Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Cranial anatomy of Andinodelphys cochabambensis, a stem metatherian from the early Palaeocene of Bolivia

(2021) Christian de Muizon et al.   GEODIVERSITAS

Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

(2021) Johanna von Seth et al.   Nature Communications

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum )

(2021) Fátima Sánchez‐Barreiro et al.   MOLECULAR ECOLOGY

A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines

(2021) Pierre-Olivier Antoine et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Ocean Carbon Storage across the middle Miocene: a new interpretation for the Monterey Event

(2020) S. M. Sosdian et al.   Nature Communications

Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros

(2020) Ashot Margaryan et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros

(2020) Edana Lord et al.   CURRENT BIOLOGY

Interspecific gene flow and the evolution of specialisation in black and white rhinoceros

(2020) Yoshan Moodley et al.   MOLECULAR BIOLOGY AND EVOLUTION

The origin of Rhinocerotoidea and phylogeny of Ceratomorpha (Mammalia, Perissodactyla)

(2020) Bin Bai et al.   Communications Biology

African Land Mammal Ages

(2020) John A. Van Couvering et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

(2019) Lei Chen et al.   SCIENCE

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

(2019) Enrico Cappellini et al.   NATURE

Gene flow analysis method, the D-statistic, is robust in a wide parameter space

(2018) Yichen Zheng et al.   BMC BIOINFORMATICS

Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis

(2018) Herman L. Mays et al.   CURRENT BIOLOGY

Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells

(2018) Tate Tunstall et al.   GENOME RESEARCH

Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World’s Rarest Hyena Species, the Brown Hyena

(2018) Michael V Westbury et al.   MOLECULAR BIOLOGY AND EVOLUTION

DiscoVista: Interpretable visualizations of gene tree discordance

(2018) Erfan Sayyari et al.   MOLECULAR PHYLOGENETICS 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

Northernmost Record of the Merck’s Rhinoceros Stephanorhinus kirchbergensis (Jäger) and Taxonomic Status of Coelodonta jacuticus Russanov (Mammalia, Rhinocerotidae)

(2018) A. V. Shpansky et al.   PALEONTOLOGICAL JOURNAL

Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions

(2018) Pavel Kosintsev et al.   Nature Ecology & Evolution

Perissodactyla (Rhinocerotidae and Equidae) from Kanapoi

(2017) Denis Geraads   JOURNAL OF HUMAN EVOLUTION

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species

(2017) Huajing Teng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

(2017) Hannes Svardal et al.   NATURE GENETICS

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Discovery of the skull of Stephanorhinus kirchbergensis (Jäger, 1839) above the Arctic Circle

(2017) Irina V. Kirillova et al.   QUATERNARY RESEARCH

A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica

(2017) Michael Westbury et al.   Nature Communications

A new genus of horse from Pleistocene North America

(2017) Peter D Heintzman et al.   eLife

Middle Pleistocene protein sequences from the rhinoceros genusStephanorhinusand the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae

(2017) Frido Welker et al.   PeerJ

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

(2017) Sarah Siu Tze Mak et al.   GigaScience

Genomic consequences of intensive inbreeding in an isolated wolf population

(2017) Marty Kardos et al.   Nature Ecology & Evolution

The Genetic Origin of Short Tail in Endangered Korean Dog, DongGyeongi

(2017) DongAhn Yoo et al.   Scientific Reports

Genomic Flatlining in the Endangered Island Fox

(2016) Jacqueline A. Robinson et al.   CURRENT BIOLOGY

The Genomes of Two Bat Species with Long Constant Frequency Echolocation Calls

(2016) Dong Dong et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus

(2016) Bettina Harr et al.   Scientific Data

Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study

(2015) Matthew Parks et al.   BMC GENOMICS

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

(2015) Eleftheria Palkopoulou et al.   CURRENT BIOLOGY

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

(2015) K. R. Veeramah et al.   GENETICS

Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus

(2015) Puli Chandramouli Reddy et al.   JOURNAL OF BIOSCIENCES

Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates

(2015) Frido Welker et al.   NATURE

Mechanisms of coexistence in diverse herbivore-carnivore assemblages: demographic, temporal and spatial heterogeneities affecting prey vulnerability

(2015) Norman Owen-Smith   OIKOS

Will current conservation responses save the Critically Endangered Sumatran rhinoceros Dicerorhinus sumatrensis?

(2015) Rasmus Gren Havmøller et al.   ORYX

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

(2015) Y. Xue et al.   SCIENCE

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle et al.   SYSTEMATIC BIOLOGY

Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic

(2015) Vincent J. Lynch et al.   Cell Reports

Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2015) Ruibang Luo et al.   GigaScience

A revision ofAceratherium blanfordiLydekker, 1884 (Mammalia: Rhinocerotidae) from the Early Miocene of Pakistan: postcranials as a key

(2015) PIERRE-OLIVIER ANTOINE et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

(2014) M. dos Reis et al.   Biology Letters

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

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

(2014) Shiping Liu et al.   CELL

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

Early Eocene fossils suggest that the mammalian order Perissodactyla originated in India

(2014) Kenneth D. Rose et al.   Nature Communications

Genome Sequencing Highlights the Dynamic Early History of Dogs

(2014) Adam H. Freedman et al.   PLoS Genetics

Hypoxia Adaptations in the Grey Wolf (Canis lupus chanco) from Qinghai-Tibet Plateau

(2014) Wenping Zhang et al.   PLoS Genetics

A new genus of Rhinocerotidae (Mammalia, Perissodactyla) from the Oligocene of Europe

(2013) Damien Becker et al.   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

Complete Genome Sequences of Elephant Endotheliotropic Herpesviruses 1A and 1B Determined Directly from Fatal Cases

(2013) G. S. Wilkie et al.   JOURNAL OF VIROLOGY

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

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

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

Minke whale genome and aquatic adaptation in cetaceans

(2013) Hyung-Soon Yim et al.   NATURE GENETICS

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

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

The tiger genome and comparative analysis with lion and snow leopard genomes

(2013) Yun Sung Cho et al.   Nature Communications

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The bonobo genome compared with the chimpanzee and human genomes

(2012) Kay Prüfer et al.   NATURE

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability

(2012) S. Brace et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The history and management of black rhino in KwaZulu-Natal: a population genetic approach to assess the past and guide the future

(2011) M. Karsten et al.   ANIMAL CONSERVATION

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

True single-molecule DNA sequencing of a pleistocene horse bone

(2011) L. Orlando et al.   GENOME RESEARCH

C14ORF179 encoding IFT43 is mutated in Sensenbrenner syndrome

(2011) H. H. Arts et al.   JOURNAL OF MEDICAL GENETICS

Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins

(2011) Enrico Cappellini et al.   JOURNAL OF PROTEOME RESEARCH

Testing for Ancient Admixture between Closely Related Populations

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

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Molecular phylogeny and evolution of the Perissodactyla

(2011) CYNTHIA C. STEINER et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

(2009) Eske Willerslev et al.   BMC EVOLUTIONARY BIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

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

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Mid-Miocene cooling and the extinction of tundra in continental Antarctica

(2008) A. R. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The earliest immigration of woolly rhinoceros (Coelodonta tologoijensis, Rhinocerotidae, Mammalia) into Europe and its adaptive evolution in Palaearctic cold stage mammal faunas

(2008) Ralf-Dietrich Kahlke et al.   QUATERNARY SCIENCE REVIEWS