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Ocean currents play a significant role in driving the long-distance dispersal (LDD), spatial distribution and phylogeographic patterns of many organisms. Integrating phylogeographic analyses and mechanistic ocean current modelling can provide novel insights into the evolutionary history of terrestrial littoral species but has been rarely applied in this context. We focused on a group of Cycas that have buoyant seeds and occupy coastal habitats. By integrating evidence from mechanistic simulations and whole plastomic data, we examined the role of ocean circulation in shaping the phylogeography of these Cycas species. Plastomes of the studied Cycas species showed extreme conservatism, following a post-Pleistocene divergence. Phylogenies revealed three subclades, corresponding to the Pacific Ocean, Sunda Shelf and Indian Ocean. The ocean modelling results indicate that hotspots of seed stranding coincide well with the contemporary distribution of the Cycas species and that drifting trajectories from the three subclades are largely confined to separate regions. These findings suggest that ocean current systems, by driving long-distance dispersal, have shaped the distribution and phylogeography for Cycas with buoyant seeds. This study highlights how the combination of genomic data and ocean drift modelling can help explain phylogeographic patterns and diversity in terrestrial littoral ecosystems.

Background Plastid genomes (plastomes) present great potential in resolving multiscale phylogenetic relationship but few studies have focused on the influence of genetic characteristics of plastid genes, such as genetic variation and phylogenetic discordance, in resolving the phylogeny within a lineage. Here we examine plastome characteristics of Cycas L., the most diverse genus among extant cycads, and investigate the deep phylogenetic relationships within Cycas by sampling 47 plastomes representing all major clades from six sections. Results All Cycas plastomes shared consistent gene content and structure with only one gene loss detected in Philippine species C. wadei. Three novel plastome regions (psbA-matK, trnN-ndhF, chlL-trnN) were identified as containing the highest nucleotide variability. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection except ndhB. Phylogenomic analyses that alternatively included concatenated and coalescent methods, both identified four clades but with conflicting topologies at shallow nodes. Specifically, we found three species-rich Cycas sections, namely Stangerioides, Indosinenses and Cycas, were not or only weakly supported as monophyly based on plastomic phylogeny. Tree space analyses based on different tree-inference methods both revealed three gene clusters, of which the cluster with moderate genetic properties showed the best congruence with the favored phylogeny. Conclusions Our exploration in plastomic data for Cycas supports the idea that plastid protein-coding genes may exhibit discordance in phylogenetic signals. The incongruence between molecular phylogeny and morphological classification reported here may largely be attributed to the uniparental attribute of plastid, which cannot offer sufficient information to resolve the phylogeny. Contrasting to a previous consensus that genes with longer sequences and a higher proportion of variances are superior for phylogeny reconstruction, our result implies that the most effective phylogenetic signals could come from loci that own moderate variation, GC content, sequence length, and underwent modest selection.

Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists. The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking. The study closes an important gap in our understanding of genome structure and evolution in seed plants.

Zamia amplifolia Hort. W. Bull ex Mast., Z. roezlii Linden, and Z. wallisii A. Braun have been unnecessarily neotypified because original material exists at K or STO. Zamia oligodonta E. Calderon & D.W. Stev. is synonymized with Z. montana A. Braun. Zamia lindenii Regel ex Andre is considered specifically distinct from Z. poeppigiana Mart. & Eichler. The genus Chigua is synonymized with Zamia and the new combination Z. restrepoi (D.W. Stev.) A. Lindst. proposed, and C. bernalli D.W. Stev. is synonymized with Z. restrepoi.

Curcuma woodii, a new species of Curcuma subg. Ecomata (Zingiberaceae) from Thailand is described and illustrated here. It differs from C. rhomba by the leaf blades abaxially pubescent, the bracts whitish green, the labellum white with orange bands at the center, the lateral staminodes white with orange dots at the apex, and the ovary nearly glabrous.