DOI: 10.5061/dryad.79cnp5j5g
title: Does tidal marsh restoration lead to the recovery of trophic pathways that support estuarine fishes?

description: Evaluation of tidal marsh restoration success is typically based on the
 recovery of habitat acreage and target species. However, food-web
 structure may provide valuable insight into ecosystem functioning
 trajectories. Here, we studied restored tidal marshes of different ages
 (new, young, old; spanning 1 to 150 years) in comparison to nearby
 reference sites along the San Francisco Estuary. We asked: (i) How does
 restoration help recover energy pathways that support fish? (ii) Do fishes
 rely more on algal vs. detrital pathways in restored sites?; and
 (iii) How does food-web structure vary as a function of species
 origin and life history? To answer these questions, we sampled fish
 (n=806) and basal resources (emergent vegetation and phytoplankton; n=109)
 seasonally over two hydrologically contrasting years. Using stable
 isotopes (𝛿13C, 𝛿15N, and 𝛿34S), we calculated fish isotopic niche
 volumes, food chain lengths, and the relative importance of algal vs.
 detrital energy pathways. We found that food chains in restored sites were
 8% shorter than in their paired reference site. Additionally, the young
 and old restored sites had 37% smaller niche volumes than their
 references, but the opposite was true for the new restored site (11%
 larger), illustrating the characteristic trophic surge of early
 succession. Fishes found in restored sites relied significantly less on
 detrital energy (7% less) than fishes found in reference sites, and
 resident fishes showed 12% higher reliance on the detrital pathway than
 transient species. Finally, most of the native niche volume overlapped
 with that of introduced fish, which was in turn 38% larger, and a similar
 pattern was observed when comparing resident to transient fish. Our
 findings demonstrate that food-web structure does not immediately recover
 with tidal marsh restoration, even if fish assemblages are species-rich,
 and show that transient trophic surges may complicate restoration success
 assessments of newly restored marshes. We contend that incorporating
 recovery of energy pathways as an indicator of performance may help
 strengthen monitoring and design of wetland ecosystem restoration
 projects.
description: Using the stable isotopes carbon (δ<sup>13</sup>C),
 nitrogen (δ<sup>15</sup>N), and sulfur
 (δ<sup>34</sup>S), we characterize and compare food webs at
 six sites (three reference, three restored) spanning the low salinity zone
 of the San Francisco Bay-Delta: upstream of the Carquinez Strait and
 downstream of the Sacramento‑San Joaquin confluence. These sites represent
 a range of restoration ages (2-50+ years since breaching) and include Tule
 Red Island (breached in October 2019) and Chipps Island (slated for
 interior restoration). We reconstruct food webs by calculating food chain
 length, isotopic niche volume, and energy pathways based on isotopic
 signatures of basal resources (e.g., phytoplankton, emergent vegetation)
 and fish. All field data were collected in Winter and Summer 2020 and
 2021.
description: # Does tidal marsh restoration lead to the recovery of trophic pathways
 that support estuarine fishes? Dataset Version and Release History \*
 Current Version: 2 \* Number: 1.1.0 \* Date: 2025-08-12 \* Persistent
 identifier: n/a \* Summary of changes: n/a \* Dataset Title: Data for the
 article "Does tidal marsh restoration lead to the recovery of trophic
 pathways that support estuarine fishes?" \* Dataset Contributors: \*
 Creators: Megan D. Pagliaro, Susan E.W. De La Cruz, Isa Woo, Jake Sousa,
 Natalie Rich,\ Lenny Grimaldo, Denise Colombano, and Albert Ruhi \* Date
 of Issue: n/a \* Publisher: n/a \* License: Use of these data is covered
 by the following license: \* Title: CC0 1.0 Universal (CC0 1.0) \*
 Specification:
 [https://creativecommons.org/publicdomain/zero/1.0/](https://creativecommons.org/publicdomain/zero/1.0/); the authors respectfully request to be contacted by researchers interested in the re-use of these data so that the possibility of collaboration can be discussed. Contact Information \* Name: Megan D Pagliaro \* Affiliations: Department of Environmental Science, Policy, and Management, University of California, Berkeley \* ORCID ID: [https://orcid.org/0000-0002-9772-8158](https://orcid.org/0000-0002-9772-8158) \* Email: [megan.pagliaro@berkeley.edu](mailto:megan.pagliaro@berkeley.edu) \* Address: e-mail preferred \* Alternative Contact: Doctoral PI \* Name: Albert Ruhi \* Affiliations: Department of Environmental Science, Policy, and Management, University of California, Berkeley \* ORCID ID: [https://orcid.org/0000-0003-4011-6457](https://orcid.org/0000-0003-4011-6457) \* Email: [albert.ruhi@berkeley.edu](mailto:albert.ruhi@berkeley.edu) \* Address: 319 Wellman Hall, University of California, Berkeley \* Contributor ORCID IDs: \* Susan De La Cruz: [https://orcid.org/\[0000-0001-6315-0864](https://orcid.org/[0000-0001-6315-0864)]([https://orcid.org/0000-0001-6315-0864](https://orcid.org/0000-0001-6315-0864)) \* Isa Woo: [https://orcid.org/\[0000-0002-8447-9236](https://orcid.org/[0000-0002-8447-9236)]([https://orcid.org/0000-0002-8447-9236](https://orcid.org/0000-0002-8447-9236)) \* Jake Sousa: n/a \* Lenny Grimaldo: [https://orcid.org/\[0000-0002-2251-3689](https://orcid.org/[0000-0002-2251-3689)]([https://orcid.org/0000-0002-2251-3689](https://orcid.org/0000-0002-2251-3689)) \* Denise Colombano: [https://orcid.org/0000-0002-7237-4859](https://orcid.org/0000-0002-7237-4859) #### Data and File Overview Summary Metrics \* File count: 16 \* Total file size: 280.96 KB \* Range of individual file sizes: 4 KB - 98 KB \* File formats: .R and .csv **Table of Contents** \* FCL_V1.01.R \* MixSIAR_BySpp_V2.00.R \* NicheVolumeAllPlots_V1.01.R \* Overlap_All_V2.00.R \* FishIsoMetadata_17Mar2025_short.csv \* FCL_Data.csv \* MetaTDF.csv \* P1_Sources_EAV.csv \* P2_Sources_EAV.csv \* P3_Sources_EAV.csv \* BR_ConsumersCNS.csv \* SH_ConsumersCNS.csv \* CH_Consumers_NoCLPLSNA.csv \* WH_Consumers_NoCLP.csv \* RY_Consumers_NoCLPLSNA.csv \* TR_Consumers_NoCLPLSNA.csv \* Recommended software/tools: RStudio 2022.10.31; R version 4.2.2 **File/Folder Details** **Details For: FCL_V1.01.R** \* Description: R script containing code that runs t-tests on food-chain length (FCL) data, and plots the FCL data. See the manuscript for details. \* Format(s): .R \* Size(s): 4.1 KB \* Dimensions: N/A \* Variables: *Input: FCL_Data.csv *Output: Faceted boxplots of FCL data annotated with results of statistical testing **Details For: MixSIAR_BySpp_V2.00.R** \* Description: R script on MixSIAR models, adapted from the ‘MixSIAR’ package and vignette. The script estimates the reliance of each consumer (fish) on two basal resources (emergent vegetation and phytoplankton) via Bayesian mixing models on C,N,S stable isotope data. P1 is Browns Island (BR) and Sherman Island (SH), P2 is Chipps Island (CH) and Wheeler Island (WH), and P3 is Ryer Island and Tule Red (TR). See the manuscript for details. \* Format(s): .R \* Size(s): 19.47 KB \* Dimensions: N/A \* Variables: \* Input: *a) Consumer data: BR_ConsumersCNS.csv, SH_ConsumersCNS.csv; CH_Consumers_NoCLPLSNA.csv WH_Consumers_NoCLP.csv; RY_Consumers_NoCLPLSNA.csv; TR_Consumers_NoCLPLSNA.csv *b) Source data: P1_Sources_EAV.csv; P2_Sources_EAV.csv; P3_Sources_EAV.csv *c) Discrimination Factor: MetaTDF.csv \* Output: Process diagnostics, summary stats, and posterior plots of Bayesian mixing models; graph of data in the form of faceted boxplots **Details For: NicheVolumeAllPlots_V1.01.R** \* Description: R script on niche volumes, adapted from the “NicheRover” R package and its vignette. The script calculates the isotopic niche volume of the fish communities at all six sites using C,N,S stable isotope data. Code also includes methodology for resampling the datasets. See the manuscript for details. \* Format(s): .R \* Size(s): 68.55 KB \* Dimensions: N/A \* Variables: \* Input: FishIsoMetadata_17Mar2025_short.csv \* Outputs: *Niche volume calculations for: *a) raw data (no resampling), pooling years *b) raw data (no resampling), separating by year *c) resampling abundance (but not species), pooling years *d) resampling abundance (but not species), separating by year *e) resampling species, pooling years *f) resampling species, separating by year; \* Final faceted boxplot graphically representing the Niche Volume results **Details For: Overlap_All_V2.00.R** *Description: R script on niche volume, adapted from the “NicheRover” package and its vignette. The script calculates the isotopic niche overlap and isotopic niche volume of fishes, using C,N,S stable isotope data. See the manuscript for details. \* Format(s): .R \* Size(s): 18.84 KB \* Dimensions: N/A \* Variables:  \* Input: FishIsoMetadata_17Mar2025_short.csv \* Outputs:  *Niche overlap and niche volume for:  *a) Native vs Non-Native species, pooling years *b) Transient vs Resident species, pooling years *c) Native vs Non-Native species, separating by year *d)Transient vs Resident species, separating by year \* Final faceted boxplot graphically representing the niche overlap and niche  volume results **Details for: FishIsoMetadata_17Mar2025_short.csv** \* Description: a comma-delimited file containing mean length (mm) and stable isotope data (‰, C,N,S) of fishes collected at six tidal marshes (Browns Island; Sherman Island; Chipps Island; Wheeler; Ryer Island; Tule Red) in winter and summer of 2021 and 2021 by the authors and contributors. See the manuscript for details. \* Format(s): .csv \* Size(s): 98 KB \* Dimensions: 807 rows x 16 columns \* Variables: \* Season: Time period of collection; Winter (January-March); Summer (May-July) \* Year: Calendar year \* Habitat: The habitat fish were collected; Interior denotes interior channel; Exterior denotes exterior shoal; Channel Mouth denotes channel mouth connecting interior channel to exterior shoal (channel mouth used in winter 2020 but removed for all other seasons) \* SiteCode: Abbreviated versions of the site names; BR = Browns Island; SH = Sherman Island; CH = Chipps Island; WH = Wheeler; RY = Ryer Island; TR = Tule Red \* Site: Names of six focal tidal marsh sites \* Pair: Sites grouped in analytical blocks with one restored and one reference marsh in close proximity. P1 = Browns and Sherman; P2 = Chipps and Wheeler; P3= Ryer and Tule Red \* SiteType: Characterizes each site as either Reference (Ref) or Restored (Res) \* PairID: Combination of Pair and SiteType, unique for each wetland \* Species: Species identity (common name) of each fish; “Tridentiger Goby” represents the pooled species Shimofuri goby and Shokihaze goby \* SppAb: Abbreviated versions of species identity (common name) \* Length: Fork length in mm of each fish (standard length used for fish with no fork in the tail) \* History: Characterization of each fish species as native or introduced (non-native) to the San Francisco \* LifeHistory: Characterization of each fish species based on life history as transient or resident \* D15N: (‰); the isotopic nitrogen value of the fish tissue \* D13C: (‰); the isotopic carbon value of the fish tissue \* D34S: (‰). The isotopic sulfur value of the fish tissue **Details for: FCL_Data.csv** \* Description: a comma-delimited file containing mean stable isotope data (‰, N) of the fishes with the highest d15N at each site each year, mean stable isotope data (‰, N) of the basal resources (referred to as “baseline”; emergent vegetation and phytoplankton) at each site each year, and calculated FCL from said data collected at six tidal marshes (Browns Island; Sherman Island; Chipps Island; Wheeler; Ryer Island; Tule Red) in 2020 and 2021 by authors and contributors. See the manuscript for details. \* Format(s): .csv \* Size(s): 8 KB \* Dimensions: 95 rows x 8 columns \* Variables: \* Year: Calendar year \* Site: Names of six focal tidal marsh sites ( Browns Island, Sherman Island, Chipps Island, Wheeler, Ryer Island, Tule Red) \* Type: Characterizes each site as either Reference (Ref) or Restored (Res) \* Pair: Sites grouped in analytical blocks with one restored and one reference marsh in close proximity. P1 = Browns and Sherman; P2 = Chipps and Wheeler; P3= Ryer and Tule Red \* Species: Species identity (common name) of each fish; “Tridentiger Goby” represents the pooled species Shimofuri goby and Shokihaze goby \* D15N Fish: (‰); the isotopic nitrogen value of the fish tissue \* D15N Baseline: (‰); the combined average of the average D15N of emergent vegetation and average D15N of phytoplankton collected at that site that year \* FCL: food chain length; FCL = ((D15N top predator fish) – (D15N baseline)/3.4) + 1 **Details for: MetaTDF.csv** \* Description: a comma-delimited file containing trophic discrimination factor stable isotope data (‰, C, N, S) used as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate reliance on each pathway (and associated uncertainty). Our MixSIAR model required the inclusion of trophic discrimination factors of 2.1±6.6 ‰ for 𝛿13C and 3.1 ± 7.5 ‰ for 𝛿15N (from the Canseco et al. 2022 meta-analysis), and 1.27±1.31 ‰ for 𝛿34S (from the Raoult et al. 2024 meta-analysis). See the manuscript for details. \* Format(s): .csv \* Size(s): 4 KB \* Dimensions: 3 rows x 7 columns \* Variables \* Source: two basal resources (referred to as “source”), imputed in the model \* MeanD13C: (‰); the mean isotopic carbon trophic discrimination factor \* MeanD15N: (‰); the mean isotopic nitrogen trophic discrimination factor \* MeanD34S: (‰); the mean isotopic sulfur trophic discrimination factor \* SDD13C: (‰); the standard deviation of the isotopic carbon trophic discrimination factor \* SDD15N: (‰); the standard deviation of the isotopic nitrogen trophic discrimination factor \* SDDD34S: (‰); the standard deviation of the isotopic sulfur trophic discrimination factor **Details for: P1_Sources_EAV.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of basal resources (phytoplankton and emergent vegetation) collected at Pair 1 sites (Browns Island (ref) and Sherman Island (res)) in winter and summer of 2021 2021 by authors and contributors. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate fish reliance on each pathway (and associated uncertainty). See the manuscript for details. \* Format(s): .csv \* Size(s): 4 KB \* Dimensions: 3 rows x 8 columns \* Variables: \* Source: the two basal resources (referred to as “source”) imputed in the model; Phyto = phytoplankton; Emergent = emergent vegetation (specifically tule and typha). \* MeanD13C: (‰); the mean isotopic carbon value of the source tissue \* MeanD15N: (‰); the mean isotopic nitrogen value of the source tissue \* MeanD34S: (‰); the mean isotopic sulfur value of the source tissue \* SDD13C: (‰); the standard deviation of the isotopic carbon value of the source tissue \* SDD15N: (‰); the standard deviation of the isotopic nitrogen value of the source tissue \* SDDD34S: (‰); the standard deviation of the isotopic sulfur value of the source tissue \* n: the number of individuals/samples being averaged **Details for: P2_Sources_EAV.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of basal resources (phytoplankton and emergent vegetation) collected at Pair 2 sites (Chipps Island (ref) and Wheeler (res)) in winter and summer of 2021 2021 by authors and contributors. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate fish reliance on each pathway (and associated uncertainty). See the manuscript for details. \* Format(s): .csv \* Size(s): 4 KB \* Dimensions: 3 rows x 8 columns \* Variables: \* Source: the two basal resources (referred to as “source”) imputed in the model; Phyto = phytoplankton; Emergent = emergent vegetation (specifically tule and typha). \* MeanD13C: (‰); the mean isotopic carbon value of the source tissue \* MeanD15N: (‰); the mean isotopic nitrogen value of the source tissue \* MeanD34S: (‰); the mean isotopic sulfur value of the source tissue \* SDD13C: (‰); the standard deviation of the isotopic carbon value of the source tissue \* SDD15N: (‰); the standard deviation of the isotopic nitrogen value of the source tissue \* SDDD34S: (‰); the standard deviation of the isotopic sulfur value of the source tissue \* n: the number of individuals/samples being averaged **Details for: P3_Sources_EAV.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of basal resources (phytoplankton and emergent vegetation) collected at Pair 3 sites (Ryer Island (ref) and Tule Red (res)) in winter and summer of 2021 by authors and contributors. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate fish reliance on each pathway (and associated uncertainty). See the manuscript for details. \* Format(s): .csv \* Size(s): 4 KB \* Dimensions: 3 rows x 8 columns \* Variables: \* Source: the two basal resources (referred to as “source”) imputed in the model; Phyto = phytoplankton; Emergent = emergent vegetation (specifically tule and typha). \* MeanD13C: (‰); the mean isotopic carbon value of the source tissue \* MeanD15N: (‰); the mean isotopic nitrogen value of the source tissue \* MeanD34S: (‰); the mean isotopic sulfur value of the source tissue \* SDD13C: (‰); the standard deviation of the isotopic carbon value of the source tissue \* SDD15N: (‰); the standard deviation of the isotopic nitrogen value of the source tissue \* SDDD34S: (‰); the standard deviation of the isotopic sulfur value of the source tissue \* n: the number of individuals/samples being averaged **Details for: BR_ConsumersCNS.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of fishes collected at Browns Island in winter and summer of 2021 and 2021 by authors and contributors. All fish used in the community analysis were included, with the exception of larval fish and fish found in 2 sites or fewer. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate reliance on each pathway (and associated uncertainty). See the manuscript for details. \* Format(s): .csv \* Size(s): 8 KB \* Dimensions: 116 rows x 4 columns \* Variables: \* SppAb: Abbreviated versions of species identity (common name) of fishes. See “FishIsoMetadata_15Aug2024_short.csv” for the corresponding full name \* D13C: (‰); the isotopic carbon value of the fish tissue \* D15N: (‰); the isotopic nitrogen value of the fish tissue \* D34S: (‰). The isotopic sulfur value of the fish tissue **Details for: SH_ConsumersCNS.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of fishes collected at Sherman Island in winter and summer of 2021 and 2021 by the authors and contributors. All fish used in the community analysis were included, with the exception of larval fish and fish found in 2 sites or fewer. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate reliance on each pathway (and associated uncertainty). See the manuscript for details. \* Format(s): .csv \* Size(s): 8 KB \* Dimensions: 130 rows x 4 columns \* Variables: \* SppAb: Abbreviated versions of species identity (common name) of fishes. See “FishIsoMetadata_15Aug2024_short.csv” for the corresponding full name \* D13C: (‰); the isotopic carbon value of the fish tissue \* D15N: (‰); the isotopic nitrogen value of the fish tissue \* D34S: (‰). The isotopic sulfur value of the fish tissue **Details for: CH_Consumers_NoCLPLSNA.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of fishes collected at Chipps Island in winter and summer of 2021 and 2021 by the authors and contributors. All fish used in the community analysis were included, with the exception of larval fish and fish found in 2 sites or fewer. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate reliance on each pathway (and associated uncertainty). See the manuscript for details. \* Format(s): .csv \* Size(s): 8 KB \* Dimensions: 143 rows x 4 columns \* Variables: \* SppAb: Abbreviated versions of species identity (common name) of fishes. See “FishIsoMetadata_15Aug2024_short.csv” for the corresponding full name \* D13C: (‰); the isotopic carbon value of the fish tissue \* D15N: (‰); the isotopic nitrogen value of the fish tissue \* D34S: (‰). The isotopic sulfur value of the fish tissue **Details for: WH_Consumers_NoCLP.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of fishes collected at Wheeler in winter and summer of 2021 and 2021 by authors and contributors. All fish used in the community analysis were included with the exception of larval fish and fish found in 2 sites or less. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate reliance on each pathway (and associated uncertainty). See the manuscript for details. \* Format(s): .csv \* Size(s): 8 KB \* Dimensions: 100 rows x 4 columns \* Variables: \* SppAb: Abbreviated versions of species identity (common name) of fishes. See “FishIsoMetadata_15Aug2024_short.csv” for corresponding full name \* D13C: (‰); the isotopic carbon value of the fish tissue \* D15N: (‰); the isotopic nitrogen value of the fish tissue \* D34S: (‰). The isotopic sulfur value of the fish tissue **Details for: RY_Consumers_NoCLPLSNA.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of fishes collected at Ryer Island in winter and summer of 2021 and 2021 by authors and contributors. All fish used in the community analysis were included, with the exception of larval fish and fish found in 2 sites or fewer. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate reliance on each pathway (and associated uncertainty). Seethe manuscript for details. \* Format(s): .csv \* Size(s): 8 KB \* Dimensions: 146 rows x 4 columns \* Variables: \* SppAb: Abbreviated versions of species identity (common name) of fishes. See “FishIsoMetadata_15Aug2024_short.csv” for the corresponding full name \* D13C: (‰); the isotopic carbon value of the fish tissue \* D15N: (‰); the isotopic nitrogen value of the fish tissue \* D34S: (‰). The isotopic sulfur value of the fish tissue **Details for: TR_Consumers_NoCLPLSNA.csv** \* Description: a comma-delimited file containing stable isotope data (‰, C,N,S) of fishes collected at Tule Red in winter and summer of 2021 and 2021 by authors and contributors. All fish used in the community analysis were included, with the exception of larval fish and fish found in 2 sites or fewer. Data format was required as an input in the ‘MixSIAR’ R package in R (Stock et al. 2022) to estimate reliance on each pathway (and associated uncertainty). See the manuscript for details. \* Format(s): .csv \* Size(s): 8 KB \* Dimensions: 96 rows x 4 columns \* Variables: \* SppAb: Abbreviated versions of species identity (common name) of fishes. See “FishIsoMetadata_15Aug2024_short.csv” for the corresponding full name \* D13C: (‰); the isotopic carbon value of the fish tissue \* D15N: (‰); the isotopic nitrogen value of the fish tissue \* D34S: (‰). The isotopic sulfur value of the fish tissue