Ancient and modern stickleback genomes reveal the demographic constraints on adaptation

Confidently identifying the correct K value using the Δ K method: When does K  = 2?

(2020) Catherine I. Cullingham et al.   MOLECULAR ECOLOGY

Present‐Day DNA Contamination in Ancient DNA Datasets

(2020) Stéphane Peyrégne et al.   BIOESSAYS

On the causes of geographically heterogeneous parallel evolution in sticklebacks

(2020) Bohao Fang et al.   Nature Ecology & Evolution

Unlocking the potential of ancient fish DNA in the genomic era

(2019) Tom Oosting et al.   Evolutionary Applications

Architecture of Parallel Adaptation in Ten Lacustrine Threespine Stickleback Populations from the White Sea Area

(2019) Nadezhda V Terekhanova et al.   Genome Biology and Evolution

A Few Stickleback Suffice for the Transport of Alleles to New Lakes

(2019) Jared Galloway et al.   G3-Genes Genomes Genetics

Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback

(2018) Matthew R. J. Morris et al.   BMC EVOLUTIONARY BIOLOGY

Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

(2018) Francisco C. Ceballos et al.   BMC GENOMICS

Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback

(2018) Susan Bassham et al.   GENETICS

Genomic parallelism and lack thereof in contrasting systems of three-spine sticklebacks

(2018) Shenglin Liu et al.   MOLECULAR ECOLOGY

Worldwide phylogeny of three-spined sticklebacks

(2018) Bohao Fang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Runs of homozygosity: windows into population history and trait architecture

(2018) Francisco C. Ceballos et al.   NATURE REVIEWS GENETICS

Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback

(2018) Susan Bassham et al.   GENETICS

Quantifying variable rates of postglacial relative sea level fall from a cluster of 24 isolation basins in southern Norway

(2018) Anders Romundset et al.   QUATERNARY SCIENCE REVIEWS

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots

(2018) Daniel J. Lawson et al.   Nature Communications

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

The K = 2 conundrum

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

Evolving New Skeletal Traits by cis -Regulatory Changes in Bone Morphogenetic Proteins

(2016) Vahan B. Indjeian et al.   CELL

Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication

(2016) Jazmín Ramos-Madrigal et al.   CURRENT BIOLOGY

Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences

(2016) Shenglin Liu et al.   MOLECULAR ECOLOGY

The genetic and molecular architecture of phenotypic diversity in sticklebacks

(2016) Catherine L. Peichel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds

(2015) Pontus Skoglund et al.   CURRENT BIOLOGY

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

(2015) Eleftheria Palkopoulou et al.   CURRENT BIOLOGY

Evolution of stickleback in 50 years on earthquake-uplifted islands

(2015) Emily A. Lescak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

(2015) Philine G. D. Feulner et al.   PLoS Genetics

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

A Holocene sea-level curve and revised isobase map based on isolation basins from near the southern tip of Norway

(2014) Anders Romundset et al.   BOREAS

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

(2014) Pontus Skoglund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Ancient DNA Damage

(2013) J. Dabney et al.   Cold Spring Harbor Perspectives in Biology

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

GLOBAL ANALYSIS OF GENES INVOLVED IN FRESHWATER ADAPTATION IN THREESPINE STICKLEBACKS (GASTEROSTEUS ACULEATUS)

(2011) Jacquelin DeFaveri et al.   EVOLUTION

Testing for Ancient Admixture between Closely Related Populations

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

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Postglacial uplift and relative sea level changes in Finnmark, northern Norway

(2011) Anders Romundset et al.   QUATERNARY SCIENCE REVIEWS

Lake Boksehandsken's earliest postglacial sediments and their palaeoenvironmental implications, Jameson Land, East Greenland

(2010) SVANTE BJÖRCK et al.   BOREAS

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

Genetics and ecological speciation

(2009) D. Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics

Mitochondrial DNA phylogeography of the three-spined stickleback (Gasterosteus aculeatus) in Europe—Evidence for multiple glacial refugia

(2007) H.S. Mäkinen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION