Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics

Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

(2017) Ethan B. Linck et al.   Ecology and Evolution

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

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

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

(2016) Tomasz Suchan et al.   PLoS One

Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing

(2015) Jose Alfredo Samaniego Castruita et al.   BMC BIOINFORMATICS

Consequences of extensive habitat fragmentation in landscape-level patterns of genetic diversity and structure in the Mediterranean esparto grasshopper

(2015) Joaquín Ortego et al.   Evolutionary Applications

Does phylogeographical structure relate to climatic niche divergence? A test using maritime pine (Pinus pinaster Ait.)

(2015) M. J. Serra-Varela et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Hybridization promotes speciation in Coenonympha butterflies

(2015) Thibaut Capblancq et al.   MOLECULAR ECOLOGY

Echoes of a distant time: effects of historical processes on contemporary genetic patterns inGalaxias plateiin Patagonia

(2015) Iván Vera-Escalona et al.   MOLECULAR ECOLOGY

Past climate change drives current genetic structure of an endangered freshwater mussel species

(2015) Kentaro Inoue et al.   MOLECULAR ECOLOGY

Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus

(2015) Aaron B. A. Shafer et al.   MOLECULAR ECOLOGY

Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape

(2015) Bertrand Gauffre et al.   MOLECULAR ECOLOGY

Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

(2015) Carlo Pacioni et al.   MOLECULAR ECOLOGY

The population demography ofBetula maximowicziana, a cool-temperate tree species in Japan, in relation to the last glacial period: its admixture-like genetic structure is the result of simple population splitting not admixing

(2015) Y. Tsuda et al.   MOLECULAR ECOLOGY

Multivariate and Propensity Score Matching Software with Automated Balance Optimization: TheMatchingPackage forR

(2015) Jasjeet S. Sekhon   Journal of Statistical Software

Pragmatic Perspective on Conservation Genetics and Demographic History of the Last Surviving Population of Kashmir Red Deer (Cervus elaphus hanglu) in India

(2015) Mukesh et al.   PLoS One

The Historical Demography and Genetic Variation of the Endangered Cycas multipinnata (Cycadaceae) in the Red River Region, Examined by Chloroplast DNA Sequences and Microsatellite Markers

(2015) Yi-Qing Gong et al.   PLoS One

The future of ancient DNA: Technical advances and conceptual shifts

(2014) Michael Hofreiter et al.   BIOESSAYS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Museum DNA reveals the demographic history of the endangered Seychelles warbler

(2014) Lewis G. Spurgin et al.   Evolutionary Applications

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

(2014) Anil Raj et al.   GENETICS

Genetic depletion at adaptive but not neutral loci in an endangered bird species

(2014) Stefanie A. Hartmann 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

Multiple independent colonization of the Canary Islands by the winged grasshopper genus Sphingonotus Fieber, 1852

(2014) Martin Husemann et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

(2014) Mandy Man-Ying Tin et al.   PLoS One

Genetic diversity, demographical history and conservation aspects of the endangered yew tree Taxus contorta (syn. Taxus fuana) in Pakistan

(2014) Ram C. Poudel et al.   Tree Genetics & Genomes

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

Is functional connectivity in common grasshopper species affected by fragmentation in an agricultural landscape?

(2013) Daniela Keller et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Genetic signature of a recent metapopulation bottleneck in the olive ridley turtle (Lepidochelys olivacea) after intensive commercial exploitation in Mexico

(2013) Clara J. Rodríguez-Zárate et al.   BIOLOGICAL CONSERVATION

The genetic structure of crossbills suggests rapid diversification with little niche conservatism

(2013) Mats Björklund et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The relevance of time series in molecular ecology and conservation biology

(2013) Jan C. Habel et al.   BIOLOGICAL REVIEWS

Palaearctic biogeography revisited: evidence for the existence of a North African refugium for Western Palaearctic biota

(2013) Martin Husemann et al.   JOURNAL OF BIOGEOGRAPHY

Morphological, ecological and genetic aspects associated with endemism in the Fly Orchid group

(2013) Yann Triponez et al.   MOLECULAR ECOLOGY

Meta-analysis reveals lower genetic diversity in overfished populations

(2013) Malin L. Pinsky et al.   MOLECULAR ECOLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

A wide geographical survey of mitochondrial DNA variation in the great spotted woodpecker complex,Dendrocopos major(Aves: Picidae)

(2012) Utku Perktaş et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Conservation of phylogeographic lineages under climate change

(2012) Manuela D’Amen et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus

(2012) Eveline Kindler et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Signature of a Pre-Human Population Decline in the Critically Endangered Reunion Island Endemic Forest Bird Coracina newtoni

(2012) Jordi Salmona et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Museums and disease: Using tissue archive and museum samples to study pathogens

(2011) Kyriakos Tsangaras et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett 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

Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion

(2011) Line V Ugelvig et al.   BMC EVOLUTIONARY BIOLOGY

Strong decline of gene diversity in local populations of the highly endangered Common hamster (Cricetus cricetus) in the western part of its European range

(2011) M. J. J. La Haye et al.   CONSERVATION GENETICS

and D do not replace FST

(2011) MICHAEL C. WHITLOCK   MOLECULAR ECOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

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

(2010) E. Paradis   BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biological collections and ecological/environmental research: a review, some observations and a look to the future

(2009) Graham H. Pyke et al.   BIOLOGICAL REVIEWS

Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies

(2009) UMA RAMAKRISHNAN et al.   MOLECULAR ECOLOGY

Transalpine colonisation and partial phylogeographic erosion by dispersal in the common vole (Microtus arvalis)

(2009) SONJA BRAAKER et al.   MOLECULAR ECOLOGY

Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

(2009) MICHAEL M. HANSEN et al.   MOLECULAR ECOLOGY

ADZE: a rarefaction approach for counting alleles private to combinations of populations

(2008) Z. A. Szpiech et al.   BIOINFORMATICS

Bayesian inference of population size history from multiple loci

(2008) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Unprecedented long-term genetic monomorphism in an endangered relict butterfly species

(2008) Jan Christian Habel et al.   CONSERVATION GENETICS

Italy as a major Ice Age refuge area for the batMyotis myotis(Chiroptera: Vespertilionidae) in Europe

(2008) MANUEL RUEDI et al.   MOLECULAR ECOLOGY

Multiple Colonizations, In Situ Speciation, and Volcanism-Associated Stepping-Stone Dispersals Shaped the Phylogeography of the Macaronesian Red Fescues (Festuca L., Gramineae)

(2008) Antonio Díaz-Pérez et al.   SYSTEMATIC BIOLOGY

Colonization and speciation on volcanic islands: phylogeography of the flightless grasshopper genusArminda(Orthoptera, Acrididae) on the Canary Islands

(2008) AXEL HOCHKIRCH et al.   SYSTEMATIC ENTOMOLOGY