2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
January 21st, 2025
Version: 2
University of California, Berkeley
ecology
biorxiv

Challenges in detecting ecological interactions using sedimentary ancient DNA data

Callahan, F. M.Open in Google Scholar•Li, J. K.Open in Google Scholar•Nielsen, R.Open in Google Scholar

With increasing availability of ancient and modern environmental DNA technology, whole-community species occurrence and abundance data over time and space is becoming more available. Sedimentary ancient DNA data can be used to infer associations between species, which can generate hypotheses about biotic interactions, a key part of ecosystem function and biodiversity science. Here, we have developed a realistic simulation to evaluate five common methods from different fields for this type of inference. We find that across all methods tested, false discovery rates of inter-species associations are high under simulation conditions where the assumptions of the methods are violated in a variety of ecologically realistic ways. Additionally, we find that for more realistic simulation scenarios, with sample sizes that are currently realistic for this type of data models are typically unable to detect interactions better than random assignment of associations. Different methods perform differentially well depending on the number of taxa in the dataset. Some methods (SPIEC-EASI, SparCC) assume that there are large numbers of taxa in the dataset, and we find that SPIEC-EASI is highly sensitive to this assumption while SparCC is not. Additionally, we find that for many methods, default calibration can result in high false discovery rates. We find that for small numbers of species, no method consistently outperforms logistic and linear regression, indicating a need for further testing and methods development.

Similar Papers

biorxiv
Thu Apr 03 2025
Genetic basis of cuticular hydrocarbon variation in the desert ant
Cuticluar hydrocarbons (CHCs) are a ubiquitous component of insect cuticles that are used for a wide range of chemical signaling functions, especially recognition. Recognition and other signals are vital for the maintainance of insularity and cooperation in social insect colonies. Therefore, we expect natural selection on the composition and variabitlity of social insect CHC profiles. Selection on...
Inbar, S.
•
Saied, B.
•
Cohen, P.
•
Frenkel, Z.
...•
Privman, E.
biorxiv
Thu Apr 03 2025
Green cities and the risk for vector-borne disease transmission for humans and animals: a scoping review
Background: Greening cities is a nature-based strategy to sustainable urban development that integrates natural elements like plants or water bodies, to mitigate climate change impacts and enhance human well-being. However, urban green infrastructures (UGIs) can influence the distribution of disease vectors, potentially affecting vector-borne diseases (VBDs). UGIs may provide new suitable environm...
Mercat, M.
•
Bartholomee, C.
•
Fournet, F.
•
Alcover Amengual, M.
...•
Simard, F.
biorxiv
Thu Apr 03 2025
Advancing ecological assessment: The integration of eDNA metabarcoding into an estuarine fish index
In the face of increasing anthropogenic pressures on estuarine ecosystems, methods to efficiently and reliably assess their ecological status are essential. This study explores the integration of environmental DNA analysis into the AZTI\'s Fish Index (AFI) to assess ecological status of estuarine ecosystems. Surface water eDNA sampling and bottom trawl surveys were performed across multiple estuar...
Bhendarkar, M.
•
Canals, O.
•
Jurado, C.
•
Mendibil, I.
...•
Rodriguez-Ezpeleta, N.
biorxiv
Thu Apr 03 2025
Mammal responses to habitat degradation induced by cashew expansion in West Africa
Tropical landscapes are perishing due to high rates of land-use change. In West Africa, Guinea-Bissau lost 77% of its closed-canopy forest over the last 25 years, mostly to the expansion of cashew monoculture. To date, understanding how species cope with such changes remains a conservation priority for the region. Here we examine mammal species composition, richness, and abundance, in addition to ...
Na Mone, D.
•
Nhasse, I.
•
Soares, J.
•
Oliveira, R.
...•
Palmeirim, A. F.
biorxiv
Thu Apr 03 2025
Strip cropping in organic agriculture results in 15% higher ground beetle richness and 30% higher activity density than monocultures
Global biodiversity is declining at an unprecedented rate, with agriculture as one of the major drivers. There is mounting evidence that intercropping can increase insect biodiversity while maintaining or increasing yield. Yet, intercropping is often considered impractical for mechanized farming systems. Strip cropping is a type of intercropping that is compatible with standard farm machinery and ...
Croijmans, L.
•
Cuperus, F.
•
van Apeldoorn, D. F.
•
Bianchi, F. J. J. A.
...•
Poelman, E.
biorxiv
Wed Apr 02 2025
Lotka-Volterra Dynamics Facilitate Sustainable Biocontrol of Wastewater Sludge Bulking
Biological wastewater treatment is driven by complex interactions between prokaryotes and eukaryotes. Occasionally, filamentous bacteria species, first and foremost Ca. Microthrix parvicella, increase in abundance and lead to detrimental wastewater sludge bulking or floating, causing environmental harm and financial losses. Current mitigation strategies rely heavily on nonspecific chemical interve...
Baltes, F.
•
Weiss, A.
•
Ettl, M.
•
Dumack, K.
biorxiv
Wed Apr 02 2025
Contrasting amphibian population trend from a protected area in Madagascar reveal severe underestimation of extinction risks
The amphibian endemic fauna from Madagascar is currently facing multiple threats, including habitat loss, climate change and invasive species. Many species are listed as threatened by the IUCN, but long-term monitoring is scarce and assessments rarely account for population trends. Using a 13-year amphibian survey in the Strict Nature Reserve of Betampona (eastern Madagascar), we assessed the popu...
Porcel, X.
•
Crottini, A.
•
Freeman, K.
•
Noel, J.
...•
Dubos, N.
biorxiv
Wed Apr 02 2025
Impacts on the microbial fungal communities across water, sediment, and amphibian hosts across an urbanization gradient waterway in Worcester, Massachusetts
In a world of increasingly urbanized environments, it is critical to understand the impact on microbial communities, including fungal communities, as a measure of ecosystem health, and to document how these environments are changing. Aquatic environments, in particular, can be highly sensitive to urbanization with removal of local habitat and inputs of wastewater and contaminants, leading to a dis...
Wheeler, S. J.
•
DelCogliano, M.
•
Hare, B.
•
Bradshaw, A. J.
...•
Tabima, J. F.
biorxiv
Wed Apr 02 2025
A Bayesian approach to include Indigenous Knowledge in habitat selection functions
Indigenous Knowledge (IK) of species-habitat relationships provides in-depth understanding of species presence. While IK and Western scientific data are rarely combined in the same model, Bayesian statistics provides a method to include IK as prior knowledge (priors) and combine it with Western data. In partnership with Inupiat hunters, we developed a method to include IK in Bayesian habitat selec...
Gryba, R.
•
Von Duyke, A. L.
•
Huntington, H. P.
•
Adams, B.
...•
Auger-Methe, M.
biorxiv
Wed Apr 02 2025
A novel protistan trait database reveals functional redundancy and complementarity in terrestrial protists (Amoebozoa & Rhizaria)
The inclusion of functional traits of protists in environmental sequencing surveys, in addition to the traditional taxonomic framework, is essential for a better understanding of their roles and impacts on ecosystem processes. We provide a database of functional traits for a widespread and important clade of protists, the Amoebozoa, based on extensive literature research in eight trait categories:...
Freudenthal, J.
•
Schlegel, M.
•
Bonkowski, M.
•
Dumack, K.