Data from: Investigating eye lens composition for stable isotope analysis in fishes: A comparison between Chondrichthyes and Actinopterygii
Data files
Jun 24, 2026 version files 7.15 MB
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laminae_data_processed.csv
7.15 MB
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README.md
3.39 KB
Abstract
Life history ecology provides a framework for understanding the complex interactions between organisms and their environments, but is challenging to resolve for long-lived and migratory species. In fishes, the combination of movement and foraging ecology is predominantly explored with stable isotope analysis (SIA) of accretionary tissues, such as otoliths. An alternative archival tissue validated for SIA in Actinopterygii (i.e., ray-finned fishes) is the proteinaceous eye lens and its growth layers (laminae). Here, we aim to expand the SIA of laminae to include Chondrichthyes (cartilaginous fishes; sharks, skates, rays, sawfish, and chimeras). We observe that urea in the eye lens drives patterns of elemental composition (i.e., C:N ratio) for Chondrichthyes, but the isotopic effect of urea is negligible. Actinopterygian fishes exhibit consistent C:N ratios across eye lenses, while chondrichthyan eye lens laminae C:N ratios decrease from the inner post-apoptotic laminae to outer pre-apoptotic laminae. After confirming the presence of urea in the Leopard Shark (Triakis semifasciata) eye lens laminae with Attenuated Total Reflectance (ATR) - Fourier Transform Infrared (FTIR) spectroscopy and urea assays, we successfully removed urea from eye lens laminae via three deionized water rinses. Subsequently, the C:N ratios of post-urea extracted Leopard Shark eye lens laminae exhibited similar patterns to actinopterygian fishes. Urea removal from Leopard Shark eye lens laminae increased in δ15N values as expected, but the isotopic effect was within analytical error. Our results indicate the utility of chondrichthyan eye lens laminae as chronological tissues for SIA. However, there are isotopic effects dependent on urea concentrations. This study demonstrates the need for inter-taxa comparison when establishing novel methodologies in SIA.
https://doi.org/10.5061/dryad.mw6m9064k
Description of the data and file structure
We evaluated the material composition of chondrichthyan eye lenses using ATR-FTIR spectroscopy. In ATR-FTIR, infrared absorption bands identify and quantify organic functional groups and inorganic ions based on reflectance and vibrational movement of chemical bonds (Lee and Chapman 1986). We collected ATR-FTIR spectra of Leopard Shark eye lens laminae (n individuals = 2; n laminae = 29) on a Bruker Vertex 70 Far-Infrared FTIR at the Nuclear Magnetic Resonance Facility of the University of California, Merced. Spectra were collected by smoothing 32 scans per sample from wavelength 400 – 4000 (cm-1) at a resolution of 4 cm-1. The FTIR spectra of isolated biomolecular compounds serve as a reference to determine individual compounds (Coates 2000; Shurvell 2006), and the size of absorbance of a band in arbitrary units (a.u.) is proportional to the concentration of the associated compound (Grunenwald et al. 2014; Lebon et al. 2016).
Spectra were corrected by flattening expected baseline absorbance bands and fitting smooth spline curves to said baseline bands (Stuart 2004; Trayler et al. 2023). We visually identified absorbance bands in ATR-FTIR spectra and detected each absorbance band’s peak (Table 2). To compare shifts in specific absorption band peaks (i.e., amide I and amide II), we normalized each lamina’s spectra to the maximum absorption value of the absorption band peak of interest. Additionally, due to the variability in the intensity of absorption band peaks (i.e., max absorbance) in raw FTIR spectra, peak-to-peak ratios are often used to standardize value comparisons between samples (Lebon et al. 2016). Because it was unclear which urea-associated peak-to-peak ratio would be best to indicate urea concentration, we ratioed the urea absorbance band peak (~ wavelength 1449 cm-1) to other individual identified peaks prominent in the spectra (e.g., amide III [1234 cm-1], carboxylate [1392 cm-1], amide II [1516 cm-1], etc.) across all laminae.
Files and variables
File: laminae_data_processed.csv
Description: Post-processed ATR-FTIR spectra of the eye lens laminae of two Leopard Sharks (Triakis semifasciata).
Variables
- file_name: Spectra file name for each sample.
- ucm_id: Leopard Shark ID #.
- layer: Eye lens laminae # (zero is the core; innermost layer).
- sample: Sample ID combination (ucm_id, L or R for left or right eye, and layer).
- diameter (mm): Eye lens laminae diameter in millimeters.
- normalized diameter (%): Eye lens laminae diameter as a normalized percent (laminae diameter divided by total eye lens capsule diameter).
- wavenumber: ATR-FTIR spectra from wavelength 400 – 4000 (cm-1) at a resolution of 4 cm-1.
- absorbance: ATR-FTIR absorbance in arbitrary units (a.u.), which is proportional to the concentration of an associated compound.
Code/software
See Trayler RB, Landa PV, Kim SL (2023). Evaluating the efficacy of collagen isolation using stable isotope analysis and infrared spectroscopy. J Archaeol Sci, 151:105727. https://doi.org/10.1016/j.jas.2023.105727.
We evaluated the material composition of chondrichthyan eye lenses using ATR-FTIR spectroscopy. In ATR-FTIR, infrared absorption bands identify and quantify organic functional groups and inorganic ions based on reflectance and vibrational movement of chemical bonds (Lee and Chapman 1986). We collected ATR-FTIR spectra of Leopard Shark eye lens laminae (n individuals = 2; n laminae = 29) on a Bruker Vertex 70 Far-Infrared FTIR at the Nuclear Magnetic Resonance Facility of the University of California, Merced. Spectra were collected by smoothing 32 scans per sample from wavelength 400 – 4000 (cm-1) at a resolution of 4 cm-1. Spectra were corrected by flattening expected baseline absorbance bands and fitting smooth spline curves to said baseline bands (Stuart 2004; Trayler et al. 2023).