Temporal matches between monarch butterfly and milkweed population changes over the past 25,000 years

Population genetics of a recent range expansion and subsequent loss of migration in monarch butterflies

(2022) William B. Hemstrom et al.   MOLECULAR ECOLOGY

Colonization and genetic diversification processes of Leishmania infantum in the Americas

(2021) Philipp Schwabl et al.   Communications Biology

Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus

(2021) Mario Vallejo-Marín et al.   Communications Biology

Changes in climate drive recent monarch butterfly dynamics

(2021) Erin R. Zylstra et al.   Nature Ecology & Evolution

Genomic evidence for gene flow between monarchs with divergent migratory phenotypes and flight performance

(2020) Venkat Talla et al.   MOLECULAR ECOLOGY

Rapid homoploid hybrid speciation in British gardens: The origin of Oxford ragwort ( Senecio squalidus )

(2020) Bruno Nevado et al.   MOLECULAR ECOLOGY

Monarch butterfly and milkweed declines substantially predate the use of genetically modified crops

(2019) J. H. Boyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Importance of Shifting Disturbance Regimes in Monarch Butterfly Decline and Recovery

(2019) Nathan L. Haan et al.   Frontiers in Ecology and Evolution

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

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

A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae

(2019) Kevin Weitemier et al.   PeerJ

Demographic inference in barn swallows using whole-genome data shows signal for bottleneck and subspecies differentiation during the Holocene

(2018) Chris C. R. Smith et al.   MOLECULAR ECOLOGY

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

(2018) Luca Venturini et al.   GigaScience

ABC random forests for Bayesian parameter inference

(2018) Louis Raynal et al.   BIOINFORMATICS

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly

(2018) Gui-Cai Xu et al.   GigaScience

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

(2018) Daniel Mapleson et al.   GigaScience

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

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

Multiple introductions, admixture and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia in Europe and Australia

(2017) Lotte A. van Boheemen et al.   MOLECULAR ECOLOGY

The K = 2 conundrum

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

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Monarch butterfly population decline in North America: identifying the threatening processes

(2017) Wayne E. Thogmartin et al.   Royal Society Open Science

Interpreting surveys to estimate the size of the monarch butterfly population: Pitfalls and prospects

(2017) John M. Pleasants et al.   PLoS One

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Linking the continental migratory cycle of the monarch butterfly to understand its population decline

(2016) Hidetoshi Inamine et al.   OIKOS

Quasi-extinction risk and population targets for the Eastern, migratory population of monarch butterflies (Danaus plexippus)

(2016) Brice X. Semmens et al.   Scientific Reports

Reliable ABC model choice via random forests

(2015) Pierre Pudlo et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

The genetics of monarch butterfly migration and warning colouration

(2014) Shuai Zhan et al.   NATURE

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Milkweed loss in agricultural fields because of herbicide use: effect on the monarch butterfly population

(2012) JOHN M. PLEASANTS et al.   Insect Conservation and Diversity

Lack of genetic differentiation between monarch butterflies with divergent migration destinations

(2012) JUSTINE I. LYONS et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

The Monarch Butterfly Genome Yields Insights into Long-Distance Migration

(2011) Shuai Zhan et al.   CELL

Decline of monarch butterflies overwintering in Mexico: is the migratory phenomenon at risk?

(2011) LINCOLN P. BROWER et al.   Insect Conservation and Diversity

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

(2011) Mark A DePristo et al.   NATURE GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

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

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

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   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

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

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS