Fossil denticles reveal how ocean productivity shapes shark baselines and recovery potential
Data files
Jun 17, 2026 version files 1.90 MB
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bchron_ages.csv
60.79 KB
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bchron_iter.csv
1.50 MB
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cross_isthmus_dd_func.csv
9.90 KB
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cross_isthmus_dd.csv
17.14 KB
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dates_pacific_panama.csv
8.23 KB
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dd_taph.csv
251.47 KB
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README.md
7.13 KB
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sampling_intervals_pacific.csv
40.04 KB
Abstract
Shark populations on coral reefs have declined globally, but few baselines exist to quantify natural variability before human impact. Using fossil dermal denticles preserved in reef sediments, we reconstructed shark communities across the Isthmus of Panama before significant exploitation (~7–3 ka) and recently (last century). We found differences in shark baselines and responses to fishing between the oceans on either side of the Isthmus. Reefs in the Pacific supported an ~20-fold higher shark abundance than Caribbean reefs before human impact. Caribbean shark populations—particularly pelagic species—have declined by 75% since the mid-Holocene, while their Pacific counterparts persisted over millennia despite higher fishing pressure. These contrasting trajectories are consistent with differences in oceanic productivity that dictate regional carrying capacities, highlighting the importance of incorporating oceanographic context into marine conservation targets.
Dataset DOI: 10.5061/dryad.931zcrjzs
Description of the data and file structure
Fossil shark dermal denticle accumulations in coral reef sediments were collected, counted, and classified to reconstruct shark communities over millennia across the Isthmus of Panama (Bocas del Toro, Caribbean and Gulf of Panama, Pacific). The provided datasets include the denticle counts and classifications used in this study as well as key contextual information.
Files and variables
File: bchron_ages.csv
Description: age outputs from age-depth models produced with the R package BChron using radiometric dates of coral fragments from reef matrix push cores in the Gulf of Panama
Variables
- region: area of study (Gulf of Panama)
- date_locality: site name
- unique: unique core interval code, comprising the sample code and depth interval
- sample: sample code (one per core)
- depth: position in core, at midpoint of interval (cm)
- interval_no: numeric classifier for each depth interval
- min: lower bound of 95 % credible interval (years BP)
- median: median predicted age (years BP)
- predicted_age_BP: mean predicted age (years BP)
- max: upper bound of 95 % credible interval (years BP)
- predicted_age_AD_BC: mean predicted age (CE/BCE)
- perc_2.5: 2.5th percentile of estimated years per interval based on modeled sedimentation rate
- perc_25: 25th percentile of estimated years per interval based on modeled sedimentation rate
- perc_50: 50th percentile of estimated years per interval based on modeled sedimentation rate
- perc_75: 75th percentile of estimated years per interval based on modeled sedimentation rate
- perc_97.5: 97.5th percentile of estimated years per interval based on modeled sedimentation rate
- predicted_age_median: median predicted age (CE/BCE)
- predicted_age_BP_median: median predicted age (years BP), same as "median"
File: cross_isthmus_dd.csv
Description: denticle counts from each sample in Caribbean and Pacific Panama
Variables
- basin: ocean basin (Caribbean, Pacific)
- region: region (Bocas del Toro, Gulf of Panama)
- site_name: site name
- sample: sample code
- depth: position in core (cm, Pacific only)
- unique: unique sample code
- type: type of sample (modern_bulk, Holocene_bulk, core)
- total_dd_count: number of intact shark dermal denticles
- sed_weight_kg: weight of sediment processed for denticles (kg)
- num_yrs_est_bulks: estimated number of years represented by bulk samples (Caribbean only)
- num_yrs_est_bulks_upper: 75th percentile of estimated number of years represented by bulk samples (Caribbean only)
- num_yrs_est_bulks_lower: 25th percentile of estimated number of years represented by bulk samples (Caribbean only)
- age_est_bulks: median estimated age of bulk samples (Caribbean only)
File: cross_isthmus_dd_func.csv
Description: classifications of denticles from a subset of samples in Caribbean and Pacific Panama
Variables
- basin: ocean basin (Caribbean, Pacific)
- region: region (Bocas del Toro, Gulf of Panama)
- site_name: site name
- sample: sample code
- depth: position in core (cm, Pacific only)
- unique: unique sample code
- abr_tot: number of abrasion strength denticles
- defense: number of defense denticles
- drag: number of drag reduction denticles
- gen_func: number of generalized functions denticles
- rabr_tot: number of ridged abrasion strength denticles
- unknown: number of unidentified denticles
- abr_pel: number of abrasion strength denticles classified to the pelagic form (subset of abr_tot)
- rabr_pel: number of ridged abrasion strength denticles classified to the pelagic form (subset of rabr_tot)
- total_dd_count: total number of intact denticles
- group: group counter, for grouping samples with low denticle counts
- age_group: time period classifier (modern, pre_exp), from age-depth model
File: dates_pacific_panama.csv
Description: U-Th dates used to run the age-depth models
Variables
- region: area of study (Gulf of Panama)
- date_locality: site name
- sample: sample code (one per core)
- horizon_cm: interval sampled (cm)
- depth: lower bound of interval (cm)
- depth_up: upper bound of interval (cm)
- depth_mid: midpoint of interval (cm)
- unique: unique core interval code, comprising the sample code and depth interval
- U_Th_age: measured age (CE/BCE)
- age_ci: 2 sigma confidence interval on age measurement
- thickness: thickness of interval sampled (cm)
- calCurve: calibration curve type
- notes: any notes associated with the sample
File: dd_taph.csv
Description: weathering scores for denticles from the same subset of samples, to assess preservation
Variables
- basin: ocean basin (Caribbean, Pacific)
- region: region (Bocas del Toro, Gulf of Panama)
- site_name: site name
- sample: sample code
- depth: position in core (cm, Pacific only)
- unique: unique sample code
- dd_no: denticle code
- dd_unique: unique denticle code
- func_morph: functional morphotype (DR = drag reduction, A = abrasion strength, RA = ridged abrasion strength, GF = generalized functions, DEFENSE = defense, UNK = unidentified, RAY = ray denticle)
- microstr: are microstructures present on the denticle crown? (Y/N)
- crown_sa: estimated size of denticle crown, calculated as sqrt(length*width) in um
- frag_base: weathering score for base (A-C, where A is the best)
- frag_crown: weathering score for crown (A-D, where A is the best)
- frag_peaks: weathering score for peaks (A-B, where A is the best)
- surf_alt: score for presence of surface alteration (A-D, where A is the best)
- discolor: score for presence of discoloration (A-C, where A is the best)
- is_frag: is the denticle fragmented such that more than ~50 % of the crown is missing (Y/N)
File: sampling_intervals_pacific.csv
Description: list of sampling intervals for the pacific cores, to match the BChron age models with the sampling intervals
Variables
- region: area of study (Gulf of Panama)
- date_locality: site name
- unique: unique core interval code, comprising the sample code and depth interval
- sample: sample code (one per core)
- depth: position in core, at midpoint of interval (cm)
- depth_upper: upper bound of interval (cm)
- depth_lower: lower bound of interval (cm)
- thickness: thickness of interval (cm)
- thick.not.5: is the thickness not 5 cm (standard cuts)? (no/yes)
- sampling_unique: unique core interval code, comprising the sample code and depth interval (of the corresponding sample, which is named by the lower depth)
File: bchron_iter.csv
Description: 1000 iterations for each core interval output by the BChron age-depth models, where each column is a unique core interval and each row is an iteration
Variables
- wide-form, with one column for every sampling interval that contains the sedimentation estimates
Note: "NA" and "." cells are used to indicate "Not Applicable" or missing data.