Publications


In review

Brazeau MD*.,Guillerme T*., Smith MR*. Morphological phylogenetic analysis with inapplicable data. In review in Systematic Biology.

* All authors contributed equally. Preprint available here. Key words: cladistic analysis, inapplicable data, character independence, phylogenetic tree search, character optimizatio.

Guillerme T. dispRity: a modular R package for measuring disparity. In review in Methods in Ecology and Evolution.

Key words: disparity, ordination, multidimensionality, disparity-through-time, palaeobiology, ecology.

2017

Healy K., Guillerme T., Kelly S., Inger R., Bearhop, S., Jackson, A. SIDER: An R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness. Ecography., doi:10.1111/ecog.03371

Key words: SIDER Trophic Enrichment Factors, Comparative Analysis, Stable Isotope Analysis. Personal contribution: co-developed the R package.

Turvey S., Crees J.J., Hansford J., Jeffree T.E., Crumpton N., Kurniawan I., Setiyabudi E., Guillerme T., Paranggarimu U., Dosseto A., van den Bergh G.D. (2017) Quaternary vertebrate faunas from Sumba, Indonesia: implications for Wallacean biogeography and evolution. Proceedings of the Royal Society of London B, 284: 1861, doi:10.1098/rspb.2017.1278

Key words: biogeography, island evolution, murid, Quaternary extinctions, Stegodon, Wallacea.. Personal contribution: ran the phylogenetic analysis.

2016

Kane A., Healy K., Guillerme T., Ruxton G., and Jackson A.L. (2016) A Recipe for Scavenging - the natural history of a behaviour. Ecography, 39: 001–011, doi:10.1111/ecog.02817

Key words: scavenging; carrion; vertebrates. Personal contribution: helping designing and writing the structure of the review. This paper was featured as the Ecography cover for February 2017. See associated blog post.

Guillerme T. and Cooper N. (2016) Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses Biology Letters, 12 20151003 doi:10.1098/rsbl.2015.1003

Key words: Total Evidence Method, phylogenetic clustering, extinct, topology, discrete anatomical matrix. This was an invited submission for a special issue: Putting fossils in trees. Presentation (08/2015) ; Blog post

Guillerme T. and Cooper N. (2016) Effects of missing data on topological inference using a Total Evidence approach. Molecular Phylogenetics and Evolution, 94:146–158 doi:10.1016/j.ympev.2015.08.023

Key words: Morphological characters, Bayesian, Maximum Likelihood, topology, fossil, living. Presentation (08/2015) ; Blog post

2014

Healy K., Guillerme T., Finlay S., Kane A., Kelly S.B.A., McClean D., Kelly D.J., Donohue I., Jackson A.L. and Cooper N. (2014) Ecology and mode of life explain lifespan variation in birds and mammals. Proceedings of the Royal Society of London B. 281(1784), 20140298, doi:10.1098/rspb.2014.0298

Key words: Longevity, extrinsic mortality, MCMCglmm, volant, non-volant. Personal contribution: collecting the data, writing the code and running the analysis. Blog post: about the paper and the collaborative project.

Softwares

Guillerme T & Healy K. (2014). mulTree: a package for running MCMCglmm analysis on multiple trees. ZENODO. 10.5281/zenodo.12902.

v1.3:

Performs MCMCglmm on multiple phylogenetic trees. This package is based on the MCMCglmm package and runs a MCMCglmm analysis on multiple trees. Related publications: Healy et al. 2014, Proceedings B., Healy 2015, Proceedings B..

Guillerme T. (2015). dispRity: a package for measuring disparity in R. ZENODO. 10.5281/zenodo.31742.

v0.3.9:

A modular package allowing to calculate disparity (as defined by user) from ordinated matrices (typically from distance matrices from cladistic/morphometric/ecological data).

Healy K, Jackson AL & Guillerme T (2016). SIDER: Stable Isotope Discrimination Estimation in R. ZENODO. 10.5281/zenodo.167079.

v0.9.1.2:

This package allows users to estimate Trophic Discrimination Factors (TDF) for species with no current measured TDF values using Bayesian imputation. This package is based on the MCMCglmm package and runs a MCMCglmm analysis on multiple trees using mulTree.

Brazeau MD, Guillerme T. (2016). morphylib: a C library for calculating tree length under parsimony with inapplicable data. ZENODO. 10.5281/zenodo.815372.

v0.9.1.2:

This library allows to count tree length under our new inapplicable algorithm. This is part of the morphyproject.