Biology subjects

Guralnick, R. P.

Publications and source records attributed to Guralnick, R. P..

At least 19 recordsLinked to original sources

bioRxiv2026

Conservation of declining Florida ecosystems is critical for an at-risk butterfly

Assessing the availability of protected habitats for at-risk species is needed to determine how the spatial distribution of land cover and land use shapes conservation outcomes. The Loammi skipper (Atrytonopsis loammi) is a nonmigratory, prairie-associated butterfly that has experienced a significant reduction in its formerly widespread southeastern United States distribution over the past several decades. Observations in recent years have been limited to a small number of isolated Florida populations, and it is unclear how much suitable habitat remains and what proportion of that habitat is protected. Here we used publicly available community science data and collected specimens to identify the predominant land cover types occupied by A. loammi. We then quantified the extent to which each of these land cover types overlap with protected areas to estimate the proportion of the butterflys current distribution that occurs on managed conservation lands. Our findings show that A. loammi relies heavily on protected lands, with over half of the total area of the most strongly associated habitats located within protected areas. Given the continued expansion of human-modified landscapes in Florida and the reliance of A. loammi on protected lands, the long-term persistence of A. loammi will likely depend on the conservation and effective management of its remaining suitable habitat. Implications for insect conservationOur results highlight the critical role of protected areas in sustaining at-risk insect populations, particularly for species with limited dispersal and shrinking ranges. More broadly, they suggest that conserving and restoring protected habitats while maintaining connectivity are essential strategies for effective insect conservation in rapidly developing regions.

ecology↗

bioRxiv2026

Large-scale atmospheric circulation cells regulate migratory dynamics of the iconic monarch butterfly

Understanding the impacts of climate on migratory dynamics is a priority for global change research, especially as phenological mismatches have been identified as a primary concern for long-distance migration. The eastern monarch (Danaus plexippus) is a flagship species for insect migration, but there has been surprisingly little research on their spring and summer migratory timing and mismatches with their key breeding resources. We show that spring, but not summer, phenological mismatch with their milkweed host plants has the potential to be a limiting factor in the eastern monarchs yearly population growth. To better understand arrival at their breeding grounds, we developed models specifically to tease apart the factors that push (from departure grounds), pull (towards arrival grounds), or facilitate flow (in the flight corridor) during migration. We found wind (flow) dynamics to be the most important factor associated with arrival timing, especially in spring. Further, we show how spring and summer migratory flyways coincide with the large-scale Hadley and Ferrel atmospheric cells respectively, and how their dynamics appear to be essential for understanding monarch migratory timing.

ecology↗

bioRxiv2026

"Fuzzy specificity" shapes diazotroph diversity and composition in nodulating plants of the Southeastern USA

Nitrogen-fixing symbioses, particularly those occurring in root nodules, are among the most consequential mutualisms in natural and agricultural systems and represent a globally important source of bioavailable nitrogen. Despite their importance, patterns of diversity and composition among diazotrophic symbionts--and the processes structuring those patterns in natural systems--remain poorly resolved, with competing hypotheses emphasizing ecological, or phylogenetic constraints on host-symbiont associations. Here, using a broad survey of nodulating plants from the southeastern United States, we examine how diazotrophic symbiont communities vary across host plant phylogeny, habitat context, and geographic origin. We find that host phylogeny is the primary determinant of symbiont composition, outweighing effects of fine-scale taxonomic identity. Symbiont associations are therefore structured mainly at deeper phylogenetic levels, consistent with phylogenetically constrained, or "fuzzy," host specificity. Likewise, nodule community diversity--potentially reflecting variation in host control over infection--differs primarily among higher-level clades rather than among closely related taxa. Habitat context also shapes nodule communities, but its influence is secondary and most evident in undisturbed environments. As well, nonnative legumes harbor distinct symbiont assemblages despite occupying similar habitats, whereas distantly related legume clades share symbionts across habitats, highlighting interactions among phylogeny, ecology, and geographic history. Overall, our results show that host phylogeny exerts the strongest influence on nodule microbial communities, likely reflecting evolutionary divergence in symbiotic function across major host lineages.

ecology↗

bioRxiv2026

Endangered Species Act listing is linked with greater research effort for U.S. butterflies

Conservation strategies for at-risk species can be aided significantly by research on topics such as ecology, life history, and threats, yet research effort is lacking for many species facing elevated extinction risk. Here we investigated whether listing under the U.S. Endangered Species Act (ESA) was associated with research effort for U.S. butterflies, and whether that effort was higher before or after ESA listing. We found that ESA-listed species had significantly more peer-reviewed publications than non-listed species after accounting for species range and taxonomic family. Further, we showed that more papers were published per year after ESA listing than before. These findings confirm that ESA-listed species benefit from greater research attention that can support data-informed conservation efforts. However, the relative scarcity of studies prior to ESA listing, as well as the lack of research for many unlisted, at-risk taxa, underscores the need for proactive, strategic research effort to inform conservation action.

zoology↗

bioRxiv2026

Local interaction networks reconstructed from global biodiversity data improve pollinator restoration decision making

Global pollinator declines threaten the health of ecosystems and food systems, underscoring the urgency of conservation actions such as habitat restoration. However, data gaps on plant use among pollinators continue to limit reliable design of restoration plant mixes. To address this, we present NECTAR (Network-Enhanced Conservation Tool for Analysis and Recommendation), a new modular framework that integrates multiple data modalities - including species distributions, phenological metrics, and phylogenetic data - to infer flower visitation and host plant interactions from spatial, temporal, and phylogenetic overlap, generating spatially explicit plant-insect interaction networks that guide planting recommendations for pollinator habitat restoration. We demonstrate the utility of NECTAR by generating a large plant-insect metaweb across California, comprising 2,473,729 spatially explicit interactions that included 3,792 pollinator species and 4,363 native plant species. NECTAR achieved high interaction recall across withheld interactions and independent datasets, substantially outperforming null models and matching or exceeding values reported in comparable studies. NECTAR's data-driven plant mix recommendations are predicted to support up to 2.4 times more pollinator species compared to existing resources and random selection of plants. This optimization facilitates the inclusion of multiple goals and constraints, and provides complementary decision-making information to existing resources. NECTAR offers a scalable, evidence-based framework for translating increasingly available global biodiversity data into locally actionable restoration guidance, with broad potential to improve pollinator habitat restoration worldwide.

ecology↗

bioRxiv2025

Petal to the metal: The slow road to automating large-scale phenology labeling for herbarium specimens

Herbarium specimens represent critical historical records of plant phenology, yet automating annotation of reproductive structures remains challenging given the diversity of floral morphologies, specimen age and quality, and image quality. Here, we present a machine learning pipeline that uses an ensemble modeling approach to detect flowers on herbarium specimens and deliver these data to the phenology research community. After testing multiple strategies for generating training data, we found in-house expert-curated annotations were essential for producing reliable results. Expert validation found relatively strong accuracy for detecting present floral structures, but still had moderately high false negative rates. Applying the ensemble to our filtered final image dataset of 22 million records resulted in 11.1 million records labeled with flowers present. However, only 2.9 million of these contained complete metadata necessary for downstream phenology research, highlighting the need for full label digitization efforts. Still, this dataset represents a large compilation of historical herbarium-derived phenology records available as a resource for the phenology community. We end by demonstrating how integrating these machine-labeled records into Phenobase, a publicly-available phenology database, expands taxonomic and temporal coverage for large-scale phenological analyses, and discuss remaining challenges and next steps.

ecology↗

bioRxiv2025

Turning a new leaf: PhenoVision provides leaf phenology data at the global scale

Plant phenology dictates many aspects of community function and ecosystem dynamics. Yet, global phenology data are still limited, especially in areas lacking monitoring programs. Here we present a new data resource, PhenoVision-Leaf, which extends a computer-vision pipeline utilizing iNaturalist digital image vouchers to produce global-scale leaf phenophase data for deciduous, woody genera. We first discuss our implementation of a new human annotation framework for leaf phenology on iNaturalist, aligning with phenophase definitions used by the larger phenology community. We then showcase the use of 165,988 crowdsourced annotated records to train a Vision Transformer model with a two-stage regime to maximize accuracy across single- and multi-image records. This approach extends Phenovision from scoring individual images to aggregating at the iNaturalist record level, better aligning with human annotation processes. Post-hoc validation showed high performance for detecting present green and colored leaves (>98% accuracy), and reasonable accuracy for breaking leaf buds (>87% accuracy). Applying PhenoVision-Leaf to over 26 million iNaturalist records yielded 5.6 million record-level phenology observations across 6,500 species and 57 families, filling geographic and taxonomic gaps. These data, now accessible through the Phenobase portal, establish a foundation for near real-time monitoring of leaf phenology, supporting global-scale synthesis analyses.

ecology↗

bioRxiv2025

Phylogeny, systematics and evolution of mimicry patterns in Neotropical limenitidine butterflies

The Neotropical butterfly genus Adelpha Hubner exhibits remarkable species diversity and striking convergence in wing colour patterns potentially explained by mimicry, making it an exceptional model for exploring trait evolution and its relationship with speciation. To date, unresolved phylogenetic relationships hinder a comprehensive understanding of the evolutionary biology of the genus. Using a novel multi-marker dataset combining one mitochondrial and 15 nuclear gene fragments, we generate the most comprehensive phylogeny of the genus Adelpha to revisit its systematics and investigate the evolution of mimicry colour patterns. Our data set encompasses 83 of the 87 known extant species and six Limenitis species that were recently excluded from Adelpha (134 of c. 160 subspecies in total), collectively displaying 14 distinct mimicry patterns. We provide conclusive evidence that corroborates previous work on the polyphyly of Adelpha as historically conceived, and describe the genus Adelphina Paez & Willmott n. gen. to stabilize the nomenclature, both genera representing Neotropical limenitidines. The comprehensive phylogeny provided in this study lays a solid foundation for future research into the processes driving diversification within these species interacting through mimicry. Ancestral character state reconstruction reveals gradual evolution of mimicry pattern. The more common mimicry pattern IPHICLUS (forewing with orange subapical spot and white band) is inferred as ancestral, but repeated convergent evolution is also recovered. Evolutionary convergence is also observed for the second most abundant mimicry pattern, COCALA (orange-white banded). Increased rates of mimicry pattern evolution are also found toward the equator. These results underscore the complexity of mimicry evolution in the Neotropical limenitidines i.e., Adelpha and Adelphina, emphasizing the need to explore its interplay with other biotic and abiotic factors.

evolutionary biology↗

bioRxiv2025

Loss of a morph is associated with asymmetric character release in a radiation of woodland salamanders

Color polymorphism, the occurrence of multiple discrete color morphs with co-adapted sets of traits within the same population, may provide the raw materials for rapid species formation. It has been hypothesized that fixation of a single morph can result in character release, whereby the monomorphic form evolves without the constraint of accommodating multiple adaptive peaks. However, the rates of evolution between populations fixed for different morphs likely depend on the specific adaptive zones occupied by each morph. We studied the evolution of dorsal color polymorphism (striped and unstriped morphs) in woodland salamanders (Plethodon), a North American radiation in which the polymorphism can be found in even the most distantly related species ([~]44 Ma divergence). We estimated a phylogenomic tree of Plethodon, representing all extant taxa with multiple samples for most species. Morphometric data suggest that between-species variation exists predominantly along an axis of relative body elongation, likely corresponding to a terrestrial-fossorial continuum. Polymorphic species occupy an intermediate phenotypic space between the evolutionary optima of striped and unstriped species, although polymorphic species did not have elevated speciation rates. Faster rates of body shape evolution were observed in unstriped species, suggesting that body elongation, which is co-adapted with the unstriped morph, is constrained by the polymorphism. Striped species had slower rates of evolution than polymorphic species, despite lacking the genetic constraints often associated with polymorphism. Our results demonstrate that rates of phenotypic evolution and speciation following character release can be asymmetric and idiosyncratic depending on the alternative adaptations of each morph.

evolutionary biology↗

bioRxiv2024

Macroevolutionary Constraint and Selection on Anti-Bat Moth Tails

Elaborate traits evolve via intense selective pressure, overpowering ecological constraints. Hindwing tails that thwart bat attack have repeatedly originated in moon moths (Saturniidae), with longer tails having greater anti-predator effect. Here, we take a macroevolutionary approach to evaluate the evolutionary balance between predation pressure and possible limiting environmental factors on tail elongation. To trace the evolution of tail length across time and space, we inferred a time-calibrated phylogeny of the entirely tailed moth group (Actias + Argema) and performed ancestral state reconstruction and biogeographical analyses. We generated metrics of predation via estimates of bat abundance from nearly 200 custom-built species distribution models and environmental metrics via estimates of bioclimatic variables associated with individual moth observations. To access community science data, we developed a novel method for measuring wing lengths from un-scaled photos. Integrating these data into phylogenetically-informed mixed models, we find a positive association between bat predation pressure and moth tail length and body size, and a negative association between environmental factors and these morphological traits. Regions with more insectivorous bats and more consistent temperatures tend to host longer-tailed moths. Our study provides insight into tradeoffs between biotic selective pressures and abiotic constraints that shape elaborate traits across the tree-of-life.

evolutionary biology↗

bioRxiv2024

Ensemble automated approaches for producing high quality herbarium digital records

One of the slowest steps in digitizing natural history collections is converting labels associated with specimens into a digital data record usable for collections management and research. Recent work has shown a path for semi-automated approaches that can find labels, OCR them and convert the raw OCR text into digital data records. Here we address how raw OCR can be converted into a digital data record via extraction into standardized Darwin Core fields. We first showcase development of a rule-based approach and compare outcomes with a large language model-based approach, in particular ChatGPT4. We next quantified error rates in a set of OCRed labels, determining omission and commission errors for both approaches and documenting other issues. For example, we find that ChatGPT4 will often create field names that are not Darwin Core compliant. Our results suggest that these approaches each have different limitations. Therefore, we developed an ensemble approach that utilizes outputs from both in order to reduce problems from each individual method. An ensemble method reduces issues with field name heterogeneity and strongly reduces information extraction errors. This suggests that such an ensemble method is likely to have particular value for creating digital data records, even for complicated label content, given that longer labels, though more error prone, are still successfully extracted. While human validation is still much needed to ensure the best possible quality, we showcase working solutions to speed digitization of herbarium specimen labels that are likely usable more broadly for all natural history collection types.

bioinformatics↗

bioRxiv2023

Phylogenetic diversity and regionalization in the temperate arid zone

Astragalus (Fabaceae) is astoundingly diverse in temperate, cold arid regions of Earth, positioning this group as a model clade for investigating the distribution of plant diversity in the face of climatic challenge. Here we identify the spatial distribution of diversity and endemism in Astragalus, using species distribution models for 752 species and a phylogenetic tree comprising 847 species. We integrated these to map centers of species richness (SR) and relative phylogenetic diversity (RPD), and used grid cell randomizations to investigate centers of endemism. We also used clustering methods to identify phylogenetic regionalizations. We then assembled predictor variables of current climate conditions to test environmental factors predicting these phylogenetic diversity results, especially temperature and precipitation seasonality. We find that SR centers are distributed globally at temperate middle latitudes in arid regions, but the Mediterranean Basin is the most important center of RPD. Endemism centers also occur globally, but Iran represents a key endemic area with a concentration of both paleo- and neoendemism. Phylogenetic regionalization recovered an east-west gradient in Eurasia and an amphitropical disjunction across North and South America; American phyloregions are overall most closely related to east and central Asia. SR, RPD, and lineage turnover are driven mostly by precipitation and seasonality, but endemism is driven primarily by diurnal temperature variation. Endemism and regionalization results point to western Asia and especially Iran as a biogeographic gateway between Europe and Asia. RPD and endemism highlight the importance of temperature and drought stress in determining plant diversity and endemism centers.

plant biology↗

bioRxiv2023

Substantial urbanization-driven declines of larval and adult moths in a subtropical environment

Recent work has shown the decline of insect abundance, diversity, and biomass, with potential implications for ecosystem services. These declines are especially pronounced in regions with high human activity, and urbanization is emerging as a significant contributing factor. However, the scale of these declines and the traits that determine variation in species-specific responses remain less well understood, especially in subtropical and tropical regions, where insect diversity is high and urban footprints are rapidly expanding. Here, we surveyed moths across an entire year in protected forested sites across an urbanization gradient to test how caterpillar and adult life stages of subtropical moths (Lepidoptera) are impacted by urbanization. Specifically, we assess how urban development affects the total abundance of caterpillars and adult moths, and quantify how richness and phylogenetic diversity of macro-moths are impacted by urban development. Additionally, we determine the effects of urban warming on species-specific adult macro-moth abundance while accounting for urban development and explore how life-history traits condition species responses to urban stressors. At the community level, we find that urban development decreases caterpillar biomass and adult moth abundance. We also find sharp declines of adults in response to urban development across the moth phylogeny, leading to a decrease in species richness and phylogenetic diversity in more urban sites. Finally, our study found that smaller macro-moths are less impacted by urban development than larger macro- moths in subtropical environments, perhaps highlighting the tradeoffs of metabolic costs of urban heat island effects favoring smaller moths over the relative benefits of dispersal for larger moths. In summary, our research underscores the far-reaching consequences of urbanization on moths and provides compelling evidence that urban forests alone may not be sufficient to safeguard biodiversity in cities.

ecology↗

bioRxiv2023

Phylogenetic diversity and regionalization of root nodule symbiosis

AimHere we determine centers of species richness (SR), relative phylogenetic diversity (RPD) and centers of paleo- and neo-endemism, and regionalizations of phylogenetic diversity in the mimosoid clade of the legumes to understand the distribution and environmental associates of mimosoids lacking RNS (root nodule symbiosis). LocationGlobal. Time periodPresent. Major taxa studiedMimosoid legumes. MethodsWe built a phylogenetic tree of 1313 species and high-quality species distribution models for 1128 species representing the phylogenetic breadth of the mimosoid clade to identify the geographic distribution of RNS. Centers of significant RPD and endemism were identified using a randomization approach, the latter using CANAPE. Phylogenetic regionalization used a distance-based phylogenetic beta-diversity approach. ResultsWe recognized nine areas of contiguous high SR as distinct SR hotspots. Non-RNS species occur mainly outside hotspots but are closely correlated with high RPD. Absence of RNS was best predicted by high precipitation, and represents multiple independent phylogenetic assemblages in different biogeographic areas. Main conclusionsSR hotspots are partly incongruent with centers of RPD and phylogenetic endemism. Lineages lacking RNS are distributed in SR hotspots in Africa and the Americas, belong to biogeographically separate species assemblages, and are, in most cases, associated with relatively moist tropical environments with low temperature seasonality and high available soil nitrogen.

ecology↗

bioRxiv2023

Rapid in-situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

O_LIThe macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. C_LIO_LIWe integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. C_LIO_LIOur results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in-situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. C_LIO_LIThe proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in-situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in-situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales. C_LI

evolutionary biology↗

bioRxiv2023

Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus

Astragalus (Fabaceae), with more than 3,000 species, represents a successful radiation of morphologically highly similar species found 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. Here, for the first time using extensive taxonomic sampling in a phylogenetic analysis, we ask whether (1) Astragalus is uniquely characterized by bursts of radiation or is instead similar to related taxa. Then we test whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats or (3) particular soils. Finally, we test (4) whether Astragalus originated in central Asia as proposed and (5) whether niche evolutionary shifts were associated with the colonization of other continents. Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but attributable to no abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. We find strong evidence for a central Asian origin and direct dispersals from this region responsible for much of the present-day distribution, highlighting the importance of central Asia as a biogeographic gateway. In contrast to diversification shifts, biogeographic shifts have a strong association with the abiotic environment. Our most important result was a fundamental divide in soil types and diurnal temperature variation between the Eastern and Western Hemisphere species; this divergence does not reflect differences in available habitat among these biogeographic domains but may reflect unique local gains of edaphic and abiotic stress adaptations. While large clades are logistically difficult to tackle, our investigation shows the importance of phylogenetic and evolutionary studies of "mega-radiations." Our findings reject any simple key innovation behind the dominance and richness of Astragalus and underline the often nuanced, multifactorial processes leading to species-rich clades.

plant biology↗

bioRxiv2023

FloraTraiter: Automated parsing of traits from descriptive biodiversity literature

Premise--Plant 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. Methods and Results--FloraTraiter was implemented through collaborative work between programmers and botanical experts, and customized for both online floras and scanned literature. We report a strategy spanning OCR, 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. Over 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. Conclusions--We identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open-source trait datasets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale.

plant biology↗

bioRxiv2023

Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae)

AO_SCPLOWBSTRACTC_SCPLOWOaks (Quercus), one of the most species-rich and ecologically dominant woody plant clades in the Northern Hemisphere, are well known for their propensity to hybridize and form syngameons, complexes where alleles are readily exchanged among closely related species. While hybridization has been extensively studied towards the tips of the oak phylogeny, the extent, timeline, and evolutionary scenarios of hybridization during the early radiation of oaks and related genera (Quercoideae) remain poorly known. Using an expansive new dataset of nuclear and chloroplast sequences (including up to 431 spp.), we conducted a multifaceted phylogenomic investigation of Quercus aimed at characterizing gene-tree and cytonuclear (chloroplast-nuclear) discordance and identifying ancient reticulation in the early evolution of the group. We document extensive nuclear gene-tree and cytonuclear discordance at deep nodes in Quercus and Quercoideae, with Quercus recovered as non-monophyletic in the chloroplast phylogeny. Analyses recovered clear signatures of gene flow against a backdrop of incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and Quercoideae during their initial radiation, dated to the early-middle Eocene. Ancestral reconstructions including fossil data suggest that the ancestors of Castanea+Castanopsis, Lithocarpus, and the Old World oak clade co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Following this initial phase of radiation and reticulation, we detected multiple niche shifts in Quercus and other Quercoideae genera that likely facilitated their expansion into new habitats arising from post-Eocene climatic changes. Our study shows that hybridization--perhaps in the form of ancient syngameons similar to those seen today--has been a common and important process throughout the evolutionary history of oaks and their close relatives.

evolutionary biology↗