Author

T. J. Davies

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Ecology· 6 Microbiology· 3 Evolutionary Biology· 1 Plant Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:ecology & biodiversity· 5 Organism:plant (other)· 5 Approach:statistical model· 5 Research Focus:host-pathogen & immune response· 4 Research Focus:benchmarking· 3 Approach:experimental assay· 3 Assay:whole-genome sequencing· 3 Research Focus:cell type annotation· 2

Frequent Co-Authors

C. C. Davis· 3 shared P. W. Fowler· 3 shared T. E. Peto· 3 shared A. E. Sheppard· 2 shared A. S. Walker· 2 shared D. W. Crook· 2 shared E. Meineke· 2 shared J. Swann· 2 shared

Activity by Year

2017-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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3 shared papersEcology

C. C. Davis

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Author profile →

11 papers

Recent·Most cited

Abnormal weather drives disease outbreaks in wild and agricultural plants

D. Kirk, J. Cohen, V. Nguyen, M. L. Childs, J. E. Farner, T. J. Davies, S. L. Flory, J. R. Rohr, M. I. O'Connor, E. A. Mordecai

The paper shows how abnormal weather influences disease outbreaks in both wild and agricultural plants, finding that historical climate affects wild plants while warming increases agricultural disease risks.

bioRxiv · Mar 17, 2023 · PreprintEcology

The evolutionary history of spines: a Cenozoic arms race with mammals

U. Gelin, T. Charles-Dominique, T. J. Davies, J.-C. Svenning, W. J. Bond, K. W. Tomlinson

This study investigates the evolutionary history of spines in plants, finding that spine diversification was driven by mammal herbivory rather than climate, with regional patterns linked to herbivore diversity.

bioRxiv · Feb 9, 2023 · PreprintEvolutionary Biology

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

T. J. Davies, J. Swann, A. E. Sheppard, H. Pickford, S. Lipworth, M. AbuOun, M. Ellington, P. W. Fowler, S. Hopkins, K. Hopkins, D. Crook, T. E. Peto, M. F. Anjum, A. S. Walker, N. Stoesser

This study evaluates four AMR gene typing methods using simulated and real E. coli data, revealing significant discrepancies and highlighting issues with current bioinformatic approaches.

bioRxiv · Nov 3, 2021 · PreprintMicrobiology

Herbarium specimens reveal herbivory patterns across the genus Cucurbita

L. A. Jenny, L. R. Shapiro, C. C. Davis, T. J. Davies, N. E. Pierce, E. Meineke

This study uses herbarium specimens to analyze herbivory patterns across Cucurbita species, finding variation in damage levels and a link between habitat type and herbivory intensity.

bioRxiv · Jul 21, 2021Ecology

Environmental DNA as a management tool fortracking artificial waterhole use in savanna ecosystems

M. J. Farrell, D. Govender, M. Hajibabaei, M. van der Bank, T. J. Davies

This study compares eDNA metabarcoding and camera traps to track mammal use of artificial waterholes in Kruger National Park, finding eDNA can detect many species but has temporal limitations.

bioRxiv · Nov 3, 2020Ecology

Re-examining Kozlov et al.: Estimation of biases in museum specimen data requires robust sampling

E. Meineke, C. C. Davis, T. J. Davies

This paper re-analyzes Kozlov et al.'s study on herbarium specimen biases, finding that herbarium specimens can accurately represent herbivory when sample sizes are adequate, contradicting the original conclusions.

bioRxiv · Sep 1, 2020 · PreprintEcology

Predicting missing links in global host-parasite networks

M. J. Farrell, M. Elmasri, D. A. Stephens, T. J. Davies

This paper predicts missing host-parasite links using network properties and phylogenetic relationships, identifying both undocumented and potential associations in global mammal-parasite networks.

bioRxiv · Feb 25, 2020Ecology

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

T. J. Davies, N. Stoesser, A. E. Sheppard, M. Abuoun, P. W. Fowler, J. Swann, P. Quan, D. Griffiths, A. Vaughan, M. Morgan, H. T. T. Phan, K. J. Jeffery, M. Andersson, M. Ellington, O. Ekelund, , A. S. Walker

This study shows that amoxicillin-clavulanate resistance in E. coli is quantitative, not binary, and that WGS-based predictions outperform traditional phenotyping methods.

bioRxiv · Feb 6, 2020Microbiology

The realised velocity of climate change reveals remarkable idiosyncrasy of species’ distributional shifts

W. D. Pearse, T. J. Davies

The paper analyzes species distributional shifts in response to climate change, finding that species track climate but not fast enough, with highly variable responses across taxa.

bioRxiv · Oct 30, 2019 · PreprintEcology

Validating a 14-drug microtitre plate containing bedaquiline and delamanid for large-scale research susceptibility testing of Mycobacterium tuberculosis

P. M. Rancoita, F. Cugnata, A. L. Gibertoni Cruz, E. Borroni, S. J. Hoosdally, T. M. Walker, C. Grazian, T. J. Davies, T. E. Peto, D. W. Crook, P. W. Fowler, D. M. Cirillo, the CRyPTIC Consortium

The paper validates a 14-drug microtitre plate for measuring MICs of anti-TB compounds in M. tuberculosis isolates, finding optimal reading with the Vizion system after 14 days incubation.

bioRxiv · Jun 15, 2018Microbiology

The unrealized potential of herbaria in global change biology

E. K. Meineke, C. C. Davis, T. J. Davies

This paper highlights the underutilized potential of herbaria for global change biology, emphasizing their value in studying ecological and evolutionary responses to climate change and other biodiversity loss drivers.

bioRxiv · Nov 14, 2017Plant Biology