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Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies

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Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies. / Cai, Wang; Pichler, Maximilian; Biggs, Jeremy et al.
In: Ecography, 04.02.2025.

Research output: Contribution to Journal/MagazineJournal articlepeer-review

Harvard

Cai, W, Pichler, M, Biggs, J, Nicolet, P, Ewald, N, Griffiths, RA, Bush, A, Leibold, MA, Hartig, F & Yu, DW 2025, 'Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies', Ecography. https://doi.org/10.1111/ecog.07461

APA

Cai, W., Pichler, M., Biggs, J., Nicolet, P., Ewald, N., Griffiths, R. A., Bush, A., Leibold, M. A., Hartig, F., & Yu, D. W. (2025). Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies. Ecography. Advance online publication. https://doi.org/10.1111/ecog.07461

Vancouver

Cai W, Pichler M, Biggs J, Nicolet P, Ewald N, Griffiths RA et al. Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies. Ecography. 2025 Feb 4. Epub 2025 Feb 4. doi: 10.1111/ecog.07461

Author

Cai, Wang ; Pichler, Maximilian ; Biggs, Jeremy et al. / Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies. In: Ecography. 2025.

Bibtex

@article{c4c3a99ab7f24684823798f43390937c,
title = "Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies",
abstract = "Technological advances are enabling ecologists to conduct large‐scale and structured community surveys. However, it is unclear how best to extract information from these novel community data. We metabarcoded 48 vertebrate species from their eDNA in 320 ponds across England and applied the {\textquoteleft}internal structure' approach, which uses joint species distribution models (JSDMs) to explain compositions as the result of four metacommunity processes: environmental filtering, dispersal, species interactions, and stochasticity. We confirm that environmental filtering plays an important role in community assembly, and find that species' estimated environmental preferences are consistent with known ecologies. We also detect negative biotic covariances between fish and amphibians after controlling for divergent environmental preferences, consistent with predator–prey interactions (likely mediated by predator avoidance behaviour), and we detect high spatial autocorrelation for the palmate newt, consistent with its hypothesised relict distribution. Promisingly, ecologically and spatially distinctive sites are better explained by their environmental covariates and geographic locations, respectively, revealing sites where environmental filtering and dispersal limitation act more strongly. These results are consistent with the recent proposal that applying JSDMs to species distribution patterns can help reveal the relative importance of environmental filtering, dispersal limitation, and biotic interaction processes for individual sites and species. Our results also highlight the value of the modern interpretation of metacommunity ecology, which embraces the fact that assembly processes differ among species and sites. We discuss how novel community data allow for several study design improvements that will strengthen the inference of metacommunity assembly processes from observational data.",
keywords = "metabarcoding, macroecology, joint species distribution model (JSDM), Triturus cristatus, biodiversity, Aquatic eDNA",
author = "Wang Cai and Maximilian Pichler and Jeremy Biggs and Pascale Nicolet and Naomi Ewald and Griffiths, {Richard A.} and Alex Bush and Leibold, {Mathew A.} and Florian Hartig and Yu, {Douglas W.}",
year = "2025",
month = feb,
day = "4",
doi = "10.1111/ecog.07461",
language = "English",
journal = "Ecography",
issn = "0906-7590",
publisher = "Wiley-Blackwell",

}

RIS

TY - JOUR

T1 - Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies

AU - Cai, Wang

AU - Pichler, Maximilian

AU - Biggs, Jeremy

AU - Nicolet, Pascale

AU - Ewald, Naomi

AU - Griffiths, Richard A.

AU - Bush, Alex

AU - Leibold, Mathew A.

AU - Hartig, Florian

AU - Yu, Douglas W.

PY - 2025/2/4

Y1 - 2025/2/4

N2 - Technological advances are enabling ecologists to conduct large‐scale and structured community surveys. However, it is unclear how best to extract information from these novel community data. We metabarcoded 48 vertebrate species from their eDNA in 320 ponds across England and applied the ‘internal structure' approach, which uses joint species distribution models (JSDMs) to explain compositions as the result of four metacommunity processes: environmental filtering, dispersal, species interactions, and stochasticity. We confirm that environmental filtering plays an important role in community assembly, and find that species' estimated environmental preferences are consistent with known ecologies. We also detect negative biotic covariances between fish and amphibians after controlling for divergent environmental preferences, consistent with predator–prey interactions (likely mediated by predator avoidance behaviour), and we detect high spatial autocorrelation for the palmate newt, consistent with its hypothesised relict distribution. Promisingly, ecologically and spatially distinctive sites are better explained by their environmental covariates and geographic locations, respectively, revealing sites where environmental filtering and dispersal limitation act more strongly. These results are consistent with the recent proposal that applying JSDMs to species distribution patterns can help reveal the relative importance of environmental filtering, dispersal limitation, and biotic interaction processes for individual sites and species. Our results also highlight the value of the modern interpretation of metacommunity ecology, which embraces the fact that assembly processes differ among species and sites. We discuss how novel community data allow for several study design improvements that will strengthen the inference of metacommunity assembly processes from observational data.

AB - Technological advances are enabling ecologists to conduct large‐scale and structured community surveys. However, it is unclear how best to extract information from these novel community data. We metabarcoded 48 vertebrate species from their eDNA in 320 ponds across England and applied the ‘internal structure' approach, which uses joint species distribution models (JSDMs) to explain compositions as the result of four metacommunity processes: environmental filtering, dispersal, species interactions, and stochasticity. We confirm that environmental filtering plays an important role in community assembly, and find that species' estimated environmental preferences are consistent with known ecologies. We also detect negative biotic covariances between fish and amphibians after controlling for divergent environmental preferences, consistent with predator–prey interactions (likely mediated by predator avoidance behaviour), and we detect high spatial autocorrelation for the palmate newt, consistent with its hypothesised relict distribution. Promisingly, ecologically and spatially distinctive sites are better explained by their environmental covariates and geographic locations, respectively, revealing sites where environmental filtering and dispersal limitation act more strongly. These results are consistent with the recent proposal that applying JSDMs to species distribution patterns can help reveal the relative importance of environmental filtering, dispersal limitation, and biotic interaction processes for individual sites and species. Our results also highlight the value of the modern interpretation of metacommunity ecology, which embraces the fact that assembly processes differ among species and sites. We discuss how novel community data allow for several study design improvements that will strengthen the inference of metacommunity assembly processes from observational data.

KW - metabarcoding

KW - macroecology

KW - joint species distribution model (JSDM)

KW - Triturus cristatus

KW - biodiversity

KW - Aquatic eDNA

U2 - 10.1111/ecog.07461

DO - 10.1111/ecog.07461

M3 - Journal article

JO - Ecography

JF - Ecography

SN - 0906-7590

ER -