Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2021.04.03.438104

Unbiased clade age estimation using a Bayesian Brownian Bridge

Silvestro, D.·Bacon, C. D.·Ding, W.·Zhang, Q.·Donoghue, P. C. J.·Antonelli, A.·Xing, Y.
View original source ↗Export metadata ↓

Abstract

In a recent paper1 we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. Applying BBB to 198 angiosperm families, we found that their fossil record is compatible with clade origins earlier than most contemporary palaeobotanical interpretations. In particular, we estimated with high probability that crown-angiosperms originated before the Cretaceous (> 145 Ma). Budd and colleagues2 critique our study, arguing that the BBB model is biased towards older estimates when fossil data are scarce or absent, that our underlying fossil dataset is unsound, that our clade age estimates are therefore biased by early diverging lineages that are underrepresented in the fossil record, and that pooling of fossil data for analysis at higher taxonomic ranks overcomes these biases. Here, we explore their points and perform new simulations to show that their critique has no merit.

Explore related subjects

paleontologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Silvestro, D., Bacon, C. D., Ding, W., Zhang, Q., Donoghue, P. C. J., Antonelli, A., Xing, Y.. 2021-04-04. Unbiased clade age estimation using a Bayesian Brownian Bridge. https://doi.org/10.1101/2021.04.03.438104

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Constraining Palaeogeography and Palaeotides for the Cambrian using cnidarian medusae

The ocean tides influence key Earth system processes at a range of spatial and temporal scales. It is known that the geometry of ocean basins is the leading controller of tidal energetics, so well-constrained palaeogeographic reconstructions and tidal properties for Earths past are imperative when investigating other Earth system processes. Here, we present a novel way to constrain both deep-time tidal model results and reconstructions, by combining palaeoecology with sedimentology. We compare new palaeo-tidal model simulations for the Cambrian period, significant for the early origin and radiation of major animal fauna, to tidal proxies. One of the most abundant soft-bodied organisms preserved during this time are cnidarian medusae (jellyfish). A total of 17 cnidarian medusae localities were obtained through the literature, which had an adequate global distribution and occurred at regular intervals throughout the period of study. In some locations there were also estimates of palaeo-tidal range. Our results show a good agreement between the simulations and proxy data. In the few locations where there is disagreement, it is proposed that the palaeogeographic reconstructions are missing details, e.g., island chains, and our results allow for the palaeogeographic reconstructions to be improved. The proxy method presented is promising and can be applied to other time-periods with different marine fossils, particularly at evolutionary and extinction periods where the marginal marine environment is of importance.

paleontology↗
bioRxiv2021

Early evolution of beetles regulated by the end-Permian deforestation

The end-Permian mass extinction (EPME) led to a severe terrestrial ecosystem collapse. However, the ecological response of insects--the most diverse group of organisms on Earth--to the EPME remains poorly understood. Here, we analyse beetle evolutionary history based on taxonomic diversity, morphological disparity, phylogeny, and ecological shifts from the Early Permian to Middle Triassic, using a comprehensive new data set. Permian beetles were dominated by xylophagous stem groups with a high diversity and disparity, which probably played an underappreciated role in the Permian carbon cycle. Our suite of analyses shows that Permian xylophagous beetles suffered a severe extinction during the EPME largely due to the collapse of forest ecosystems, resulting in an Early Triassic gap of xylophagous beetles. New xylophagous beetles appeared widely in the early Middle Triassic, which is consistent with the restoration of forest ecosystems. Our results highlight the ecological significance of insects in deep-time terrestrial ecosystems.

paleontology↗
bioRxiv2021

Belemnite phylogeny and decline during the mid-Cretaceous

Belemnites are common fossil coleoid cephalopods of the Mesozoic. They began to diversify in the Triassic-Early Jurassic and maintained this diversity until the early Early Cretaceous. During the mid-Cretaceous, they declined in diversity and distribution, being restricted to only the Boreal and Austral Realm since the Turonian. Here, I present the first cladistic analysis of belemnite phylogeny, spanning taxa representative of the whole diversity and stratigraphic range of the group. This analysis shows that the usually applied subdivision of all belemnites into "Belemnitina" and "Belemnopseina" is not supported. A newly identified clade, the Pseudoalveolata, is suggested here. Pseudoalveolate belemnites represent the last remaining belemnites after the Aptian. Oceanic anoxia and warming are likely the main cause of the mid-Cretaceous belemnite decline, resulting in the Aptian-Albian dominance of the warm-adapted pseudoalveolate genus Neohibolites. The rise of teleost fish diversity during the mid-Cretaceous is discussed and its relevance for belemnite evolution. Some teleosts (e.g., Enchodus) might have taken over the mesopredator niches left by belemnites during the mid-Cretaceous, being better adapted to warming seas. Belemnites were not able to recover their earlier widespread distribution and diversity and the last remaining, disjunctly distributed families, the northern Belemnitellidae and southern Dimitobelidae, became extinct at the K/Pg-boundary.

paleontology↗