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Abstract PremiseCompetition 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. MethodsWe 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. ResultsOf all native species,Doryopteris angelicahad the lowest percentage of occurrences of naturalized species in its suitable area whileD. decorahad the highest. However, allDoryopterisspp. had a higher percentage overlap, whilePellaea ternifoliahad a lower percentage overlap, than expected by chance.Doryopteris decoraandD. decipienshad the lowest proportions (<20%) of suitable area covering native habitat. DiscussionAreas 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. 

Summary The effects of single chromosome number change—dysploidy – mediating diversification remain poorly understood. Dysploidy modifies recombination rates, linkage, or reproductive isolation, especially for one‐fifth of all eukaryote lineages with holocentric chromosomes. Dysploidy effects on diversification have not been estimated because modeling chromosome numbers linked to diversification with heterogeneity along phylogenies is quantitatively challenging.We propose a new state‐dependent diversification model of chromosome evolution that links diversification rates to dysploidy rates considering heterogeneity and differentiates between anagenetic and cladogenetic changes. We apply this model toCarex(Cyperaceae), a cosmopolitan flowering plant clade with holocentric chromosomes.We recover two distinct modes of chromosomal evolution and speciation inCarex. In one diversification mode, dysploidy occurs frequently and drives faster diversification rates. In the other mode, dysploidy is rare, and diversification is driven by hidden, unmeasured factors. When we use a model that excludes hidden states, we mistakenly infer a strong, uniformly positive effect of dysploidy on diversification, showing that standard models may lead to confident but incorrect conclusions about diversification.This study demonstrates that dysploidy can have a significant role in speciation in a large plant clade despite the presence of other unmeasured factors that simultaneously affect diversification. 

Abstract Geological events such as mountain uplift affect how, when, and where species diversify, but measuring those effects is a longstanding challenge. Andean orogeny impacted the evolution of regional biota by creating barriers to gene flow, opening new habitats, and changing local climate. B⁢o⁢m⁢a⁢r⁢e⁢a (Alstroemeriaceae) are tropical plants with (often) small, isolated ranges; in total, B⁢o⁢m⁢a⁢r⁢e⁢a species occur from central Mexico to central Chile. This genus appears to have evolved rapidly and quite recently, and rapid radiations are often challenging to resolve with traditional phylogenetic inference. In this study, we apply phylogenomics—with hundreds of loci, gene-tree-based data curation, and a multispecies-coalescent approach—to infer the phylogeny of B⁢o⁢m⁢a⁢r⁢e⁢a. We use this phylogeny to untangle the potential drivers of diversification and biogeographic history. In particular, we test if Andean orogeny contributed to the diversification of B⁢o⁢m⁢a⁢r⁢e⁢a. We find that B⁢o⁢m⁢a⁢r⁢e⁢a originated in the central Andes during the mid-Miocene, then spread north, following the trajectory of mountain uplift. Furthermore, Andean lineages diversified faster than non-Andean relatives. B⁢o⁢m⁢a⁢r⁢e⁢a thus demonstrates that—at least in some cases—geological change rather than environmental stability has driven high species diversity in a tropical biodiversity hotspot. These results also demonstrate the utility (and danger) of genome-scale data for making macroevolutionary inferences. 

Abstract Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these shifts may coincide with key evolutionary events such as the development of novel morphological characters, the acquisition of adaptive traits, polyploidization or other structural genomic changes, or dispersal to a new habitat and subsequent increase in environmental niche space. However, while multiple methods now exist to estimate diversification rates and identify shifts using phylogenetic topologies, the appropriate use and accuracy of these methods are hotly debated. Here we test whether five Bayesian methods—Bayesian Analysis of Macroevolutionary Mixtures (BAMM), two implementations of the Lineage-Specific Birth–Death–Shift model (LSBDS and PESTO), the approximate Multi-Type Birth–Death model (MTBD; implemented in BEAST2), and the Cladogenetic Diversification Rate Shift model (ClaDS2)—produce comparable results. We apply each of these methods to a set of 65 empirical time-calibrated phylogenies and compare inferences of speciation rate, extinction rate, and net diversification rate. We find that the five methods often infer different speciation, extinction, and net-diversification rates. Consequently, these different estimates may lead to different interpretations of the macroevolutionary dynamics. The different estimates can be attributed to fundamental differences among the compared models. Therefore, the inference of shifts in diversification rates is strongly method dependent. We advise biologists to apply multiple methods to test the robustness of the conclusions or to carefully select the method based on the validity of the underlying model assumptions to their particular empirical system. 

Underground storage organs occur in phylogenetically diverse plant taxa and arise from multiple tissue types including roots and stems. Thickening growth allows underground storage organs to accommodate carbohydrates and other nutrients and requires proliferation at various lateral meristems followed by cell expansion. The WOX-CLE module regulates thickening growth via the vascular cambium in several eudicot systems, but the molecular mechanisms of proliferation at other lateral meristems are not well understood. In potato, onion, and other systems, members of the phosphatidylethanolamine-binding protein (PEBP) gene family induce underground storage organ development in response to photoperiod cues. While molecular mechanisms of tuber development in potato are well understood,we lack detailed mechanistic knowledge for the extensive morphological and taxonomic diversity of underground storage organs in plants. 

Recent field research on the eastern slopes of the Andes resulted in the discovery of a new species ofBomareafrom the Cerro Candelaria Reserve in the Tungurahua province of Ecuador.Bomarea pastazensisis 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).