Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Environmental palaeogenomic reconstruction of an Ice Age algal population

(2021) Youri Lammers et al.   Communications Biology

An annotated draft genome for the Andean bear, Tremarctos ornatus

(2021) Nedda F Saremi et al.   JOURNAL OF HEREDITY

A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA

(2021) Joshua D Kapp et al.   JOURNAL OF HEREDITY

Evidence of human occupation in Mexico around the Last Glacial Maximum

(2020) Ciprian F. Ardelean et al.   NATURE

THE INTCAL20 NORTHERN HEMISPHERE RADIOCARBON AGE CALIBRATION CURVE (0–55 CAL kBP)

(2020) Paula J Reimer et al.   RADIOCARBON

Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set

(2020) Tyler J. Murchie et al.   QUATERNARY RESEARCH

Hybridization capture of larch ( Larix Mill) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest

(2020) Luise Schulte et al.   Molecular Ecology Resources

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia

(2019) M. C. Stahlschmidt et al.   Scientific Reports

Saving Old Bones: a non-destructive method for bone collagen prescreening

(2019) Matt Sponheimer et al.   Scientific Reports

A tale of four bears: Environmental signal on the phylogeographical patterns within the extant Ursus species

(2019) Carlos Luna‐Aranguré et al.   JOURNAL OF BIOGEOGRAPHY

Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

(2018) Engy Ahmed et al.   QUATERNARY SCIENCE REVIEWS

Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation

(2018) Anuj Srivastava et al.   DNA RESEARCH

The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA

(2017) Joanna R. Freeland   GENOME

Tracing the peopling of the world through genomics

(2017) Rasmus Nielsen et al.   NATURE

A non-destructive DNA sampling technique for herbarium specimens

(2017) Lara D. Shepherd   PLoS One

Neandertal and Denisovan DNA from Pleistocene sediments

(2017) Viviane Slon et al.   SCIENCE

The evolutionary history of bears is characterized by gene flow across species

(2017) Vikas Kumar et al.   Scientific Reports

A basal ursine bear (Protarctos abstrusus) from the Pliocene High Arctic reveals Eurasian affinities and a diet rich in fermentable sugars

(2017) Xiaoming Wang et al.   Scientific Reports

Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America

(2016) Kieren J. Mitchell et al.   Biology Letters

Combining bleach and mild predigestion improves ancient DNA recovery from bones

(2016) Sanne Boessenkool et al.   Molecular Ecology Resources

Postglacial viability and colonization in North America’s ice-free corridor

(2016) Mikkel W. Pedersen et al.   NATURE

Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska

(2016) Russell W. Graham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4,000 years ago

(2016) Frederik Valeur Seersholm et al.   Nature Communications

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture

(2015) Emily E. Puckett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Ancient and modern environmental DNA

(2014) Mikkel Winther Pedersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

(2014) B. Shapiro et al.   SCIENCE

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Mitochondrial Phylogenomics of Modern and Ancient Equids

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

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mid-Pliocene warm-period deposits in the High Arctic yield insight into camel evolution

(2013) Natalia Rybczynski et al.   Nature Communications

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

(2012) M. Kearse et al.   BIOINFORMATICS

Delineating genetic groupings in continuously distributed species across largely homogeneous landscapes: a study of American black bears (Ursus americanus) in Ontario, Canada

(2012) A. Pelletier et al.   CANADIAN JOURNAL OF ZOOLOGY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome

(2011) Jiajie Zhang et al.   BMC BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

(2009) Johannes Krause et al.   BMC EVOLUTIONARY BIOLOGY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Non-Destructive Sampling of Ancient Insect DNA

(2009) Philip Francis Thomsen et al.   PLoS One

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL