Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change

Genomic and Fitness Consequences of Genetic Rescue in Wild Populations

(2020) Sarah W. Fitzpatrick et al.   CURRENT BIOLOGY

Conterminous United States land cover change patterns 2001–2016 from the 2016 National Land Cover Database

(2020) Collin Homer et al.   ISPRS JOURNAL OF PHOTOGRAMMETRY AND REMOTE SENSING

Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature

(2020) Tianyan Yang et al.   Animals

Comparative transcriptomic and proteomic analyses provide insights into functional genes for hypoxic adaptation in embryos of Tibetan chickens

(2020) Ying Zhang et al.   Scientific Reports

Mixed support for gene flow as a constraint to local adaptation and contributor to the limited geographic range of an endemic salamander

(2020) Steven J. Micheletti et al.   MOLECULAR ECOLOGY

LFMM 2: Fast and accurate inference of gene-environment associations in genome-wide studies

(2019) Kevin Caye et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

(2019) Bruno Contreras-Moreira et al.   MOLECULAR ECOLOGY

A chromosome-scale assembly of the axolotl genome

(2019) Jeramiah J. Smith et al.   GENOME RESEARCH

Conserving adaptive potential: lessons from Tasmanian devils and their transmissible cancer

(2019) Paul A. Hohenlohe et al.   CONSERVATION GENETICS

Back to the future: conserving functional and phylogenetic diversity in amphibian-climate refuges

(2019) Ricardo Lourenço-de-Moraes et al.   BIODIVERSITY AND CONSERVATION

Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections

(2019) Orly Razgour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic analysis reveals variant association with high altitude adaptation in native chickens

(2019) Hamed Kharrati-Koopaee et al.   Scientific Reports

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

Sampling strategy optimization to increase statistical power in landscape genomics: a simulation‐based approach

(2019) Oliver Selmoni et al.   Molecular Ecology Resources

YTHDF1 links hypoxia adaptation and non-small cell lung cancer progression

(2019) Yulin Shi et al.   Nature Communications

These aren't the loci you're looking for: Principles of effective SNP filtering for molecular ecologists

(2018) Shannon J. O'Leary et al.   MOLECULAR ECOLOGY

Soil Property and Class Maps of the Conterminous United States at 100-Meter Spatial Resolution

(2018) Amanda Ramcharan et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Navigating the Interface Between Landscape Genetics and Landscape Genomics

(2018) Andrew Storfer et al.   Frontiers in Genetics

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

Putatively adaptive genetic variation in the giant California sea cucumber ( Parastichopus californicus ) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

(2018) Amanda Xuereb et al.   MOLECULAR ECOLOGY

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata)

(2017) Charles Babin et al.   Genome Biology and Evolution

Parallel habitat acclimatization is realized by the expression of different genes in two closely related salamander species (genus Salamandra)

(2017) D J Goedbloed et al.   HEREDITY

WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas

(2017) Stephen E. Fick et al.   INTERNATIONAL JOURNAL OF CLIMATOLOGY

Ten Years of Landscape Genomics: Challenges and Opportunities

(2017) Yong Li et al.   Frontiers in Plant Science

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire et al.   Current Zoology

High fitness costs of climate change-induced camouflage mismatch

(2016) Marketa Zimova et al.   ECOLOGY LETTERS

Demographic history and adaptation account for clock gene diversity in humans

(2016) I Dall'Ara et al.   HEREDITY

Climatic niche breadth can explain variation in geographical range size of alpine and subalpine plants

(2016) Fangyuan Yu et al.   INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE

An approach for identifying cryptic barriers to gene flow that limit species' geographic ranges

(2016) Steven J. Micheletti et al.   MOLECULAR ECOLOGY

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire et al.   Current Zoology

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Detecting adaptive evolution based on association with ecological gradients: Orientation matters!

(2015) E Frichot et al.   HEREDITY

A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)

(2015) Steven J. Micheletti et al.   MOLECULAR ECOLOGY

A practical guide to environmental association analysis in landscape genomics

(2015) Christian Rellstab et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Accelerating extinction risk from climate change

(2015) M. C. Urban   SCIENCE

Genetic rescue to the rescue

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

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

Modeling Percent Tree Canopy Cover

(2015) John W. Coulston et al.   PHOTOGRAMMETRIC ENGINEERING AND REMOTE SENSING

LANDSCAPE GENOMICS OFPOPULUS TRICHOCARPA: THE ROLE OF HYBRIDIZATION, LIMITED GENE FLOW, AND NATURAL SELECTION IN SHAPING PATTERNS OF POPULATION STRUCTURE

(2014) Armando Geraldes et al.   EVOLUTION

THE EVOLUTION OF ENVIRONMENTAL TOLERANCE AND RANGE SIZE: A COMPARISON OF GEOGRAPHICALLY RESTRICTED AND WIDESPREADMIMULUS

(2014) Seema N. Sheth et al.   EVOLUTION

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Research Review: Polygenic methods and their application to psychiatric traits

(2014) Naomi R. Wray et al.   JOURNAL OF CHILD PSYCHOLOGY AND PSYCHIATRY

Rhythmic U2af26 Alternative Splicing Controls PERIOD1 Stability and the Circadian Clock in Mice

(2014) Marco Preußner et al.   MOLECULAR CELL

Coming to Terms with the Concept of Moving Species Threatened by Climate Change – A Systematic Review of the Terminology and Definitions

(2014) Maria H. Hällfors et al.   PLoS One

EXAMINING THE FULL EFFECTS OF LANDSCAPE HETEROGENEITY ON SPATIAL GENETIC VARIATION: A MULTIPLE MATRIX REGRESSION APPROACH FOR QUANTIFYING GEOGRAPHIC AND ECOLOGICAL ISOLATION

(2013) Ian J. Wang   EVOLUTION

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

NeEstimatorv2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

(2013) C. Do et al.   Molecular Ecology Resources

Population Genetic Studies Revealed Local Adaptation in a High Gene-Flow Marine Fish, the Small Yellow Croaker (Larimichthys polyactis)

(2013) Le Wang et al.   PLoS One

Batrachochytrium salamandrivorans sp. nov. causes lethal chytridiomycosis in amphibians

(2013) A. Martel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ten years of landscape genetics

(2013) Stéphanie Manel et al.   TRENDS IN ECOLOGY & EVOLUTION

diveRsity: AnRpackage for the estimation and exploration of population genetics parameters and their associated errors

(2013) Kevin Keenan et al.   Methods in Ecology and Evolution

Expression Profiling Reveals Novel Hypoxic Biomarkers in Peripheral Blood of Adult Mice Exposed to Chronic Hypoxia

(2012) Matias Mosqueira et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Dispersal will limit ability of mammals to track climate change in the Western Hemisphere

(2012) C. A. Schloss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Do species’ traits predict recent shifts at expanding range edges?

(2011) Amy L. Angert et al.   ECOLOGY LETTERS

Rapid Range Shifts of Species Associated with High Levels of Climate Warming

(2011) I.-C. Chen et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended

(2010) Maxime Bonhomme et al.   GENETICS

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Evolution and Ecology of Species Range Limits

(2009) Jason P. Sexton et al.   Annual Review of Ecology Evolution and Systematics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Assisted migration of plants: Changes in latitudes, changes in attitudes

(2009) Pati Vitt et al.   BIOLOGICAL CONSERVATION

Spatial patterns of variation due to natural selection in humans

(2009) John Novembre et al.   NATURE REVIEWS GENETICS

Dissolved oxygen requirements for hatching success of two ambystomatid salamanders in restored ephemeral ponds

(2009) Allison B. Sacerdote et al.   WETLANDS

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

(2008) Thibaut Jombart   BIOINFORMATICS

A Meta-Analysis of the Effects of Ultraviolet B Radiation and Its Synergistic Interactions with pH, Contaminants, and Disease on Amphibian Survival

(2008) BETSY A. BANCROFT et al.   CONSERVATION BIOLOGY

Genetic variation across species’ geographical ranges: the central–marginal hypothesis and beyond

(2008) C. G. ECKERT et al.   MOLECULAR ECOLOGY

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

Climatic change and wetland desiccation cause amphibian decline in Yellowstone National Park

(2008) S. K. McMenamin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA