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A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471250953.bi1110s43openalex-snapshot

From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

inferredcites →https://doi.org/10.1002/evl3.99openalex-snapshot

Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish

inferredcites →https://doi.org/10.1007/978-3-319-24277-4openalex-snapshot

ggplot2

inferredcites →https://doi.org/10.1007/s00227-020-03705-xopenalex-snapshot

Adaptive evolution of low-salinity tolerance and hypoosmotic regulation in a euryhaline teleost, Takifugu obscurus

inferredcites →https://doi.org/10.1016/j.ajhg.2015.12.022openalex-snapshot

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

inferredcites →https://doi.org/10.1016/j.cell.2023.01.042openalex-snapshot

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation

inferredcites →https://doi.org/10.1016/j.csbj.2017.10.001openalex-snapshot

Challenges in the Setup of Large-scale Next-Generation Sequencing Analysis Workflows

inferredcites →https://doi.org/10.1016/j.cub.2018.08.066openalex-snapshot

Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes

inferredcites →https://doi.org/10.1016/j.cub.2018.12.044openalex-snapshot

A Single Interacting Species Leads to Widespread Parallel Evolution of the Stickleback Genome

inferredcites →https://doi.org/10.1016/j.cub.2021.02.027openalex-snapshot

Ancient and modern stickleback genomes reveal the demographic constraints on adaptation

inferredcites →https://doi.org/10.1016/j.tree.2013.09.008openalex-snapshot

Genome sequencing and population genomics in non-model organisms

inferredcites →https://doi.org/10.1017/s0016672300014634openalex-snapshot

The hitch-hiking effect of a favourable gene

inferredcites →https://doi.org/10.1038/351652a0openalex-snapshot

Adaptive protein evolution at the Adh locus in Drosophila

inferredcites →https://doi.org/10.1038/nature10944openalex-snapshot

The genomic basis of adaptive evolution in threespine sticklebacks

inferredcites →https://doi.org/10.1038/nature13408openalex-snapshot

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

inferredcites →https://doi.org/10.1038/nature13685openalex-snapshot

Comparative population genomics in animals uncovers the determinants of genetic diversity

inferredcites →https://doi.org/10.1038/nature14181openalex-snapshot

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

inferredcites →https://doi.org/10.1038/nature19057openalex-snapshot

Analysis of protein-coding genetic variation in 60,706 humans

inferredcites →https://doi.org/10.1038/nature21347openalex-snapshot

Tracing the peopling of the world through genomics

inferredcites →https://doi.org/10.1038/ncomms10474openalex-snapshot

Evolutionary signals of selection on cognition from the great tit genome and methylome

inferredcites →https://doi.org/10.1038/ncomms13195openalex-snapshot

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

inferredcites →https://doi.org/10.1038/ng.2588openalex-snapshot

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

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An intercross population study reveals genes associated with body size and plumage color in ducks

inferredcites →https://doi.org/10.1038/s41467-018-06159-4openalex-snapshot

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

inferredcites →https://doi.org/10.1038/s41467-021-21379-xopenalex-snapshot

Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

inferredcites →https://doi.org/10.1038/s41467-021-21697-0openalex-snapshot

Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes

inferredcites →https://doi.org/10.1038/s41559-017-0437-7openalex-snapshot

Variation and constraints in hybrid genome formation

inferredcites →https://doi.org/10.1038/s41559-018-0717-xopenalex-snapshot

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

inferredcites →https://doi.org/10.1038/s41559-019-0814-5openalex-snapshot

Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence

inferredcites →https://doi.org/10.1038/s41586-020-2845-0openalex-snapshot

Contrasting signatures of genomic divergence during sympatric speciation

inferredcites →https://doi.org/10.1038/s41586-020-2873-9openalex-snapshot

Dense sampling of bird diversity increases power of comparative genomics

inferredcites →https://doi.org/10.1038/s41586-021-03265-0openalex-snapshot

Climate-driven flyway changes and memory-based long-distance migration

inferredcites →https://doi.org/10.1038/s41586-021-03451-0openalex-snapshot

Towards complete and error-free genome assemblies of all vertebrate species

inferredcites →https://doi.org/10.1038/s41586-023-06045-0openalex-snapshot

A genomic mutational constraint map using variation in 76,156 human genomes

inferredcites →https://doi.org/10.1038/s41587-019-0053-yopenalex-snapshot

How bioinformatics and open data can boost basic science in countries and universities with limited resources

inferredcites →https://doi.org/10.1038/s41592-021-01254-9openalex-snapshot

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

inferredcites →https://doi.org/10.1038/s41598-020-75387-wopenalex-snapshot

Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes

inferredcites →https://doi.org/10.1038/s43588-021-00085-0openalex-snapshot

Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools

inferredcites →https://doi.org/10.1038/sdata.2019.21openalex-snapshot

The variable quality of metadata about biological samples used in biomedical experiments

inferredcites →https://doi.org/10.1038/srep14256openalex-snapshot

Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas

inferredcites →https://doi.org/10.1073/pnas.1220835110openalex-snapshot

Frequent adaptation and the McDonald–Kreitman test

inferredcites →https://doi.org/10.1073/pnas.1617728114openalex-snapshot

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

inferredcites →https://doi.org/10.1073/pnas.1702909114openalex-snapshot

Spatially restricted dental regeneration drives pufferfish beak development

inferredcites →https://doi.org/10.1073/pnas.1908332116openalex-snapshot

Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin

inferredcites →https://doi.org/10.1073/pnas.2107934118openalex-snapshot

Poor data stewardship will hinder global genetic diversity surveillance

inferredcites →https://doi.org/10.1073/pnas.2115635118openalex-snapshot

The Earth BioGenome Project 2020: Starting the clock

inferredcites →https://doi.org/10.1073/pnas.2202862119openalex-snapshot

An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice

inferredcites →https://doi.org/10.1086/519795openalex-snapshot

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btaa222openalex-snapshot

GenMap: ultra-fast computation of genome mappability

inferredcites →https://doi.org/10.1093/bioinformatics/btac600openalex-snapshot

grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads

inferredcites →https://doi.org/10.1093/bioinformatics/btac667openalex-snapshot

Metadata retrieval from sequence databases with ffq

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btq351openalex-snapshot

BigWig and BigBed: enabling browsing of large distributed datasets

inferredcites →https://doi.org/10.1093/bioinformatics/btq559openalex-snapshot

Robust relationship inference in genome-wide association studies

inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot

The variant call format and VCFtools

inferredcites →https://doi.org/10.1093/bioinformatics/btt637openalex-snapshot

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

inferredcites →https://doi.org/10.1093/bioinformatics/btv098openalex-snapshot

Sambamba: fast processing of NGS alignment formats

inferredcites →https://doi.org/10.1093/bioinformatics/btx699openalex-snapshot

Mosdepth: quick coverage calculation for genomes and exomes

inferredcites →https://doi.org/10.1093/bioinformatics/bty560openalex-snapshot

fastp: an ultra-fast all-in-one FASTQ preprocessor

inferredcites →https://doi.org/10.1093/bioinformatics/bty633openalex-snapshot

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

inferredcites →https://doi.org/10.1093/g3journal/jkad117openalex-snapshot

Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data

inferredcites →https://doi.org/10.1093/gbe/evaa065openalex-snapshot

Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations

inferredcites →https://doi.org/10.1093/gbe/evx067openalex-snapshot

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations

inferredcites →https://doi.org/10.1093/gbe/evz110openalex-snapshot

Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis

inferredcites →https://doi.org/10.1093/gbe/evz249openalex-snapshot

Genome assembly of the common pheasant Phasianus colchicus, a model for speciation and ecological genomics

inferredcites →https://doi.org/10.1093/genetics/123.3.585openalex-snapshot

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

inferredcites →https://doi.org/10.1093/gigascience/giab008openalex-snapshot

Twelve years of SAMtools and BCFtools

inferredcites →https://doi.org/10.1093/gigascience/giy049openalex-snapshot

Population genomic data reveal genes related to important traits of quail

inferredcites →https://doi.org/10.1093/gigascience/giz111openalex-snapshot

Genomic evidence of neo-sex chromosomes in the eastern yellow robin

inferredcites →https://doi.org/10.1093/molbev/msq249openalex-snapshot

Estimation of the Neutrality Index

inferredcites →https://doi.org/10.1093/molbev/msv078openalex-snapshot

Purifying Selection Maintains Dosage-Sensitive Genes during Degeneration of the Threespine Stickleback Y Chromosome

inferredcites →https://doi.org/10.1093/molbev/msy181openalex-snapshot

The Origin of a New Sex Chromosome by Introgression between Two Stickleback Fishes

inferredcites →https://doi.org/10.1093/molbev/msy194openalex-snapshot

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

inferredcites →https://doi.org/10.1093/nar/gkaa892openalex-snapshot

Database resources of the National Center for Biotechnology Information

inferredcites →https://doi.org/10.1093/nar/gkh073openalex-snapshot

Database resources of the National Center for Biotechnology Information: update

inferredcites →https://doi.org/10.1093/nar/gkq1019openalex-snapshot

The Sequence Read Archive

inferredcites →https://doi.org/10.1093/nar/gkr1006openalex-snapshot

The International Nucleotide Sequence Database Collaboration

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025634openalex-snapshot

Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans

inferredcites →https://doi.org/10.1098/rspb.2018.0206openalex-snapshot

Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas

inferredcites →https://doi.org/10.1098/rspb.2018.1246openalex-snapshot

Signatures of human-commensalism in the house sparrow genome

inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot

Fast model-based estimation of ancestry in unrelated individuals

inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

inferredcites →https://doi.org/10.1101/gr.196485.115openalex-snapshot

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

inferredcites →https://doi.org/10.1109/mic.2011.64openalex-snapshot

Globus Online: Accelerating and Democratizing Science through Cloud-Based Services

inferredcites →https://doi.org/10.1111/1755-0998.12498openalex-snapshot

Whole‐genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations

inferredcites →https://doi.org/10.1111/1755-0998.13070openalex-snapshot

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

inferredcites →https://doi.org/10.1111/ahg.12383openalex-snapshot

Thousands of missing variants in the UK Biobank are recoverable by genome realignment

inferredcites →https://doi.org/10.1111/eva.12659openalex-snapshot

Recent advances in conservation and population genomics data analysis

inferredcites →https://doi.org/10.1111/evo.13175openalex-snapshot

Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes

inferredcites →https://doi.org/10.1111/evo.14120openalex-snapshot

Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population

inferredcites →https://doi.org/10.1111/mec.12693openalex-snapshot

Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics

inferredcites →https://doi.org/10.1111/mec.13827openalex-snapshot

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

inferredcites →https://doi.org/10.1111/mec.15310openalex-snapshot

Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe

inferredcites →https://doi.org/10.1111/mec.15885openalex-snapshot

Sex‐linked genetic diversity and differentiation in a globally distributed avian species complex

inferredcites →https://doi.org/10.1111/mec.16077openalex-snapshot

A beginner's guide to low‐coverage whole genome sequencing for population genomics

inferredcites →https://doi.org/10.1126/sciadv.1602996openalex-snapshot

The genomic mosaicism of hybrid speciation

inferredcites →https://doi.org/10.1126/sciadv.abg5391openalex-snapshot

Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes

inferredcites →https://doi.org/10.1126/science.1253226openalex-snapshot

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

inferredcites →https://doi.org/10.1126/science.aac9927openalex-snapshot

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

inferredcites →https://doi.org/10.1126/science.aad0843openalex-snapshot

Stable recombination hotspots in birds

inferredcites →https://doi.org/10.1126/science.aal3298openalex-snapshot

Recent natural selection causes adaptive evolution of an avian polygenic trait

inferredcites →https://doi.org/10.1126/science.aar5273openalex-snapshot

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

inferredcites →https://doi.org/10.1126/science.abn5642openalex-snapshot

Genetic diversity loss in the Anthropocene

inferredcites →https://doi.org/10.1136/jmg.35.4.273openalex-snapshot

Alport syndrome, mental retardation, midface hypoplasia, and elliptocytosis: a new X linked contiguous gene deletion syndrome?

inferredcites →https://doi.org/10.1145/2076450.2076468openalex-snapshot

Software as a service for data scientists

inferredcites →https://doi.org/10.1186/s12859-019-3169-7openalex-snapshot

Recommendations for performance optimizations when using GATK3.8 and GATK4

inferredcites →https://doi.org/10.1186/s12859-021-04407-xopenalex-snapshot

Comparison of sequencing data processing pipelines and application to underrepresented African human populations

inferredcites →https://doi.org/10.1186/s12864-021-07710-2openalex-snapshot

Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China

inferredcites →https://doi.org/10.1186/s13059-014-0557-1openalex-snapshot

Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species

inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot

Second-generation PLINK: rising to the challenge of larger and richer datasets

inferredcites →https://doi.org/10.1201/9780429447273openalex-snapshot

Interactive Web-Based Data Visualization with R, plotly, and shiny

inferredcites →https://doi.org/10.12688/f1000research.29032.1openalex-snapshot

Sustainable data analysis with Snakemake

inferredcites →https://doi.org/10.12688/f1000research.29032.2openalex-snapshot

Sustainable data analysis with Snakemake

inferredcites →https://doi.org/10.1371/journal.pbio.1002112openalex-snapshot

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

inferredcites →https://doi.org/10.1371/journal.pbio.2001627openalex-snapshot

Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments

inferredcites →https://doi.org/10.1371/journal.pgen.1004223openalex-snapshot

Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species

inferredcites →https://doi.org/10.1371/journal.pgen.1004966openalex-snapshot

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

inferredcites →https://doi.org/10.1371/journal.pgen.1006044openalex-snapshot

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

inferredcites →https://doi.org/10.1534/g3.113.008722openalex-snapshot

Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish

inferredcites →https://doi.org/10.18637/jss.v021.i11openalex-snapshot

boa : An R Package for MCMC Output Convergence Assessment and Posterior Inference

inferredcites →https://doi.org/10.18637/jss.v021.i12openalex-snapshot

Reshaping Data with the reshape Package

inferredcites →https://doi.org/10.21105/joss.01686openalex-snapshot

Welcome to the Tidyverse

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.32614/rj-2013-014openalex-snapshot

ggmap: Spatial Visualization with ggplot2

inferredcites →https://doi.org/10.3389/fgene.2019.00736openalex-snapshot

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy

inferredcites →https://doi.org/10.48550/arxiv.1303.3997openalex-snapshot

Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

inferredcites →https://doi.org/10.7554/elife.23907openalex-snapshot

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

inferredcites →https://doi.org/10.7554/elife.43785openalex-snapshot

Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks

inferredcites →https://doi.org/10.7554/elife.54462openalex-snapshot

The evolutionary history and genomics of European blackcap migration

inferredcites →https://doi.org/10.7554/elife.61076openalex-snapshot

Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci

inferredcites →https://doi.org/10.7554/elife.67509openalex-snapshot

Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin’s Paradox

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3897/zookeys.1244.141409zenodo-depositor-declared

A new species of Anemonefish from French Polynesia, Amphiprion maohiensis, (Pomacentridae, Amphiprioninae), the Polynesian anemonefish

inferred← citeshttps://doi.org/10.1002/ece3.71846openalex-snapshot

Genomic Landscape of High‐Altitude Adaptation in East African Mountain Honey Bees ( Apis mellifera )

inferred← citeshttps://doi.org/10.1007/s10592-026-01814-6openalex-snapshot

Genomic survey of the ex situ Palm Cockatoo (Probosciger aterrimus) population identifies an undiscovered species-level lineage endemic to Yapen Island

inferred← citeshttps://doi.org/10.1016/j.cub.2026.02.022openalex-snapshot

Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus

inferred← citeshttps://doi.org/10.1016/j.cub.2026.07.022openalex-snapshot

Genomic targets of hurricane-induced selection on clinging performance in an island lizard

inferred← citeshttps://doi.org/10.1016/j.egg.2026.100491openalex-snapshot

Genome-wide SNP discovery and genetic variation analysis in Cymodocea nodosa using public resequencing data

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SNP discovery and applications in plant genetics for sustainable food security: A review

inferred← citeshttps://doi.org/10.1016/j.isci.2025.113202openalex-snapshot

cAMP-related second messenger pathways modulate hearing function in Aedes aegypti mosquitoes

inferred← citeshttps://doi.org/10.1038/s41437-025-00808-3openalex-snapshot

Parallel clines of chromosomal inversion frequencies in seaweed flies are associated with thermal variation

inferred← citeshttps://doi.org/10.1038/s41467-026-74605-9openalex-snapshot

Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea

inferred← citeshttps://doi.org/10.1038/s41477-026-02220-zopenalex-snapshot

Elucidation of gene clusters underlying withanolide biosynthesis in ashwagandha through yeast metabolic engineering

inferred← citeshttps://doi.org/10.1038/s41559-025-02919-wopenalex-snapshot

Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism

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Next-generation data filtering in the genomics era

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Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone

inferred← citeshttps://doi.org/10.1073/pnas.2602084123openalex-snapshot

The dynamic genomes of Salvinia reshape our understanding of fern chromosome evolution

inferred← citeshttps://doi.org/10.1093/aob/mcag011openalex-snapshot

Late Cretaceous origins for major nightshade lineages from total-evidence timetree analysis

inferred← citeshttps://doi.org/10.1093/bioadv/vbae098openalex-snapshot

loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing

inferred← citeshttps://doi.org/10.1093/evlett/qraf011openalex-snapshot

k-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species

inferred← citeshttps://doi.org/10.1093/evlett/qraf013openalex-snapshot

Diverging Arabidopsis populations quickly accumulate pollen-acting genetic incompatibilities

inferred← citeshttps://doi.org/10.1093/evolinnean/kzag010openalex-snapshot

Sexual signal divergence and reproductive isolation in an adaptive radiation of a Hawaiian spider

inferred← citeshttps://doi.org/10.1093/g3journal/jkae042openalex-snapshot

Chromosome-level genome assembly of the European green woodpecker Picus viridis

inferred← citeshttps://doi.org/10.1093/g3journal/jkag142openalex-snapshot

MKado: a toolkit for McDonald–Kreitman tests of natural selection

inferred← citeshttps://doi.org/10.1093/g3journal/jkag209openalex-snapshot

A Mid-Atlantic Brook Trout ( Salvelinus fontinalis ) genome to advance conservation and comparative genomics

inferred← citeshttps://doi.org/10.1093/gbe/evae174openalex-snapshot

Draft Genome of Akame (Lates Japonicus) Reveals Possible Genetic Mechanisms for Long-Term Persistence and Adaptive Evolution with Low Genetic Diversity

inferred← citeshttps://doi.org/10.1093/gbe/evaf158openalex-snapshot

Evolutionary Consequences of Unusually Large Pericentric TE-rich Regions in the Genome of a Neotropical Fig Wasp

inferred← citeshttps://doi.org/10.1093/gbe/evag103openalex-snapshot

A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them

inferred← citeshttps://doi.org/10.1093/gbe/evag259openalex-snapshot

Is faster-X adaptation due to large-effect mutations? An empirical test of a new theory

inferred← citeshttps://doi.org/10.1093/genetics/iyaf217openalex-snapshot

Sex-specific recombination landscape in a species with holocentric chromosomes

inferred← citeshttps://doi.org/10.1093/genetics/iyag196openalex-snapshot

Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography

inferred← citeshttps://doi.org/10.1093/icb/icae056openalex-snapshot

Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc

inferred← citeshttps://doi.org/10.1093/jhered/esae023openalex-snapshot

A draft reference genome assembly of California Pipevine, Aristolochia californica Torr.

inferred← citeshttps://doi.org/10.1093/jhered/esaf018openalex-snapshot

Genomic data from the extinct California brown bear suggests a source population for reintroduction to California

inferred← citeshttps://doi.org/10.1093/molbev/msae229openalex-snapshot

Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee

inferred← citeshttps://doi.org/10.1093/molbev/msae266openalex-snapshot

Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk

inferred← citeshttps://doi.org/10.1093/molbev/msaf016openalex-snapshot

Positive Selection on Mammalian Immune Genes—Effects of Gene Function and Selective Constraint

inferred← citeshttps://doi.org/10.1093/molbev/msaf282openalex-snapshot

Efficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More)

inferred← citeshttps://doi.org/10.1093/molbev/msag004openalex-snapshot

Estimating the Reduction in Genetic Diversity from Background Selection under Non-equilibrium Demography and Partial Selfing

inferred← citeshttps://doi.org/10.1093/molbev/msag017openalex-snapshot

Germline de novo mutation rate of the highly heterozygous amphioxus genome

inferred← citeshttps://doi.org/10.1093/molbev/msag212openalex-snapshot

Adaptation to seasonal drought in Arabis alpina is linked to the demographic history and climatic changes since the last glacial maximum

inferred← citeshttps://doi.org/10.1093/ornithology/ukag028openalex-snapshot

Phylogenetic relationships, hybridization, and genetic structuring in “Cassidix” grackles

inferred← citeshttps://doi.org/10.1093/pcp/pcag074openalex-snapshot

CRISPR/Cas9-mediated genome editing reveals the involvement of a polyphenol oxidase in the shikonin-specific biosynthesis in Lithospermum erythrorhizon

inferred← citeshttps://doi.org/10.1098/rspb.2025.2899openalex-snapshot

Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics

inferred← citeshttps://doi.org/10.1101/2024.05.17.594778openalex-snapshot

Previously unmeasured genetic diversity explains part of Lewontin’s paradox in a k -mer-based meta-analysis of 112 plant species

inferred← citeshttps://doi.org/10.1101/2024.12.20.629758openalex-snapshot

pipemake: A pipeline creation tool using Snakemake for reproducible analysis of biological datasets

inferred← citeshttps://doi.org/10.1101/2025.02.20.639311openalex-snapshot

Filling the gap in the Neotropics: new firefly species provide insights into Central American biodiversity

inferred← citeshttps://doi.org/10.1101/2025.05.15.654353openalex-snapshot

Efficient Estimation of Nucleotide Diversity and Divergence using Depth Information

inferred← citeshttps://doi.org/10.1101/2025.08.12.669975openalex-snapshot

Introgression and Parental Conflict Underlie Repeated Occurrences of Postzygotic Isolation

inferred← citeshttps://doi.org/10.1101/2025.10.03.680100openalex-snapshot

Parallel polygenic urban adaptation despite high gene flow in a coastal marine invertebrate

inferred← citeshttps://doi.org/10.1101/2025.10.03.680265openalex-snapshot

Gut microbiome-derived prolyl peptidases from Segatella copri and Stenotrophomonas maltophilia degrade immunogenic gliadin peptides and restore intestinal barrier integrity in a Celiac disease model

inferred← citeshttps://doi.org/10.1101/2025.11.26.690832openalex-snapshot

SaVor - A Reproducible Structural Variant Calling and Benchmarking Platform from Short-Read Data

inferred← citeshttps://doi.org/10.1111/1755-0998.13893openalex-snapshot

Genomics and conservation: Guidance from training to analyses and applications

inferred← citeshttps://doi.org/10.1111/1755-0998.70119openalex-snapshot

SwarmGenomics : A Unified Pipeline for Individual‐Based Whole‐Genome Analyses

inferred← citeshttps://doi.org/10.1111/eva.70255openalex-snapshot

Whole Genome Analyses of the Endangered Northern Abalone ( Haliotis kamtschatkana ) Reveal Population Differentiation and a Genomic Signature of a Dramatic Population Decline

inferred← citeshttps://doi.org/10.1111/jpy.70124openalex-snapshot

Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches

inferred← citeshttps://doi.org/10.1111/mec.17362openalex-snapshot

Limited genomic signatures of population collapse in the critically endangered black abalone ( Haliotis cracherodii )

inferred← citeshttps://doi.org/10.1111/mec.17650openalex-snapshot

Seascape Genomics of Red Abalone: Limited Range‐Wide Population Structure and Evidence for Local Adaptation

inferred← citeshttps://doi.org/10.1111/mec.17758openalex-snapshot

The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids

inferred← citeshttps://doi.org/10.1111/mec.70073openalex-snapshot

Population Genomics, Local Adaptation and Cryptic Speciation in a Temperate Reef Fish, the Black Surfperch, Embiotoca jacksoni , Using Genome‐Wide Resequencing

inferred← citeshttps://doi.org/10.1111/mec.70093openalex-snapshot

Patterns of Genetic Diversity Within Three California Quail Species Are Best Explained by Climate and Landscape Changes

inferred← citeshttps://doi.org/10.1111/mec.70218openalex-snapshot

Chromosome‐Level Genomics and Historical Museum Collections Reveal New Insights Into the Population Structure and Chromosome Evolution of Waterbuck

inferred← citeshttps://doi.org/10.1111/mec.70385openalex-snapshot

From Lineage Discovery to Conservation Prioritisation: An Integrative Genomic Framework Applied to a Model Damselfly System

inferred← citeshttps://doi.org/10.1126/sciadv.adj6823openalex-snapshot

A nuclear genome assembly of an extinct flightless bird, the little bush moa

inferred← citeshttps://doi.org/10.1126/sciadv.adv1159openalex-snapshot

Aboral cell types of Clytia and coral larvae have shared features and link taurine to the regulation of settlement

inferred← citeshttps://doi.org/10.1126/sciadv.adv1982openalex-snapshot

Ancient inversion polymorphisms are locally adaptive in a widespread butterfly species

inferred← citeshttps://doi.org/10.1186/s12859-025-06242-wopenalex-snapshot

Learning-based parallel acceleration for HaplotypeCaller

inferred← citeshttps://doi.org/10.1186/s12915-025-02156-4openalex-snapshot

Convergent evolution of noncoding elements associated with short tarsus length in birds

inferred← citeshttps://doi.org/10.1371/journal.pgen.1011062openalex-snapshot

Inferring multi-locus selection in admixed populations

inferred← citeshttps://doi.org/10.1371/journal.pone.0358232openalex-snapshot

Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations

inferred← citeshttps://doi.org/10.3120/0024-9637-250014openalex-snapshot

INVESTIGATING PUTATIVE HYBRIDS OF FREMONTODENDRON DECUMBENS AND F. CALIFORNICUM IN THE SIERRA FOOTHILLS

inferred← citeshttps://doi.org/10.64898/2026.01.22.701211openalex-snapshot

A pistil peptide toxin–pollen antidote system for reproductive barrier

inferred← citeshttps://doi.org/10.64898/2026.02.02.703194openalex-snapshot

Evaluating the applicability of kinship analyses for sedimentary ancient DNA datasets

inferred← citeshttps://doi.org/10.64898/2026.02.28.708717openalex-snapshot

selscape: A Snakemake Workflow for Investigating Genomic Landscapes of Natural Selection

inferred← citeshttps://doi.org/10.64898/2026.03.02.709016openalex-snapshot

A Global Genomic Resource for Outcrossing Arabidopsis lyrata and Arabidopsis arenosa

inferred← citeshttps://doi.org/10.64898/2026.03.04.709719openalex-snapshot

The complete chloroplast genome of Garcinia binucao (Blanco) Choisy, an indigenous fruit from the Philippines

inferred← citeshttps://doi.org/10.64898/2026.03.17.712489openalex-snapshot

Introgression across ploidies contributes to genetic diversity in introduced urban Capsella bursa-pastoris

inferred← citeshttps://doi.org/10.64898/2026.04.10.717634openalex-snapshot

Coupling of electron-bifurcation modules powers aromatic ring reduction beyond the biological redox window

inferred← citeshttps://doi.org/10.64898/2026.04.27.721231openalex-snapshot

Large population sizes shape genome evolution in barnacles

inferred← citeshttps://doi.org/10.64898/2026.05.27.728286openalex-snapshot

Pleiotropy constrains the evolution of immune system plasticity while promoting domain modularity

inferred← citeshttps://doi.org/10.64898/2026.05.28.728377openalex-snapshot

Genomic connectivity and the spread of adaptive insecticide resistance alleles in Anopheles arabiensis from East Africa

inferred← citeshttps://doi.org/10.64898/2026.06.08.730324openalex-snapshot

Yersinia pestis lipoprotein SlyB promotes plague pathogenesis via envelope stress tolerance

inferred← citeshttps://doi.org/10.64898/2026.06.30.735478openalex-snapshot

Ecological genomics of a novel host-parasitoid arms-race in nature

inferred← citeshttps://doi.org/10.64898/2026.07.31.741990openalex-snapshot

Intra-specific evidence to support the drift-barrier hypothesis of mutation rate evolution

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