Partial genomic survival of cave bears in living brown bears

Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age

(2018) James A Cahill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors

(2016) Michael Dannemann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

(2016) Sriram Sankararaman et al.   CURRENT BIOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears

(2016) Gloria G. Fortes et al.   MOLECULAR ECOLOGY

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

(2015) James A. Cahill et al.   MOLECULAR ECOLOGY

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

(2014) Konrad Lohse et al.   GENETICS

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

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

Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex

(2013) Mathias Stiller et al.   QUATERNARY INTERNATIONAL

Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution

(2013) James A. Cahill et al.   PLoS Genetics

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

Mammalian hybrid zones: a review

(2011) Quinn R. Shurtliff   MAMMAL REVIEW

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Craniometrical variability in the cave bears (Carnivora, Ursidae): Multivariate comparative analysis

(2011) Gennady F. Baryshnikov et al.   QUATERNARY INTERNATIONAL

Middle Palaeolithic human occupation of the high altitude region of Hovk-1, Armenia

(2011) R. Pinhasi et al.   QUATERNARY SCIENCE REVIEWS

Withering Away--25,000 Years of Genetic Decline Preceded Cave Bear Extinction

(2010) M. Stiller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics