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

Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands

(2019) Whitney L.E. Tsai et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Earth history and the passerine superradiation

(2019) Carl H. Oliveros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

(2019) Mark T. Swanson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods

(2019) Andrea Lienhard et al.   PeerJ

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci

(2019) Marshal Hedin et al.   PeerJ

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

(2019) Christian Kehlmaier et al.   Scientific Reports

A demonstration of unsupervised machine learning in species delimitation

(2019) Shahan Derkarabetian et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Entomological Collections in the Age of Big Data

(2018) Andrew Edward Z. Short et al.   Annual Review of Entomology

Exon-capture based phylogeny and diversification of the venomous gastropods (Neogastropoda, Conoidea)

(2018) J Abdelkrim et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae)

(2018) Marshal Hedin et al.   ZooKeys

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

(2018) Shahan Derkarabetian et al.   ZooKeys

On the universality of target-enrichment baits for phylogenomic research

(2018) Silas Bossert et al.   Methods in Ecology and Evolution

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

(2018) Marshal Hedin et al.   Scientific Reports

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

Parasitoid biology preserved in mineralized fossils

(2018) Thomas van de Kamp et al.   Nature Communications

Advancing mite phylogenomics: Designing ultraconserved elements for acari phylogeny

(2018) Matthew H. Van Dam et al.   Molecular Ecology Resources

The history and impact of digitization and digital data mobilization on biodiversity research

(2018) Gil Nelson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog (Sarcohyla; Hylidae)

(2018) Eugenia Zarza et al.   PeerJ

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

(2017) Clio Der Sarkissian et al.   Molecular Ecology Resources

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

(2017) Andrea M. Quattrini et al.   Molecular Ecology Resources

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

(2017) Sara Ruane et al.   Molecular Ecology Resources

Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA

(2017) John S. Sproul et al.   Molecular Ecology Resources

Dry habitats were crucibles of domestication in the evolution of agriculture in ants

(2017) Michael G. Branstetter et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient DNA Resolves the History of Tetragnatha (Araneae, Tetragnathidae) Spiders on Rapa Nui

(2017) Darko Cotoras et al.   Genes

The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling

(2016) Ward C. Wheeler et al.   CLADISTICS

High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements

(2016) Haw Chuan Lim et al.   Molecular Ecology Resources

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

(2016) James Starrett et al.   Molecular Ecology Resources

Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga

(2016) Bonnie B. Blaimer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

The use of museum specimens with high-throughput DNA sequencers

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

Impact of enrichment conditions on cross-species capture of fresh and degraded DNA

(2015) Johanna L. A. Paijmans et al.   Molecular Ecology Resources

Sequence capture of ultraconserved elements from bird museum specimens

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

DNA barcodes from century-old type specimens using next-generation sequencing

(2015) Sean W. J. Prosser et al.   Molecular Ecology Resources

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes

(2015) Fábio Raposo do Amaral et al.   PLoS One

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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A molecular phylogenetic approach to the New Zealand species of Enantiobuninae (Opiliones : Eupnoi : Neopilionidae)

(2014) Sebasti�n V�lez et al.   INVERTEBRATE SYSTEMATICS

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

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

Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography

(2014) Rosa Fernández et al.   PLoS One

PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics

(2013) Kevin M. Kocot et al.   Evolutionary Bioinformatics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

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

(2013) Martijn Staats et al.   PLoS One

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol

(2013) Jeremy Miller et al.   ZooKeys

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Molecular phylogeny of the leiobunine harvestmen of eastern North America (Opiliones: Sclerosomatidae: Leiobuninae)

(2012) Mercedes Burns et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science

(2012) Nico Cellinese et al.   ZooKeys

No specimen left behind: industrial scale digitization of natural history collections

(2012) Vladimir Blagoderov et al.   ZooKeys

Molecular systematics of sclerosomatid harvestmen (Opiliones, Phalangioidea, Sclerosomatidae): Geography is better than taxonomy in predicting phylogeny

(2011) Marshal Hedin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores

(2009) Gonzalo Giribet et al.   CLADISTICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH