DOI: 10.5061/dryad.4f4qrfjqg
title: Bulk tissue versus amino acid carbon stable isotopes to reveal the diet and basal resource use of an invasive rodent

description: Stable isotope analysis is widely used to reconstruct food webs,
 characterize trophic relationships, and estimate dietary composition.
 However, bulk tissue stable isotope analysis (BSIA) can yield diffuse or
 imprecise estimates when dietary sources are isotopically similar. We
 compared carbon stable isotope analysis of amino acids (δ13C-EAA values)
 with BSIA (δ13C and δ15N values) to estimate diet composition and basal
 resource use of non-native, invasive house mice (Mus musculus) on Sand
 Island, part of a remote atoll in the north Pacific Ocean. We aimed to
 assess whether δ13C-EAA values could improve source differentiation and
 yield more precise diet estimates and to evaluate whether δ13C-EAA
 fingerprints could provide insight into the origin and use of basal
 resources by mice. We applied a Bayesian mixing model using δ13C-EAA
 values from a subset of 10 mice and associated diet items, with sample
 selection guided by existing BSIA and next-generation sequencing datasets.
 Diet estimates from the δ13C-EAA model closely resembled those from the
 BSIA-based model (n = 90): arthropods dominated the mouse diet, with
 smaller contributions from seabirds and plants. Moreover, estimates from
 the δ13C-EAA model were more consistent and precise than those from a BSIA
 model using the same 10 individuals, underscoring the value of informed
 sample selection. Although the use of δ13C-EAA values did not
 substantially improve separation among isotopically similar sources, it
 reinforced our previous findings. We also used δ13C-EAA fingerprinting to
 reconstruct basal resource use. Mice obtained most of their essential
 amino acids from aquatic basal sources—likely through direct consumption
 of seabird tissues or indirect consumption of scavenging
 arthropods—whereas terrestrial resources contributed far less. These
 findings highlight the role of marine-derived nutrients in this food web
 and suggest that mice may reroute energy and nutrients in the Sand Island
 system by exploiting marine subsidies. Collectively, our results suggest
 that δ13C-EAA values are most effective when paired with pre-existing
 ecological knowledge, especially for omnivores in complex food webs.
 Applied judiciously, this method may strengthen ecological inferences and
 provide additional insight into impacts of invasive species—particularly
 in vulnerable island ecosystems.
description: # Bulk tissue versus amino acid carbon stable isotopes to reveal the diet
 and basal resource use of an invasive rodent Dataset DOI:
 [10.5061/dryad.4f4qrfjqg](10.5061/dryad.4f4qrfjqg) ## Description of the
 data and file structure For this study, we used existing samples of house
 mouse hair and known diet items (including plants, arthropods, and mōlī
 feathers) from Sand Island of Kuaihelani, collected between April 2018 to
 November 2021 (Holthuijzen et al. 2023). Hair and fecal samples were
 obtained from 318 mice captured via a series of traplines across four main
 habitat types, set approximately every eight weeks. Our experimental
 design allowed us to account for differences in food source composition,
 availability, and accessibility throughout the island. All samples were
 dried and homogenized before analysis; samples were processed for carbon
 isotope analysis of amino acids at the Stable Isotope Facility at the
 University of California, Davis. ### Files and variables #### File:
 TableS1.csv **Description:** **Table S1**. NGS data of arthropods consumed
 by the herbland house mouse sample subset (*n* = 10). “FOO” indicates
 frequency of occurrence for a specific taxon; “%FOO” indicates percentage
 frequency of occurrence for a specific taxon. ##### Variables * Order =
 order of each taxon * Family = family of each taxon * Genus = genus of
 each taxon * Species = species of each taxon * FOO = frequency of
 occurrence for each taxon * %FOO = percentage frequency of occurrence for
 each taxon #### File: TableS2.csv **Description:** **Table S2**. NGS data
 of plants consumed by the herbland house mouse sample subset (*n* = 10).
 “FOO” indicates frequency of occurrence for a specific taxon; “%FOO”
 indicates percentage frequency of occurrence for a specific taxon. #####
 Variables * Order = order of each taxon * Family = family of each taxon *
 Genus = genus of each taxon * Species = species of each taxon * FOO =
 frequency of occurrence for each taxon * %FOO = percentage frequency of
 occurrence for each taxon #### File: TableS3.csv **Description:** **Table
 S3**. Means and standard deviations for amino acid *δ*^13^C values of
 mouse samples (*n* = 10) and diet item samples (*n* = 26). Relevant
 metadata are also included for each sample, including species name, sample
 mass, tissue type(s) analyzed, date collected, and location collected.
 ##### Variables * CSIA_ID, Submission_ID, Original_ID = various IDs used
 to identify individual house mouse and diet item samples * Species =
 species of each taxon (house mouse or diet item) * Order = order of each
 taxon * CSIA_sample_mass_mg = mass of each sample in milligrams for carbon
 stable isotope analysis of amino acids * CSIA_tissue = type of tissue of
 each sample used for carbon stable isotope analysis of amino acids *
 CSIA_comments = comments on the composition of each sample  * Group1 =
 mice and diet item samples (grouped into four categories *a posteriori*
 for reporting) * Group2 = mice and diet item samples (grouped into five
 categories for diet reconstruction) * Date_collected = date each sample
 was collected * Location_collected = description of where each sample was
 collected on Sand Island * Latitude, Longitude = coordinates of the exact
 location where each sample was collected on Sand Island * Sex, Age = sex
 and age of house mouse and Laysan albatross samples * Trap = ID of trap
 where arthropods or house mice were captured * Trapline_ID = ID of
 trapline where arthropods or house mice were captured * Habitat_type =
 habitat type where each sample was obtained * Trapping_session = trapping
 session during which each sample was obtained * BSIA_sample_mass_mg = mass
 of each sample in milligrams for bulk tissue stable isotope analysis *
 %N, δ15N_vs_AIR_(‰) = bulk tissue %N and *δ*^15^N value for each sample *
 %C, δ13C_vs_VPDB_(‰) = bulk tissue %C and *δ*^13^C value for each sample *
 BSIA_tissue = type of tissue of each sample used for bulk tissue stable
 isotope analysis * Remaining columns = mean and SD *δ*^13^C values for
 each amino acid (designated by a three-letter code) for each sample  ####
 File: TableS4.csv **Description:** **Table S4**. *δ*^13^C values of
 isoleucine (Ile), leucine (Leu), lysine (Lys), phenylalanine (Phe),
 threonine (Thr), and valine (Val) for samples compiled from previously
 published studies. Each sample is assigned to a basal resource category
 (aquatic, bacterial, fungal, or terrestrial) based on classifications
 reported in the original studies. ##### Variables * Citation = citation of
 published study  * Group = classification of each sample into one of four
 basal resource categories (aquatic, bacterial, fungal, or terrestrial)  *
 Taxon = taxon of each sample * Origin = location where each sample was
 collected * Remaining columns = *δ*^13^C-EAA values of Ile, Leu, Lys, Phe,
 Thr, and Val for each sample #### File: TableS5.csv
 **Description:** **Table S5**. Summary of the estimated contributions from
 four (combined) source groups overall and among individual house mice (*n*
 = 10) based on mean-centered *δ*^13^C-EAA values. Source contributions are
 reported (in %) as mean values, standard deviation, and at various
 quantiles. ##### Variables * ID = overall (i.e., "global" in the
 mixing model) and ID for each individual house mouse sample * Source = one
 of four diet source groups (arthropods, C~3~ plants, C~4~ plants, and mōlī
 / Laysan albatross) * Mean = mean estimate of each diet source
 contribution * SD = SD of each diet source contribution * Remaining
 columns = quantiles of each diet source contribution #### File:
 TableS6.csv **Description:** **Table S6**. Summary of the estimated
 contributions from five source groups overall and among individual house
 mice (*n* = 10) based on mean-centered *δ*^13^C-EAA values. Source
 contributions are reported (in %) as mean values, standard deviation, and
 at various quantiles. ##### Variables * ID = overall (i.e.,
 "global" in the mixing model) and ID for each individual house
 mouse sample * Source = one of five diet source groups (C~3~ plants, C~4~
 plants, Diptera-Ixodida, Hymenoptera-Isopoda, and mōlī / Laysan albatross)
 * Mean = mean estimate of each diet source contribution * SD = SD of each
 diet source contribution * Remaining columns = quantiles of each diet
 source contribution #### File: TableS7.csv **Description:** **Table S7**.
 Summary of the estimated contributions from four source groups overall and
 among individual house mice (*n* = 10) based on bulk tissue *δ*^13^C and
 *δ*^15^N values. Source contributions are reported (in %) as mean values,
 standard deviation, and at various quantiles. ##### Variables * ID =
 overall (i.e., "global" in the mixing model) and ID for each
 individual house mouse sample * Source = one of four diet source groups
 (arthropods, C~3~ plants, C~4~ plants, and mōlī / Laysan albatross) * Mean
 = mean estimate of each diet source contribution * SD = SD of each diet
 source contribution * Remaining columns = quantiles of each diet source
 contribution #### File: TableS8.csv **Description:** **Table S8**. Summary
 of the estimated contributions from basal resource categories overall and
 among individual house mice (*n* = 10) based on mean-centered *δ*^13^C-EAA
 values. Basal resource contributions are reported (in %) as mean values,
 standard deviation, and credible interval. ##### Variables * ID = overall
 (i.e., "global" in the mixing model) and ID for each individual
 house mouse sample * Basal resource = one of two basal resource categories
 (aquatic or terrestrial) * Mean = mean estimate of each basal resource
 contribution * SD = SD of each basal resource contribution * Remaining
 columns = quantiles of each basal resource contribution #### File:
 House_Mouse_Metadata.csv **Description:** **House mouse metadata**.
 Metadata on house mouse (*Mus musculus*) samples collected from Sand
 Island between April 2018 to May 2019 (*n* = 318). Metadata include
 individual IDs, species scientific name, order, sex, and age, as well as
 information regarding the date and location collected. ##### Variables *
 SIA ID, NGS ID = various IDs used to identify individual house mouse
 samples for stable isotope analysis (SIA) and next-generation sequencing
 (NGS) * Scientific Name = species of each taxon (*Mus musculus*) * Order =
 order of each taxon (Rodentia) * Date Collected = date each sample was
 collected * Sex, Age = sex and age of each house mouse sample * Trap = ID
 of trap where each sample was captured * Trapline ID = ID of trapline
 where each sample was captured * Habitat Type = habitat type where each
 sample was obtained * Trapping Session = trapping session during which
 each sample was obtained * Latitude, Longitude = coordinates ofthe  exact
 location where each sample was collected on Sand Island #### File:
 House_Mouse_SIA_Data.csv **Description:** **House mouse bulk tissue stable
 isotope data**. Bulk tissue stable isotope data (*δ*^13^C and *δ*^15^N
 values) for house mice (*Mus musculus*) collected from Sand Island between
 April 2018 to May 2019 (*n* = 318). ##### Variables * SIA ID = ID used to
 identify individual house mouse samples for stable isotope analysis (SIA)
 * Sample Mass (mg) = mass of each sample in milligrams for bulk tissue
 stable isotope analysis * % N, δ15N vs AIR (‰) = bulk tissue %N
 and *δ*^15^N value for each sample * % C, δ13C vs VPDB (‰) = bulk tissue
 %C and *δ*^13^C value for each sample * Tissue = type of tissue of each
 sample used for bulk tissue stable isotope analysis * Notes = Comments on
 individual samples regarding values or analysis #### File: R_script.R
 **Description:** R script associated with figures and analyses for the
 associated manuscript. ## Code/software * PRIMER-e v7 * R v4.1.2 (all
 packages listed in R script) ## Access information Other publicly
 accessible locations of the data used in this manuscript: * Holthuijzen,
 W. A., E. N. Flint, S. J. Green, J. H. Plissner, D. Simberloff, D.
 Sweeney, C. A. Wolf, and H. P. Jones. 2023a. An invasive appetite:
 combining molecular and stable isotope analyses to reveal the diet of
 introduced house mice (*Mus Musculus*) on a small, subtropical island.
 PLoS ONE 18(10):e0293092. * Holthuijzen, W. A., E. N. Flint, S. J. Green,
 J. H. Plissner, D. Simberloff, D. Sweeney, C. A. Wolf, and H. P. Jones.
 2023b. An invasive appetite: combining molecular and stable isotope
 analyses to reveal the diet of introduced house mice (*Mus Musculus*) on a
 small, subtropical island [Dataset]. Dryad: 10.5061/dryad.q573n5tnn