Myth or relict: Does ancient DNA detect the enigmatic Upland seal?

Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species

“…One exception is that of OBI, which also had one if the highest proportion of correct assignments with microsatellite data (68.8%; Dussex et al., ). This result is in line with the suggestion that OBI may represent a refugium from sealing (Dussex et al., ; Salis et al., ; Smith, ) and thus a colony with a higher proportion of private alleles, thus increasing the proportion of pups correctly assigned. While colony‐level assignment for species may be unfeasible with the tools presently available, our results suggest that outlier loci assignment techniques could enable confident assignment in the future (e.g., Nielsen et al., ).…”

“…For our analyses of population structure, we evaluated genetic variation at the colony and genetic cluster levels. Three main clusters were defined based on previous NZFS genetic studies (Dussex et al., ; Salis et al., ) as well as the results presented here: NZ‐North‐West (OBI: Open Bay Island; CF: Cape Foulwind; WP: Wekakura Point), NZ‐North‐East (CP: Cape Palliser; OP: Ohau Point), previously identified as a zone of admixture (Dussex et al., ) and NZ‐South (East Coast to south coast colonies; HB: Horseshoe Bay; VB: Victory Beach; NP: Nugget Point) (Figure ).…”

“…Here, we did not attempt to reiterate the demographic model comparisons described in these studies, but rather to estimate demographic parameters based on SNP data for the most likely scenarios inferred in these studies. We thus designed a scenarios including a Polynesian‐induced decline (~500–1,000 years ago; Emami‐Khoyi et al., ), and a European‐induced decline (~125–250 years ago; Dussex et al., ) followed by range‐wide recolonization from a single refugium and subsequent population divergence with a NZ‐North (OBI, CF, WK, CP, OP) and NZ‐South cluster (HB,VB,NP) (Dussex et al., ; Salis et al., ) (Supporting Information Figure , Table ). We also designed a null model of constant effective population size though time followed by the same population divergence.…”

“…() and Salis et al. () microsatellite and mt DNA results, and the dotted line represents the approximate limit of the admixture zone between the two main clusters. Arrows depict the post‐sealing recolonization scenario from hypothetical south‐western South Island refugia depicted with a star inferred by ABC analyses (Dussex et al., ; this study) [Colour figure can be viewed at wileyonlinelibrary.com]…”

“…However, previous studies on pinniped species with histories of intense exploitation have shown a lack of (e.g., Arctocephalus gazella , Hoffman, Grant, Forcada, & Phillips, ) or only moderate fine‐scale structure (e.g., Arctocephalus tropicalis , Wynen et al., ; Halichoerus grypus , Fietz et al., ). Research based on modern and ancient DNA suggests that, while there was a shift in the genetic composition of NZFS in southern New Zealand resulting from the demographic decline, this decline may not have been long enough to induce a significant loss of genetic diversity as evidenced by comparable levels of genetic diversity in modern and ancient populations (Salis et al., ). This result is in stark contrast with the severe demographic decline and near range‐wide extirpation in the 1800s.…”