Lessons learned from organizing and teaching virtual phylogenetics workshops

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The Liliid and the Oddity: Macroevolution and development of underground storage organs in the order Liliales

Traditional botany focuses on the morphology, anatomy, and evolution of above-ground plant parts, but remarkable variation also exists underground. Underground storage organs (USOs), one example of understudied underground botany, include corms, bulbs, rhizomes, and stem- and root-derived tubers. These odd organs characterize geophytes, plants that produce perennating buds below ground and often store nutrients such as starch and water in USOs. Diverse underground morphology is particularly evident in the monocotyledenous order Liliales.In this dissertation, I examine the evolution and development of USOs across the order Liliales, or the ’liliids’. In Chapter 1, I take a macroevolutionary perspective to ask if plants with different USOs are evolving towards different climatic niche adaptive peaks across the order. I find that the presence of root tubers, especially rotund root tubers, is associated with lower temperature seasonality. Furthermore, I develop and describe a new analysis pipeline in statistical comparative phylogenetics for testing adaptive hypotheses. In Chapter 2, I zoom in on a particular liliid geophyte, Bomarea multiflora, to identify genes underlying root tuber formation by comparing the transcriptomes of root tubers vs. fibrous roots. I compare the genes identified in this study with patterns from USOs produced by other taxa to characterize to what extent processes are shared across non-homologous USOs and across deep evolutionary divergences. I find that many processes are shared despite these differences, indicating that parallel molecular mechanisms may underlie USO development. In Chapter 3, I describe a new R package, RevGadgets, that can process and visualize the output of complex phylogenetic analyses from the RevBayes phylogenetic graphical modelling software. RevGadgets is designed to provide user-friendly modular workflows and thus increase accessibility to more complex phylogenetic models. I illustrate core RevGadgets functionality through six use cases and provide examples of code and resulting figures.Together, these projects bring light to the outstanding diversity of below ground forms and begin the work of characterizing the evolution and development of this diversity. This work also illustrates the utility of establishing reproducible and user-friendly pipelines to increase the accessibility and versatility of complex statistical methods in comparative biology

The Liliid and the Oddity: Macroevolution and development of underground storage organs in the order Liliales

Traditional botany focuses on the morphology, anatomy, and evolution of above-ground plant parts, but remarkable variation also exists underground. Underground storage organs (USOs), one example of understudied underground botany, include corms, bulbs, rhizomes, and stem- and root-derived tubers. These odd organs characterize geophytes, plants that produce perennating buds below ground and often store nutrients such as starch and water in USOs. Diverse underground morphology is particularly evident in the monocotyledenous order Liliales.In this dissertation, I examine the evolution and development of USOs across the order Liliales, or the ’liliids’. In Chapter 1, I take a macroevolutionary perspective to ask if plants with different USOs are evolving towards different climatic niche adaptive peaks across the order. I find that the presence of root tubers, especially rotund root tubers, is associated with lower temperature seasonality. Furthermore, I develop and describe a new analysis pipeline in statistical comparative phylogenetics for testing adaptive hypotheses. In Chapter 2, I zoom in on a particular liliid geophyte, Bomarea multiflora, to identify genes underlying root tuber formation by comparing the transcriptomes of root tubers vs. fibrous roots. I compare the genes identified in this study with patterns from USOs produced by other taxa to characterize to what extent processes are shared across non-homologous USOs and across deep evolutionary divergences. I find that many processes are shared despite these differences, indicating that parallel molecular mechanisms may underlie USO development. In Chapter 3, I describe a new R package, RevGadgets, that can process and visualize the output of complex phylogenetic analyses from the RevBayes phylogenetic graphical modelling software. RevGadgets is designed to provide user-friendly modular workflows and thus increase accessibility to more complex phylogenetic models. I illustrate core RevGadgets functionality through six use cases and provide examples of code and resulting figures.Together, these projects bring light to the outstanding diversity of below ground forms and begin the work of characterizing the evolution and development of this diversity. This work also illustrates the utility of establishing reproducible and user-friendly pipelines to increase the accessibility and versatility of complex statistical methods in comparative biology

Bomarea pastazensis (Alstroemeriaceae), an exceptionally small new species from the eastern Andean slopes of Ecuador

Recent field research on the eastern slopes of the Andes resulted in the discovery of a new species of Bomarea from the Cerro Candelaria Reserve in the Tungurahua province of Ecuador. Bomarea pastazensis is the second smallest species in the genus and differs from the smallest by the presence of glutinous trichomes on the ovary, glabrous sepals, and greenish-yellow petals with purple spots. Based on IUCN guidelines, a preliminary conservation status is assigned as Vulnerable (VU)

Conservation applications of niche modeling: Native and naturalized ferns may compete for limited Hawaiian dryland habitat

Abstract Premise Competition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land‐use change and competition from naturalized species in determining habitat availability. Methods We used fine‐resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantified the degree to which naturalized ferns tend to occupy areas suitable for native species and mapped the remaining available habitat given land‐use change. Results Of all native species, Doryopteris angelica had the lowest percentage of occurrences of naturalized species in its suitable area while D. decora had the highest. However, all Doryopteris spp. had a higher percentage overlap, while Pellaea ternifolia had a lower percentage overlap, than expected by chance. Doryopteris decora and D. decipiens had the lowest proportions (<20%) of suitable area covering native habitat. Discussion Areas characterized by shared environmental preferences of native and naturalized ferns may decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of place‐based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem

RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes

10.1111/2041-210X.13750METHODS IN ECOLOGY AND EVOLUTION132314-32

Lessons learned from organizing and teaching virtual phylogenetics workshops

In 2020 and 2021, the COVID-19 pandemic led to an abrupt overhaul of many academic practices, including the transition of scientific events, such as workshops, to a fully virtual format. We describe our experiences organizing and teaching online-only statistical phylogenetics workshops and the lessons we learned along the way. We found that online workshops present some specific challenges, but format choices and rigorous planning can alleviate many of the concerns typically associated with a virtual medium. In addition, online workshops have unique advantages such as the flexibility they offer to participants and instructors and their accessibility to non-traditional and underprivileged audiences. We hope that our experience will encourage workshop organizers to consider online-only events as an integral part of potential training opportunities rather than simply a stop-gap solution for unusual circumstances. In addition, we hope to prompt broader discussion about integrating aspects of online workshops into traditional in-person courses to make training opportunities more flexible and inclusive.This preprint is made available through EcoEvoRxiv Preprints at doi:10.32942/osf.io/kp8sz. Posted with permission. CC-By Attribution-ShareAlike 4.0 Internationa