Effects of plastic ingestion on blood chemistry, gene expression and body condition in wedge-tailed shearwaters (Ardenna pacifica)

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Biodiversity and Conservation

Main article text

 

Introduction

Materials and Methods

Study site

Blood sampling

Morphometric data

Gastric lavage

DNA purification and polymerase chain reaction

RNA isolation and sequencing

Data analysis

Results

Sex determination through PCR

Stomach contents from gastric lavage

Blood analytics, morphometric and stomach contents

Relationships between blood analytics, morphometric and stomach contents

RNA-seq analyses

Discussion

Conclusion

Supplemental Information

Supplemental information

DOI: 10.7717/peerj.18566/supp-1

Plastic samples

Plastic collected from stomach contents from WTSH under microscope (magnification 40x).

DOI: 10.7717/peerj.18566/supp-2

Individual t-test analysis of each blood analyte and weight

(A–K) Blood analyte plotted against presence and absence of plastic with error bars. Any test that showed a slight significance value is noted with an asterisk on the individual chart. (L) Weight plotted against presence or absence of plastic.

DOI: 10.7717/peerj.18566/supp-3

Logistic linear model analyses

Analyses did not reveal statistically significant relationships. (A) Presence or absence of plastic and weight of bird ( p-value = 0.08601). (B) Presence or absence of plastic and total carbon dioxide ( p-value = 0.07327).

DOI: 10.7717/peerj.18566/supp-4

PCA analyses blood analytes

(A) Blood analytes with variables of presence of plastic using PCA 1 and PCA 2. (B) Blood analytes with variables of presence of plastic using PCA 3 and PCA 4. (C) Blood analytes with variables of sex using PCA 1 and PCA 2. (D) Blood analytes with variables of sex using PCA 3 and PCA 4.

DOI: 10.7717/peerj.18566/supp-5

PCA analyses of morphometrics measurements

(A) Morphometric measurements with variables of presence of plastic using PCA 1 and PCA 2. (B) Morphometric measurements with variables of presence of plastic using PCA 3 and PCA 4. (C) Morphometrics measurements with variables of sex using PCA 1 and PCA 2. (D) Morphometric measurements with variables of sex using PCA 3 and PCA 4.

DOI: 10.7717/peerj.18566/supp-6

Average Phred score per samples

Phred score is used for nucleotide quality assessment of sequencing.

DOI: 10.7717/peerj.18566/supp-7

Reads per sample

This measurement assesses an inferred sequence of base pairs that correspond to a single DNA fragment.

DOI: 10.7717/peerj.18566/supp-8

Multiple mapped reads

Multiple mapped reads describe reads that map more than once in different genomic regions. This is the number of multiple mapped reads from the prepared library that are aligned to the Cory Shearwater reference genome.

DOI: 10.7717/peerj.18566/supp-9

Uniquely mapped reads

Uniquely mapped reads have one exact location within the reference genome which they map to. This is the number of uniquely mapped reads from the prepared library that are aligned to the Cory Shearwater reference genome.

DOI: 10.7717/peerj.18566/supp-10

Genes differentially expressed between individuals of the same sex with and without plastic

(A) Heatmap showing the 14 significantly expressed genes in males. (B) Heatmap showing the 4 significant differentially expressed genes in females.

DOI: 10.7717/peerj.18566/supp-11

Genes differentially expressed between sex divided into samples that had ingested plastic and samples that did not have plastic

(A) Heatmap showing the 11 significant differentially expressed genes in all of the samples containing plastic separated by sex. (B) Heatmap showing the 43 significant differentially expressed genes in all samples that do not contain plastic separated by sex.

DOI: 10.7717/peerj.18566/supp-12

Gene enrichment analysis results for bird weight

(A) Manhattan plot showing results of enrichment analysis and the databases used. (B) Terms with significant values from the enrichment analysis in the differentially expressed genes between weight categories

DOI: 10.7717/peerj.18566/supp-13

Genes differentially expressed and enrichment analysis for the entire data set

(A) Heatmap showing that plastic and size factor of libraries do not explain the differentially expressed gene profiles. The heatmap shows the top 20 genes with the highest statistical power. (B) Enrichment analysis and significant terms for the 6 differentially expressed genes shown on the heatmap above.

DOI: 10.7717/peerj.18566/supp-14

Table summarizing differential genetic expression analyses run

The test/experiment column describes the three main analyses that we conducted and the variables that were used for each test. Transcripts represent the count of transcripts that were aligned with the reference genome. Net transcripts represent the count of transcripts that were represented or quantifiable in all of the samples. Outlier transcripts and outlier genes represent the count of transcripts that differentiated within the respective test. p-value represents the two p-values we used to determine significance of the results. We used both a marginal pvalue (0.1) and a standard value (0.05).

DOI: 10.7717/peerj.18566/supp-15

Model outputs

This table provides the model output statistics for each of the analyses run. The “Variable” indicates the analyte or variable tested against the “Dependent variable”. Significance ( p < 0.05) is indicated by *. “Std Error” is “standard error”. The specific analyses is listed under “Model Type”.

DOI: 10.7717/peerj.18566/supp-16

Summary of values from blood analytes

This table provides the mean, standard deviation (abb. SD) and p-values from the t-tests for each of the blood chemistry analytes and weight. The plus sign (+) indicated the values for individuals with plastic. The minus sign (-) indicates the values for individuals without plastic. The blood analytes measured were sodium (Na mmol/L), potassium (K mmol/L), chloride (Cl mmol/L), ionized calcium (iCa mmol/L), total carbon dioxide (TCO2), glucose (Glu mg/dL), Urea nitrogen/urea (BUN mg/dL), creatine (Crea mg/dL), hematocrit (Hct%PCU), hemoglobin (Hb g/dL), anion gap (AnGap mmol/L) and are ordered respectively in the table.

DOI: 10.7717/peerj.18566/supp-17

RIN values

RIN values assign a numerical value to the quality of the RNA that we worked with. A RIN value of 8 and above indicated higher quality and integrity of RNA and values below 5 indicated some levels of RNA degradations. Numerical values for sequence reads, Phred scores, uniquely mapped reads, and multiple mapped reads.

DOI: 10.7717/peerj.18566/supp-18

Additional Information and Declarations

Competing Interests

Scott Edwards is an Academic Editor for PeerJ. The authors declare that they have no other competing interests.

Author Contributions

Nicole Mejia conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Flavia Termignoni-Garcia performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Jennifer Learned conceived and designed the experiments, performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Jay Penniman performed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Scott V. Edwards conceived and designed the experiments, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The Harvard University Faculty of Arts and Science Standing Committee on the Use of Animals and Teaching provided full approval for this research (project number 24-06).

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Field experiments were approved by the Hawaii Division of Forestry and Wildlife (permit number: 08487).

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The raw transcriptome data for this project are available at NCBI SRA: PRJNA1152110; SAMN43336009SAMN43336036.

Data Availability

The following information was supplied regarding data availability:

The scripts are available at GitHub and Zenodo:

https://github.com/nicolemejia6180/Scripts-for-Wedge-Tailed-Shearwater-Plastic-Analyses.

– Mejia, N. (2024). Scripts for Wedge-Tailed Shearwater Plastic Analyses. Zenodo. https://doi.org/10.5281/zenodo.13621264.

Funding

This work was supported by the Harvard College Office of Undergraduate Research and Fellowships and the Harvard University Museum of Comparative Zoology. The Wetmore Colles Fund of the Museum of Comparative Zoology at Harvard funded the open access charges, article processing fees and the graphical abstract. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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