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Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor‐quality samples
Author(s) -
Morin Phillip A.,
Forester Brenna R.,
Forney Karin A.,
Crossman Carla A.,
HancockHanser Brittany L.,
Robertson Kelly M.,
BarrettLennard Lance G.,
Baird Robin W.,
Calambokidis John,
Gearin Pat,
Hanson M. Bradley,
Schumacher Cassie,
Harkins Timothy,
Fontaine Michael C.,
Taylor Barbara L.,
Parsons Kim M.
Publication year - 2021
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.15827
Subject(s) - porpoise , biological dispersal , range (aeronautics) , genetic structure , biology , population , ecology , gene flow , geography , mtdna control region , isolation by distance , genetic variation , fishery , haplotype , harbour , genotype , genetics , materials science , demography , sociology , computer science , gene , programming language , composite material
Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes ( N = 271 samples) in addition to mitochondrial (mtDNA) sequence data ( N = 413 samples) to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We confirmed an overall pattern of strong isolation‐by‐distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct ( F ST = 0.02 [microhaplotypes]; 0.31 [mtDNA]), with both reduced genetic variability and high frequency of an otherwise rare mtDNA haplotype. At the northern end of our study range, we found significant genetic differentiation of samples from the Strait of Georgia, previously identified as a potential biogeographical boundary or secondary contact zone between harbor porpoise populations. Association of microhaplotypes with remotely sensed environmental variables indicated potential local adaptation, especially at the southern end of the species’ range. These results inform conservation and management for this nearshore species, illustrate the value of genomic methods for detecting patterns of genetic structure within a continuously distributed marine species, and highlight the power of microhaplotype genotyping for detecting genetic structure in harbor porpoises despite reliance on poor‐quality samples.