The role of introgression and ecotypic parallelism in delineating intraspecific conservation units

admixr—R package for reproducible analyses using ADMIXTOOLS

(2019) Martin Petr et al.   BIOINFORMATICS

Insights from genomes into the evolutionary importance and prevalence of hybridization in nature

(2019) Scott A. Taylor et al.   Nature Ecology & Evolution

The Caribou (Rangifer tarandus) Genome

(2019) Rebecca S. Taylor et al.   Genes

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Improving conservation policy with genomics: a guide to integrating adaptive potential into U.S. Endangered Species Act decisions for conservation practitioners and geneticists

(2018) W. C. Funk et al.   CONSERVATION GENETICS

Genomics and conservation units: The genetic basis of adult migration timing in Pacific salmonids

(2018) Robin S. Waples et al.   Evolutionary Applications

Lines on a map: conservation units, meta-population dynamics, and recovery of woodland caribou in Canada

(2018) Byron V. Weckworth et al.   Ecosphere

Parallel plumage colour evolution and introgressive hybridization in wheatears

(2018) Manuel Schweizer et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Evolutionary reconstruction supports the presence of a Pleistocene Arctic refugium for a large mammal species

(2017) Cornelya F. C. Klütsch et al.   JOURNAL OF BIOGEOGRAPHY

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

(2017) Sangeet Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revisiting Adaptive Potential, Population Size, and Conservation

(2017) Ary A. Hoffmann et al.   TRENDS IN ECOLOGY & EVOLUTION

Redefining the Role of Admixture and Genomics in Species Conservation

(2017) Bridgett M. vonHoldt et al.   Conservation Letters

Draft genome of the reindeer (Rangifer tarandus)

(2017) Zhipeng Li et al.   GigaScience

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

(2017) Vikas Kumar et al.   Scientific Reports

Łeghágots'enetę (learning together): the importance of indigenous perspectives in the identification of biological variation

(2016) Jean L. Polfus et al.   ECOLOGY AND SOCIETY

Genetically informed ecological niche models improve climate change predictions

(2016) Dana H. Ikeda et al.   GLOBAL CHANGE BIOLOGY

Ancient diversification in glacial refugia leads to intraspecific diversity in a Holarctic mammal

(2016) Jean L. Polfus et al.   JOURNAL OF BIOGEOGRAPHY

The probability of parallel genetic evolution from standing genetic variation

(2016) A. MacPherson et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

The eastern migratory caribou: the role of genetic introgression in ecotype evolution

(2016) Cornelya F. C. Klütsch et al.   Royal Society Open Science

The silent extinction: climate change and the potential hybridization-mediated extinction of endemic high-mountain plants

(2015) José M. Gómez et al.   BIODIVERSITY AND CONSERVATION

Adaptive introgression as a resource for management and genetic conservation in a changing climate

(2015) Jill A. Hamilton et al.   CONSERVATION BIOLOGY

A framework to guide the conservation of species hybrids based on ethical and ecological considerations

(2015) Raeya N. Jackiw et al.   CONSERVATION BIOLOGY

Hybridization and the species problem in conservation

(2015) Benjamin M. Fitzpatrick et al.   Current Zoology

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

(2015) M. Malinsky et al.   SCIENCE

Genetic rescue to the rescue

(2015) Andrew R. Whiteley et al.   TRENDS IN ECOLOGY & EVOLUTION

Hybridization and the species problem in conservation

(2015) Benjamin M. Fitzpatrick et al.   Current Zoology

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

How important is intraspecific genetic admixture to the success of colonising populations?

(2014) Marc Rius et al.   TRENDS IN ECOLOGY & EVOLUTION

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Reconstruction of caribou evolutionary history in Western North America and its implications for conservation

(2012) BYRON V. WECKWORTH et al.   MOLECULAR ECOLOGY

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Loss of Mhc and Neutral Variation in Peary Caribou: Genetic Drift Is Not Mitigated by Balancing Selection or Exacerbated by Mhc Allele Distributions

(2012) Sabrina S. Taylor et al.   PLoS One

Phylogeographical Analysis of mtDNA Data Indicates Postglacial Expansion from Multiple Glacial Refugia in Woodland Caribou (Rangifer tarandus caribou)

(2012) Cornelya F. C. Klütsch et al.   PLoS One

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Conservation of caribou (Rangifer tarandus) in Canada: an uncertain future1This review is part of the virtual symposium “Flagship Species – Flagship Problems” that deals with ecology, biodiversity and management issues, and climate impacts on species at risk and of Canadian importance, including the polar bear (Ursus maritimus), Atlantic cod (Gadus morhua), Piping Plover (Charadrius melodus), and caribou (Rangifer tarandus).

(2011) M. Festa-Bianchet et al.   CANADIAN JOURNAL OF ZOOLOGY

Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice

(2011) Ying Song et al.   CURRENT BIOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic rescue guidelines with examples from Mexican wolves and Florida panthers

(2009) Philip W. Hedrick et al.   CONSERVATION GENETICS

Global declines of caribou and reindeer

(2009) LIV SOLVEIG VORS et al.   GLOBAL CHANGE BIOLOGY

Climate change induced hybridization in flying squirrels

(2009) COLIN J. GARROWAY et al.   GLOBAL CHANGE BIOLOGY

Survival in the Rockies of an endangered hybrid swarm from diverged caribou (Rangifer tarandus) lineages

(2009) ALLAN D. McDEVITT et al.   MOLECULAR ECOLOGY

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

The Last Glacial Maximum

(2009) P. U. Clark et al.   SCIENCE

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS