Application of next-generation sequencing to the study of non-model insects

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

(2016) Andrew Donovan Young et al.   BMC EVOLUTIONARY BIOLOGY

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Genomic divergence and lack of introgressive hybridization between two 13-year periodical cicadas support life cycle switching in the face of climate change

(2016) Takuya Koyama et al.   MOLECULAR ECOLOGY

Genome-wide sequence data suggest the possibility of pollinator sharing by host shift in dioecious figs (Moraceae,Ficus)

(2016) Nakatada Wachi et al.   MOLECULAR ECOLOGY

Lack of genetic variation prevents adaptation at the geographic range margin in a damselfly

(2016) Yuma Takahashi et al.   MOLECULAR ECOLOGY

Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga

(2016) Bonnie B. Blaimer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Harnessing the power of RADseq for ecological and evolutionary genomics

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

No evidence for extensive horizontal gene transfer in the genome of the tardigradeHypsibius dujardini

(2016) Georgios Koutsovoulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius

(2016) Jeffrey A. Rosenfeld et al.   Nature Communications

The Report of My Death was an Exaggeration: A Review for Researchers Using Microsatellites in the 21st Century

(2016) Richard G. J. Hodel et al.   Applications in Plant Sciences

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

(2016) Tom O. Delmont et al.   PeerJ

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data

(2016) Lauren Coombe et al.   PLoS One

Collections-based research in the genomic era

(2015) Sven Buerki et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

(2015) Bonnie B. Blaimer et al.   BMC EVOLUTIONARY BIOLOGY

Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

(2015) Scott P. Egan et al.   ECOLOGY LETTERS

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

Rapid diversification associated with ecological specialization in NeotropicalAdelphabutterflies

(2015) Emily R. Ebel et al.   MOLECULAR ECOLOGY

High-throughput DNA barcoding for ecological network studies

(2015) Hirokazu Toju   POPULATION ECOLOGY

Development of microsatellite markers for two endangered grassland butterflies, Melitaea ambigua and M. protomedia (Nymphalidae), using Ion Torrent next-generation sequencing

(2015) Naoyuki Nakahama et al.   Conservation Genetics Resources

MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform

(2015) Yoshihisa Suyama et al.   Scientific Reports

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

Rapid Convergent Evolution in Wild Crickets

(2014) Sonia Pascoal et al.   CURRENT BIOLOGY

Genome size increase in the phytophagous ladybird beetleHenosepilachna vigintioctomaculataspecies complex (Coleoptera: Coccinellidae)

(2014) Kei W. Matsubayashi et al.   ENTOMOLOGICAL SCIENCE

Population genomics of parallel hybrid zones in the mimetic butterflies,H. melpomeneandH. erato

(2014) Nicola J. Nadeau et al.   GENOME RESEARCH

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud et al.   MOLECULAR BIOLOGY AND EVOLUTION

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock

(2014) Tetsumi Takahashi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Complementary molecular information changes our perception of food web structure

(2014) Helena K. Wirta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics provides strong evidence for relationships of butterflies and moths

(2014) A. Y. Kawahara et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

(2014) Joanna L. Kelley et al.   Nature Communications

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Phylogenomics Resolves Evolutionary Relationships among Ants, Bees, and Wasps

(2013) Brian R. Johnson et al.   CURRENT BIOLOGY

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

Genome sizes of three species in the subtribe Carabina (Coleoptera: Carabidae)

(2012) Teiji Sota et al.   ENTOMOLOGICAL SCIENCE

LARGE-SCALE CANDIDATE GENE SCAN REVEALS THE ROLE OF CHEMORECEPTOR GENES IN HOST PLANT SPECIALIZATION AND SPECIATION IN THE PEA APHID

(2012) Carole M. Smadja et al.   EVOLUTION

The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets

(2012) Christelle Godel et al.   FASEB JOURNAL

Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

(2012) Leigh A. Nelson et al.   GENE

Genome-wide patterns of divergence and gene flow across a butterfly radiation

(2012) Nicola J. Nadeau et al.   MOLECULAR ECOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Simultaneous genome sequencing of symbionts and their hosts

(2012) Sujai Kumar et al.   SYMBIOSIS

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

(2011) Seth M. Bybee et al.   Genome Biology and Evolution

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

A guide to the genomics of ecological speciation in natural animal populations

(2010) Amber M. Rice et al.   ECOLOGY LETTERS

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Rapid Microsatellite Development for Water Striders by Next-Generation Sequencing

(2010) Jen C. Perry et al.   JOURNAL OF HEREDITY

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

(2010) M. J. T. N. Timmermans et al.   NUCLEIC ACIDS RESEARCH

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations

(2010) Nicola J. Nadeau et al.   TRENDS IN GENETICS

Microsatellite discovery by deep sequencing of enriched genomic libraries

(2009) Quentin C. Santana et al.   BIOTECHNIQUES

What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae)

(2009) David A Rasmussen et al.   BMC GENOMICS

Parallel tagged sequencing on the 454 platform

(2008) Matthias Meyer et al.   Nature Protocols

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One