Transcriptome sequencing data provides a solid base to understand the phylogenetic relationships, biogeography and reticulated evolution of the genus Zamia L. (Cycadales: Zamiaceae).

Background and aims: Cycad is a key lineage to understand the early evolution of seed plants and their response to past environmental changes. However, tracing the evolutionary trajectory of cycad species is challenging when the robust relationships at inter- or infrageneric level are not well resolved.

Methods: Here, using 2,901 single-copy nuclear genes, we explored the species relationships and gene flow within the second largest genus of cycads, i.e., Zamia, based on phylotranscriptomic analyses of 90% extant Zamia species. Based on a well-resolved phylogenetic framework, we performed gene flow analyses, molecular dating, and biogeographical reconstruction to examine the spatiotemporal evolution of Zamia. We also performed ancestral state reconstruction (ASR) of a total of 62 traits of the genus to comprehensively investigate its morphological evolution.

Key results: Zamia is comprised of seven major clades corresponding to seven distinct distribution areas in the Americas, with at least three reticulation nodes revealed in this genus. Extant lineages of Zamia initially diversified around 18.4-32.6 (29.14) million years ago (MA) in the Mega-Mexico, and then expanded eastward into the Caribbean and southward into Central and South America. ASR revealed homoplasy in most of the morphological characters.

Conclusions: This study revealed congruent phylogenetic relationships from comparative methods/datasets, with some conflicts being the result of incomplete lineage sorting and ancient/recent hybridization events. The strong association between the clades and the biogeographic areas suggested that ancient dispersal events shaped the modern distribution pattern, and regional climatic factors may have resulted in the following in-situ diversification. Climate cooling starting during the mid Miocene is associated with the global expansion of Zamia to the tropical South America that have dramatically driven lineage diversification in the New World flora, as well as the extinction of cycad species in the nowadays cooler regions of both hemispheres as indicated by the fossil records.