Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears

Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates

(2020) Axel Barlow et al.   Genes

Direct estimation of mutations in great apes reconciles phylogenetic dating

(2019) Søren Besenbacher et al.   Nature Ecology & Evolution

Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations

(2019) Gui-Lian Sheng et al.   CURRENT BIOLOGY

The presence and impact of reference bias on population genomic studies of prehistoric human populations

(2019) Torsten Günther et al.   PLoS Genetics

Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear

(2019) Joscha Gretzinger et al.   Scientific Reports

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

A comprehensive genomic history of extinct and living elephants

(2018) Eleftheria Palkopoulou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene

(2018) Gui-Lian Sheng et al.   Genes

Cranial and mandibular morphology of Middle Pleistocene cave bears (Ursus deningeri): implications for diet and evolution

(2018) Anneke H. van Heteren et al.   HISTORICAL BIOLOGY

Partial genomic survival of cave bears in living brown bears

(2018) Axel Barlow et al.   Nature Ecology & Evolution

Morphometry of upper cheek teeth of cave bears (Carnivora, Ursidae)

(2018) Gennady F. Baryshnikov et al.   BOREAS

Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker

(2017) Remi Allio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas

(2017) Yibo Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution

(2017) Matthias Meyer et al.   eLife

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

(2017) Vikas Kumar et al.   Scientific Reports

The mutation rate in human evolution and demographic inference

(2016) Aylwyn Scally   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

(2016) Matthias Meyer et al.   NATURE

Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds

(2015) Pontus Skoglund et al.   CURRENT BIOLOGY

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone

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The future of ancient DNA: Technical advances and conceptual shifts

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

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Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes

(2014) Adrien Rieux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome flux and stasis in a five millennium transect of European prehistory

(2014) Cristina Gamba et al.   Nature Communications

A mitochondrial genome sequence of a hominin from Sima de los Huesos

(2013) Matthias Meyer et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

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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

Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

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mapDamage: testing for damage patterns in ancient DNA sequences

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FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

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

The power of genetic monitoring for studying demography, ecology and genetics of a reintroduced brown bear population

(2010) M. DE BARBA et al.   MOLECULAR ECOLOGY

The Sequence Alignment/Map format and SAMtools

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Fast and accurate short read alignment with Burrows-Wheeler transform

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

(2009) Johannes Krause et al.   BMC EVOLUTIONARY BIOLOGY

Genetic Variation, Relatedness, and Effective Population Size of Polar Bears (Ursus maritimus) in the southern Beaufort Sea, Alaska

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Gene flow and species delimitation

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