Jason E. Bond1*
Matjaž Kuntner2,3,4,5- 1Department of Entomology and Nematology, University of California Davis, Davis, CA, United States
- 2Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
- 3Jovan Hadži Institute of Biology, ZRC SAZU, Ljubljana, Slovenia
- 4Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei, China
- 5Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
The chelicerate class Arachnida is a diverse, ancient, and ecologically important lineage of largely terrestrial taxa comprising >12 orders, with spiders (Araneae) and mites (acarines) composing over 80% of the ~120,000 nominal species (Kuntner, 2022; Sharma and Gavish-Regev, 2025); many more species and higher-level taxonomic groups (genera and families) remain to be discovered (Opatova et al., 2020; Hebets et al., 2024; Dunlop and Garwood, 2024). Methodological innovation in sequencing (Starrett et al., 2017; Garb et al., 2018) and morphological imaging (Wood and Parkinson, 2019; Rix et al., 2021; Loria et al., 2024) over the last 10–15 years has been incredibly transformative for arthropod systematic and evolutionary studies. The Morphology, Systematics, and Evolution section of Frontiers in Arachnid Science seeks to publish papers that capitalize on these new and transformative approaches. No doubt papers in this section may broadly overlap with other sections (e.g., Ecology and Behavior (Schausberger, 2022); Diversity, Conservation and Biogeography (Agnarsson, 2023); Genetics and Biomaterials (Blamires, 2024)), however, the primary focus of this section will include systematic, evolutionary, and comparative papers.
We would especially welcome papers addressing the following three grand challenges:
1. Broadly resolving phylogenetic relationships across all hierarchical levels of the arachnid tree of life
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 data sets 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 with a 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), is expected to advance arachnid genomics considerably. Developing new pipelines for data analysis and cost-effective 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., 2020; 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 at enhancing the robustness of hypotheses being proposed. Analytical approaches should be well-justified and include relevant relative support values (i.e., optimality criterion should be justified but there are no journal-specific preferences).
2. Employing accurate species delimitation and resolving cryptic diversity
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 21st 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 ground-dwelling araneomorph spiders has been well known for over a quarter of a 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 oversplits 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.
3. Investigating trait evolution and linking phenotype to genotype
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 differences (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 and Michalik, 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 et al., 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 et al., 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; 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, and life history characteristics; linking of 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; Wolff et al., 2019; Wolf 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, and anatomical features across multiple taxa and are not typically descriptions of characters that are restricted to a single species.
To conclude, 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 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 data sets 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 morphology, systematics, and evolution.
Author contributions
JB: Writing – original draft. MK: Writing – original draft.
Funding
The author(s) declared that financial support was not received for this work and/or its publication.
Conflict of interest
The authors declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
The authors JB, MK declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.
Generative AI statement
The author(s) declared that generative AI was not used in the creation of this manuscript.
Any alternative text (alt text) provided alongside figures in this article has been generated by Frontiers with the support of artificial intelligence and reasonable efforts have been made to ensure accuracy, including review by the authors wherever possible. If you identify any issues, please contact us.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
References
Agnarsson I. (2023). Grand challenges in research on arachnid diversity, conservation, and biogeography. Front. Arachn Sci. 2. doi: 10.3389/frchs.2023.1101141
Agnarsson I. and Kuntner M. (2007). Taxonomy in a changing world: seeking solutions for a science in crisis. Syst. Biol. 56, 531–539. doi: 10.1080/10635150701424546
Audisio P. (2017). Insect taxonomy, biodiversity research and the new taxonomic impediments. Fragm Entomol. 49, 121. doi: 10.4081/fe.2017.252
Ballesteros J. A., Santibáñez-López C. E., Baker C. M., Benavides L. R., Cunha T. J., Gainett G., et al. (2022). Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida. Mol. Biol. Evol. 39, msac021. doi: 10.1093/molbev/msac021
Blamires S. J. (2024). Grand challenges in arachnid genetics and biomaterials. Front. Arachn Sci. 3. doi: 10.3389/frchs.2024.1356170
Bond J. E., Garrison N. L., Hamilton C. A., Godwin R. L., Hedin M., and Agnarsson I. (2014). Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution. Curr. Biol. 24, 1765–1771. doi: 10.1016/j.cub.2014.06.034
Bond J. E., Godwin R. L., Colby J. D., Newton L. G., Zahnle X. J., Agnarsson I., et al. (2021). Improving taxonomic practices and enhancing its extensibility—an example from araneology. Diversity 14, 5. doi: 10.3390/d14010005
Bond J. E., Hedin M. C., Ramirez M. G., and Opell B. D. (2001). Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus. Mol. Ecol. 10, 899–910. doi: 10.1046/j.1365-294X.2001.01233.x
Bond J. E. and Stockman A. K. (2008). An integrative method for delimiting cohesion species: finding the population-species interface in a group of Californian trapdoor spiders with extreme genetic divergence and geographic structuring. Syst. Biol. 57, 628–646. doi: 10.1080/10635150802302443
Bryant M. J., Coello A. M., Glendening A. M., Hilliman S. A. III, Jara C. F., Pring S. S., et al. (2024). Unveiling the genetic blueprint of a desert scorpion: a chromosome-level genome of Hadrurus arizonensis provides the first reference for Parvorder Iurida. Genome Biol. Evol. 16, evae097. doi: 10.1093/gbe/evae097
Cazzaniga N. and Prendini L. (2024). Integrative systematics reveals cryptic diversity in Paraphrynus whip spiders (Amblypygi: Phrynidae) from Southwestern North America. Diversity 16, 669. doi: 10.3390/d16110669
Christophoryová J., Krajčovičová K., Šťáhlavský F., Španiel S., and Opatova V. (2023). Integrative taxonomy approach reveals cryptic diversity within the phoretic pseudoscorpion genus Lamprochernes (Pseudoscorpiones: Chernetidae). Insects 14, 122. doi: 10.3390/insects14020122
Derkarabetian S., Lord A., Angier K., Frigyik E., and Giribet G. (2023). An Opiliones-specific ultraconserved element probe set with a near-complete family-level phylogeny. Mol. Phylog Evol. 187, 107887. doi: 10.1016/j.ympev.2023.107887
Dunlop J. A. and Garwood R. J. (2024). A review of fossil scorpion higher systematics. PeerJ 12, e18557. doi: 10.7717/peerj.18557
Faircloth B. C., Branstetter M. G., White N. D., and Brady S. G. (2015). Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol. Ecol. Res. 15, 489–501. doi: 10.1111/1755-0998.12328
Garb J. E., Haney R. A., Schwager E. E., Gregorič M., Kuntner M., Agnarsson I., et al. (2019). The transcriptome of Darwin’s bark spider silk glands predicts proteins contributing to dragline silk toughness. Commun. Biol. 2, 275. doi: 10.1038/s42003-019-0496-1
Garb J. E., Sharma P. P., and Ayoub N. A. (2018). Recent progress and prospects for advancing arachnid genomics. Curr. Opin. Insect Sci 25, 51–57. doi: 10.1016/j.cois.2017.11.005
Garrison N. L., Brewer M. S., and Bond J. E. (2020). Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex. BMC Evol. Biol. 20, 68. doi: 10.1186/s12862-020-01606-7
Garrison N. L., Rodriguez J., Agnarsson I., Coddington J. A., Griswold C. E., Hamilton C. A., et al. (2016). Spider phylogenomics: untangling the spider tree of life. PeerJ 4, e1719. doi: 10.7717/peerj.1719
Gorneau J. A., Crews S. C., Cala-Riquelme F., Montana K. O., Spagna J. C., Ballarin F., et al. (2023). Webs of intrigue: museum genomics elucidate relationships of the marronoid spider clade (Araneae). Ins Syst. Div. 7, 5. doi: 10.1093/isd/ixad021
Hebets E. A., Oviedo-Diego M., Cargnelutti F., Bollatti F., Calbacho-Rosa L., Mattoni C. I., et al. (2024). A scientist’s guide to Solifugae: how solifuges could advance research in ecology, evolution, and behaviour. Zool. J. Linn. Soc 202, zlad174. doi: 10.1093/zoolinnean/zlad174
Kulkarni S., Wood H. M., and Hormiga G. (2023). Advances in the reconstruction of the spider tree of life: a roadmap for spider systematics and comparative studies. Cladistics 39, 479–532. doi: 10.1111/cla.12557
Kulkarni S., Wood H., Lloyd M., and Hormiga G. (2020). Spider-specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae). Mol. Ecol. Res. 20, 185–203. doi: 10.1111/1755-0998.13099
Kuntner M. (2022). The seven grand challenges in arachnid science. Front. Arachn Sci. 1. doi: 10.3389/frchs.2022.1082700
Kuntner M., Čandek K., Gregorič M., Turk E., Hamilton C. A., Chamberland L., et al. (2023). Increasing information content and diagnosability in family-level classifications. Syst. Biol. 72, 964–971. doi: 10.1093/sysbio/syad021
Kuntner M., Hamilton C. A., Cheng R.-C., Gregorič M., Lupše N., Lokovšek T., et al. (2019). Golden orbweavers ignore biological rules: phylogenomic and comparative analyses unravel a complex evolution of sexual size dimorphism. Syst. Biol. 68, 555–572. doi: 10.1093/sysbio/syy082
Long E. J., Edgecombe G. D., Clark B., Hatch C., Ball A. D., and Ma X. (2024). Mouthpart morphology and feeding structures in the palaeocharinid trigonotarbids of the Rhynie chert: insights from comparisons to modern arachnids. Palaeontology 67, e12717. doi: 10.1111/pala.12717
Loria S. F., Ehrenthal V. L., and Esposito L. A. (2024). Revisiting the scorpion central nervous system using microCT. Sci. Rep. 14, 27961. doi: 10.1038/s41598-024-76917-6
Lozano-Fernandez J., Tanner A. R., Giacomelli M., Carton R., Vinther J., Edgecombe G. D., et al. (2019). Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nat. Commun. 10, 2295. doi: 10.1038/s41467-019-10244-7
Magalhaes I. L. F., Azevedo G. H. F., Michalik P., and Ramírez M. J. (2020). The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic. Biol. Rev. 95:184–217. doi: 10.1111/brv.12559
Munegowda C., Pechmann M., Prpic-Schäper N., and Turetzek N. (2025). Gene and genome duplication in spiders. J. Exp. Zool Pt B. 344:379–393. doi: 10.1002/jez.b.23304
Newton L. G., Starrett J., Jochim E. E., and Bond J. E. (2023). Phylogeography and cohesion species delimitation of California endemic trapdoor spiders within the Aptostichus icenoglei sibling species complex (Araneae: Mygalomorphae: Euctenizidae). Ecol. Evol. 13, e10025. doi: 10.1002/ece3.10025
Opatova V., Hamilton C. A., Hedin M., De Oca L. M., Král J., and Bond J. E. (2020). Phylogenetic systematics and evolution of the spider infraorder Mygalomorphae using genomic scale data. Syst. Biol. 69, 671–707. doi: 10.1093/sysbio/syz064
Ramirez M. and Michalik P. (2019). The spider anatomy ontology (SPD)—a versatile tool to link anatomy with cross-disciplinary data. Diversity 11, 202. doi: 10.3390/d11100202
Rivera‐Quiroz F. A. and Miller J. A. (2022). Micro‐CT visualization of the CNS: Performance of different contrast‐enhancing techniques for documenting the spider brain. J of Comparative Neurology. 530(14), 2474–2485. doi: 10.1002/cne.25343
Rix M. G., Wood H. M., Harvey M. S., and Michalik P. (2021). Micro-computed tomography reveals a remarkable twin intromittent organ in spiders – a novelty for arachnids with direct sperm transfer. Front. Ecol. Evol. 9. doi: 10.3389/fevo.2021.794708
Schausberger P. (2022). Grand challenges and bold opportunities in arachnid ecology and behavior. Front. Arachn Sci. 1. doi: 10.3389/frchs.2022.1097945
Sharma P. P., Ballesteros J. A., and Santibáñez-López C. E. (2021). What is an “arachnid”? consensus, consilience, and confirmation bias in the phylogenetics of Chelicerata. Diversity 13, 568. doi: 10.3390/d13110568
Sharma P. P. and Gavish-Regev E. (2025). The evolutionary biology of Chelicerata. Ann. Rev. Entomol. 70, 143–163. doi: 10.1146/annurev-ento-022024-011250
Starrett J., Derkarabetian S., Hedin M., Bryson R. W., McCormack J. E., and Faircloth B. C. (2017). High phylogenetic utility of an ultraconserved element probe set designed for Arachnida. Mol. Ecol. Res. 17, 812–823. doi: 10.1111/1755-0998.12621
Starrett J., Jochim E. E., Quayle I. L., Zahnle X. J., and Bond J. E. (2024). Microgeographic population structuring in a genus of California trapdoor spiders and discovery of an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.). Ecol. Evol. 14(3), e10983. doi: 10.1002/ece3.10983
Starrett J., McGinley R. H., Hebets E. A., and Bond J. E. (2022). Phylogeny and secondary sexual trait evolution in Schizocosa wolf spiders (Araneae, Lycosidae) shows evidence for multiple gains and losses of ornamentation and species delimitation uncertainty. Mol. Phyl Evol. 169, 107397. doi: 10.1016/j.ympev.2022.107397
Sukumaran J. and Knowles L. L. (2017). Multispecies coalescent delimits structure, not species. Proc. Natl. Acad. Sci. U.S.A. 114, 1607–1612. doi: 10.1073/pnas.1607921114
Van Dam M. H., Trautwein M., Spicer G. S., and Esposito L. (2019). Advancing mite phylogenomics: designing ultraconserved elements for Acari phylogeny. Mol. Ecol. Res. 19, 465–475. doi: 10.1111/1755-0998.12962
Wolff J. O., Paterno G. B., Liprandi D., Ramírez M. J., Bosia F., Meijden A., et al. (2019). Evolution of aerial spider webs coincided with repeated structural optimization of silk anchorages. Evolution 73, 2122–2134. doi: 10.1111/evo.13834
Wolff J. O., Wierucka K., Uhl G., and Herberstein M. E. (2021). Building behavior does not drive rates of phenotypic evolution in spiders. Proc. Natl. Acad. Sci. U.S.A. 118, e2102693118. doi: 10.1073/pnas.2102693118
Wood H. M. and Parkinson D. Y. (2019). Comparative morphology of cheliceral muscles using high-resolution X-ray microcomputed-tomography in palpimanoid spiders (Araneae, Palpimanoidea). J. Morph 280, 232–243. doi: 10.1002/jmor.20939
Yu K.-P., Cheng R.-C., Haddad C. R., Tanikawa A., Pett B. L., Piacentini L. N., et al. (2025). Systematics and evolutionary history of raft and nursery-web spiders (Araneae: Dolomedidae and Pisauridae). Zool. Scr 54, 421–435. doi: 10.1111/zsc.12719
Yu K.-P. and Kuntner M. (2024). Discovering unknown Madagascar biodiversity: integrative taxonomy of raft spiders (Pisauridae: Dolomedes). PeerJ 12, e16781. doi: 10.7717/peerj.16781
Keywords: arachnid evolution, species delimitation, taxonomy, genomics, comparative method
Citation: Bond JE and Kuntner M (2025) Grand challenges in morphology, systematics, and evolution. Front. Arachn. Sci. 4:1713046. doi: 10.3389/frchs.2025.1713046
Received: 25 September 2025; Accepted: 26 November 2025; Revised: 25 November 2025;
Published: 19 December 2025.
Edited and reviewed by:
Peter Schausberger, University of Vienna, AustriaCopyright © 2025 Bond and Kuntner. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Jason E. Bond, amJvbmRAdWNkYXZpcy5lZHU=