The evolutionary history of vines in a neotropical biodiversity hotspot: Phylogenomics and biogeography of a large passion flower clade (Passiflora section Decaloba)

Pliocene seeds of Passiflora subgenus Decaloba (Gray Fossil Site, Tennessee) and the impact of the fossil record on understanding the diversification and biogeography of Passiflora

PREMISE

Passiflora is a diverse genus of ~570 extant species primarily distributed in the Americas, from the eastern United States to Argentina and Chile. Nevertheless, the known fossil record of Passiflora is small. To date, only two fossil seed species have been unequivocally assigned to the genus. In this contribution, rare sulcate seeds from Gray Fossil Site are described as a third fossil seed species of Passiflora.

METHODS

Three partial seeds with sulcate sculpture from Gray Fossil Site, early Pliocene, Tennessee, USA, were examined, photographed, and measured. They were compared to samples of sulcate seeds from six extant Passiflora species in supersection Decaloba. A broader survey of sulcate seeds produced by modern species in the subgenera Decaloba, Deidamioides, and Tryphostemmatoides was done using published illustrations and descriptions.

RESULTS

The Gray Fossil Site seeds are described as Passiflora sulcatasperma, sp. nov., and assigned to subgenus Decaloba, supersection Decaloba. They are characterized by their small size, elliptical shape, ridged-and-sulcate sculpture, rugulose ridges, and thin palisade seed coat.

CONCLUSIONS

The two largest subgenera of Passiflora can be identified from Neogene fossils. Subgenus Decaloba is represented by two fossil seed species, P. bulgarica (Miocene, Bulgaria) and P. sulcatasperma (Pliocene, USA). Subgenus Passiflora is represented by fossil pollen (Miocene, Argentina and Brazil) and P. appalachiana seeds (Pliocene, USA). The distributions of fossil and modern species suggest that Passiflora may have used both North Atlantic and Antarctic routes to expand into Europe and the Asian-Oceanian Paleotropics, respectively.

Phylogenomics and the flowering plant tree of life

The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.

Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation

BACKGROUND AND AIMS

The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centred rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution.

METHODS

Targeted sequence capture using a probe-set recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance.

KEY RESULTS

While silica-dried leaf tissue resulted in longer assembled sequence data, the inclusion of herbarium samples improved taxonomic representation. Relationships among baccate lineages are similar to those inferred in previous studies, although they differ for lineages within and among capsular clades. We improve the phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant.

CONCLUSIONS

This first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict and well-supported differences between analyses based on different nuclear loci. Together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is probably present in many other species-rich Andean plant radiations.

Estimation of Current and Future Suitable Areas for Tapirus pinchaque in Ecuador

At present, climate change is a direct threat to biodiversity and its effects are evidenced by an increasingly accelerated loss of biodiversity. This study identified the main threats presently facing the Tapirus pinchaque species in Ecuador, generated predictive models regarding its distribution, and analyzed the protected areas as a conservation tool. The methodology was based on a literature review and the application of binary predictive models to achieve these objectives. The main results indicate that the T. pinchaque is seriously threatened, mainly by changes in land use. In addition, three models were selected that show current and future suitable areas for the conservation of the species. Its current distribution amounts to 67,805 km2, 33% (22,872 km2) of which is located in 31 of the 61 protected areas. Finally, it is important to take timely actions focused on biodiversity conservation, considering the importance of balance in ecosystems to the humans dependent thereof, and the results regarding the changes in the current and future distribution areas of the mountain tapir are a great contribution to be used as a management tool for its conservation.