2024

Cooke NP, Murray M, Cassidy LM, Mattiangeli V, Okazaki K, Kasai K, Gakuhari T, Bradley DG, Nakagome S. Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan. iScience. 2024 May 21;27(6):110050. PMID: 38883821

Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, ...Orlando L. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature. 2024 Jul;631(8022):819-825. PMID: 38843826

Bagnasco G, Marzullo M, Cattaneo C, Biehler-Gomez L, Mazzarelli D, Ricciardi V, Müller W, Coppa A, McLaughlin R, Motta L, Prato O, Schmidt F, Gaveriaux F, Marras GB, Millet MA, Madgwick R, Ballantyne R, Makarewicz CA, Trentacoste A, Reimer P, Mattiangeli V, Bradley DG, Malone C, Esposito C, Breslin EM, Stoddart S. Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth-seventh century BC, central Italy). Sci Rep. 2024 May 28;14(1):11895. PMID: 38806487

Sandoval-Castellanos E, Hare AJ, Lin AT, Dimopoulos EA, Daly KG, Geiger S, Mullin VE, Wiechmann I, Mattiangeli V, Lühken G, Zinovieva NA, Zidarov P, Çakırlar C, Stoddart S, Orton D, Bulatović J, Mashkour M, Sauer EW, Horwitz LK, Horejs B, Atici L, Özkaya V, Mullville J, Parker Pearson M, Mainland I, Card N, Brown L, Sharples N, Griffiths D, Allen D, Arbuckle B, Abell JT, Duru G, Mentzer SM, Munro ND, Uzdurum M, Gülçur S, Buitenhuis H, Gladyr E, Stiner MC, Pöllath N, Özbaşaran M, Krebs S, Burger J, Frantz L, Medugorac I, Bradley DG, Peters J. Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries). Sci Adv. 2024 Apr 12;10(15) PMID: 38608027

Martiniano R, Haber M, Almarri MA, Mattiangeli V, Kuijpers MCM, Chamel B, Breslin EM, Littleton J, Almahari S, Aloraifi F, Bradley DG, Lombard P, Durbin R. Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. Cell Genom. 2024 Mar 13;4(3):100507. PMID: 3841744

2023

Cooke NP, Mattiangeli V, Cassidy LM, Okazaki K, Kasai K, Bradley DG, Gakuhari T, Nakagome S. Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands. Evol Hum Sci. 2023 Jul 10;5:e23. PMID: 37587935

Jackson I, Mattiangeli V, Cassidy LM, Murphy E, Bradley DG. Millennium-old pathogenic Mendelian mutation discovery for multiple osteochondromas from a Gaelic Medieval graveyard. Eur J Hum Genet. 2023 Feb;31(2):248-251. PMID: 36443465

2022

Daly KG, Arbuckle BS, Rossi C, Mattiangeli V, Lawlor PA, Mashkour M, Sauer E, Lesur J, Atici L, Erek CM, Bradley DG. A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics. Elife. 2022 Oct 3;11 PMID: 36190761

Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Telles Antunes M, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Öztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, Orlando L. The genomic history and global expansion of domestic donkeys. Science. 2022 Sep 9;377(6611):1172-1180. PMID: 36074859

Erven JAM, Çakirlar C, Bradley DG, Raemaekers DCM, Madsen O. Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel. Front Genet. 2022 Jul 12;13:872486. PMID: 35903348

Ward JA, McHugo GP, Dover MJ, Hall TJ, Ng'ang'a SI, Sonstegard TS, Bradley DG, Frantz LAF, Salter-Townshend M, MacHugh DE. Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations. iScience. 2022 Jun 26;25(7):104672. PMID: 35832892

VarGoats Consortium; Nijman IJ, Rosen BD, Bardou P, Faraut T, Cumer T, Daly KG, Zheng Z, Cai Y, Asadollahpour H, Kul BÇ, Zhang WY, E G, Ayin A, Baird H, Bakhtin M, Bâlteanu VA, Barfield D, Berger B, Blichfeldt T, Boink G, Bugiwati SRA, Cai Z, Carolan S, Clark E, Cubric-Curik V, Dagong MIA, Dorji T, Drew L, Guo J, Hallsson J, Horvat S, Kantanen J, Kawaguchi F, Kazymbet P, Khayatzadeh N, Kim N, Shah MK, Liao Y, Martínez A, Masangkay JS, Masaoka M, Mazza R, McEwan J, Milanesi M, Omar FM, Nomura Y, Ouchene-Khelifi NA, Pereira F, Sahana G, Salavati M, Sasazaki S, Da Silva A, Simčič M, Sölkner J, Sutherland A, Tigchelaar J, Zhang H; Econogene Consortium; Ajmone-Marsan P, Bradley DG, Colli L, Drögemüller C, Jiang Y, Lei C, Mannen H, Pompanon F, Tosser-Klopp G, Lenstra JA. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions. Mol Ecol. 2022 Aug;31(16):4364-4380. PMID: 35751552

Ariano B, Mattiangeli V, Breslin EM, Parkinson EW, McLaughlin TR, Thompson JE, Power RK, Stock JT, Mercieca-Spiteri B, Stoddart S, Malone C, Gopalakrishnan S, Cassidy LM, Bradley DG. Ancient Maltese genomes and the genetic geography of Neolithic Europe. Curr Biol. 2022 Jun 20;32(12) PMID: 35588742

Dulias K, Foody MGB, Justeau P, Silva M, Martiniano R, Oteo-García G, Fichera A, Rodrigues S, Gandini F, Meynert A, Donnelly K, Aitman TJ; Scottish Genomes Partnership, Chamberlain A, Lelong O, Kozikowski G, Powlesland D, Waddington C, Mattiangeli V, Bradley DG, Bryk J, Soares P, Wilson JF, Wilson G, Moore H, Pala M, Edwards CJ, Richards MB. Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney. Proc Natl Acad Sci U S A. 2022 Feb 22;119(8) PMID: 35131896

Bradley DG. Bronze Age genomes reveal migration to Britain. Nature. 2022 Jan;601(7894):512-513. PMID: 34937885

2021

Sinding M-H, Ciucani M, Ramos-Madrigal J,Carmagnini A, RasmussenJA, Feng S, Chen G, Vieira FG, Mattiangeli V, Rajinder K.Ganjo RK, Larson G, Sicheritz-Pontén T, Petersen B, Frantz L, Gilbert MTP, Bradley DG Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos IScience 2021 Oct 6: 103226 PMID: 103226

Cooke NP, Mattiangeli V, Cassidy LM, Okazaki K, Stokes CA, Onbe S, Hatakeyama S, Machida K, Kasai K, Tomioka N, Matsumoto A, Ito M, Kojima Y, Bradley DG, Gakuhari T, Nakagome S. Ancient genomics reveals tripartite origins of Japanese populations. Sci Adv. 2021 Sep 17;7(38) PMID: 34533991

Rossi C, Ruß-Popa G, Mattiangeli V, McDaid F, Hare AJ, Davoudi H, Laleh H, Lorzadeh Z, Khazaeli R, Fathi H, Teasdale MD, A'ali A, Stöllner T, Mashkour M, Daly KG. Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrabad, Iran. Biol Lett. 2021 Jul;17(7) PMID: 34256582 https://pubmed.ncbi.nlm.nih.gov/34256582/

Daly KG, Mattiangeli V, Hare AJ, Davoudi H, Fathi H, Doost SB, Amiri S, Khazaeli R, Decruyenaere D, Nokandeh J, Richter T, Darabi H, Mortensen P, Pantos A, Yeomans L, Bangsgaard P, Mashkour M, Zeder MA, Bradley DG. Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains. Proc Natl Acad Sci U S A. 2021 Jun 22;118(25) . PMID: 34099576 Free PMC article.

Rey-Iglesia A, Lister AM, Campos PF, Brace S, Mattiangeli V, Daly KG, Teasdale MD, Bradley DG, Barnes I, Hansen AJ. Exploring the phylogeography and population dynamics of the giant deer (Megaloceros giganteus) using Late Quaternary mitogenomes. Proc Biol Sci. 2021 May 12;288(1950) PMID: 33977786

Frantz LAF, Bradley DG, Larson G, Orlando L. Animal domestication in the era of ancient genomics. Nat Rev Genet. 2020 Aug;21(8):449-460. PMID: 32265525

2020

Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Bus MM, de Barros Damgaard P, Martiniano R, Renaud G, Bhérer C, Moreno-Mayar JV, Fotakis AK, Allen M, Allmäe R, Molak M, Cappellini E, Scorrano G, McColl H, Buzhilova A, Fox A, Albrechtsen A, Schütz B, Skar B, Arcini C, Falys C, Jonson CH, Blaszczyk D, Pezhemsky D, Turner-Walker G, Gestsdóttir H, Lundstrøm I, Gustin I, Mainland I, Potekhina I, Muntoni IM, Cheng J, Stenderup J, Ma J, Gibson J, Peets J, Gustafsson J, Iversen KH, Simpson L, Strand L, Loe L, Sikora M, Florek M, Vretemark M, Redknap M, Bajka M, Pushkina T, Søvsø M, Grigoreva N, Christensen T, Kastholm O, Uldum O, Favia P, Holck P, Sten S, Arge SV, Ellingvåg S, Moiseyev V, Bogdanowicz W, Magnusson Y, Orlando L, Pentz P, Jessen MD, Pedersen A, Collard M, Bradley DG, Jørkov ML, Arneborg J, Lynnerup N, Price N, Gilbert MTP, Allentoft ME, Bill J, Sindbæk SM, Hedeager L, Kristiansen K, Nielsen R, Werge T, Willerslev E. Population genomics of the Viking world. Nature. 2020 Sep;585(7825):390-396. PMID: 32939067

Kontopoulos I, Penkman K, Mullin VE, Winkelbach L, Unterländer M, Scheu A, Kreutzer S, Hansen HB, Margaryan A, Teasdale MD, Gehlen B, Street M, Lynnerup N, Liritzis I, Sampson A, Papageorgopoulou C, Allentoft ME, Burger J, Bradley DG, Collins MJ. Screening archaeological bone for palaeogenetic and palaeoproteomic studies. PLoS One. 2020 Jun 25;15(6) PMID: 32584871

Cassidy LM, Ó Maoldúin R, Kador T, Lynch A, Jones C, Woodman PC, Murphy E, Ramsey G, Dowd M, Noonan A, Campbell C, Jones ER, Mattiangeli V, Bradley DG. A dynastic elite in monumental Neolithic society. Nature. 2020 Jun;582(7812) PMID: 32555485

Mattiangeli V, Cooke NP, Ó Maoldúin R, Sikora M, Mulhall M, Bradley DG, Teasdale MD. Genomic analysis of Irish bog butter. Journal of Archaeological Science: Reports. Volume 31, June 2020, 102368 102368

Zheng Z, Wang X, Li M, Li Y, Yang Z, Wang X, Pan X, Gong M, Zhang Y, Guo Y, Wang Y, Liu J, Cai Y, Chen Q, Okpeku M, Colli L, Cai D, Wang K, Huang S, Sonstegard TS, Esmailizadeh A, Zhang W, Zhang T, Xu Y, Xu N, Yang Y, Han J, Chen L, Lesur J, Daly KG, Bradley DG, Heller R, Zhang G, Wang W, Chen Y, Jiang Y. The origin of domestication genes in goats. Sci Adv. 2020 May 20;6(21) PMID: 32671210

2019

Frantz LAF, Haile J, Lin AT, Scheu A, Geörg C, Benecke N, Alexander M, Linderholm A, Mullin VE, Daly KG, Battista VM, Price M, Gron KJ, Alexandri P, Arbogast RM, Arbuckle B, B?l??escu A, Barnett R, Bartosiewicz L, Baryshnikov G, Bonsall C, Bori? D, Boronean? A, Bulatovi? J, Çakirlar C, Carretero JM, Chapman J, Church M, Crooijmans R, De Cupere B, Detry C, Dimitrijevic V, Dumitra?cu V, du Plessis , Edwards CJ, Erek CM, Erim-Özdo?an A, Ervynck A, Fulgione D, Gligor M, Götherström A, Gourichon L, Groenen MAM, Helmer D, Hongo H, Horwitz LK, Irving-Pease EK, Lebrasseur O, Lesur J, Malone C, Manaseryan N, Marciniak A, Martlew H, Mashkour M, Matthews R, Matuzeviciute GM, Maziar S, Meijaard E McGovern T, Megens HJ, Miller R, Mohaseb AF, Orschiedt J, Orton D, Papathanasiou A, Pearson MP, Pinhasi R, Radmanovi? D, Ricaut FX, Richards M, Sabin R, Sarti L, Schier W, Sheikhi S, Stephan E, Stewart JR, Stoddart S, Tagliacozzo A, Tasi? N, Trantalidou K, Tresset A, Valdiosera C, van den Hurk Y, Van Poucke S, Vigne JD, Yanevich A, Zeeb-Lanz A, Triantafyllidis A, Gilbert MTP, Schibler J, Rowley-Conwy P, Zeder M, Peters J, Cucchi T, Bradley DG, Dobney K Burger J, Evin A, Girdland-Flink L, Larson G. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe. Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17231-17238. DOI: 10.1073/pnas.1901169116.

Verdugo MP, Mullin VE, Scheu A, Mattiangeli V, Daly KG, Maisano Delser P, Hare AJ, Burger J, Collins MJ, Kehati R, Hesse P, Fulton D, Sauer EW, Mohaseb FA, Davoudi H, Khazaeli R, Lhuillier J, Rapin C, Ebrahimi S, Khasanov M, Vahidi SMF, MacHugh DE, Ertu?rul O, Koukouli-Chrysanthaki C, Sampson A, Kazantzis G, Kontopoulos I, Bulatovic J, Stojanovi? I, Mikdad A, Benecke N, Linstädter J, Sablin M, Bendrey R, Gourichon L, Arbuckle BS, Mashkour M, Orton D, Horwitz LK, Teasdale MD, Bradley DG. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science. 2019 Jul 12;365(6449):173-176. DOI: 10.1126/science.aav1002
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Ring SC, Purfield DC, Good M, Breslin P, Ryan E, Blom A, Evans RD, Doherty ML, Bradley DG, Berry DP. Variance components for bovine tuberculosis infection and multi-breed genome-wide association analysis using imputed whole genome sequence data. PLoS One. 2019 Feb 14;14(2) PMID:30763354

2018

Maixner F, Turaev D, Cazenave-Gassiot A, Janko M, Krause-Kyora B, Hoopmann MR, Kusebauch U, Sartain M, Guerriero G, O'Sullivan N, Teasdale M, Cipollini G, Paladin A, Mattiangeli V, Samadelli M, Tecchiati U, Putzer A, Palazoglu M, Meissen J, Lösch S, Rausch P, Baines JF, Kim BJ, An HJ, Gostner P, Egarter-Vigl E, Malfertheiner P, Keller A, Stark RW, Wenk M, Bishop D, Bradley DG, Fiehn O, Engstrand L, Moritz RL, Doble P, Franke A, Nebel A, Oeggl K, Rattei T, Grimm R, Zink A. The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals Curr Biol. 2018 Jul 23;28(14):2348-2355.e9. PMID:30017480

Daly KG, Maisano Delser P, Mullin VE, Scheu A, Mattiangeli V, Teasdale MD, Hare AJ, Burger J, Verdugo MP, Collins MJ, Kehati R, Erek CM, Bar-Oz G, Pompanon F, Cumer T, Çak?rlar C, Mohaseb AF, Decruyenaere D, Davoudi H, Çevik Ö, Rollefson G, Vigne JD, Khazaeli R, Fathi H, Doost SB, Rahimi Sorkhani R, Vahdati AA, Sauer EW, Azizi Kharanaghi H, Maziar S, Gasparian B, Pinhasi R, Martin L, Orton D, Arbuckle BS, Benecke N, Manica A, Horwitz LK, Mashkour M, Bradley DG. Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science. 2018 Jul 6;361(6397):85-88. PMID:29976826

Chen N, Cai Y, Chen Q, Li R, Wang K, Huang Y, Hu S, Huang S, Zhang H, Zheng Z, Song W, Ma Z, Ma Y, Dang R, Zhang Z, Xu L, Jia Y, Liu S, Yue X, Deng W, Zhang X, Sun Z, Lan X, Han J, Chen H, Bradley DG, Jiang Y, Lei C. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat Commun. 2018 Jun 14;9(1):2337. PMID:29904051

Schroeder H, Sikora M, Gopalakrishnan S, Cassidy LM, Maisano Delser P, Sandoval Velasco M, Schraiber JG, Rasmussen S, Homburger JR, Ávila-Arcos MC, Allentoft ME, Moreno-Mayar JV, Renaud G, Gómez-Carballa A, Laffoon JE, Hopkins RJA, Higham TFG, Carr RS, Schaffer WC, Day JS, Hoogland M, Salas A, Bustamante CD, Nielsen R, Bradley DG, Hofman CL, Willerslev E. Origins and genetic legacies of the Caribbean Taino. Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2341-2346. PMID:29463742

Byrne RP, Martiniano R, Cassidy LM, Carrigan M, Hellenthal G, Hardiman O, Bradley DG, McLaughlin RL. Insular Celtic population structure and genomic footprints of migration. PLoS Genet. 2018 Jan 25;14(1) PMID:29370172

2017

Teasdale, M.D., Fiddyment, S., Vnoucek, J., Mattiangeli, V., Speller, C., Binois, A., Carver, M., Dand, C., Newfield, T.P., Webb, C.C., Bradley, D.G., Collins, M.J. The York Gospels: a one thousand year biological palimpsest. R. Soc. open sci. 4: 170988. DOI: 10.1098/rsos.170988
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Martiniano, R., Cassidy, L.M., Ó'Maoldúin, R., McLaughlin, R., Silva, N.M., Manco, L., Fidalgo, D., Pereira, T., Coelho, M.J., Serra, M., Burger, J., Parreira, R., Moran, E., Valera, A.C., Porfirio, E., Boaventura, R., Silva, A.M., Bradley, D.G. The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods. PLoS Genet. 2017 Jul 27;13(7) PMID 28749934
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McLaughlin, R.L., Schijven, D., van Rheenen, W., van Eijk, K.R., O'Brien, M., Kahn, R.S., Ophoff, R.A., Goris, A., Bradley, D.G., Al-Chalabi, A., van den Berg, L.H., Luykx, J.J., Hardiman, O., Veldink, J.H., Project MinE GWAS Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium. Genetic correlation between amyotrophic lateral sclerosis and schizophrenia. Nat Commun. 2017 Mar 21;8:14774. PMID 28322246

Cassidy, L.M., Teasdale, M.D., Carolan, S., Enright, R., Werner, R., Bradley, D.G., Finlay,E.K., Mattiangeli, V. Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland. Biology Letters 2017 Mar;13(3). PMID:28250207

Jones, E.R., Zarina, G., Moiseyev, V., Lightfoot, E., Nigst, P.R., Manica, A., Pinhasi, R., Bradley, D.G. The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers. Current Biology, 2017 Feb 20;27(4):576-582. doi: 10.1016/j.cub.2016.12.060. PMID28162894

Siska,V., Jones,E.R., Jeon,S., Bhak,Y, Kim,H-M., Cho,Y.S., Kim,H., Lee,K.,Veselovskaya,E.,Balueva,T.,Gallego-Llorente,M., Hofreiter,M., Bradley,D.G., Eriksson,A.,Pinhasi,R.,Bhak,J. and Manica, A. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. Science Advances 01 Feb 2017: Vol. 3, no. 2, e1601877,doi: 10.1126/sciadv.1601877 PMID28164156
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2016