Flanagan SP, Jones AG. 2019. The future of parentage analysis: from microsatellites to SNPs and beyond. Molecular Ecology. 28(3): 544-567. link to paper, my summary

Jost L, Archer F, Flanagan SP, Gaggiotti O, Hoban S, Latch E. 2018. Differentiation measures for conservation genetics. Evolutionary Applications. 11: 1139-1148. pdf, link to paper, my summary

Flanagan SPForester BRLatch EKAitken SNHoban S. 2017. Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservationEvolutionary Applications. 1110351052. pdf, link to paper, my summary

Flanagan SP, and Jones AG. 2017. Substantial differences in bias between single-digest and double-digest RAD-seq: A case study. Molecular Ecology Resources. 18: 264-280. link to papermy summary, associated code, gwscaR, data, genomic data

Flanagan SP, and Jones AG. 2017. Constraints on the FST-heterozygosity outlier approach. Journal of Heredity. 108(5): 561-573. doi: 10.1093/jhered/esx048  pdflink to paper, my summary, associated code, data

Flanagan SP, and Jones AG. 2017. Genome-wide selection components analysis in a fish with male pregnancy. Evolution.  71: 1096–1105. DOI: 10.1111/evo.13173 pdflink to paper, my summary, associated code, data, genomic data

Flanagan SP, Rosenqvist G, and Jones AG. 2017. Mate quality and timing of reproduction affects sexual selection in a sex-role-reversed pipefish. Behavioral Ecology and Sociobiology. 71(1): 1-10. doi: 10.1007/s00265-016-2255-3 pdflink to paper, press release, data

Flanagan SP. 2017. Pipefish pairing. Biosphere Magazine. 23. link to article


Flanagan SP, Rose E, and Jones AG. 2016. Population genomics reveals multiple drivers of population differentiation in a sex-role-reversed pipefish. Molecular Ecology. 25(20): 5043-5072. doi: 10.1111/mec.13794 pdflink to paper, my summary, data, genomic data, associated code

Titon SCM, de Assis VR, Titon Jr B, Barsotti AMG, Flanagan SP, and Gomes FR. 2016. Calling rate, corticosterone plasma levels and immunocompetence of Hypsiboas albopunctatus. Comparative Biochemistry and Physiology: Part A. 201: 53-60. link to paper

Rose E, Flanagan SP, and Jones AG. 2015. The effects of synthetic estrogen on the sexually dimorphic liver transcriptome of the sex-role-reversed Gulf pipefish. PLoS One. 10(10): e0139401. pdfmy summary, associated code

Flanagan SP, and Jones AG. 2015. Identifying signatures of sexual selection using genome-wide selection components analysis. Ecology and Evolution. 5(13): 2722-2744. doi: 10.1002/ece3.1546. pdf, my summary, data, associated code

Flanagan SP, Johnson JB, Rose E, and Jones AG. 2014. Sexual selection on female ornaments in the sex-role-reversed Gulf pipefish (Syngnathus scovelli). Journal of Evolutionary Biology. 27 (11): 2457-2467. pdf, data

Flanagan SP, and Bevier CR. 2014. Do male activity and territory quality affect female association time in the Brown Anole, Anolis sagrei? Ethology. 120 (4): 365-374. link to paper

Flanagan SP, Wilson WH, Jones KL, and Lance SL. 2010. Development and characterization of twelve polymorphic microsatellite loci in the Bog Copper, Lycaena epixanthe. Conservation Genetics Resources. 2(1): 159-161. pdf

***Please contact me if you require access to a PDF***