• Mining threatens Colombian ecosystems

      Pérez-Escobar, Oscar Alejandro; Cámara-Leret, Rodrigo; Antonelli, Alexandre; Bateman, Richard M.; Bellot, Sidonie; Chomicki, Guillaume; Cleef, Antoine; Diazgranados, Mauricio; Dodsworth, Steven; Jaramillo, Carlos; et al. (American Association for the Advancement of Science, 2018-03-30)
    • The origin and diversification of the hyperdiverse flora in the Chocó biogeographic region

      Pérez-Escobar, Oscar Alejandro; Lucas, Eve; Jaramillo, Carlos; Monro, Alexandre; Morris, Sarah K.; Bogarín, Diego; Greer, Deborah; Dodsworth, Steven; Aguilar-Cano, José; Sanchez Meseguer, Andrea; et al. (Frontiers, 2019-12-06)
      Extremely high levels of plant diversity in the American tropics are derived from multiple interactions between biotic and abiotic factors. Previous studies have focused on macro-evolutionary dynamics of the Tropical Andes, Amazonia, and Brazil’s Cerrado and Atlantic forests during the last decade. Yet, other equally important Neotropical biodiversity hotspots have been severely neglected. This is particularly true for the Chocó region on the north-western coast of South and Central America. This geologically complex region is Earth’s ninth most biodiverse hotspot, hosting approximately 3% of all known plant species. Here, we test Gentry’s [1982a,b] hypothesis of a northern Andean-Central American Pleistocene origin of the Chocoan flora using phylogenetic reconstructions of representative plant lineages in the American tropics. We show that plant diversity in the Chocó is derived mostly from Andean immigrants. Contributions from more distant biogeographical areas also exist but are fewer. We also identify a strong floristic connection between the Chocó and Central America, revealed by multiple migrations into the Chocó during the last 5 Ma. The dated phylogenetic reconstructions suggest a Plio-Pleistocene onset of the extant Chocó flora. Taken together, these results support to a limited extend Gentry’s hypothesis of a Pleistocene origin and of a compound assembly of the Chocoan biodiversity hotspot. Strong Central American–Chocoan floristic affinity may be partly explained by the accretion of a land mass derived from the Caribbean plate to north-western South America. Additional densely sampled phylogenies of Chocoan lineages also well represented across the Neotropics could enlighten the role of land mass movements through time in the assembly of floras in Neotropical biodiversity hotspots.
    • Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

      Serna-Sánchez, Maria Alejandra; Pérez-Escobar, Oscar A.; Bogarín, Diego; Torres-Jimenez, María Fernanda; Alvarez-Yela, Astrid Catalina; Arcila-Galvis, Juliana E.; Hall, Climbie F.; de Barros, Fábio; Pinheiro, Fábio; Dodsworth, Steven; et al. (SpringerNature, 2021-03-25)
      Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
    • A roadmap for global synthesis of the plant tree of life

      Eiserhardt, Wolf L.; Antonelli, Alexandre; Bennett, Dominic J.; Botigue, Laura R.; Burleigh, J. Gordon; Dodsworth, Steven; Enquist, Brian J.; Forest, Felix; Kim, Jan T.; Kozlov, Alexey M.; et al. (Wiley, 2018-03-31)
      Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.