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Highly Parallel Genomic Selection Response in Replicated Drosophila melanogaster Populations with Reduced Genetic Variation

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Identification of Haplotypes Associated With Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole-Genome Resequencing

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Variation in genomic vulnerability to climate change across temperate populations of eelgrass (Zostera marina)

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Regulation of transposable elements: Interplay between TE‐encoded regulatory sequences and host‐specific trans‐acting factors in Drosophila melanogaster

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Microevolutionary selection dynamics acting on immune genes of the green‐veined white butterfly, Pieris napi

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Pleiotropic effects of regulatory variation in tan result in correlation of two pigmentation traits in Drosophila melanogaster

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Rapid adaptation and extinction in synchronized outdoor evolution experiments of Arabidopsis

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Population-specific thermal responses contribute to regional variability in arbovirus transmission with changing climates

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Genomics of Recombination Rate Variation in Temperature-EvolvedDrosophila melanogasterPopulations

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The effects of genetic drift and genomic selection on differentiation and local adaptation of the introduced populations of Aedes albopictus in southern Russia

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Neutral and adaptive drivers of genomic change in introduced brook trout ( Salvelinus fontinalis ) populations revealed by pooled sequencing

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Molecular parallelism in signaling function across different sexually selected ornaments in a warbler

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Evolution and genomic basis of the plant-penetrating ovipositor: a key morphological trait in herbivorous Drosophilidae

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Genomic and Transcriptome Analysis Reveals the Biosynthesis Network of Cordycepin in Cordyceps militaris

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A method for single pair mating in an obligate parasitic nematode

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Genome-Wide Mapping of Gene–Phenotype Relationships in Experimentally Evolved Populations

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Readapting to DCV Infection without Wolbachia: Frequency Changes of Drosophila Antiviral Alleles Can Replace Endosymbiont Protection

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Genetic and Genome Analyses Reveal Genetically Distinct Populations of the Bee Pathogen Nosema ceranae from Thailand

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Population genomics of honey bees reveals a selection signature indispensable for royal jelly production

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Genome scan detection of selective sweeps among biotypes of the soybean aphid, Aphis glycines, with differing virulence to resistance to A. glycines (Rag) traits in soybean, Glycine max

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Within-population sperm competition intensity does not predict asymmetry in conpopulation sperm precedence

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Genetic × environment variation in sheep lines bred for divergent resistance to strongyle infection

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Detection of whole genome selection signatures of Pakistani Teddy goat

Saif, R., Henkel, J., Mahmood, T., Ejaz, A., Ahmad, F., & Zia, S. (2021) · Molecular Biology Reports · doi:10.1007/s11033-021-06726-x · Cited by 12

Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss

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Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes

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Whole-genome screening for near-diagnostic genetic markers for four western European white oak species identification

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Genome scans for selection signatures identify candidate virulence genes for adaptation of the soybean cyst nematode to host resistance

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Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma

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Advances in finding Alba: the locus affecting life history and color polymorphism in a Colias butterfly

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A genetic reconstruction of the invasion of the calanoid copepod Pseudodiaptomus inopinus across the North American Pacific Coast

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Using Pool-seq to Search for Genomic Regions Affected by Hybrid Inviability in the copepod T. californicus

Lima, T. G., & Willett, C. S. (2018) · Journal of Heredity · doi:10.1093/jhered/esx115 · Cited by 11

Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches

Nunez, J. C. B., Elyanow, R., Ferranti, D. A., & Rand, D. M. (2018) · Population genomics · doi:10.1007/13836_2018_58 · Cited by 11

Elevated Heterozygosity in Adults Relative to Juveniles Provides Evidence of Viability Selection on Eagles and Falcons

Doyle, J. M., Willoughby, J. R., Bell, D. A., Bloom, P. H., Bragin, E. A., Fernández, N. B., Katzner, T. E., Leonard, K., & DeWoody, J. A. (2019) · Journal of Heredity · doi:10.1093/jhered/esz048 · Cited by 12

Genome‐wide re‐sequencing and transcriptome analysis reveal candidate genes associated with the pendulous comb phenotype in domestic chickens

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Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population

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Genomic evidence for adaptive differentiation among Microhyla fissipes populations: Implications for conservation

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Transcriptional dynamics following freezing stress reveal selection for mechanisms of freeze tolerance at the poleward range margin in the cold water intertidal barnacle Semibalanus balanoidesPreprint

Marshall, K. E., Dowle, E., Petrunina, A. S., Kolbasov, G. A., & Chan, B. K. K. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/449330 · Cited by 12

Bait‐ER: A Bayesian method to detect targets of selection in Evolve‐and‐Resequence experiments

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Genomic signatures of adaptation to novel environments: hatchery and life history-associated loci in landlocked and anadromous Atlantic salmon ( Salmo salar )

Harder, A. M., & Christie, M. R. (2022) · Canadian Journal of Fisheries and Aquatic Sciences · doi:10.1139/cjfas-2021-0066 · Cited by 10

Bulk segregant linkage mapping for rodent and human malaria parasites

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Assessing the relative importance of stressors to the benthic index, M-AMBI: An example from U.S. estuaries

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Release from sexual selection leads to rapid genome-wide evolution in Aedes aegypti

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Comparative genomics of rainbow trout ( Oncorhynchus mykiss ): Is the genetic architecture of migratory behavior conserved among populations?

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Mitonuclear interactions shape both direct and parental effects of diet on fitness and involve a SNP in mitoribosomal 16s rRNA

Dobson, A. J., Voigt, S., Kumpitsch, L., Langer, L., Voigt, E., Ibrahim, R., Dowling, D. K., & Reinhardt, K. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002218 · Cited by 10

Parental care shapes the evolution of molecular genetic variation

Rahia Mashoodh, A., Trowsdale, A. T., Manica, A., & Kilner, R. M. (2023) · Evolution Letters · doi:10.1093/evlett/qrad039 · Cited by 10

Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish

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Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation

Woronowicz, K. C., Esin, E. V., Маркевич, Г. Н., Martinez, C. S., McMenamin, S. K., Daane, J. M., Harris, M. P., & Shkil, F. N. (2024) · Development · doi:10.1242/dev.203002 · Cited by 10

Comparative analysis of two phenologically divergent populations of the pine processionary moth (Thaumetopoea pityocampa) by de novo transcriptome sequencing

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Regulatory and sequence evolution in response to selection for improved associative learning ability in Nasonia vitripennis

Kraaijeveld, K., Oostra, V., Liefting, M., Wertheim, B., de Meijer, E., & Ellers, J. (2018) · BMC Genomics · doi:10.1186/s12864-018-5310-9 · Cited by 10

Large-scale genome investigations reveal insights into domestication of cultivated mushrooms

Fu, Y., Dai, Y., Chethana, K. W. T., Li, Z., Sun, L., Li, C., Yu, H., Yang, R., Tan, Q., Bao, D., et al. (2022) · Mycosphere · doi:10.5943/mycosphere/si/1f/4 · Cited by 10

Phase variable colony variants are conserved across Gardnerella spp. and exhibit different virulence-associated phenotypes

Garcia, E. M., Klimowicz, A. K., Edupuganti, L., Topf, M. A., Bhide, S. R., Slusser, D. J., Leib, S. M., Coddington, C. L., Matveyev, A. V., Buck, G. A., et al. (2024) · mSphere · doi:10.1128/msphere.00450-24 · Cited by 10

Adaptive evolution of stress response genes in parasites aligns with host niche diversity

Cruz‐Laufer, A. J., Vanhove, M. P. M., Bachmann, L., Barson, M., Bassirou, H., Nyom, A. R. B., Geraerts, M., Hahn, C., Huyse, T., Kasembele, G. K., et al. (2025) · BMC Biology · doi:10.1186/s12915-024-02091-w · Cited by 9

Genomic Signatures of Selection between Urban and Rural Populations of Black Garden Ant Lasius niger

Konorov, E. A. (2018) · Russian Journal of Genetics · doi:10.1134/s1022795418020102 · Cited by 9

Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation

Grande, F. D., Jamilloux, V., Choisne, N., Calchera, A., Rolshausen, G., Petersen, M., Schulz, M., Nilsson, M. A., & Schmitt, I. (2021) · Biology · doi:10.3390/biology11010024 · Cited by 9

Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations

Wit, J., Workentine, M. L., Redman, E., Laing, R., Stevens, L., Cotton, J. A., Chaudhry, U. N., Ali, Q., Andersen, E. C., Yeaman, S., et al. (2022) · International Journal for Parasitology · doi:10.1016/j.ijpara.2022.07.004 · Cited by 9

Genomic differentiation in Pacific cod using P ool‐ S eq

Spies, I., Tarpey, C. M., Kristiansen, T., Fisher, M. C., Rohan, S. K., & Hauser, L. (2022) · Evolutionary Applications · doi:10.1111/eva.13488 · Cited by 9

Sex chromosomes in the tribe Cyprichromini (Teleostei: Cichlidae) of Lake Tanganyika

Behrens, K. A., Koblmüller, S., & Kocher, T. D. (2022) · Scientific Reports · doi:10.1038/s41598-022-23017-y · Cited by 9

Synthesizing historic and current evidence for anadromy in a northern pike (Esox lucius L.) meta-population inhabiting brackish lagoons of the southern Baltic Sea, with implications for management

Roser, P., Dhellemmes, F., Rittweg, T. D., Möller, S., Winkler, H., Lukyanova, O., Niessner, D., Schütt, J., Kühn, C., Dennenmoser, S., et al. (2023) · Fisheries Research · doi:10.1016/j.fishres.2023.106670 · Cited by 9

Evidence of introgression, ecological divergence and adaptation inAsteriassea stars

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Sexually discordant selection is associated with trait-specific morphological changes and a complex genomic response

Audet, T., Krol, J., Pelletier, K., Stewart, A. D., & Dworkin, I. M. (2024) · Evolution · doi:10.1093/evolut/qpae071 · Cited by 9

Genome Scans Reveal Homogenization and Local Adaptations in Populations of the Soybean Cyst Nematode

St-Marseille, A.-F. G., Lord, É., Véronneau, P., Jacques Brodeur, B., & Mimee, B. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00987 · Cited by 9

Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations of Haemonchus contortus

Khan, S., Zhao, X., Hou, Y., Yuan, C., Li, Y., Luo, X., Liu, J., & Feng, X. (2019) · Journal of Biosciences · doi:10.1007/s12038-019-9917-z · Cited by 9

Genomics of Early Cardiac Dysfunction and Mortality in Obese Drosophila melanogaster

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Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)

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Evolutionary Change in the Eastern Oyster,Crassostrea Virginica, Following Low Salinity Exposure

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Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature

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Investigating the genetics of B ti resistance using m RNA tag sequencing: application on laboratory strains and natural populations of the dengue vector A edes aegypti

Paris, M., Marcombe, S., Coissac, É., Corbel, V., David, J., & Després, L. (2013) · Evolutionary Applications · doi:10.1111/eva.12082 · Cited by 9

Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas

Deitz, K. C., Athrey, G., Jawara, M., Overgaard, H. J., Matías, A., & Slotman, M. A. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.031906 · Cited by 9

Bucking the trend of pollinator decline: the population genetics of a range expanding bumblebee

Huml, J. V., Ellis, J. S., Lloyd, K. L., Benefer, C. M., Kiernan, M., Brown, M. J. F., & Knight, M. E. (2021) · Evolutionary Ecology · doi:10.1007/s10682-021-10111-2 · Cited by 9

Sex-linked DNA marker screening and characterization in albino northern snakehead (Channa argus var.) via third-generation sequencing and pool resequencing

Dai, S., Chen, M., Zheng, S., Su, J. Q., Wu, J., Han, L., Zhou, C., Zou, Y., Wang, D., & Li, M. (2024) · Aquaculture · doi:10.1016/j.aquaculture.2024.741449 · Cited by 8

Genome‐wide differentiation corresponds to climatic niches in two species of lichen‐forming fungi

Wong, E. L. Y., Valim, H. F., & Schmitt, I. (2024) · Environmental Microbiology · doi:10.1111/1462-2920.16703 · Cited by 8

Ethanol resistance in Drosophila melanogaster has increased in parallel cold‐adapted populations and shows a variable genetic architecture within and between populations

Sprengelmeyer, Q. D., & Pool, J. E. (2021) · Ecology and Evolution · doi:10.1002/ece3.8228 · Cited by 8

Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa

Forde, S. H., von der Heyden, S., Moan, A. L., Nielsen, E. S., Durholtz, D., Kainge, P., Kathena, J. N., Lipiński, M. R., Ndjaula, H. O. N., Matthee, C. A., et al. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13820 · Cited by 8

Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence

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Circadian clock‐ and temperature‐associated genes contribute to overall genomic differentiation along elevation in lichenized fungi

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Genome-wide association studies unveil major genetic loci driving insecticide resistance in Anopheles funestus in four eco-geographical settings across Cameroon

Mahamat, G., Kengne-Ouafo, J. A., Tchouakui, M., Wondji, M. J., Mugenzi, L. M. J., Hearn, J., Boyomo, O., & Wondji, C. S. (2024) · BMC Genomics · doi:10.1186/s12864-024-11148-7 · Cited by 8

Detection of genetic variation affecting milk coagulation properties in Danish Holstein dairy cattle by analyses of pooled whole-genome sequences from phenotypically extreme samples (pool-seq)1

Bertelsen, H. P., Gregersen, V. R., Poulsen, N. A., Nielsen, R. O., Das, A., Madsen, L. B., Buitenhuis, B., Holm, L.-E., Panitz, F., Larsen, L. B., et al. (2016) · Journal of Animal Science · doi:10.2527/jas.2015-9884 · Cited by 8

A Population Genomic Investigation of Immune Cell Diversity and Phagocytic Capacity in a Butterfly

Keehnen, N. L. P., Fors, L., Järver, P., Spetz, A., Nylin, S., Theopold, U., & Wheat, C. W. (2021) · Genes · doi:10.3390/genes12020279 · Cited by 8

The Genomics and Population Genomics of the Light Brown Apple Moth, Epiphyas postvittana, an Invasive Tortricid Pest of Horticulture

Thrimawithana, A. H., Wu, C., Christeller, J. T., Simpson, R. M., Hilario, E., Tooman, L. K., Begum, D., Jordan, M. D., Crowhurst, R. N., Newcomb, R. D., et al. (2022) · Insects · doi:10.3390/insects13030264 · Cited by 8

Introgression of a synthetic sex ratio distortion transgene into different genetic backgrounds of Anopheles coluzzii

Pollegioni, P., Persampieri, T., Minuz, R. L., Bucci, A., Trusso, A., Martino, S. D., Leo, C., Bruttini, M., Ciolfi, M., Waldvogel, A., et al. (2022) · Insect Molecular Biology · doi:10.1111/imb.12813 · Cited by 8

Historic DNA uncovers genetic effects of climate change and landscape alteration in two wild bee species

Brasil, S. N. R., Kelemen, E. P., & Rehan, S. M. (2022) · Conservation Genetics · doi:10.1007/s10592-022-01488-w · Cited by 8

Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild-caught populations of Drosophila melanogaster

Pelletier, K., Pitchers, W., Mammel, A., Northrop‐Albrecht, E. J., Márquez, E. J., Moscarella, R. A., Houle, D., & Dworkin, I. M. (2023) · Genetics · doi:10.1093/genetics/iyad050 · Cited by 9

Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish

Chen, A., Wang, R., Liu, S., Peatman, E., Sun, L., Bao, L., Jiang, C., Li, C., Li, Y., Zeng, Q., et al. (2016) · Molecular Genetics and Genomics · doi:10.1007/s00438-015-1162-z · Cited by 8

The genetic architecture in Saccharomyces cerevisiae that contributes to variation in drug response to the antifungals benomyl and ketoconazole

Roberts, C. A., Miller, J. H., & Atkinson, P. H. (2017) · FEMS Yeast Research · doi:10.1093/femsyr/fox027 · Cited by 8

A Test for Gene Flow among Sympatric and Allopatric Hawaiian Picture-Winged Drosophila

Kang, L., Garner, H. R., Price, D. K., & Michalak, P. (2017) · Journal of Molecular Evolution · doi:10.1007/s00239-017-9795-7 · Cited by 8

Uterine leiomyosarcoma metastasis to the breast.

Hsiao, H. H., Liu, Y. C., Hou, M., & Lin, S. (2008) · PubMed · Cited by 8

Postglacial ecotype formation under outcrossing and self‐fertilization inArabidopsis lyrata

Lucek, K., Hohmann, N., & Willi, Y. (2019) · Molecular Ecology · doi:10.1111/mec.15035 · Cited by 8

Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake’s sediment

Cordellier, M., Wojewodzic, M. W., Wessels, M., Kuster, C., & von Elert, E. (2021) · Zoology · doi:10.1016/j.zool.2021.125895 · Cited by 8

Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae

Li, K., Yan, W., Zhang, L. Z., Zeng, Z. J., Evans, J. D., & Huang, Q. (2021) · Microbial Ecology · doi:10.1007/s00248-021-01827-3 · Cited by 8

Drosophila yakuba mayottensis, a new model for the study of incipient ecological speciation

Yassin, A. (2016) · Fly · doi:10.1080/19336934.2016.1221550 · Cited by 8

Convergent Adaptation to Quantitative Host Resistance in a Major Plant Pathogen

Carlier, J. P., Bonnot, F., Roussel, V., Ravel, S., Martínez, R. T., Vicente, L. P., Abadie, C., & Wright, S. (2021) · mBio · doi:10.1128/mbio.03129-20 · Cited by 8

Transposable element dynamics are consistent across the Drosophila phylogeny, despite drastically differing contentPreprint

Hill, T. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/651059 · Cited by 8

Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflowerPreprint

Wilkinson, M. J., Roda, F., Walter, G. M., James, M. E., Nipper, R. W., Walsh, J., Allen, S. L., North, H. L., Beveridge, C. A., & Ortíz-Barrientos, D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/845354 · Cited by 8

Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscuriorPreprint

Errbii, M., Gadau, J., Becker, K., Schrader, L., & Oettler, J. (2024) · Genome Research · doi:10.1101/gr.278392.123 · Cited by 8

Analyses of emerging macrocyclic lactone resistance: Speed and signature of ivermectin and moxidectin selection and evidence of a shared genetic locus

McIntyre, J., Morrison, A. A., Maitland, K., Devaney, E., Cotton, J. A., Britton, C., Kaplan, R. M., Bartley, D., & Laing, R. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013578 · Cited by 7

Allelically and Differentially Expressed Genes After Infection of Edwardsiella ictaluri in Channel Catfish as Determined by Bulk Segregant RNA-Seq

Jin, Y., Zhou, T., Jiang, W., Li, N., Xu, X., Tan, S., Shi, H., Yang, Y., Yuan, Z., Wang, W., et al. (2022) · Marine Biotechnology · doi:10.1007/s10126-022-10094-3 · Cited by 7

A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?

Arnqvist, G., & Sayadi, A. (2022) · Ecology and Evolution · doi:10.1002/ece3.9440 · Cited by 7

Comparing the Utility of Microsatellites and Single Nucleotide Polymorphisms in Conservation Genetics: Insights from a Study on Two Freshwater Fish Species in France

Prunier, J. G., Veyssière, C., Loot, G., & Blanchet, S. (2023) · Diversity · doi:10.3390/d15050681 · Cited by 10

Genetic constraints in genes exhibiting splicing plasticity in facultative diapause

Steward, R., Pruisscher, P., Roberts, K. T., & Wheat, C. W. (2024) · Heredity · doi:10.1038/s41437-024-00669-2 · Cited by 7

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