Research/Scholarly/Creative Works

• Johnson BD., Anderson AP., Small CM., Rose E., Flanagan SP., Hendrickson-Rose C. and Jones AG. (2022) The evolution of the testis transcriptome in pregnant male pipefishes and seahorses. Evolution 76(9): 2162-2180. http://dx.doi.org/10.1111/evo.14579. (Journal Articles)

• Pullen M., Gerber D., Thomsen MS. and Flanagan SP. (2022) Seasonal Dynamics of Faunal Diversity and Population Ecology in an Estuarine Seagrass Bed. Estuaries and Coasts 45(8): 2578-2591. http://dx.doi.org/10.1007/s12237-022-01103-8. (Journal Articles)

• Flanagan SP., Rose E. and Jones AG. (2021) The population genomics of repeated freshwater colonizations by Gulf pipefish. Molecular Ecology 30(7): 1672-1687. http://dx.doi.org/10.1111/mec.15841. (Journal Articles)

• Howell L., LaRue M. and Flanagan SP. (2021) Environmental DNA as a tool for monitoring Antarctic vertebrates. New Zealand Journal of Zoology 48(3-4): 245-262. http://dx.doi.org/10.1080/03014223.2021.1900299. (Journal Articles)

• Anderson AP., Rose E., Flanagan SP. and Jones AG. (2020) The estrogen-responsive transcriptome of female secondary sexual traits in the gulf pipefish. Journal of Heredity 111(3): 294-306. http://dx.doi.org/10.1093/JHERED/ESAA008. (Journal Articles)

• Flanagan S. (2020) Quantitative Genetics of Behavior. In Choe JC (Ed.), Encyclopedia of Animal Behavior (2nd Edition ed.): 80-93.Elsevier Academic Press. (Chapters)

• Lerch BA., Dautel KA., Brewer S., Liang A., Siewe N. and Flanagan S. (2020) Space, density and extra-pair matings have opposing impacts on male and female reproductive success. Population Ecology 62(2): 269-283. http://dx.doi.org/10.1002/1438-390X.12047. (Journal Articles)

• Wright AM., Schwartz RS., Oaks JR., Newman CE. and Flanagan SP. (2020) The why, when, and how of computing in biology classrooms. F1000Research 8 http://dx.doi.org/10.12688/f1000research.20873.1. (Journal Articles)

• Flanagan SP. and Jones AG. (2019) The future of parentage analysis: From microsatellites to SNPs and beyond. Molecular Ecology 28(3): 544-567. http://dx.doi.org/10.1111/mec.14988. (Journal Articles)

• Flanagan SP. and Jones AG. (2018) Substantial differences in bias between signal-digest and double-digest RAD-seq libraries: A case study. Molecular Ecology Resources 18(2): 264-280. http://dx.doi.org/10.0.4.87/1755-0998.12734. (Journal Articles)

• Jost L., Archer F., Flanagan S., Gaggiotti O., Hoban S. and Latch E. (2018) Differentiation measures for conservation genetics. Evolutionary Applications 11(7): 1139-1148. http://dx.doi.org/10.1111/eva.12590. (Journal Articles)

• Flanagan S. (Ed.) (2017) gwscaR: Genome-wide selection components analysis in R. . (Software / Code)

• Flanagan SP. (2017) Pipefish Pairing. Biosphere 23 [Magazine article]. (Other)

• Flanagan SP. (Ed.) (2017) fsthet: Generating smoothed quantiles for the FST-heterozygosity distribution. . (Software / Code)

• Flanagan SP. and Jones AG. (2017) Constraints on the F-ST-Heterozygosity Outlier Approach. Journal of Heredity 108(5): 561-573. http://dx.doi.org/10.1093/jhered/esx048. (Journal Articles)

• Flanagan SP. and Jones AG. (2017) Genome-wide selection components analysis in a fish with male pregnancy. Evolution 71(4): 1096-1105. http://dx.doi.org/10.1111/evo.13173. (Journal Articles)

• Flanagan SP., Forester BR., Latch EK., Aitken SN. and Hoban S. (2017) Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation. Evolutionary Applications early access online http://dx.doi.org/10.1111/eva.12569. (Journal Articles)

• Flanagan SP., Rosenqvist G. and Jones AG. (2017) Mate quality and the temporal dynamics of breeding in a sex-role-reversed pipefish, S. typhle. Behavioral Ecology and Sociobiology 71 28 http://dx.doi.org/10.1007/s00265-016-2255-3. (Journal Articles)

• 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. http://dx.doi.org/10.1111/mec.13794. (Journal Articles)

• Monteiro Titon SC., de Assis VR., Titon Junior B., Giorgi Barsotti AM., Flanagan SP. and Gomes FR. (2016) Calling rate, corticosterone plasma levels and immunocompetence of Hypsiboas albopunctatus. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology 201: 53-60. http://dx.doi.org/10.1016/j.cbpa.2016.06.023. (Journal Articles)

• Flanagan SP. and Jones AG. (2015) Identifying signatures of sexual selection using genomewide selection components analysis. Ecology and Evolution 5(13): 2722-2744. http://dx.doi.org/10.1002/ece3.1546. (Journal Articles)

• Rose E., Flanagan SP. and Jones AG. (2015) The Effects of Synthetic Estrogen Exposure on the Sexually Dimorphic Liver Transcriptome of the Sex-Role-Reversed Gulf Pipefish. PLoS ONE 10(10) e0139401 http://dx.doi.org/10.1371/journal.pone.0139401. (Journal Articles)

• Flanagan SP. and Bevier CR. (2014) Do Male Activity Level And Territory Quality Affect Female Association Time in The Brown Anole, Anolis sagrei? Ethology 120(4): 365-374. http://dx.doi.org/10.1111/eth.12213. (Journal Articles)

• 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. http://dx.doi.org/10.1111/jeb.12487. (Journal Articles)

• 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. http://dx.doi.org/10.1007/s12686-010-9206-5. (Journal Articles)

Student Supervision

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Completed
• Masters - Gerber D: Determining effects of temperature and heatwaves on estuarine foundation species and associated animal communities (2021)
• Masters - Howell L: Environmental DNA as a tool for in-field monitoring of Antarctic vertebrates. (2021)
• Masters - Pullen M: Community composition of native New Zealand seagrass, Zostera muelleri (2021)
• Summer Student - Freeman C: Evolution of pigmentation genes in sex-role reversed pipefish (2019)

Review and Refereeing

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• Animal Conservation ( 2018 - 2023)
• Aquaculture Research ( 2016 - 2023)
• Ecology and Evolution ( 2018 - 2023)
• Evolutionary Applications ( 2018 - 2023)
• Heredity ( 2017 - 2023)
• International Journal of Molecular Sciences ( 2016 - 2023)
• Journal of Ethology ( 2018 - 2023)
• Molecular Ecology ( 2016 - 2023)
• Molecular Ecology Resources ( 2017 - 2023)

Future Research

• diversity and biogeography of New Zealand pipefish
• evolution of female ornamentation in pipefish
• comparative genomics of female ornamentation