the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 30 Mar 2026
A Community-Trait-Phylogenetic Framework: Ecological and Evolutionary Integration for Soil Microarthropod Assembly
Abstract. Why does a single square meter of forest soil harbour thousands of animal species? Fifty years after Jonathan M. Anderson raised this question, soil ecology still struggles with a fragmented view on the coexistence of species. Researchers often study taxonomy, functional traits, and phylogeny in isolation. Each approach adds insight but leaves gaps in the picture of soil biodiversity.
In this paper, I propose a Community-Trait-Phylogenetic Ecology framework that integrates evolutionary and ecological perspectives to explain how soil animal communities form and persist. The framework combines three research fields:
- Biogeography – describes species composition across local, regional, and global scales.
- Functional traits – divided into α‑niche traits (resource use) and β‑niche traits (environmental tolerance), showing whether resource partitioning or filtering by environment drives community assembly.
- Phylogeny – shapes trait expression and defines the pool of species.
Evidence from the dominant soil microarthropods, springtails (Hexapoda: Collembola) and oribatid mites (Acari: Oribatida), shows the value of this framework. Global data synthesis reveals a mismatch between density and diversity, which challenges traditional biogeographic predictions. Trait analyses show that environmental filtering occurs at global scales. At regional and local scales, cryptic species that diverged millions of years ago coexist with distinct habitat preferences. In addition, ancient and recent lineages coexist across elevations. Morphological and physiological traits usually follow phylogenetic constraints. In contrast, trophic traits show high flexibility, which allows closely related species to coexist.
This integrative view shifts soil animal ecology from describing patterns to understanding the mechanisms responsible for them. It also supports predictions of community responses to climate change and land‑use change. Finally, it can guide conservation strategies for soil habitats that protect species, functional, and evolutionary diversity of soil biota.
Status: final response (author comments only)
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RC1: 'Comment on egusphere-2026-777', Anonymous Referee #1, 21 Apr 2026
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AC1: 'Reply on RC1', Ting-Wen Chen, 17 Aug 2026
Reviewer's comment: I really liked this paper for its original approach and integrative nature. It is worth publishing with little revision. Some suggestions follow below.
> Thank you very much for your positive assessment and constructive suggestions. I address each point below and indicate the corresponding changes implemented in the upcoming revised manuscript.
Reviewer's comment: Line 29: I believe the main reason why Joe Anderson called the species richness of soil invertebrates an “enigma” was that it seemed to conflict with the then popular concept of limiting similarity, as formulated by Gause and elaborated by ecologists such as G.E. Hutchinson (1959) and R. MacArthur (1967). So it might be appropriate to refer to one of these classical papers.
> This is an excellent point! In the revision, I will explicitly connect Anderson’s “enigma” to the classical limiting‑similarity framework and cite key formulations by Gause, Hutchinson (1959), and MacArthur (1967) to clarify the conceptual tension.
Reviewer's comment: Line 49: determination = identification
> This will be corrected.
Reviewer's comment: Line 90: Variations = Variation
> This will be corrected.
Reviewer's comment: Line 110: show strong = show a strong
> This will be corrected.
Reviewer's comment: Line 111: signal = signals
> This will be corrected.
Reviewer's comment: Line 121: I think it would be helpful here to indicate what are the “traditional perspectives” that you refer to. Can you mention a key paper that has promoted this argument, e.g. that the common linear rank abundance graphs (that also hold for Collembola and Oribatida) suggest that higher overall abundance implies more scope for rare species.
> Thank you for this suggestion. I will remove the vague term “traditional” and explicitly refer to the “more‑individuals hypothesis”.
Reviewer's comment: Line 143: I don’t understand what you mean by “more directly”. More than what? Can something be more direct than direct? Delete “more”.
> Agreed. The word “more” will be deleted.
Reviewer's comment: Line 152: The study = Studies
> This will be corrected.
Reviewer's comment: Line 185: “physiological functions” – what about morphological traits?
> Ture. I will expand the text to include both physiological functions and morphological traits.
Reviewer's comment: Line 219: What is missing here is a prospect that depicts how the new framework can be used in practice. I understand that you cannot include a complete data analysis in this paper, but maybe you can refer to ongoing work or papers to come that report a statistical analysis proving the correctness of the framework presented in this paper.
> Thank you for raising this important point. As a concrete starting point, I will add a brief note pointing readers to a preliminary implementation sketch in Chapter 6 (p. 147) of my dissertation at the University of Göttingen, and to the empirical application in Xie et al. (2022, Journal of Biogeography), which is already cited in the manuscript. I will also clarify that a full tutorial with step‑by‑step statistical analyses would exceed the scope of this conceptual paper and is better suited to a separate methods article. To lower the entry barrier in the meantime, I will add a short glossary of key terms and concepts to help soil ecologists navigate the interdisciplinary vocabulary and analytical techniques required to apply the framework.
Citation: https://doi.org/10.5194/egusphere-2026-777-AC1
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AC1: 'Reply on RC1', Ting-Wen Chen, 17 Aug 2026
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RC2: 'Comment on egusphere-2026-777', Elizabeth Bach, 02 Jul 2026
Dear Dr. Chen,
I have reviewed your manuscript “A community-trait-phylogenetic framework: Ecological and evolutionary integration for soil microarthropod assembly” submitted to SOIL. The proposed framework seeks to advance mechanistic understanding of high rates of soil biodiversity at multiple scales by integrating ecological, evolutionary, and biogeographical selections on species and traits. The manuscript provides new insights that could inspire the soil ecological community to synthesize and explore data in new ways that could lead to new insights into the mechanisms supporting high soil biodiversity. The high-level example from existing springtail and oribatid mite data provide important grounding for the framework, demonstrating how researchers could integrate broad mechanisms to lead to new insights.
To apply this framework will require teams of scientists with expansive knowledge, to bring together the evolutionary, ecological, and biogeographical components and sort through complex data to determine which traits/community interactions/distributions are influenced by which forces. The examples from springtails and oribatid mites are important opportunities to pursue these deeper insights, but it will be a high bar to meet for future data sets. On the other hand, soil biodiversity work is more expansive and collaborative now than ever before, and this framework provides a potentially useful approach for the next generation of soil ecological knowledge. As mentioned, trait-based ecology is often heralded as simplifying the process of understanding biodiversity patterns, especially for small and difficult to identify taxa. However, for this framework, it seems trait data would need to be coupled with some taxonomic/evolutionary data, which seems like species identification will be necessary. The manuscript is a bit ambiguous on the depth and breadth of soil ecological and evolutionary knowledge is needed to collectively adapt the framework. Some taxonomic identification will be needed to infer evolutionary relationships (as well as strong phylogenetic understanding of soil taxonomic groups that are under-studied). For example, “However, until today evolutionary perspectives are little considered by soil ecologists as it requires specific conceptual and practical skills.” (lines 63-64). It’s not clear to me what the “specific conceptual and practical skills” are. The author hints at the history of soil ecology and evolutionary work happening separately but doesn’t really address the challenges and practicalities of bringing these experts together.
I appreciate the call that this framework can provide an opportunity for conservation work to integrate both ecological and evolutionary processes in protecting and sustaining soil biodiversity now and in the future (lines 204-209). This is a tantalizing thought provided without an example of how or if conservation practitioners and strategists are likely to receive, understand, and apply the conclusions of such studies. I recognize that may be beyond the scope of the manuscript, but to mention this as a strength of the framework does leave the reader wanting some additional context. It would be incredibly exciting to have more conservation priorities informed by soil biodiversity and the processes that support it.
Citation: https://doi.org/10.5194/egusphere-2026-777-RC2 -
AC2: 'Reply on RC2', Ting-Wen Chen, 06 Sep 2026
I thank the reviewer for the thoughtful and constructive evaluation of the manuscript. I appreciate the recognition of the framework’s ambition to integrate ecological, evolutionary, and biogeographical processes, as well as the value of the springtail and oribatid mite examples. Below I respond to each major point and describe the corresponding revisions I will make.
Reviewer’s comment:
The proposed framework seeks to advance mechanistic understanding of high rates of soil biodiversity at multiple scales by integrating ecological, evolutionary, and biogeographical selections on species and traits. The manuscript provides new insights that could inspire the soil ecological community to synthesize and explore data in new ways that could lead to new insights into the mechanisms supporting high soil biodiversity. The high-level example from existing springtail and oribatid mite data provide important grounding for the framework, demonstrating how researchers could integrate broad mechanisms to lead to new insights.
> I am grateful for this positive assessment.
Reviewer’s comment:
To apply this framework will require teams of scientists with expansive knowledge, to bring together the evolutionary, ecological, and biogeographical components and sort through complex data to determine which traits/community interactions/distributions are influenced by which forces. The examples from springtails and oribatid mites are important opportunities to pursue these deeper insights, but it will be a high bar to meet for future data sets.
> I agree that full implementation is demanding. In response, I will explicitly define a “minimum viable team” and “minimum viable dataset” to avoid implying that all components must be realized at once. I will add a new subsection titled “Practical implementation: minimum viable team and data,” which will outline:
- Minimum team roles: taxonomy/phylogeny specialists, trait ecologists, biogeographers/spatial statisticians, and data engineers (for ontologies and database integration).
- Minimum data requirements: species-level (or near-species) identification sufficient for reliable phylogenetic inference; a core set of functional traits related to environmental tolerance, resource acquisition, dispersal, and life history (or any other trait-based framework for soil organisms); standardized sampling designs at multiple spatial, temporal, and taxonomic/phylogenetic scales; time-calibrated phylogenies or suitable molecular proxies for phylogenetic backbones.
- A phased strategy: initial tests focusing on a single taxonomic group (e.g., oribatid mites or a springtail family) at regional scales, followed by extension to multiple groups and cross-continental analyses.
These additions will make the pathway from concept to practice more concrete and achievable.
Reviewer’s comment:
However, for this framework, it seems trait data would need to be coupled with some taxonomic/evolutionary data, which seems like species identification will be necessary. Some taxonomic identification will be needed to infer evolutionary relationships (as well as strong phylogenetic understanding of soil taxonomic groups that are under-studied).
> I agree and appreciate this important clarification. The framework is not intended to replace taxonomy with traits, but to use traits as mechanistic bridges built upon a robust taxonomic (and phylogenetic) foundation for understanding community assembly mechanisms. In that revised text, I will emphasize that taxonomic units, ideally species or near-species entities that can be mapped to interpretable clades, are informative for inferring phylogenetic relationships. For understudied groups, I will note that taxonomy can serve as a proxy for phylogey when molecular data are incomplete for taxa in the species pool. These revisions will make clear that taxonomic identification remains essential, while also offering pragmatic strategies for data-limited contexts.
Reviewer’s comment:
The manuscript is a bit ambiguous on the depth and breadth of soil ecological and evolutionary knowledge is needed to collectively adapt the framework. For example, ‘However, until today evolutionary perspectives are little considered by soil ecologists as it requires specific conceptual and practical skills.’ (lines 63–64). It’s not clear to me what the ‘specific conceptual and practical skills’ are.
> I thank the reviewer for highlighting this ambiguity. I will rewritw and expand this passage to specify the required knowledge and skills more concretely. I wll also include a short glossary of key terms and concepts to help soil ecologists navigate the interdisciplinary vocabulary and analytical techniques required to apply the framework.
Reviewer’s comment:
The author hints at the history of soil ecology and evolutionary work happening separately but doesn’t really address the challenges and practicalities of bringing these experts together.
> I agree that this aspect is underdeveloped. I will add a new (but short) paragraph on “Practical pathways and bottlenecks for cross-disciplinary collaboration,” which will address:
Main challenges, including:
- Differences in terminology and ontologies (the same term meaning different concepts across fields),
- Inconsistent data standards (sampling designs, trait definitions, phylogeny construction methods), and
- Academic incentive structures that undervalue long-term taxonomic work and data integration.
Potential feasible pathways, including:
- Building collaborations among experts with different expertise around shared research questions (e.g., community assembly along elevational gradients) and share data dictionaries and analysis pipelines,
- Modular division of labor (taxonomy, traits, phylogeny, modeling) with regular integration points through meetings or workshops, and
- Leveraging existing platforms and networks (global soil biodiversity initiatives, regional databases) to reduce startup costs.
I will also explicitly acknowledge limitations; for example, in many regions and taxa, basic taxonomic and phylogenetic knowledge remains insufficient, so full implementation of the framework will necessarily be gradual.
Reviewer’s comment:
I appreciate the call that this framework can provide an opportunity for conservation work to integrate both ecological and evolutionary processes in protecting and sustaining soil biodiversity now and in the future (lines 204–209). This is a tantalizing thought provided without an example of how or if conservation practitioners and strategists are likely to receive, understand, and apply the conclusions of such studies. I recognize that may be beyond the scope of the manuscript, but to mention this as a strength of the framework does leave the reader wanting some additional context. It would be incredibly exciting to have more conservation priorities informed by soil biodiversity and the processes that support it.
> I appreciate this constructive suggestion and agree that the conservation implications should be more than conceptual. I will expand the conservation paragraph to include a brief but concrete application scenario illustrating how the framework could be translated into conservation decision support. Specifically, I will add a short example (presented as a boxed text) on prioritizing soil biodiversity conservation in agricultural landscapes. The framework can be used to identify hotspots characterized by high evolutionary distinctiveness, high functional diversity, and high biogeographic rarity. These hotspots can then be overlaid with existing land-use and protected-area networks to propose priority management units. I will also discuss linking trait–function relationships (e.g., organic matter decomposition) to ecosystem-service risks that can be communicated to policymakers and agricultural agencies. I will note current limitations: most conservation decisions still prioritize aboveground biodiversity and habitat types, and integrating soil biota requires demonstration cases and shared indicators. I will position the framework as having the potential to be incorporated into an indicator architecture that could be co-developed with conservation practitioners.
Reviewer’s comment:
The manuscript is a bit ambiguous on the depth and breadth of soil ecological and evolutionary knowledge is needed to collectively adapt the framework.
> To address this, I will more clearly distinguish between the “vision level” and the “operational level”. I will add a sentense stating that the goal is to propose a framework, not to claim full implementation. I will also add a “Limitations and next steps” subsection that explicitly identifies current constraints, including taxonomic gaps, the scarcity and fragmented availability of trait data, and phylogenetic uncertainty, and outlines feasible short-term research steps.
I hope these revisions and clarifications will address the reviewer’s concerns and make the framework more actionable. I am grateful for the reviewer’s insightful comments, which substantially improve the manuscript.
Citation: https://doi.org/10.5194/egusphere-2026-777-AC2
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AC2: 'Reply on RC2', Ting-Wen Chen, 06 Sep 2026
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I really liked this paper for its original approach and integrative nature. It is worth publishing with little revision. Some suggestions follow below.
Line 29: I believe the main reason why Joe Anderson called the species richness of soil invertebrates an “enigma” was that it seemed to conflict with the then popular concept of limiting similarity, as formulated by Gause and elaborated by ecologists such as G.E. Hutchinson (1959) and R. MacArthur (1967). So it might be appropriate to refer to one of these classical papers.
Line 49: determination = identification
Line 90: Variations = Variation
Line 110: show strong = show a strong
Line 111: signal = signals
Line 121: I think it would be helpful here to indicate what are the “traditional perspectives” that you refer to. Can you mention a key paper that has promoted this argument, e.g. that the common linear rank abundance graphs (that also hold for Collembola and Oribatida) suggest that higher overall abundance implies more scope for rare species.
Line 143: I don’t understand what you mean by “more directly”. More than what? Can something be more direct than direct? Delete “more”.
Line 152: The study = Studies
Line 185: “physiological functions” – what about morphological traits?
Line 219: What is missing here is a prospect that depicts how the new framework can be used in practice. I understand that you cannot include a complete data analysis in this paper, but maybe you can refer to ongoing work or papers to come that report a statistical analysis proving the correctness of the framework presented in this paper.