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      An invasive appetite: Combining molecular and stable isotope analyses to reveal the diet of introduced house mice ( Mus musculus) on a small, subtropical island

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          Abstract

          House mice ( Mus musculus) pose a conservation threat on islands, where they adversely affect native species’ distributions, densities, and persistence. On Sand Island of Kuaihelani, mice recently began to depredate nesting adult mōlī (Laysan Albatross, Phoebastria immutabilis). Efforts are underway to eradicate mice from Sand Island, but knowledge of mouse diet is needed to predict ecosystem response and recovery following mouse removal. We used next-generation sequencing to identify what mice eat on Sand Island, followed by stable isotope analysis to estimate the proportions contributed by taxa to mouse diet. We collected paired fecal and hair samples from 318 mice between April 2018 to May 2019; mice were trapped approximately every eight weeks among four distinct habitat types to provide insight into temporal and spatial variation. Sand Island’s mice mainly consume arthropods, with nearly equal (but substantially smaller) contributions of C 3 plants, C 4 plants, and mōlī. Although seabird tissue is a small portion of mouse diet, mice consume many detrital-feeding arthropods in and around seabird carcasses, such as isopods, flesh flies, ants, and cockroaches. Additionally, most arthropods and plants eaten by mice are non-native. Mouse diet composition differs among habitat types but changes minimally throughout the year, indicating that mice are not necessarily limited by food source availability or accessibility. Eradication of house mice may benefit seabirds on Sand Island (by removing a terrestrial, non-native predator), but it is unclear how arthropod and plant communities may respond and change. Non-native and invasive arthropods and plants previously consumed (and possibly suppressed) by mice may be released post-eradication, which could prevent recovery of native taxa. Comprehensive knowledge of target species’ diet is a critical component of eradication planning. Dietary information should be used both to identify and to monitor which taxa may respond most strongly to invasive species removal and to assess if proactive, pre-eradication management activities are warranted.

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          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            DADA2: High resolution sample inference from Illumina amplicon data

            We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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              Cutadapt removes adapter sequences from high-throughput sequencing reads

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Formal analysisRole: InvestigationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Funding acquisitionRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Formal analysisRole: InvestigationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                19 October 2023
                2023
                : 18
                : 10
                : e0293092
                Affiliations
                [1 ] Department of Ecology & Evolutionary Biology, University of Tennessee at Knoxville, Knoxville, Tennessee, United States of America
                [2 ] Marine National Monuments of the Pacific, U.S. Fish and Wildlife Service, Honolulu, Hawaiʻi, United States of America
                [3 ] Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, United States of America
                [4 ] Midway Atoll National Wildlife Refuge, U.S. Fish and Wildlife Service, Waipahu, Hawaiʻi, United States of America
                [5 ] Institute for Health Research & Policy, University of Illinois at Chicago, Chicago, Illinois, United States of America
                [6 ] Island Conservation, Santa Cruz, California, United States of America
                [7 ] Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
                [8 ] Institute for the Study of the Environment, Sustainability, and Energy, Northern Illinois University, DeKalb, Illinois, United States of America
                Shiv Nadar University, INDIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0002-4280-3288
                https://orcid.org/0000-0003-2781-359X
                https://orcid.org/0000-0002-1424-9291
                https://orcid.org/0000-0002-5512-9958
                Article
                PONE-D-23-12674
                10.1371/journal.pone.0293092
                10586637
                37856477
                e8866732-605b-4a6e-95a0-d15a44806a23

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 26 April 2023
                : 4 October 2023
                Page count
                Figures: 4, Tables: 3, Pages: 28
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: DG#-1842161
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100007058, Northern Illinois University;
                Award ID: Elwood and Ruth Briles Memorial Fund
                Award Recipient :
                Funded by: Sigma Xi
                Award ID: G20200315103593991
                Award Recipient :
                Funded by: Island Conservation
                Award Recipient :
                This research was funded the National Science Foundation Graduate Research Fellowship Program (DG#-1842161; https://www.nsfgrfp.org/; WAH), Northern Illinois University Elwood and Ruth Briles Memorial Fund ( https://niu.academicworks.com/opportunities/17418; WAH), Sigma Xi Grants in Aid of Research (G20200315103593991; https://www.sigmaxi.org/programs/grants-in-aid-of-research; WAH), and Island Conservation ( https://www.islandconservation.org/; WAH). Bioinformatics analysis in this article was performed by the University of Illinois at Chicago (UIC) Research Informatics Core, supported in part by the National Center for Advancing Translational Sciences (NCATS) through Grant No. UL1TR002003. The funding sources financially supported the data collection and analysis in this manuscript but did not have any other involvement in the study design, decision to publish, or preparation of the manuscript. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation, U.S. Fish and Wildlife Service, or Island Conservation. Mention of trade names or commercial products does not constitute their endorsement.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Biology and Life Sciences
                Zoology
                Animals
                Invertebrates
                Arthropoda
                Earth Sciences
                Geomorphology
                Topography
                Landforms
                Islands
                Biology and Life Sciences
                Nutrition
                Diet
                Medicine and Health Sciences
                Nutrition
                Diet
                Biology and Life Sciences
                Ecology
                Community Ecology
                Trophic Interactions
                Ecology and Environmental Sciences
                Ecology
                Community Ecology
                Trophic Interactions
                Ecology and Environmental Sciences
                Species Colonization
                Invasive Species
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Birds
                Seabirds
                Biology and Life Sciences
                Zoology
                Animals
                Vertebrates
                Amniotes
                Birds
                Seabirds
                Physical Sciences
                Physics
                Particle Physics
                Composite Particles
                Atoms
                Isotopes
                Stable Isotopes
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                Sequencing techniques
                DNA sequencing
                Next-Generation Sequencing
                Research and analysis methods
                Molecular biology techniques
                Sequencing techniques
                DNA sequencing
                Next-Generation Sequencing
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Transcriptome Analysis
                Next-Generation Sequencing
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Transcriptome Analysis
                Next-Generation Sequencing
                Custom metadata
                All relevant data are available at Dryad and are accessible at the following link: https://doi.org/10.5061/dryad.q573n5tnn. The data file in Dryad contains five spreadsheets: House Mouse Metadata; Plant ASV Table; Arthropod ASV Table; House Mouse SIA Data; and Diet Item SIA Data.

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