Population genomics of grey wolves and wolf-like canids in North America

Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

(2018) Matthew T. Oetjens et al.   BMC GENOMICS

Excess of genomic defects in a woolly mammoth on Wrangel island

(2017) Rebekah L. Rogers et al.   PLoS Genetics

Comment on “Whole-genome sequence analysis shows two endemic species of North American wolf are admixtures of the coyote and gray wolf”

(2017) Paul A. Hohenlohe et al.   Science Advances

Response to Hohenloheet al.

(2017) Bridgett M. vonHoldt et al.   Science Advances

Considering all the evidence: a reply to Sefc and Koblmüller (2016)

(2016) L. Y. Rutledge et al.   Biology Letters

Ancient hybrid origin of the eastern wolf not yet off the table: a comment on Rutledgeet al. (2015)

(2016) Kristina M. Sefc et al.   Biology Letters

Admixture mapping identifies introgressed genomic regions in North American canids

(2016) Bridgett M. vonHoldt et al.   MOLECULAR ECOLOGY

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

(2016) B. M. vonHoldt et al.   Science Advances

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

RAD sequencing and genomic simulations resolve hybrid origins within North AmericanCanis: Figure 1.

(2015) L. Y. Rutledge et al.   Biology Letters

Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species

(2015) Klaus-Peter Koepfli et al.   CURRENT BIOLOGY

Worldwide patterns of genomic variation and admixture in gray wolves

(2015) Zhenxin Fan et al.   GENOME RESEARCH

Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves

(2015) Rena M. Schweizer et al.   MOLECULAR ECOLOGY

Genetic subdivision and candidate genes under selection in North American grey wolves

(2015) Rena M. Schweizer et al.   MOLECULAR ECOLOGY

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

(2015) Clare D. Marsden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Genetic rescue in Isle Royale wolves: genetic analysis and the collapse of the population

(2014) Philip W. Hedrick et al.   CONSERVATION GENETICS

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

Genome Sequencing Highlights the Dynamic Early History of Dogs

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

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

(2013) Filipe G. Vieira et al.   GENOME RESEARCH

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

The genomics of selection in dogs and the parallel evolution between dogs and humans

(2013) Guo-dong Wang et al.   Nature Communications

Conservation genomics in perspective: A holistic approach to understanding Canis evolution in North America

(2012) Linda Y. Rutledge et al.   BIOLOGICAL CONSERVATION

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Invasion of eastern Greenland by the high arctic wolfCanis lupus arctos

(2012) Ulf Marquard-Petersen   WILDLIFE BIOLOGY

Y-chromosome evidence supports widespread signatures of three-species Canis hybridization in eastern North America

(2012) Paul J. Wilson et al.   Ecology and Evolution

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

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

A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids

(2011) Bridgett M. vonHoldt et al.   GENOME RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes

(2010) Linda Y Rutledge et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Congenital bone deformities and the inbred wolves (Canis lupus) of Isle Royale

(2009) Jannikke Räikkönen et al.   BIOLOGICAL CONSERVATION

Origin and status of the Great Lakes wolf

(2009) STEPHAN KOBLMÜLLER et al.   MOLECULAR ECOLOGY

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Native Great Lakes wolves were not restored

(2007) J. A Leonard et al.   Biology Letters

Captive breeding and the reintroduction of Mexican and red wolves

(2007) P. W. HEDRICK et al.   MOLECULAR ECOLOGY