DOI: 10.5061/dryad.t76hdr85k
title: The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution

description: The Pacific harbor seal (Phoca vitulina richardii) occurs in the Mexican
 Pacific region at the southernmost edge of the subspecies’ distribution,
 along 700 km of coastline and on nine islands west of the Baja California
 peninsula. Its abundance corresponds to 3% of its total abundance in the
 north Pacific Ocean. The species is considered relatively sedentary and
 highly philopatric, which make it vulnerable to stochastic processes;
 thus, reproductive and genetic isolation of the Mexican Pacific colonies
 is expected. This study aimed to genetically characterize the harbor seal
 in the Mexican Pacific to inform conservation efforts.  We
 estimated the levels of genetic diversity for five colonies, using a
 572-base pair mitochondrial DNA control region fragment and nine
 microsatellite loci. We examined the population genetic structure and its
 phylogeographic patterns. We found 15 variable sites that defined 18
 mitochondrial DNA haplotypes. Results show one of the lowest levels of
 diversity reported for the species (overall haplotype diversity h = 0.626
 ± SD 0.041; overall nucleotide diversity π = 0.0018 ± SD 0.0013; mean
 expected heterozygosity HE = 0.537). We found a stronger genetic structure
 with both markers than in the larger regions of the north Pacific, from
 Alaska to California. The Pacific harbor seal colonies found in Mexico may
 have their origins in northern colonies, via a founder event. We found
 only four haplotypes in common with those observed (451) along the rest of
 the Pacific colonies, while nine of the 14 haplotypes exclusive to the
 Mexican Pacific are private.
description: This README file was generated on 2024-01-17 by Alicia Abadía-Cardoso.
 GENERAL INFORMATION 1. Title of Dataset: The genetic diversity,
 phylogeography, and population structure of Pacific harbor seals reveal
 isolation at the southern end of their distribution 2. Author Information
 A. Principal Investigator Contact Information Name: Yolanda Schramm\
 Institution: Universidad Autónoma de Baja California Address: Ensenada,
 Baja California, Mexico Email: 3. Date of
 data collection (single date, range, approximate date): 2014-2016 4.
 Geographic location of data collection: Baja California, Mexico (Todos
 Santos Island, Punta Banda Estuary, San Jerónimo Island, Natividad Island,
 and San Roque Island) 5. Information about funding sources that supported
 the collection of the data: National Science and Technology Council (Fondo
 SEP-CONACyT call CB-2012-01, project 179451) SHARING/ACCESS INFORMATION 1.
 Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0)
 Public Domain 2. Links to publications that cite or use the data:
 Fernández-Martín, E.M., Schramm, Y., Heckel, G. et al. The genetic
 diversity, phylogeography, and population structure of Pacific harbor
 seals reveal isolation at the southern end of their distribution. Conserv
 Genet 24, 839–854 (2023).
 . 1. Links to other
 publicly accessible locations of the data: None 2. Links/relationships to
 ancillary data sets: None 3. Was data derived from another source? No A.
 If yes, list source(s): NA 4. Recommended citation for this dataset:
 Fernández-Martín, Eva María; Schramm, Yolanda; Heckel, Gisela;
 Abadía-Cardoso, Alicia (Forthcoming 2024). Phoca vitulina microsatellites
 genotypes [Dataset]. Dryad.
 DATA & FILE OVERVIEW
 1. File Name: Fernandez-Martin_etal_Phoca_vitulina.txt 2. Relationship
 between files, if important: None 3. Additional related data collected
 that was not included in the current data package: None 4. Are there
 multiple versions of the dataset? No A. If yes, name of file(s) that was
 updated: NA i. Why was the file updated? NA ii. When was the file updated?
 NA
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Fernandez-Martin_etal_Phoca_vitulina.txt
 This dataset includes genotypes from 7 microsatellite loci presented in a
 two-column format. 1. Column A: ID of individuals collected (N=175). ID
 codes indicate the collecton site (ITS: Todos Santos Island, EPB: Punta
 Banda Estuary, ISJ: San Jerónimo Island, IN: Natividad Island, and ISR:
 San Roque Island) 2. Number of variables: 7 microsatellite loci
 (biallelic) * Columns B and C: Genotypes from microsatellite Hg61 *
 Columns D and E: Genotypes from microsatellite Hg810 * Columns F and G:
 Genotypes from microsatellite M11A * Columns H and I: Genotypes from
 microsatellite ZcwE12 * Columns J and K: Genotypes from microsatellite
 Pv11 * Columns L and M: Genotypes from microsatellite Pv9 * Columns N and
 O: Genotypes from microsatellite PvcA 3. Missing data codes: NA (not
 applicable) 4. Specialized formats or other abbreviations used: None