Biology subjects

Hopkins, M. J.

Publications and source records attributed to Hopkins, M. J..

4 recordsLinked to original sources

bioRxiv2025

Combining fossil taxa with and without morphological data improves dated phylogenetic analyses

The fossilized birth-death (FBD) model has become an increasingly popular method for inferring dated phylogenies. This is because it is especially useful for incorporating fossil data into such analyses, integrating fossils along with their age information directly into the tree as tips or sampled ancestors. Two approaches are common for placing fossil taxa in trees: inference based on morphological character data or using taxonomic constraints to control their topological placement. These approaches have historically been treated as alternatives, though combining the two is theoretically possible. For phylogenetic inference of entirely extinct organisms, additional related fossil taxa other than those for which morphology is available are generally overlooked. Here, we implement a combined approach on an empirical dataset for a group of trilobites. We use a morphological matrix and ages for 56 taxa and age information for another 196 taxa from the Paleobiology Database. To evaluate the effects of a combined approach, we conducted FBD dated phylogenetic analyses using a combined approach with morphology and taxonomic constraints and compared them to analyses of taxa with morphology alone. We find that a combined approach yields topologies that are more stratigraphically congruent, substantially more precise parameter estimates (e.g., divergence times), and more informative tree distributions. These findings are a consequence of the substantial increase in stratigraphic age information and a more representative sample of their temporal distributions.

evolutionary biology↗

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↗

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↗

bioRxiv2018

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process

Fossil information is essential for estimating species divergence times, and can be integrated into Bayesian phylogenetic inference using the fossilized birth-death (FBD) process. An important aspect of palaeontological data is the uncertainty surrounding specimen ages, which can be handled in different ways during inference. The most common approach is to fix fossil ages to a point estimate within the known age interval. Alternatively, age uncertainty can be incorporated by using priors, and fossil ages are then directly sampled as part of the inference. This study presents a comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process. Based on simulations, we find that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils. Second, we show a comparison using an empirical dataset of extant and fossil cetaceans, which confirms that different methods of handling fossil age uncertainty lead to large differences in estimated node ages. Stratigraphic age uncertainty should thus not be ignored in divergence time estimation and instead should be incorporated explicitly.

paleontology↗