The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates

Decoding deception: the binding affinity of cuttlefish ink on shark smell receptors

Chemical signaling can play a crucial role in predator-prey dynamics. Here, we present evidence that ink from the common cuttlefish (Sepia officinalis) targets olfactory receptor proteins in sharks, potentially acting as a predator deterrent. We apply in silico 3D docking analysis to investigate the binding affinity of various odorant molecules to shark olfactory receptors of 2 shark species: cloudy catshark (Scyliorhinus torazame) and white shark (Carcharodon carcharias). Pavoninin-4 (a known shark repellent compound) displayed selectivity in binding to receptors in the white shark. In contrast, the primary component of cuttlefish ink, melanin, displayed the highest binding affinities to all shark olfactory receptor proteins in both species. Taurine, another important ink component, exhibited standard to strong bindings for both species. Trans-4,5-epoxy-(E)-2-decenal ("blood decenal"), an odorant associated with the smell of blood, displayed strong binding affinities to all shark olfactory receptors, similar to that of melanin. These findings provide new insights into the molecular interplay between cephalopod inking behavior and their shark predators, with cuttlefish ink likely exploiting the narrow band of the shark olfactory repertoire.

A timescale for placental mammal diversification based on Bayesian modeling of the fossil record

The timing of the placental mammal radiation has been the focus of debate over the efficacy of competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that placental mammals originated before the Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from the Late Cretaceous to the Jurassic. However, the absence of definitive fossils of placentals before the K-Pg boundary is compatible with a post-Cretaceous origin. Nevertheless, lineage divergence must occur before it can be manifest phenotypically in descendent lineages. This, combined with the non-uniformity of the rock and fossil records, requires the fossil record to be interpreted rather than read literally. To achieve this, we introduce an extended Bayesian Brownian bridge model that estimates the age of origination and, where applicable, extinction through a probabilistic interpretation of the fossil record. The model estimates the origination of placentals in the Late Cretaceous, with ordinal crown groups originating at or after the K-Pg boundary. The results reduce the plausible interval for placental mammal origination to the younger range of molecular clock estimates. Our findings support both the Long Fuse and Soft Explosive models of placental mammal diversification, indicating that the placentals originated shortly prior to the K-Pg mass extinction. The origination of many modern mammal lineages overlapped with and followed the K-Pg mass extinction.

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.