Cornwell, W. | bioRxiv Science

bioRxiv2024

APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census

Here we present "APCalign", an R package and accompanying browser-sourced application to align and update scientific names for Australian vascular plants to the most likely currently accepted name using the Australian Plant Census (APC) or a name in the Australian Plant Names Index (APNI). Scientific names are the label assigned to unique taxon concepts by the scientific community, but this common terminology is most useful if a taxon concept is consistently referred to by the same name. These links can be broken due to either spelling mistakes or taxonomic changes. Automated tools are required to resolve taxon lists, aligning and updating long lists of possibly erroneous scientific names to the most likely currently accepted names. It is essential that tools specific to the APC/APNI be developed, as these lists specify an endorsed national-level nomenclature used in government legislation and include the uniquely Australian concept of phrase names, absent in global taxonomic datasets. To align input names to names within the APC or APNI, "APCalign" works progressively through a sequence of checks that combine different permutations of the input name, exact versus fuzzy matches, matches that consider the entire name input versus a subset of words, and character strings that indicate a name can only be resolved to a genus or family. The aligned names are then, when possible, updated to a currently accepted taxon concept within the APC. This package should facilitate all research outputs that require diverse scientific name lists to be merged or outdated lists to be updated.

plant biology↗

bioRxiv2023

Insects pollinated flowering plants for most of angiosperm evolutionary history

O_LIPollination is a fundamental process driving the speciation of angiosperms (flowering plants). Most contemporary angiosperms are insect pollinated, but abiotic pollination by wind or water and vertebrate pollination by birds or mammals occurs in many lineages. We model the evolution of pollination across angiosperms and quantify the timing and environmental associations of pollination shifts. C_LIO_LIWe use a robust dated phylogeny and trait-independent species-level sampling across all families of angiosperms to model the evolution of pollination modes. Data on the pollination system or syndrome of 1160 species were collated from primary literature. C_LIO_LIAngiosperms were ancestrally insect pollinated, and insects have pollinated angiosperms for approximately 86% of angiosperm evolutionary history. Wind pollination evolved at least 42 times, with few reversals back to animal pollination. Transitions between insect and vertebrate pollination were more frequent: vertebrate pollination evolved at least 39 times from an insect pollinated ancestor with at least 26 reversals. The probability of wind pollination increases with habitat openness (measured by Leaf Area Index) and with distance from the equator. C_LIO_LIOur reconstruction of pollination across angiosperms sheds light on a key question in angiosperm macroevolution, highlighting the long history of interactions between insect pollinators and angiosperms still vital to global biodiversity today. C_LI

evolutionary biology↗