Grand Challenges in Arachnid Morphology, Systematics, and Evolution

Jason E Bond^1,2*Matjaz Kuntner³

• ¹University of California, Davis, Davis, United States
• ²University of California Davis Department of Entomology & Nematology, Davis, United States
• ³Nacionalni institut za biologijo, Ljubljana, Slovenia

A fully resolved and time-calibrated arachnid tree of life that includes all extant species should be an aim of the systematic arachnid community as this would significantly facilitate research across all fields of arachnid ecology, evolution, genomics, and material science. Minimally, a resolved arachnid tree containing all nominal genera would also be aspirational. Despite development of large genomic datasets in recent years, major branches on the arachnid tree of life remain unresolved and require refinement (Lozano-Fernandez et al. 2019;Sharma et al. 2021;Ballesteros et al. 2022;Sharma and Gavish-Regev 2025;Yu et al. 2025); for example, in spiders, family level delimitations continue to be refined and in further need of resolution (Bond et al. 2014;Garrison et al. 2016;Opatova et al. 2020;Kuntner et al. 2023); relationships across the arachnid orders (e.g., the placement of horseshoe crabs and monophyly of acarines) (Sharma et al. 2021;Sharma and Gavish-Regev 2025) are still ostensibly contentious and conflicting with morphology and the fossil record. Questions regarding what data and how many loci are needed to resolve relationships spanning such deep phylogenetic scales are largely unanswered. As whole genome sequencing becomes more accessible and broader knowledge of genome sizes, the development of new markers and loci like ultra conserved elements (Faircloth et al. 2015;Starrett et al. 2017;Van Dam et al. 2019;Kulkarni et al. 2020;Zhang et al. 2023;Derkarabetian et al. 2023;Kulkarni et al. 2023), along with the use of low coverage genome scans (Gorneau et al. 2023) are expected to advance arachnid genomics considerably. Developing new pipelines for data analysis and cost-eqective approaches to data capture will also advance the field. Finally, molecular clock estimates across analyses vary widely likely owing to ancient origins, highly variable branch lengths, and scarcity of critical calibration points. Thus better and more integrated fossil data are needed to resolve time point calibrations across the arachnid tree of life (Magalhaes et al. 2019;Dunlop and Garwood 2024).We envision that papers addressing these challenges will be phylogenetic treatments employing next generation sequencing technologies to create large multilocus data sets, genomic or subgenomic, of extant taxa. Typically, phylogenetic systematic analyses should comprise large, exemplar-based taxon sampling and multiple gene evidence aimed to enhance robustness of hypotheses being proposed. Analytical approaches should be welljustified and include relevant relative support values (i.e., optimality criterion should be justified but there are no journal specific preferences). The discovery and description of species is a foundational step germane to all comparative evolutionary and ecological studies (Bond et al. 2021). Description of planetary arachnid species-level diversity should be an aspirational goal for the 21 st century. Concomitantly, the confounding problem of species crypsis, morphologically indistinguishable taxa that are independent evolutionary lineages, is commonly acknowledged across many arachnid orders where species boundaries have been explored using phylogeographic and population genetic approaches. For example, species crypsis in mygalomorph and grounddwelling araneomorph spiders has been well known for over a quarter of century (Bond et al. 2001) yet remains largely an unresolved problem. Although it is agreed that integrative approaches to species delimitation that examine multiple lines of evidence (e.g., genomic, morphological, behavioral, and ecological) are challenging (Bond and Stockman 2008), species delimitation based only on molecular markers using objective criteria often oversplit taxa (Sukumaran and Knowles 2017), whereas integrative approaches often rely on subjective decisions (Christophoryová et al. 2023;Newton et al. 2023;Starrett et al. 2024). Nevertheless, studies employing multiple lines of evidence with explicit underlying species conceptualization (Newton et al. 2023;Yu and Kuntner 2024;Cazzaniga and Prendini 2024) further advance the development of integrative approaches and establish robust testable hypotheses of species boundaries. Although species discovery remains one of the most significant challenges to understanding planetary biodiversity, the enormity of the problem continues to be bottlenecked by limited expertise and funding despite the global biodiversity crisis and acknowledged need for trained taxonomists; the taxonomic impediment remains a pervasive problem across all arachnid taxa (Agnarsson and Kuntner 2007;Audisio 2017;Bond et al. 2021), with countless species remaining to be discovered and described.We invite papers that focus on the species problem in arachnids. Specifically, studies that aim to define and delimit species using an integrative framework that considers genomic scale data and other data sources -morphology, ecology -are solicited. Single gene, i.e., DNA barcoding papers, that are not broadly integrative with other large data sets are more likely to be considered suitable for more taxonomically oriented journals. The editors welcome comprehensive and integrative taxonomic treatments that adhere to the types of papers that can be submitted to Frontiers. Although important, single species descriptions lacking a broader context are discouraged. This challenge calls for placing arachnid morphological diversity into an evolutionary context using a comparative framework. Although all arachnids share a highly conserved chelicerate body plan, it is highly modified across the various orders with dramatic diqerences (Rivera-Quiroz and Miller 2022) in appendage specialization, sensory organs, respiratory structures, etc. First, we envision as a goal to establish a broad and comprehensive overview and understanding of arachnid anatomy and morphological characters, a well-established anatomical ontology (e.g., spiders, sensu Ramirez et al. 2019), and resolve deep homology questions aimed toward distinguishing convergence across lineages (the latter would incorporate fossils as critical tests). Second, we envision that next steps include linking genomes and genome structure (Bryant 2024;Munegowda et al. 2025), development, and morphology to infer arachnid key innovation evolution and diversification (e.g., spinnerets and silk, venom, chelae, chemical defense, sensory systems). Key elements to addressing a grand challenge of understanding arachnid morphological evolution would employ whole genome sequencing (Bryant 2024) and tests of selection (Garrison et al. 2020); modern imaging approaches that leverage 3D reconstruction (Rix et al. 2021;Long et al. 2024), and AI/machine learning; developing a broad understanding of the arachnid extended phenotype (sexual dimorphism and mating strategies), prey capture (e.g., webs and spinning behavior in spiders), host-parasite interactions, life history characteristics; linking function, ecology, behavior, and evolution in a holistic/multimodal framework; and ultimately, integration of large qualitative and quantitative morphological data sets with phylogenies (Challenge #1) for comparative analysis (Kuntner et al. 2019;Garb et al. 2019;Wolq et al. 2019Wolq et al. , 2021;;Starrett et al. 2022).We are keenly interested in papers that explore trait evolution across a broad range of related taxa. Typically, such papers will employ cutting edge approaches to evaluating morphology and character state reconstruction. Evolutionary genomic studies that connect morphology, phenotype, and extended phenotype with underlying genomic data are also solicited. Papers will likely examine traits, morphology, anatomical features across multiple taxa and are not typically descriptions of characters that are restricted to a single species. Advances in sequencing, imaging technologies, and AI approaches such as machine learning have transformed systematics and evolutionary studies, creating new opportunities to integrate genomic, morphological, and ecological data. The Arachnid Morphology, Systematics, and Evolution section of Frontiers in Arachnid Science seeks to highlight studies that exploit these approaches, focusing on phylogenetically informed systematics, integrative species delimitation, and comparative analyses of trait evolution, including the extended phenotype. Herein we formulate three grand challenges to frame a call for papers in this section. First, constructing a robust, time-calibrated arachnid tree of life is a critical goal, requiring comprehensive genomic sampling, improved analytical pipelines, and integration of fossils to resolve major branches and their timing. Second, accurate species delimitation is essential given widespread cryptic diversity, necessitating multi-evidence approaches combining genomic, morphological, and ecological data while addressing the shortage of trained taxonomists. Third, linking phenotype to genotype through a comparative framework is key to understanding arachnid innovations and extended phenotypes, requiring whole-genome sequencing, advanced imaging, machine learning, and large-scale morphological datasets to connect form, function, ecology, and evolution. We envision this section showcasing studies that harness cutting-edge genomic sequencing and imaging technologies within integrative phylogenetic frameworks, driving transformative advances in our understanding of arachnid morphology, systematics, and evolution.