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

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 40,166

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

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

Taillebois, L., Sabatino, S. J., Manicki, A., Daverat, F., Nachón, D. J., & Lepais, O. (2019) · Evolutionary Applications · doi:10.1111/eva.12889 · Cited by 22

Shared genetic susceptibilities for irritable bowel syndrome and depressive disorder in Chinese patients uncovered by pooled whole-exome sequencing

Zhu, S., He, M., Liu, Z., Qin, Z., Wang, Z., & Duan, L. (2020) · Journal of Advanced Research · doi:10.1016/j.jare.2020.01.016 · Cited by 23

Instability of natural selection at candidate barrier loci underlying speciation in wood ants

Kulmuni, J., Nouhaud, P., Pluckrose, L., Satokangas, I., Dhaygude, K., & Butlin, R. K. (2020) · Molecular Ecology · doi:10.1111/mec.15606 · Cited by 22

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spiderStegodyphus dumicola

Aagaard, A., Liu, S., Tregenza, T., Lund, M., Schramm, A., Verhoeven, K. J. F., Bechsgaard, J., & Bilde, T. (2022) · Molecular Ecology · doi:10.1111/mec.16696 · Cited by 22

Population Genomics Analysis of Legume Host Preference for Specific Rhizobial Genotypes in theRhizobium leguminosarumbv.viciaeSymbioses

Jorrín, B., & Imperial, J. (2014) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-09-14-0296-fi · Cited by 22

Differential divergence in autosomes and sex chromosomes is associated with intra‐island diversification at a very small spatial scale in a songbird lineage

Bourgeois, Y., Bertrand, J. A. M., Delahaie, B., Holota, H., Thébaud, C., & Milá, B. (2020) · Molecular Ecology · doi:10.1111/mec.15396 · Cited by 22

Whole‐genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

Saha, A., Andersson, A., Kurland, S., Keehnen, N. L. P., Kutschera, V. E., Hössjer, O., Ekman, D. S., Karlsson, S., Kardos, M. D., Ståhl, G., et al. (2021) · Molecular Ecology · doi:10.1111/mec.16252 · Cited by 21

Identification of male sex-specific markers using genome re-sequencing in the Chinese longsnout catfish Leiocassis longirostris

Luo, H., Li, Y., Zheng, S., Zhou, J. T., Zou, X., Li, C., Ye, H., Li, Z., Zhou, C., Lv, G., et al. (2022) · Aquaculture · doi:10.1016/j.aquaculture.2022.738392 · Cited by 21

Reconstructing queen genotypes by pool sequencing colonies in eusocial insects: Statistical Methods and their application to honeybee

Eynard, S. E., Alain Vignal, A., Basso, B., Conte, Y. L., Decourtye, A., Genestout, L., Labarthe, E., Mondet, F., Canale‐Tabet, K., & Servin, B. (2022) · Molecular Ecology Resources · doi:10.1111/1755-0998.13685 · Cited by 21

Characterization of the sex determining region of channel catfish (Ictalurus punctatus) and development of a sex-genotyping test

Wen, M., Pan, Q., Larson, W. A., Eché, C., & Guiguen, Y. (2022) · Gene · doi:10.1016/j.gene.2022.146933 · Cited by 21

Genomic adaptive potential to cold environments in the invasive red swamp crayfish

Sato, D. X., Matsuda, Y., Usio, N., Funayama, R., Nakayama, K., & Makino, T. (2023) · iScience · doi:10.1016/j.isci.2023.107267 · Cited by 21

Transgenerational adaptation to ocean acidification determines the susceptibility of filter-feeding rotifers to nanoplastics

Kim, M., Lee, Y. H., Lee, Y., Byeon, E., Kim, D., Wang, M., Hagiwara, A., Aranda, M., Wu, R. S. S., Park, H. G., et al. (2023) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2023.132593 · Cited by 21

Genomics, environment and balancing selection in behaviourally bimodal populations: The caribou case

Cavedon, M., Gubili, C., Heppenheimer, E., vonHoldt, B. M., Mariani, S., Hebblewhite, M., Hegel, T. M., Hervieux, D., Serrouya, R., Steenweg, R. W., et al. (2019) · Molecular Ecology · doi:10.1111/mec.15039 · Cited by 25

Compensatory trans -regulatory alleles minimizing variation in TDH3 expression are common within Saccharomyces cerevisiae

Metzger, B. P. H., & Wittkopp, P. J. (2019) · Evolution Letters · doi:10.1002/evl3.137 · Cited by 21

Understanding the Genetic Domestication History of the Jianchang Duck by Genotyping and Sequencing of Genomic Genes Under Selection

Wang, L., Guo, J., Xi, Y., Ma, S., Li, Y., He, H., Wang, J., Han, C., Bai, L., Mustafa, A., et al. (2020) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.400893 · Cited by 21

Novel quality metrics allow identifying and generating high‐quality assemblies of piRNA clusters

Wierzbicki, F., Schwarz, F., Cannalonga, O., & Kofler, R. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13455 · Cited by 22

Consequences of coupled barriers to gene flow for the build‐up of genomic differentiation

Kunerth, H. D., Bogdanowicz, S. M., Searle, J. B., Harrison, R. G., Coates, B. S., Kozak, G. M., & Dopman, E. B. (2022) · Evolution · doi:10.1111/evo.14466 · Cited by 21

Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila

Moerman, F., Fronhofer, E. A., Altermatt, F., & Wagner, A. (2021) · Journal of Animal Ecology · doi:10.1111/1365-2656.13598 · Cited by 20

An Experimental Test of Adaptive Introgression in Locally Adapted Populations of Splash Pool Copepods

Griffiths, J. S., Kawji, Y., & Kelly, M. W. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa289 · Cited by 20

Development of SNP markers for identification of thermo-resistant families of the Pacific oyster Crassostrea gigas based on RNA-seq

Juárez, O. E., Escobedo‐Fregoso, C., Arredondo-Espinoza, R., & Ibarra, A. M. (2021) · Aquaculture · doi:10.1016/j.aquaculture.2021.736618 · Cited by 20

The molecular architecture of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping

Shahrestani, P., King, E. G., Ramezan, R., Phillips, M., Riddle, M., Thornburg, M., Greenspan, Z. S., Estrella, Y., Garcia, K., Chowdhury, P., et al. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab324 · Cited by 20

A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl

Liu, S., Chen, H., Ouyang, J., Huang, M., Zhang, H., Zheng, S., Xi, S., Tang, H., Gao, Y., Xiong, Y., et al. (2022) · GigaScience · doi:10.1093/gigascience/giac018 · Cited by 20

Genetic fine‐mapping reveals single nucleotide polymorphism mutations in the MC1R regulatory region associated with duck melanism

Liu, H., Xi, Y., Tang, Q., Qi, J., Zhou, Z., Guo, Z., Fan, W., Hu, J., Xu, Y., Liang, S., et al. (2023) · Molecular Ecology · doi:10.1111/mec.16924 · Cited by 20

Genetic erosion reduces biomass temporal stability in wild fish populations

Prunier, J. G., Chevalier, M., Raffard, A., Loot, G., Poulet, N., & Blanchet, S. (2023) · Nature Communications · doi:10.1038/s41467-023-40104-4 · Cited by 21

High light intensity plays a major role in emergence of population level variation in Arabidopsis thaliana along an altitudinal gradient

Tyagi, A., Yadav, A., Tripathi, A. M., & Roy, S. (2016) · Scientific Reports · doi:10.1038/srep26160 · Cited by 20

Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species

Bowman, L. L., Kondrateva, E. S., Timofeyev, M. A., & Yampolsky, L. Y. (2018) · Molecular Ecology · doi:10.1111/mec.14704 · Cited by 20

Population Genomics on the Fly: Recent Advances in Drosophila

Haudry, A., Laurent, S., & Kapun, M. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0199-0_15 · Cited by 20

Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence

Oppold, A., Schmidt, H., Rose, M., Hellmann, S. L., Dolze, F., Ripp, F., Weich, B., Schmidt‐Ott, U., Schmidt, E. R., Kofler, R., et al. (2017) · Molecular Ecology · doi:10.1111/mec.14111 · Cited by 21

Extreme-QTL mapping of monepantel resistance in Haemonchus contortus

Niciura, S. C. M., Tizioto, P. C., Moraes, C. V., Cruvinel, G. G., de Albuquerque, A. C. A., Santana, R. C. M., Chagas, A. C. D. S., Esteves, S. N., Benavides, M. V., & do Amarante, A. F. T. (2019) · Parasites & Vectors · doi:10.1186/s13071-019-3663-9 · Cited by 20

Applying genomic data to seagrass conservation

Phair, N. L., Nielsen, E. S., & von der Heyden, S. (2021) · Biodiversity and Conservation · doi:10.1007/s10531-021-02184-w · Cited by 20

RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout

Paneru, B., Al-Tobasei, R., Kenney, B., Leeds, T. D., & Salem, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-09515-4 · Cited by 20

Polymorphism of Sex Determination Amongst Wild Populations Suggests its Rapid Turnover Within the Nile Tilapia Species

Triay, C., Courcelle, M., Caminade, P., Bezault, É., Baroiller, J., Kocher, T. D., & D'Cotta, H. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.820772 · Cited by 19

Genetic Variation in Heat Tolerance of the Coral Platygyra Daedalea Indicates Potential for Adaptation to Ocean Warming

Elder, H., Weis, V. M., Montalvo-Proaño, J., Mocellin, V. J. L., Baird, A. H., Meyer, E., & Bay, L. K. (2022) · Frontiers in Marine Science · doi:10.3389/fmars.2022.925845 · Cited by 19

Genomic profiling of climate adaptation in Aedes aegypti along an altitudinal gradient in Nepal indicates nongradual expansion of the disease vector

Kramer, I., Pfenninger, M., Feldmeyer, B., Dhimal, M., Gautam, I., Shreshta, P., Baral, S., Phuyal, P., Hartke, J., Magdeburg, A., et al. (2022) · Molecular Ecology · doi:10.1111/mec.16752 · Cited by 19

What can be learned by scanning the genome for molecular convergence in wild populations?

Fraser, B. A., & Whiting, J. R. (2019) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14177 · Cited by 21

Ecological Load and Balancing Selection in Circumboreal Barnacles

Nunez, J. C. B., Rong, S., Damian‐Serrano, A., Burley, J. T., Elyanow, R., Ferranti, D. A., Neil, K. B., Glenner, H., Rosenblad, M. A., Blomberg, A., et al. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa227 · Cited by 19

Little parallelism in genomic signatures of local adaptation in two sympatric, cryptic sister species

Hartke, J., Waldvogel, A., Sprenger, P. P., Schmitt, T., Menzel, F., Pfenninger, M., & Feldmeyer, B. (2020) · Journal of Evolutionary Biology · doi:10.1111/jeb.13742 · Cited by 19

Mapping Small Effect Mutations in Saccharomyces cerevisiae : Impacts of Experimental Design and Mutational Properties

Duveau, F., Metzger, B. P. H., Gruber, J. D., Mack, K. L., Sood, N., Brooks, T. E., & Wittkopp, P. J. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.011783 · Cited by 19

Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature

Langmüller, A. M., Nolte, V., Galagedara, R., Poupardin, R., Dolezal, M., & Schlötterer, C. (2020) · BMC Biology · doi:10.1186/s12915-020-00882-5 · Cited by 18

Increased time sampling in an evolve‐and‐resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change

Phillips, M., Kutch, I. C., Long, A. D., & Burke, M. K. (2020) · Molecular Ecology · doi:10.1111/mec.15687 · Cited by 18

Identification of quantitative trait loci associated with calmness and gentleness in honey bees using whole‐genome sequences

Guichard, M., Dainat, B., Eynard, S. E., Alain Vignal, A., Servin, B., & Neuditschko, M. (2021) · Animal Genetics · doi:10.1111/age.13070 · Cited by 18

Sensory‐based quantification of male colour patterns in Trinidadian guppies reveals no support for parallel phenotypic evolution in multivariate trait space

Yong, L., Croft, D. P., Troscianko, J. T., Ramnarine, I. W., & Wilson, A. J. (2021) · Molecular Ecology · doi:10.1111/mec.16039 · Cited by 19

ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp

Elkrewi, M., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., Fraïssé, C., Sax, L., Huylmans, A. K., Hontoria, F., et al. (2022) · Genetics · doi:10.1093/genetics/iyac123 · Cited by 20

Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole‐genome sequencing data

Gmel, A. I., Guichard, M., Dainat, B., Williams, G. R., Eynard, S. E., Alain Vignal, A., Servin, B., & Neuditschko, M. (2023) · Ecology and Evolution · doi:10.1002/ece3.9723 · Cited by 18

Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats

Paccard, A., Hanson, D., Stuart, Y. E., von Hippel, F. A., Kalbe, M., Klepaker, T., Skúlason, S., Kristjánsson, B. K., Bolnick, D. I., Hendry, A. P., et al. (2019) · Journal of Heredity · doi:10.1093/jhered/esz056 · Cited by 20

From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles

Nunez, J. C. B., Rong, S., Ferranti, D. A., Damian‐Serrano, A., Neil, K. B., Glenner, H., Elyanow, R., Brown, B. R. P., Rosenblad, M. A., Blomberg, A., et al. (2021) · Molecular Ecology · doi:10.1111/mec.15949 · Cited by 18

First identification of two co-existing genome-wide significant sex quantitative trait loci (QTL) in red tilapia using integrative QTL mapping

Zhu, Z.-X., 中山大学生命科学学院有害生物控制与资源利用国家重点实验室, 中., Lin, Y., Ai, C. H., Xiong, Y.-Y., Huang, D., Yao, Y.-Y., Liu, T.-D., Chen, C.-H., Lin, H., et al. (2022) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2021.402 · Cited by 18

Transcriptome annotation and marker discovery in white bass ( M orone chrysops) and striped bass ( M orone saxatilis)

Li, C., Beck, B. H., Fuller, S. A., & Peatman, E. (2014) · Animal Genetics · doi:10.1111/age.12211 · Cited by 18

Identification of polymorphisms in the bovine collagenous lectins and their association with infectious diseases in cattle

Fraser, R. S., Lumsden, J. S., & Lillie, B. N. (2018) · Immunogenetics · doi:10.1007/s00251-018-1061-7 · Cited by 20

Signatures of Selection in the Genomes of Chinese Chestnut (Castanea mollissima Blume): The Roots of Nut Tree Domestication

LaBonte, N. R., Zhao, P., & Woeste, K. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00810 · Cited by 18

Complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global change stressors

Brennan, R. S., deMayo, J. A., Finiguerra, M. B., Baumann, H., Dam, H. G., & Pespeni, M. H. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2422782122 · Cited by 17

Nucleotide diversity inflation as a genome-wide response to experimental lifespan extension in Drosophila melanogaster

Michalak, P., Kang, L., Sarup, P. M., Schou, M. F., & Loeschcke, V. (2017) · BMC Genomics · doi:10.1186/s12864-017-3485-0 · Cited by 17

Identifying Signatures of Selection Related to Comb Development

Tu, Y., Liu, Y., Zhang, M., Shan, Y., Ji, G., Ju, X., Zou, J., & Shu, J. (2019) · The Journal of Poultry Science · doi:10.2141/jpsa.0190104 · Cited by 17

Local adaptation of life cycles in a butterfly is associated with variation in several circadian clock genes

Lindestad, O., Nylin, S., Wheat, C. W., & Gotthard, K. (2021) · Molecular Ecology · doi:10.1111/mec.16331 · Cited by 17

Effects of evolutionary history on genome wide and phenotypic convergence in Drosophila populations

Phillips, M., Rutledge, G. A., Kezos, J. N., Greenspan, Z. S., Talbott, A., Matty, S., Arain, H., Mueller, L. D., Rose, M. R., & Shahrestani, P. (2018) · BMC Genomics · doi:10.1186/s12864-018-5118-7 · Cited by 17

Interactions between cytoplasmic and nuclear genomes confer sex‐specific effects on lifespan in Drosophila melanogaster

Vaught, R. C., Voigt, S., Dobler, R., Clancy, D. J., Reinhardt, K., & Dowling, D. K. (2020) · Journal of Evolutionary Biology · doi:10.1111/jeb.13605 · Cited by 17

Beyond fruit-flies: population genomic advances in non-Drosophila arthropods

Hasselmann, M., Luca Ferretti, A., & Zayed, A. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elv010 · Cited by 16

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. (2023) · BMC Biology · doi:10.1186/s12915-023-01611-4 · Cited by 16

Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic CO2 seeps

Leiva, C., Pérez‐Portela, R., & Lemer, S. (2023) · Communications Biology · doi:10.1038/s42003-023-05103-7 · Cited by 16

Transposable elements impact the population divergence of rice blast fungus Magnaporthe oryzae

lin, L., Sun, T., Guo, J., Lin, L., Chen, M., Wang, Z., Bao, J., Norvienyeku, J., Han, Y., Han, Y., et al. (2024) · mBio · doi:10.1128/mbio.00086-24 · Cited by 16

Sequence‐Based Multi Ancestry Association Study Reveals the Polygenic Architecture of Varroa destructor Resistance in the Honeybee Apis mellifera

Eynard, S. E., Mondet, F., Basso, B., Bouchez, O., Conte, Y. L., Dainat, B., Decourtye, A., Genestout, L., Guichard, M., Guillaume, F., et al. (2024) · Molecular Ecology · doi:10.1111/mec.17637 · Cited by 16

Genetic footprints of adaptive divergence in the bracovirus of Cotesia sesamiae identified by targeted resequencing

Gauthier, J., Gayral, P., Ru, B. P. L., Jancek, S., Dupas, S., Kaiser, L., Gyapay, G., & Herniou, E. A. (2018) · Molecular Ecology · doi:10.1111/mec.14574 · Cited by 16

Genome-wide analysis of the response to ivermectin treatment by a Swedish field population of Haemonchus contortus

Baltrušis, P., Doyle, S. R., Halvarsson, P., & Höglund, J. (2021) · International Journal for Parasitology Drugs and Drug Resistance · doi:10.1016/j.ijpddr.2021.12.002 · Cited by 16

Whole genome sequencing and RNA-seq evaluation allowed to detect Cd adaptation footprint in Chironomus riparius

Doria, H. B., Hannappel, P., & Pfenninger, M. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.152843 · Cited by 16

The Transposition Rate Has Little Influence on the Plateauing Level of the P-element

Kofler, R., Nolte, V., & Schlötterer, C. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac141 · Cited by 17

Genomic evidence of paternal genome elimination in the globular springtail Allacma fusca

Jaroň, K. S., Hodson, C. N., Ellers, J., Baird, S. J. E., & Ross, L. (2022) · Genetics · doi:10.1093/genetics/iyac117 · Cited by 17

Monitoring rapid evolution of plant populations at scale with Pool-SequencingPreprint

Czech, L., Peng, Y., Spence, J. P., Lang, P. L. M., Bellagio, T., Hildebrandt, J. C., Fritschi, K., Schwab, R., Rowan, B. A., Weigel, D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.02.477408 · Cited by 16

Allelic variation in a cluster of epsilon glutathione S-transferase genes contributes to DDT and pyrethroid resistance in the major African malaria vector Anopheles funestus

Kouamo, M., Ibrahim, S. S., Muhammad, A., Mahamat, G., Hearn, J., & Wondji, C. S. (2025) · BMC Genomics · doi:10.1186/s12864-025-11637-3 · Cited by 15

Geographic Origin and Vertical Transmission of Leishmania infantum Parasites in Hunting Hounds, United States

Franssen, S. U., Sanders, M. J., Berriman, M., Petersen, C. A., & Cotton, J. A. (2022) · Emerging infectious diseases · doi:10.3201/eid2806.211746 · Cited by 15

New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data

Kurland, S., Saha, A., Keehnen, N. L. P., Celorio‐Mancera, M. D. L. P., Díez‐del‐Molino, D., Ryman, N., & Laikre, L. (2023) · Molecular Ecology · doi:10.1111/mec.17213 · Cited by 15

Selection against domestication alleles in introduced rabbit populations

Andrade, P., Alves, J. M., Pereira, P., Rubin, C., da Silva, E. A., Sprehn, C. G., Enbody, E. D., Afonso, S., Faria, R., Zhang, Y., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02443-3 · Cited by 15

Small and genetically highly structured populations in a long-legged bee, Rediviva longimanus, as inferred by pooled RAD-seq

Kahnt, B., Theodorou, P., Soro, A., Hollens‐Kuhr, H., Kuhlmann, M., Pauw, A., & Paxton, R. J. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1313-z · Cited by 15

Optimizing the Power to Identify the Genetic Basis of Complex Traits with Evolve and Resequence Studies

Vlachos, C., & Kofler, R. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz183 · Cited by 15

Population Genomics of Filamentous Plant Pathogens—A Brief Overview of Research Questions, Approaches, and Pitfalls

Everhart, S. E., Gambhir, N., & Stam, R. (2020) · Phytopathology · doi:10.1094/phyto-11-20-0527-fi · Cited by 17

Pooled Sequencing Analysis of Geese (Anser cygnoides) Reveals Genomic Variations Associated With Feather Color

Ren, S., Lyu, G., Irwin, D. M., Liu, X., Feng, C., Luo, R., Zhang, J., Sun, Y., Shang, S., Zhang, S. Y., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.650013 · Cited by 15

Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

Alshwairikh, Y. A., Kroeze, S. L., Olsson, J., Stephens-Cárdenas, S. A., Swain, W. L., Waits, L. P., Horn, R. L., Narum, S. R., & Seaborn, T. (2021) · Ecology and Evolution · doi:10.1002/ece3.8324 · Cited by 15

Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations

Adams, P. E., Crist, A. B., Young, E. M., Willis, J. H., Phillips, P. C., & Fierst, J. L. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab330 · Cited by 16

High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance

Yoshida, Y., Shaikhutdinov, N., Kozlova, O., Itoh, M., Tagami, M., Murata, M., Nishiyori-Sueki, H., Kojima-Ishiyama, M., Noma, S., Cherkasov, A. V., et al. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac029 · Cited by 17

Impacts of Sex Ratio Meiotic Drive on Genome Structure and Function in a Stalk-Eyed Fly

Reinhardt, J. A., Baker, R. H., Zimin, A. V., Ladias, C., Paczolt, K. A., Werren, J. H., Hayashi, C. Y., & Wilkinson, G. S. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad118 · Cited by 15

Genome‐Wide Adaptation to a Complex Environmental Gradient in a Keystone Phytoplankton Species

Pinseel, E., Ruck, E. C., Nakov, T., Jonsson, P. R., Kourtchenko, O., Kremp, A., Pinder, M. I. M., Roberts, W. R., Sjöqvist, C., Töpel, M., et al. (2025) · Molecular Ecology · doi:10.1111/mec.17817 · Cited by 15

High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium

Bukowicki, M., Franssen, S. U., & Schlötterer, C. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12516 · Cited by 15

Genetic costructure in a meta‐community under threat of habitat fragmentation

Kort, H. D., Baguette, M., Prunier, J. G., Tessier, M., Monsimet, J., Turlure, C., & Stevens, V. M. (2018) · Molecular Ecology · doi:10.1111/mec.14569 · Cited by 15

Patterns of transposable element variation and clinality in Drosophila

Adrion, J. R., Begun, D. J., & Hahn, M. W. (2018) · Molecular Ecology · doi:10.1111/mec.14961 · Cited by 15

Genomic divergence and adaptive convergence in Drosophila simulans from Evolution Canyon, Israel

Kang, L., Rashkovetsky, E., Michalak, K., Garner, H. R., Mahaney, J. E., Rzigalinski, B. A., Korol, A. B., Nevo, E., & Michalak, P. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1720938116 · Cited by 15

Shared Mutations in a Novel Glutaredoxin Repressor of Multicellular Trichome Fate Underlie Parallel Evolution of Antirrhinum Species

Tan, Y. C., Barnbrook, M., Wilson, Y., Molnár, A., Bukys, A., & Hudson, A. (2020) · Current Biology · doi:10.1016/j.cub.2020.01.060 · Cited by 15

Supporting Fisheries Management With Genomic Tools: A Case Study of Kingklip (Genypterus capensis) Off Southern Africa

Schulze, M. J., von der Heyden, S., Japp, D. W., Singh, L., Durholtz, D., Kapula, V. K., Ndjaula, H. O. N., & Henriques, R. (2020) · Frontiers in Marine Science · doi:10.3389/fmars.2020.557146 · Cited by 15

Genetic stability of Aedes aegypti populations following invasion by wMel Wolbachia

Lau, M., Schmidt, T. L., Yang, Q., Chung, J., Sankey, L., Ross, P. A., & Hoffmann, A. A. (2021) · BMC Genomics · doi:10.1186/s12864-021-08200-1 · Cited by 15

BSA-Seq Discovery and Functional Analysis of Candidate Hessian Fly (Mayetiola destructor) Avirulence Genes

Navarro-Escalante, L., Zhao, C., Shukle, R. H., & Stuart, J. J. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.00956 · Cited by 14

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) · Genetics Selection Evolution · doi:10.1186/s12711-023-00858-3 · Cited by 14

Dynamics of Dark-Fly Genome Under Environmental Selections

Izutsu, M., Toyoda, A., Fujiyama, A., Agata, K., & Fuse, N. (2015) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.023549 · Cited by 17

Low concordance of short‐term and long‐term selection responses in experimental Drosophila populations

Langmüller, A. M., & Schlötterer, C. (2020) · Molecular Ecology · doi:10.1111/mec.15579 · Cited by 14

Pronounced Plastic and Evolutionary Responses to Unpredictable Thermal Fluctuations in Drosophila simulans

Sørensen, J. G., Manenti, T., Bechsgaard, J., Schou, M. F., Kristensen, T. N., & Loeschcke, V. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.555843 · Cited by 14

A region of the sex chromosome associated with population differences in diapause induction contains highly divergent alleles at clock genes

Pruisscher, P., Nylin, S., Wheat, C. W., & Gotthard, K. (2020) · Evolution · doi:10.1111/evo.14151 · Cited by 14

New Sex Chromosomes in Lake Victoria Cichlid Fishes (Cichlidae: Haplochromini)

Kocher, T. D., Behrens, K. A., Conte, M. A., Aibara, M., Mrosso, H. D. J., Green, E. C. J., Kidd, M. R., Nikaido, M., & Koblmüller, S. (2022) · Genes · doi:10.3390/genes13050804 · Cited by 14

Evolutionary Divergence and Radula Diversification in Two Ecomorphs from an Adaptive Radiation of Freshwater Snails

Hilgers, L., Hartmann, S. A., Pfaender, J., Lentge-Maaß, N., Marwoto, R. M., von Rintelen, T., & Hofreiter, M. (2022) · Genes · doi:10.3390/genes13061029 · Cited by 14

Comparison of whole mitochondrial genome sequences from two clades of the invasive ascidian, Didemnum vexillum

Smith, K. F., Abbott, C. L., Saito, Y., & Fidler, A. E. (2014) · Marine Genomics · doi:10.1016/j.margen.2014.11.007 · Cited by 14

A novel sex-linked mutant affecting tail formation in Hongshan chicken

Wang, Q., Pi, J., Pan, A., Shen, J., & Qu, L. (2017) · Scientific Reports · doi:10.1038/s41598-017-10943-5 · Cited by 14

Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

McCallum, J. A., Laing, W. A., Bulley, S. M., Thomson, S. J., Catanach, A. S., Shaw, M. L., Knäbel, M., Tahir, J., Deroles, S. C., Timmerman‐Vaughan, G. M., et al. (2019) · Plants · doi:10.3390/plants8070237 · Cited by 14

Massive postglacial gene flow between European white oaks uncovered genes underlying species barriersPreprint

Leroy, T., Rougemont, Q., Dupouey, J., Bodénès, C., Lalanne, C., Belser, C., Labadie, K., Provost, G. L., Aury, J., Kremer, A., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/246637 · Cited by 15

Thermal acclimation uncovers a simple genetic basis of adaptation to high temperature in a cosmopolitan pest

You, S., Lei, G., Zhou, H., Li, J., Chen, S., Huang, J., Vasseur, L., Gurr, G. M., You, M., & Chen, Y. (2024) · iScience · doi:10.1016/j.isci.2024.109242 · Cited by 13

Tutorial

Kofler, R., Ram Vinay, P., Schlötterer, C., & Barrett, J. (2011)

assessPool: a flexible pipeline for population genomic analyses of pooled sequencing dataPreprint

Freel, E. B., Conklin, E. E., Kraft, D. W., Whitney, J., Knapp, I. S. S., Forsman, Z. H., & Toonen, R. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.09.617480 · Cited by 2

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

Kofler, R., Orozco‐terWengel, P., Maio, N. D., Pandey, R. V., Nolte, V., Futschik, A., Kosiol, C., & Schlötterer, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0015925 · Cited by 576

Measuring Genetic Differentiation from Pool-seq Data

Hivert, V., Leblois, R., Petit, E. J., Gautier, M., & Vitalis, R. (2018) · Genetics · doi:10.1534/genetics.118.300900 · Cited by 184

npstat: An Efficient Tool to Explore the Population Genome Variability and Divergence Using Pool Sequencing Data

Ramos-Onsins, S. E., Guirao‐Rico, S., Hafez, A. I., & Luca Ferretti, A. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4583-3_3 · Cited by 1