Publications

You can also find my articles on my Google Scholar profile.

Journal Articles

MAST: Phylogenetic inference with mixtures across sites and trees

Published in Systematic Biology, 2024

We introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST). […] The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites.

Recommended citation: Thomas K F Wong, Caitlin Cherryh, Allen G Rodrigo, Matthew W Hahn, Bui Quang Minh, Robert Lanfear 2024. MAST: Phylogenetic Inference with Mixtures Across Sites and Trees. Systematic Biology. 73:375–391.
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Evolving thermal thresholds explain the distribution of temperature sex reversal in an Australian dragon lizard

Published in Diversity and Distributions, 2021

Species with temperature-dependent sex determination (TSD) are particularly vulnerable to climate change because a resultant skew in population sex ratio can have severe demographic consequences and increase vulnerability to local extinction. […] Our study demonstrates that complex evolutionary processes need to be incorporated into modelling biological responses to future climate scenarios.

Recommended citation: Megan A Castelli, Arthur Georges, Caitlin Cherryh, Dan F Rosauer, Stephen D Sarre, Isabella Contador-Kelsall, Clare E Holleley 2021. Evolving thermal thresholds explain the distribution of temperature sex reversal in an Australian dragon lizard. Diversity and Distributions. 27:427–438.
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A test statistic to quantify treelikeness in phylogenetics

Published in bioRxiv, 2021

To quantify and test for treelikeness in alignments, we develop and assess a test statistic to quantify treelikeness, which we call the tree proportion.

Recommended citation: Caitlin Cherryh, Bui Quang Minh, Rob Lanfear 2021. A test statistic to quantify treelikeness in phylogenetics. bioRxiv [Preprint]
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Thesis

Systematic bias in phylogenetic methods: investigating the adequacy of the treelikeness assumption

Published in ANU Open Research Repository, 2024

This thesis shows the diverse impacts of the treelikeness assumption on phylogenetic inference and suggest that treelikeness should be considered during phylogenetic tree inference.

Recommended citation: Caitlin Cherryh 2024. Systematic bias in phylogenetic methods: investigating the adequacy of the treelikeness assumption. PhD thesis. Australian National University. Available at https://doi.org/10.25911/GKN2-9F44
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