Ancestry Publications

Diaz-Papkovich Alex, A Anderson-Trocmé, Luke L et al.

Journal of human genetics

Cardinali Irene, I Bodner, Martin M et al.

Frontiers in genetics

van der Valk Tom, T Vezzi, Francesco F et al.

Molecular ecology resourcesMol Ecol ResourIndex hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.117111811171-118110.1111/1755-0998.13009The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low-quantity and low-quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.© 2019 John Wiley & Sons Ltd.van der ValkTomT0000-0001-6582-3452Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.VezziFrancescoFScience for Life Laboratory, Solna, Sweden.OrmestadMattiasMScience for Life Laboratory, Solna, Sweden.DalénLoveLDepartment of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.GuschanskiKaterinaK0000-0002-8493-5457Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.engJan Löfqvist Endowments of the Royal Physiographic Society of Lund2015-676Svenska Forskningsrådet Formas2016-00835Svenska Forskningsrådet FormasScience for Life LaboratoryKnut and Alice Wallenberg FoundationNational Genomics Infrastructure funded by the Swedish Research CouncilUppsala Multidisciplinary Center for Advanced Computational ScienceJournal Article20190505EnglandMol Ecol Resour1014656041755-098X0DNA, Ancient9007-49-2DNAIMAnimalsDNADNA Barcoding, TaxonomicDNA, AncientGorilla gorillageneticsHigh-Throughput Nucleotide SequencingmethodsSequence Analysis, DNAmethodsancient DNAindex switchingmultiplexingmuseum specimensnext-generation sequencingread misassignment201891020192282019228201939602021876020193960ppublish3084809210.1111/1755-0998.13009REFERENCES

de-Dios Toni, T van Dorp, Lucy L et al.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

Kopelman Naama M, NM Stone, Lewi L et al.

European journal of human genetics : EJHG

Jatupol Kampuansai, Wibhu Kutanan, Eszter Dudás et al.

Molecular genetics and genomics : MGG

North Sea

Pérez-Ramallo, P., García-Martínez de Lagrán, I., Rojo-Guerra, M.A. et al.

Forensic Science International: Genetics Supplement Series

Spain

Souza Aracele Maria de, AM Resende, Sarah Stela SS et al.

Genetics and molecular biology

Vai Stefania, S Brunelli, Andrea A et al.

European journal of human genetics : EJHG

Walther Parson, Mayra Eduardoff, Catarina Xavier et al.

Forensic science international. Genetics

Russia

Li Jiawei, J Zhang, Ye Y et al.

American journal of physical anthropologyAm J Phys AnthropolThe genome of an ancient Rouran individual reveals an important paternal lineage in the Donghu population.895905895-90510.1002/ajpa.23491Following the Xiongnu and Xianbei, the Rouran Khaganate (Rouran) was the third great nomadic tribe on the Mongolian Steppe. However, few human remains from this tribe are available for archaeologists and geneticists to study, as traces of the tombs of these nomadic people have rarely been found. In 2014, the IA-M1 remains (TL1) at the Khermen Tal site from the Rouran period were found by a Sino-Mongolian joint archaeological team in Mongolia, providing precious material for research into the genetic imprint of the Rouran.The mtDNA hypervariable sequence I (HVS-I) and Y-chromosome SNPs were analyzed, and capture of the paternal non-recombining region of the Y chromosome (NRY) and whole-genome shotgun sequencing of TL1 were performed. The materials from three sites representing the three ancient nationalities (Donghu, Xianbei, and Shiwei) were selected for comparison with the TL1 individual.The mitochondrial haplotype of the TL1 individual was D4b1a2a1. The Y-chromosome haplotype was C2b1a1b/F3830 (ISOGG 2015), which was the same as that of the other two ancient male nomadic samples (ZHS5 and GG3) related to the Xianbei and Shiwei, which were also detected as F3889; this haplotype was reported to be downstream of F3830 by Wei et al. ().We conclude that F3889 downstream of F3830 is an important paternal lineage of the ancient Donghu nomads. The Donghu-Xianbei branch is expected to have made an important paternal genetic contribution to Rouran. This component of gene flow ultimately entered the gene pool of modern Mongolic- and Manchu-speaking populations.© 2018 Wiley Periodicals, Inc.LiJiaweiJAncient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China.College of Life Science, Jilin University, Changchun 130012, People's Republic of China.ZhangYeYAncient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China.ZhaoYongbinYLife Science College, Jilin Normal University, Siping 136000, People's Republic of China.ChenYongzhiYDirector, Inner Mongolian Museum, Hohhot 010011, People's Republic of China.OchirAACoordinator, International Institute for Study of Nomadic Civilization, 210620A, Ulaanbaatar 11, Mongolia.SarenbiligeEditorial department, Cultural Relics and Archaeological Institute of Inner Mongolia, Hohhot 010010, People's Republic of China.ZhuHongHAncient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China.ZhouHuiH0000-0001-5858-5636Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China.College of Life Science, Jilin University, Changchun 130012, People's Republic of China.engJournal ArticleResearch Support, Non-U.S. Gov't20180421United StatesAm J Phys Anthropol04006540002-94830DNA, Ancient0DNA, MitochondrialIMAnthropology, PhysicalAsian PeoplegeneticsChromosomes, Human, YgeneticsDNA, AncientanalysisDNA, MitochondrialgeneticsGenetics, PopulationGenomegeneticsHaplotypesgeneticsHumansMaleMongoliaPhylogenyTransients and MigrantsNRY captureRouran Khaganateancient DNAnomadic population20171152018372018452018424602018121560201842360ppublish2968113810.1002/ajpa.23491REFERENCES

Schrider Daniel R, DR Kern, Andrew D AD

Trends in genetics : TIG