Biology subjects

Beck, R. M. D.

Publications and source records attributed to Beck, R. M. D..

7 recordsLinked to original sources

bioRxiv2025

Dental topography and diet in marsupials and comparisons with primates

Dental topography is a powerful tool for investigating the relationship between diet and tooth shape in mammals. Here, we test whether dental topographic metrics (DTMs) can accurately predict diet in marsupials based on 81 lower molars from 43 extant species in 12 families (representing six of the seven extant orders), and compare them to DTMs of primates with similar diets. Specific DTMs tested included Dirichlet normal energy (DNE) and variants (ariaDNE, convex DNE, and ariaDNE CV), orientation patch count rotated (OPCR), and Relief Index (RFI). We also investigate the use of the ratio of trigonid to talonid height (TriTaHI) as an additional DTM. Highest dietary classification accuracy using a leave-one-out quadratic discriminant function analysis for marsupials was reached when ariaDNE, RFI, molar size, and TriTaHI of lower second and third molars were combined, resulting in 69.2% dietary accuracy. In contrast, the primate sample of lower second molars reached the highest classification accuracy of 80.4% when only ariaDNE, RFI, and molar size were used. Notably, 3D meshes from epoxy casts showed consistently higher OPCR and ariaDNE CV values than meshes from original specimens. When using a cross-validated approach, using the primate sample to predict marsupial diets and vice versa, only ariaDNE, RFI, and molar size were needed to obtain the maximum classification accuracy (69.7% when classifying primates using the marsupial training set; and 61.8% vice versa). The comparative dataset of this study will be very useful for studies aiming to reconstruct the diets of fossil mammals that lack phylogenetically close extant analogues.

evolutionary biology↗

bioRxiv2024

Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil specimens and to estimate divergence times. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation post mortem. Moreover, some of the enamelome genes are paralogous or may coevolve. This raises the question as to whether the enamelome provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments (MSAs) for each protein and estimated the evolutionary rate for each site and examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1-2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We found that the composition of the proteome influences the phylogenetic placement of Tarsiiformes. For the inference of molecular phylogenies based on paleoproteomic data, we recommend characterizing the evolution of the proteomes from the closest extant relatives to maximize the reliability of phylogenetic inference.

evolutionary biology↗

bioRxiv2023

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

Dental topographic metrics (DTMs), which quantify different aspects of the shape of teeth, are powerful tools for studying dietary adaptation and evolution in mammals. However, comparative samples of scanned mammal teeth suitable for analysis with DTMs remain limited in size and scope, with little or no representation of some major lineages, even within well-studied clades such as primates. In addition, current DTM protocols usually rely on proprietary software, which may be unavailable to many researchers for reasons of cost. We address these issues in the context of a DTM analysis of the primate clade Platyrrhini ("New World monkeys") by: 1) presenting a large comparative sample of scanned second lower molars (m2s) of callitrichids (marmosets and tamarins), which were previously underrepresented in publicly available platyrrhine datasets; and 2) giving full details of an entirely freeware pipeline for DTM analysis. We also present an updated discrete dietary classification scheme for extant platyrrhines, based on cluster analysis of dietary data extracted from 98 primary studies. Our freeware pipeline performs equally well in dietary classification accuracy of an existing sample of platyrrhine m2s (excluding callitrichids) as a published protocol that uses proprietary software, at least when multiple DTMs are combined. Individual DTMs however, sometimes showed very different results in classification accuracies between that of our freeware pipeline and that of the proprietary protocol, most likely due to the differences in the smoothing functions used. The addition of callitrichids still resulted in high classification accuracy in predicting diet with combined DTMs, although accuracy was considerably higher when molar size was included (90%) than excluded (73%). We conclude that our new freeware DTM pipeline is capable of accurately predicting diet in platyrrhines based on tooth shape and size, and so is suitable for inferring probable diet of taxa for which direct dietary information is unavailable, such as fossil species.

evolutionary biology↗

bioRxiv2021

Total evidence tip-dating phylogeny of platyrrhine primates and 27 well-justified fossil calibrations for primate divergences

Phylogenies with estimates of divergence times are essential for investigating many evolutionary questions. In principle, "tip-dating" is arguably the most appropriate approach, with fossil and extant taxa analyzed together in a single analysis, and topology and divergence times estimated simultaneously. However, "node-dating" (as used in many molecular clock analyses), in which fossil evidence is used to calibrate the age of particular nodes a priori, will probably remain the dominant approach, due to various issues with analyzing morphological and molecular data together. Tip-dating may nevertheless play a key role in robustly identifying fossil taxa that can be used to inform node-dating calibrations. Here, we present tip-dating analyses of platyrrhine primates (so-called "New World monkeys") based on a total evidence dataset of 418 morphological characters and 10.2 kb of DNA sequence data from 17 nuclear genes, combined from previous studies. The resultant analyses support a late Oligocene or early Miocene age for crown Platyrrhini (composite age estimate: 20.7-28.2 Ma). Other key findings include placement of the early Miocene putative cebid Panamacebus outside crown Platyrrhini, equivocal support for Proteropithecia being a pitheciine, and support for a clade comprising three subfossil platyrrhines from the Caribbean (Xenothrix, Antillothrix and Paralouatta), related to Callicebinae. Based on these results and the available literature, we provide a list of 27 well-justified node calibrations for primate divergences, following best practices: 17 within Haplorhini, five within Strepsirrhini, one for crown Primates, and four for deeper divergences within Euarchontoglires. In each case, we provide a hard minimum bound, and for 23 of these we also provide a soft maximum bound and a suggested prior distribution. For each calibrated node, we provide the age of the oldest fossil of each daughter lineage that descends from it, which allows use of the "CladeAge" method for specifying priors on node ages.

evolutionary biology↗

bioRxiv2020

Global elongation and high shape flexibility as an evolutionary hypothesis of accommodating mammalian brains into skulls

Little is known about how the large brains of mammals are accommodated into the dazzling diversity of their skulls. It has been suggested that brain shape is influenced by relative brain size, that it evolves or develops according to extrinsic or intrinsic mechanical constraints, and that its shape can provide insights into its proportions and function. Here, we characterise the shape variation among 84 marsupial cranial endocasts of 57 species including fossils, using 3D geometric morphometrics and virtual dissections. Statistical shape analysis revealed four main patterns: over half of endocast shape variation ranges between elongate and straight to globular and inclined; little allometric variation with respect to centroid size, and none for relative volume; no association between locomotion and endocast shape; limited association between endocast shape and previously published histological cortex volumes. Fossil species tend to have smaller cerebral hemispheres. We find divergent endocast shapes in closely related species and within species, and diverse morphologies superimposed over the main variation. An evolutionarily and individually malleable brain with a fundamental tendency to arrange into a spectrum of elongate-to-globular shapes - possibly mostly independent of brain function - may explain the accommodation of brains within the enormous diversity of mammalian skull form.

evolutionary biology↗

bioRxiv2019

Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals

ABSTRACTThe incorporation of stratigraphic data into phylogenetic analysis has a long history of debate, but is not currently standard practice for palaeontologists. Bayesian tip-dating (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip-dating affects the recovery of evolutionary relationships has yet to be fully explored. Here we show, through analysis of several datasets with multiple phylogenetic methods, that topologies produced by tip-dating are outliers when compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip-dating have better fit to stratigraphy than trees recovered by other methods, due to trees with better stratigraphic fit being assigned a higher prior probability. Differences in stratigraphic fit and tree topology between tip-dating and other methods appear to be concentrated in parts of the tree with weaker character signal and a stronger influence of the prior, as shown by successive deletion of the most incomplete taxa from a sauropod dataset. Tip-dating applied to Mesozoic mammals firmly rejects a monophyletic Allotheria, and strongly supports diphyly of haramiyidans, with the late Triassic Haramiyavia and Thomasia forming a clade with tritylodontids, which is distant from the middle Jurassic euharamiyidans. This result is not sensitive to the controversial age of the eutherian Juramaia. A Test of the age of Juramaia using a less restrictive prior reveals strong support from the data for an Early Cretaceous age. Our results suggest that tip-dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit a prior expectation that can be overturned by strong evidence from character data.View Full Text

paleontology↗

bioRxiv2018

Improvements in the fossil record may largely resolve the conflict between morphological and molecular estimates of mammal phylogeny

Morphological phylogenies of mammals continue to show major conflicts with the robust molecular consensus view of their relationships. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships, particularly for fossil taxa for which, in most cases, molecular data is unlikely to ever become available. We tested this under a hypothetical \"best case scenario\" by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive molecular phylogeny of mammals, and then seeing what effect inclusion of these predicted ancestors had on unconstrained analyses of morphological data. We found that this resulted in topologies that are highly congruent with the molecular consensus, even when simulating the effect of incomplete fossilisation. Most strikingly, several analyses recovered monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record may be sufficient to largely reconcile morphological and molecular phylogenies of mammals, even with current morphological character sets.

evolutionary biology↗