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

Eye can see clearly now: Identifying the locus associated with a white‐eye mutation in honey bees ( Apis mellifera )

Shultz, R. R., Ryals, D. K., Patterson, P., Nixon, J. M., Gilchrist, I. R., & Harpur, B. A. (2025) · Insect Molecular Biology · doi:10.1111/imb.70019 · Cited by 2

Life History and Smoltification Shape Genomic Signatures of Thermal Tolerance in Chinook Salmon

Metzger, D. C. H., Healy, T. M., Wellband, K. W., & Schulte, P. M. (2026) · Molecular Ecology · doi:10.1111/mec.70233 · Cited by 2

Beyond acute toxicity: evolutionary response by rapid polygenic adaptation to a complex environmental stressor in Chironomus riparius

Rigano, L., Schmitz, M., Hollert, H., & Pfenninger, M. (2026) · Environmental Toxicology and Chemistry · doi:10.1093/etojnl/vgag010 · Cited by 2

The life history of recessive deleterious alleles as seen through the eyes of a honey bee ( Apis mellifera )

Shultz, R. R., Nixon, J. M., Ryals, D. K., Buschkoetter, A. C., Gilchrist, I. R., Given, K., Metz, B. N., Magaña, A. A., Moon, K., Thanepohn, B., et al. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag156 · Cited by 2

Evidences of Z- and W-Linked Regions on the Genome of Fenneropenaeus chinensis

Wang, Q., Lv, J., Ren, X., Wang, J., Jia, S., He, Y., & Li, J. (2021) · Frontiers in Marine Science · doi:10.3389/fmars.2021.743727 · Cited by 2

Transcriptomic signatures and genomic regions associated with growth in the flatfish Senegalese sole

Gayo, P., Berbel, C., & Manchado, M. (2024) · Aquaculture · doi:10.1016/j.aquaculture.2024.741234 · Cited by 3

Insect Models to Study Human Lipid Metabolism Disorders

Rundell, T. B., & Baranski, T. (2024) · Advances in experimental medicine and biology · doi:10.1007/5584_2024_827 · Cited by 2

Population differences in reproductive resource allocation and heterosis in the invasive vector Aedes albopictus

Khorramnejad, A., Alfaro, C., Quaranta, S., Lozada-Chávez, A. N., Gasmi, L., Perdomo, H. D., Chiarelli, L. R., & Bonizzoni, M. (2026) · Parasites & Vectors · doi:10.1186/s13071-025-07235-7 · Cited by 2

Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana

Andrade, P., Lyra, M. L., Zina, J., Bastos, D. F. D. O., Brunetti, A. E., Baêta, D., Afonso, S., Brunes, T. O., Taucce, P. P. G., Carneiro, M., et al. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac270 · Cited by 2

A critically endangered estuarine limpet’s only two populations are genomically and morphologically distinct

de Coito, P., Emami‐Khoyi, A., Hedderson, T. A. J., Toonen, R. J., Teske, P. R., & Branch, G. M. (2023) · Aquatic Conservation Marine and Freshwater Ecosystems · doi:10.1002/aqc.3993 · Cited by 2

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) · Parasites & Vectors · doi:10.1186/s13071-024-06300-x · Cited by 2

GTP cyclohydrolase II ( gch2 ) and axanthism in ball pythons: A new vertebrate model for pterin‐based pigmentation

García‐Elfring, A., Roffey, H. L., Abergas, J. M., Hendry, A. P., & Barrett, R. D. H. (2025) · Animal Genetics · doi:10.1111/age.70011 · Cited by 2

Next-Generation Sequencing Data Analysis on Pool-Seq and Low-Coverage Retinoblastoma Data

Özdoğan, G. Ö., & Kaya, H. (2020) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-020-00374-8 · Cited by 2

Phenotypic features, transcriptomic signatures and genomic regions associated with body ellipticity in the flatfish Senegalese sole

Gayo, P., Berbel, C., Maldonado, J. G., Claros, M. G., & Manchado, M. (2024) · Aquaculture · doi:10.1016/j.aquaculture.2024.740590 · Cited by 2

A missense mutation in the tyrosinase gene explains acromelanism in domesticated canaries

Guimarães‐Moreira, M., Marques, C. I., Afonso, S., Lacerda, B., Carneiro, M., & Araújo, P. M. (2024) · Animal Genetics · doi:10.1111/age.13481 · Cited by 2

Climate change driven hyposalinity as a selective agent in the littoral mesoherbivore Idotea balthica

Rugiu, L., Wit, P. D., Kostian, I., & Jormalainen, V. (2020) · Marine Environmental Research · doi:10.1016/j.marenvres.2020.105216 · Cited by 2

Different Genomic Changes Underlie Adaptive Evolution in Populations of Contrasting History

Seabra, S. G., Fragata, I., Santos, M. A., Faria, G. S., Santos, M. A., Sousa, V. C., Simões, P., & Matos, M. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz076 · Cited by 2

Extensive genetic differentiation between homomorphic sex chromosomes in the mosquito vector, Aedes aegyptiPreprint

Fontaine, A., Filipović, I., Fansiri, T., Hoffmann, A. A., Cheng, C., Kirkpatrick, M., Rašić, G., & Lambrechts, L. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/060061 · Cited by 2

Unravelling the genomic basis and evolution of the pea aphid male wing dimorphismPreprint

Li, B., Bickel, R. D., Parker, B. J., Vellichirammal, N. N., Grantham, M. E., Simon, J., Stern, D. L., & Brisson, J. A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/156133 · Cited by 2

New WGS data and annotation of the heterosomal vs. autosomal localization of Ostrinia scapulalis (Lepidoptera, Crambidae) nuclear genomic scaffolds

Brousseau, L., Nidelet, S., & Streiff, R. (2018) · Data in Brief · doi:10.1016/j.dib.2018.08.011 · Cited by 2

The genomics of development rate variation in Cochliomyia macellaria (Diptera: Calliphoridae)

Lewis, S. E. (2018) · ProQuest Demo Repository · doi:10.7912/c2r36k · Cited by 2

Exploiting next generation sequencing techniques (NGS) to identify molecular markers for monitoring the resistance of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) to insecticides and Bt proteins

Nascimento, A. G. (2019) · doi:10.11606/t.11.2019.tde-03012019-160052 · Cited by 2

The mechanism underlying strigolactone diversification in sorghum and its role in resistance against the parasitic weed Striga hermonthica

Shimels, M. Z. (2019) · doi:10.18174/498779 · Cited by 2

A genomic analysis of parasite-mediated population differentiation in a metapopulationPreprint

Halter, M., Pasquier, L. D., Ebert, D., & Fields, P. D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.10.483675 · Cited by 2

Polygenic architecture of adaptation to a high-altitude environment for Drosophila melanogaster wing shape and sizePreprint

Pelletier, K., Bilodeau, M., Pellizzari-Delano, I. E., Siemon, M. D., Huang, Y., Pool, J. E., & Dworkin, I. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.08.579525 · Cited by 2

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

Ancient MAX Effector Variants of a Fungal Pathogen Evade Apoplastic Immunity in ApplePreprint

Sannier, M., Benmamar, S., Collemare, J., Lemaire, C., Caffier, V., Duplaix, C., Shiller, J. B., Mathieu‐Bégné, E., Vayssières, A., Schouten, H. J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.25.695362 · Cited by 2

Coexisting Y haplotypes reveal cyclic sex chromosome differentiation around a shared sex-determining regionPreprint

Carpentier, F., Houtain, A., Unal, E., Doucette, K. L., Fontserè, R., Brelsford, A., Toups, M. A., Perrin, N., Veltsos, P., & Ma, W. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.31.697208 · Cited by 2

Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci

Marconcini, M., Cruchet, S., Goswami, S., Viswanatha, R., Butnaru, M., De, J., Roselli, C., Hadjieconomou, D., Perrimon, N., Mohr, S. E., et al. (2026) · eLife · doi:10.7554/elife.111773.3 · Cited by 2

Pool-Seq genomic based analytical approaches can yield novel insights into unculturable taxa: an example from the red snow algae Sanguina nivaloides

Tucker, A. E., & Brown, S. P. (2023) · Botany Letters · doi:10.1080/23818107.2023.2267661 · Cited by 1

Population Genetics to Population Genomics: Revisiting Multispecies Connectivity of the Hawaiian Archipelago

Freel, E. B., Conklin, E. E., Knapp, I. S. S., Kraft, D. W., Johnston, E. C., Forsman, Z. H., Coleman, R. R., Whitney, J., Iacchei, M. J., Bowen, B. W., et al. (2025) · Fishes · doi:10.3390/fishes10120623 · Cited by 1

On the distribution and diversity of tissue-specific somatic mutations in honey bee (Apis mellifera) drones

Shultz, R. R., Carey, A., Ragheb, K., Robinson, J. P., & Harpur, B. A. (2024) · Insectes Sociaux · doi:10.1007/s00040-024-00948-5 · Cited by 1

Development of single nucleotide polymorphisms markers associated with disease resistance towards Pseudomonas koreensis in empurau (Tor tambroides) using T-Plex ARMS PCR assay

Lau, M. M. L., Chung, H. H., Kho, C. J. Y., Gan, H. M., & Zulkharnain, A. (2025) · Aquaculture International · doi:10.1007/s10499-025-02055-z · Cited by 1

Global stock structure of the Silky shark (Carcharhinus falciformis, Carcharhinidae) assessed with high-throughput DNA sequencing

Kraft, D. W., Conklin, E. E., Freel, E. B., Hutchinson, M., Spaet, J. L. Y., Toonen, R. J., Forsman, Z. H., Grant, M. I., Filmalter, J. D., Hyde, J. R., et al. (2025) · PeerJ · doi:10.7717/peerj.19493 · Cited by 1

Over-expression and increased copy numbers of a cytochrome P450 and two UDP-glucuronosyltransferase genes in macrocyclic lactone resistant Psoroptes ovis of cattle

Hearn, J., van Mol, W., Meyermans, R., Bartley, K., Alioto, T., Gómez‐Garrido, J., Cruz, F., Ferreira, F. C., Gut, M., Gut, I., et al. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1012963 · Cited by 1

Divergence and Parallelism in Two Tropical Drosophilids Simultaneously Invading a Desert Environment

El-Sabrout, A. M., Moreno, C., Temperville, M., Ferreira, E. A., Ogereau, D., Hassani, I. M., Ravaomanarivo, L. H. R., Bastide, H., Abou-Youssef, A. Y., & Yassin, A. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf146 · Cited by 1

Comparative Genomic Analysis of Co‐Occurring Hybrid Zones of House Mouse Parasites Pneumocystis murina and Syphacia obvelata Using Genome Polarisation

Petružela, J., Nürnberger, B., Ribas, A., Koutsovoulos, G., Čížková, D., Fornůsková, A., Aghová, T., Blaxter, M., de Bellocq, J. G., & Baird, S. J. E. (2025) · Molecular Ecology · doi:10.1111/mec.70044 · Cited by 1

Contemporary Evolution of an At‐Risk Stickleback Population During a Severe Drought

Sanderson, S., Eckert, L., Barrett, R. D. H., Reimchen, T. E., & Hendry, A. P. (2026) · Evolutionary Applications · doi:10.1111/eva.70189 · Cited by 1

Transcriptome analysis for growth-related genes and SNPs in the Indian catfish Clarias magur

Haldar, C., Ram, R., Pavan‐Kumar, A., Gireesh-Babu, P., KORINGA, P. G., Joshi, C., & Chaudhari, A. (2026) · Aquaculture · doi:10.1016/j.aquaculture.2026.743769 · Cited by 1

Experimental evolution of the host range dynamics in two isolates of potato virus Y

de Morais, I. J., Silva, J. M. F., Inoue-Nagata, A. K., & Elena, S. F. (2026) · Virus Evolution · doi:10.1093/ve/veag010 · Cited by 1

The Genetic Architecture of Venom Resistance: A Novel Approach to Target Identification and Coevolutionary Discovery

Ward, M. J., Ellsworth, S. A., King, E. G., Ng’oma, E., Nystrom, G. S., Lawrence, K. C., Maquet, L., Oliver, A., Margres, M. J., Parkinson, C. L., et al. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag048 · Cited by 1

Evidence that standing genetic variation contributes to parallel evolution of body size in a Lake Tanganyika cichlid

Takahashi, T. (2026) · Hydrobiologia · doi:10.1007/s10750-026-06181-4 · Cited by 1

Re‐Interpreting Genetic Offset: Quantifying the Least Required Evolutionary Rate Under Climate Change at the Mediterranean Range Margin of European Beech

Morando‐Milà, J., Grau, O., Ulaszewski, B., Vilà‐Cabrera, A., Peñuelas, J., Jump, A. S., & Scotti, I. (2026) · Evolutionary Applications · doi:10.1111/eva.70230 · Cited by 1

Geographic differentiation of ectoparasitic flatworms in the pelagic zone of Lake Tanganyika, Africa

Kmentová, N., Thys, K. J. M., Hahn, C., Vorel, J., Bachmann, L., Koblmüller, S., Steenberge, M. W. V., Manda, A. C., Makasa, L., N'sibula, T. M., et al. (2026) · Frontiers in Zoology · doi:10.1186/s12983-026-00602-9 · Cited by 1

Experimental Evolution Under Biased Sex Ratios: Phenotypic and Genomic Responses in the Bulb Mite, Rhizoglyphus robini

Chmielewski, S., Parrett, J. M., Konczal, M., Szubert‐Kruszyńska, A., Łukasiewicz, A., & Radwan, J. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag151 · Cited by 1

Beyond fixation: persistent genetic variation under intense selection

Arnold, K. R., Greenspan, Z. S., Robinson, R. D., Pupo, A., Chavarin, V. V., Chang, K. S., Cannell, C. O., Qi, M., Mueller, L. D., Rose, M. R., et al. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag188 · Cited by 1

Whole-genome sequencing data confirms the uniqueness of Ireland’s native honey bee

Smith, S., Valentine, A., Verspuij, M., Binetti, C., Moro, A., Browne, K. A., Loughlin, E. M., Neuditschko, M., & Mccormack, G. P. (2026) · Scientific Reports · doi:10.1038/s41598-026-64520-w · Cited by 1

Genomics of Plant Gene Banks: Prospects for Managing and Delivering Diversity in the Digital Age

Richards, C. M. (2021) · Population genomics · doi:10.1007/13836_2021_95 · Cited by 1

Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host–Symbiont Coevolution

Matthews, A. E., Boves, T. J., Percy, K. L., Schelsky, W. M., & Wijeratne, A. (2023) · Life · doi:10.3390/life13102054 · Cited by 1

Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing

Sun, H., Zhang, J., Zhang, H.-X., Xu, Q., & Lu, D. (2023) · Parasite · doi:10.1051/parasite/2023061 · Cited by 1

Identification of a Unique Genomic Region in Sweet Chestnut (Castanea sativa Mill.) That Controls Resistance to Asian Chestnut Gall Wasp Dryocosmus kuriphilus Yasumatsu

Gaudet, M., Pollegioni, P., Ciolfi, M., Mattioni, C., Cherubini, M., & Beritognolo, I. (2024) · Plants · doi:10.3390/plants13101355 · Cited by 1

Tyrp1 is the mendelian determinant of the Axolotl (Ambystoma mexicanum) copper mutant

Cecil, R. F., Strohl, L., Thomas, M. K., Schwartz, J. L., Timoshevskaya, N. Y., Smith, J. J., & Voss, S. R. (2024) · Scientific Reports · doi:10.1038/s41598-024-73283-1 · Cited by 1

Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei

Errbii, M., Myrie, A., Robinson, D. E., Schultner, E., Schrader, L., & Oettler, J. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae217 · Cited by 1

Genomic response to sex-separated gene pools

Melo-Gavin, C., Grieshop, K., & Agrawal, A. F. (2026) · Evolution · doi:10.1093/evolut/qpag156 · Cited by 1

Aphid herbivory on macrophytes drives adaptive evolution in an aquatic community via indirect effects

Schäfer, M. K. H., Malacrinò, A., Walcher, C., Spaak, P., Serwaty-Sarazov, M., Kaeser, S., Kozakiewicz, T., Dambone-Bösch, C., Dexter, E., Hottinger, J. W., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2502742122 · Cited by 1

Phenotypic drought stress prediction of European beech (Fagus sylvatica) by genomic prediction and remote sensing

Pfenninger, M., Langan, L., Feldmeyer, B., Fussi, B., Hoffmann, J., Granado, R., Hetzer, J., Šeho, M., Mellert, K. H., & Hickler, T. (2025) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2025.1704275 · Cited by 1

Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Wasala, S. K., Howe, D. K., Dandurand, L., Zasada, I. A., & Denver, D. R. (2021) · Pathogens · doi:10.3390/pathogens10030363 · Cited by 1

Reduced representation sequencing accurately quantifies relative abundance and reveals population-level variation in Pseudo-nitzschia spp.

Kenkel, C. D., Smith, J. L., Hubbard, K. A., Chadwick, C., Lorenzen, N., Tatters, A. O., & Caron, D. A. (2022) · Harmful Algae · doi:10.1016/j.hal.2022.102314 · Cited by 1

Going down the rabbit hole: a review on methods characterizing selection and demography in natural populationsPreprint

Bourgeois, Y., Hazzouri, K. M., & Warren, B. H. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/052761 · Cited by 1

Experimental support that natural selection has shaped the latitudinal distribution of mitochondrial haplotypes in Australian Drosophila melanogasterPreprint

Camus, M. F., Wolff, J. N., Sgrò, C. M., & Dowling, D. K. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/103606 · Cited by 1

SNP Identification from Next‐Generation Sequencing Datasets

Zeng, Q., Sun, L., Fu, Q., Liu, S., & Liu, Z. (2017) · Wiley eBooks · doi:10.1002/9781118782392.ch17 · Cited by 1

On the evolution of azole resistance in Aspergillus fumigatus

Zhang, J. (2016) · doi:10.18174/385509 · Cited by 1

Identifying genomic markers associated with female re-mating rate in Drosophila pseudoobscura by replicated bulk segregant analysisPreprint

Wiberg, R. A. W., Price, T. A. R., Wedell, N., & Ritchie, M. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.20.049940 · Cited by 1

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

Brookes, B. (2020) · Spectrum Research Repository (Concordia University) · Cited by 1

Evidence of divergent selection in a parasite due to its host immunological respondPreprint

Shim, K. C., Weber, J. N., den Haan, S., & Bolnick, D. I. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.15.492026 · Cited by 1

Unprecedented Number of Recurrent Mutations Drive the Rapid Evolution of Pesticide Resistance in a Notorious PestPreprint

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.106288.1 · Cited by 1

Genomic basis of adaptation to constant and fluctuating environments in a global pest of cerealsPreprint

Laska-Modzelewska, A., Konczal, M., Rombauts, S., Radwan, J., Lewandowski, M., Raubic, J., & Skoracka, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.08.698337 · Cited by 1

From constraint to opportunity: Relaxing sexual antagonism reveals adaptive potential maintained by balancing selectionPreprint

Zwoinska, M. K., Wiberg, R. A. W., Trabert, M., Kaufmann, P., & Immonen, E. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.04.703537 · Cited by 1

Diversité génomique, évolution et adaptation de la tique Ixodes ricinus

Charrier, P. (2018) · doi:10.70675/924c0ab2z0a01z436dz9a28z52aa07eb82a1 · Cited by 1

Bioinformatic analysis of whole genome sequencing data

Maqbool, K. (2014) · Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences))

The genetics of hybrid incompatibility early in the 'speciation continuum'

Watson, E. T. (2014) · UTA ResearchCommons (University of Texas Arlington)

Migratory divides and the genetic basis of reproductive isolation

Delmore, K. E. (2016) · cIRcle (University of British Columbia) · doi:10.14288/1.0166416

Applications of Supercomputers in Population Genetics

Dumancas, G. G. (2015) · Advances in systems analysis, software engineering, and high performance computing book series · doi:10.4018/978-1-4666-7461-5.ch007

Probabilistic Viral Quasispecies Assembly

Töpfer, A., & Beerenwinkel, N. (2016) · Wiley eBooks · doi:10.1002/9781119272182.ch16

Short title: The vgll3 locus in salmon controls age at maturity

Ayllón, F., Kjærner‐Semb, E., Furmanek, T., Wennevik, V., Dahle, G., Taranger, G. L., Glover, K. A., Almén, M. S., Edvardsen, R. B., & Wargelius, A. (2015)

CUTTING EDGE INNOVATION: DISSECTING THE GENETIC BASIS OF A PLANT-PIERCING OVIPOSITOR IN AN HERBIVOROUS FLY

Ray, J. F. (2016) · UA Campus Repository (The University of Arizona)

An evolutionary and functional genomics study of Noccaea caerulescens, a heavy metal hyperaccumulating plant species

Wang, Y. (2016) · doi:10.18174/385510

Genetic dissection of a major polymorphism underlying population divergence in sexually selected pheromones in Drosophila serrata

Rusuwa, B. (2013) · The University of Queensland · doi:10.14264/uql.2016.1017

An Efficient Pipeline for Assaying Whole-Genome Plastid Variation for Population Genetics and Phylogeography

Kohrn, B. F. (2000) · doi:10.15760/etd.5891

Genomic Analysis of Chronic Heat Stress Resistance in the Nematode Caenorhabditis remanei

Claridge, S. E. (2017) · Scholars' Bank (University of Oregon)

Genetic and Genome Analyses of Native Populations of the Honeybee Pathogen Nosema ceranae

Peters, M. J. (2018) · uO Research (University of Ottawa) · doi:10.20381/ruor-22304

Peer Review #2 of "Shared genomic outliers across two divergent population clusters of a highly threatened seagrass (v0.1)"

(2019) · PeerJ · doi:10.7287/peerj.6806v0.1/reviews/2

Local adaptation and reproductive isolation in the copepod Tigriopus californicus

Lima, T. G. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/rgdy-rn25

Genome-wide changes in genetic diversity in a population of Myotis lucifugus affected by white-nose syndromePreprint

Lilley, T. M., Wilson, I. W., Field, K. A., Reeder, D. M., Vodzak, M. E., Turner, G. G., Kurta, A., Blomberg, A. S., Hoff, S., Herzog, C., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/764647

Natural Variation and Evolutionary Responses to Climate Change Stressors in Marine Invertebrates

Griffiths, J. S. (2020) · doi:10.31390/gradschool_dissertations.5168

Peer Review #2 of "Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis) (v0.2)"

(2020) · PeerJ · doi:10.7287/peerj.10186v0.2/reviews/2

Peer Review #1 of "Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis) (v0.2)"

(2020) · PeerJ · doi:10.7287/peerj.10186v0.2/reviews/1

Peer Review #2 of "Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis) (v0.1)"

(2020) · PeerJ · doi:10.7287/peerj.10186v0.1/reviews/2

Peer Review #1 of "Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis) (v0.1)"

(2020) · PeerJ · doi:10.7287/peerj.10186v0.1/reviews/1

Vulnerability, resilience and adaptation: the future for the seagrass, Zostera capensis

Phair, N. L. (2018) · SUNScholar (Stellenbosch University)

Deep Unsupervised Identification of Selected SNPs between Adapted Populations on Pool-seq DataPreprint

Siekiera, J., & Krämer, S. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2101.00004

Genomic data shed light on sex-determination in Australian freshwater Percichthyid fish species: Many ways to be a malePreprint

Pavlova, A., Harrisson, K. A., Turakulov, R. I., Lee, Y. P., Ingram, B. A., Gilligan, D. M., Sunnucks, P., & Gan, H. M. (2021) · doi:10.22541/au.161410988.87857941/v1

Genetic and Biochemical Characterization of Phospholipase Associated Metabolic Dysfunction in Drosophila melanogaster

Williams, S. P. (2021)

30a-E-7 クォーク模型によるΣ^-p相互作用の散乱偏極量

藤田, 匡., 藤原, 義., 仲本, 朝., & 鈴木, 宜. (1998) · 日本物理学会講演概要集

Labile sex chromosomes and a novel candidate sex-determination gene in the Australian freshwater fish family PercichthyidaePreprint

Pavlova, A., Harrisson, K. A., Turakulov, R. I., Lee, Y. P., Ingram, B. A., Gilligan, D. M., Sunnucks, P., & Gan, H. M. (2021) · doi:10.22541/au.162696809.95212733/v1

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.104368.1

Applications of Supercomputers in Population Genetics

Dumancas, G. G. (2019) · IGI Global eBooks · doi:10.4018/978-1-5225-8903-7.ch028

Peer Review #1 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/1

Peer Review #1 of "Shared genomic outliers across two divergent population clusters of a highly threatened seagrass (v0.1)"

(2019) · PeerJ · doi:10.7287/peerj.6806v0.1/reviews/1

Peer Review #3 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/3

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