Cited by 815Genetic diversity and population structureGenomics and Phylogenetic StudiesGenetic Mapping and Diversity in Plants and Animals

The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

Open access

Kofler, Robert, Pandey, Ram Vinay, Schlötterer, Christian·2011·Bioinformatics

DOI 10.1093/bioinformatics/btr589PMC PMC3232374

Open this paper in CoChat — free account Open PDF

Abstract

SUMMARY: Sequencing pooled DNA samples (Pool-Seq) is the most cost-effective approach for the genome-wide comparison of population samples. Here, we introduce PoPoolation2, the first software tool specifically designed for the comparison of populations with Pool-Seq data. PoPoolation2 implements a range of commonly used measures of differentiation (F(ST), Fisher's exact test and Cochran-Mantel-Haenszel test) that can be applied on different scales (windows, genes, exons, SNPs). The result may be visualized with the widely used Integrated Genomics Viewer. AVAILABILITY AND IMPLEMENTATION: PoPoolation2 is implemented in Perl and R. It is freely available on http://code.google.com/p/popoolation2/ CONTACT: christian.schloetterer@vetmeduni.ac.at SUPPLEMENTARY INFORMATION: Manual: http://code.google.com/p/popoolation2/wiki/Manual Test data and tutorial: http://code.google.com/p/popoolation2/wiki/Tutorial Validation: http://code.google.com/p/popoolation2/wiki/Validation.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/bioinformatics/btr589

Cites

23 of 23 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 40,207
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
Excoffier, L., & Lischer, H. E. L. (2010) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2010.02847.x · Cited by 16,266
GENEPOP (version 1.2): population genetic software for exact tests and ecumenicism
Raymond, M., & Rousset, F. (1995) · Journal of Heredity · doi:10.1093/oxfordjournals.jhered.a111573 · Cited by 16,187
Integrative genomics viewer
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390
Principles of Population Genetics.
Cormack, R. M., Hartl, D. L., & Clark, A. G. (1990) · Biometrics · doi:10.2307/2531471 · Cited by 5,283
Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.
Lander, E. S., & Botstein, D. (1989) · Genetics · doi:10.1093/genetics/121.1.185 · Cited by 5,236
On the Interpretation of χ 2 from Contingency Tables, and the Calculation of P
Fisher, R. A. (1922) · Journal Of The Royal Statistical Society · doi:10.2307/2340521 · Cited by 2,975
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
Begun, D. J., Holloway, A. K., Stevens, K., Hillier, L. W., Poh, Y.-P., Hahn, M. W., Nista, P. M., Jones, C. D., Kern, A. D., Dewey, C. N., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050310 · Cited by 637

Flagged first, then by citations

Show all 23 references

Sorted by citations

Items 701–782 of 782

Faculty Opinions recommendation of Recurrent specialization on a toxic fruit in an island Drosophila population.
Linnen, C. R. (2016) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.726263824.793525267
Faculty Opinions recommendation of Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster.
Chevin, L. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736618952.793565848
Investigating the Quantitative Trait Loci Contributing to Individual Variation in Drug Response
Roberts, C. A. (2015) · doi:10.26686/wgtn.17014628
Faculty Opinions recommendation of The genomic basis of Red Queen dynamics during rapid reciprocal host-pathogen coevolution.
Herman, M. A. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734713338.793555864
Peer Review #2 of "The effects of genetic drift and genomic selection on differentiation and local adaptation of the introduced populations of Aedes albopictus in southern Russia (v0.1)"
(2021) · PeerJ · doi:10.7287/peerj.11776v0.1/reviews/2
Development of linkage InDel markers of the white petal gene based on whole-genome re-sequencing data in Brassica napus L.
Wang, R., Xue, C. H. E. N., Guo, Q.-Q., Zhou, R., Lei, C. H. E. N., & Jia-Na, L. I. (2022) · ACTA AGRONOMICA SINICA · doi:10.3724/sp.j.1006.2022.14025
High nucleotide diversity accompanies differential DNA methylation in naturally diverging populationsPreprint
Ord, J., Gossmann, T. I., & Adrian‐Kalchhauser, I. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.08.511291
Transgenerational genomic analyses reveal allelic oscillation and purifying selection in a gut parasite Nosema ceranae
Wei, X., Zheng, J., Evans, J. D., & Huang, Q. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.927892
ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language
Mas-Sandoval, À., Jin, C., Fracassetti, M., & Fumagalli, M. (2022) · F1000Research · doi:10.12688/f1000research.104368.2
621. Statistics for an accurate genome wide association study on Varroa resistance trait in a French honeybee
Eynard, S. E., Alain Vignal, A., Agez, Y., Basso, B., Bouchez, O., Bulach, T., Conte, Y. L., Dainat, B., Decourtye, A., Genestout, L., et al. (2022) · World Congress on Genetics Applied to Livestock Production (WCGALP) · doi:10.3920/978-90-8686-940-4_621
Polygenic adaptation to overnutrition reveals a role for cholinergic signaling in longevityPreprint
Rundell, T. B., Brunelli, M., Alvi, A., Safian, G., Capobianco, C., Tu, W., Subedi, S. D., Fiumera, A. C., & Musselman, L. P. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.14.544888
ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language
Mas-Sandoval, À., Jin, C., Fracassetti, M., & Fumagalli, M. (2023) · F1000Research · doi:10.12688/f1000research.104368.3
poolHelper : An R package to help in designing Pool‐Seq studies
Carvalho, J., Faria, R., Butlin, R. K., & Sousa, V. C. (2023) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.14185
A high-quality assembly reveals genomic characteristics, phylogenetic status and causal genes for white feather of Indian peafowlPreprint
Liu, S., Chen, H., Ouyang, J., Huang, M., Zhang, H., Zheng, S., Xi, S., Tang, H., Gao, Y., Xiong, Y., et al. (2024) · doi:10.22541/au.170666290.06903129/v1
Natural variation in phospholipase IPLA2-VIA contributes to starvation sensitivity in Drosophila melanogasterPreprint
Williams, S. B., Franklin, B., Lemieux, F. A., & Rand, D. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.05.602254
Pooled whole genome sequencing method (Pool-Seq) to identify genomic regions associated to Dryocosmus kuriphilus Yasumatsu resistance in European Castanea sativa Mill.
Gaudet, M., Pollegioni, P., Ciolfi, M., Cherubini, M., Mattioni, C., Villani, F., & Beritognolo, I. (2024) · Acta Horticulturae · doi:10.17660/actahortic.2024.1400.8
Long-term blood-free rearing of Anopheles mosquitoes with no effect on fitness, Plasmodium infectivity nor microbiota composition
Marques, J., Seabra, S. G., Almeida, I., Gomes, J., Alves, A. C., & Silveira, H. (2024) · Scientific Reports · doi:10.1038/s41598-024-70090-6
Convergence of gut phage communities but not bacterial communities following wild mouse bacteriophage transplantation into captive house mice
Čížková, D., Payne, P., Bryjová, A., Ďureje, Ľ., Piálek, J., & Kreisinger, J. (2024) · The ISME Journal · doi:10.1093/ismejo/wrae178 · Cited by 1
Breeding season temporal and spatial trends in continental-scale migration of the monarch butterfly
Fisher, K. E., Filandro, A., Bradbury, S. P., Wanamaker, A. D., & Coates, B. S. (2024) · Environmental Entomology · doi:10.1093/ee/nvae076
Population genomics of the invasive Argentine ant ( Linepithema humile ) – adaptive evolution in introduced supercolonies despite low genetic diversityPreprint
Päkkilä, I., Paviala, J., Pedersen, J. S., Helanterä, H., & Viljakainen, L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.29.620798
Enhancing detection of polygenic adaptation: a comparative study of machine learning and statistical approaches using simulated evolve-and-resequence data
Caliendo, C., Gerber, S., & Pfenninger, M. (2026) · BMC Genomics · doi:10.1186/s12864-026-13163-2
Acompanhando a evolução de clinas genômicas em Drosophila melanogaster por meio de amostragens históricas
Miranda, V. C. C. (2025) · doi:10.11606/d.41.2025.tde-13062025-173146
Wildlife Forensics in the Genomic Era: Molecular Strategies for Anti-Poaching InvestigationsPreprint
Arvind Prabhu., T. (2025) · Research Square · doi:10.21203/rs.3.rs-6891725/v1
Host-specific adaptation and fitness trade-off of Barley Yellow Dwarf Viruses suggested by experimental evolution through aphid inoculation on multiple Poaceae speciesPreprint
Tamisier, L., Colson, C., Maclot, F., Zhang, P., Wang, X., Francis, F., Baurain, D., & Massart, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.20.660669
Recurrent Mutations Drive the Rapid Evolution of Pesticide Resistance in the Two-spotted Spider Mite Tetranychus urticaePreprint
Cao, L., Chen, J.-C., Thia, J. A., Schmidt, T. L., ffrench‐Constant, R. H., Zhang, L.-X., Yu, Y., Yuan, M.-C., Zhang, J., Zhang, X., et al. (2025) · eLife · doi:10.7554/elife.106288.2
Polymorphism in a metabolic gene involved in sexual selection shapes global gene expression profiles in the bulb mite males
Plesnar‐Bielak, A., Chmielewski, S., Dudek, K., Unnikrishnan, P., Cygnar, G., & Konczal, M. (2025) · Journal of Evolutionary Biology · doi:10.1093/jeb/voaf109
Elucidating the genetic architecture of migratory timing in a songbird migrant, the great reed warbler, Acrocephalus arundinaceus
Fackler, E. R., Kishkinev, D., Procházka, P., & Fitak, R. R. (2025) · Biology Open · doi:10.1242/bio.062039
Independent Mutations in the LRP2 Gene Mediating Telescope Eyes and Celestial Eyes in Goldfish
Li, R., Zhang, B., Sun, Y., & Li, J. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262110625
Gene flow erodes spatial genomic clines while selection preserves adaptive loci over hundreds of generationsPreprint
Miranda, V. H., Ribeiro, T. D. S., Alves, J. M., Eanes, W. F., Brud, E., Veeramah, K. R., Pool, J. E., Rodrigues, M. F., & Cogni, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.28.691231
Identification of Freezing Tolerance QTLs in Tripsacum dactyloides Using Open-Pollinated Bulk Segregant AnalysisPreprint
El-Walid, M., Gault, C. M., Costich, D. E., Lepak, N. K., Budka, J. S., Stitzer, M. C., Giri, A., Rees, E. R., Romay, M. C., Buckler, E. S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.10.693030
Additional file 1 of The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime
Otte, K. A., Nolte, V., Mallard, F., & Schlötterer, C. (2021) · Figshare · doi:10.6084/m9.figshare.14998766
Self-citation
Additional file 3 of A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits
Poklukar, K., Mestre, C., Škrlep, M., Čandek-Potokar, M., Óvilo, C., Fontanesi, L., Riquet, J., Bovo, S., Schiavo, G., Ribani, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26650980
Additional file 5 of A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits
Poklukar, K., Mestre, C., Škrlep, M., Čandek-Potokar, M., Óvilo, C., Fontanesi, L., Riquet, J., Bovo, S., Schiavo, G., Ribani, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26650986
Additional file 3 of The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime
Otte, K. A., Nolte, V., Mallard, F., & Schlötterer, C. (2021) · Figshare · doi:10.6084/m9.figshare.14998772
Self-citation
Additional file 1 of A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits
Poklukar, K., Mestre, C., Škrlep, M., Čandek-Potokar, M., Óvilo, C., Fontanesi, L., Riquet, J., Bovo, S., Schiavo, G., Ribani, A., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24770393
Additional file 4 of A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits
Poklukar, K., Mestre, C., Škrlep, M., Čandek-Potokar, M., Óvilo, C., Fontanesi, L., Riquet, J., Bovo, S., Schiavo, G., Ribani, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26650983
Additional file 2 of Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs
Momeni, J., Parejo, M., Nielsen, R. O., Langa, J., Montes, I., Papoutsis, L., Farajzadeh, L., Bendixen, C., Căuia, E., Charrière, J.-D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13710770
Additional file 2 of Natural variation in Drosophila shows weak pleiotropic effects
Christodoulaki, E., Nolte, V., Lai, W.-Y., & Schlötterer, C. (2022) · Figshare · doi:10.6084/m9.figshare.19778337
Self-citation
Additional file 1 of Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)
Grummer, J. A., Whitlock, M. C., Schulte, P. M., & Taylor, E. B. (2021) · Figshare · doi:10.6084/m9.figshare.14471519
Additional file 1 of Natural variation in Drosophila shows weak pleiotropic effects
Christodoulaki, E., Nolte, V., Lai, W.-Y., & Schlötterer, C. (2022) · Figshare · doi:10.6084/m9.figshare.19778334
Self-citation
Additional file 1 of Fine-scale adaptive divergence and population genetic structure of Aedes aegypti in Metropolitan Manila, Philippines
Muharromah, A. F., Carvajal, T. M., Regilme, M. A. F., & Watanabe, K. (2024) · Figshare · doi:10.6084/m9.figshare.26723037
Additional file 2 of A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits
Poklukar, K., Mestre, C., Škrlep, M., Čandek-Potokar, M., Óvilo, C., Fontanesi, L., Riquet, J., Bovo, S., Schiavo, G., Ribani, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.24770681
Additional file 4 of Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs
Momeni, J., Parejo, M., Nielsen, R. O., Langa, J., Montes, I., Papoutsis, L., Farajzadeh, L., Bendixen, C., Căuia, E., Charrière, J.-D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13710791
Additional file 3 of Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs
Momeni, J., Parejo, M., Nielsen, R. O., Langa, J., Montes, I., Papoutsis, L., Farajzadeh, L., Bendixen, C., Căuia, E., Charrière, J.-D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13710773
Additional file 1 of Balancing selection on an MYB transcription factor maintains the twig trichome color variation in Melastoma normale
Huang, G., Wu, W., Chen, Y., Zhi, X., Zou, P., Ning, Z., Fan, Q., Liu, Y., Deng, S., Zeng, K., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26591624
Tracking the evolution of genomic clines of Drosophila melanogaster using historical sampling
Miranda, V. H. (2025) · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
The genomic basis of local adaptation to photoperiod across altitude in a self-fertilizing monkeyflowerPreprint
Love, J. M., Mahesh, A., & Ferris, K. G. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.14.699501
Pollution‐Driven Selection in a Non‐Biting Midge: Genome‐Wide Responses to Bacillus thuringiensis israelensis and Copper
Röder, N., Kolbenschlag, S., Pietz, S., Brennan, R. S., Bundschuh, M., Pfenninger, M., & Schwenk, K. (2026) · Molecular Ecology · doi:10.1111/mec.70263
Genomic analysis of DDT resistance identifies importance of glutathione transferases in driving evolutionary response to vector control in the malaria vector Anopheles gambiae
Al‐Yazeedi, T., Morris, M., Muhammad, A., Alkhnbashi, O. S., Dyer, N. A., & Ranson, H. (2026) · BMC Genomics · doi:10.1186/s12864-026-13466-4
Hyperdivergent haplotypes control melanic camouflage in a polymorphic moth
Livraghi, L., Cassily, J. L., Brayer, M., Carter, A., Alqassar, J. D., Sim, S. B., Geib, S. M., Hanly, J. J., & Martin, A. (2026) · Current Biology · doi:10.64898/2026.02.24.707733
Genome Sequencing and Genome‐Wide Analysis Uncover Candidate Genes and Loci Linked to Key Production Traits in the Philippine Black Tiger Shrimp ( Penaeus monodon )
Cadorna, K., Aguinaldo, Z.-Z. A., de la Cruz, M. P. E., Pasaquian, H. M. E., Corre, V. L., Parado-Estepa, F. D., Amar, E. C., Maningas, M. B. B., & Lluisma, A. O. (2026) · Animal Genetics · doi:10.1002/age.70082
Development of genomic tools in the Manila clam, Ruditapes philippinarum, to investigate resistance to major pathogens and potential selection for aquaculture
Smits, M. (2019) · doi:10.70675/43f89a4azc5e5z4649zafecz0b22d08ec983
Analyse de la différenciation génétique à l'ère des nouvelles technologies de séquençage
Hivert, V. (2018) · doi:10.70675/fcd25408z226az46dfz815bz96f32c906273
Etude de l'adaptation aux résistances variétales chez le champignon Pseudocercospora fijiensis, agent causal de la maladie des raies noires du bananier
Dumartinet, T. (2021) · doi:10.70675/e82cb95fza363z44edzbe25z4ac07b8ab630
Microévolution des déterminismes sexuels chez le poisson Tétra Mexicain, Astyanax mexicanus
Imarazene, B. (2020) · doi:10.70675/513bc8fazc3cez4acbz837dz8d0ffd5ca1dd
Bases génétiques du déterminisme du sexe chez le tilapia du Nil en populations naturelles
Triay, C. (2021) · doi:10.70675/eb748549z374bz4020zbe2cz56bd9cbdc19a
Application of whole-eDNA sequencing for monitoring broodstock genetic diversity in breeding groups of gilthead seabream (Sparus aurata)
Bertolini, F., Taurisano, V., Bovo, S., Vegni, J., Napolitano, R., Martinoli, M., Capoccioni, F., & Fontanesi, L. (2026) · Aquaculture · doi:10.1016/j.aquaculture.2026.743980
Génomique de la résistance aux insecticides chez la punaise de lit Cimex lectularius
Haberkorn, C. (2023) · theses.fr (ABES) · doi:10.70675/e800fb57z2c19z40abz8285zc538251d131b
Balancing Selection on a Single Locus Controls Colour Polymorphism in a Reptile via Tubulin Modification
Xie, H., Wu, D., Wen, G., Liang, X., Luo, S., Yang, C., Elmer, K. R., & Du, W. (2026) · Molecular Ecology · doi:10.1111/mec.70373
A Whole‐Genome Investigation of Mitonuclear Discordance in the Trematode Parasite Atriophallophorus winterbourni
Zajac, N., Feijen, F. A. A., & Jokela, J. (2026) · Molecular Ecology · doi:10.1111/mec.70391
Genetic rescue increases long-term fitness despite elevating putative genetic load in a male-dimorphic mite
Parrett, J. M., Konczal, M., Kulczak, M., & Radwan, J. (2026) · Nature Ecology & Evolution · doi:10.1038/s41559-026-03080-8
Genomic Patterns of Parallel Divergence Across Demographically Heterogeneous Stickleback Populations in Eastern Canada
García‐Elfring, A., Paccard, A., & Barrett, R. D. H. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag083
Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel
Pimenta, J., Miranda, I., Farelo, L., Alvarenga, M. M., Mills, L. S., & Melo‐Ferreira, J. (2026) · Evolution · doi:10.1093/evolut/qpag110
Reviewer #1 (Public review): Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci
(2026) · eLife · doi:10.7554/elife.111773.1.sa1
eLife Assessment: Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci
Courtier‐Orgogozo, V. (2026) · eLife · doi:10.7554/elife.111773.1.sa2
Reviewer #2 (Public review): Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci
(2026) · eLife · doi:10.7554/elife.111773.1.sa0
Standing Genomic Variation inferred by popGWAS Predicts Seedling Drought Survival Experiment in Fagus sylvaticaPreprint
Eberhardt, L., Reuss, F., & Pfenninger, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.13.738179
Interactions Between Inbreeding, Fitness and the Bacterial Microbiome in Aedes aegypti Mosquitoes
Ross, P. A., de Jonge, N., Yang, Q., Paris, V., Kristensen, T. N., & Hoffmann, A. A. (2026) · Evolutionary Applications · doi:10.1111/eva.70308
IMPACTS OF MULTIPLE COASTAL STRESSORS ACROSS LIFE-HISTORY STAGES IN THE EASTERN OYSTER
Zyck, A. (2025) · doi:10.23860/diss-4470
Contrasting Oviposition Preference Despite Limited Chemosensory Receptor Gene Differentiation in Two Cryptic Anopheles Species
Ambadiang, M. M., Fouet, C., Ashu, F. A., Rios, D. E., Kulkarni, A., Roy, S., Bouaka, C. U. T., Penlap-Beng, V., & Kamdem, C. (2026) · Molecular Ecology · doi:10.1111/mec.70512
Polygenic adaptation from standing variation underlies rapid evolution under anthropogenic selection in an agricultural weedPreprint
Neto, C., Baussay, A., & Neve, P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.18.745463
Evolution of virulence of a plant RNA virus in developmental stage-structured host populations
Carrasco, J. L., Toft, C., & Elena, S. F. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag225
The Spatial and Temporal Repeatability of Genomic Responses to Natural Selection as Demonstrated in Stickleback Populations Experiencing Highly Dynamic Environments
Hickox, M. K., Munch, S. B., García‐Elfring, A., Palkovacs, E. P., Hendry, A. P., & Barrett, R. D. H. (2026) · Molecular Ecology · doi:10.1111/mec.70528
Reviewer #2 (Public review): Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci
(2026) · eLife · doi:10.7554/elife.111773.2.sa1
Climate‐Driven Niche Tracking and Genomic Resilience Shape Future Distribution of a Widespread Agricultural Weed
Neto, C., Zheng, Q., & Neve, P. (2026) · Molecular Ecology · doi:10.1111/mec.70547
PoLoCo: a reproducible pooled low-coverage workflow for draft genome assembly and allele frequency analysis from ethanol-preserved small non-model invertebrates
Shuvo, M. J., Segelbacher, G., & Geue, J. C. (2026) · Gigabyte · doi:10.46471/gigabyte.195
Additive in size, synergistic in composition: selection across the eastern oyster larval genome under coastal acidification and sewage effluentPreprint
Puritz, J. B., Harvey, J. A., & Lotterhos, K. E. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.10.08.757713
Whole genome pool sequencing reveals genomic variation in field Haemonchus contortus isolates in Sweden
Liu, N., Baltrušis, P., Ohlsson, Å., Höglund, J., & Mikko, S. (2026) · BMC Genomics · doi:10.1186/s12864-026-13449-5
Data from: Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps
Fischer, M. C., Rellstab, C., Tedder, A., Zoller, S., Gugerli, F., Shimizu, K. K., Holderegger, R., & Widmer, A. (2013) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.b2k47
Data from: Towards understanding the genetic basis of mouth asymmetry in the scale-eating cichlid Perissodus microlepis
Raffini, F., Fruciano, C., Franchini, P., & Axel, M. (2016) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.fp0b8.1
Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations
Franssen, S. U., Nolte, V., Tobler, R., & Schlötterer, C. (2015) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.403b2.1
Self-citation
Evolutionary genetics and genomics of flower colour loci in an Antirrhinum hybrid zone
Tavares, H. (2014) · UEA Digital Repository (University of East Anglia)

Authors: Kofler, R., Pandey, R. V., & Schlötterer, C.
Affiliations: University of Veterinary Medicine Vienna (AT)
Corresponding author: Schlötterer, Christian
ORCID: Kofler, Robert
Pandey, Ram Vinay
Schlötterer, Christian
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2011-10-23
Volume: 27
Issue: 24
Pages: 3435-3436
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btr589
PMC: PMC3232374
OpenAlex: W2161950199
Cited by: 815
References: 23
Citations by year: 2026: 44 · 2025: 48 · 2024: 68 · 2023: 54 · 2022: 86 · 2021: 83 · 2020: 88 · 2019: 77 · 2018: 64 · 2017: 54 · 2016: 62 · 2015: 34 · 2014: 22 · 2013: 26 · 2012: 2
FWCI: 9.98
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/3.0 (vor, 1806 d)
Locations: Bioinformatics (publishedVersion, cc-by-nc)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: Austrian Science Fund (P 22725, P19467)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords: pooled DNA sequencing, genetic differentiation, F(ST), Fisher's exact test, Cochran-Mantel-Haenszel test, population genetics software
MeSH terms: Animals, Drosophila melanogaster, Genetics, Population, Software, Arabidopsis, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks