Data from: Genetic and evolutionary divergence of harbor seals (Phoca vitulina) in Iliamna Lake, Alaska ...

• Main Authors: O'Corry-Crowe, Greg, Ferrer, Tatiana, Boveng, Peter, Hauser, Donna, Withrow, Dave, Burkanov, Vladimir, Quinn, Thomas
• Format: Dataset
• Language: English
• Published: Dryad 2024
• Subjects: Genetic; evolutionary; divergences; Phoca vitulina; Iliamna Lake; Seals; FOS Biological sciences; Pacific; Alaska
• Online Access: https://dx.doi.org/10.5061/dryad.6hdr7sr8f; https://datadryad.org/stash/dataset/doi:10.5061/dryad.6hdr7sr8f

Freshwater populations of typically marine species present unique opportunities to investigate biodiversity, evolutionary divergence, and the adaptive potential and niche width of species. A few pinniped species have populations that reside solely in freshwater. The harbor seals inhabiting Iliamna Lake, Alaska constitute one such population. Their remoteness, however, has long hindered scientific inquiry. We used DNA from seal scat and from tissue samples provided by Indigenous hunters to screen for mitochondrial DNA and microsatellite variation within Iliamna Lake and eight regions across the Pacific Ocean. The Iliamna seals: (1) were substantially and significantly discrete from all other populations ( Fst-mtDNA= 0.544, Φst-mtDNA = 0.541, Fst-microsatellites = 0.308), (2) formed a discrete genetic cluster separate from all marine populations (modal ∆k=2, PC1=14.8%), and had (3) less genetic diversity (Hd, π, Hexp) and (4) higher inbreeding (F) than marine populations. These findings are both striking and ... : Samples were collected from six locations between 1996 and 2017 (Figure 1). DNA was extracted from 222 ILS scat and 13 tissue samples using QIAamp® Fast DNA Stool Mini Kit and DNeasy® Blood and Tissue purification kit (Qiagen), respectively. A 435bp fragment of the mitochondrial control region and adjacent proline tRNA gene (mtDNA) was amplified and both forward and reverse strands were sequenced on a Genetic Analyzer 3130 (Applied Biosystems) according to published methods [13]. Twelve independent microsatellite loci, originally developed on pinnipeds and previously optimized for P. vitulina [14,15], were multiplexed and screened for genotypic variation: Hg3.6, Hg4.2, Hg6.1, Hg6.3, Hg8.9, Hg8.10, BG, SGPv9, SGPv11, Pvc19, Pvc78, and Lc28 [14,16,17,18,19] (Table S1). This 12-locus panel was successfully used to identify duplicate samples. The quality and quantity of DNA recovered from scat was much lower than from tissue samples, often resulting in poorer quality allele amplification and sequences. A ...