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Abstract Nitrogen (N)-fixing symbiosis is critical to terrestrial ecosystems, yet possession of this trait is known for few plant species. Broader presence of the symbiosis is often indirectly determined by phylogenetic relatedness to taxa investigated via manipulative experiments. This data gap may ultimately underestimate phylogenetic, spatial, and temporal variation in N-fixing symbiosis. Still needed are simpler field or collections-based approaches for inferring symbiotic status. N-fixing plants differ from non-N-fixing plants in elemental and isotopic composition, but previous investigations have not tested predictive accuracy using such proxies. Here we develop a regional field study and demonstrate a simple classification model for fixer status using nitrogen and carbon content measurements, and stable isotope ratios (δ¹⁵N and δ¹³C), from field-collected leaves. We used mixed models and classification approaches to demonstrate that N-fixing phenotypes can be used to predict symbiotic status; the best model required all predictors and was 80–94% accurate. Predictions were robust to environmental context variation, but we identified significant variation due to native vs. non-native (exotic) status and phylogenetic affinity. Surprisingly, N content—not δ¹⁵N—was the strongest predictor, suggesting that future efforts combine elemental and isotopic information. These results are valuable for understudied taxa and ecosystems, potentially allowing higher-throughput field-based N-fixer assessments. 

Abstract PremiseEndophytic plant‐microbe interactions range from mutualistic relationships that confer important ecological and agricultural traits to neutral or quasi‐parasitic relationships. In contrast to root‐associated endophytes, the role of environmental and host‐related factors in the acquisition of leaf endophyte communities at broad spatial and phylogenetic scales remains sparsely studied. We assessed endofoliar diversity to test the hypothesis that membership in these microbial communities is driven primarily by abiotic environment and host phylogeny. MethodsWe used a broad geographic coverage of North America in the genusHeucheraL. (Saxifragaceae), representing 32 species and varieties across 161 populations. Bacterial and fungal communities were characterized using 16S and ITS amplicon sequencing, respectively, and standard diversity metrics were calculated. We assembled environmental predictors for microbial diversity at collection sites, including latitude, elevation, temperature, precipitation, and soil parameters. ResultsAssembly patterns differed between bacterial and fungal endophytes. Host phylogeny was significantly associated with bacteria, while geographic distance was the best predictor of fungal community composition. Species richness and phylogenetic diversity were consistent across sites and species, with only fungi showing a response to aridity and precipitation for some metrics. Unlike what has been observed with root‐associated microbial communities, in this system microbes show no relationship with pH or other soil factors. ConclusionsOverall, this work improves our understanding of the large‐scale patterns of diversity and community composition in leaf endophytes and highlights the relative significance of environmental and host‐related factors in driving different microbial communities within the leaf microbiome. 

Abstract PremisePlant trait data are essential for quantifying biodiversity and function across Earth, but these data are challenging to acquire for large studies. Diverse strategies are needed, including the liberation of heritage data locked within specialist literature such as floras and taxonomic monographs. Here we report FloraTraiter, a novel approach using rule‐based natural language processing (NLP) to parse computable trait data from biodiversity literature. MethodsFloraTraiter was implemented through collaborative work between programmers and botanical experts and customized for both online floras and scanned literature. We report a strategy spanning optical character recognition, recognition of taxa, iterative building of traits, and establishing linkages among all of these, as well as curational tools and code for turning these results into standard morphological matrices. ResultsOver 95% of treatment content was successfully parsed for traits with <1% error. Data for more than 700 taxa are reported, including a demonstration of common downstream uses. ConclusionsWe identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open‐source trait data sets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale. 

ABSTRACT Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages ofQuercusand relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages ofQuercusand relatives in Quercoideae during their initial radiation, dated to the Early‐Middle Eocene. Ancestral reconstructions including fossils suggest ancestors ofCastanea + Castanopsis,Lithocarpus, and the Old World oak clade probably co‐occurred in North America and Eurasia, while the ancestors ofChrysolepis, Notholithocarpus, and the New World oak clade co‐occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups. 

Abstract PremiseAstragalus(Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid‐adapted clade and what sets it apart from close relatives with far less species richness. MethodsHere, for the first time using extensive phylogenetic sampling, we asked whether (1)Astragalusis uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity ofAstragalusis attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whetherAstragalusoriginated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents. ResultsOur results point to the importance of heterogeneity in the diversification ofAstragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway. ConclusionsOur investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging “mega‐radiations.” Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species‐rich clades. 

Abstract Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.] 

Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality (“greenness”) as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies. 

Abstract Old, climatically buffered, infertile landscapes (OCBILs) have been hypothesized to harbour an elevated number of persistent plant lineages and are predicted to occur across different parts of the globe, interspersed with other types of landscapes. We tested whether the mean age of a plant community is associated with occurrence on OCBILs, as predicted by climatic stability and poor soil environments. Using digitized occurrence data for seed plants occurring in Australia (7033 species), sub-Saharan Africa (3990 species) and South America (44 482 species), regions that comprise commonly investigated OCBILs (Southwestern Australian Floristic Region, Greater Cape Floristic Region and campos rupestres), and phylogenies pruned to match the species occurrences, we tested for associations between environmental data (current climate, soil composition, elevation and climatic stability) and two novel metrics developed here that capture the age of a community (mean tip length and mean node height). Our results indicate that plant community ages are influenced by a combination of multiple environmental predictors that vary globally; we did not find statistically strong associations between the environments of OCBIL areas and community age, in contrast to the prediction for these landscapes. The Cape Floristic Region was the only OCBIL that showed a significant, although not strong, overlap with old communities.