Ancient introgression underlying the unusual mito‐nuclear discordance and coat phenotypic variation in the Moupin pika

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Ring distribution patterns—diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin

(2021) Yanqun Wang et al.   MOLECULAR ECOLOGY

ENMeval 2.0: redesigned for customizable and reproducible modeling of species’ niches and distributions

(2021) Jamie M. Kass et al.   Methods in Ecology and Evolution

Chromosome-Level Reference Genome Assembly for the American Pika (Ochotona princeps)

(2021) Bryson M F Sjodin et al.   JOURNAL OF HEREDITY

Positive responses from giant pandas to the Natural Forest Conservation Programme based on slope utilisation

(2021) Mingsheng Hong et al.   Global Ecology and Conservation

Recovering signals of ghost archaic introgression in African populations

(2020) Arun Durvasula et al.   Science Advances

The origin and spread of locally adaptive seasonal camouflage in snowshoe hares

(2020) Matthew R. Jones et al.   AMERICAN NATURALIST

Ghost Introgression: Spooky Gene Flow in the Distant Past

(2020) Jente Ottenburghs   BIOESSAYS

Out of Tibet: Genomic Perspectives on the Evolutionary History of Extant Pikas

(2020) XiaoYun Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates

(2020) Rachel C. M. Warnock et al.   PALEOBIOLOGY

Recent demographic history inferred by high-resolution analysis of linkage disequilibrium

(2020) Enrique Santiago et al.   MOLECULAR BIOLOGY AND EVOLUTION

Retreat of large carnivores across the giant panda distribution range

(2020) Sheng Li et al.   Nature Ecology & Evolution

Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

(2020) Milan Malinsky et al.   Molecular Ecology Resources

Genetics and Evolution of Mammalian Coat Pigmentation

(2020) Eduardo Eizirik et al.   Annual Review of Animal Biosciences

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

(2019) Guanliang Meng et al.   NUCLEIC ACIDS RESEARCH

More grist for the mill? Species delimitation in the genomic era and its implications for conservation

(2019) David W. G. Stanton et al.   CONSERVATION GENETICS

‘Ghost introgression’ as a cause of deep mitochondrial divergence in a bird species complex

(2019) Dezhi Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary history of field mice (Murinae: Apodemus), with emphasis on morphological variation among species in China and description of a new species

(2019) Deyan Ge et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

UNC13C Suppress Tumor Progression via Inhibiting EMT Pathway and Improves Survival in Oral Squamous Cell Carcinoma

(2019) Bharath Kumar Velmurugan et al.   Frontiers in Oncology

Introgression drives repeated evolution of winter coat color polymorphism in hares

(2019) Iwona Giska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ShinyGO: a graphical gene-set enrichment tool for animals and plants

(2019) Steven Xijin Ge et al.   BIOINFORMATICS

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep

(2018) Christina Marie Rochus et al.   BMC GENOMICS

Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture

(2018) Sharon R. Browning et al.   CELL

The Value of Ecosystem Services from Giant Panda Reserves

(2018) Fuwen Wei et al.   CURRENT BIOLOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

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

Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves

(2018) Rena M Schweizer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergence of biannual moulting strategies across birds and mammals

(2018) Roxanne S. Beltran et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MAGI2 is an independent predictor of biochemical recurrence in prostate cancer

(2018) Stephanie N. David et al.   PROSTATE

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

(2018) Matthew R. Jones et al.   SCIENCE

Molecular phylogeny, morphological diversity, and systematic revision of a species complex of common wild rat species in China (Rodentia, Murinae)

(2018) Deyan Ge et al.   JOURNAL OF MAMMALOGY

Multilocus phylogeny and taxonomy of pikas of the subgenus Ochotona (Lagomorpha, Ochotonidae)

(2018) Andrey A. Lissovsky et al.   ZOOLOGICA SCRIPTA

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

(2018) Milan Malinsky et al.   Nature Ecology & Evolution

Beyond mean allelic effects: A locus at the major color gene MC1R associates also with differing levels of phenotypic and genetic (co)variance for coloration in barn owls

(2017) Luis M. San-Jose et al.   EVOLUTION

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

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

Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing

(2017) Lin Zeng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of novel mimicry rings facilitated by adaptive introgression in tropical butterflies

(2017) Juan Enciso-Romero et al.   MOLECULAR ECOLOGY

Warm-cold colonization: response of oaks to uplift of the Himalaya-Hengduan Mountains

(2017) Hong-Hu Meng et al.   MOLECULAR ECOLOGY

Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot

(2017) Yaowu Xing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Climatologies at high resolution for the earth’s land surface areas

(2017) Dirk Nikolaus Karger et al.   Scientific Data

Multiscale partitioning of small mammal β-diversity provides novel insights into the Quaternary faunal history of Qinghai-Tibetan Plateau and Hengduan Mountains

(2016) Zhixin Wen et al.   JOURNAL OF BIOGEOGRAPHY

Making sense of genomic islands of differentiation in light of speciation

(2016) Jochen B. W. Wolf et al.   NATURE REVIEWS GENETICS

Dynamics of mtDNA introgression during species range expansion: insights from an experimental longitudinal study

(2016) V. Mastrantonio et al.   Scientific Reports

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach

(2015) José Melo-Ferreira et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Experimental validation of candidate schizophrenia gene CALN1 as a target for microRNA-137

(2015) Shihui Xia et al.   NEUROSCIENCE LETTERS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity forMaxentecological niche models

(2014) Robert Muscarella et al.   Methods in Ecology and Evolution

ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis

(2013) W. He et al.   GENETICS AND MOLECULAR RESEARCH

Taxonomic revision of pikas Ochotona (Lagomorpha, Mammalia) at the species level

(2013) Andrey A. Lissovsky   MAMMALIA

BLAST: a more efficient report with usability improvements

(2013) Grzegorz M. Boratyn et al.   NUCLEIC ACIDS RESEARCH

Evolutionary History of Lagomorphs in Response to Global Environmental Change

(2013) Deyan Ge et al.   PLoS One

GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework

(2013) Donovan H. Parks et al.   PLoS One

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

(2012) Pablo Cingolani et al.   FLY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Reevaluation of several taxa of Chinese lagomorphs (Mammalia: Lagomorpha) described on the basis of pelage phenotype variation

(2011) Deyan Ge et al.   MAMMALIAN BIOLOGY

Testing for Ancient Admixture between Closely Related Populations

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

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat

(2010) AMY S. TURMELLE et al.   MOLECULAR ECOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

WHEN COLD IS BETTER: CLIMATE-DRIVEN ELEVATION SHIFTS YIELD COMPLEX PATTERNS OF DIVERSIFICATION AND DEMOGRAPHY IN AN ALPINE SPECIALIST (AMERICAN PIKA,OCHOTONA PRINCEPS)

(2009) Kurt E. Galbreath et al.   EVOLUTION

Inferring divergence times within pikas (Ochotona spp.) using mtDNA and relaxed molecular dating techniques

(2009) Hayley C. Lanier et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Genetic Basis of Phenotypic Convergence in Beach Mice: Similar Pigment Patterns but Different Genes

(2008) C. C. Steiner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogeny of five species ofDremomys(Rodentia: Sciuridae), inferred from cytochromebgene sequences

(2008) Song Li et al.   ZOOLOGICA SCRIPTA