Molecular and morphological clocks for estimating evolutionary divergence times

Barba-Montoya, José; Tao, Qiqing; Kumar, Sudhir

doi:10.1186/s12862-021-01798-6

Cited by 9 publications

(6 citation statements)

References 48 publications

(99 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Without these calibrations, the divergence time estimates are far younger than expected; for example, a phylogenetic reconstruction with no additional calibration of certain genera places the divergence between leporids and ochotonids at around 10.9 million years. This reflects the young estimates for clade divergence that morphological data alone, with a poor sampling of fossil specimens, tends to produce ( Barba-Montoya, Tao & Kumar, 2021 ). By placing a few key calibrations on large extant genera, we compute a tree with estimations that are concordant with previous studies.…”

Section: Resultsmentioning

confidence: 92%

The evolution of unique cranial traits in leporid lagomorphs

Wood-Bailey

Cox

Sharp

2022

PeerJ

View full text Add to dashboard Cite

Background The leporid lagomorphs (rabbits and hares) are adapted to running and leaping (some more than others) and consequently have unique anatomical features that distinguish them from ochotonid lagomorphs (pikas) and from their rodent relatives. Two traits that have received some attention are fenestration of the lateral wall of the maxilla and facial tilting. These features are known to correlate with specialised locomotory form in that the faster running species will generally have fenestration that occupies the dorsal and the anteroventral surface of the maxillary corpus and a more acute facial tilt angle. Another feature is an intracranial joint that circumscribes the back of the skull, thought to facilitate skull mobility. This joint separates the anterior portion of the cranium (including the dentition, rostrum and orbit) from the posterior portion of the cranium (which encompasses the occipital and the auditory complex). Aside from the observation that the intracranial joint is absent in pikas (generalist locomotors) and appears more elaborate in genera with cursorial and saltatorial locomotory habits, the evolutionary history, biomechanical function and comparative anatomy of this feature in leporids lacks a comprehensive evaluation. Methodology The present work analysed the intracranial joint, facial tilting and lateral fenestration of the wall of the maxilla in the context of leporid evolutionary history using a Bayesian inference of phylogeny (18 genera, 23 species) and ancestral state reconstruction. These methods were used to gather information about the likelihood of the presence of these three traits in ancestral groups. Results Our phylogenetic analyses found it likely that the last common ancestor of living leporids had some facial tilting, but that the last common ancestor of all lagomorphs included in the dataset did not. We found that it was likely that the last common ancestor of living leporids had fenestration that occupies the dorsal, but not the anteroventral, surface of the maxillary corpus. We also found it likely that the last common ancestor of living leporids had an intracranial joint, but that the last common ancestor of all living lagomorphs did not. These findings provide a broader context to further studies of evolutionary history and will help inform the formulation and testing of functional hypotheses.

show abstract

Section: Resultsmentioning

confidence: 92%

The evolution of unique cranial traits in leporid lagomorphs

Wood-Bailey

Cox

Sharp

2022

PeerJ

View full text Add to dashboard Cite

show abstract

“…Relaxed clock models applying various rate smoothing functions at different scales are an acknowledgement of this phenomenon (Lartillot et al, 2016; Lepage et al, 2007; Tiley et al, 2020; Yang, 1994). At the other extreme, there are moves to discern the operation of morphological clocks (Lee, 2016; Lee et al, 2014; Zhang & Wang, 2019), such that a straightforward distinction between clock‐like patterns in molecules and putatively stochastic/punctuated patterns in morphology may be an oversimplification (Barba‐Montoya et al, 2021). The difference is therefore quantitative rather than strictly qualitative.…”

Section: Discussionmentioning

confidence: 99%

Why should we compare morphological and molecular disparity?

et al. 2023

View full text Add to dashboard Cite

Indices of morphological disparity seek to summarise the highly multivariate morphological variation across groups of species within clades, time bins or other groups. Morphological variation can be quantified using geometric morphometric, outline or surface‐based methods. These are most effective when morphological differences are relatively modest and there are numerous ubiquitous landmarks and phase aligned features of shape variation. The most disparate samples, such as those across classes and phyla, typically necessitate the use of discrete characters. Unfortunately, such characters are often compiled subjectively in a manner reflecting the level of morphological and taxonomic focus and the intensity of taxon sampling. Sampling intensity is often highly variable within a single data set, especially in repurposed and amalgamated cladistic matrices. Here, we propose indices of molecular disparity analogous to those of morphological disparity. Despite numerous shortcomings discussed here, molecular sequence data can be obtained in a more objective, automated and scalable manner than morphological data. Comparisons of the morphological and molecular disparity of subclades in 16 large data sets suggest that molecular disparity is less susceptible to sampling biases than morphological disparity. Moreover, distance matrices inferred from individual genes tend to correlate strongly with each other and with distances from all concatenated genes. By contrast, morphological and molecular disparity are typically not significantly correlated across subclades, such that comparisons for groups can help to give a fuller picture of their evolution. For example, within mammals, Afrotheria have conspicuously high morphological disparity but modest molecular disparity, suggesting unusually high morphological plasticity. Even more strikingly, the molecular disparity of rodents is over five times that for Artiodactyla, despite having only half of their morphological disparity. These contrasts suggest the differential operation of geometric, biomechanical, ontogenetic and environmental constraints on form. Given the increasing abundance of total evidence datasets in the literature and the widespread and sometimes uncritical repurposing of discrete morphological matrices, we propose the comparison of morphological and molecular disparity as a useful tool to understand subclade evolution more fully.

show abstract

“…2017; Parins‐Fukuchi & Brown 2017; Barba‐Montoya et al . 2021), and morphological data need to allow accurate inference of the phylogenetic position of fossil terminals (Sansom et al . 2010; Sansom & Wills 2013; Guillerme & Cooper 2016; Luo et al .…”

Section: Discussionmentioning

confidence: 99%

“…This finding is particularly noteworthy as our simulation pipeline incorporated all major caveats thought to complicate the use of morphological clocks: we incorporated adaptive phenotypic variation, used overly simplistic models of character change, and did not enforce constancy of evolutionary rates (Sanderson 1998; Beck & Lee 2014; Parins‐Fukuchi & Brown 2017; Barba‐Montoya et al . 2021).…”

Section: Discussionmentioning

confidence: 99%

Inaccurate fossil placement does not compromise tip‐dated divergence times

Mongiardino Koch,

Garwood,

Parry

2023

Palaeontology

View full text Add to dashboard Cite

Time‐scaled phylogenies underpin the interrogation of evolutionary processes across deep timescales, as well as attempts to link these to Earth's history. By inferring the placement of fossils and using their ages as temporal constraints, tip dating under the fossilized birth–death (FBD) process provides a coherent prior on divergence times. At the same time, it also links topological and temporal accuracy, as incorrectly placed fossil terminals should misinform divergence times. This could pose serious issues for obtaining accurate node ages, yet the interaction between topological and temporal error has not been thoroughly explored. We simulate phylogenies and associated morphological datasets using methodologies that incorporate evolution under selection, and are benchmarked against empirical datasets. We find that datasets of 300 characters and realistic levels of missing data generally succeed in inferring the correct placement of fossils on a constrained extant backbone topology, and that true node ages are usually contained within Bayesian posterior distributions. While increased fossil sampling improves the accuracy of inferred ages, topological and temporal errors do not seem to be linked: analyses in which fossils resolve less accurately do not exhibit elevated errors in node age estimates. At the same time, inferred divergence times are biased, probably due to a mismatch between the FBD prior and the shape of our simulated trees. While these results are encouraging, suggesting that even fossils with uncertain affinities can provide useful temporal information, they also emphasize that palaeontological information cannot overturn discrepancies between model priors and the true diversification history.

show abstract

Molecular and morphological clocks for estimating evolutionary divergence times

Cited by 9 publications

References 48 publications

The evolution of unique cranial traits in leporid lagomorphs

The evolution of unique cranial traits in leporid lagomorphs

Why should we compare morphological and molecular disparity?

Inaccurate fossil placement does not compromise tip‐dated divergence times

Contact Info

Product

Resources

About