Determinants of genetic variation across eco-evolutionary scales in pinnipeds

Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data

(2019) Vera M. Warmuth et al.   Molecular Ecology Resources

The determinants of genetic diversity in butterflies

(2019) Alexander Mackintosh et al.   Nature Communications

The inference of gray whale (Eschrichtius robustus) historical population attributes from whole-genome sequences

(2018) Anna Brüniche-Olsen et al.   BMC EVOLUTIONARY BIOLOGY

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding

(2018) Emily Humble et al.   G3-Genes Genomes Genetics

Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history

(2018) M. A. Stoffel et al.   Nature Communications

Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds

(2017) Fidel Botero-Castro et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

(2017) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

The mutation rate in human evolution and demographic inference

(2016) Aylwyn Scally   CURRENT OPINION IN GENETICS & DEVELOPMENT

Making sense of the relationships between Ne, Nb and Nc towards defining conservation thresholds in Atlantic salmon (Salmo salar)

(2016) A-L Ferchaud et al.   HEREDITY

Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes

(2016) Emeric Figuet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Making sense of genetic estimates of effective population size

(2016) Robin S. Waples   MOLECULAR ECOLOGY

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex

(2015) A Brelsford et al.   HEREDITY

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

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

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

(2015) Russell B. Corbett-Detig et al.   PLOS BIOLOGY

Accelerated modern human-induced species losses: Entering the sixth mass extinction

(2015) G. Ceballos et al.   Science Advances

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

DISENTANGLING THE CONTRIBUTION OF SEXUAL SELECTION AND ECOLOGY TO THE EVOLUTION OF SIZE DIMORPHISM IN PINNIPEDS

(2014) Oliver Krüger et al.   EVOLUTION

Purifying Selection, Drift, and Reversible Mutation with Arbitrarily High Mutation Rates

(2014) Brian Charlesworth et al.   GENETICS

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

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

Taxonomic status of two subspecies of South American fur seals:Arctocephalus australis australis vs.A. a. gracilis

(2014) Larissa Rosa de Oliveira et al.   MARINE MAMMAL SCIENCE

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies

(2014) Tommi Nyman et al.   Ecology and Evolution

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Simple life-history traits explain key effective population size ratios across diverse taxa

(2013) R. S. Waples et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping

(2012) Jonathan Romiguier et al.   PLoS One

Effective/census population size ratio estimation: a compendium and appraisal

(2012) Friso P. Palstra et al.   Ecology and Evolution

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

Global threats to pinnipeds

(2011) Kit M. Kovacs et al.   MARINE MAMMAL SCIENCE

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

(2010) L. Chikhi et al.   GENETICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

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

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence?

(2008) FRISO P. PALSTRA et al.   MOLECULAR ECOLOGY