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JOURNAL ARTICLE
Benet Oriol Sabat, Daniel Mas Montserrat, Xavier Giro-I-Nieto, Alexander G Ioannidis
MOTIVATION: Local ancestry inference (LAI) is the high resolution prediction of ancestry labels along a DNA sequence. LAI is important in the study of human history and migrations, and it is beginning to play a role in precision medicine applications including ancestry-adjusted genome-wide association studies (GWASs) and polygenic risk scores (PRSs). Existing LAI models do not generalize well between species, chromosomes or even ancestry groups, requiring re-training for each different setting...
September 16, 2022: Bioinformatics
#22
JOURNAL ARTICLE
Lara R Arauna, Jacob Bergstedt, Jeremy Choin, Javier Mendoza-Revilla, Christine Harmant, Maguelonne Roux, Alex Mas-Sandoval, Laure Lémée, Heidi Colleran, Alexandre François, Frédérique Valentin, Olivier Cassar, Antoine Gessain, Lluis Quintana-Murci, Etienne Patin
The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands ∼3,000 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity...
September 8, 2022: Current Biology: CB
#23
JOURNAL ARTICLE
Iosif Lazaridis, Songül Alpaslan-Roodenberg, Ayşe Acar, Ayşen Açıkkol, Anagnostis Agelarakis, Levon Aghikyan, Uğur Akyüz, Desislava Andreeva, Gojko Andrijašević, Dragana Antonović, Ian Armit, Alper Atmaca, Pavel Avetisyan, Ahmet İhsan Aytek, Krum Bacvarov, Ruben Badalyan, Stefan Bakardzhiev, Jacqueline Balen, Lorenc Bejko, Rebecca Bernardos, Andreas Bertsatos, Hanifi Biber, Ahmet Bilir, Mario Bodružić, Michelle Bonogofsky, Clive Bonsall, Dušan Borić, Nikola Borovinić, Guillermo Bravo Morante, Katharina Buttinger, Kim Callan, Francesca Candilio, Mario Carić, Olivia Cheronet, Stefan Chohadzhiev, Maria-Eleni Chovalopoulou, Stella Chryssoulaki, Ion Ciobanu, Natalija Čondić, Mihai Constantinescu, Emanuela Cristiani, Brendan J Culleton, Elizabeth Curtis, Jack Davis, Tatiana I Demcenco, Valentin Dergachev, Zafer Derin, Sylvia Deskaj, Seda Devejyan, Vojislav Djordjević, Kellie Sara Duffett Carlson, Laurie R Eccles, Nedko Elenski, Atilla Engin, Nihat Erdoğan, Sabiha Erir-Pazarcı, Daniel M Fernandes, Matthew Ferry, Suzanne Freilich, Alin Frînculeasa, Michael L Galaty, Beatriz Gamarra, Boris Gasparyan, Bisserka Gaydarska, Elif Genç, Timur Gültekin, Serkan Gündüz, Tamás Hajdu, Volker Heyd, Suren Hobosyan, Nelli Hovhannisyan, Iliya Iliev, Lora Iliev, Stanislav Iliev, İlkay İvgin, Ivor Janković, Lence Jovanova, Panagiotis Karkanas, Berna Kavaz-Kındığılı, Esra Hilal Kaya, Denise Keating, Douglas J Kennett, Seda Deniz Kesici, Anahit Khudaverdyan, Krisztián Kiss, Sinan Kılıç, Paul Klostermann, Sinem Kostak Boca Negra Valdes, Saša Kovačević, Marta Krenz-Niedbała, Maja Krznarić Škrivanko, Rovena Kurti, Pasko Kuzman, Ann Marie Lawson, Catalin Lazar, Krassimir Leshtakov, Thomas E Levy, Ioannis Liritzis, Kirsi O Lorentz, Sylwia Łukasik, Matthew Mah, Swapan Mallick, Kirsten Mandl, Kristine Martirosyan-Olshansky, Roger Matthews, Wendy Matthews, Kathleen McSweeney, Varduhi Melikyan, Adam Micco, Megan Michel, Lidija Milašinović, Alissa Mittnik, Janet M Monge, Georgi Nekhrizov, Rebecca Nicholls, Alexey G Nikitin, Vassil Nikolov, Mario Novak, Iñigo Olalde, Jonas Oppenheimer, Anna Osterholtz, Celal Özdemir, Kadir Toykan Özdoğan, Nurettin Öztürk, Nikos Papadimitriou, Niki Papakonstantinou, Anastasia Papathanasiou, Lujana Paraman, Evgeny G Paskary, Nick Patterson, Ilian Petrakiev, Levon Petrosyan, Vanya Petrova, Anna Philippa-Touchais, Ashot Piliposyan, Nada Pocuca Kuzman, Hrvoje Potrebica, Bianca Preda-Bălănică, Zrinka Premužić, T Douglas Price, Lijun Qiu, Siniša Radović, Kamal Raeuf Aziz, Petra Rajić Šikanjić, Kamal Rasheed Raheem, Sergei Razumov, Amy Richardson, Jacob Roodenberg, Rudenc Ruka, Victoria Russeva, Mustafa Şahin, Ayşegül Şarbak, Emre Savaş, Constanze Schattke, Lynne Schepartz, Tayfun Selçuk, Ayla Sevim-Erol, Michel Shamoon-Pour, Henry M Shephard, Athanasios Sideris, Angela Simalcsik, Hakob Simonyan, Vitalij Sinika, Kendra Sirak, Ghenadie Sirbu, Mario Šlaus, Andrei Soficaru, Bilal Söğüt, Arkadiusz Sołtysiak, Çilem Sönmez-Sözer, Maria Stathi, Martin Steskal, Kristin Stewardson, Sharon Stocker, Fadime Suata-Alpaslan, Alexander Suvorov, Anna Szécsényi-Nagy, Tamás Szeniczey, Nikolai Telnov, Strahil Temov, Nadezhda Todorova, Ulsi Tota, Gilles Touchais, Sevi Triantaphyllou, Atila Türker, Marina Ugarković, Todor Valchev, Fanica Veljanovska, Zlatko Videvski, Cristian Virag, Anna Wagner, Sam Walsh, Piotr Włodarczak, J Noah Workman, Aram Yardumian, Evgenii Yarovoy, Alper Yener Yavuz, Hakan Yılmaz, Fatma Zalzala, Anna Zettl, Zhao Zhang, Rafet Çavuşoğlu, Nadin Rohland, Ron Pinhasi, David Reich, Ruben Davtyan
We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia...
August 26, 2022: Science
#24
JOURNAL ARTICLE
Shan Shan Dai, Xierzhatijiang Sulaiman, Jainagul Isakova, Wei Fang Xu, Najmudinov Tojiddin Abdulloevich, Manilova Elena Afanasevna, Khudoidodov Behruz Ibrohimovich, Xi Chen, Wei Kang Yang, Ming Shan Wang, Quan Kuan Shen, Xing Yan Yang, Yong Gang Yao, Almaz A Aldashev, Abdusattor Saidov, Wei Chen, Lu Feng Cheng, Min Sheng Peng, Ya Ping Zhang
The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians...
August 25, 2022: Molecular Biology and Evolution
#25
JOURNAL ARTICLE
Xiaoming Zhang, Xueping Ji, Chunmei Li, Tingyu Yang, Jiahui Huang, Yinhui Zhao, Yun Wu, Shiwu Ma, Yuhong Pang, Yanyi Huang, Yaoxi He, Bing Su
Southern East Asia is the dispersal center regarding the prehistoric settlement and migrations of modern humans in Asia-Pacific regions. However, the settlement pattern and population structure of paleolithic humans in this region remain elusive, and ancient DNA can provide direct information. Here, we sequenced the genome of a Late Pleistocene hominin (MZR), dated ∼14.0 thousand years ago from Red Deer Cave located in Southwest China, which was previously reported possessing mosaic features of modern and archaic hominins...
June 21, 2022: Current Biology: CB
#26
JOURNAL ARTICLE
Siddhartha P Kar, Pedro M Quiros, Muxin Gu, Tao Jiang, Jonathan Mitchell, Ryan Langdon, Vivek Iyer, Clea Barcena, M S Vijayabaskar, Margarete A Fabre, Paul Carter, Slavé Petrovski, Stephen Burgess, George S Vassiliou
Clonal hematopoiesis (CH), the clonal expansion of a blood stem cell and its progeny driven by somatic driver mutations, affects over a third of people, yet remains poorly understood. Here we analyze genetic data from 200,453 UK Biobank participants to map the landscape of inherited predisposition to CH, increasing the number of germline associations with CH in European-ancestry populations from 4 to 14. Genes at new loci implicate DNA damage repair (PARP1, ATM, CHEK2), hematopoietic stem cell migration/homing (CD164) and myeloid oncogenesis (SETBP1)...
August 2022: Nature Genetics
#27
JOURNAL ARTICLE
Yue-Chen Liu, Rosalind Hunter-Anderson, Olivia Cheronet, Joanne Eakin, Frank Camacho, Michael Pietrusewsky, Nadin Rohland, Alexander Ioannidis, J Stephen Athens, Michele Toomay Douglas, Rona Michi Ikehara-Quebral, Rebecca Bernardos, Brendan J Culleton, Matthew Mah, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly Callan, Ann Marie Lawson, Kirsten Mandl, Megan Michel, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Kenneth Kidd, Judith Kidd, Theodore G Schurr, Kathryn Auckland, Adrian V S Hill, Alexander J Mentzer, Consuelo D Quinto-Cortés, Kathryn Robson, Douglas J Kennett, Nick Patterson, Carlos D Bustamante, Andrés Moreno-Estrada, Matthew Spriggs, Miguel Vilar, Mark Lipson, Ron Pinhasi, David Reich
Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago...
July 2022: Science
#28
JOURNAL ARTICLE
Ying Li, Jee Hyun Kim, Hailong Li, Yuxi Peng, Min Chen, Weihong Zhu, Puneet Pandey, Gleb Sedash, Tianming Wang, Yury Darman, Hang Lee
Given current anthropogenic pressures and climate change, wildlife range expansion offers a second chance for species conservation. The water deer Hydropotes inermis is a native to China and the Korean peninsula, but populations in North Korea and mainland China have declined drastically in recent years. However, the range of this species appears to be rapidly expanding northward. In this study, we employed camera traps and molecular technology to assess the status, phylogeny, and genetic ancestry of the newly recorded population...
May 28, 2022: Animals: An Open Access Journal From MDPI
#29
JOURNAL ARTICLE
Tunde I Huszar, Walter F Bodmer, Katarzyna Hutnik, Jon H Wetton, Mark A Jobling
Short tandem repeat (STR) polymorphisms are traditionally assessed by measuring allele lengths via capillary electrophoresis (CE). Massively parallel sequencing (MPS) reveals differences among alleles of the same length, thus improving discrimination, but also identifying groups of alleles likely related by descent. These may have relatively restricted geographical distributions and thus MPS could detect population structure more effectively than CE-based analysis. We addressed this question by applying an MPS multiplex, the Promega PowerSeq™ Auto/Mito/Y System prototype, to 362 individuals chosen to represent a wide geographical spread from the People of the British Isles (PoBI) cohort, which represents at least three generations of local rural ancestry...
July 2022: Forensic Science International. Genetics
#30
JOURNAL ARTICLE
Manjusha Chintalapati, Nick Patterson, Priya Moorjani
Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on ~1,100 ancient genomes, we reconstruct major gene flow events during European Holocene...
May 30, 2022: ELife
#31
JOURNAL ARTICLE
Zoltán Maróti, Endre Neparáczki, Oszkár Schütz, Kitti Maár, Gergely I B Varga, Bence Kovács, Tibor Kalmár, Emil Nyerki, István Nagy, Dóra Latinovics, Balázs Tihanyi, Antónia Marcsik, György Pálfi, Zsolt Bernert, Zsolt Gallina, Ciprián Horváth, Sándor Varga, László Költő, István Raskó, Péter L Nagy, Csilla Balogh, Albert Zink, Frank Maixner, Anders Götherström, Robert George, Csaba Szalontai, Gergely Szenthe, Erwin Gáll, Attila P Kiss, Bence Gulyás, Bernadett Ny Kovacsóczy, Szilárd Sándor Gál, Péter Tomka, Tibor Török
Huns, Avars, and conquering Hungarians were migration-period nomadic tribal confederations that arrived in three successive waves in the Carpathian Basin between the 5th and 9th centuries. Based on the historical data, each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations have been debated. Recently, hundreds of ancient genomes were analyzed from Central Asia, Mongolia, and China, from which we aimed to identify putative source populations for the above-mentioned groups...
May 19, 2022: Current Biology: CB
#32
JOURNAL ARTICLE
Bruno Ariano, Valeria Mattiangeli, Emily M Breslin, Eóin W Parkinson, T Rowan McLaughlin, Jess E Thompson, Ronika K Power, Jay T Stock, Bernardette Mercieca-Spiteri, Simon Stoddart, Caroline Malone, Shyam Gopalakrishnan, Lara M Cassidy, Daniel G Bradley
Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society...
June 20, 2022: Current Biology: CB
#33
JOURNAL ARTICLE
Ainash Childebayeva, Adam Benjamin Rohrlach, Rodrigo Barquera, Maïté Rivollat, Franziska Aron, András Szolek, Oliver Kohlbacher, Nicole Nicklisch, Kurt W Alt, Detlef Gronenborn, Harald Meller, Susanne Friederich, Kay Prüfer, Marie-France Deguilloux, Johannes Krause, Wolfgang Haak
Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany...
June 2, 2022: Molecular Biology and Evolution
#34
JOURNAL ARTICLE
Lucija Barbarić, Ivana Horjan-Zanki
Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains unidentified. The aim of this study was to assess the applicability of massively parallel sequencing (MPS) approach in the forensic cases of five drowned individuals recovered on the Western Balkan migration route. Besides capillary electrophoresis (CE)-based genetic profiling (aSTR, Y STR, and mitochondrial control region sequencing) of postmortem samples, we applied ForenSeq DNA Signature Prep Kit/Primer Mix B on MiSeqFGx platform and concomitant ForenSeq Universal Analysis (UAS) software...
January 2023: International Journal of Legal Medicine
#35
JOURNAL ARTICLE
Chengyuan Mao, Xinwei Li, Yun Su, Haiyang Luo, Liyuan Fan, Huimin Zheng, Yu Fan, Zhihua Yang, Shuo Zhang, Zhengwei Hu, Xiaoyan Hao, Changhe Shi, Yuming Xu
Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant cerebellar ataxia accompanied by extracerebellar signs and other neurological disorders. It is caused by an expansion of the ATTCT pentanucleotide repeat in intron 9 of ATXN10. Cases of SCA10, formerly confined to America, have been reported in Europe and Asia. In the present study, we aim to report an atypical SCA10 family in China and provide a reference for the diagnosis of SCA10 in Asia by comparing their clinical and genetic features with former SCA10 pedigrees...
April 19, 2022: Cerebellum
#36
JOURNAL ARTICLE
Guido Alberto Gnecchi-Ruscone, Anna Szécsényi-Nagy, István Koncz, Gergely Csiky, Zsófia Rácz, A B Rohrlach, Guido Brandt, Nadin Rohland, Veronika Csáky, Olivia Cheronet, Bea Szeifert, Tibor Ákos Rácz, András Benedek, Zsolt Bernert, Norbert Berta, Szabolcs Czifra, János Dani, Zoltán Farkas, Tamara Hága, Tamás Hajdu, Mónika Jászberényi, Viktória Kisjuhász, Barbara Kolozsi, Péter Major, Antónia Marcsik, Bernadett Ny Kovacsóczy, Csilla Balogh, Gabriella M Lezsák, János Gábor Ódor, Márta Szelekovszky, Tamás Szeniczey, Judit Tárnoki, Zoltán Tóth, Eszter K Tutkovics, Balázs G Mende, Patrick Geary, Walter Pohl, Tivadar Vida, Ron Pinhasi, David Reich, Zuzana Hofmanová, Choongwon Jeong, Johannes Krause
The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region...
April 14, 2022: Cell
#37
JOURNAL ARTICLE
John King N Layos, Ronel B Geromo, Dinah M Espina, Masahide Nishibori
The Philippine archipelago was believed to have never been connected to the Asian continent even during the severe Quaternary sea-level drops. As a result, the history of domestic pig (Sus scrofa) dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine domestic pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boar corresponding to their geographic origin...
2022: PloS One
#38
JOURNAL ARTICLE
Douglas J Kennett, Mark Lipson, Keith M Prufer, David Mora-Marín, Richard J George, Nadin Rohland, Mark Robinson, Willa R Trask, Heather H J Edgar, Ethan C Hill, Erin E Ray, Paige Lynch, Emily Moes, Lexi O'Donnell, Thomas K Harper, Emily J Kate, Josue Ramos, John Morris, Said M Gutierrez, Timothy M Ryan, Brendan J Culleton, Jaime J Awe, David Reich
The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations...
March 22, 2022: Nature Communications
#39
JOURNAL ARTICLE
Katharina Dulias, M George B Foody, Pierre Justeau, Marina Silva, Rui Martiniano, Gonzalo Oteo-García, Alessandro Fichera, Simão Rodrigues, Francesca Gandini, Alison Meynert, Kevin Donnelly, Timothy J Aitman, Andrew Chamberlain, Olivia Lelong, George Kozikowski, Dominic Powlesland, Clive Waddington, Valeria Mattiangeli, Daniel G Bradley, Jaroslaw Bryk, Pedro Soares, James F Wilson, Graeme Wilson, Hazel Moore, Maria Pala, Ceiridwen J Edwards, Martin B Richards
Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From ∼3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By ∼2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC...
February 22, 2022: Proceedings of the National Academy of Sciences of the United States of America
#40
JOURNAL ARTICLE
Anna E White, Toni de-Dios, Pablo Carrión, Gian Luca Bonora, Laia Llovera, Elisabetta Cilli, Esther Lizano, Maral K Khabdulina, Daniyar T Tleugabulov, Iñigo Olalde, Tomàs Marquès-Bonet, François Balloux, Davide Pettener, Lucy van Dorp, Donata Luiselli, Carles Lalueza-Fox
The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins...
December 14, 2021: Biology
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