Estimating demographic parameters for bearded seals, Erignathus barbatus, in Alaska using close-kin mark-recapture methods
Data files
Nov 05, 2024 version files 30.94 MB
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bearded_genos.csv
30.57 MB
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README.md
3.72 KB
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Samples.csv
362.34 KB
Abstract
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.
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).
