Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses

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

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

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

(2014) Shiping Liu et al.   CELL

Sequencing the Mouse Y Chromosome Reveals Convergent Gene Acquisition and Amplification on Both Sex Chromosomes

(2014) Y.Q. Shirleen Soh et al.   CELL

An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

(2014) R. Scozzari et al.   GENOME RESEARCH

Molecular Phylogeny and SNP Variation of Polar Bears (Ursus maritimus), Brown Bears (U. arctos), and Black Bears (U. americanus) Derived from Genome Sequences

(2014) Matthew A. Cronin et al.   JOURNAL OF HEREDITY

Inter- and Intraspecies Phylogenetic Analyses Reveal Extensive X–Y Gene Conversion in the Evolution of Gametologous Sequences of Human Sex Chromosomes

(2014) Beniamino Trombetta et al.   MOLECULAR BIOLOGY AND EVOLUTION

Brown and Polar Bear Y Chromosomes Reveal Extensive Male-Biased Gene Flow within Brother Lineages

(2014) Tobias Bidon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow

(2014) Verena E. Kutschera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators

(2014) Daniel W. Bellott et al.   NATURE

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle

(2014) Songlin Chen et al.   NATURE GENETICS

Comparative primate genomics: emerging patterns of genome content and dynamics

(2014) Jeffrey Rogers et al.   NATURE REVIEWS GENETICS

The impact of whole-genome sequencing on the reconstruction of human population history

(2014) Krishna R. Veeramah et al.   NATURE REVIEWS GENETICS

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Six novel Y chromosome genes in Anopheles mosquitoes discovered by independently sequencing males and females

(2013) Andrew Brantley Hall et al.   BMC GENOMICS

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

(2013) G. Li et al.   GENOME RESEARCH

Efficient identification of Y chromosome sequences in the human andDrosophilagenomes

(2013) Antonio Bernardo Carvalho et al.   GENOME RESEARCH

Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome

(2013) Mannis van Oven et al.   HUMAN MUTATION

Y Chromosome Analysis of Dingoes and Southeast Asian Village Dogs Suggests a Neolithic Continental Expansion from Southeast Asia Followed by Multiple Austronesian Dispersals

(2013) Benjamin N. Sacks et al.   MOLECULAR BIOLOGY AND EVOLUTION

A sensitive and specific multiplex PCR approach for sex identification of ursine and tremarctine bears suitable for non-invasive samples

(2013) Tobias Bidon et al.   Molecular Ecology Resources

Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration

(2013) Doris Bachtrog   NATURE REVIEWS GENETICS

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

(2013) Barbara Wallner et al.   PLoS One

Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions

(2013) Pille Hallast et al.   PLoS Genetics

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

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

Genomics and Genetics of Human and Primate Y Chromosomes

(2012) Jennifer F. Hughes et al.   Annual Review of Genomics and Human Genetics

Identification of avian W-linked contigs by short-read sequencing

(2012) Nancy Chen et al.   BMC GENOMICS

A calibrated human Y-chromosomal phylogeny based on resequencing

(2012) W. Wei et al.   GENOME RESEARCH

Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

(2012) Jennifer F. Hughes et al.   NATURE

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba 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

Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage

(2012) F. Hailer et al.   SCIENCE

Carnivore-Specific SINEs (Can-SINEs): Distribution, Evolution, and Genomic Impact

(2011) K. B. Walters-Conte et al.   JOURNAL OF HEREDITY

The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important

(2010) E. M. Kvikstad et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

(2010) Jennifer F. Hughes et al.   NATURE

Gene Conversion between the X Chromosome and the Male-Specific Region of the Y Chromosome at a Translocation Hotspot

(2009) Zoë H. Rosser et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

The quest for Y-chromosomal markers - methodological strategies for mammalian non-model organisms

(2009) MAJA P. GREMINGER et al.   Molecular Ecology Resources

Origin and evolution of Y chromosomes: Drosophila tales

(2009) A. Bernardo Carvalho et al.   TRENDS IN GENETICS

A system for sex determination from degraded DNA: a useful tool for palaeogenetics and conservation genetics of ursids

(2008) Marie Pagès et al.   CONSERVATION GENETICS

Unequal Rates of Y Chromosome Gene Divergence during Speciation of the Family Ursidae

(2008) Shigeki Nakagome et al.   MOLECULAR BIOLOGY AND EVOLUTION

Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny

(2007) Marie Pagès et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION