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

A reference‐free approach to analyze RADseq data using standard Next Generation Sequencing toolkits

(2021) Rasmus Heller et al.   Molecular Ecology Resources

Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

(2020) Christian A. Totoiu et al.   PLoS One

Uneven missing data skews phylogenomic relationships within the lories and lorikeets

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

Preservation-Induced Morphological Change in Salamanders and Failed DNA Extraction from a Decades-Old Museum Specimen: Implications for Plethodon ainsworthi

(2020) Todd W. Pierson et al.   JOURNAL OF HERPETOLOGY

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

Natural history collections are critical resources for contemporary and future studies of urban evolution

(2020) Allison J. Shultz et al.   Evolutionary Applications

Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs ( Rhacophorus )

(2020) Kyle A. O’Connell et al.   MOLECULAR ECOLOGY

Genomics of natural history collections for understanding evolution in the wild

(2020) Lua Lopez et al.   Molecular Ecology Resources

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

(2019) Ke Bi et al.   PLoS Genetics

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

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

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

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

(2019) Samuel T. Turvey et al.   Ecology and Evolution

Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

(2019) Paul M. Hime et al.   G3-Genes Genomes Genetics

Genomic impact of severe population decline in a nomadic songbird

(2019) Ross Crates et al.   PLoS One

ipyrad: Interactive assembly and analysis of RADseq datasets

(2019) Deren A R Eaton et al.   BIOINFORMATICS

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

Museum specimens provide phylogenomic data to resolve relationships of sack-bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae)

(2018) Ryan A. St Laurent et al.   SYSTEMATIC ENTOMOLOGY

The use of museum skins for genomic analyses of temporal genetic diversity in wild species

(2018) Astrid Vik Stronen et al.   Conservation Genetics Resources

Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution

(2018) Marshal Hedin et al.   Scientific Reports

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

(2018) Bruno A. S. de Medeiros et al.   PeerJ

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

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

(2018) Tobias Andermann et al.   PeerJ

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

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

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

Museum samples could help to reconstruct the original distribution of Salmo trutta complex in Italy

(2017) A. Splendiani et al.   JOURNAL OF FISH BIOLOGY

Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

(2017) Rayna C. Bell et al.   MOLECULAR ECOLOGY

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

(2017) Sara Ruane et al.   Molecular Ecology Resources

Trehalose improves PCR amplification of vertebrate nuclear DNA from historical allozymes

(2017) Michael L. Yuan et al.   Conservation Genetics Resources

Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics

(2017) Sarah Schmid et al.   Ecology and Evolution

How and how much does RAD-seq bias genetic diversity estimates?

(2016) Marie Cariou et al.   BMC EVOLUTIONARY BIOLOGY

Natural history collections as windows on evolutionary processes

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

Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes

(2016) Fátima Sánchez Barreiro et al.   Molecular Ecology Resources

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

(2016) Sandra L. Hoffberg et al.   Molecular Ecology Resources

Exon capture optimization in amphibians with large genomes

(2016) Evan McCartney-Melstad et al.   Molecular Ecology Resources

Reticulation, divergence, and the phylogeography–phylogenetics continuum

(2016) Scott V. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

(2015) O. A. Ali et al.   GENETICS

The use of museum specimens with high-throughput DNA sequencers

(2015) Andrew S. Burrell et al.   JOURNAL OF HUMAN 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

Widespread rapid reductions in body size of adult salamanders in response to climate change

(2014) Nicholas M. Caruso et al.   GLOBAL CHANGE BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

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

Unexpected Rarity of the Pathogen Batrachochytrium dendrobatidis in Appalachian Plethodon Salamanders: 1957–2011

(2014) Carly Muletz et al.   PLoS One

Genetic utility of natural history museum specimens: endangered fairy shrimp (Branchiopoda, Anostraca)

(2014) Adam Wall et al.   ZooKeys

Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues

(2013) Stefan Paireder et al.   ANALYTICAL BIOCHEMISTRY

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

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

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

(2013) Martijn Staats et al.   PLoS One

Non-formalin fixative versus formalin-fixed tissue: A comparison of histology and RNA quality

(2012) Daniel Groelz et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

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

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

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A reduced representation approach to population genetic analyses and applications to human evolution

(2011) F. Luca et al.   GENOME RESEARCH

Oldies (but Goldies!): Extracting DNA from Cryopreserved Allozyme Homogenates

(2011) Marina P. Arbetman et al.   JOURNAL OF HEREDITY

Museum genomics: low-cost and high-accuracy genetic data from historical specimens

(2011) KEVIN C. ROWE et al.   Molecular Ecology Resources

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Detecting range shifts from historical species occurrences: new perspectives on old data

(2009) Morgan W. Tingley et al.   TRENDS IN ECOLOGY & EVOLUTION

The Effect of Ancient DNA Damage on Inferences of Demographic Histories

(2008) E. Axelsson et al.   MOLECULAR BIOLOGY AND EVOLUTION