Sequence capture of ultraconserved elements from bird museum specimens

Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura)

(2015) Guillaume Besnard et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The use of museum samples for large-scale sequence capture: a study of congeneric horseshoe bats (family Rhinolophidae)

(2015) Sebastian E. Bailey et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico

(2015) Loubab Zedane et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

(2015) Carly F. Graham et al.   Molecular Ecology Resources

The future of ancient DNA: Technical advances and conceptual shifts

(2014) Michael Hofreiter et al.   BIOESSAYS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact

(2014) Fiona C Gowen et al.   BMC EVOLUTIONARY BIOLOGY

From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition

(2014) Guillaume Besnard et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

The relevance of time series in molecular ecology and conservation biology

(2013) Jan C. Habel et al.   BIOLOGICAL REVIEWS

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

Genomics and museum specimens

(2013) Michael W. Nachman   MOLECULAR ECOLOGY

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

Mitochondrial Phylogenomics of Modern and Ancient Equids

(2013) Julia T. Vilstrup et al.   PLoS One

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

(2013) Brant C. Faircloth et al.   PLoS One

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

(2013) Martijn Staats et al.   PLoS One

Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs

(2013) O. Thalmann et al.   SCIENCE

Next-Generation Museomics Disentangles One of the Largest Primate Radiations

(2013) Katerina Guschanski et al.   SYSTEMATIC BIOLOGY

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

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Long identical multispecies elements in plant and animal genomes

(2012) J. Reneker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

(2011) V. C. Mason et al.   GENOME RESEARCH

Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach

(2011) Martyna Molak et al.   JOURNAL OF MOLECULAR EVOLUTION

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

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

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

(2011) María C. Ávila-Arcos et al.   Scientific Reports

CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS

(2010) John E. McCormack et al.   EVOLUTION

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

GENETIC DIVERGENCE AND DIFFERENTIATION WITHIN THE WESTERN SCRUB-JAY (APHELOCOMA CALIFORNICA)

(2008) KATHLEEN SEMPLE DELANEY et al.   AUK

The Effect of Ancient DNA Damage on Inferences of Demographic Histories

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

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

(2007) S. Stephen et al.   MOLECULAR BIOLOGY AND EVOLUTION