The Flanagan Lab

The Flanagan Lab

Dr. Sarah Flanagan is a Senior Lecturer Above the Bar in the School of Biological Sciences at the University of Canterbury. The lab is focused on understanding the evolution of complex, multivariate traits (such as mating display traits), primarily relying on population and quantitative genetics, genomic datasets, simulation modeling.

Publications

Authors whose names are in green are trainees supervised by Sarah. Co-first authorship is denoted by *.

Peer-reviewed papers

  1. Gwatkin GSM, Hickcox RP, Niebuhr CN, Strang AJ, Flanagan SP, and LaRue MA. 2026. Little penguins select more isolated nest boxes for breeding, but lay date influences breeding success. Journal of Wildlife Management, e70230. link to paper, PDF
  2. Holser RR, Hickcox RP, Costa DP, Hildebrand T, Flanagan SP, LaRue MA (2026) Field immobilisation of adult Weddell seals using intramuscular butorphanol and midazolam. Veterinary Record link to paper, PDF
  3. Tosto N, Rose E, Mason H,Flanagan SP (2025) Sex-biased gene expression in the northern pipefish (Syngnathus fuscus), a species with male pregnancy, is widespread and linked to tissue specificity. Sexual Development link to paper
  4. Flanagan SP, Chaturvedi S, Palma-Silva C, Rennison D, Rogers S, Singh P (2025) Ecology of gene expression. Molecular Ecology 34:e70035 link to paper, PDF
  5. Godsoe W, Allen W, Waller L, Barratt B, Flanagan SP, Marion ZH, Tylianakis JM, Moltchanova E, Dickie IA (2025) Rapid shifts in relative abundance obscure temporal diversity changes in a metacommunity. Ecology and Evolution 2025; 15:e71694 link to paper, PDF
  6. Flanagan SP, Alonzo SH. (2024) Supergenes are not necessary to explain the maintenance of complex alternative phenotypes. Proceedings of the Royal Society B. 291: 20241715. link to paper, PDF, supplemental material, shiny app to inspect model conditions, associated code
  7. Tosto N, Rose E, Mason H, Mank J, Flanagan SP (2024) Sexual selection on non-ornamental traits is underpinned by evidence of genetic constraints on sex-biased expression in dusky pipefish. Molecular Ecolology e17550. link to paper, PDF
  8. van Eyndhoven F, Cameron EZ, Flanagan SP. (2023) High rates of male courtship in a female-ornamented pipefish. The Royal Society Open Science. 10: 231428. 231428.link to paper, PDF, associated code, data, article in The Conversation about the research
  9. Tosto NM, Rose E, Flanagan SP, Mason HD. (2023) The development of a quantification method for measuring iridescence using sexually selected traits in the Gulf pipefish (Syngnathus scovelli). Frontiers in Marine Science. 10: 1127790 link to paper, PDF
  10. Tosto NM, Beasley ER, Wong BBM, Mank JE, Flanagan SP (2023) The roles of sexual selection and sexual conflict in shaping patterns of genome and transcriptome variation. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-023-02019-7. link to paper
  11. 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. DOI: 10.1111/evo.14579. link to paper, PDF
  12. Pullen M, Gerber D, Thomsen MS, Flanagan SP (2022) Seasonal dynamics of faunal diversity and population ecology in an estuarine seagrass bed. Estuaries and Coasts. DOI: 10.1007/s12237-022-01103-8. link to paper (open access), PDF, associated code, data, my summary, a one-page summary
  13. Howell LA, LaRue M, Flanagan SP (2021) Environmental DNA as a tool for monitoring Antarctic vertebrates. New Zealand Journal of Zoology. DOI: 10.1080/03014223.2021.1900299. link to paper, PDF, my summary
  14. Flanagan SP, Rose E, Jones AG (2021) The population genomics of repeated freshwater colonizations by Gulf pipefish. Molecular Ecology. DOI: 10.1111/mec.15841 link to paper, PDF
  15. Anderson AP, Flanagan SP, Rose E, Jones AG. 2020. The estrogen-responsive transcriptome of female secondary sexual traits in the Gulf pipefish, Journal of Heredity, esaa008, link to paper, AGA's blog post about the paper
  16. Lerch B, Dautel KA, Brewer S, Liang A, Siewe N, Flanagan SP. 2020. Space, density, and extra-pair matings have opposing impacts on male and female reproductive success. Population Ecology. link to paper, PDF
  17. Wright AM, Schwartz RS, Oaks JR, Newman CE, Flanagan SP. The why, when, and how of computing in biology classrooms [version 2; peer review: 2 approved]. F1000Research 2019, 8:1854. link to paper (open access)
  18. Flanagan SP, and Jones AG. 2019. The future of parentage analysis: Moving from microsatellites to SNPs and beyond. Molecular Ecology. 28(3): 544-567 doi: 10.1111/mec.14988 link to paper, my summary
  19. Jost L, Archer F, Flanagan SP, Gaggiotti O, Hoban S, Latch E. 2018. Differentiation measures for conservation genetics. Evolutionary Applications. 11: 1139-1148. doi: 10.1111/eva.12590. pdf, link to paper, my summary
  20. Flanagan SP*, Forester BR*, Latch EK, Aitken SN, Hoban S. 2017. Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation. Evolutionary Applications. 11: 1035–1052. doi: 10.1111/eva.12569. pdf, link to paper, my summary
  21. 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. doi: 10.1111/1755-0998.12734. link to paper, my summary, associated code, gwscaR, data, genomic data
  22. 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  pdf, link to paper, my summary, associated code, data
  23. 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 pdf, link to paper, my summary, associated code, data, genomic data
  24. 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 pdf, link to paper, press release, data
  25. 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 pdf, link to paper, my summary, data, genomic data, associated code


  26. 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
  27. 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. pdf, my summary, associated code
  28. 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. link to paper, pdf, my summary, data, associated code
  29. 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
  30. 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
  31. 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

Other outputs

  1. Flanagan SP 2023. Male pregnancy and weird courtship wiggles: how NZ’s wide-bodied pipefish confounds expectations. The Conversation. link
  2. Thomsen M, Moser A, Pullen M, Gerber D, & Flanagan SP . 2020. Seagrass beds provide habitat for crabs, shrimps and fish in two estuaries on the South Island of New Zealand. bioRxiv. link to paper, PDF
  3. Flanagan, SP 2019. Quantitative Genetics of Behavior. In: Choe, J.C. (Ed.), Encyclopedia of Animal Behavior, (2nd ed.). vol. 2, pp. 80–93. Elsevier, Academic Press. link to paper, PDF
  4. Flanagan SP. 2017. Pipefish pairing. Biosphere Magazine. 23. PDF (opens in a new tab)

Theses

  1. Beasley, ER. 2025. A taste for the beautiful : differential expression in genes, traits, and behaviours in three congeneric species of pipefish in the genus Stigmatopora. link
  2. Gwatkin, GSM. 2025. Interactions between kororā/little penguins (Eudyptula minor) and their terrestrial environment at Pōhatu/Flea Bay, Banks Peninsula. link
  3. Tosto, NM. 2024. Deciphering the evolutionary tapestry of sexual dimorphism: From gene expression to sexual selection in pipefish.
  4. O'Neill, R. 2023. Quantifying the reproductive ecology and immune-related gill gene regulation in Stigmatopora macropterygia. link
  5. Cox, A. 2023. Insight into the effectomes of Aotearoa Phythophthora cinnamomi isolates by comparative genomics. link
  6. van Eyndhoven, F. 2022. The role of the novel female ornament in the wide-bodied pipefish, Stigmatapora nigra. http://dx.doi.org/10.26021/12821 link
  7. Howell, L. 2021. Detecting Antarctic and New Zealand vertebrates using environmental DNA (eDNA). http://dx.doi.org/10.26021/10882. link
  8. Gerber, DA (co-supervised by [Mads Thomsen](https://www.thomsenlab.com/)). 2021. Associations between estuarine foundation species and their effect on biodiversity across latitudes and seasons. http://dx.doi.org/10.26021/11369 link
  9. Pullen, M. 2021. The use of seagrass (Zostera muelleri) habitat types by seagrass communities in New Zealand. http://dx.doi.org/10.26021/11188. link

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