Fragmented habitat compensates for the adverse effects of genetic bottleneck

Abstract

According to the population genetics theory, population subdivision helps organisms retain genetic diversity, crucial for adaptation in a changing environment. Habitat shape is thought to be important for generating and maintaining population subdivision, but empirical cases are needed to test this assumption. We studied Saimaa ringed seals, land-locked in a labyrinthine lake and recovering from a drastic bottleneck, by whole-genome sequencing 105 individuals and additional individuals from three other ringed seal subspecies. We analyzed the distribution of variation and the genetic relatedness among the individuals in relation to the habitat shape. Despite a severe history of a genetic bottleneck with prevalent homozygosity in Saimaa ringed seals, we found evidence for population structure mirroring the subregions of the lake. Highlighting the significance of habitat connectivity in conservation biology and the power of genomic tools in understanding its impact, the genome wide analyses showed the subpopulations to have retained unique variation and largely complementary patterns of homozygosity, giving hope to this endangered species.

Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population

“…1000 generations. Our results are in line with earlier studies showing low genetic diversity in the population (Palo et al 2003;Valtonen et al 2012;Martinez-Bakker et al 2013;Nyman et al 2014;Savriama et al 2018;Stoffel et al 2018;Peart et al 2020;Löytynoja et al 2022). The diversity loss has been attributed to either a founder event after the colonization bottleneck, gradual erosion of diversity over a long isolation, or a more recent anthropogenic bottleneck caused by targeted hunting in the 1900s (Palo et al 2003;Nyman et al 2014;Stoffel et al 2018;Peart et al 2020).…”

“…The results are in line with several previous studies documenting reduced genetic diversity and significant population sub structuring in Saimaa ringed seals (Palo et al 2003;Valtonen et al 2012Valtonen et al , 2014Löytynoja et al 2022). Mitochondrial diversity patterns in the Saimaa population suggest that female seals are highly philopatric, staying and reproducing in their natal regions (Valtonen et al 2012).…”

“…org/). The reference genome was built by scaffolding the 2183 contiguous sequences of the original draft assembly (Löytynoja et al 2022) with a novel linkage disequilibrium (LD) -based method (Kivikoski et al 2021) into 41 super scaffolds totaling 2,33 giga base pairs (Gbp). We then performed a joint variant calling pipeline of the Genome Analysis Toolkit (Van der Auwera and O'Connor 2020), which produced Variant Call Format (VCF) files for the next stage of the analysis.…”

“…Mitochondrial diversity patterns in the Saimaa population suggest that female seals are highly philopatric, staying and reproducing in their natal regions (Valtonen et al 2012). Furthermore, nuclear markers show highly significant population structure (Valtonen et al 2014;Löytynoja et al 2022), indicating that sporadic trips made by single individuals between water basins (Biard et al 2022)…”

“…The longest RoH in mammal genomes may exceed 10 million base pairs (Mbp) (Purfield et al 2012;Grossen et al 2017). In the Saimaa ringed seal population, a genome-wide SNP and RoH analysis in comparison to the neighboring Arctic (P. h. hispida), Baltic (P. h. botnica) and Ladoga (P. h. ladogensis) subspecies shows evidence of lost genetic diversity and contemporary inbreeding (Löytynoja et al 2022).…”