Ancestry Publications

Foster Nicole R, NR Holman, Luke E LE et al.

Molecular ecology resources

Tulloch Rachel L, RL Rojahn, Jack J et al.

Molecular ecology resources

Gilardet Alexandre, A Lord, Edana E et al.

Molecular ecology resources

Straube Nicolas, N Lyra, Mariana L ML et al.

Molecular ecology resourcesMol Ecol ResourSuccessful application of ancient DNA extraction and library construction protocols to museum wet collection specimens.229923152299-231510.1111/1755-0998.13433Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.StraubeNicolasN0000-0001-7047-1084University Museum of Bergen, Bergen, Norway.SNSB Bavarian State Collection of Zoology, München, Germany.LyraMariana LML0000-0002-7863-4965Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany.PaijmansJohanna L AJLA0000-0002-1938-7052Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.PreickMichaelaMDepartment of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.BaslerNikolasNDepartment of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.PennerJohannesJMuseum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany.RödelMark-OliverMOMuseum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.WestburyMichael VMV0000-0003-0478-3930Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.HaddadCélio F BCFBDepartamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.BarlowAxelADepartment of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.HofreiterMichaelMDepartment of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.eng#2013/50741-7Fundação de Amparo à Pesquisa do Estado de São Paulo#2017/2616-8Fundação de Amparo à Pesquisa do Estado de São Paulo#2018/15425-0Fundação de Amparo à Pesquisa do Estado de São Paulo351649567Deutsche Forschungsgemeinschaft431589/2016-0Conselho Nacional de Desenvolvimento Científico e Tecnológico306623/2018-8Conselho Nacional de Desenvolvimento Científico e TecnológicoJournal Article20210616EnglandMol Ecol Resour1014656041755-098X0DNA, Ancient0DNA, MitochondrialIMDNA, AncientDNA, MitochondrialgeneticsMuseumsSequence Analysis, DNASpecimen Handlingancient DNAarchival DNAbiological collectionformalinsingle-stranded DNA librarytarget capture20215920211720215142021527602021918602021526721ppublish3403673210.1111/1755-0998.13433REFERENCES

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