Biology subjects

Gardner, E. M.

Publications and source records attributed to Gardner, E. M..

3 recordsLinked to original sources

bioRxiv2020

Phylogenomics of Brosimum Sw. (Moraceae) and allied genera, including a revised subgeneric system

We present a phylogenomic study of Brosimum and the allied genera Trymatococcus and Helianthostylis, with near-complete taxon sampling. Distributed from Mexico and the Greater Antilles to the Amazon, this clade contains the underutilized crop ramon (bread nut) (Brosimum alicastrum) as well as other species valued for timber or medicinal uses. Target enrichment for 333 genes produced a well-resolved phylogenetic tree and showed that Trymatoccocus and Helianthostylis are nested within Brosimum. We present a revised subgeneric classification of Brosimum based on phylogenetic and morphological considerations, including the reduction of Trymatococcus and Helianthostylis to subgenera. The monophyletic subgenera can be diagnosed based on stipule, pistillode, and cotyledon synapomorphies. Divergence date estimates suggest a Miocene origin for Brosimum, and ancestral area reconstruction indicated that all four subgenera originated and initially diversified in Amazonia before dispersing into other parts of South and Central America. ResumenPresentamos un estudio filogenomico del genero Brosimum y sus aliados, Trymatococcus y Helianthostylis, y que incluye practicamente todas las especies descritas. Su distribucion va desde Mexico y las Antillas Mayores hasta el Amazonas y comprende especies como el ramon (B. alicastrum), un cultivo infrautilizado, y otras especies empleadas como madera o en medicina. La secuenciacion masiva dirigida de 333 marcadores nucleares de copia unica permitio la reconstruccion de una filogenia bien resuelta, en la que se demuestra que Trymatococcus y Helianthostylis estan anidados en Brosimum. Presentamos, por lo tanto, una clasificacion revisada a nivel de especies, teniendo en cuenta los resultados moleculares y las caracteristicas morfologicas, y donde Trymatococcus y Helianthostylis pasan a ser subgeneros de Brosimum. Estos subgeneros monofileticos pueden ser identificados por caracteres de las estipulas y de los pistilodios.

plant biology↗

bioRxiv2020

Repeated parallel losses of inflexed stamens in Moraceae: phylogenomics and generic revision of the tribe Moreae and the reinstatement of the tribe Olmedieae (Moraceae)

We present a densely-sampled phylogenomic study of the mulberry tribe (Moreae, Moraceae), an economically important clade with a global distribution, revealing multiple losses of inflexed stamens, a character traditionally used to circumscribe Moreae. Inflexed stamens facilitate ballistic pollen release and are associated with wind pollination, and the results presented here suggest that losses of this character state may have evolved repeatedly in Moraceae. Neither Moreae nor several of its major genera (Morus, Streblus, Trophis) were found to be monophyletic. A revised system for a monophyletic Moreae is presented, including the reinstatement of the genera Ampalis, Maillardia, Taxotrophis, and Paratrophis, and the recognition of the new genus Afromorus, based on Morus subgenus Afromorus. Pseudostreblus is reinstated and transferred to the Parartocarpeae, and Sloetiopsis is reinstated and transferred to the Dorstenieae. The tribe Olmediae is reinstated, replacing the Castilleae, owing to the reinstatement of the type genus Olmedia, and its exclusion from Moreae. Streblus s.s. is excluded from Moreae and transferred to the Olmediae, which is characterized primarily by involucrate inflorescences without regard to stamen position. Eight new combinations are made.

plant biology↗

bioRxiv2019

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.

evolutionary biology↗