Perspectives in plant evolutionary genetics: A field guide in 15 “easy steps” to modern tools in evolutionary genetics and genomics

The Earth BioGenome Project 2020: Starting the clock

(2022) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae)

(2021) I. M. De-la-Cruz et al.   Scientific Reports

Transcriptome of weeping pinyon pine, Pinus pinceana, shows differences across heterogeneous habitats

(2021) Laura Figueroa-Corona et al.   TREES-STRUCTURE AND FUNCTION

The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

(2021) Josué Barrera-Redondo et al.   Horticulture Research

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

(2021) Shanlin Liu et al.   CELL

Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics

(2021) Jorge Cruz-Nicolás et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The evolutionary genomics of species’ responses to climate change

(2021) Jonás A. Aguirre-Liguori et al.   Nature Ecology & Evolution

Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico

(2021) Carmina Martínez-González et al.   Frontiers in Ecology and Evolution

Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations

(2021) Cristóbal Hernández-Álvarez et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae)

(2021) Sabina Irene Lara-Cabrera et al.   Frontiers in Plant Science

Phylogenetic tree building in the genomic age

(2020) Paschalia Kapli et al.   NATURE REVIEWS GENETICS

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

(2020) Paul M Hime et al.   SYSTEMATIC BIOLOGY

Hybridization Between Yuccas From Baja California: Genomic and Environmental Patterns

(2020) Maria Clara Arteaga et al.   Frontiers in Plant Science

The relevance of gene flow with wild relatives in understanding the domestication process

(2020) Alejandra Moreno-Letelier et al.   Royal Society Open Science

Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes

(2020) Thibaut Capblancq et al.   Annual Review of Ecology Evolution and Systematics

The Plant Microbiome: From Ecology to Reductionism and Beyond

(2020) Connor R. Fitzpatrick et al.   Annual Review of Microbiology

Plant–microbiome interactions: from community assembly to plant health

(2020) Pankaj Trivedi et al.   NATURE REVIEWS MICROBIOLOGY

Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners

(2020) Josué Barrera-Redondo et al.   Frontiers in Genetics

Genomic and chemical evidence for local adaptation in resistance to different herbivores in Datura stramonium

(2020) Ivan M. De‐la‐Cruz et al.   EVOLUTION

Reference genome and demographic history of the most endangered marine mammal, the vaquita

(2020) Phillip A. Morin et al.   Molecular Ecology Resources

Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize

(2020) Jonás A. Aguirre-Liguori et al.   Frontiers in Genetics

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

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

The genome of Cucurbita argyrosperma (silver-seed gourd) reveals faster rates of protein-coding gene and long noncoding RNA turnover and neofunctionalization within Cucurbita

(2019) Josué Barrera-Redondo et al.   Molecular Plant

A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

(2019) Stéphane Compant et al.   Journal of Advanced Research

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies ( Zea mays parviglumis and Zea mays mexicana )

(2019) Jonás A. Aguirre‐Liguori et al.   MOLECULAR ECOLOGY

Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize

(2019) Jonás A. Aguirre-Liguori et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gazing into the anthosphere: considering how microbes influence floral evolution

(2019) María Rebolleda‐Gómez et al.   NEW PHYTOLOGIST

Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS

(2019) Lang Wu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Floral organs act as environmental filters and interact with pollinators to structure the yellow monkeyflower ( Mimulus guttatus ) floral microbiome

(2019) María Rebolleda Gómez et al.   MOLECULAR ECOLOGY

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Genomic landscape of the global oak phylogeny

(2019) Andrew L. Hipp et al.   NEW PHYTOLOGIST

Evolutionary response to herbivory: population differentiation in microsatellite loci, tropane alkaloids and leaf trichome density in Datura stramonium

(2019) I. M. De-la-Cruz et al.   Arthropod-Plant Interactions

The search for loci under selection: trends, biases and progress

(2018) Collin W. Ahrens et al.   MOLECULAR ECOLOGY

Heritability estimates from genomewide relatedness matrices in wild populations: Application to a passerine, using a small sample size

(2018) C. Perrier et al.   Molecular Ecology Resources

Historical biogeography and phylogeny of Cucurbita : insights from ancestral area reconstruction and niche evolution

(2018) Gabriela Castellanos-Morales et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Practical considerations for plant phylogenomics

(2018) Michael R. McKain et al.   Applications in Plant Sciences

Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics

(2018) Ovidiu Paun et al.   NEW PHYTOLOGIST

Evolutionary and ecological functional genomics, from lab to the wild

(2018) Maricris L. Zaidem et al.   PLANT JOURNAL

Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem

(2018) Eneas Aguirre-von-Wobeser et al.   PLoS One

Co-niche construction between hosts and symbionts: ideas and evidence

(2017) Renee M. Borges   JOURNAL OF GENETICS

Connecting genomic patterns of local adaptation and niche suitability in teosintes

(2017) J. A. Aguirre-Liguori et al.   MOLECULAR ECOLOGY

Signatures of local adaptation in lowland and highland teosintes from whole-genome sequencing of pooled samples

(2017) M.-A. Fustier et al.   MOLECULAR ECOLOGY

The K = 2 conundrum

(2017) Jasmine K. Janes et al.   MOLECULAR ECOLOGY

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

(2017) Dario Copetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

(2017) Kelly Swarts et al.   SCIENCE

Seasonal Changes in a Maize-Based Polyculture of Central Mexico Reshape the Co-occurrence Networks of Soil Bacterial Communities

(2017) Eria A. Rebollar et al.   Frontiers in Microbiology

Domestication Genomics of the Open-Pollinated Scarlet Runner Bean (Phaseolus coccineus L.)

(2017) Azalea Guerra-García et al.   Frontiers in Plant Science

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae)

(2016) Michael R. McKain et al.   AMERICAN JOURNAL OF BOTANY

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

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Use of molecular and environmental analyses for integrated in situ and ex situ conservation: The case of the Mexican prairie dog

(2016) Gabriela Castellanos-Morales et al.   BIOLOGICAL CONSERVATION

Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication

(2016) Jazmín Ramos-Madrigal et al.   CURRENT BIOLOGY

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

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae)

(2016) Karolina Heyduk et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

epiGBS: reference-free reduced representation bisulfite sequencing

(2016) Thomas P van Gurp et al.   NATURE METHODS

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding

(2016) Miguel Vallebueno-Estrada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment

(2016) Qin Xu et al.   Scientific Reports

Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture

(2015) Karolina Heyduk et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Climate change, genetic markers and species distribution modelling

(2015) Nicholas J. Gotelli et al.   JOURNAL OF BIOGEOGRAPHY

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

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

Mycorrhizal ecology and evolution: the past, the present, and the future

(2015) Marcel G. A. van der Heijden et al.   NEW PHYTOLOGIST

A new FST-based method to uncover local adaptation using environmental variables

(2015) Pierre de Villemereuil et al.   Methods in Ecology and Evolution

DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data

(2014) Jean-Marie Cornuet et al.   BIOINFORMATICS

Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation

(2014) Matthew C. Fitzpatrick et al.   ECOLOGY LETTERS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

Recent novel approaches for population genomics data analysis

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

The genetics of Mexico recapitulates Native American substructure and affects biomedical traits

(2014) A. Moreno-Estrada et al.   SCIENCE

Population genomics from pool sequencing

(2013) Luca Ferretti et al.   MOLECULAR ECOLOGY

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

Ecological niche models in phylogeographic studies: applications, advances and precautions

(2013) Diego F. Alvarado-Serrano et al.   Molecular Ecology Resources

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

Genome size variation in wild and cultivated maize along altitudinal gradients

(2013) Concepción M. Díez et al.   NEW PHYTOLOGIST

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Estimating heritability using genomic data

(2013) John Stanton-Geddes et al.   Methods in Ecology and Evolution

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

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

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

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

Ecological niche similarities of Peponapis bees and non-domesticated Cucurbita species

(2011) T.C. Giannini et al.   ECOLOGICAL MODELLING

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

How many flowering plants are pollinated by animals?

(2011) Jeff Ollerton et al.   OIKOS

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

Approximate Bayesian Computation in Evolution and Ecology

(2010) Mark A. Beaumont   Annual Review of Ecology Evolution and Systematics

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

(2010) Thibaut Jombart et al.   BMC GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

(2010) Angélica Cibrián-Jaramillo et al.   Genome Biology and Evolution

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis)

(2010) Jason A. Holliday et al.   NEW PHYTOLOGIST

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants

(2008) Matthieu G Conte et al.   BMC GENOMICS

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce

(2008) MARIE-CLAIRE NAMROUD et al.   MOLECULAR ECOLOGY