Tasks performed
As a postdoctoral researcher within FEZ, James' tasks include:
- Developing new methodologies to better ameliorate phylogenetic reconstruction artifacts.
- Better understanding the phylogenetic relationships of Lophotrochozoa.
- Collaborating with other groups with related interests to share methods, information and results.
Background
James completed his PhD at Bristol University in 2014, studying the evolution of the visual protein opsin across animal life, with a particular focus on ecdysozoans: the group of animals that includes insects, crustaceans and tardigrades.
Following this, he obtained a JSPS postdoctoral fellowship at Keio University Institute of Advanced Biosciences in Japan, where he worked on the evolution of terrestrialisation in tardigrades.
James' research interests broadly revolve around protein evolution and the evolution of major transitions, particularly within the invertebrates. To accomplish this, he uses a range of molecular and fossil-informed strategies and methodologies, and is also interested in the development of new methodologies to tackle the problems that occur when using these tools, such as long branch attraction and compositional heterogeneity.
Selected publications
Fleming, J.F. and Struck, T.H., 2023. nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets. BMC bioinformatics, 24(1), pp.1-25.
Fleming, J., Eriksen, P.M. and Struck, T.H., 2023. Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric. F1000Research, 12, p.945.
Fleming, J.F., Valero‐Gracia, A. and Struck, T.H., 2023. Identifying and addressing methodological incongruence in phylogenomics: A review. Evolutionary Applications.
Fleming, J.F., 2023. The wealth of shared resources: Improving molecular taxonomy using eDNA and public databases. Zoologica Scripta, 52(3), pp.226-234.
Fleming, J.F., Pisani, D. and Arakawa, K., 2021. New Tardigrade opsins and differential expression analyses show ontogenic variation in light perception. Genome biology and evolution, 13(8), p.evab164.
Fleming, J.F. and Arakawa, K., 2021. Systematics of tardigrada: A reanalysis of tardigrade taxonomy with specific reference to Guil et al.(2019). Zoologica scripta, 50(3), pp.376-382.
Fleming, J.F., Feuda, R., Roberts, N.W. and Pisani, D., 2020. A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans. Genome biology and evolution, 12(2), pp.3906-3916.
Fleming, J.F., Kristensen, R.M., Sørensen, M.V., Park, T.Y.S., Arakawa, K., Blaxter, M., Rebecchi, L., Guidetti, R., Williams, T.A., Roberts, N.W. and Vinther, J., 2018. Molecular palaeontology illuminates the evolution of ecdysozoan vision. Proceedings of the Royal Society B, 285(1892), p.20182180.
Howard, R.J., Giacomelli, M., Lozano-Fernandez, J., Edgecombe, G.D., Fleming, J.F., Kristensen, R.M., Ma, X., Olesen, J., Sørensen, M.V., Thomsen, P.F. and Wills, M.A., 2022. The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data. Journal of the Geological Society, 179(4), pp.jgs2021-107.
Kakui, K., Fleming, J.F., Mori, M., Fujiwara, Y. and Arakawa, K., 2021. Comprehensive transcriptome sequencing of Tanaidacea with proteomic evidences for their silk. Genome biology and evolution, 13(12), p.evab281.
Lozano-Fernandez, J., Giacomelli, M., Fleming, J.F., Chen, A., Vinther, J., Thomsen, P.F., Glenner, H., Palero, F., Legg, D.A., Iliffe, T.M. and Pisani, D., 2019. Pancrustacean evolution illuminated by taxon-rich genomic-scale data sets with an expanded remipede sampling. Genome biology and evolution, 11(8), pp.2055-2070.
Puttick, M.N., O'Reilly, J.E., Tanner, A.R., Fleming, J.F., Clark, J., Holloway, L., Lozano-Fernandez, J., Parry, L.A., Tarver, J.E., Pisani, D. and Donoghue, P.C., 2017. Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data. Proceedings of the Royal Society B: Biological Sciences, 284(1846), p.20162290.
O'Reilly, J.E., Puttick, M.N., Parry, L., Tanner, A.R., Tarver, J.E., Fleming, J., Pisani, D. and Donoghue, P.C., 2016. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data. Biology letters, 12(4), p.20160081.
Published
Dec. 15, 2020 1:53 PM
- Last modified
Aug. 23, 2023 10:46 AM
