Biology subjects

Wright, D. F.

Publications and source records attributed to Wright, D. F..

3 recordsLinked to original sources

bioRxiv2024

Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data

Understanding the evolution and phylogenetic distribution of morphologic traits is fundamental to macroevolutionary research. Despite decades of major advances and key insights from molecular systematics, organismal anatomical features remain a key source of biological data for both inferring phylogenies and investigating patterns of trait evolution among fossil and extant species. In palaeobiology, morphologic characters are typically the only source of information available for reconstructing evolutionary trees. Systematists working with fossil data must make decisions regarding how morphological characters are modeled, whether they are coded as continuous or categorical, and how to address biological sources of rate variation. To determine the impact of how different models of morphological evolution influence phylogenetic inferences and downstream comparative analyses of fossil data, we compared a series of increasingly complex model configurations of character evolution to a dataset of Cambrian-Ordovician trilobites containing both discrete morphological characters and continuous traits. Model configurations vary in complexity, ranging from simple constant rate scenarios with only discrete categorical traits, to complex evolutionary models including both discrete and quantitative traits across multiple ecological partitions while accounting for multiple sources of rate variation. We compared topological distributions across model configurations by visualizing their distances in multidimensional treespace. Results indicate support for rate-variable models and partitioning characters. However, inclusion of continuous traits dramatically alters macroevolutionary inferences. Character model complexity also has a major impact on which regions of treespace are explored, suggesting a critical need to carefully model morphologic evolution even when systematists are only interested in patterns of phylogenetic relationships alone.

evolutionary biology↗

bioRxiv2022

H4K20me3 controls Ash1-mediated H3K36me3 and transcriptional silencing in facultative heterochromatin

Facultative heterochromatin controls development and differentiation in many eukaryotes. In metazoans, plants, and many filamentous fungi, facultative heterochromatin is characterized by transcriptional repression and enrichment with nucleosomes that are trimethylated at histone H3 lysine 27 (H3K27me3). While loss of H3K27me3 results in derepression of transcriptional gene silencing in many species, additional up- and downstream layers of regulation are necessary to mediate control of transcription in chromosome regions enriched with H3K27me3. Here, we investigated the effects of one histone mark on histone H4, namely H4K20me3, in the fungus Zymoseptoria tritici, a globally important pathogen of wheat. Deletion of kmt5, the gene encoding the sole methyltransferase responsible for H4K20 methylation, resulted in global derepression of transcription, especially in regions of facultative heterochromatin. Reversal of silencing in the absence of H4K20me3 not only affected genes but also a large number of novel, previously undetected, non-coding transcripts generated from regions of facultative heterochromatin on accessory chromosomes. Transcriptional activation in kmt5 deletion strains was accompanied by a complete loss of Ash1-mediated H3K36me3 and chromatin reorganization affecting H3K27me3 and H3K4me2 distribution in regions of facultative heterochromatin. Strains with a H4K20M mutation in the single histone H4 gene of Z. tritici recapitulated these chromatin changes, suggesting that H4K20me3 is essential for Ash1-mediated H3K36me3. The {Delta}kmt5 mutants we obtained are more sensitive to genotoxic stressors and both, {Delta}kmt5 and {Delta}ash1, showed greatly increased rates of accessory chromosome loss. Taken together, our results provide insights into a novel, and unsuspected, mechanism controlling the assembly and maintenance of facultative heterochromatin. SignificanceFacultative heterochromatin contains genes important for specific developmental or life cycle stages. Transcriptional regulation of these genes is influenced by chromatin structure. Here, we report that a little studied histone modification, trimethylation of lysine 20 on histone H4 (H4K20me3), is enriched in facultative heterochromatin and important for transcriptional repression in these regions in an important agricultural pathogen. Furthermore, normal levels of H4K20me3 are essential for deposition of another repressive histone mark, Ash1-mediated H3K36me3, and affect the distribution of other marks including H3K27me3. We conducted the first genome-wide assessment of H4K20 methylation levels in a fungus, and our discoveries reveal that multiple chromatin modifications are required to establish transcriptional silencing, providing the framework to understand epistasis relationships among these histone marks.

genetics↗

bioRxiv2020

Ignoring fossil age uncertainty leads to inaccurate topology and divergence times in time calibrated tree inference

Time calibrated trees are challenging to estimate for many extinct groups of species due to the incompleteness of the rock and fossil records. Additionally, the precise age of a sample is typically not known as it may have occurred at any time during the time interval spanned by the rock layer. Bayesian phylogenetic approaches provide a coherent framework for incorporating multiple sources of evidence and uncertainty. In this study, we simulate datasets with characteristics typical of Palaeozoic marine invertebrates, in terms of character and taxon sampling. We use these datasets to examine the impact of different age handling methods on estimated topologies and divergence times obtained using the fossilized birth-death process. Our results reiterate the importance of modeling fossil age uncertainty, although we find that the overall impact of fossil age uncertainty depends on both fossil taxon sampling and character sampling. When character sampling is low, different approaches to handling fossil age uncertainty make little to no difference in the accuracy and precision of the results. However, when character sampling is high, sampling the fossil ages as part of the inference gives topology and divergence times estimates that are as good as those obtained by fixing ages to the truth, whereas fixing fossil ages to incorrect values results in higher error and lower coverage. Modeling fossil age uncertainty is thus critical, as fixing incorrect fossil ages will negate the benefits of improved fossil and character sampling.

evolutionary biology↗