Search

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution.

The New World warblers (Parulidae) are a model group for ecological and evolutionary analyses. However, current phylogenetic relationships across this family are based upon few loci. Here we use ultraconserved elements (UCEs) to estimate a rigorous species-level phylogeny for the family. As is true for many groups, high-quality tissues were unavailable for some taxa. Thus, we explored methods for incorporating sequences derived from historical (toe pad) samples to expand the phylogenetic datasets. We recovered an average of 4,186 UCE loci and mitochondrial bycatch data (supplemented with published mitochondrial data) from 96% of all currently recognized species. We found that the UCE phylogeny built with alignments with less than 70% of gaps and ambiguities recovered the most robust phylogenetic relationships for this family, representing 101 species. Using this phylogeny as a topological backbone and adding ten fair quality "bad" samples effectively generated an overall well supported phylogeny, representing 108 species (∼90% of all species). Based on this tree, we then added in seven poor quality "ugly" samples and six of those were placed within their expected genera. We also explored the phylogenetic positions of the likely extinct Leucopeza semperi and the endangered Catharopeza bishopi where limited data was obtained. Overall, taxonomic placements in our UCE trees largely correspond to previously published studies with the recovery of all currently recognized genera as monophyletic except for Basileuterus which was rendered paraphyletic by B. lachrymosus. Our study provides insights in understanding the phylogenetic relationships of a model Passeriformes family and outlines effective practices for managing sparse genomic data sourced from historical museum specimens. Variable topological arrangements across datasets and analyses reflect the evolutionary complexity of this group and provide future topics for in-depth studies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Islands are well known for their unique biodiversity and significance in evolutionary and ecological studies. Nevertheless, the extinction of island species accounts for most human-caused extinctions in recent time scales, which have accelerated in recent centuries. Pigeons and doves (Columbidae) are noteworthy for the high number of island endemics, as well as for the risks those species have faced since human arrival. On Caribbean islands, no other columbid has generated more phylogenetic interest and uncertainty than the blue-headed quail-dove, Starnoenas cyanocephala . This endangered Cuban endemic has been considered more similar, both behaviourally and phenotypically, to Australasian species than to the geographically closer 'quail-dove' ( Geotrygon s.l.) species of the Western Hemisphere. Here, we use whole genome sequencing from Starnoenas and other newly sequenced columbids in combination with sequence data from previous publications to investigate its relationships. Phylogenomic analyses, which represent 35 of the 51 genera currently comprising the Columbidae, reveal that the blue-headed quail-dove is the sole representative of a lineage diverging early in the radiation of columbids. Starnoenas is sister to the species-rich subfamily Columbinae, which is found worldwide. As a highly distinctive evolutionary lineage lacking close modern relatives, we recommend elevating the conservation priority of Starnoenas .

Urbanization in temperate climates often advances the beginning and peak of biological events due to multiple factors, especially urban heat islands. However, the effect of urbanization on insect phenology remains understudied in more tropical areas, where temperature may be a weaker phenological cue. We surveyed moths across an urban gradient in a subtropical city weekly for a year to test how impervious surface and canopy cover impact phenology at the caterpillar and adult life stages. For macro-moths, we also examine how these effects vary with life history traits. When pooling all individuals, we found no effect of urbanization proxy variables on timing of caterpillar or adult phenology. At the species-specific level, we found timing of peak adult macro-moths is influenced by canopy cover, which also interacts with two traits: temperature niche and body size. Cold-adapted species delay timing of peak abundance in more shaded sites, while warm-adapted species were not affected. Smaller species, associated with lower dispersal ability, were more phenologically sensitive to canopy cover than larger bodied species. These results highlight the importance of canopy cover within cities and its interaction with species' traits in mediating impact of urbanization on moth phenology in subtropical systems., (© 2024 The Author(s). Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

Premise: 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. Here, we address how herbarium specimen labels can be converted into digital data records via extraction into standardized Darwin Core fields., Methods: We first showcase the development of a rule-based approach and compare outcomes with a large language model-based approach, in particular ChatGPT4. We next quantified omission and commission error rates across target fields for a set of labels transcribed using optical character recognition (OCR) for both approaches. For example, we find that ChatGPT4 often creates field names that are not Darwin Core compliant while rule-based approaches often have high commission error rates., Results: Our results suggest that these approaches each have different strengths and limitations. We therefore developed an ensemble approach that leverages the strengths of each individual method and documented that ensembling strongly reduced overall information extraction errors., Discussion: This work shows that an ensemble approach has particular value for creating high-quality digital data records, even for complicated label content. While human validation is still needed to ensure the best possible quality, automated approaches can speed digitization of herbarium specimen labels and are likely to be broadly usable for all natural history collection types., (© 2024 The Author(s). Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

How landscape composition and configuration impact the distribution of multi-vector and multi-host mosquito vector-borne disease systems, such as West Nile virus (WNV), remains challenging because of complex habitat and resource requirements by hosts and vectors that affect transmission opportunities. We examined correlations between landscape composition and configuration and 2018 WNV sentinel chicken seroconversion in Florida, USA across the state and within five National Oceanic Atmospheric Administration (NOAA) bioclimatic regions to understand strength and variation of landscape effects during an elevated transmission year. Although few landscape studies have examined WNV in Florida, we expected higher percentages of residential or medium-developed landscapes and more fragmented landscapes would be positively correlated with WNV seroconversion owing to the main mosquito vector habitats and avian host distributions. However, we expected to find variation in the importance of forest, wetland, and agriculture landscapes across bioclimatic regions in the state. WNV seroconversion rates were calculated using Florida 2018 Department of Health WNV sentinel chicken seroconversion data from 187 flocks maintained by mosquito control programs. Percent land cover and edge density metrics were calculated for multiple land cover classes and within multiple buffer distances from chicken coops using 2019 National Land Cover Data. We used binomial generalized linear mixed effects models to calculate the importance of landscape metrics to WNV seroconversion. We found no statewide predictors of seroconversion, but as expected, the importance of landscape varied across regions. In the north-central part of the state, we found higher seroconversion in less populated suburban areas while higher seroconversion in south-central Florida was correlated with fragmented forested areas within 0.5 km of coops and intact woody wetland areas within 2 km of coops. This work corroborates previous findings that consistent landscape predictors of WNV are difficult to identify across broader geographic areas and sets the stage for additional work that incorporates climate and landscapes interactions for a greater understanding of WNV ecology in this geographic region., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Tavares et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Biological nitrogen fixation is a fundamental part of ecosystem functioning. Anthropogenic nitrogen deposition and climate change may, however, limit the competitive advantage of nitrogen-fixing plants, leading to reduced relative diversity of nitrogen-fixing plants. Yet, assessments of changes of nitrogen-fixing plant long-term community diversity are rare. Here, we examine temporal trends in the diversity of nitrogen-fixing plants and their relationships with anthropogenic nitrogen deposition while accounting for changes in temperature and aridity. We used forest-floor vegetation resurveys of temperate forests in Europe and the United States spanning multiple decades. Nitrogen-fixer richness declined as nitrogen deposition increased over time but did not respond to changes in climate. Phylogenetic diversity also declined, as distinct lineages of N-fixers were lost between surveys, but the "winners" and "losers" among nitrogen-fixing lineages varied among study sites, suggesting that losses are context dependent. Anthropogenic nitrogen deposition reduces nitrogen-fixing plant diversity in ways that may strongly affect natural nitrogen fixation.

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 of Quercus and 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 of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early-Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably 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. 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., (© 2024 Institute of Botany, Chinese Academy of Sciences.)

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 (δ 15 N and δ 13 C), 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 δ 15 N-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., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

The angiosperm family Elaeagnaceae comprises three genera and ca . 100 species distributed mainly in Eurasia and North America. Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted, limiting the application and preservation of natural genetic resources. Here, we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand inter- and intrageneric relationships, as well as the origin and biogeographical history of the family. For this purpose, we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and, along with current distributional data, infer historical biogeographical processes. Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera. Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia . The intrageneric relationships of Elaeagnus and Hippophae were also well resolved. High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus , and our analyses suggest putative ancient and recent hybridization. We inferred that Elaeagnaceae originated at ca . 90.48 Ma (95% CI = 89.91-91.05 Ma), and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution. This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date, offers new insights into previously unresolved relationships in Elaeagnus , and provides a foundation for further studies on classification, evolution, biogeography, and conservation of Elaeagnaceae., Competing Interests: No conflict of interest exits with the submission of this manuscript, and it has been approved by all authors for publication., (© 2024 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltdé.)

Insects often exhibit irruptive population dynamics determined by environmental conditions. We examine if populations of the Culex tarsalis mosquito, a West Nile virus (WNV) vector, fluctuate synchronously over broad spatial extents and multiple timescales and whether climate drives synchrony in Cx. tarsalis, especially at annual timescales, due to the synchronous influence of temperature, precipitation, and/or humidity. We leveraged mosquito collections across 9 National Ecological Observatory Network (NEON) sites distributed in the interior West and Great Plains region USA over a 45-month period, and associated gridMET climate data. We utilized wavelet phasor mean fields and wavelet linear models to quantify spatial synchrony for mosquitoes and climate and to calculate the importance of climate in explaining Cx. tarsalis synchrony. We also tested whether the strength of spatial synchrony may vary directionally across years. We found significant annual synchrony in Cx. tarsalis, and short-term synchrony during a single period in 2018. Mean minimum temperature was a significant predictor of annual Cx. tarsalis spatial synchrony, and we found a marginally significant decrease in annual Cx. tarsalis synchrony. Significant Cx. tarsalis synchrony during 2018 coincided with an anomalous increase in precipitation. This work provides a valuable step toward understanding broadscale synchrony in a WNV vector., (© 2024. The Author(s).)

Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for the NFC and an RNS trait database to reconstruct the evolution of RNS. Our analysis identifies evolutionary rate heterogeneity associated with a two-step process: An ancestral precursor state transitioned to a more labile state from which RNS was rapidly gained at multiple points in the NFC. We illustrate how a two-step process could explain multiple independent gains and losses of RNS, contrary to recent hypotheses suggesting one gain and numerous losses, and suggest a broader phylogenetic and genetic scope may be required for genome-phenome mapping., (© 2024. The Author(s).)

Despite experimental and observational studies demonstrating that biodiversity enhances primary productivity, the best metric for predicting productivity at broad geographic extents-functional trait diversity, phylogenetic diversity, or species richness-remains unknown. Using >1.8 million tree measurements from across eastern US forests, we quantified relationships among functional trait diversity, phylogenetic diversity, species richness, and productivity. Surprisingly, functional trait and phylogenetic diversity explained little variation in productivity that could not be explained by tree species richness. This result was consistent across the entire eastern United States, within ecoprovinces, and within data subsets that controlled for biomass or stand age. Metrics of functional trait and phylogenetic diversity that were independent of species richness were negatively correlated with productivity. This last result suggests that processes that determine species sorting and packing are likely important for the relationships between productivity and biodiversity. This result also demonstrates the potential confusion that can arise when interdependencies among different diversity metrics are ignored. Our findings show the value of species richness as a predictive tool and highlight gaps in knowledge about linkages between functional diversity and ecosystem functioning., Competing Interests: Competing interests statement:The authors declare no competing interest.

Premise: Astragalus (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., Methods: Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is 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 of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents., Results: Our results point to the importance of heterogeneity in the diversification of Astragalus, 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., Conclusions: Our 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., (© 2024 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

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 biomass of caterpillars, abundance of adult moths and quantify how richness and phylogenetic diversity of macro-moths are impacted by urban development. Additionally, we explore how life-history traits condition species' responses to urban development. At the community level, we find that urban development decreases caterpillar biomass and adult moth abundance. We also find sharp declines of adult macro-moths in response to urban development across the 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 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., (Global Change Biology© 2024 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

The 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. We 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. Our 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 the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The 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., (© 2024 The Authors New Phytologist © 2024 New Phytologist Foundation.)

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: 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 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., Results: 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 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., (© 2024 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Humans did not arrive on most of the world's islands until relatively recently, making islands favorable places for disentangling the timing and magnitude of natural and anthropogenic impacts on species diversity and distributions. Here, we focus on Amazona parrots in the Caribbean, which have close relationships with humans (e.g., as pets as well as sources of meat and colorful feathers). Caribbean parrots also have substantial fossil and archaeological records that span the Holocene. We leverage this exemplary record to showcase how combining ancient and modern DNA, along with radiometric dating, can shed light on diversification and extinction dynamics and answer long-standing questions about the magnitude of human impacts in the region. Our results reveal a striking loss of parrot diversity, much of which took place during human occupation of the islands. The most widespread species, the Cuban Parrot, exhibits interisland divergences throughout the Pleistocene. Within this radiation, we identified an extinct, genetically distinct lineage that survived on the Turks and Caicos until Indigenous human settlement of the islands. We also found that the narrowly distributed Hispaniolan Parrot had a natural range that once included The Bahamas; it thus became "endemic" to Hispaniola during the late Holocene. The Hispaniolan Parrot also likely was introduced by Indigenous people to Grand Turk and Montserrat, two islands where it is now also extirpated. Our research demonstrates that genetic information spanning paleontological, archaeological, and modern contexts is essential to understand the role of humans in altering the diversity and distribution of biota.

Predicting potential distributions of species in new areas is challenging. Physiological data can improve interpretation of predicted distributions and can be used in directed distribution models. Nonnative species provide useful case studies. Panther chameleons (Furcifer pardalis) are native to Madagascar and have established populations in Florida, USA, but standard correlative distribution modeling predicts no suitable habitat for F. pardalis there. We evaluated commonly collected thermal traits- thermal performance, tolerance, and preference-of F. pardalis and the acclimatization potential of these traits during exposure to naturally-occurring environmental conditions in North Central Florida. Though we observed temperature-dependent thermal performance, chameleons maintained similar thermal limits, performance, and preferences across seasons, despite long-term exposure to cool temperatures. Using the physiological data collected, we developed distribution models that varied in restriction: time-dependent exposure near and below critical thermal minima, predicted activity windows, and predicted performance thresholds. Our application of commonly collected physiological data improved interpretations on potential distributions of F. pardalis, compared with correlative distribution modeling approaches that predicted no suitable area in Florida. These straightforward approaches can be applied to other species with existing physiological data or after brief experiments on a limited number of individuals, as demonstrated here., (© 2023. Springer Nature Limited.)

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.]., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

Changes in phenology in response to ongoing climate change have been observed in numerous taxa around the world. Differing rates of phenological shifts across trophic levels have led to concerns that ecological interactions may become increasingly decoupled in time, with potential negative consequences for populations. Despite widespread evidence of phenological change and a broad body of supporting theory, large-scale multitaxa evidence for demographic consequences of phenological asynchrony remains elusive. Using data from a continental-scale bird-banding program, we assess the impact of phenological dynamics on avian breeding productivity in 41 species of migratory and resident North American birds breeding in and around forested areas. We find strong evidence for a phenological optimum where breeding productivity decreases in years with both particularly early or late phenology and when breeding occurs early or late relative to local vegetation phenology. Moreover, we demonstrate that landbird breeding phenology did not keep pace with shifts in the timing of vegetation green-up over a recent 18-y period, even though avian breeding phenology has tracked green-up with greater sensitivity than arrival for migratory species. Species whose breeding phenology more closely tracked green-up tend to migrate shorter distances (or are resident over the entire year) and breed earlier in the season. These results showcase the broadest-scale evidence yet of the demographic impacts of phenological change. Future climate change-associated phenological shifts will likely result in a decrease in breeding productivity for most species, given that bird breeding phenology is failing to keep pace with climate change.

Butterflies are a diverse and charismatic insect group that are thought to have evolved with plants and dispersed throughout the world in response to key geological events. However, these hypotheses have not been extensively tested because a comprehensive phylogenetic framework and datasets for butterfly larval hosts and global distributions are lacking. We sequenced 391 genes from nearly 2,300 butterfly species, sampled from 90 countries and 28 specimen collections, to reconstruct a new phylogenomic tree of butterflies representing 92% of all genera. Our phylogeny has strong support for nearly all nodes and demonstrates that at least 36 butterfly tribes require reclassification. Divergence time analyses imply an origin ~100 million years ago for butterflies and indicate that all but one family were present before the K/Pg extinction event. We aggregated larval host datasets and global distribution records and found that butterflies are likely to have first fed on Fabaceae and originated in what is now the Americas. Soon after the Cretaceous Thermal Maximum, butterflies crossed Beringia and diversified in the Palaeotropics. Our results also reveal that most butterfly species are specialists that feed on only one larval host plant family. However, generalist butterflies that consume two or more plant families usually feed on closely related plants., (© 2023. The Author(s).)

Studies of long-term trends in phenology often rely on climatic averages or accumulated heat, overlooking climate variability. Here we test the hypothesis that unusual weather conditions are critical in driving adult insect phenology. First, we generate phenological estimates for Lepidoptera (moths and butterflies) across the Eastern USA, and over a 70 year period, using natural history collections data. Next, we assemble a set of predictors, including the number of unusually warm and cold days prior to, and during, the adult flight period. We then use phylogenetically informed linear mixed effects models to evaluate effects of unusual weather events, climate context, species traits, and their interactions on flight onset, offset and duration. We find increasing numbers of both warm and cold days were strong effects, dramatically increasing flight duration. This strong effect on duration is likely driven by differential onset and termination dynamics. For flight onset, impact of unusual climate conditions is dependent on climatic context, but for flight cessation, more unusually cold days always lead to later termination particularly for multivoltine species. These results show that understanding phenological responses under global change must account for unusual weather events, especially given they are predicted to increase in frequency and severity., (© 2023. The Author(s).)

Phenology of adult host-seeking female mosquitoes is a critical component for understanding potential for vector-borne pathogen maintenance and amplification in the natural environment. Despite this importance, long-term multi-species investigations of mosquito phenologies across environments and differing species' life history traits are rare. Here we leverage long-term mosquito control district monitoring data to characterize annual phenologies of 7 host-seeking female mosquito species over a 20-year time period in suburban Illinois, USA. We also assembled data on landscape context, categorized into low and medium development, climate variables including precipitation, temperature and humidity, and key life history traits, i.e. overwintering stage and Spring-Summer versus Summer-mid-Fallseason fliers. We then fit linear mixed models separately for adult onset, peak abundances, and flight termination with landscape, climate and trait variables as predictors with species as a random effect. Model results supported some expectations, including warmer spring temperatures leading to earlier onset, warmer temperatures and lower humidity leading to earlier peak abundances, and warmer and wetter fall conditions leading to later termination. However, we also found sometimes complex interactions and responses contrary to our predictions. For example, temperature had generally weak support on its own, impacting onset and peak abundance timing; rather temperature has interacting effects with humidity or precipitation. We also found higher spring precipitation, especially in low development contexts, generally delayed adult onset, counter to expectations. These results emphasize the need to consider how traits, landscape and climatic factors all interact to determine mosquito phenology, when planning management strategies for vector control and public health protection., (© 2023. The Author(s).)

Natural history collections (NHC) provide a wealth of information that can be used to understand the impacts of global change on biodiversity. As such, there is growing interest in using NHC data to estimate changes in species' distributions and abundance trends over historic time horizons when contemporary survey data are limited or unavailable. However, museum specimens were not collected with the purpose of estimating population trends and thus can exhibit spatiotemporal and collector-specific biases that can impose severe limitations to using NHC data for evaluating population trajectories. Here we review the challenges associated with using museum records to track long-term insect population trends, including spatiotemporal biases in sampling effort and sparse temporal coverage within and across years. We highlight recent methodological advancements that aim to overcome these challenges and discuss emerging research opportunities. Specifically, we examine the potential of integrating museum records and other contemporary data sources (e.g. collected via structured, designed surveys and opportunistic citizen science programs) in a unified analytical framework that accounts for the sampling biases associated with each data source. The emerging field of integrated modelling provides a promising framework for leveraging the wealth of collections data to accurately estimate long-term trends of insect populations and identify cases where that is not possible using existing data sources., (© 2022 The Authors. Journal of Animal Ecology © 2022 British Ecological Society.)

Animal colour is a complex trait shaped by multiple selection pressures that can vary across geography. The thermal melanism hypothesis predicts that darker coloration is beneficial to animals in colder regions because it allows for more rapid solar absorption. Here, we use community science images of three closely related species of North American ratsnakes (genus Pantherophis ) to examine if climate predicts colour variation across range-wide scales. We predicted that darker individuals are found in colder regions and higher elevations, in accordance with the thermal melanism hypothesis. Using an unprecedented dataset of over 8000 images, we found strong support for temperature as a key predictor of darker colour, supporting thermal melanism. We also found that elevation and precipitation are predictive of colour, but the direction and magnitude of these effects were more variable across species. Our study is the first to quantify colour variation in Pantherophis ratsnakes, highlighting the value of community science images for studying range-wide colour variation.

Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources assemble species-level trait data, but the data and metadata underlying those trait measurements are often not reported. Here, we introduce FuTRES (Functional Trait Resource for Environmental Studies; pronounced few-tress), an online datastore and community resource for individual-level trait reporting that utilizes a semantic framework. FuTRES already stores millions of trait measurements for paleobiological, zooarchaeological, and modern specimens, with a current focus on mammals. We compare dynamically derived extant mammal species' body size measurements in FuTRES with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. We then show that individual-level data improve estimates of body mass-including uncertainty-for zooarchaeological specimens. FuTRES facilitates trait data integration and discoverability, accelerating new research agendas, especially scaling from intra- to interspecific trait variability., Competing Interests: The authors declare no competing interests., (© 2022 The Authors.)

Data availability limits phenological research at broad temporal and spatial extents. Butterflies are among the few taxa with broad-scale occurrence data, from both incidental reports and formal surveys. Incidental reports have biases that are challenging to address, but structured surveys are often limited seasonally and may not span full flight phenologies. Thus, how these data source compare in phenological analyses is unclear. We modeled butterfly phenology in relation to traits and climate using parallel analyses of incidental and survey data, to explore their shared utility and potential for analytical integration. One workflow aggregated "Pollard" surveys, where sites are visited multiple times per year; the other aggregated incidental data from online portals: iNaturalist and eButterfly. For 40 species, we estimated early (10%) and mid (50%) flight period metrics, and compared the spatiotemporal patterns and drivers of phenology across species and between datasets. For both datasets, inter-annual variability was best explained by temperature, and seasonal emergence was earlier for resident species overwintering at more advanced stages. Other traits related to habitat, feeding, dispersal, and voltinism had mixed or no impacts. Our results suggest that data integration can improve phenological research, and leveraging traits may predict phenology in poorly studied species., (© 2022. The Author(s).)

Openly available community science digital vouchers provide a wealth of data to study phenotypic change across space and time. However, extracting phenotypic data from these resources requires significant human effort. Here, we demonstrate a workflow and computer vision model for automatically categorizing species color pattern from community science images. Our work is focused on documenting the striped/unstriped color polymorphism in the Eastern Red-backed Salamander ( Plethodon cinereus ). We used an ensemble convolutional neural network model to analyze this polymorphism in 20,318 iNaturalist images. Our model was highly accurate (∼98%) despite image heterogeneity. We used the resulting annotations to document extensive niche overlap between morphs, but wider niche breadth for striped morphs at the range-wide scale. Our work showcases key design principles for using machine learning with heterogeneous community science image data to address questions at an unprecedented scale., Competing Interests: The authors declare no competing interests., (© 2022 The Authors.)

Insect phenological lability is key for determining which species will adapt under environmental change. However, little is known about when adult insect activity terminates and overall activity duration. We used community-science and museum specimen data to investigate the effects of climate and urbanisation on timing of adult insect activity for 101 species varying in life history traits. We found detritivores and species with aquatic larval stages extend activity periods most rapidly in response to increasing regional temperature. Conversely, species with subterranean larval stages have relatively constant durations regardless of regional temperature. Species extended their period of adult activity similarly in warmer conditions regardless of voltinism classification. Longer adult durations may represent a general response to warming, but voltinism data in subtropical environments are likely underreported. This effort provides a framework to address the drivers of adult insect phenology at continental scales and a basis for predicting species response to environmental change., (© 2021 John Wiley & Sons Ltd.)

Color polymorphic animals offer a unique system for studying intraspecific phenotypic responses to climate change. Discrete color morphs are easy to identify, and correlated trait responses of morphs can indicate how climate warming may facilitate long-term maintenance of polymorphisms. We use a historical dataset spanning 43 years to examine temporal shifts in color morph frequency and body size in response to climate in the Eastern Red-backed Salamander, Plethodon cinereus, which contains a widespread striped/unstriped color polymorphism. We created a pipeline to extract high-throughput trait data from fluid-preserved museum specimens where we batch-photographed salamanders, de-aggregated individual specimens from photographs, and solicited help of community scientists to score color morphs. We used a linear modeling framework that includes information about spatial population structure to demonstrate that color morph frequency and body size vary in response to climate, elevation, and over time, with an overall trend of higher frequency and decreased body size of the striped morph, but increased size of the unstriped morph. These surprising results suggest that morphs may be responding to multiple climate and geographic drivers through co-adapted morphological changes. This work highlights new practices of extracting trait data from museum specimens to demonstrate species phenotypes response to climate change., (© 2021. The Author(s).)

Yucca in the American desert Southwest typically flowers in early spring, but a well-documented anomalous bloom event occurred during an unusually cold and wet late fall and early winter 2018-2019. We used community science photographs to generate flowering presence and absence data. We fit phenoclimatic models to determine which climate variables are explanatory for normal flowering, and then we tested if the same conditions that drive normal blooming also drove the anomalous blooming event. Flowering for Yucca brevifolia (Joshua tree) and Yucca schidigera (Mojave yucca) is driven by complex, nonlinear interactions between daylength, temperature, and precipitation. To our surprise, early-season flowering odds are highest in colder and drier conditions, especially for Joshua trees, but increase with precipitation late-season. However, the models used to fit normal blooming overpredicted the number of anomalous blooms compared to what was actually observed. Thus, predicting anomalous flowering events remains a challenge for quantitative phenological models. Because our model overpredicted the number of anomalous blooms, there are likely other factors, such as biotic interactions or other seasonal factors, which may be especially important in controlling what is presumed to be rare, out-of-season flowering in desert-adapted Yucca., (© 2021. The Author(s).)

Anthropogenically-driven climate warming is a hypothesized driver of animal body size reductions. Less understood are effects of other human-caused disturbances on body size, such as urbanization. We compiled 140,499 body size records of over 100 North American mammals to test how climate and human population density, a proxy for urbanization, and their interactions with species traits, impact body size. We tested three hypotheses of body size variation across urbanization gradients: urban heat island effects, habitat fragmentation, and resource availability. Our results demonstrate that both urbanization and temperature influence mammalian body size variation, most often leading to larger individuals, thus supporting the resource availability hypothesis. In addition, life history and other ecological factors play a critical role in mediating the effects of climate and urbanization on body size. Larger mammals and species that utilize thermal buffering are more sensitive to warmer temperatures, while flexibility in activity time appears to be advantageous in urbanized areas. This work highlights the value of using digitized, natural history data to track how human disturbance drives morphological variation., (© 2021. The Author(s).)

Animals and plants are shifting the timing of key life events in response to climate change, yet despite recent documentation of escalating phenological change, scientists lack a full understanding of how and why phenological responses vary across space and among species. Here, we used over 7 million community-contributed bird observations to derive species-specific, spatially explicit estimates of annual spring migration phenology for 56 bird species across eastern North America. We show that changes in the spring arrival of migratory birds are coarsely synchronized with fluctuations in vegetation green-up and that the sensitivity of birds to plant phenology varied extensively. Bird arrival responded more synchronously with vegetation green-up at higher latitudes, where phenological shifts over time are also greater. Critically, species' migratory traits explained variation in sensitivity to green-up, with species that migrate more slowly, arrive earlier and overwinter further north showing greater responsiveness to earlier springs. Identifying how and why species vary in their ability to shift phenological events is fundamental to predicting species' vulnerability to climate change. Such variation in sensitivity across taxa, with long-distance neotropical migrants exhibiting reduced synchrony, may help to explain substantial declines in these species over the last several decades.

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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Kates, Doby, Siniscalchi, LaFrance, Soltis, Soltis, Guralnick and Folk.)

Worldwide decline in biodiversity during the Holocene has impeded a comprehensive understanding of pre-human biodiversity and biogeography. This is especially true on islands, because many recently extinct island taxa were morphologically unique, complicating assessment of their evolutionary relationships using morphology alone. The Caribbean remains an avian hotspot but was more diverse before human arrival in the Holocene. Among the recently extinct lineages is the enigmatic genus Nesotrochis, comprising three flightless species. Based on morphology, Nesotrochis has been considered an aberrant rail (Rallidae) or related to flufftails (Sarothruridae). We recovered a nearly complete mitochondrial genome of Nesotrochis steganinos from fossils, discovering that it is not a rallid but instead is sister to Sarothruridae, volant birds now restricted to Africa and New Guinea, and the recently extinct, flightless Aptornithidae of New Zealand. This result suggests a widespread or highly dispersive most recent common ancestor of the group. Prior to human settlement, the Caribbean avifauna had a far more cosmopolitan origin than is evident from extant species.

Shifts in reproductive timing are among the most commonly documented responses of organisms to global climate change. However, our knowledge of these responses is biased towards taxa that are easily observable and abundant in existing biodiversity data sets. Mammals are common subjects in reproductive biology, but mammalian phenology and its drivers in the wild remain poorly understood because many species are small, secretive, or too labor-intensive to monitor. We took an informatics-based approach to reconstructing breeding phenology in the widespread North American deer mouse (Peromyscus maniculatus) using individual-level reproductive observations from digitized museum specimens and field censuses spanning >100 yr and >45 degrees of latitude. We reconstructed female phenology in different regions and tested the importance of three environmental variables (photoperiod, temperature, precipitation) as breeding cues. Photoperiod and temperature were strong positive and negative breeding cues, respectively, whereas precipitation was not a significant predictor of breeding phenology. However, phenologies and the use of environmental cues varied substantially among regions, and we found evidence that these cueing repertoires are tuned to ecosystem-specific limiting conditions. Our results reiterate the importance of ecological context in optimizing reproduction and demonstrate how harmonization across biodiversity data resources allows new insight into phenology and its drivers in wild mammals., (© 2020 by the Ecological Society of America.)

Premise: Large phylogenetic data sets have often been restricted to small numbers of loci from GenBank, and a vetted sampling-to-sequencing phylogenomic protocol scaling to thousands of species is not yet available. Here, we report a high-throughput collections-based approach that empowers researchers to explore more branches of the tree of life with numerous loci., Methods: We developed an integrated Specimen-to-Laboratory Information Management System (SLIMS), connecting sampling and wet lab efforts with progress tracking at each stage. Using unique identifiers encoded in QR codes and a taxonomic database, a research team can sample herbarium specimens, efficiently record the sampling event, and capture specimen images. After sampling in herbaria, images are uploaded to a citizen science platform for metadata generation, and tissue samples are moved through a simple, high-throughput, plate-based herbarium DNA extraction and sequencing protocol., Results: We applied this sampling-to-sequencing workflow to ~15,000 species, producing for the first time a data set with ~50% taxonomic representation of the "nitrogen-fixing clade" of angiosperms., Discussion: The approach we present is appropriate at any taxonomic scale and is extensible to other collection types. The widespread use of large-scale sampling strategies repositions herbaria as accessible but largely untapped resources for broad taxonomic sampling with thousands of species., (© 2021 Folk et al. Applications in Plant Sciences is published by Wiley Periodicals LLC on behalf of the Botanical Society of America.)

A wave of green leaves and multi-colored flowers advances from low to high latitudes each spring. However, little is known about how flowering offset (i.e., ending of flowering) and duration of populations of the same species vary along environmental gradients. Understanding these patterns is critical for predicting the effects of future climate and land-use change on plants, pollinators, and herbivores. Here, we investigated potential climatic and landscape drivers of flowering onset, offset, and duration of 52 plant species with varying key traits. We generated phenology estimates using >270,000 community-science photographs and a novel presence-only phenometric estimation method. We found longer flowering durations in warmer areas, which is more obvious for summer-blooming species compared to spring-bloomers driven by their strongly differing offset dynamics. We also found that higher human population density and higher annual precipitation are associated with delayed flowering offset and extended flowering duration. Finally, offset of woody perennials was more sensitive than herbaceous species to both climate and urbanization drivers. Empirical forecast models suggested that flowering durations will be longer in 2030 and 2050 under representative concentration pathway (RCP) 8.5, especially for summer-blooming species. Our study provides critical insight into drivers of key flowering phenophases and confirms that Hopkins' Bioclimatic Law also applies to flowering durations for summer-blooming species and herbaceous spring-blooming species., (© 2020 John Wiley & Sons Ltd.)

The complex forces that shape butterfly wings have long been a subject of experimental and comparative research. Butterflies use their wings for flight, camouflage, mate recognition, warning, and mimicry. However, general patterns and correlations among wing shape and size evolution are still poorly understood. We collected geometric morphometric measurements from over 1400 digitized museum specimens of Papilio swallowtails and combined them with phylogenetic data to test two hypotheses: 1) forewing shape and size evolve independently of hindwing shape and size and 2) wing size evolves more quickly than wing shape. We also determined the major axes of wing shape variation and discovered that most shape variability occurs in hindwing tails and adjacent areas. We conclude that forewing shape and size are functionally and biomechanically constrained, whereas hindwings are more labile, perhaps in response to disruptive selective pressure for Batesian mimicry or against predation. The development of a significant, re-usable, digitized data resource will enable further investigation on tradeoffs between flight performance and ecological selective pressures, along with the degree to which intraspecific, local-scale selection may explain macroevolutionary patterns. [Batesian mimicry; Lepidoptera; geometric morphometrics; museum specimens.]., (© The Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: Plastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of pseudogenization and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context., Results: We find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the ndh complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional., Conclusions: Saniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, perhaps related to its extreme habitat specialization, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.

Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids-a clade of ~25% of all angiosperm species-to understand global patterns of diversification and its climatic association. Our approach incorporates historical global temperature, assessment of species' temperature niche, and two broad-scale characterizations of tropical versus non-tropical niche occupancy. We find the diversification rates of most subclades dramatically increased over the last 15 million years (Myr) during cooling associated with global expansion of temperate habitats. Climatic niche is negatively associated with diversification rates, with tropical rosids forming older communities and experiencing speciation rates ~2-fold below rosids in cooler climates. Our results suggest long-term cooling had a disproportionate effect on non-tropical diversification rates, leading to dynamic young communities outside of the tropics, while relative stability in tropical climes led to older, slower-evolving but still species-rich communities.

Premise: Digitization and imaging of herbarium specimens provides essential historical phenotypic and phenological information about plants. However, the full use of these resources requires high-quality human annotations for downstream use. Here we provide guidance on the design and implementation of image annotation projects for botanical research., Methods and Results: We used a novel gold-standard data set to test the accuracy of human phenological annotations of herbarium specimen images in two settings: structured, in-person sessions and an online, community-science platform. We examined how different factors influenced annotation accuracy and found that botanical expertise, academic career level, and time spent on annotations had little effect on accuracy. Rather, key factors included traits and taxa being scored, the annotation setting, and the individual scorer. In-person annotations were significantly more accurate than online annotations, but both generated relatively high-quality outputs. Gathering multiple, independent annotations for each image improved overall accuracy., Conclusions: Our results provide a best-practices basis for using human effort to annotate images of plants. We show that scalable community science mechanisms can produce high-quality data, but care must be taken to choose tractable taxa and phenophases and to provide informative training material., (© 2020 Brenskelle et al. Applications in Plant Sciences is published by Wiley Periodicals, LLC on behalf of the Botanical Society of America.)

Premise: Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results., Methods: We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR)., Results: We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa., Conclusions: We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies., (© 2020 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Quaternary paleontological and archaeological evidence often is crucial for uncovering the historical mechanisms shaping modern diversity and distributions. We take an interdisciplinary approach using multiple lines of evidence to understand how past human activity has shaped long-term animal diversity in an island system. Islands afford unique opportunities for such studies given their robust fossil and archaeological records. Herein, we examine the only non-volant terrestrial mammal endemic to the Bahamian Archipelago, the hutia Geocapromys ingrahami. This capromyine rodent once inhabited many islands but is now restricted to several small cays. Radiocarbon dated fossils indicate that hutias were present on the Great Bahama Bank islands before humans arrived at AD ~800-1000; all dates from other islands post-date human arrival. Using ancient DNA from a subset of these fossils, along with modern representatives of Bahamian hutia and related taxa, we develop a fossil-calibrated phylogeny. We found little genetic divergence among individuals from within either the northern or southern Bahamas but discovered a relatively deep North-South divergence (~750 ka). This result, combined with radiocarbon dating and archaeological evidence, reveals a pre-human biogeographic divergence, and an unexpected human role in shaping Bahamian hutia diversity and biogeography across islands.

Premise: Citizen science platforms for sharing photographed digital vouchers, such as iNaturalist, are a promising source of phenology data, but methods and best practices for use have not been developed. Here we introduce methods using Yucca flowering phenology as a case study, because drivers of Yucca phenology are not well understood despite the need to synchronize flowering with obligate pollinators. There is also evidence of recent anomalous winter flowering events, but with unknown spatiotemporal extents., Methods: We collaboratively developed a rigorous, consensus-based approach for annotating and sharing whole plant and flower presence data from iNaturalist and applied it to Yucca records. We compared spatiotemporal flowering coverage from our annotations with other broad-scale monitoring networks (e.g., the National Phenology Network) in order to determine the unique value of photograph-based citizen science resources., Results: Annotations from iNaturalist were uniquely able to delineate extents of unusual flowering events in Yucca . These events, which occurred in two different regions of the Desert Southwest, did not appear to disrupt the typical-period flowering., Discussion: Our work demonstrates that best practice approaches to scoring iNaturalist records provide fine-scale delimitation of phenological events. This approach can be applied to other plant groups to better understand how phenology responds to changing climate., (© 2020 Barve et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.)

Plant and animal phenology is shifting in response to urbanization, with most hypotheses focusing on the 'urban heat island' (UHI) effect as the driver. However, generalities regarding the direction and magnitude of phenological response to urbanization have not yet emerged because most studies have focused on remote-sensed vegetative phenologies or at local scales with relatively few species. Furthermore, how urbanization interacts with broad-scale climate gradients remains an unknown but important component of anthropogenically driven phenological change. Here, we used a database with >22 million in situ plant phenological observations from the United States and Europe to study the joint influence of varying human population density, which serves as an urbanization measure, and of regional temperature on median flowering and leaf-out dates across a wide plant phylogenetic spectrum. Separately, increasing population density and warmer regional temperature both advanced plant flowering and leaf-out. However, the influence of human population density on plant flowering and leaf-out depends on the regional temperature: high population density advanced plant phenology in cold areas but this effect disappeared or even reversed in warm areas. UHI effects (as measured by daily land surface temperature) alone cannot explain the overall influence of urbanization on plant phenology, suggesting that urbanization also affects plant phenology via other mechanisms. Shorter plants with large specific leaf areas and early flower or leaf-out dates were most affected by urbanization and temperature changes. Our study provides strong empirical evidence that the influence of urbanization on plant phenology varies with regional temperature. Therefore, robust understanding and accurate prediction of phenological changes must take this interaction into account.

Since the late Pleistocene humans have caused the extinction of species across our planet. Placing these extinct species in the tree of life with genetic data is essential to understanding the ecological and evolutionary implications of these losses. While ancient DNA (aDNA) techniques have advanced rapidly in recent decades, aDNA from tropical species, especially birds, has been historically difficult to obtain, leaving a gap in our knowledge of the extinction processes that have influenced current distributions and biodiversity. Here we report the recovery of a nearly complete mitochondrial genome from a 2,500 year old (late Holocene) bone of an extinct species of bird, Caracara creightoni, recovered from the anoxic saltwater environment of a blue hole in the Bahamas. Our results suggest that this extinct species is sister (1.6% sequence divergence) to a clade containing the extant C. cheriway and C. plancus. Caracara creightoni shared a common ancestor with these extant species during the Pleistocene (1.2-0.4 MYA) and presumably survived on Cuba when the Bahamas was mostly underwater during Quaternary interglacial intervals (periods of high sea levels). Tropical blue holes have been collecting animals for thousands of years and will continue to improve our understanding of faunal extinctions and distributions. In particular, new aDNA techniques combined with radiocarbon dating from Holocene Bahamian fossils will allow us to place other extinct (species-level loss) and extirpated (population-level loss) vertebrate taxa in improved phylogenetic, evolutionary, biogeographic, and temporal contexts., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing environment., Competing Interests: The authors have declared that no competing interests exist.