Causes and consequences of fine-scale population structure in a critically endangered freshwater seal

Abstract

BackgroundSmall, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland.ResultsMicrosatellite diversity within the subspecies (HE = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (FST = 0.107) than in maternally inherited mtDNA (FST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females.ConclusionsGenetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.

Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies

“…In addition, the labyrinthine shape of Lake Saimaa has been shown to impose population fragmentation on the seals (Valtonen et al. , ), which could speed up genetic erosion in relation to the presumedly more panmictic Ladoga population ( cf . Amos and Harwood ; Caballero et al.…”

“…; Valtonen et al. ; see also O'Corry‐Crowe ), especially remembering that the reduced nuclear variation is paralleled by losses in mitochondrial haplotype (33.9%) and nucleotide (89.4%) diversity (Valtonen et al. ).…”

“…Microsatellite variation was inferred at 17 variable loci; detailed methods and data characteristics are described in Valtonen et al. (). The possibility of genotyping errors was investigated by analyzing the data in MICRO‐CHECKER v. 2.2.3 (van Oosterhout et al.…”

“…On this account, we combined new data from 17 microsatellite loci (Valtonen et al. ) with previously published mitochondrial control‐region sequence data (Valtonen et al. ) to estimate the divergence times and past effective population sizes of the three focal subspecies.…”

Multi‐level patterns in population genetics: Variogram series detects a hidden isolation‐by‐distance‐dominated structure of Scandinavian brown bears Ursus arctos

“…To estimate IBD, we correlated geographical distance with the genetic divergence index Rousset's â (Rousset, ), an individual‐based analogue to F ST /(1‐ F ST ) for continuously distributed populations (Figure a,b). Rousset's â has the advantage of not relying on a reference population (Vekemans & Hardy, ) and has been used in previous studies (Coulon et al., ; Leblois, Rousset, Tikel, Moritz, & Estoup, ; Schwalm, Waits, & Ballard, ; Valtonen et al., ). We used an asymptotically increasing shape of the IBD model, which is clearly supported by the data (Figure ).…”