Genomic data can be used to identify patterns of selection from the background patterns caused by neutral evolutionary processes (genetic drift, mutation, and recombination). Our lab uses these tools to ask questions about the relative importance of different types of selection, the impacts of spatial variation in environments, and to compare patterns of differentiation at the genomic level to differentiation at the phenotypic level. Our work on the Gulf pipefish is building a compelling that will help elucidate how different selection pressures impact the Gulf pipefish genome, and whether patterns of adaptation and sexual selection are repeatable across populations.
That being said, The general dynamics of local adaptation, population differentiation, and novel trait evolution are best understood if multiple evolutionary trajectories are compared. To that end, the lab is developing comparative population genomics and transcriptomics studies using other Syngnathid fishes.
Some relevant papers from the lab include:
Jost L, Archer F, Flanagan SP, Gaggiotti O, Hoban S, Latch E. 2018. Differentiation measures for conservation genetics. Evolutionary Applications . 00:1-10. https://doi.org/10.1111/eva.12590. pdf, link to paper, my summary
Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation. Evolutionary Applications. 00: 1–18. https://doi.org/10.1111/eva.12569. pdf, link to paper, my summary, , , , . 2017.
Flanagan SP, and Jones AG. 2017. Substantial differences in bias between single-digest and double-digest RAD-seq: A case study. Molecular Ecology Resources. 00:1–17. https://doi-org.proxy.lib.utk.edu:2050/10.1111/1755-0998.12734. link to paper, my summary, associated code, gwscaR, data, genomic 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 pdf, link to paper, my summary, associated code, data, genomic data
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
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