoneking M.

Genome Res. 2016 Apr;26(4):417-26. doi: 10.1101/gr.203216.115. Epub 2016 Feb 25.


Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver.

Engelken J, Espadas G, Mancuso FM, Bonet N, Scherr AL, Jímenez-Álvarez V, Codina-Solà M, Medina-Stacey D, Spataro N, Stoneking M, Calafell F, Sabidó E, Bosch E.

Mol Biol Evol. 2016 Mar;33(3):738-54. doi: 10.1093/molbev/msv267. Epub 2015 Nov 17.


A founder effect for p47(phox)Trp193Ter chronic granulomatous disease in Kavkazi Jews.

de Boer M, Tzur S, van Leeuwen K, Dencher PC, Skorecki K, Wolach B, Gavrieli R, Nasidze I, Stoneking M, Tanck MW, Roos D.

Blood Cells Mol Dis. 2015 Dec;55(4):320-7. doi: 10.1016/j.bcmd.2015.07.014. Epub 2015 Jul 23.


Denisovan Ancestry in East Eurasian and Native American Populations.

Qin P, Stoneking M.

Mol Biol Evol. 2015 Oct;32(10):2665-74. doi: 10.1093/molbev/msv141. Epub 2015 Jun 23.


A novel candidate region for genetic adaptation to high altitude in Andean populations.

Valverde G, Zhou H, Lippold S, de Filippo C, Tang K, López Herráez D, Li J, Stoneking M.

PLoS One. 2015 May 11;10(5):e0125444. doi: 10.1371/journal.pone.0125444. eCollection 2015.


Evaluating intra- and inter-individual variation in the human placental transcriptome.

Hughes DA, Kircher M, He Z, Guo S, Fairbrother GL, Moreno CS, Khaitovich P, Stoneking M.

Genome Biol. 2015 Mar 19;16:54. doi: 10.1186/s13059-015-0627-z.


Genome-wide insights into the genetic history of human populations.

Pugach I, Stoneking M.

Investig Genet. 2015 Apr 1;6:6. doi: 10.1186/s13323-015-0024-0. eCollection 2015.


Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations.

Li M, Schröder R, Ni S, Madea B, Stoneking M.

Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2491-6. doi: 10.1073/pnas.1419651112. Epub 2015 Feb 9.


Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa.

Li J, Quinque D, Horz HP, Li M, Rzhetskaya M, Raff JA, Hayes MG, Stoneking M.

BMC Microbiol. 2014 Dec 17;14:316. doi: 10.1186/s12866-014-0316-1.


Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.

Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PL, Li M, Reis S, Bernardo DV, DeGiorgio M, Duggan AT, Bastos M, Wang Y, Stenderup J, Moreno-Mayar JV, Brunak S, Sicheritz-Ponten T, Hodges E, Hannon GJ, Orlando L, Price TD, Jensen JD, Nielsen R, Heinemeier J, Olsen J, Rodrigues-Carvalho C, Lahr MM, Neves WA, Kayser M, Higham T, Stoneking M, Pena SD, Willerslev E.

Curr Biol. 2014 Nov 3;24(21):R1035-7. doi: 10.1016/j.cub.2014.09.078. Epub 2014 Oct 23.


New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa.

Macholdt E, Slatkin M, Pakendorf B, Stoneking M.

Am J Phys Anthropol. 2015 Apr;156(4):661-4. doi: 10.1002/ajpa.22675. Epub 2014 Dec 2. Erratum in: Am J Phys Anthropol. 2015 Sep;158(1):172.


Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.

Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schröder R, Stoneking M.

Investig Genet. 2014 Sep 24;5:13. doi: 10.1186/2041-2223-5-13. eCollection 2014.


Variation and signatures of selection on the human face.

Guo J, Tan J, Yang Y, Zhou H, Hu S, Hashan A, Bahaxar N, Xu S, Weaver TD, Jin L, Stoneking M, Tang K.

J Hum Evol. 2014 Oct;75:143-52. doi: 10.1016/j.jhevol.2014.08.001. Epub 2014 Sep 1.


Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies.

Henne K, Li J, Stoneking M, Kessler O, Schilling H, Sonanini A, Conrads G, Horz HP.

BMC Evol Biol. 2014 Aug 22;14:190. doi: 10.1186/s12862-014-0190-3.


Recent developments in the genetic history of East Asia and Oceania.

Duggan AT, Stoneking M.

Curr Opin Genet Dev. 2014 Dec;29:9-14. doi: 10.1016/j.gde.2014.06.010. Epub 2014 Aug 23. Review.


Reconstructing Austronesian population history in Island Southeast Asia.

Lipson M, Loh PR, Patterson N, Moorjani P, Ko YC, Stoneking M, Berger B, Reich D.

Nat Commun. 2014 Aug 19;5:4689. doi: 10.1038/ncomms5689.


Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing.

Giuliani C, Barbieri C, Li M, Bucci L, Monti D, Passarino G, Luiselli D, Franceschi C, Stoneking M, Garagnani P.

Aging (Albany NY). 2014 Jun;6(6):454-67.


Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa.

Barbieri C, Vicente M, Oliveira S, Bostoen K, Rocha J, Stoneking M, Pakendorf B.

PLoS One. 2014 Jun 5;9(6):e99117. doi: 10.1371/journal.pone.0099117. eCollection 2014.


Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion.

Duggan AT, Evans B, Friedlaender FR, Friedlaender JS, Koki G, Merriwether DA, Kayser M, Stoneking M.

Am J Hum Genet. 2014 May 1;94(5):721-33. doi: 10.1016/j.ajhg.2014.03.014. Epub 2014 Apr 10.


Tracing pastoralist migrations to southern Africa with lactase persistence alleles.

Macholdt E, Lede V, Barbieri C, Mpoloka SW, Chen H, Slatkin M, Pakendorf B, Stoneking M.

Curr Biol. 2014 Apr 14;24(8):875-9. doi: 10.1016/j.cub.2014.03.027. Epub 2014 Apr 3.


Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea.

van Oven M, Brauer S, Choi Y, Ensing J, Schiefenhövel W, Stoneking M, Kayser M.

Eur J Hum Genet. 2014 Dec;22(12):1393-403. doi: 10.1038/ejhg.2014.38. Epub 2014 Mar 12.


Early Austronesians: into and out of Taiwan.

Ko AM, Chen CY, Fu Q, Delfin F, Li M, Chiu HL, Stoneking M, Ko YC.

Am J Hum Genet. 2014 Mar 6;94(3):426-36. doi: 10.1016/j.ajhg.2014.02.003.


Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa.

Engelken J, Carnero-Montoro E, Pybus M, Andrews GK, Lalueza-Fox C, Comas D, Sekler I, de la Rasilla M, Rosas A, Stoneking M, Valverde MA, Vicente R, Bosch E.

PLoS Genet. 2014 Feb 20;10(2):e1004128. doi: 10.1371/journal.pgen.1004128. eCollection 2014 Feb.

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