Brian J. Stucky's research while affiliated with Florida Museum of Natural History and other places

Publications (50)

Preprint
Urbanization is quickly becoming one of the most important drivers of global environmental change as human population and economic development rapidly increase. However, the effects of urbanization on plant phenology, especially leaf senescence and the length of growing season across large spatial scales, are still understudied. Previous work sugge...
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Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsul...
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Unlike other European domesticates introduced in the Americas after the European invasion, equids (Equidae) were previously in the Western Hemisphere but were extinct by the late Holocene era. The return of equids to the Americas through the introduction of the domestic horse ( Equus caballus ) is documented in the historical literature but is not...
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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 scien...
Preprint
Full-text available
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 scien...
Article
Full-text available
Aim Urbanization is becoming one of the most important drivers of global environmental change as human population and economic development rapidly increase. However, the effects of urbanization on plant phenology are still poorly understood, especially for leaf senescence and growing season length across large spatial scales. We aimed to fill this...
Article
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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...
Article
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Phenological data (i.e., data on growth and reproductive events of organisms) are increasingly being used to study the effects of climate change, and biodiversity specimens have arisen as important sources of phenological data. However, phenological data are not expressly treated by the Darwin Core standard (Wieczorek et al. 2012), and specimen-bas...
Article
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The availability of citizen science data has resulted in growing applications in biodiversity science. One widely used platform, iNaturalist, provides millions of digitally vouchered observations submitted by a global user base. These observation records include a date and a location but otherwise do not contain any information about the sampling p...
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Synopsis Despite efforts to integrate research across different subdisciplines of biology, the scale of integration remains limited. We hypothesize that future generations of Artificial Intelligence (AI) technologies specifically adapted for biological sciences will help enable the reintegration of biology. AI technologies will allow us not only to...
Preprint
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 urbanization on timing of adult insect activity for...
Article
Full-text available
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 remai...
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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 an...
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The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heter...
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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 resear...
Article
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Machine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens-preserved plant material curated in natural history collections-but ML techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as...
Article
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Twenty-nine Pacarina (Hemiptera: Cicadidae) adults, 12 males and 17 females, emerged from the soil of a potted Dracaena trifasciata (Asparagaceae) in Arraiján, Republic of Panama, providing the first rearing records and the first definitive host plant records for any species of Pacarina . These reared Pacarina appear to be morphologically distinct...
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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 opp...
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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 th...
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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 o...
Preprint
Full-text available
Broad-scale plant flowering phenology data has predominantly come from geographically and taxonomically restricted monitoring networks. However, platforms such as iNaturalist, where citizen scientists upload photographs and curate identifications, provide a promising new source of data. Here we develop a general set of best practices for scoring iN...
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Ideally, an information system that automates the integration of disparate datasets should be able to minimize the loss of information from any one dataset, achieve computational complexity suitable for working with large datasets, be flexible enough to easily incorporate new data sources, and produce output that is easily analyzed and understood b...
Article
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Recent progress in using deep learning techniques to automate the analysis of complex image data is opening up exciting new avenues for research in biodiversity science. However, potential applications of machine learning methods in biodiversity research are often limited by the relative scarcity of data suitable for training machine learning model...
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Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty i...
Data
Ontology competency questions, user domains or groups, and example use cases
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Premise of the Study The Plant Phenology Ontology (PPO) was originally developed to integrate phenology observations of whole plants across different global observation networks. Here we describe a new release of the PPO and associated data pipelines that supports integration of phenology observations from herbarium specimens, which provide histori...
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Plant phenology – the timing of plant life-cycle events, such as flowering or leafing out – plays a fundamental role in the functioning of terrestrial ecosystems, including human agricultural systems. Because plant phenology is often linked with climatic variables, there is widespread interest in developing a deeper understanding of global plant ph...
Article
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Premise of the Study | Herbarium specimens provide a robust record of historical plant phenology (the timing of seasonal events such as flowering or fruiting). However, the difficulty of aggregating phenological data from specimens arises from a lack of standardized scoring methods and definitions for phenological states across the collections comm...
Article
Full-text available
The study of plant phenology is concerned with the timing of plant life-cycle events, such as leafing out, flowering, and fruiting. Today, thanks to data digitization and aggregation initiatives, phenology monitoring networks, and the efforts of citizen scientists, more phenologically relevant plant data is available than ever before. Until recentl...
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Ontologies offer multiple benefits for biodiversity data processing and analysis, including precisely defined vocabularies, robust pathways for data integration, and support for automated machine reasoning. However, ontologies have yet to be widely deployed for biodiversity data processing and analysis. Reasons for this include: specialized skills...
Article
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Ontologies (formal descriptions of the concepts and relationships that can exist in knowledge domains) provide the conceptual foundations for modern knowledge representation systems and knowledge bases, and they are a core component of automated reasoning pipelines that infer new facts from existing data. Although a variety of software tools are av...
Conference Paper
Full-text available
Report on Results of a Hackathon to Progress with the Training Resources for Natural Language Processing (NLP) in Ecology
Article
Parasitoids that locate their hosts by eavesdropping on the acoustic signals of other insects can be collected in traps baited with audio signals that mimic the sounds of the parasitoid's hosts. I describe a new acoustic trap designed to capture Emblemasoma erro Aldrich (Diptera: Sarcophagidae), an eavesdropping parasitoid of cicadas whose phonotac...
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Females of several species of dipteran parasitoids use long-range hearing to locate hosts for their offspring by eavesdropping on the acoustic mating calls of other insects. Males of these acoustic eavesdropping parasitoids also have physiologically functional ears, but so far, no adaptive function for male hearing has been discovered. I investigat...
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Background: 'Eavesdropping' parasitoids find their hosts by homing in on the communication signals of other insects. These parasitoids often exploit chemical communication, but at least some species of the sarcophagid genusEmblemasomaeavesdropon the acoustic communications of cicadas. Despite considerable scientific interest in acoustic parasitoid...
Article
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The biodiversity informatics community has discussed aspirations and approaches for assigning globally unique identifiers (GUIDs) to biocollections for nearly a decade. During that time, and despite misgivings, the de facto standard identifier has become the "Darwin Core Triplet", which is a concatenation of values for institution code, collection...
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Recent years have brought great progress in efforts to digitize the world’s biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web technologies have been widely recognized by biodiversity scientists for their potential to help solve this problem, yet these technologies h...
Article
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The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science sugge...
Data
Calling song of Tibicen neomexicensis sp. n. (doi: 10.3897/zookeys.337.5950.app1) File format: Waveform Audio File Format (wav).
Article
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AbstractTibicen neomexicensis sp. n., a new species of cicada found in the Sacramento Mountains of southcentral New Mexico, is described. Tibicen neomexicensis closely resembles Tibicen chiricahua Davis morphologically, but males of the two species have highly distinct calling songs that differ in phrasal structure, amplitude burst rates, and pulse...
Data
Calling song of Tibicen chiricahua Davis. (doi: 10.3897/zookeys.337.5950.app2) File format: Waveform Audio File Format (wav).
Article
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“If names be not correct, language is not in accordance with the truth of things. If language be not in accordance with the truth of things, affairs cannot be carried on to success.” - Confucius, Analects, Book XIII, Chapter 3, verses 4-7, translated by James Legge Two workshops (hereafter described as “workshops”) were held in 2012, which brough...
Article
Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few nonproprietary software tools are available to assist with this process. SeqTrace is a new, free, and open-source software application that is designed to automate t...
Article
Tibicen pruinosus (Say)—a large, arboreal cicada typically found in the central United States—is reported for the first time from Colorado. This new state record represents a significant western extension of this cicada's known range. Also reported are new records from Kansas that link the Colorado population to the previously known distribution of...

Citations

... Additionally, after arriving in the Americas over 21k years ago (Bennett et al., 2021;Pigati et al., 2023), humans played an important role in modifying the distribution of fire and herbivore 'consumer regimes', by regulating the frequency, timing, and extent of both fire, via intentional burning, and herbivory, via management of wild and domestic herbivores (Nowacki et al., 2012;Roos et al., 2018). Beginning with the introduction of cattle by Europeans in the 16 th century (Delsol et al., 2023;Rouse, 1977), intensively managed and spatially constrained domestic livestock production systems have largely replaced free roaming herds of large herbivores in North America. Acknowledgement of widespread ecological impacts caused by altered fire patterns and herbivore communities has prompted calls for and motivated initiatives aimed at restoring ancient consumer regimes (Fuhlendorf et al., 2009;Lorimer et al., 2015). ...
... To date archaeological investigations in the archipelago have mainly focused on the earlier Indigenous societies, neglecting the subsequent periods (Arnay-de-la-Rosa 2009; González Marrero and Tejera Gaspar 2011;Mitchell 2023). Despite the key role of these islands in the development of animal translocation between continents (Delsol et al. 2022;López et al. 2013;McTavish et al. 2013;Olalde et al. 2015;Reitz 1992;Speller et al. 2013), local zooarchaeological research is basically limited to either Indigenous sites or sites from the fifteenth century corresponding to the period of contact between the Europeans and the Native populations (Castellano Alonso et al. 2016. Additionally, while historical written sources of the Modern Era of the Canary Islands provide valuable insights into human-animal interactions, they are often biased, limited in scope, or subject to interpretation. ...
... In addition, approaches have been developed to not only recognise objects in multimedia data sources, but also to differentiate by anomalies or other species-specific features such as plant or animal colours (e.g. Hantak et al., 2022;Perez-Udell et al., 2023). Ultimately, the ever-improving models used to generate ecological networks also help to turn information into knowledge. ...
... Some studies found opposite effects between daytime and nighttime temperatures across different natural ecosystems [14][15][16][17] , while others did not find such contrasting patterns 18,19 . Additionally, there are studies suggesting that urbanization, as measured using population density or urban fraction (UF), may have an equally substantial, or even a greater, impact on phenological shifts compared to UHI effects 20,21 , particularly in a climate-dependent context 22 . Confounding factors in urban areas may challenge the notion of treating the UHI effect on phenology in the same manner as the future warming environment 23 . ...
... Moreover, global warming may increase both the population growth and metabolic rates of insects. 5,59,60 This would be a challenge to sustainable approaches for meeting the increasing food demand because the most sustainable method would be increasing crop yields rather than reclaiming more land surface for crop production. 8,9 Thus, the emergence and spread of crop pests threatens global food security, 7 and soybean cultivated areas located in midlatitudes appear to be facing greater food security risks. ...
... Each photo includes detailed metadata: copyright status, location, uploader, time, and taxonomic classification. This diversity in image sources makes iNaturalist an excellent dataset for training AI models intended for real-world applications [37,24,7,3]. Despite its vast and diverse data, iNaturalist is not directly optimized for AI researchers: arranging this data for use in AI models like CLIP is not straightforward. ...
... In conclusion, AI has greatly affected medicine and biology, from detecting illnesses, medication discovery, and development to predicting protein structures and drug discovery. As AI technology matures, these areas will use it more, creating more inventive and efficient (Hamet & Tremblay, 2017;Hassoun et al., 2021). We offer some examples as illustrations, arranged in approximate order of increasing difficulty of implementation. ...
... Future analyses of extinct birds would greatly benefit from an integrative approach. In addition to classical morphological, chronological, and palaeoecological perspectives (e.g., Cooper et al. 1996;Tokita et al. 2017;Oswald et al. 2021), they should include genomic, epigenomic, and/or proteomic analyses of fossil and subfossil remains. Such approaches may in the future allow (1) reconstructing phylogenetic relationships and origins of extinct lineages, (2) distinguishing between true island-restricted radiations and independent waves of colonization, (3) estimating times of colonization and informing us of diversification processes, (4) determining the genetic diversity lost over time, and (5) uncovering genomic regions involved in the evolution of conspicuous and hidden "island syndrome" traits, suchas flightlessness and sedentarism, which could explain the effects of lowering or erasing gene flow among nearby populations favoring avian radiations (Burga et al. 2017;Horn et al. 2019). ...
... However, field-based phenological records documenting the onset and termination of phenophases across multiple species are limited in geographic or taxonomic scope (Sherry et al. 2011, Crimmins et al. 2013, Bock et al. 2014, and frequently focus on repeated observation of specific individuals rather than local populations. While modern observation networks such as the USA-NPN and iNaturalist have greatly broadened the spatial and taxonomic breadth of records capable of evaluating the timing of flowering onset, duration and termination, (Rosemartin et al. 2014, Pearse et al. 2019, Li et al. 2021, these data are limited in their temporal depth, and still exhibit significant taxonomic and spatial gaps. To date, this has limited our ability to assess climate-driven shifts in phenological synchrony across regions and taxa, highlighting the need for taxonomically and spatially extensive data sources that offer the capacity to estimate the duration of targeted phenophases. ...
... Following Semantic Web standards 80 , PKT-KG defines a KG as K = 〈T, A〉, where T is the TBox and A is the ABox. The TBox represents the taxonomy of a particular domain 81,82 . It describes classes, properties or relationships, and assertions that are assumed to generally hold within a domain (e.g., a gene is a heritable unit of DNA located in the nucleus of cells [ Fig. 7a]). ...