Gonzalez-Ramirez, I. S. | Search bioRxiv

bioRxiv2025

Late Cretaceous origins for major nightshade lineages from total evidence timetree analysis

Background and AimsThe timing of the radiation of nightshades (Solanaceae) has been contentious in the literature, with estimates of the crown age ranging from ca. 30 to 70 Mya (mid-Oligocene to late Cretaceous). The tempo of diversification of major lineages within the family (e.g., berries, tobaccos) has been equally challenging to resolve, in large part because of the paucity of fossil information. Recently described fossils present an opportunity to revisit the timing of nightshade diversification using more powerful model-based methods. Here, we simultaneously infer divergence times within Solanaceae and the placement of a select set of well-preserved and morphologically diverse fruit and seed fossils. MethodsWe assembled a family-wide morphological dataset, including 17 categorical and eight continuous characters, for 134 living and 14 fossil Solanaceae taxa, as well as sequence data for the extant taxa. We implemented a Bayesian total evidence dating analysis in RevBayes using (a time continuous and a time heterogeneous) fossilized birth-death model and models of character evolution for each type of data. Key ResultsThe origin of Solanaceae was [~]98 Mya, and the major splits were roughly three-fold older than previously estimated. Although the 14 fossil taxa were phylogenetically placed with different degrees of confidence, we identified a fruit fossil and a seed fossil whose affinities were strongly supported. Moreover, most of the fossils lacking a precise placement were nevertheless confidently inferred to belong to the large berry clade. ConclusionsOur study provides an example of how a sophisticated model used on a carefully assembled dataset can shed light on the timing of the evolution of a group, while accounting for phylogenetic uncertainty. The timetree we present here provides a temporal framework for further research, from comparative genomics and patterns of diversification to trait evolution and biogeography.

evolutionary biology↗

bioRxiv2024

Spatial Phylogenetics with Continuous Data: an Application to California Bryophytes

Spatial phylogenetics is premised on the idea that species are not discrete categorical entities but instead lie on a hierarchical evolutionary continuum that contains rich biological information valuable for quantifying spatial biodiversity patterns. Yet while spatial phylogenetic approaches use quantitative information to represent phylogenetic patterns, most have continued to rely on methods that discard valuable information about spatial patterns by converting continuous variables into binary categories. This includes representing geographic ranges using binary presence-absence data, classifying statistical significance into categories, and quantifying biogeographic gradients into discrete regions. In this paper we show how a full suite of spatial phylogenetic analyses, including analyses of alpha and beta diversity, neo- and paleo-endemism, biogeographic hypothesis testing, and spatial conservation prioritization, can be implemented with "smooth" methods that never remove information content by categorizing continuous data. Our analysis focuses on the bryophytes of California, an understudied group in a global plant biodiversity hotspot. Using a time-calibrated phylogeny and species distribution models for 548 species of mosses and liverworts, we profile the evolutionary diversity, compositional turnover, and conservation value of bryophyte communities across the state. Our results highlight important patterns in the diversity of this key plant group, while our methods can serve as a model for future studies seeking to maximize the information content of spatial phylogenetic analyses.

evolutionary biology↗