DOI: 10.5061/dryad.34tmpg4r5
title: Dataset for: Estimating pregnancy rate from blubber progesterone levels of a blindly biopsied beluga population poses methodological, analytical and statistical challenges

description: 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 &lt;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.
description: This study used three sample groups:
 SLE<sub>carcasses</sub>, NUN<sub>carcasses</sub>,
 and SLE<sub>biopsies</sub> (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. SLE<sub>carcasses </sub>were from
 individuals with known pregnancy status, whereas NUN<sub>carcasses
 </sub>and SLE<sub>biopsies </sub>were from individuals
 of unknown pregnancy status.  
description: R software, Numbers or Microsoft Excel are required. 
description: # 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&gt;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.