DOI: 10.5061/dryad.z08kprrpw
title: Estimating demographic parameters for bearded seals, Erignathus barbatus, in Alaska using close-kin mark-recapture methods

description: Reliable estimates of population abundance and demographics are essential
 for managing harvested species. Ice-associated phocids, “ice seals”, are a
 vital resource for subsistence-dependent coastal Native communities in
 western and northern Alaska, USA. In 2012, the Beringia distinct
 population segment of the bearded seal, Erignathus barbatus nauticus, was
 listed as “threatened” under the U.S. Endangered Species Act requiring
 greater scrutiny for management assessments. We sought to estimate
 requisite population parameters from harvested seals by using close-kin
 mark-recapture (CKMR) methods, the first such application for marine
 mammals. Samples from 1,758 bearded seals harvested by Bering, Chukchi,
 and Beaufort Sea communities during 1998–2020 were genotyped, genetically
 sexed, and aged by tooth annuli. After rigorous quality control, kin
 relationships were established for 1,484 seals including two parent
 offspring pairs (POPs) and 25 potential second-order kin pairs. Most of
 the second-order kin were half-sibling pairs (HSPs), but four were
 potential grandparent-grandchild pairs (GGPs). There were no full sibling
 pairs, suggesting a lack of mate fidelity. Mitochondrial DNA analysis
 identified 17 potential HSPs as paternally related, providing substantial
 evidence of persistent heterogeneity in reproductive success among adult
 males. The statistical CKMR model incorporates probabilities associated
 with POPs, HSPs, and GGPs and assumes known ages and a stable population.
 Our top model accommodates heterogeneity in adult male breeding success
 and yields an abundance estimate of ~409,000 with a coefficient of
 variation (CV) = 0.35, which is substantially greater than the
 “non-heterogeneity” model estimate of ~232,000 (CV = 0.21), an important
 difference for managing a harvested species. Using CKMR methods with
 harvested species provides estimates of abundance with the added
 opportunity to acquire information about adult survival, fecundity, and
 breeding success that could be applied to other species of concern, marine
 and terrestrial.
description: # Estimating Demographic Parameters for Bearded Seals, *Erignathus
 barbatus*, in Alaska using Close-Kin Mark-Recapture Methods
 [https://doi.org/10.5061/dryad.z08kprrpw](https://doi.org/10.5061/dryad.z08kprrpw) ## Description: ### Samples.csv Associated information for the 1,484 genotyped seals used in the models including location of harvest, year of harvest, date of harvest, age at harvest, tooth or claw age, tooth age quality, type of tissue analyzed for genetics, the archiving lab, and the genetically determined sex. #### *Column names and description:* * *Record* – Integer value (1-1484), used to track samples while sorting data. * *Well* – location of sample within sample plate (see Appendix_2). * *Dart_job* – Character assigned to the 2 DArT’s jobs comprising our data (DArTcap analysis: ‘DArT 9.13E+11 and DArTseq analysis: '9.11E+11). - *Our_plate* – The plate number assigned to samples.  Cap1-Cap16 (DArTcap analysis) and 1 – 3 (DArTseq analysis). * *Our_sample* – Unique ID assigned to each seal. - *Fishtot* – Total number of reads per sample used to normalize all samples to a common read depth.  The terminology “fish” reflects initial application to fish populations. * *File* – Data file provided by DART. - *MD5* – Similar to DArT_job, characters assigned to the two DArT jobs: 07ccd032f47248dc13be14c102f98e47 for the DArTcap analysis and 3267afdd4ebe40784c3181a50b0660bc for the DArTseq analysis. * *TargetID* – Unique to each sample. - *UID* – ID combining sample ID, well location, and plate number. * *SP* – Species of seal.  All assigned BARBATUS. - *Lcode* – Coastal Alaskan village closest to the seal’s harvest location. * *lat* – Latitude of the village closest to the seal’s harvest location. - *lon* –Longitude of the village closest to the seal’s harvest location. * *MONTH* – Month of harvest. - *DATE* – Date of harvest. * *YEAR* – Year of harvest. - *AgeCombined* – The seal’s age (in years) as determined by analysis of teeth or, or in lieu of a tooth age, claws. * *AgeType* – Basis for age (tooth or claw). - *ToothAgeQuality* – Reliability of tooth age assignments from highest, code A, to the lowest, code C. Provided by Matson’s Lab. * Age1 – The youngest age (in years) when assigned an age range by Matson’s Lab. - *Age2* – The oldest age (in years) when assigned an age range by Matson’s Lab. * *Aging comments* – Seal specific aging analysis comments provided by Matson’s Lab. - *SexDArT* – The genetically determined sex assigned by DArT. * *SLcm* – Seal length in cm. - *Batch* – Analytical batch. 1 = DArTseq analysis, 2 = DArTcap analysis. * *PlateIDcombined* – Unique plate number (1-19) assigned to the combination of DArTseq (1-3) and DArTcap (Cap1-Cap16) plates. - *Tissue* – Type of tissue genetically analyzed. * *Weightg* – Weight of sample in grams sent to DArT. - *Comments* – Additional relevant information for a sample. * *Source* – Source of the sample if not archived at ADF&G.  University of Alaska Museum (UAM) or Southwest Fisheries Science Center (SWFSC). - *npoly* – polyploidy (yes = 1, No = 0).  #### *Blank Cells* Blank cells represent non applicable as in Age1 and Age2 columns, indicate Alaska Department of Fish and Game (ADF&G) in the Source column, or reflect unavailable data in remaining columns with blanks. ### bearded\_genos.csv This large table gives bearded seal genotypes. Each individual is represented by a row, while each 2-column pair represents a different locus. For instance: L252.1 and L252.2 represent the two alleles found at locus 251. Possible alleles are 'A', 'B' and '0' (null).