http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Avilés, J. M., Cruz-Miralles, Á., Ducrest, A.-L., Simon, C., Roulin, A., Wakamatsu, K., & Parejo, D. (2019). Redness variation in the Eurasian scops-owl otus scops is due to pheomelanin but is not associated with variation in the melanocortin-1 receptor gene (MC1R). Ardeola, 67 (1), 3-13.
Benton, M. J., Dhouailly, D., Jiang, B., & McNamara, M. (2019). The early origin of feathers. Trends in ecology & evolution, 34 (9), 856-869.
Blem, C. R. (1976). Patterns of lipid storage and utilization in birds.American Zoologist, 16 (4), 671-684.
Britton, S., & Davidowitz, G. (2023). The effect of diet on melanin pigmentation in animals. Functional ecology, 37 (2), 206-217. doi:https://doi.org/10.1111/1365-2435.14209
Brommer, J. E., Ahola, K., & Karstinen, T. (2005). The colour of fitness: plumage coloration and lifetime reproductive success in the tawny owl. Proceedings of the Royal Society B: Biological Sciences, 272 (1566), 935-940.
Chaisson, M. J., & Tesler, G. (2012). Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC bioinformatics, 13 (1), 1-18.
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience, 4 (1), s13742-13015-10047-13748.
Chen, N. (2004). Using Repeat Masker to identify repetitive elements in genomic sequences. Current protocols in bioinformatics, 5 (1), 4.10. 11-14.10. 14.
Cui, L., Lv, C., Zhang, J., Mo, C., Lin, D., Li, J., & Wang, Y. (2017). Characterization of melanin-concentrating hormone (MCH) and its receptor in chickens: Tissue expression, functional analysis, and fasting-induced up-regulation of hypothalamic MCH expression. Gene, 615 , 57-67.
D’Alba, L., & Shawkey, M. D. (2019). Melanosomes: biogenesis, properties, and evolution of an ancient organelle. Physiological reviews, 99 (1), 1-19.
Diniz, G. B., & Bittencourt, J. C. (2019). The melanin-concentrating hormone (MCH) system: a tale of two peptides. Frontiers in Neuroscience, 13 , 1280.
Ducrest, A.-L., Keller, L., & Roulin, A. (2008). Pleiotropy in the melanocortin system, coloration and behavioural syndromes. Trends in ecology & evolution, 23 (9), 502-510.
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32 (5), 1792-1797.
Excoffier, L., & Lischer, H. E. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular ecology resources, 10 (3), 564-567.
Field, D. J., D’Alba, L., Vinther, J., Webb, S. M., Gearty, W., & Shawkey, M. D. (2013). Melanin concentration gradients in modern and fossil feathers. PLoS One, 8 (3), e59451.
Fogelholm, J., Henriksen, R., Höglund, A., Huq, N., Johnsson, M., Lenz, R., . . . Wright, D. (2020). CREBBP and WDR 24 identified as candidate genes for quantitative variation in red-brown plumage colouration in the chicken. Scientific reports, 10 (1), 1161.
Galeotti, P., Rubolini, D., Dunn, P. O., & Fasola, M. (2003). Colour polymorphism in birds: causes and functions. Journal of Evolutionary Biology, 16 (4), 635-646.
Galván, I., Rodríguez‐Martínez, S., & Carrascal, L. M. (2018). Dark pigmentation limits thermal niche position in birds. Functional ecology, 32 (6), 1531-1540.
Guo, Y., Huang, Y., Hou, L., Ma, J., Chen, C., Ai, H., . . . Ren, J. (2017). Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches.Genetics Selection Evolution, 49 , 1-11.
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29 (8), 1072-1075. doi:10.1093/bioinformatics/btt086
Hoffman, J. I., Krause, E. T., Lehmann, K., & Krüger, O. (2014). MC1R genotype and plumage colouration in the zebra finch (Taeniopygia guttata): population structure generates artefactual associations.PLoS One, 9 (1), e86519.
Hofreiter, M., & Schöneberg, T. (2010). The genetic and evolutionary basis of colour variation in vertebrates. Cellular and Molecular Life Sciences, 67 , 2591-2603.
Johnsson, M., Jonsson, K. B., Andersson, L., Jensen, P., & Wright, D. (2016). Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken. G3 Genes|Genomes|Genetics, 6 (2), 311-319. doi:10.1534/g3.115.024299
Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24 (11), 1403-1405.
Karell, P., Ahola, K., Karstinen, T., Valkama, J., & Brommer, J. E. (2011). Climate change drives microevolution in a wild bird.Nature communications, 2 (1), 1-7.
Kerje, S., Lind, J., Schütz, K., Jensen, P., & Andersson, L. (2003). Melanocortin 1‐receptor (MC1R) mutations are associated with plumage colour in chicken. Animal genetics, 34 (4), 241-248.
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature biotechnology, 37 (5), 540-546.
Koskenpato, K., Ahola, K., Karstinen, T., & Karell, P. (2016). Is the denser contour feather structure in pale grey than in pheomelanic brown tawny owls Strix aluco an adaptation to cold environments? Journal of Avian Biology, 47 (1), 1-6.
Koskenpato, K., Lehikoinen, A., Lindstedt, C., & Karell, P. (2020). Gray plumage color is more cryptic than brown in snowy landscapes in a resident color polymorphic bird. Ecology and evolution, 10 (4), 1751-1761.
Kowata, K., Nakaoka, M., Nishio, K., Fukao, A., Satoh, A., Ogoshi, M., . . . Takeuchi, S. (2014). Identification of a feather β-keratin gene exclusively expressed in pennaceous barbule cells of contour feathers in chicken. Gene, 542 (1), 23-28.
Li, H. (2012). seqtk Toolkit for processing sequences in FASTA/Q formats. GitHub, 767 , 69.
Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997 .
Liu, H., Xi, Y., Tang, Q., Qi, J., Zhou, Z., Guo, Z., . . . Liang, S. (2023). Genetic fine‐mapping reveals single nucleotide polymorphism mutations in the MC1R regulatory region associated with duck melanism.Molecular ecology, 32 (12), 3076-3088.
Lucassen, M., Koschnick, N., Eckerle, L., & Portner, H.-O. (2006). Mitochondrial mechanisms of cold adaptation in cod (Gadus morhua L.) populations from different climatic zones. Journal of Experimental Biology, 209 (13), 2462-2471.
MacDougall-Shackleton, E. A., Blanchard, L., & Gibbs, H. L. (2003). Unmelanized plumage patterns in Old World leaf warblers do not correspond to sequence variation at the melanocortin-1 receptor locus (MC1R). Molecular Biology and Evolution, 20 (10), 1675-1681.
Margalida, A., Negro, J. J., & Galván, I. (2008). Melanin-based color variation in the bearded vulture suggests a thermoregulatory function.Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 149 (1), 87-91.
McNamara, M. E., Rossi, V., Slater, T. S., Rogers, C. S., Ducrest, A.-L., Dubey, S., & Roulin, A. (2021). Decoding the evolution of melanin in vertebrates. Trends in ecology & evolution, 36 (5), 430-443.
Mundy, N. I. (2005). A window on the genetics of evolution: MC1R and plumage colouration in birds. Proceedings of the Royal Society B: Biological Sciences, 272 (1573), 1633-1640.
Passarotto, A., Rodríguez‐Caballero, E., Cruz‐Miralles, Á., & Avilés, J. M. (2022). Ecogeographical patterns in owl plumage colouration: Climate and vegetation cover predict global colour variation.Global ecology and biogeography, 31 (3), 515-530.
Paysan-Lafosse, T., Blum, M., Chuguransky, S., Grego, T., Pinto, B. L., Salazar, Gustavo A., . . . Bateman, A. (2022). InterPro in 2022.Nucleic acids research, 51 (D1), D418-D427. doi:10.1093/nar/gkac993
Poleti, M. D., Regitano, L. C., Souza, G. H., Cesar, A. S., Simas, R. C., Silva-Vignato, B., . . . Coutinho, L. L. (2018). Longissimus dorsi muscle label-free quantitative proteomic reveals biological mechanisms associated with intramuscular fat deposition. Journal of proteomics, 179 , 30-41.
Rochette, N. C., Rivera‐Colón, A. G., & Catchen, J. M. (2019). Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Molecular ecology, 28 (21), 4737-4754.
Roulin, A. (2014). Melanin‐based colour polymorphism responding to climate change. Global Change Biology, 20 (11), 3344-3350.
Roulin, A., & Ducrest, A.-L. (2013). Genetics of colouration in birds. Paper presented at the Seminars in cell & developmental biology.
Salis, P., Lorin, T., Laudet, V., & Frédérich, B. (2019). Magic traits in magic fish: understanding color pattern evolution using reef fish.Trends in Genetics, 35 (4), 265-278.
San-Jose, L. M., Ducrest, A.-L., Ducret, V., Simon, C., Richter, H., Wakamatsu, K., & Roulin, A. (2017). MC1R variants affect the expression of melanocortin and melanogenic genes and the association between melanocortin genes and coloration. Molecular ecology, 26 (1), 259-276. doi:https://doi.org/10.1111/mec.13861
San-Jose, L. M., & Roulin, A. (2018). Toward understanding the repeated occurrence of associations between melanin-based coloration and multiple phenotypes. The American Naturalist, 192 (2), 111-130.
Sheehan, M. J., & Bergman, T. J. (2016). Is there an evolutionary trade-off between quality signaling and social recognition?Behavioral Ecology, 27 (1), 2-13.
Shoval, O., Sheftel, H., Shinar, G., Hart, Y., Ramote, O., Mayo, A., . . . Alon, U. (2012). Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science, 336 (6085), 1157-1160.
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31 (19), 3210-3212. doi:10.1093/bioinformatics/btv351
Stanke, M., & Morgenstern, B. (2005). AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.Nucleic acids research, 33 (suppl_2), W465-W467.
Sun, R., Xia, X., Chong, K. C., Zee, B. C.-Y., Wu, W. K. K., & Wang, M. H. (2019). wtest: an integrated R package for genetic epistasis testing.BMC Medical Genomics, 12 (9), 1-6.
Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38 (7), 3022-3027.
Terrill, R. S., & Shultz, A. J. (2023). Feather function and the evolution of birds. Biological reviews, 98 (2), 540-566.
Wang, M. H., Sun, R., Guo, J., Weng, H., Lee, J., Hu, I., . . . Zee, B. C.-Y. (2016). A fast and powerful W-test for pairwise epistasis testing.Nucleic acids research, 44 (12), e115-e115.
Wernimont, S. M., Clark, A. G., Stover, P. J., Wells, M. T., Litonjua, A. A., Weiss, S. T., . . . Schwartz, J. (2011). Folate network genetic variation, plasma homocysteine, and global genomic methylation content: a genetic association study. BMC medical genetics, 12 (1), 1-11.
Wittke-Thompson, J. K., Pluzhnikov, A., & Cox, N. J. (2005). Rational inferences about departures from Hardy-Weinberg equilibrium. The American Journal of Human Genetics, 76 (6), 967-986.
Yuan, X., Cui, H., Jin, Y., Zhao, W., Liu, X., Wang, Y., . . . Zhao, G. (2022). Fatty acid metabolism-related genes are associated with flavor-presenting aldehydes in Chinese local chicken. Frontiers in Genetics, 13 , 902180.
Zhang, W., Wu, C., Ni, R., Yang, Q., Luo, L., & He, J. (2021). Formimidoyltransferase cyclodeaminase prevents the starvation-induced liver hepatomegaly and dysfunction through downregulating mTORC1.PLoS genetics, 17 (12), e1009980. doi:10.1371/journal.pgen.1009980
Zhou, X., & Stephens, M. (2012). Genome-wide efficient mixed-model analysis for association studies. Nature genetics, 44 (7), 821-824.