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method_refs.txt
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method_refs.txt
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Barnett, D. W., E. K. Garrison, A. R. Quinlan, M. P. Stromberg, and G. T. Marth. 2011. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics 27:1691–1692.
Broman, K. W., H. Wu, S. Sen, and G. A. Churchill. 2003. R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890.
Broman, K. W., and S. Sen. 2009. A guide to QTL mapping with R/qtl. Springer, Dordrecht.
Chang, C. C., C. C. Chow, L. C. Tellier, S. Vattikuti, S. M. Purcell, and J. J. Lee. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4.
Clark, B. W., C. W. Matson, D. Jung, and R. T. Di Giulio. 2010. AHR2 mediates cardiac teratogenesis of polycyclic aromatic hydrocarbons and PCB-126 in Atlantic killifish (Fundulus heteroclitus). Aquat. Toxicol. 99:232–240.
Faust, G. G., and I. M. Hall. 2014. SAMBLASTER: Fast duplicate marking and structural variant read extraction. Pp. 2503–2505 in Bioinformatics.
Garrison, E. 2018. freebayes: Bayesian haplotype-based genetic polymorphism discovery and genotyping.
Kosambi, D. D. 1943. The estimation of map distances from recombination values. Annals of Eugenics 12:172–175.
Miller, J. T., N. M. Reid, D. E. Nacci, and A. Whitehead. 2019. Developing a High-Quality Linkage Map for the Atlantic Killifish Fundulus heteroclitus. G3 9:2851–2862.
Miller, M. R., J. P. Dunham, A. Amores, W. A. Cresko, and E. A. Johnson. 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research 17:240–248.
Oziolor, E. M., E. Bigorgne, L. Aguilar, S. Usenko, and C. W. Matson. 2014. Evolved resistance to PCB- and PAH-induced cardiac teratogenesis, and reduced CYP1A activity in Gulf killifish (Fundulus grandis) populations from the Houston Ship Channel, Texas. Aquat. Toxicol. 150:210–219.
Oziolor, E. M., N. M. Reid, S. Yair, K. M. Lee, S. Guberman VerPloeg, P. C. Bruns, J. R. Shaw, A. Whitehead, and C. W. Matson. 2019. Adaptive introgression enables evolutionary rescue from extreme environmental pollution. Science 364:455–457.
Reid, N. M., D. A. Proestou, B. W. Clark, W. C. Warren, J. K. Colbourne, J. R. Shaw, S. I. Karchner, M. E. Hahn, D. Nacci, M. F. Oleksiak, D. L. Crawford, and A. Whitehead. 2016. The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 354:1305–1308.
Rubin, C.-J., H.-J. Megens, A. M. Barrio, K. Maqbool, S. Sayyab, D. Schwochow, C. Wang, Ö. Carlborg, P. Jern, C. B. Jørgensen, A. L. Archibald, M. Fredholm, M. A. M. Groenen, and L. Andersson. 2012. Strong signatures of selection in the domestic pig genome. PNAS 109:19529–19536. National Academy of Sciences.
Tang, H., X. Zhang, C. Miao, J. Zhang, R. Ming, J. C. Schnable, P. S. Schnable, E. Lyons, and J. Lu. 2015. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol. 16:3.
Whitehead, A., D. A. Triant, D. Champlin, and D. Nacci. 2010. Comparative transcriptomics implicates mechanisms of evolved pollution tolerance in a killifish population. Molecular Ecology 19:5186–5203
Whitehead, A., W. Pilcher, D. Champlin, and D. Nacci. 2012. Common mechanism underlies repeated evolution of extreme pollution tolerance. P Roy Soc B-Biol Sci 279:427–433.
Xu, S. 2008. Quantitative Trait Locus Mapping Can Benefit From Segregation Distortion. Genetics 180:2201–2208. Genetics.