Search for: All records

Summary Natural history collections (NHCs) are essential for studying biodiversity. Although spatial, temporal, and taxonomic biases in NHCs affect analyses, the influence of collector practices on biases remains largely unexplored.We utilized one million digitized specimens collected in the northeastern United States byc.10 000 collectors to investigate how collector practices shape spatial, temporal, and taxonomic biases in NHCs; and similarities and differences between practices of more‐ and less‐prolific collectors.We identified six common collector practices, or collection norms: collectors generally collected different species, from multiple locations, from sites sampled by others, during the principal growing season, species identifiable outside peak collecting months, and species from species‐poor families and genera. Some norms changed over decades, with different taxa favored during different periods. Collection norms have increased taxonomic coverage in NHCs; however, collectors typically avoided large, taxonomically complex groups, causing their underrepresentation in NHCs. Less‐prolific collectors greatly enhanced coverage by collecting during more months and from less‐sampled locations.We assert that overall collection biases are shaped by shared predictable collection norms rather than random practices of individual collectors. Predictable biases offer an opportunity to more effectively address biases in future biodiversity models. 

Abstract PremisePteridophytes—vascular land plants that disperse by spores—are a powerful system for studying plant evolution, particularly with respect to the impact of abiotic factors on evolutionary trajectories through deep time. However, our ability to use pteridophytes to investigate such questions—or to capitalize on the ecological and conservation‐related applications of the group—has been impaired by the relative isolation of the neo‐ and paleobotanical research communities and by the absence of large‐scale biodiversity data sources. MethodsHere we present the Pteridophyte Collections Consortium (PCC), an interdisciplinary community uniting neo‐ and paleobotanists, and the associated PteridoPortal, a publicly accessible online portal that serves over three million pteridophyte records, including herbarium specimens, paleontological museum specimens, and iNaturalist observations. We demonstrate the utility of the PteridoPortal through discussion of three example PteridoPortal‐enabled research projects. ResultsThe data within the PteridoPortal are global in scope and are queryable in a flexible manner. The PteridoPortal contains a taxonomic thesaurus (a digital version of a Linnaean classification) that includes both extant and extinct pteridophytes in a common phylogenetic framework. The PteridoPortal allows applications such as greatly accelerated classic floristics, entirely new “next‐generation” floristic approaches, and the study of environmentally mediated evolution of functional morphology across deep time. DiscussionThe PCC and PteridoPortal provide a comprehensive resource enabling novel research into plant evolution, ecology, and conservation across deep time, facilitating rapid floristic analyses and other biodiversity‐related investigations, and providing new opportunities for education and community engagement. 

Abstract Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods^1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome^3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins^5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes⁸. This 15-fold increase in genus-level sampling relative to comparable nuclear studies⁹provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade. 

PremiseComprising five families that vastly differ in species richness—ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species—members of the Gentianales are often among the most species‐rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family‐level relationships within Gentianales have been presented in previous studies. MethodsHere we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off‐target reads for most taxa and infer phylogenetic trees for comparison with the nuclear‐derived trees. ResultsWe recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order’s classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). ConclusionsThe higher‐level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.