Understanding the origin of species with genome-scale data: modelling gene flow

Approximate Bayesian Computation

(2013) Mikael Sunnåker et al.   PLoS Computational Biology

Length Distributions of Identity by Descent Reveal Fine-Scale Demographic History

(2012) Pier Francesco Palamara et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identity by Descent Between Distant Relatives: Detection and Applications

(2012) Sharon R. Browning et al.   Annual Review of Genetics

Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation

(2012) Sen Li et al.   BMC GENETICS

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

(2012) Joseph Lachance et al.   CELL

HYBRID SPECIATION AND INDEPENDENT EVOLUTION IN LINEAGES OF ALPINE BUTTERFLIES

(2012) Chris C. Nice et al.   EVOLUTION

Population Genetics Models of Local Ancestry

(2012) S. Gravel   GENETICS

Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion

(2012) S. Lukic et al.   GENETICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Inferring Population Histories Using Genome-Wide Allele Frequency Data

(2012) Mathieu Gautier et al.   MOLECULAR BIOLOGY AND EVOLUTION

A likelihood-based comparison of population histories in a parasitoid guild

(2012) Konrad Lohse et al.   MOLECULAR ECOLOGY

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

(2012) A. Eriksson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Date of Interbreeding between Neandertals and Modern Humans

(2012) Sriram Sankararaman et al.   PLoS Genetics

Population Genomics of Inversion Polymorphisms in Drosophila melanogaster

(2012) Russell B. Corbett-Detig et al.   PLoS Genetics

Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

(2012) John E. Pool et al.   PLoS Genetics

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

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

A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

(2012) Thomas Mailund et al.   PLoS Genetics

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

(2011) Laurent Excoffier et al.   BIOINFORMATICS

An Accurate Sequentially Markov Conditional Sampling Distribution for the Coalescent With Recombination

(2011) J. S. Paul et al.   GENETICS

A Hierarchical Bayesian Model for Next-Generation Population Genomics

(2011) Z. Gompert et al.   GENETICS

A General Method for Calculating Likelihoods Under the Coalescent Process

(2011) K. Lohse et al.   GENETICS

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

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

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

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

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

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-equilibrium allele frequency spectra via spectral methods

(2011) Sergio Lukić et al.   THEORETICAL POPULATION BIOLOGY

Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

(2011) Thomas Mailund et al.   PLoS Genetics

Dating the age of admixture via wavelet transform analysis of genome-wide data

(2011) Irina Pugach et al.   GENOME BIOLOGY

Divergence with Gene Flow: Models and Data

(2010) Catarina Pinho et al.   Annual Review of Ecology Evolution and Systematics

Approximate Bayesian Computation in Evolution and Ecology

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

Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations

(2010) P. Beerli et al.   GENETICS

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

Reconstructing Population Histories from Single Nucleotide Polymorphism Data

(2010) J. Siren et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantifying population structure using the F-model

(2010) OSCAR E. GAGGIOTTI et al.   Molecular Ecology Resources

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

(2010) Bridgett M. vonHoldt et al.   NATURE

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Adaptation genomics: the next generation

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

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Estimating Divergence Parameters With Small Samples From a Large Number of Loci

(2009) Y. Wang et al.   GENETICS

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

Statistical inferences in phylogeography

(2009) RASMUS NIELSEN et al.   MOLECULAR ECOLOGY

Darwin's bridge between microevolution and macroevolution

(2009) David N. Reznick et al.   NATURE

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Correcting the Site Frequency Spectrum for Divergence-Based Ascertainment

(2009) Andrew D. Kern   PLoS One

An approximate likelihood for genetic data under a model with recombination and population splitting

(2009) D. Davison et al.   THEORETICAL POPULATION BIOLOGY

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

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

Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts

(2008) J. E. Pool et al.   GENETICS

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS

Bayesian inference of fine-scale recombination rates using population genomic data

(2008) Y. Wang et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Can one learn history from the allelic spectrum?

(2008) Simon Myers et al.   THEORETICAL POPULATION BIOLOGY

Coalescent genealogy samplers: windows into population history

(2008) Mary K. Kuhner   TRENDS IN ECOLOGY & EVOLUTION

Inferring Human Colonization History Using a Copying Model

(2008) Garrett Hellenthal et al.   PLoS Genetics