Dataset for: Estimating pregnancy rate from blubber progesterone levels of a blindly biopsied beluga population poses methodological, analytical and statistical challenges
Cite this dataset
Renaud, Limoilou-Amelie (2023). Dataset for: Estimating pregnancy rate from blubber progesterone levels of a blindly biopsied beluga population poses methodological, analytical and statistical challenges [Dataset]. Dryad. https://doi.org/10.5061/dryad.34tmpg4r5
Abstract
Beluga (Delphinapterus leucas) from the St. Lawrence Estuary, Canada, have been declining since the early 2000s, suggesting recruitment issues as a result of low fecundity, abnormal abortion rates or poor calf or juvenile survival. Pregnancy is difficult to observe in cetaceans, making the ground-truthing of pregnancy estimates in wild individuals challenging. Blubber progesterone concentrations were contrasted among 62 SLE beluga with a known reproductive state (i.e., pregnant, resting, parturient, and lactating females), that were found dead in 1997–2019. The suitability of a threshold obtained from decaying carcasses to assess reproductive state and pregnancy rate of freshly-dead or free-ranging and blindly-sampled beluga was examined using three statistical approaches and two datasets (135 freshly-harvested carcasses in Nunavik, and 65 biopsy-sampled SLE beluga). Progesterone concentrations in decaying carcasses were considerably higher in known-pregnant (mean ± sd: 365 ± 244 ng g-1 of tissue) than resting (3.1 ± 4.5 ng g-1 of tissue) or lactating (38.4 ± 100 ng g-1 of tissue) females. An approach based on statistical mixtures of distributions and a logistic regression was compared to the commonly-used, fixed threshold approach (here, 100 ng g-1) for discriminating pregnant from non-pregnant females. The error rate for classifying individuals of known reproductive status was the lowest for the fixed threshold and logistic regression approaches, but the mixture approach required limited a priori knowledge for clustering individuals of unknown pregnancy status. Mismatches in assignations occurred at lipid content <10% of sample weight. Our results emphasize the importance of reporting lipid contents and progesterone concentrations in both units (ng g-1 of tissue and ng g-1 of lipid) when sample mass is low. By highlighting ways to circumvent potential biases in field sampling associated with capturability of different segments of a population, this study also enhances the usefulness of the technique for estimating pregnancy rate of free-ranging population.
README: Dataset for: Estimating pregnancy rate from blubber progesterone levels of a blindly biopsied beluga population poses methodological, analytical and statistical challenges
variable description for the clean_df_dryad.csv dataframe
- sample: Unique ID given to blubber sample. This alphanumeric combination starts with DL, abbreviation for latin Delphinapterus leucas, then the 4 or 2 last digits for the year, then the sequential sample number for the current sampling season (or year), like this: DL1997-002.
- date: Date of blubber sampling, as YYYY-MM-DD date format. Year should generally fit the first numbers of sample ID.
- age: Age, in years, as estimated from counts of dentinal growth layer groups following Lesage et al. (2014).
- sex: Sex, as genetically confirmed or from examination of reproductive tracts of stranded beluga whales.
- maturity: Whether an individual was mature or immature, based on a combination of body color, age and examination of reproductive tracts.
- color: Whether the animal was white, offwhite or grey. Calves are excluded from this dataset. It is assumed that beluga turn dark grey after a year or two, and progressively lighten in colour as they approach sexual maturity.
- progesterone_ng_g: This is the mean concentration of the duplicate samples processed in the lab using the ELISA. Concentration units are converted from pg per mL to ng per g of blubber. Resuspension volume, a factor of 1000, and wet sample mass in g, are used to convert units in pg per mL into ng per g (concentration_ng_ml*0.5/sample_mass_g). The volume in which the sample is resuspended is 0.5mL.
- coeff_variation: Variation accross duplicates processed on the ELISA. Samples with a CV>15% were automatically discarded and reprocessed. Coefficients of variation for biopsies are to be updated and some are missing.
- log_progesterone: Logarithmic transformation of progesterone concentration in ng per g of blubber.
- corrected_progesterone: Progesterone_ng_g divided by extraction efficiency (0.88 in Nunavik and SLE carcasses, and 74% in SLE biopsies).
- gLipid_per_gTissue: the lipidic content of the blubber sample, calculated as the difference between the final sample mass once the progesterone is extracted, and the initial sample mass. This is used to correct for progesterone concentration in ng per g of blubber, by dividing by this value.
- pregnant: whether the female was pregnant or not at sampling, as a factor.
- known_status: Reproductive status resulting from the examination of reproductive tracts in SLE carcasses. Left as NA for SLE biopsies and NUN carcasses are these were free-ranging (alive) and recently killed for subsistence, respectively.
- dataset: Whether blubber samples were collected from the long-term monitoring of St. Lawrence Estuary beluga carcasses, the Nunavik subsistence beluga hunt or from free-ranging, live St. Lawrence Estuary beluga whales.
Methods
This study used three sample groups: SLEcarcasses, NUNcarcasses, and SLEbiopsies (n = 62, 135, and 65, respectively), collected via the SLE carcass recovery program, Nunavik subsistence harvests, and biopsy sampling of the free-ranging SLE population. SLEcarcasses were from individuals with known pregnancy status, whereas NUNcarcasses and SLEbiopsies were from individuals of unknown pregnancy status.
Usage notes
R software, Numbers or Microsoft Excel are required.
Funding
Fisheries and Oceans Canada, Species at Risk
Fisheries and Oceans Canada, Whale Initiatives
Fisheries and Oceans Canada, Results Fund
Nunavik Marine Region Wildlife Board