Mining museums for historical DNA: advances and challenges in museomics

Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches

(2021) Sharon A. Appleyard et al.   JOURNAL OF FISH BIOLOGY

Examining Natural History through the Lens of Palaeogenomics

(2021) Kieren J. Mitchell et al.   TRENDS IN ECOLOGY & EVOLUTION

Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

(2021) Cody W. Thompson et al.   mBio

Genetic barcoding of museum eggshell improves data integrity of avian biological collections

(2021) Alicia Grealy et al.   Scientific Reports

Genomics Reveals the Origins of Historical Specimens

(2021) Qian Cong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Million-year-old DNA sheds light on the genomic history of mammoths

(2021) Tom van der Valk et al.   NATURE

High‐throughput methods for efficiently building massive phylogenies from natural history collections

(2021) Ryan A. Folk et al.   Applications in Plant Sciences

Systematic benchmark of ancient DNA read mapping

(2021) Adrien Oliva et al.   BRIEFINGS IN BIOINFORMATICS

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens

(2021) Christoph Mayer et al.   SYSTEMATIC ENTOMOLOGY

On the potential of Angiosperms353 for population genomic studies

(2021) Madeline Slimp et al.   Applications in Plant Sciences

Genomic library preparation and hybridization capture of formalin‐fixed tissues and allozyme supernatant for population genomics and considerations for combining capture‐ and RADseq‐based single nucleotide polymorphism data sets

(2021) Kyle A. O’Connell et al.   Molecular Ecology Resources

Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement

(2021) Emily Roycroft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

(2020) Angela McGaughran   BMC GENOMICS

Museum Epigenomics: Charting the Future by Unlocking the Past

(2020) Erin E. Hahn et al.   TRENDS IN ECOLOGY & EVOLUTION

Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates

(2020) Axel Barlow et al.   Genes

Uneven missing data skews phylogenomic relationships within the lories and lorikeets

(2020) Brian Tilston Smith et al.   Genome Biology and Evolution

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

(2020) Jocelyn P. Colella et al.   Molecular Ecology Resources

Hybridization ddRAD‐sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA

(2020) Patricia L. M. Lang et al.   Molecular Ecology Resources

Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland

(2020) Jérémy Gauthier et al.   Molecular Ecology Resources

Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community

(2020) Vanessa C. Bieker et al.   Molecular Ecology Resources

Shuttered natural history museums fight for survival

(2020) Elizabeth Pennisi   SCIENCE

Genomics of natural history collections for understanding evolution in the wild

(2020) Lua Lopez et al.   Molecular Ecology Resources

The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes

(2020) Dawson M White et al.   SYSTEMATIC BIOLOGY

The evolution of a tropical biodiversity hotspot

(2020) Michael G. Harvey et al.   SCIENCE

A molecular phylogeny of historical and contemporary specimens of an under‐studied micro‐invertebrate group

(2020) Russell J. S. Orr et al.   Ecology and Evolution

Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change

(2019) Ke Bi et al.   PLoS Genetics

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

(2019) Shawn M. Billerman et al.   Molecular Ecology Resources

Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

(2019) Sangeet Lamichhaney et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression

(2019) Christian Kehlmaier et al.   Scientific Reports

The presence and impact of reference bias on population genomic studies of prehistoric human populations

(2019) Torsten Günther et al.   PLoS Genetics

Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction

(2019) Nicolas Dussex et al.   Biology Letters

Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

(2019) Kyle M. Ewart et al.   Molecular Ecology Resources

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

(2019) Shahan Derkarabetian et al.   Molecular Ecology Resources

More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens

(2019) Whitney L. E. Tsai et al.   Molecular Ecology Resources

Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation

(2019) Allison Q. Byrne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies

(2019) Bruna Trevisan et al.   PeerJ

The enigmatic Crimean green lizard ( Lacerta viridis magnifica ) is extinct but not valid: Mitogenomics of a 120‐year‐old museum specimen reveals historical introduction

(2019) Christian Kehlmaier et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

The Limits of Hyb-Seq for Herbarium Specimens: Impact of Preservation Techniques

(2019) Laura L. Forrest et al.   Frontiers in Ecology and Evolution

Museum epigenomics: Characterizing cytosine methylation in historic museum specimens

(2019) Tricia L. Rubi et al.   Molecular Ecology Resources

How old can we go? Evaluating the age limit for effective DNA recovery from historical insect specimens

(2019) Melanie M.L. Lalonde et al.   SYSTEMATIC ENTOMOLOGY

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project

(2018) Pauline Robbe et al.   GENETICS IN MEDICINE

Performance of commonly requested destructive museum samples for mammalian genomic studies

(2018) Molly M McDonough et al.   JOURNAL OF MAMMALOGY

A perfect storm for mammalogy: declining sample availability in a period of rapid environmental degradation

(2018) Jason L Malaney et al.   JOURNAL OF MAMMALOGY

Next-generation museum genomics: Phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)

(2018) Hannah M. Wood et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool

(2018) Ulrike Taron et al.   Genes

Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards

(2018) Jimmy A. McGuire et al.   PeerJ

Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

(2018) Vanessa C. Bieker et al.   Botany Letters

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas

(2018) Tom van der Valk et al.   CURRENT BIOLOGY

Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing

(2018) Nadin Rohland et al.   Nature Protocols

Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples

(2018) Simon Haile et al.   NUCLEIC ACIDS RESEARCH

Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene

(2018) C. Jonathan Schmitt et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens

(2017) Sara Ruane et al.   Molecular Ecology Resources

AntCaller: an accurate variant caller incorporating ancient DNA damage

(2017) Boyan Zhou et al.   MOLECULAR GENETICS AND GENOMICS

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

(2017) Priscilla C. Silva et al.   Neotropical Ichthyology

Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

(2017) Ethan B. Linck et al.   Ecology and Evolution

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

(2017) Charles Y. Feigin et al.   Nature Ecology & Evolution

Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar

(2016) Christian Silva et al.   ANNALS OF BOTANY

Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

(2016) Melissa T. R. Hawkins et al.   BMC EVOLUTIONARY BIOLOGY

Old and new DNA unweave the phylogenetic position of the eastern Atlantic gall crabDetocarcinus balssi(Monod, 1956) (Decapoda: Cryptochiridae)

(2016) Sancia E. T. van der Meij et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Natural history collections as windows on evolutionary processes

(2016) Michael W. Holmes et al.   MOLECULAR ECOLOGY

Opinion: Specimen collections should have a much bigger role in infectious disease research and response

(2016) Diane DiEuliis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retrieval of hundreds of nuclear loci from herbarium specimens

(2016) Michelle L. Hart et al.   TAXON

Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections

(2016) David K Yeates et al.   Current Opinion in Insect Science

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

(2016) Tomasz Suchan et al.   PLoS One

Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens

(2016) Bonnie B. Blaimer et al.   PLoS One

The Nagoya Protocol on Access and Benefit Sharing

(2015) Myrna E. Watanabe   BIOSCIENCE

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence capture of ultraconserved elements from bird museum specimens

(2015) John E. McCormack et al.   Molecular Ecology Resources

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

(2015) Sarah M. Hykin et al.   PLoS One

Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization

(2014) H. Do et al.   CLINICAL CHEMISTRY

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

(2014) Mandy Man-Ying Tin et al.   PLoS One

Drastic population fluctuations explain the rapid extinction of the passenger pigeon

(2014) C.-M. Hung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

Preservation of RNA and DNA from mammal samples under field conditions

(2013) Miguel Camacho-Sanchez et al.   Molecular Ecology Resources

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

(2013) Martijn Staats et al.   PLoS One

One Hundred Twenty Years of Koala Retrovirus Evolution Determined from Museum Skins

(2012) M. C. Avila-Arcos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient DNA Recovers the Origins of Māori Feather Cloaks

(2011) K. Hartnup et al.   MOLECULAR BIOLOGY AND EVOLUTION

Searching for DNA in museum specimens: a comparison of sources in a mammal species

(2009) M. CASAS-MARCE et al.   Molecular Ecology Resources

DNA damage in preserved specimens and tissue samples: a molecular assessment

(2008) Juergen Zimmermann et al.   Frontiers in Zoology

Ancient DNA and conservation: lessons from the endangered kiwi of New Zealand

(2008) L. D SHEPHERD et al.   MOLECULAR ECOLOGY