References
Barrett, R. D. H., & Schluter, D. (2008). Adaptation from standing genetic variation. Trends Ecol. Evol. , 23 , 38–44.
Bassham, S., Catchen, J., Lescak, E., von Hippel, F. A., & Cresko, W. A. (2018). Repeated selection of alternatively adapted haplotypes creates sweeping genomic remodeling in stickleback. Genetics ,209 (3), 921–939. doi: 10.1534/genetics.117.300610
Bell, M. A., Orti, G., Walker, J. A., & Koenings, J. P. (1993). Evolution of pelvic reduction in threespine stickleback fish: a test of competing hypotheses. Evolution , 47 , 906–914. doi: 10.2307/2410193
Berner, D. (2019). Allele frequency difference AFD - an intuitive alternative to FST for quantifying genetic population differentiation.Genes , 10 (4), 308.
Berner, D. (2021). Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin.Nat. Commun. , 12 , 2806.
Berner, D., & Roesti, M. (2017). Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate. Mol. Ecol. ,26 , 6351–6369.
Bolnick, D. I., & Nosil, P. (2007). Natural selection in populations subject to a migration load. Evolution , 61 (9), 2229–2243.
Bourgeois, J. F., Blouw, D. M., Koenings, J. P., & Bell, M. A. (1994). Multivariate analysis of geographic covariance between phenotypes and environments in the threespine stickleback, Gasterosteus aculeatus , from the Cook Inlet area, Alaska. Can. J. Zool. ,72 , 1497–1509. doi: 10.1139/z94-198
Campbell, R. N. (1985). Morphological variation in the three-spined stickleback (Gasterosteus aculeatus ) in Scotland.Behaviour , 93 , 161–168. doi: 10.1163/156853986X00838
Catchen, J. M., Bassham, S., Wilson, T., Currey, M., O’Brien, C., Yeates, Q., & Cresko, W. A. (2013). The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Mol. Ecol. ,22 (11), 2864–2883. doi: 10.1111/mec.12330
Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villareal Jr, G., Dickson, M., Grimwood, J., … Kingsley, D. M. (2005). Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science , 307 , 1928–1933.
Fang, B., Kemppainen, P., Momigliano, P., Feng, X., & Merilä, J. (2020). On the causes of geographically heterogeneous parallel evolution in sticklebacks. Nat. Ecol. Evol. doi: 10.1038/s41559-020-1222-6
Galloway, J., Cresko, W. A., & Ralph, P. (2020). A few stickleback suffice for the transport of alleles to new lakes. G3: Genes, Genomes, Genetics , 10 (2), 505–514. doi: 10.1101/713040
Giles, N. (1983). The possible role of environmental calcium levels during the evolution of phenotypic diversity in Outer Hebridean populations of the three-spined stickleback, Gasterosteus aculeatus . J. Zool. , 199 , 535–544.
Glazer, A. M., Killingbeck, E. E., Mitros, T., Rokhsar, D. S., & Miller, C. T. (2015). Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing. G3-Genes Genomes Genetics , 5 (7), 1463–1472. doi: 10.1534/g3.115.017905
[dataset] Haenel, Q., Guerard, L., MacColl, A. D. C., & Berner, D. (2021). Individual whole-genome sequence data for North Uist freshwater and Atlantic marine stickleback. https://www.ebi.ac.uk/ena/browser/view/ PRJEB42736
Haenel, Q., Roesti, M., Moser, D., MacColl, A. D. C., & Berner, D. (2019a). Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish. Evol. Lett. , 3 , 28–42.
[dataset] Haenel, Q., Roesti, M., Moser, D., MacColl, A. D. C., & Berner, D. (2019b). Individual whole-genome sequence data for North Uist marine stickleback. https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA485717
Hermisson, J., & Pennings, P. S. (2005). Soft sweeps: molecular population genetics of adaptation from standing genetic variation.Genetics , 169 (4), 2335–2352.
Hohenlohe, P. A., Bassham, S., Etter, P. D., Stiffler, N., Johnson, E. A., & Cresko, W. A. (2010). Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. ,6 (2), e1000862. Retrieved from http://dx.doi.org/10.1371%2Fjournal.pgen.1000862
Jones, F. C., Chan, Y. F., Schmutz, J., Grimwood, J., Brady, S. D., Southwick, A. M., … Kingsley, D. M. (2012a). A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Curr. Biol. , 22 (1), 83–90. Retrieved from http://linkinghub.elsevier.com/retrieve/pii/S0960982211013273
Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., … Kingsley, D. M. (2012b). The genomic basis of adaptive evolution in threespine sticklebacks. Nature ,484 (7392), 55–61. Retrieved from http://dx.doi.org/10.1038/nature10944
Kirch, M., Romundset, A., Gilbert, M. T. P., Jones, F. C., & Foote, A. D. (2021). Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Curr. Biol. , 31 (9), 2027–2036. doi: 10.1016/j.cub.2021.02.027
Klepaker, T., Ostbye, K., Spence, R., Warren, M., Przybylski, M., & Smith, C. (2016). Selective agents in the adaptive radiation of Hebridean sticklebacks. Evol. Ecol. Res. , 17 , 243–262.
Kremer, A., & Le Corre, V. (2012). Decoupling of differentiation between traits and their underlying genes in response to divergent selection. Heredity , 108 (4), 375–385. doi: 10.1038/hdy.2011.81
Latta, R. G. (1998). Differentiation of allelic frequencies at quantitative trait loci affecting locally adaptive traits. Am. Nat. , 151 (3), 283–292. doi: 10.1086/286119
Le Corre, V., & Kremer, A. (2012). The genetic differentiation at quantitative trait loci under local adaptation. Mol. Ecol. ,21 (7), 1548–1566. doi: 10.1111/j.1365-294X.2012.05479.x
Lescak, E. A., Bassham, S. L., Catchen, J., Gelmond, O., Sherbick, M. L., von Hippel, F. A., & Cresko, W. A. (2015). Evolution of stickleback in 50 years on earthquake-uplifted islands. Proc. Natl. Acad. Sci. USA , 112 , E7204–E7212. doi: 10.1073/pnas.1512020112
Magalhaes, I. S., Agostino, D. D., Hohenlohe, P. A., & Maccoll, A. D. C. (2016). The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland. Mol. Ecol. , 25 (17), 4319–4336. doi: 10.1111/mec.13746
Magalhaes, I. S., Whiting, J. R., D’Agostino, D., Hohenlohe, P. A., Mahmud, M., Bell, M. A., … MacColl, A. D. C. (2021). Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations. Nat. Ecol. Evol. , 5 (2), 251–261. doi: 10.1038/s41559-020-01341-8
Mäkinen, H. S., Cano, J. M., & Merilä, J. (2006). Genetic relationships among marine and freshwater populations of the European three-spined stickleback (Gasterosteus aculeatus ) revealed by microsatellites.Mol. Ecol. , 15 (6), 1519–1534. doi: 10.1111/j.1365-294X.2006.02871.x
Matschiner, M. (2016). Fitchi: Haplotype genealogy graphs based on the Fitch algorithm. Bioinformatics , 32 (8), 1250–1252. doi: 10.1093/bioinformatics/btv717
Matuszewski, S., Hermisson, J., & Kopp, M. (2015). Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum. Genetics , 200 (4), 1255–1274. doi: 10.1534/genetics.115.178574
Messer, P. W., & Petrov, D. A. (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol. Evol. ,28 (11), 659–669. doi: 10.1016/j.tree.2013.08.003
Morgan, M., Pages, H., Obenchain, V., & Hayden, N. (2017). Rsamtools: binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. R Package Version 1.3.0  (http://Bioconductor.Org/Packages/Release/Bioc/Html/Rsamtools.Html) .
Orr, H. A., & Betancourt, A. J. (2001). Haldane’s sieve and adaptation from the standing genetic variation. Genetics , 157 (2), 875–884.
Paradis, E., & Schliep, K. (2018). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics ,35 , 526–528.
R Core Team (2019). R: A language and environment for statistical computing . Vienna, Austria: R Foundation for Statistical Computing. https ://www.R-proje ct.org/
Roesti, M., Gavrilets, S., Hendry, A. P., Salzburger, W., & Berner, D. (2014). The genomic signature of parallel adaptation from shared genetic variation. Mol. Ecol. , 23 , 3944–3956.
Roesti, M., Kueng, B., Moser, D., & Berner, D. (2015). The genomics of ecological vicariance in threespine stickleback fish. Nat. Commun. , 6 , 8767. doi: 10.1038/ncomms9767 http://www.nature.com/articles/ncomms9767#supplementary-information
Roesti, M., Moser, D., & Berner, D. (2013). Recombination in the threespine stickleback genome - patterns and consequences. Mol. Ecol. , 22 , 3014–3027.
Scheet, P., & Stephens, M. (2006). A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. , 78 (4), 629–644. doi: 10.1086/502802
Schliep, K. (2011). phangorn: phylogenetic analysis in R.Bioinformatics , 27 (4), 592–593.
Schluter, D., & Conte, G. L. (2009). Genetics and ecological speciation. Proc. Natl. Acad. Sci. USA , 106 , 9955–9962. doi: 10.1073/pnas.0901264106
Spence, R., Wootton, R. J., Barber, I., Przybylski, M., & Smith, C. (2013). Ecological causes of morphological evolution in the three-spined stickleback. Ecol. Evol. , 3 (6), 1717–1726. doi: 10.1002/ece3.581
Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics ,30 (9), 1312–1313. doi: 10.1093/bioinformatics/btu033
Terekhanova, N. V., Barmintseva, A. E., Kondrashov, A. S., Bazykin, G. A., Mugue, N. S., & Alba, M. (2019). Architecture of parallel adaptation in ten lacustrine threespine stickleback populations from the White Sea area. Genome Biol. Evol. , 11 (9), 2605–2618. doi: 10.1093/gbe/evz175
Waterston, A. R., Holden, A. V, Campbell, R. N., & Maitland, P. S. (1979). Inland waters of the Outer Hebrides. P. Roy. Soc. Edinb. B , 77 , 329–351.
Yeaman, S. (2015). Local adaptation by alleles of small effect.Am. Nat. , 186 (S1), S74–S89. doi: 10.1086/682405
Yeaman, S., & Whitlock, M. C. (2011). The genetic architecture of adaptation under migration-selection balance. Evolution ,65 (7), 1897–1911. doi: 10.1111/j.1558-5646.2011.01269.x