Lorena Endara

Orchid phylogenomics and multiple drivers of their extraordinary diversification

Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras), and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp−1 My−1) is 6.8 times that at the Asparagales crown.

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield phylogenetic structure at various levels of a tree (i.e., along the spine and at the tips of the branches). Here, we demonstrate the phylogenetic utility of a heretofore unused portion of a plastid protein-coding gene, hypothetical chloroplast open reading frame 1 (ycf1), in orchids. All portions of ycf1 examined are highly variable, yet alignable across Orchidaceae, and are phylogenetically informative at the level of species. In Orchidaceae, ycf1 is more variable than matK both in total number of parsimony informative characters and in percent variability. The nrITS region is more variable than ycf1, but is more difficult to align. Although we only demonstrate the phylogenetic utility of ycf1 in orchids, it is likely to be similarly useful among other plant taxa.

MatrixConverter: Facilitating construction of phenomic character matrices.

Premise of the study: While numerous software packages enable scientists to evaluate molecular data and transform them for phylogenetic analyses, few such tools exist for phenomic data. We introduce MatrixConverter, a program that helps expedite and facilitate the transformation of raw phenomic character data into discrete character matrices that can be used in most evolutionary inference programs. Methods and Results: MatrixConverter is an open source program written in Java; a platform-independent binary executable, as well as sample data sets and a users manual, are available at https://github.com/gburleigh/MatrixConverter/tree/master/distribution. MatrixConverter has a simple, intuitive user interface that enables the user to immediately begin scoring phenomic characters. We demonstrate the performance of MatrixConverter on a phenomic data set from cycads. Conclusions: New technologies and software make it possible to obtain phenomic data from species across the tree of life, and MatrixConverter helps to transform these new data for evolutionary or ecological inference.

OTO: Ontology Term Organizer.

BackgroundThe need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most software tools for ontology construction are designed for knowledge engineers and not for domain experts to use. The differences in the opinions of different domain experts and in the terminology usages in source literature are rarely addressed by existing software.MethodsOTO software was developed based on the Agile principles. Through iterations of software release and user feedback, new features are added and existing features modified to make the tool more intuitive and efficient to use for small and large data sets. The software is open source and built in Java.ResultsOntology Term Organizer (OTO; http://biosemantics.arizona.edu/OTO/) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts’ opinions. The organized terms may be fed into formal ontologies to boost their coverage. All datasets organized on OTO are publicly available.ConclusionOTO has been used to organize the terms extracted from thirty volumes of Flora of North America and Flora of China combined, in addition to some smaller datasets of different taxon groups. User feedback indicates that the tool is efficient and user friendly. Being open source software, the application can be modified to fit varied term organization needs for different domains.

Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing

Premise of the Study Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi‐automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms. Methods and Results Our protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon‐by‐character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae. Conclusions The NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses.

Community assembly of the ferns of Florida

PREMISE OF THE STUDY Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. METHODS We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic distances and functional trait data for both spatial scales and compared the results to null models to assess significance. KEY RESULTS Our results for over vs. underdispersion in functional and phylogenetic diversity differed depending on spatial scale and metric considered. At the county scale, MPD revealed evidence for phylogenetic overdispersion, while MNTD revealed phylogenetic and functional underdispersion, and at the conservation area scale, MPD revealed phylogenetic and functional underdispersion while MNTD revealed evidence only of functional underdispersion. CONCLUSIONS Our results are consistent with environmental filtering playing a larger role at the smaller, conservation area scale. The smaller spatial units are likely composed of fewer local habitat types that are selecting for closely related species, with the larger-scale units more likely to be composed of multiple habitat types that bring together a larger pool of species from across the phylogeny. Several aspects of fern biology, including their unique physiology and water relations and the importance of the independent gametophyte stage of the life cycle, make ferns highly sensitive to local, microhabitat conditions.

New Mining Concessions Could Severely Decrease Biodiversity and Ecosystem Services in Ecuador

Ecuador has among the world’s highest biodiversity, despite being a tiny fraction of the world’s land area. The threat of extinction for some of this biodiversity has dramatically increased since April 2016, during which time the Ecuadorian government has opened around 13% of the country to mining exploration, with many of the concessions in previously protected forests. Herein, we describe the system of protected lands in Ecuador, their mining laws, and outline the scale of threat by comparing the mammals, amphibians, reptiles, birds, and orchids from several now threatened protected areas, classed as “Bosques Protectores,” in the northwestern montane cloud forests. Together, these reserves form a buffer and a southern corridor for the still-protected Cotacachi-Cayapas Ecological Reserve, which is otherwise now surrounded by mining concessions. We gathered published literature, “gray literature,” information from reserve records and websites, and our previously unpublished observations to make comparative species tables for each reserve. Our results reveal the potential losses that mining could cause: eight critically endangered species, including two primates (brown-headed spider monkey and white-fronted capuchin), 37 endangered species, 153 vulnerable, 89 near threatened, and a large number of less threatened species. Our data show that each reserve protects a unique subset of taxa in this region of highly localized endemics and the reserves also generate sustainable income for local people. The short-term national profits from mining will not compensate for the permanent biodiversity losses, and the long-term ecosystem service and economic losses at the local and regional level.