Complex origins and history of the relict Fennoscandian ringed seals

not-yet-known not-yet-known not-yet-known unknown Spatiotemporal environmental heterogeneity is a major evolutionary driver, which can cause profound phylogeographic complexity, particularly at the periphery of species ranges. Ringed seals display a highly disjoint distribution with an abundant subspecies occurring throughout the circumpolar Arctic, as well as three relict subspecies in Fennoscandia; the Baltic Sea, Lake Saimaa and Lake Ladoga. Traditionally regarded as originating from a single colonisation event from the paleo-Skagerrak-Kattegat region after the Last Glacial Maximum (LGM), recent studies have challenged this perception. Here, we analyse 246 mitogenomes and 180 skulls to unravel the diversity and spatiotemporal pattern of diversification in Fennoscandian ringed seals. Contrary to previous assumptions, our results reveal a complex evolutionary history characterised by several Fennoscandian colonisation events and pre-LGM diversification from Arctic ringed seals. We hypothesis that Lake Saimaa seals originate directly from the Arctic, possibly via the Karelia seaway, Ladoga via a similar route as well as from paleo-Skagerrak-Kattegat-Baltic, while the Baltic ringed seal have mixed evolutionary origins, which may be traced to distinct European glacial refugia, as well as ongoing gene-flow with the Arctic. Lake Saimaa and to some extent Lake Ladoga ringed seals have experienced a loss of diversity and evolved divergent skull morphologies as a result of colonisation bottlenecks, isolation and dietary specialisation, while Baltic Sea ringed seals have retained remarkably high levels of diversity. Our study supports the current classification of Lake Saimaa, Lake Ladoga and Baltic Sea ringed seals as distinct subspecies, and highlights the need for management and conservation efforts to mitigate cumulative impacts of human activities and climate change on Fennoscandian ringed seals. TITLE Complex origins and history of the relict Fennoscandian ringed seals AUTHORS Morten Tange Olsen 1,2*, Ari Löytynoja 3, Mia Valtonen 4, Steen W. Knudsen 5, Sofie Bang 1, Casper Gunnersen 1, Aqqalu Rosing-Asvid 6, Steven H. Ferguson 7, Rune Dietz 2, Kit M. Kovacs 8, Christian Lydersen 8, Jukka Jernvall 3, Petri Auvinen 3 and Anders Galatius 2 not-yet-known not-yet-known not-yet-known unknown AFFILIATIONS 1Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen K, Denmark. 2Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, DK-4000, Roskilde Denmark 3Institute of Biotechnology, University of Helsinki, Viikinkaari 5D, 00790 Helsinki, Finland 4Wildlife Ecology Group, Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland 5NIVA Denmark Water Research, Njalsgade 76, DK-2300 Copenhagen, Denmark 6Department of Birds and Mammals, Greenland Institute of Natural Resources, Nuuk, Greenland. 7Fisheries and Oceans Canada, Winnipeg, MB, R3T 2N6, Canada 8Norwegian Polar Institute, Fram Centre, N-9296 Tromsø, Norway CORRESPONDING AUTHOR *Morten Tange Olsen, [email protected] KEY WORDS Climate change, Quaternary, morphometrics, phylogeography, subspeciation RUNNING HEAD Fennoscandian ringed seals

Spatiotemporal environmental heterogeneity is a major evolutionary driver, which can cause profound phylogeographic complexity, particularly at the periphery of species ranges. Ringed seals display a highly disjoint distribution with an abundant subspecies occurring throughout the circumpolar Arctic, as well as three relict subspecies in Fennoscandia; the Baltic Sea, Lake Saimaa and Lake Ladoga. Traditionally regarded as originating from a single colonisation event from the paleo-Skagerrak-Kattegat region after the Last Glacial Maximum (LGM), recent studies have challenged this perception. Here, we analyse 246 mitogenomes and 180 skulls to unravel the diversity and spatiotemporal pattern of diversification in Fennoscandian ringed seals. Contrary to previous assumptions, our results reveal a complex evolutionary history characterised by several Fennoscandian colonisation events and pre-LGM diversification from Arctic ringed seals. We hypothesis that Lake Saimaa seals originate directly from the Arctic, possibly via the Karelia seaway, Ladoga via a similar route as well as from paleo-Skagerrak-Kattegat-Baltic, while the Baltic ringed seal have mixed evolutionary origins, which may be traced to distinct European glacial refugia, as well as ongoing gene-flow with the Arctic. Lake Saimaa and to some extent Lake Ladoga ringed seals have experienced a loss of diversity and evolved divergent skull morphologies as a result of colonisation bottlenecks, isolation and dietary specialisation, while Baltic Sea ringed seals have retained remarkably high levels of diversity. Our study supports the current classification of Lake Saimaa, Lake Ladoga and Baltic Sea ringed seals as distinct subspecies, and highlights the need for management and conservation efforts to mitigate cumulative impacts of human activities and climate change on Fennoscandian ringed seals.

The distribution and genetic diversity of the Earth’s flora and fauna was influenced greatly by Late Quaternary environmental fluctuations (Hewitt 2000). Many terrestrial species follow a general pattern, in which cold-adapted species expand their range towards lower latitudes during glacial periods and retract to high-latitude (or alpine) refugia during interglacial periods (Stewart et al. 2010). However, spatiotemporal environmental heterogeneity and physical geography introduces the possibility of creating refugia at high latitudes during glacial periods, and at low latitudes during interglacial periods, thus increasing the phylogeographic complexity and overall genotypic and phenotypic diversity of some species. In particular, this seems to be the case for many Arctic and boreal marine species, with cryptic diversity and complex phylogeography reported for invertebrates (Tempestini, Pinchuk et al. 2020), fish (Madsen, Nelson et al. 2016, Jacobsen, Jensen et al. 2022), pinnipeds (Carr, Duggan et al. 2015, Rosing‐Asvid, Löytynoja et al. 2023, Ruiz-Puerta, Keighley et al. 2023) and cetaceans (Louis, Skovrind et al. 2020, Skovrind, Louis et al. 2021, Olsen, Nielsen et al. 2022). Identifying such diversity and understanding how it was formed is central to our understanding of a species’ ecology and evolution, as well as for formulating efficient management and conservation strategies to meet the challenges of the biodiversity and climate crisis. The ringed seal (Pusa hispida, (Schreber 1775)) is one of the most widespread mammals in the northern hemisphere and a key species in the marine food-web (Durner, Douglas et al. 2017, Hamilton, Kovacs et al. 2017). The species is highly adapted to polar conditions, capable of maintaining breathing holes in sea ice and hence occupying areas of seasonal or continuous ice-cover, allowing it to overwinter in the High Arctic and possibly persisting at high latitudes during glacial periods (Davies 1958, Rosing‐Asvid, Löytynoja et al. 2023). The reproductive success of ringed seals is tied to stability of sea ice and adequate snow cover, with birth and lactation taking place in subnivean snow lairs on the sea ice (McLaren 1958, Smith and Lydersen 1991, Hammill 2009). Intriguingly, while an Arctic subspecies ( Pusa hispida hispida ) occurs throughout the circumpolar Arctic, contemporary ringed seals have a disjoint distribution with multiple additional “relict” subspecies inhabiting sub-Arctic and cold-temperate environments of the Baltic Sea ( P. h. botnica ), Lake Ladoga (P. h. ladogensis ), and Lake Saimaa ( P. h. saimensis ), as well as the Sea of Okhotsk ( P. h. ochotensis ) (Davies 1958) (Figure 1). In addition, the ringed seal’s “sister species”, the Baikal seal ( P. sibirica ), might have evolved from such an ancient relict ringed seal population (Sasaki, Numachi et al. 2003, Palo and Väinölä 2006). The three Fennoscandian ringed seal subspecies (i.e. Baltic, Ladoga and Saimaa) are generally assumed to have colonised their current ranges after the LGM from glacial refugia in the North Sea-Skagerrak-Kattegat region of northern Europe (Davies 1958, Palo, Mäkinen et al. 2001, Sommer and Benecke 2003, Valtonen, Palo et al. 2012, Ukkonen, Aaris-Sørensen et al. 2014). This could have occurred via river outlets through central Sweden (Närke Strait) and/or the Danish Straits (Dana River) into the Baltic Sea and further into Lake Saimaa and Lake Ladoga, with each of the three Fennoscandian subspecies becoming isolated as the main species distribution retracted north and isostatic rebound formed the Ladoga and Saimaa lakes. However, genetic studies have suggested that periodic gene flow has occurred from both the Arctic and Lake Ladoga to the Baltic Sea (Palo, Mäkinen et al. 2001, Martinez-Bakker, Sell et al. 2013, Nyman, Valtonen et al. 2014), and recent demographic reconstructions indicate that the origin of the Saimaa subspecies may predate the LGM (Löytynoja, Rastas et al. 2023). Thus, the colonisation of Fennoscandia by ringed seals may be more complex than first assumed, perhaps involving refugia in glacial lakes at the edge of the Fennoscandian Ice Sheet (Heino, Nyman et al. 2023), and/or interglacial dispersal routes directly from the Arctic through Karelia. In addition to affecting genetic diversity, spatiotemporal environmental and geographical heterogeneity may have influenced the ringed seal’s phenotypic diversity. In particular, differences in marine and freshwater habitat size and characteristics, such as bathymetry, temperature and salinity, are expected to affect the available prey base and in turn drive the evolution of different foraging strategies and morphologies. For example, analyses of body size variation among Arctic ringed seals suggest that pack-ice seals generally are smaller than fast ice ringed seals and these differences appear to also be reflected in their skull morphology (Finley, Miller et al. 1983). Ringed seals in eastern Canada show a marked latitudinal gradient in body size, growth rates and life history (Ferguson, Zhu et al. 2018, Ferguson, Yurkowski et al. 2019, Ferguson, Yurkowski et al. 2020). At a wider geographical scale, the body size of animals in West Greenland and the High Arctic (Northwest Greenland and Northeast Canada), and to some extent Svalbard, appear to be larger than the average, while animals in Alaska and the White Sea are smaller (Kovacs, Citta et al. 2021). Likewise, analyses of Fennoscandian ringed seals suggest that Ladoga ringed seals are smaller than other subspecies, Saimaa ringed seals are similar to other medium-sized Arctic ringed seals, but smaller than those in the Baltic Sea, which are comparable in size to the large ringed seals found in the Canadian High Arctic (Helle 1979, McLaren 1993, Auttila, Kurkilahti et al. 2016, Ferguson, Zhu et al. 2018). Similarly, the skull morphology appears to vary among Fennoscandian and Arctic ringed seals, with Saimaa and Ladoga seals, but not Baltic seals, differing from each other and the Arctic subspecies (Amano, Hayano et al. 2002). Nevertheless, it is unclear if these cases of body size and skull shape variation reflect phenotypic plasticity in response to environmental condition, genetic adaptations, or a combination of the two (but see Rosing‐Asvid, Löytynoja et al. 2023). Thus, although Fennoscandian and Arctic ringed seals have previously been subject to both genetic (Palo, Mäkinen et al. 2001, Palo, Hyvärinen et al. 2003, Davis, Stirling et al. 2008, Valtonen, Palo et al. 2012, Martinez-Bakker, Sell et al. 2013, Nyman, Valtonen et al. 2014, Heino, Nyman et al. 2023, Rosing‐Asvid, Löytynoja et al. 2023, Sundell, Kammonen et al. 2023) and morphological (Helle 1979, Finley, Miller et al. 1983, McLaren 1993, Amano, Hayano et al. 2002, Auttila, Kurkilahti et al. 2016, Ferguson, Zhu et al. 2018, Kovacs, Citta et al. 2021) analyses, several questions about their evolutionary history remain unanswered. Here, we combine analyses of 246 mitogenomes with morphological measurements from 180 skulls to shed new light on the phylogeography of Fennoscandian ringed seals and their genotypic and phenotypic diversity. Specifically, we seek to: i) use mitogenomic data to infer the timing and route(s) of ringed seal colonisation of Fennoscandia and to determine whether this occurred as a single stepwise event or through repeated colonisation waves; ii) assess putative differences in skull morphology to infer the role of dietary specialisation in the diversification of Fennoscandian ringed seals; and iii) discuss the implications of our findings for the status and fate of Fennoscandian ringed seals in a warming world. Compared to previous work, our study expands the genetic and morphological sample size from all three Fennoscandian subspecies and substantially increases the genetic sample size from the Atlantic Arctic. Notably, we fill a major geographical gap in previous studies by including mitogenome and morphological data from East Greenland ringed seals, which are among the Arctic ringed seals that have the shortest (waterway) distance to Fennoscandia and hence might be a possible source of founders and migrants.

Mitogenome analyses Sampling, DNA extraction and sequencing Ringed seal tissue samples for mitogenome analyses were collected from all three Fennoscandian subspecies and across the Atlantic range of the Arctic subspecies (Figure 1; Table 1). DNA from Svalbard, the Baltic Sea, Lake Ladoga and Lake Saimaa was extracted using NucleoSpin Tissue Kit (Macherey-Nagel) and sequenced as described in Savriama et al. (2018), Löytynoja et al. (2023) and Sundell et al. (2023), while DNA was extracted from the Greenlandic and Canadian samples using the Thermo Scientific KingFisher Cell and Tissue DNA Kit (Germany), as described in Rosing-Asvid et al. (2023). DNA libraries from the Greenlandic and Canadian samples were built using the blunt end single tube (BEST) protocol (Carøe, Gopalakrishnan et al. 2018) and sequenced on the Illumina HiSeq4000 platform using paired end 150 bp at the National High-throughput DNA Sequencing Centre, University of Copenhagen, Denmark. Data filtering and mapping Sequence reads were mapped to a Baltic Sea ringed seal mitogenome (NC_008433; Arnason, Gullberg et al. 2006) using Geneious Prime 2019.0.4 (https://www.geneious.com). We focused our analyses on the 12 coding regions (i.e. ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5 and CYTB) to obtain a dataset comprising 246 mitogenomes at a length of 10,713 bp (Supplementary File S1). While this reduction of the data might deflate estimates of mitogenome diversity, it should still allow for inferring the phylogeography of ringed seal subspecies. DNAsp (Rozas, Ferrer-Mata et al. 2017) was used for calculating the number of variable sites (S), haplotypes (h), haplotype diversity (H d ), nucleotide diversity (π), average number of differences (K) for each location, and the Atlantic Arctic as a whole. PopArt (Leigh and Bryant 2015) was used to create a median-joining network (Bandelt, Forster et al. 1999) for graphically displaying haplotype richness and diversity. Finally, genetic differentiation between sample sites was estimated by K ST (Hudson, Boos et al. 1992) using 1000 permutations to determine significance of the observed values. Moreover, we estimated the net number of nucleotide substitutions per site, d A (Nei 1987, equation 10.21) for a tentative evaluation of subspecies status (Morin, Martien et al. 2023). The phylogenetic analyses were conducted on a reduced dataset of ringed seal 141 mitogenomes in which identical haplotypes from the Lake Saimaa subspecies were removed as they are phylogenetically uninformative and removing them ease computation and visualisation . We used BEAST2.5.2. (Bouckaert, Vaughan et al. 2019) to construct a phylogenetic tree and estimate divergence times among major ringed seal lineages. First, the data were partitioned into both codon position and individual genes with the time-tree and clock model linked for all the partitions. As initial trials with a relaxed clock and a random local clock had difficulties stabilizing for the posteriors, priors and likelihoods, we used a strict clock model, no calibration of nodes and a HKY nucleotide substitution model with estimated frequencies, a fixed mutation rate and a Gamma category count of 4. The tree prior was set to Birth Death Model with a 1/x distribution, with a chain length at 40,000,000 and logging of every 1000 th tree, resulting in 40,000 trees. Tracer (Rambaut, Drummond et al. 2018) was used to explore the outputs from the Bayesian analysis and to asses that the effective sample size (ESS) was >200 for all parameters. The tree file was processed in TreeAnnotator v2.5.2, with a 10% burn-in, a posterior probability limit of 0, using Maximum clade credibility with node heights set to mean heights. The resulting tree was visualized in Figtree v. 1.4.4 (Rambaut 2006-2018). In addition, to supplement the Bayesian phylogeny, we constructed a maximum likelihood tree using PhyML with a GTR model, 4 substitution rate categories and 1000 bootstrap iterations (Guindon, Dufayard et al. 2010). In order to rescale the root (“crown age”) of our ringed seal Bayesian phylogeny, we performed a time-calibrated multi-species Bayesian phylogenetic analyses in BEAST2 using an alignment of mitogenomes from eight related phocid seal species with 36 of our ringed seal mitogenomes representing the main evolutionary lineages A-H identified in the ringed seal phylogenetic analysis (Supplementary File S2). We linked clock and tree models, used a HKY model with four gamma categories, and as priors a Birth-Death model with gamma shaped birth and death rates. To time the tree, we defined prior calibration points for four monophyletic groups: Phocini (mean=5.215 Mya; 95%HPD=2.24-8.00 Mya; normal with sigma=1.7, offset=0.0), Phocina (mean=2.375 Mya; 95%HPD=1.14-3.61 Mya; normal with sigma=0.75, offset=0.0), ringed seal and Baikal seal (mean=1.89 Mya; 95%HPD=1.28-2.55; normal with sigma=0.4, offset=0.0) and finally our 36 ringed seal mitogenomes to obtain a ringed seal crown age (median=0.882; 95%HPD=0.265-2.56; gamma with offset=0.2; alpha=1.2; beta=0.7). These calibration point priors are based on the divergence times inferred from pinniped-specific mitogenome analyses (Fulton and Strobeck 2010), which we preferred over the generally much older dates provided by TimeTree v. 5 (Kumar, Suleski et al. 2022), as the former will push the ringed seal crown age as well as the divergence times of different ringed seal subspecies and major evolutionary lineages towards younger, rather than older, more controversial dates. The multi-species time-calibrated Bayesian analysis was characterised by high ESS values (Supplementary Table S2), and pointed to a crown age for the sampled ringed seals at 538 kya (95% HPD interval = 322-741 kya) (Supplementary Figure S2), which we used to rescale the root of the ringed seal mitogenome Bayesian phylogeny. not-yet-known not-yet-known not-yet-known unknown 1 Skull geometric morphometrics 1 Skull geometric morphometrics Sampling A total of 180 ringed seal skulls from the Baltic Sea (N=49), Lake Ladoga (N=28), Lake Saimaa (N=24), East Greenland (N=60), and the High Arctic (Northwest Greenland and Eastern Canadian Arctic) (N=19), were measured, including 46 females, 62 males and 72 specimens of unknown sex (Figure 1; Supplementary File S3). To avoid excessive allometric variation in the sample, only adult and subadult animals were included, with subadults being defined by centroid size close to the range of known adults, as described below. The skull specimens are held at the Natural History Museum of Denmark and the Museum of Natural History in Helsinki, Finland; none of them were sampled for the mitogenome analyses. Thirty-one anatomical cranial landmarks were defined that could be unequivocally located and that were presumed to be homologous among all skulls (Supplementary Figure S1, Supplementary File S3). Three-dimensional coordinates of the landmarks were registered with a Microscribe® 3D digitizer. The raw landmark coordinates were run through the generalized least-squares Procrustes superimposition (Rohlf and Slice 1990) using the MorphoJ-program (Klingenberg 2011), which was also used for all initial analyses. The Procrustes procedure used here was amended to deal with the redundancy of data points caused by the symmetry of the vertebrate skull (Klingenberg, Barluenga et al. 2002). To exclude size-related variation, all further analyses were performed on the residuals of a multivariate regression of skull shape (i.e. Procrustes coordinates) on size (i.e. the logarithm of centroid size, CS; the square root of the summed squared distances of all landmarks to the centroid of the configuration). To ensure independence of vectors describing sexual and geographical differences, the directionality of a vector describing shape differences between males and females at each locality was compared to the vectors describing shape differences among areas. The respective vectors were defined by linear discriminant analysis vectors between males and females and linear discriminant analysis vectors between the five sampling areas. Finding that geographical differences were unrelated to sex (see below), it was decided to pool sexes for geographical comparisons to improve sample sizes and include specimens with unknown sex. Multivariate comparisons were performed on the first 10 components of a principal components analysis (PCA) to reduce the number of variables relative to the number of observations in the smaller samples from Northwest Greenland and Canada, Lake Ladoga and Lake Saimaa. These 10 PCs accounted for 67% of the total variance in the dataset. All subsequent PCs each accounted for less than 3.5% of total variance. Shape differences between the five sampling areas were explored using the first 10 PCs with R v4.3 (R Development Core Team 2015). A canonical variates analysis with classification of each specimen to the most likely geographical area by jackknife cross-validation based on Mahalanobis distance (Lachenbruch 1967), was used to assess the success rate of assignment of skulls to the area of origin by shape. Success rates were also assessed by jackknife reclassification of pairwise comparisons between the potential subspecies, that is, Arctic, Baltic, Ladoga and Saimaa ringed seals, respectively. Hotelling’s T 2 tests were used for pairwise comparisons for statistically significant shape differences between all pairs of sampling areas. Student’s t -tests were used to compare centroid sizes between all areas. The variation of skull shapes within each area was also assessed by computing the Procrustes distance of each specimen to its group mean shape. Like the analysis of centroid sizes, Student’s t -tests were used to compare the levels of variation in skull shape between areas.

Mitogenome analyses Diversity and differentiation The mitochondrial haplotype ( H d ) and nucleotide diversity (π) of Baltic Sea ringed seals was surprisingly high, with almost every animal having a unique haplotype (Table 1). In contrast, Lake Ladoga seals had relatively high haplotype diversity and low levels of nucleotide diversity, whereas Saimaa ringed seals had both low haplotype and nucleotide diversity with only 7 unique haplotypes found among a sample of 112 animals. The estimates of pairwise differentiation ( K ST ) were high, and statistically different for all comparisons between the Baltic Sea, Lake Ladoga, Lake Saimaa and Arctic ringed seals (Table 2). The highest level of pairwise genetic differentiation was found between Baltic Sea and Lake Saimaa ringed seals, as well as between Lake Saimaa and Lake Ladoga ringed seals, whereas the lowest level was estimated between the Arctic and the Baltic Sea. Likewise, estimates of d A were higher for Lake Ladoga and Lake Saimaa ringed seals and generally lower for comparisons including Baltic Sea ringed seals (Table 2). Within the Arctic, estimates of K ST and d A were close to zero, with only Ulukhaktok (Eastern Beaufort Sea, Canada) showing some level of genetic differentiation from other Arctic localities, although this was not statistically significant (Supplementary Table S1). Haplotype network and phylogeny The median-joining haplotype network suggested the existence of eight evolutionary lineages, consisting of six major and two minor lineages across the sample range (Figure 2). These include: lineage A dominated by Lake Ladoga haplotypes, but also containing Arctic and Baltic haplotypes; lineage B dominated by Baltic haplotypes and a few Arctic ones; lineages C and F with Arctic haplotypes; lineage D containing all the Lake Saimaa haplotypes, as well as a few Arctic haplotypes at the base; a mixed lineage G with haplotypes from most sample regions, except Lake Saimaa; and finally two minor lineages E and H consisting of Arctic haplotypes. Arctic ringed seals appear to occupy the central positions of the network, whereas seals in the Baltic Sea, Lake Ladoga and Lake Saimaa occupy the tips, suggesting that Arctic haplotypes are ancestral. The ringed seal Bayesian and maximum likelihood phylogenetic analyses confirmed the existence of the ringed seal lineages identified in the haplotype network (Figure 3; Supplementary Figure S3; Supplementary Figure S4; Supplementary Table S3). The crown age (root) estimated in the multispecies phylogeny at 538 kya marks an early split between two ringed seal superclades I and II within which the Arctic lineages C, E, F and H emerge 250-500 kya, and the remaining Arctic and Fennoscandian lineages A, B and D appearing 150-50 kya. Mitogenome lineage G, comprising a mix of Arctic and Fennoscandian seals, diverged early from other lineages at circa 470 kya, but diverged into sublineages much later at circa 100 kya. In Fennoscandia, the sublineage D2 leading to Saimaa ringed seals diverged from Arctic ringed seals in lineage D1 about 70 kya and diverged into distinct haplotypes about 33 kya. The Ladoga seals (and a few Arctic and Baltic seals) in sublineages A1-A2 split from the Arctic lineage A3 about 86 kya. Notably, the A2 lineage, consisting exclusively of Ladoga and a few Baltic seals, but no Arctic ringed seals, emerged about 63 kya and diverged into distinct haplotypes about 30 kya. Baltic ringed seal haplotypes were assigned to multiple distinct lineages, but predominantly belong to lineage B, which diverged from other ringed seals about 163 kya. This group diverged further into sublineages B1 and B2 about 49 kya. Lineage G was characterised by low internal resolution, except for three well-supported sublineages G1, G3 and G5 comprising mainly Baltic animals, which appear to diverge from Arctic seals in lineage G about 15-18 kya. Skull geometric morphometrics The vectors describing shape difference between males and females and the differences between the ringed seal distribution areas were largely independent. All vectors describing geographical differences among the five sample areas had angles between 85.7° and 98.6° (with 90° representing complete independence) when compared to the vector describing male-female differences, except for the pairs Saimaa-Ladoga (56.9°) and Saimaa-East Greenland (108.0°). A jack-knife reclassification of skulls based on sex yielded a success rate of 63.9%, demonstrating very modest sexual dimorphism and large shape overlap between sexes. Thus, sexes were pooled for further analysis of shape. Geographical differences in skull shape, diversity and size Highly significant shape differences ( p <0.000001) were detected among all areas, except between Arctic localities (High Arctic vs East Greenland), which had a more moderate p-value ( p = 0.013). These values were in turn reflected in the Procrustes and Mahalanobis distances among the regions, with the largest shape distances found between the Lake Ladoga and Lake Saimaa populations, and the smallest distance between East Greenland and the High Arctic (Table 3). The success of reclassification of specimens to geographical area of origin by shape using jack-knife cross-validation varied from 48% and 53% for East Greenland and the High Arctic, respectively, 59% for Baltic Sea, 82% and 88% for Ladoga and Saimaa seals, respectively (Table 4). Assignment success was between 79% and 90% for all pairwise comparisons, with the lowest being between the Arctic and the Baltic subspecies, where the more divergent lake subspecies were not involved (Table 5). These values reiterate that despite the highly statistically significant differences in skull morphology, there are substantial overlaps of shape between most of the sampled areas. This is also illustrated by plots of the first eight principal components, accounting for 58.7% of total variance of the residual shape after correction for allometry (Figure 4). Subsequent PCs all accounted for <4% of variance and did not show patterns related to geography. Differences between area-specific shapes and the grand mean of shapes among areas were small (Supplementary Figure S5). The morphological differences are most noticeable for the landlocked ringed seals, where Lake Ladoga skulls display a somewhat longer, laterally narrower, and dorsally compressed skull compared to the grand mean. Lake Saimaa skulls showed an opposite tendency, being somewhat shorter and dorsally expanded with slightly larger eye orbits compared to the grand mean. The largest skulls were found in the High Arctic of Northwest Greenland and Northeast Canada, whereas the other areas did not differ much in average skull size (Figure 5A). The Baltic Sea sample showed the largest variation in skull size, whereas the landlocked subspecies showed the lowest levels of variation (Figure 5B). The average shape variation within areas as defined by Procrustes distance to sample mean was larger than the between-sample Procrustes distances, again highlighting modest geographic variation in ringed seal skull shapes.

Fennoscandian phylogeography suggests cryptic refugia and colonisation routes The origin of Fennoscandian ringed seals has been the subject of much scientific investigation and debate (e.g. Davies 1958, Palo, Mäkinen et al. 2001, Sommer and Benecke 2003, Valtonen, Palo et al. 2012, Martinez-Bakker, Sell et al. 2013, Nyman, Valtonen et al. 2014, Ukkonen, Aaris-Sørensen et al. 2014, Heino, Nyman et al. 2023). In our mitogenome analyses, we detected multiple levels of phylogenetic structure with eight distinct evolutionary lineages, which largely grouped into two superlineages; I (lineages A-B) and II (lineages C-H). The three Fennoscandian subspecies showed some a phylogeographic patterning, whereas no clear phylogeographic pattern is detected in the Arctic subspecies with animals from Canada, Greenland and Svalbard scattered across all eight phylogenetic lineages. Our genetic data strongly point towards a more complex origin of Fennoscandian ringed seals than previously assumed, which we tentatively attribute to the existence of multiple colonisation routes and waves, as well as glacial refugia at the edge of the Fennoscandian Ice Sheet (Figure 6). Saimaa ringed seals Like previous studies, we found that the Saimaa subspecies was highly genetically (and to an extent morphologically) distinct from other subspecies. It was characterised by high pairwise estimates of genetic differentiation and formed a single monophyletic sublineage (D2) nested deep within multiple largely Arctic lineages (C, D1, E and F). Recent analyses by Heino et al. (2023) based on ~700 bp mtDNA control region data found multiple Baltic Sea haplotypes nested within Saimaa haplotypes, however our and most other studies find Saimaa to be monophyletic. Like us, Heino et al. (2023) found Saimaa ringed seals nested deep within Arctic haplotypes, which we interpret to mean that Saimaa ringed seals originated during a single colonisation event from an Arctic-like source (Figure 6), contrasting with most other previous interpretations which have pointed to a Skagerrak-Kattegat origin. The exact source of the Saimaa subspecies remains obscure, potentially due to insufficient sample coverage from significant portions of the ringed seal’s Russian range, the notable mitogenome homogeneity observed in Arctic ringed seals, or the possibility that the source population has become extinct over time. Regardless of its origin, evidence is mounting that the Saimaa subspecies is substantially older than previously assumed. Recent nuclear genome analyses indicate that the subspecies has followed a distinct demographic trajectory at least since the LGM and possibly up to 50-60 kya or older (Löytynoja, Rastas et al. 2023). Similarly, demographic modelling using microsatellite markers suggested a Saimaa-Baltic divergence c. 95 kya, although the authors interpreted this – at the time unexpectedly old divergence time estimate – as bias caused by the use of unusual high mutation rates (Valtonen, Palo et al. 2012). Moreover, a recent study of seal lice in Fennoscandian ringed seals support a split of these from Arctic seal lice about 96 kya, and that seal lice in Saimaa seals have followed their own demographic trajectory for 60-80 ky (Sromek, Johnson et al. 2024). Our mitogenome data suggest that sublineages D1 and D2, consisting of Arctic and Saimaa haplotypes, respectively, diverged from other ringed seals about 289 kya, that D1 and D2 diverged about 69 kya and that the single Svalbard haplotype at the root of D2 split at 46 kya, after which Saimaa seals comprise a monophyletic clade. Thus, we too find that the mitogenome lineage of the Saimaa ringed seal has a pre-LGM origin. The length of the lineage (branch) leading to lineage D following its split from lineage C at 289 kya points to a long period of isolation and low abundance (bottleneck) before ultimately colonising Lake Saimaa. We hypothesize that the Arctic ringed seals, which gave rise to the Saimaa D2 sublineage, could have colonised the region from the Barents Sea and White Sea through the Karelia seaway, which connected the Pre-White Sea and the Pre-Baltic Sea region, including Ladoga and Saimaa, during the Eemian interglacial (130-115 kya) (Funder, Demidov et al. 2002, Lebas, Gromig et al. 2021). Subsequently, these could have maintained large viable populations at the north- and southeastern edge of the Fennoscandian Ice Sheet. This region was ice-free during the Early Weichselian glaciation (109-71 kya) (Svendsen, Alexanderson et al. 2004, Andren, Bjorck et al. 2011), and much of the eastern Baltic Sea, Karelia and White Sea region was characterised by a vast network of enclosed marine seas and ice-dammed lakes up until the Middle Weichselian about 60-50 kya (Mangerud, Jakobsson et al. 2004, Helmens and Engels 2010). Likewise, the period 55-35 kya was characterized by long climatic interstadials, in which time was sufficient to efficiently reduce the size of the Fennoscandian ice sheet (Kleman, Hättestrand et al. 2021), and even the LGM 30-20 kya was characterised by large glacial lake systems at the ice-margin (Hughes, Gyllencreutz et al. 2016, Patton, Hubbard et al. 2017). At the end of the LGM (19 kya), the southeastern edge of the Fennoscandian Ice Sheet was characterised by a continuous presence of a vast system of ice-lakes (Gorlach, Hang et al. 2017). Several of these ice-lakes were similar in size to present day Lake Saimaa (4,400 km²), and a few even similar to present day Lake Ladoga (17,700 km²) (Gorlach, Hang et al. 2017), and could thus easily have supported viable “pre-Saimaa” seal populations that tracked the receding LGM ice sheet and its associated glacial lakes to ultimately colonise present day Lake Saimaa during the Holocene. Ladoga ringed seals Ladoga ringed seals were also characterised by high levels of genetic (and morphological) differentiation in our analyses, albeit not at the same levels as estimated for the Saimaa subspecies. Our results indicate that the origin of Lake Ladoga ringed seals is more complex than previously assumed with Ladoga seals comprising a mix of very different evolutionary lineages with possible distinct histories of refugia and colonisation (Figure 6). In sublineage G1, two haplotypes are found in Lake Ladoga, whereas the rest occur in the Baltic Sea and the Arctic. Consistent with earlier studies (Palo, Mäkinen et al. 2001, Nyman, Valtonen et al. 2014), we interpret this as indicative of a post-LGM (Holocene) colonisation from the Baltic Sea, e.g. during the Baltic Ice Lake stage, during which present day Lake Ladoga and the Baltic Sea formed a combined waterbody (Vassiljev, Saarse et al. 2011, Ukkonen, Aaris-Sørensen et al. 2014). Such periodic gene flow with the Baltic may still be ongoing. However, while the Ladoga seals in lineage G appear to be of post-LGM origin, most other Ladoga seal haplotypes occur in two other sublineages, A1 and A3, together with the mainly Arctic sublineages A2 and A4 from which they diverged about 24 kya and at least 30 kya (but possibly up to 63 kya), respectively. Thus, similarly to the D2 haplotypes found in Saimaa seals, the A1 and A3 haplotypes in Ladoga seals appear have an Arctic pre-LGM origin, rather than a post-LGM Baltic origin. The A lineage split from the B lineage about 163 kya and has a crown age at about 86 kya, and may thus have entered Fennoscandia from the Arctic via the White Sea and the Karelia Seaway during the Eemian interglacial and found refuge in enclosed seas and/or glacial lakes during the Weichselian and LGM, like hypothesised for the Saimaa seal. Alternatively, as discussed below, the A1 and A3 haplotypes in Ladoga seals may be traced to a cryptic northwestern European refugium. Baltic ringed seals In contrast to Lake Saimaa and Lake Ladoga ringed seals being dominated by haplotypes from one and two lineages, respectively, the Baltic Sea subspecies carries haplotypes from four distinct lineages (A, B, F and G), suggesting a mixed origin of Baltic Sea ringed seals. The Baltic haplotypes in lineages A, F and G appear to be of relatively recent origin, diverging 20-10 kya from Arctic seals. This in agreement with previous accounts on the post-LGM colonisation of the Baltic Sea by ringed seals from the Skagerrak-Kattegat region (Figure 6). Indeed, while the earliest zooarchaeological remains of ringed seals in the Baltic Sea date to c. 10,440 kya, much older remains dating to at least 45,000 kya have been recovered in the neighbouring Skagerrak and Kattegat, documenting the existence of a ringed seal population in the region during the last glacial period (Ukkonen, Aaris-Sørensen et al. 2014). Not all Baltic ringed seals appear to share this origin. Most notably, nearly half of the Baltic ringed seals carry lineage B haplotypes, which are found almost exclusively in the Baltic Sea. Lineage B consists of two sublineages B1 and B2, which diverged 49 kya, and itself appears to have separated about 163 kya from lineage A haplotypes found in Arctic, Ladoga and a few other Baltic seals, . The shape of the subtree leading to lineage B, characterised by a long branch length extending over the current B1 and B2 sublineages, indicates that the ancestral B haplotypes experienced a long period of isolation and low abundance (bottleneck) before colonising the Baltic Sea. Such isolation could have occurred in a cryptic refugium located at the edge of the Fennoscandian Ice Sheet (Figure 6). The North Sea (Sejrup, Nygård et al. 2009, Patton, Hubbard et al. 2017, Panin, Astakhov et al. 2020), The Channel River (or “Fleuve Manche”) (Toucanne, Zaragosi et al. 2009, Toucanne, Rodrigues et al. 2023), or the extensive mosaic of glacial lakes described at the southwestern ice margin in present-day Germany and the Netherlands (Lang, Lauer et al. 2018) could all have supported such an isolated ringed seal populations. Seals from either of these hypothesized glacial refugia could have gradually moved into the Pre-Skagerrak-Kattegat to intermix with Baltic A, F and G haplotypes and colonise the Baltic Sea when it deglaciated during the Holocene. Morphological variation: adaptation, plasticity or chance? The results of our morphological analyses support the genetic data; the landlocked Saimaa and Ladoga ringed seal subspecies are the most morphologically divergent and showed the lowest levels of within-group morphological variation. This complements the genetic results that the Saimaa subspecies has followed its own evolutionary trajectory and likely went through bottlenecks. Lake Saimaa skulls were shorter and dorsally expanded compared to the average skull shape across our overall sample with somewhat larger eye orbits. As suggested in previous analyses (Amano, Hayano et al. 2002), the distinct skull morphology of Saimaa seals – with relatively larger eyes and brains – may be adaptations for navigation in the murky and labyrinthine lake environment. In contrast, Lake Ladoga skulls display a somewhat longer, laterally narrower, and dorsally compressed skull compared to the grand mean. It is possible that these morphological adaptations arose prior to colonising Lake Saimaa and Lake Ladoga, respectively, perhaps during long periods of isolation in glacial refugia at the edge of the Fennoscandian Ice Sheet. Baltic Sea ringed seals showed the largest within-group variation in skull size and shape, corresponding with their relatively high mitogenome diversity; they were not highly distinct from Arctic seals. Multiple colonisation events of the Baltic region might have introduced diverse phenotypes and genotypes, boosting the Baltic subspecies’ overall genetic and morphological diversity. This diversity might have been maintained by Baltic ringed seals occupying multiple smaller pockets of suitable habitat with substantial variation in environmental conditions and prey-bases in three main population centres in the Bothnian Bay, Finnish Archipelago Sea and Gulf of Riga, as well as a small, declining presence of ringed seals in the Gulf of Finland. The skulls of High Arctic ringed seals had a wide size range, but were on average larger than skulls from all other areas, in agreement with previous observations of body and skull size in the Arctic (Finley, Miller et al. 1983, Ferguson, Zhu et al. 2018, Kovacs, Citta et al. 2021). This may reflect the large source area for this sample and perhaps also the latitudinal size cline found in eastern Canada (Ferguson, Zhu et al. 2018, Ferguson, Yurkowski et al. 2019). It is unclear whether this cline reflects phenotypic plasticity or natural selection. Recent genetic and ecological data suggest the existence of a distinct “Kangia” ringed seal ecotype that inhabits the Ilulissat Icefjord in West Greenland (Rosing‐Asvid, Löytynoja et al. 2023). The body size of these Kangia seals is as large as to that of High Arctic ringed seals (Kovacs, Citta et al. 2021) and preliminary morphometric analyses indicate that their skulls are also distinctive (M.T. Olsen, unpublished data). It is likely that at least some of the morphological variation observed among Arctic ringed seals has a genetic background. Interspecific variation in skull morphology of phocid seals (and many other vertebrates) is strongly linked to feeding ecology, with most species occupying distinct morphospaces and relatively easy to visually identify to species (Kienle and Berta 2016). However, the intraspecific variation in phocid skull morphology is often modest, and how this links to function is generally poorly understood (Galatius, Svendsen et al. 2022). Ringed seals are typically described as opportunistic foragers, using a combination of biting and suction to ingest a range of fish and invertebrate species (Siegstad, Neve et al. 1998, Holst, Stirling et al. 2001, Kienle and Berta 2016, Scharff-Olsen, Galatius et al. 2018). This might buffer against divergence and adaptations in larger areas with a wide array of potential prey items, such as the Arctic and to some extent the Baltic Sea, while the landlocked subspecies in Lake Saimaa and Lake Ladoga may have adapted to a limited local prey diversity. Unfortunately, there is no investigation of the diet of Lake Ladoga seals available to evaluate this. However, Lake Saimaa seals are known to have a relatively simple diet with smelt ( Osmerus eperlanus ), ruff ( Gymnocephalus cernuus ) and perch ( Flerva fluviatilis ) making up more than 70% of prey (Auttila, Sinisalo et al. 2015). We propose that this forced dietary specialisation might have been a driver of its morphological skull diversification. We note that marine populations of ringed seals, as well as other pinniped species, are known to occasionally visit and forage in rivers and adjoining lakes (Roffe and Mate 1984), so we would not expect an immediate strong selection on skull morphology caused by salinity changes when the Saimaa and Ladoga ancestors moved from marine to freshwater. The status and fate of Fennoscandian ringed seals? Historical catch records indicate that the long-term population size of Baltic Sea ringed seals was in the hundreds of thousands (Kvist 1991, Kokko, Helle et al. 1999), but that its population size was reduced to about 5,000 animals in the 1960s-1980s due to hunting and organochloride pollution (Bergman and Olsson 1986, Harding and Härkönen 1999). Its abundance has increased in recent decades, currently numbering 20,000-30,000 animals, of which the majority reside in the Bothnian Bay, 1,500 live in the Estonian part of the Gulf of Riga, 200-300 live in the Archipelago Sea, and less than 100 in the Gulf of Finland (HELCOM 2023). Nevertheless, Baltic ringed seals continue to face challenges and fall short of attaining good environmental status. New pollutants are emerging in the Baltic Sea ecosystem (Sonne, Siebert et al. 2020), pathogens might be introduced from sympatric seal and bird species (Sonne, Lakemeyer et al. 2020), and overexploitation of fish stocks affects the quality and quantity of important prey species and in turn the nutritional status and reproductive success of Baltic ringed seals (Kauhala, Bergenius et al. 2019). Climate change is already severely affecting the southern Baltic distributional areas, where mild winters have greatly reduced the extent of sea ice with overlying snow for breeding lairs (Meier, Kniebusch et al. 2022). The relatively high levels of phenotypic and genetic diversity reported here and elsewhere (Palo, Mäkinen et al. 2001, Amano, Hayano et al. 2002, Martinez-Bakker, Sell et al. 2013) may provide some resilience to human impacts and environmental variation in Baltic ringed seals. Still, it is imperative that management and conservation measures are kept in place and adapted to address changes in the intensity of different impacts such as climate change. It has been debated whether Baltic ringed seals constitute a subspecies or a population (Palo, Mäkinen et al. 2001, Amano, Hayano et al. 2002, Martinez-Bakker, Sell et al. 2013). For cetaceans, guidelines for taxonomy propose a classification of the population/subspecies boundary at d A > 0.0006 for mitogenomes (Morin, Martien et al. 2023) and percent diagnosability (PD) > 80% for morphological data (Taylor, Archer et al. 2017). Using these criteria, our results indicate that Baltic Sea ringed seals meet the subspecies criteria based on mitogenome data ( d A = 0.0013-0.0066), while diagnosability based on morphometrics was close to this threshold, at least in pairwise comparisons (PD = 78.9%-88.1%). The landlocked Lake Saimaa ringed seal subspecies is characterised by extremely low levels of diversity, with little variation in skull shape, and very low haplotype and nucleotide diversity in a sample of more than hundred animals. These findings are similar to previous genetic studies (Palo, Hyvärinen et al. 2003, Valtonen, Palo et al. 2012, Nyman, Valtonen et al. 2014, Heino, Nyman et al. 2023, Löytynoja, Rastas et al. 2023, Sundell, Kammonen et al. 2023), which all suggest that Saimaa ringed seals have experienced bottlenecks during colonisation, and as a consequence of more recent human impacts and climate change (Kunnasranta, Niemi et al. 2021). In Saimaa, dedicated conservation and management measures by researchers and volunteers have supported breeding efforts in years with insufficient snow and/or ice cover by shovelling snow piles and construction of floating man-made “nest boxes” with some success (Kunnasranta, Niemi et al. 2021). In addition, rehabilitation, captive breeding and translocation (within Lake Saimaa and/or to other lake systems), is being considered to facilitate population growth and maintain genetic diversity in the subspecies (Sundell, Kammonen et al. 2023). However, due to its very low abundance estimated at only 400-500 animals, the most important conservation priority is to mitigate the risk of stochastic effects, including spread of diseases and regulating fishing and recreation in key habitats and seasons (Kunnasranta, Niemi et al. 2021). Lake Saimaa ringed seals clearly meet the subspecies criteria proposed for cetaceans for mitogenome data genetic ( d A = 0.0036-0.0099) and morphological distinctiveness (PD = 84.6%-90.3%), and we note that it in some pairwise comparisons also meet the species criteria at d A > 0.008 (Morin, Martien et al. 2023), while falling slightly below the species diagnosability criteria for morphological data at > 95% (Taylor, Archer et al. 2017). Lake Ladoga seals are slightly more genetically and morphologically diverse than Lake Saimaa seals, possibly due to a larger founding population, less severe impacts of human activities, and perhaps also occasional gene-flow from Baltic Sea ringed seals. Hunting of the Lake Ladoga subspecies led to population declines from about 20,000 animals in the early 20 th century to about 4,000 animals in the 1970s, but since their protection in the 1980s, abundance increased to about 5,000 animals in the 1990s and up to 8,000 animals in 2012, with most occurring in the northern part of the lake (Sipilä and Hyvärinen 1998, Trukhanova, Gurarie et al. 2013). As with other Fennoscandian ringed seals, the Lake Ladoga subspecies is threatened by bycatch, recreational activities and climate change through loss of ice and snow cover during the breeding season (Trukhanova, Andrievskaya et al. 2021). In our analyses, the Lake Ladoga ringed seals meet the subspecies criteria for both mitogenome ( d A = 0.0023-0.0099) and morphological data (PD = 84.6%-88.8%), and management should be undertaken accordingly. Climate change is already affecting Fennoscandian ringed seals, particularly regarding declines in suitable breeding habitats with sufficient ice and snow cover, and these effects will only increase in the future (Meier, Kniebusch et al. 2022). All Fennoscandian ringed seals, along with some Arctic counterparts (e.g. Northwest Greenland, Svalbard, White Sea and Bering Sea), resort to using land as a haul-out platform during the summer when sea ice is unavailable (Lydersen, Vaquie-Garcia et al. 2017, Olsen MT pers. obs., Gryba, Huntington et al. 2021, Kunnasranta, Niemi et al. 2021, Melnikov 2022, Svetochev, Kavtsevich et al. 2022, Trukhanova, Bakunovich et al. 2024). Though breeding on land has only recently been reported for the Lake Ladoga ringed seal (Loseva, Chirkova et al. 2022), our and previous studies document the long-term persistence of Fennoscandia ringed seals through interglacials and Holocene warm periods (e.g. Sommer and Benecke 2003, Ukkonen, Aaris-Sørensen et al. 2014, Heino, Nyman et al. 2023, Löytynoja, Rastas et al. 2023). Thus, while land-based breeding is likely associated with a substantial reduction in reproductive success, there is ground for some optimism for the future of Fennoscandian ringed seals, contingent upon the effective reduction of other anthropogenic pressures, including bycatch, disturbance of resting and breeding sites, competition for food, and pollution (Reusch, Dierking et al. 2018, Sonne, Siebert et al. 2020).

AND FURTHER RESEARCH Evidence is accumulating that the evolutionary histories of the three Fennoscandian ringed seal subspecies is more complex than previously assumed, characterised by several periods of isolation and connection during glacials and interglacials. Our finding that the diversification of Fennoscandian ringed seals predate the LGM is controversial given the lack of ringed seal zooarchaeological material from this period. However, prior to and during the LGM, we expect very few if any prehistoric human settlements that could account for deposition of bone remains, and natural deposits are likely to be widely scattered and thus rarely unearthed. Moreover, while our genetic analyses are limited in their reliance on maternally inherited mitogenome markers and rather simplistic model assumptions for the ringed seal phylogenetic analysis, the tree was dated by comprehensive time-calibrated multi-species phylogenetic analysis, and divergence times supported by recent analyses of nuclear genomes (Löytynoja et al. 2023; Sromek et al. 2024) and historic mtDNA data (Heino et al. 2023). Importantly, we argue that the biology of the ringed seal makes it fully capable of surviving long glacial and interglacial periods in even small isolated glacial refugia. Evidently, ringed seals have been maintaining small isolated populations for millennia in the Saimaa and Ladoga lakes, as well as in Arctic glacial fjord systems (Rosing-Asvid et al. 2023), and the long-term existence of lake populations is also known for harbour seals ( Phoca vitulina ), including the Lac des Loups Marins (Ungava) and Iliamna seals (Smith, Lavigne et al. 1994, Ferrer, Boveng et al. 2024). Future research endeavours incorporating full nuclear genome data hold promise for providing additional insights into the evolutionary history of Fennoscandian ringed seals. Such studies may also include more detailed morphological and isotopic analyses to generate hypotheses regarding the role of foraging and other adaptations in the diversification process, contributing to a more comprehensive understanding of the complex evolutionary dynamics within this species. Finally, we note that the Fennoscandian region holds other relict marine species (e.g. Funder et al. 2002), which may also be characterised by a more complex history of evolution and colonisation than previously assumed.

The authors thank staff at the Natural History Museum of Denmark and the Finnish Museum of Natural History for access to the ringed seal skull collections, as well as Tina B. Brand, Pernille Selmer Olsen and Lasse Vinner at the Globe Institute, University of Copenhagen, for their guidance on genome sequencing. The study was supported by a Carlsberg Foundation Semper Ardens Accelerate (grant CF21-0425) to MTO, as well as funding to MTO and RD from the BONUS BALTHEALTH project, BONUS (Art. 185), funded jointly by the EU, Innovation Fund Denmark (grants 6180-00001B and 6180-00002B), Forschungszentrum Jülich GmbH, German Federal Ministry of Education and Research (grant FKZ 03F0767A), Academy of Finland (grant 311966) and Swedish Foundation for Strategic Environmental Research (MISTRA). The Greenland Institute of Natural Resources funded the collection and sequencing of Greenland ringed seal samples and the Norwegian Polar Institute supported Svalbard collections. We thank Jane ja Aatos Erkon Säätiö (JAES) (4-2013, 5-2017) for funding provided to JJ and PA, and the LIFE Programme of the European Commission (LIFE19NAT/FI/000832) for funding to PA. AUTHOR CONTRIBUTIONS MTO and AG conceived and designed the study; MTO, MV, ARA, RDI, SF, JJ, KK, CL and PA provided genetic samples and funding; MTO, AL, SWK and SB analysed the genetic data; AG and CG performed the geometric morphometric analyses; MTO and AG drafted the manuscript; all authors provided editorial inputs and approved of the final version of the manuscript. not-yet-known not-yet-known not-yet-known unknown COMPETING INTERESTS The authors declare no conflicts of interest. DATA ACCESSIBILITY Mitogenomes and morphometric data are attached as supplementary files. not-yet-known not-yet-known not-yet-known unknown 1 REFERENCES https://indicators.helcom.fi/indicator/ringed-seal-abundance/ 1 REFERENCES not-yet-known not-yet-known not-yet-known unknown 1 Amano, M., A. Hayano and N. Miyazaki (2002). ”Geographic Variation in the Skull of the Ringed Seal, Pusa Hispida .” Journal of Mammalogy 83 (2): 370-380.Andren, T., S. Bjorck, E. Andren, D. Conley, L. Zillen and J. Anjar (2011). The Development of the Baltic Sea Basin During the Last 130 ka. Baltic Sea Basin. J. Harff, S. Bjorck and P. Hoth: 75-+.Arnason, U., A. Gullberg, A. Janke, M. Kullberg, N. Lehman, E. A. Petrov and R. Väinölä (2006). ”Pinniped phylogeny and a new hypothesis for their origin and dispersal.” Molecular Phylogenetics and Evolution 41 (2): 345-354.Auttila, M., M. Kurkilahti, M. Niemi, R. Levänen, T. Sipilä, M. Isomursu, J. Koskela and M. Kunnasranta (2016). ”Morphometrics, body condition, and growth of the ringed seal (Pusa hispida saimensis ) in Lake Saimaa: Implications for conservation.” Marine mammal science 32 (1): 252-267.Auttila, M., T. Sinisalo, M. Valtonen, M. Niemi, M. Viljanen, M. Kurkilahti and M. Kunnasranta (2015). ”Diet composition and seasonal feeding patterns of a freshwater ringed seal (Pusa hispida saimensis ).” Marine Mammal Science 31 (1): 45-65.Bandelt, H.-J., P. Forster and A. Röhl (1999). ”Median-joining networks for inferring intraspecific phylogenies.” Molecular Biology and Evolution 16 (1): 37-48.Bergman, A. and M. Olsson (1986). ”Pathology of Baltic grey seal and ringed seal females with special reference to adrenocortical hyperplasia: is environmental pollution the cause of a widely distributed disease syndrome?” Riistatieteellisia Julkaisuja 44 : 47-62.Bouckaert, R., T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kühnert, N. De Maio, M. Matschiner, F. K. Mendes, N. F. Müller, H. A. Ogilvie, L. du Plessis, A. Popinga, A. Rambaut, D. Rasmussen, I. Siveroni, M. A. Suchard, C.-H. Wu, D. Xie, C. Zhang, T. Stadler and A. J. Drummond (2019). ”BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.” PLOS Computational Biology 15 (4): e1006650.Carr, S. M., A. T. Duggan, G. B. Stenson and H. D. Marshall (2015). ”Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus ).” PLOS ONE 10 (8): e0134207.Carøe, C., S. Gopalakrishnan, L. Vinner, S. S. T. Mak, M. H. S. Sinding, J. A. Samaniego, N. Wales, T. Sicheritz-Pontén and M. T. P. Gilbert (2018). ”Single-tube library preparation for degraded DNA.” Methods in Ecology and Evolution 9 (2): 410-419.Davies, J. L. (1958). ”Pleistocene geography and the distribution of northern pinnipeds.” Ecology 39 (1): 97-113.Davis, C. S., I. Stirling, C. Strobeck and D. W. Coltman (2008). ”Population structure of ice-breeding seals.” Molecular Ecology 17 (13): 3078-3094.Durner, G. M., D. C. Douglas, S. E. Albeke, J. P. Whiteman, S. C. Amstrup, E. Richardson, R. R. Wilson and M. Ben-David (2017). ”Increased Arctic sea ice drift alters adult female polar bear movements and energetics.” Glob Chang Biol 23 (9): 3460-3473.Ferguson, S. H., D. J. Yurkowski, B. G. Young, A. T. Fisk, D. C. Muir, X. Zhu and G. W. Thiemann (2020). ”Comparing temporal patterns in body condition of ringed seals living within their core geographic range with those living at the edge.” Ecography 43 (10): 1521-1535.Ferguson, S. H., D. J. Yurkowski, B. G. Young, C. Willing, X. Zhu, D. C. Muir, A. T. Fisk and G. W. Thiemann (2019). ”Do intraspecific life history patterns follow interspecific predictions? A test using latitudinal variation in ringed seals.” Population Ecology 61 (4): 371-382.Ferguson, S. H., X. Zhu, B. G. Young, D. J. Yurkowski, G. W. Thiemann, A. T. Fisk and D. C. Muir (2018). ”Geographic variation in ringed seal (Pusa hispida ) growth rate and body size.” Canadian journal of zoology 96 (7): 649-659.Ferrer, T., P. Boveng, D. D. Hauser, D. Withrow, V. Burkanov, T. P. Quinn and G. O’Corry-Crowe (2024). ”Genetic and evolutionary divergence of harbour seals (Phoca vitulina) in Iliamna Lake, Alaska.” Biology Letters 20 (10): 20240166.Finley, K. J., G. W. Miller, R. A. Davis and W. R. Koski (1983). ”A distinctive large breeding population of ringed seals (Phoca hispida ) inhabiting the Baffin Bay pack ice.” Arctic 36 (2): 162-173.Fulton, T. L. and C. Strobeck (2010). ”Multiple fossil calibrations, nuclear loci and mitochondrial genomes provide new insight into biogeography and divergence timing for true seals (Phocidae, Pinnipedia).” Journal of Biogeography 37 (5): 814-829.Funder, S., I. Demidov and Y. Yelovicheva (2002). ”Hydrography and mollusc faunas of the Baltic and the White Sea–North Sea seaway in the Eemian.” Palaeogeography, Palaeoclimatology, Palaeoecology 184 (3-4): 275-304.Galatius, A., M. S. Svendsen, D. Messer, M. Valtonen, M. McGowen, R. Sabin, V. A. Dahl, A. B. Dahl and M. T. Olsen (2022). ”Range-wide variation in Grey Seal (Halichoerus grypus) skull morphology.” Zoology 153 : 126023.Gorlach, A., T. Hang and V. Kalm (2017). ”GIS‐based reconstruction of Late Weichselian proglacial lakes in northwestern Russia and Belarus.” Boreas 46 (3): 486-502.Gryba, R., H. P. Huntington, A. Von Duyke, B. Adams, B. Frantz, J. Gatten, Q. Harcharek, H. Olemaun, R. Sarren and J. Skin (2021). ”Indigenous Knowledge of bearded seal (Erignathus barbatus), ringed seal (Pusa hispida), and spotted seal (Phoca largha) behaviour and habitat use near Utqiaġvik, Alaska, USA.” Arctic Science 7 (4): 832-858.Guindon, S., J.-F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk and O. Gascuel (2010). ”New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.” Systematic biology 59 (3): 307-321.Hamilton, C. D., K. M. Kovacs, R. A. Ims, J. Aars and C. Lydersen (2017). ”An Arctic predator-prey system in flux: climate change impacts on coastal space use by polar bears and ringed seals.” J Anim Ecol 86 (5): 1054-1064.Hammill, M. O. (2009). Ringed Seal: Pusa hispida. Encyclopedia of Marine Mammals (Second Edition). W. F. Perrin, B. Würsig and J. G. M. Thewissen. London, Academic Press: 972-974.Harding, K. C. and T. J. Härkönen (1999). ”Development in the Baltic grey seal (Halichoerus grypus ) and ringed seal (Phoca hispida ) populations during the 20th century.” Ambio 28 (7): 619-627.Heino, M. T., T. Nyman, J. U. Palo, J. Harmoinen, M. Valtonen, M. Pilot, S. Översti, E. Salmela, M. Kunnasranta and R. Väinölä (2023). ”Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections.” Ecology and Evolution 13 (1): e9720.HELCOM (2023). ”Population trends and abundance of seals. HELCOM core indicator report. Online. .”.Helle, E. (1979). ”Growth and size of the ringed seal Phoca (Pusa) hispida Schreber in the Bothnian Bay, Baltic.”Helmens, K. F. and S. Engels (2010). ”Ice‐free conditions in eastern Fennoscandia during early Marine Isotope Stage 3: lacustrine records.” Boreas 39 (2): 399-409.Hewitt, G. (2000). ”The genetic legacy of the Quaternary ice ages.” Nature 405 (6789): 907-913.Holst, M., I. Stirling and K. A. Hobson (2001). ”Diet of ringed seals (Phoca hispida ) on the east and west sides of the North Water Polynya, northern Baffin Bay.” Marine Mammal Science 17 (4): 888-908.Hudson, R. R., D. D. Boos and N. L. Kaplan (1992). ”A statistical test for detecting geographic subdivision.” Molecular Biology and Evolution 9 (1): 138-151.Hughes, A. L. C., R. Gyllencreutz, O. S. Lohne, J. Mangerud and J. I. Svendsen (2016). ”The last Eurasian ice sheets - a chronological database and time-slice reconstruction, DATED-1.” Boreas 45 (1): 1-+.Jacobsen, M. W., N. W. Jensen, R. Nygaard, K. Præbel, B. Jónsson, N. H. Nielsen, J. M. Pujolar, D. J. Fraser, L. Bernatchez and M. M. Hansen (2022). ”A melting pot in the Arctic: Analysis of mitogenome variation in Arctic char (Salvelinus alpinus ) reveals a 1000‐km contact zone between highly divergent lineages.” Ecology of Freshwater Fish 31 (2): 330-346.Kauhala, K., M. Bergenius, M. Isomursu and J. Raitaniemi (2019). ”Reproductive rate and nutritional status of Baltic ringed seals.” Mammal research 64 : 109-120.Kienle, S. S. and A. Berta (2016). ”The better to eat you with: the comparative feeding morphology of phocid seals (Pinnipedia, Phocidae).” Journal of Anatomy 228 (3): 396-413.Kleman, J., M. Hättestrand, I. Borgström, D. Fabel and F. Preusser (2021). ”Age and duration of a MIS 3 interstadial in the Fennoscandian Ice Sheet core area–Implications for ice sheet dynamics.” Quaternary Science Reviews 264 : 107011.Klingenberg, C. P. (2011). ”MorphoJ: an integrated software package for geometric morphometrics.” Molecular ecology resources 11 (2): 353-357.Klingenberg, C. P., M. Barluenga and A. Meyer (2002). ”Shape analysis of symmetric structures: quantifying variation among individuals and asymmetry.” Evolution 56 (10): 1909-1920.Kokko, H., E. Helle, J. Lindström, E. Ranta, T. Sipilä and F. Courchamp (1999). Backcasting population sizes of ringed and grey seals in the Baltic and Lake Saimaa during the 20th century. Annales Zoologici Fennici, JSTOR.Kovacs, K. M., J. Citta, T. Brown, R. Dietz, S. Ferguson, L. Harwood, M. Houde, E. V. Lea, L. Quakenbush and F. Riget (2021). ”Variation in body size of ringed seals (Pusa hispida hispida ) across the circumpolar Arctic: evidence of morphs, ecotypes or simply extreme plasticity?” Polar Research 40 .Kumar, S., M. Suleski, J. M. Craig, A. E. Kasprowicz, M. Sanderford, M. Li, G. Stecher and S. B. Hedges (2022). ”TimeTree 5: an expanded resource for species divergence times.” Molecular biology and evolution 39 (8): msac174.Kunnasranta, M., M. Niemi, M. Auttila, M. Valtonen, J. Kammonen and T. Nyman (2021). ”Sealed in a lake—Biology and conservation of the endangered Saimaa ringed seal: A review.” Biological Conservation 253 : 108908.Kvist, R. (1991). ”Sealing and sealing methods in the Bay of Bothnia 1551-70.” Polar Record 27 (163): 339-344.Lachenbruch, P. A. (1967). ”An almost unbiased method of obtaining confidence intervals for the probability of misclassification in discriminant analysis.” Biometrics: 639-645.Lang, J., T. Lauer and J. Winsemann (2018). ”New age constraints for the Saalian glaciation in northern central Europe: Implications for the extent of ice sheets and related proglacial lake systems.” Quaternary Science Reviews 180 : 240-259.Lebas, E., R. Gromig, S. Krastel, B. Wagner, G. Fedorov, C. Görtz, T. Averes, D. Subetto, M. Naumenko and M. Melles (2021). ”Pre-glacial and post-glacial history of the Scandinavian Ice Sheet in NW Russia–Evidence from Lake Ladoga.” Quaternary Science Reviews 251 : 106637.Leigh, J. W. and D. Bryant (2015). ”POPART: full-feature software for haplotype network construction.” Methods in Ecology and Evolution 6 (9): 1110-1116.Loseva, A., O. Chirkova and E. Akhatov (2022). ”Ladoga Ringed Seal (Pusa hispida ladogensis ) Can Breed on Land.” Arctic 75 (4): 480-490.Louis, M., M. Skovrind, J. A. Samaniego Castruita, C. Garilao, K. Kaschner, S. Gopalakrishnan, J. S. Haile, C. Lydersen, K. M. Kovacs and E. Garde (2020). ”Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros .” Proceedings of the Royal Society B 287 (1925): 20192964.Lydersen, C., J. Vaquie-Garcia, E. Lydersen, G. N. Christensen and K. M. Kovacs (2017). ”Novel terrestrial haul-out behaviour by ringed seals (Pusa hispida ) in Svalbard, in association with harbour seals (Phoca vitulina).” Polar Research 36 (1): 1374124.Löytynoja, A., P. Rastas, M. Valtonen, J. Kammonen, L. Holm, M. T. Olsen, L. Paulin, J. Jernvall and P. Auvinen (2023). ”Fragmented habitat compensates for the adverse effects of genetic bottleneck.” Current Biology 33 (6): 1009-1018. e1007.Madsen, M. L., R. J. Nelson, S.-E. Fevolden, J. S. Christiansen and K. Præbel (2016). ”Population genetic analysis of Euro-Arctic polar cod Boreogadus saida suggests fjord and oceanic structuring.” Polar Biology 39 (6): 969-980.Mangerud, J., M. Jakobsson, H. Alexanderson, V. Astakhov, G. K. Clarke, M. Henriksen, C. Hjort, G. Krinner, J.-P. Lunkka and P. Möller (2004). ”Ice-dammed lakes and rerouting of the drainage of northern Eurasia during the Last Glaciation.” Quaternary Science Reviews 23 (11-13): 1313-1332.Martinez-Bakker, M. E., S. K. Sell, B. J. Swanson, B. P. Kelly and D. A. Tallmon (2013). ”Combined genetic and telemetry data reveal high rates of gene flow, migration, and long-distance dispersal potential in Arctic ringed seals (Pusa hispida ).” PLoS One 8 (10): e77125.McLaren, I. (1993). ”Growth in pinnipeds.” Biological Reviews of the Cambridge Philosophical Society 68 (1): 1-79.McLaren, I. A. (1958). The biology of the ringed seal (Phoca hispida Schreber ) in the eastern Canadian Arctic, Fisheries Research Board of Canada Ottawa.Meier, H. M., M. Kniebusch, C. Dieterich, M. Gröger, E. Zorita, R. Elmgren, K. Myrberg, M. P. Ahola, A. Bartosova and E. Bonsdorff (2022). ”Climate change in the Baltic Sea region: a summary.” Earth System Dynamics 13 (1): 457-593.Melnikov, V. V. (2022). ”Observations of Ringed Seal (Phoca hispida) in the Nearshore Waters of the Chukotka Peninsula.” Arctic 75 (4): 431-448.Morin, P. A., K. K. Martien, A. R. Lang, B. L. Hancock-Hanser, V. L. Pease, K. M. Robertson, M. Sattler, E. Slikas, P. E. Rosel and C. S. Baker (2023). ”Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes.” Journal of Heredity 114 (6): 612-624.Nyman, T., M. Valtonen, J. Aspi, M. Ruokonen, M. Kunnasranta and J. U. Palo (2014). ”Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies.” Ecology and Evolution 4 (17): 3420-3434.Olsen, M. T., N. H. Nielsen, V. Biard, J. Teilmann, M. C. Ngô, G. Víkingsson, T. Gunnlaugsson, G. Stenson, J. Lawson and L. Lah (2022). ”Genetic and behavioural data confirm the existence of a distinct harbour porpoise ecotype in West Greenland.” Ecological Genetics and Genomics 22 : 100108.Palo, J. U., H. Hyvärinen, E. Helle, H. S. Mäkinen and R. Väinölä (2003). ”Postglacial loss of microsatellite variation in the landlocked Lake Saimaa ringed seal.” Conservation Genetics 4 (2): 117-128.Palo, J. U., H. S. Mäkinen, E. Helle, O. Stenman and R. Väinola (2001). ”Microsatellite variation in ringed seals (Phoca hispida ): genetic structure and history of the Baltic Sea population.” Heredity 86 (5): 609-617.Palo, J. U. and R. Väinölä (2006). ”The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences.” Biological Journal of the Linnean Society 88 (1): 61-72.Panin, A. V., V. I. Astakhov, E. Lotsari, G. Komatsu, J. Lang and J. Winsemann (2020). ”Middle and Late Quaternary glacial lake-outburst floods, drainage diversions and reorganization of fluvial systems in northwestern Eurasia.” Earth-Science Reviews 201 : 103069.Patton, H., A. Hubbard, K. Andreassen, A. Auriac, P. L. Whitehouse, A. P. Stroeven, C. Shackleton, M. Winsborrow, J. Heyman and A. M. Hall (2017). ”Deglaciation of the Eurasian ice sheet complex.” Quaternary Science Reviews 169 : 148-172.Rambaut, A. (2006-2018). FigTree: Tree Figure Drawing Tool, v.1.4.4.Rambaut, A., A. J. Drummond, D. Xie, G. Baele and M. A. Suchard (2018). ”Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.” Systematic Biology 67 (5): 901-904.Reusch, T. B., J. Dierking, H. C. Andersson, E. Bonsdorff, J. Carstensen, M. Casini, M. Czajkowski, B. Hasler, K. Hinsby and K. Hyytiäinen (2018). ”The Baltic Sea as a time machine for the future coastal ocean.” Science advances 4 (5): eaar8195.Roffe, T. J. and B. R. Mate (1984). ”Abundances and feeding habits of pinnipeds in the Rogue River, Oregon.” The Journal of Wildlife Management: 1262-1274.Rohlf, F. J. and D. Slice (1990). ”Extensions of the Procrustes Method for the Optimal Superimposition of Landmarks.” Systematic Biology 39 (1): 40-59.Rosing‐Asvid, A., A. Löytynoja, P. Momigliano, R. G. Hansen, C. H. Scharff‐Olsen, M. Valtonen, J. Kammonen, R. Dietz, F. F. Rigét and S. H. Ferguson (2023). ”An evolutionarily distinct ringed seal in the Ilulissat Icefjord.” Molecular Ecology.Rozas, J., A. Ferrer-Mata, J. C. Sánchez-DelBarrio, S. Guirao-Rico, P. Librado, S. E. Ramos-Onsins and A. Sánchez-Gracia (2017). ”DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.” Molecular Biology and Evolution 34 (12): 3299-3302.Ruiz-Puerta, E. J., X. Keighley, S. P. Desjardins, A. B. Gotfredsen, S. E. Pan, B. Star, S. Boessenkool, J. H. Barrett, M. L. McCarthy and L. W. Andersen (2023). ”Holocene deglaciation drove rapid genetic diversification of Atlantic walrus.” Proceedings of the Royal Society B 290 (2007): 20231349.Sasaki, H., K. Numachi and M. A. Grachev (2003). ”The origin and genetic relationships of the Baikal seal, Phoca sibirica, by restriction analysis of mitochondrial DNA.” Zoological Science 20 (11): 1417-1422.Savriama, Y., M. Valtonen, J. I. Kammonen, P. Rastas, O.-P. Smolander, A. Lyyski, T. J. Häkkinen, I. J. Corfe, S. Gerber, I. Salazar-Ciudad, L. Paulin, L. Holm, A. Löytynoja, P. Auvinen and J. Jernvall (2018). ”Bracketing phenogenotypic limits of mammalian hybridization.” Royal Society Open Science 5 (11): 180903.Scharff-Olsen, C. H., A. Galatius, J. Teilmann, R. Dietz, S. M. Andersen, S. Jarnit, A.-M. Kroner, A. B. Botnen, K. Lundström, P. R. Møller, M. T. Olsen and N. Handling editor: Simon (2018). ”Diet of seals in the Baltic Sea region: a synthesis of published and new data from 1968 to 2013.” ICES Journal of Marine Science: fsy159-fsy159.Schreber, J. C. D. (1775). Die Säugetiere in Abbildungen nach der Natur mit Beschreibungen.Sejrup, H., A. Nygård, A. Hall and H. Haflidason (2009). ”Middle and Late Weichselian (Devensian) glaciation history of south-western Norway, North Sea and eastern UK.” Quaternary Science Reviews 28 (3-4): 370-380.Siegstad, H., P. B. Neve, M. P. Heide-Jorgensen and T. Harkonen (1998). ”Diet of the ringed seal (Phoca hispida ) in Greenland.” NAMMCO Scientific Publications 1 : 229-241.Sipilä, T. and H. Hyvärinen (1998). ”Status and biology of Saimaa (Phoca hispida saimensis ) and Ladoga (Phoca hispida ladogensis ) ringed seals.” NAMMCO Scientific Publications 1 : 83-99.Skovrind, M., M. Louis, M. V. Westbury, C. Garilao, K. Kaschner, J. A. S. Castruita, S. Gopalakrishnan, S. W. Knudsen, J. S. Haile and L. Dalén (2021). ”Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations.” Molecular Ecology 30 (11): 2543-2559.Smith, R. J., D. M. Lavigne and W. R. Leonard (1994). ”Subspecific status of the freshwater harbor seal (Phoca vitulina mellonae): A re‐assessment.” Marine mammal science 10 (1): 105-110.Smith, T. G. and C. Lydersen (1991). ”Availability of suitable land-fast ice and predation as factors limiting ringed seal populations, Phoca hispida, in Svalbard.” Polar Research 10 (2): 585-594.Sommer, R. and N. Benecke (2003). ”Post-glacial history of the European seal fauna on the basis of sub-fossil records.” Beitraege zur Archaeozoologie und Praehistorischen Anthropologie 4 : 16-28.Sonne, C., J. Lakemeyer, J.-P. Desforges, I. Eulaers, S. Persson, I. Stokholm, A. Galatius, S. Gross, K. Gonnsen and K. Lehnert (2020). ”A review of pathogens in selected Baltic Sea indicator species.” Environment international 137 : 105565.Sonne, C., U. Siebert, K. Gonnsen, J.-P. Desforges, I. Eulaers, S. Persson, A. Roos, B.-M. Bäcklin, K. Kauhala and M. T. Olsen (2020). ”Health effects from contaminant exposure in Baltic Sea birds and marine mammals: A review.” Environment international 139 : 105725.Sromek, L., K. P. Johnson, M. Kunnasranta, E. Ylinen, S. Virrueta Herrera, E. Andrievskaya, V. Alexeev, O. Rusinek, A. Rosing‐Asvid and T. Nyman (2024). ”Population genomics of seal lice provides insights into the postglacial history of northern European seals.” Molecular ecology: e17523.Sundell, T., J. I. Kammonen, E. Mustanoja, V. Biard, M. Kunnasranta, M. Niemi, M. Nykänen, T. Nyman, J. U. Palo and M. Valtonen (2023). ”Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population.” Conservation Genetics 24 (2): 155-165.Svendsen, J. I., H. Alexanderson, V. I. Astakhov, I. Demidov, J. A. Dowdeswell, S. Funder, V. Gataullin, M. Henriksen, C. Hjort, M. Houmark-Nielsen, H. W. Hubberten, Ó. Ingólfsson, M. Jakobsson, K. H. Kjær, E. Larsen, H. Lokrantz, J. P. Lunkka, A. Lyså, J. Mangerud, A. Matiouchkov, A. Murray, P. Möller, F. Niessen, O. Nikolskaya, L. Polyak, M. Saarnisto, C. Siegert, M. J. Siegert, R. F. Spielhagen and R. Stein (2004). ”Late Quaternary ice sheet history of northern Eurasia.” Quaternary Science Reviews 23 (11): 1229-1271.Svetochev, V. N., N. N. Kavtsevich and O. N. Svetocheva (2022). ”Seasonal distribution of ringed seal in the White Sea monitored by satellite tagging.” Czech Polar Reports 12 (2): 160–171-160–171.Taylor, B. L., F. I. Archer, K. K. Martien, P. E. Rosel, B. L. Hancock-Hanser, A. R. Lang, M. S. Leslie, S. L. Mesnick, P. A. Morin, V. L. Pease, W. F. Perrin, K. M. Robertson, K. M. Parsons, A. Viricel, N. L. Vollmer, F. Cipriano, R. R. Reeves, M. Krützen and C. S. Baker (2017). ”Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data.” Marine Mammal Science 33 (S1): 132-155.Tempestini, A., A. I. Pinchuk and F. Dufresne (2020). ”Spatial genetic structure in Themisto libellula (Amphipoda: Hyperiidae) from the coastal Gulf of Alaska, Bering and Chukchi seas.” Polar Biology 43 (11): 1795-1804.Toucanne, S., T. Rodrigues, G. Menot, G. Soulet, S. Cheron, I. Billy, F. Eynaud, P. Antoine, J. S. S. Damste and E. Bard (2023). ”Marine Isotope Stage 4 (71–57 ka) on the Western European margin: Insights to the drainage and dynamics of the Western European Ice Sheet.” Global and Planetary Change 229 : 104221.Toucanne, S., S. Zaragosi, J.-F. Bourillet, P. Gibbard, F. Eynaud, J. Giraudeau, J. Turon, M. Cremer, E. Cortijo and P. Martinez (2009). ”A 1.2 Ma record of glaciation and fluvial discharge from the West European Atlantic margin.” Quaternary Science Reviews 28 (25-26): 2974-2981.Trukhanova, I. S., E. M. Andrievskaya and V. A. Alekseev (2021). ”Bycatch in Lake Ladoga Fisheries Remains a Threat to Ladoga Ringed Seal (Pusa hispida ladogensis ) Population.” Aquatic Mammals 47 (5).Trukhanova, I. S., P. M. Bakunovich and M. V. Sokolovskaya (2024). ”Haul-out site use by Ladoga ringed seal (Pusa hispida ladogensis ) on the islands of the Valaam Archipelago.” Limnology 25 (1): 25-36.Trukhanova, I. S., E. Gurarie and R. A. Sagitov (2013). ”Distribution of hauled-out Ladoga ringed seals (Pusa hispida ladogensis ) in spring 2012.” Arctic: 417-428.Ukkonen, P., K. Aaris-Sørensen, L. Arppe, L. Daugnora, A. Halkka, L. Lõugas, M. J. Oinonen, M. Pilot and J. Storå (2014). ”An Arctic seal in temperate waters: History of the ringed seal (Pusa hispida ) in the Baltic Sea and its adaptation to the changing environment.” The Holocene.Valtonen, M., J. Palo, M. Ruokonen, M. Kunnasranta and T. Nyman (2012). ”Spatial and temporal variation in genetic diversity of an endangered freshwater seal.” Conservation Genetics 13 (5): 1231-1245.Vassiljev, J., L. Saarse and A. Rosentau (2011). ”Palaeoreconstruction of the Baltic Ice Lake in the Eastern Baltic.” The Baltic Sea Basin: 189-202. 1 Amano, M., A. Hayano and N. Miyazaki (2002). ”Geographic Variation in the Skull of the Ringed Seal, Pusa Hispida .” Journal of Mammalogy 83 (2): 370-380.Andren, T., S. Bjorck, E. Andren, D. Conley, L. Zillen and J. Anjar (2011). The Development of the Baltic Sea Basin During the Last 130 ka. Baltic Sea Basin. J. Harff, S. Bjorck and P. Hoth: 75-+.Arnason, U., A. Gullberg, A. Janke, M. Kullberg, N. Lehman, E. A. Petrov and R. Väinölä (2006). ”Pinniped phylogeny and a new hypothesis for their origin and dispersal.” Molecular Phylogenetics and Evolution 41 (2): 345-354.Auttila, M., M. Kurkilahti, M. Niemi, R. Levänen, T. Sipilä, M. Isomursu, J. Koskela and M. Kunnasranta (2016). ”Morphometrics, body condition, and growth of the ringed seal (Pusa hispida saimensis ) in Lake Saimaa: Implications for conservation.” Marine mammal science 32 (1): 252-267.Auttila, M., T. Sinisalo, M. Valtonen, M. Niemi, M. Viljanen, M. Kurkilahti and M. Kunnasranta (2015). ”Diet composition and seasonal feeding patterns of a freshwater ringed seal (Pusa hispida saimensis ).” Marine Mammal Science 31 (1): 45-65.Bandelt, H.-J., P. Forster and A. Röhl (1999). ”Median-joining networks for inferring intraspecific phylogenies.” Molecular Biology and Evolution 16 (1): 37-48.Bergman, A. and M. Olsson (1986). ”Pathology of Baltic grey seal and ringed seal females with special reference to adrenocortical hyperplasia: is environmental pollution the cause of a widely distributed disease syndrome?” Riistatieteellisia Julkaisuja 44 : 47-62.Bouckaert, R., T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kühnert, N. De Maio, M. Matschiner, F. K. Mendes, N. F. Müller, H. A. Ogilvie, L. du Plessis, A. Popinga, A. Rambaut, D. Rasmussen, I. Siveroni, M. A. Suchard, C.-H. Wu, D. Xie, C. Zhang, T. Stadler and A. J. Drummond (2019). ”BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.” PLOS Computational Biology 15 (4): e1006650.Carr, S. M., A. T. Duggan, G. B. Stenson and H. D. Marshall (2015). ”Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus ).” PLOS ONE 10 (8): e0134207.Carøe, C., S. Gopalakrishnan, L. Vinner, S. S. T. Mak, M. H. S. Sinding, J. A. Samaniego, N. Wales, T. Sicheritz-Pontén and M. T. P. Gilbert (2018). ”Single-tube library preparation for degraded DNA.” Methods in Ecology and Evolution 9 (2): 410-419.Davies, J. L. (1958). ”Pleistocene geography and the distribution of northern pinnipeds.” Ecology 39 (1): 97-113.Davis, C. S., I. Stirling, C. Strobeck and D. W. Coltman (2008). ”Population structure of ice-breeding seals.” Molecular Ecology 17 (13): 3078-3094.Durner, G. M., D. C. Douglas, S. E. Albeke, J. P. Whiteman, S. C. Amstrup, E. Richardson, R. R. Wilson and M. Ben-David (2017). ”Increased Arctic sea ice drift alters adult female polar bear movements and energetics.” Glob Chang Biol 23 (9): 3460-3473.Ferguson, S. H., D. J. Yurkowski, B. G. Young, A. T. Fisk, D. C. Muir, X. Zhu and G. W. Thiemann (2020). ”Comparing temporal patterns in body condition of ringed seals living within their core geographic range with those living at the edge.” Ecography 43 (10): 1521-1535.Ferguson, S. H., D. J. Yurkowski, B. G. Young, C. Willing, X. Zhu, D. C. Muir, A. T. Fisk and G. W. Thiemann (2019). ”Do intraspecific life history patterns follow interspecific predictions? A test using latitudinal variation in ringed seals.” Population Ecology 61 (4): 371-382.Ferguson, S. H., X. Zhu, B. G. Young, D. J. Yurkowski, G. W. Thiemann, A. T. Fisk and D. C. Muir (2018). ”Geographic variation in ringed seal (Pusa hispida ) growth rate and body size.” Canadian journal of zoology 96 (7): 649-659.Ferrer, T., P. Boveng, D. D. Hauser, D. Withrow, V. Burkanov, T. P. Quinn and G. O’Corry-Crowe (2024). ”Genetic and evolutionary divergence of harbour seals (Phoca vitulina) in Iliamna Lake, Alaska.” Biology Letters 20 (10): 20240166.Finley, K. J., G. W. Miller, R. A. Davis and W. R. Koski (1983). ”A distinctive large breeding population of ringed seals (Phoca hispida ) inhabiting the Baffin Bay pack ice.” Arctic 36 (2): 162-173.Fulton, T. L. and C. Strobeck (2010). ”Multiple fossil calibrations, nuclear loci and mitochondrial genomes provide new insight into biogeography and divergence timing for true seals (Phocidae, Pinnipedia).” Journal of Biogeography 37 (5): 814-829.Funder, S., I. Demidov and Y. Yelovicheva (2002). ”Hydrography and mollusc faunas of the Baltic and the White Sea–North Sea seaway in the Eemian.” Palaeogeography, Palaeoclimatology, Palaeoecology 184 (3-4): 275-304.Galatius, A., M. S. Svendsen, D. Messer, M. Valtonen, M. McGowen, R. Sabin, V. A. Dahl, A. B. Dahl and M. T. Olsen (2022). ”Range-wide variation in Grey Seal (Halichoerus grypus) skull morphology.” Zoology 153 : 126023.Gorlach, A., T. Hang and V. Kalm (2017). ”GIS‐based reconstruction of Late Weichselian proglacial lakes in northwestern Russia and Belarus.” Boreas 46 (3): 486-502.Gryba, R., H. P. Huntington, A. Von Duyke, B. Adams, B. Frantz, J. Gatten, Q. Harcharek, H. Olemaun, R. Sarren and J. Skin (2021). ”Indigenous Knowledge of bearded seal (Erignathus barbatus), ringed seal (Pusa hispida), and spotted seal (Phoca largha) behaviour and habitat use near Utqiaġvik, Alaska, USA.” Arctic Science 7 (4): 832-858.Guindon, S., J.-F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk and O. Gascuel (2010). ”New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.” Systematic biology 59 (3): 307-321.Hamilton, C. D., K. M. Kovacs, R. A. Ims, J. Aars and C. Lydersen (2017). ”An Arctic predator-prey system in flux: climate change impacts on coastal space use by polar bears and ringed seals.” J Anim Ecol 86 (5): 1054-1064.Hammill, M. O. (2009). Ringed Seal: Pusa hispida. Encyclopedia of Marine Mammals (Second Edition). W. F. Perrin, B. Würsig and J. G. M. Thewissen. London, Academic Press: 972-974.Harding, K. C. and T. J. Härkönen (1999). ”Development in the Baltic grey seal (Halichoerus grypus ) and ringed seal (Phoca hispida ) populations during the 20th century.” Ambio 28 (7): 619-627.Heino, M. T., T. Nyman, J. U. Palo, J. Harmoinen, M. Valtonen, M. Pilot, S. Översti, E. Salmela, M. Kunnasranta and R. Väinölä (2023). ”Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections.” Ecology and Evolution 13 (1): e9720.HELCOM (2023). ”Population trends and abundance of seals. HELCOM core indicator report. Online. .”.Helle, E. (1979). ”Growth and size of the ringed seal Phoca (Pusa) hispida Schreber in the Bothnian Bay, Baltic.”Helmens, K. F. and S. Engels (2010). ”Ice‐free conditions in eastern Fennoscandia during early Marine Isotope Stage 3: lacustrine records.” Boreas 39 (2): 399-409.Hewitt, G. (2000). ”The genetic legacy of the Quaternary ice ages.” Nature 405 (6789): 907-913.Holst, M., I. Stirling and K. A. Hobson (2001). ”Diet of ringed seals (Phoca hispida ) on the east and west sides of the North Water Polynya, northern Baffin Bay.” Marine Mammal Science 17 (4): 888-908.Hudson, R. R., D. D. Boos and N. L. Kaplan (1992). ”A statistical test for detecting geographic subdivision.” Molecular Biology and Evolution 9 (1): 138-151.Hughes, A. L. C., R. Gyllencreutz, O. S. Lohne, J. Mangerud and J. I. Svendsen (2016). ”The last Eurasian ice sheets - a chronological database and time-slice reconstruction, DATED-1.” Boreas 45 (1): 1-+.Jacobsen, M. W., N. W. Jensen, R. Nygaard, K. Præbel, B. Jónsson, N. H. Nielsen, J. M. Pujolar, D. J. Fraser, L. Bernatchez and M. M. Hansen (2022). ”A melting pot in the Arctic: Analysis of mitogenome variation in Arctic char (Salvelinus alpinus ) reveals a 1000‐km contact zone between highly divergent lineages.” Ecology of Freshwater Fish 31 (2): 330-346.Kauhala, K., M. Bergenius, M. Isomursu and J. Raitaniemi (2019). ”Reproductive rate and nutritional status of Baltic ringed seals.” Mammal research 64 : 109-120.Kienle, S. S. and A. Berta (2016). ”The better to eat you with: the comparative feeding morphology of phocid seals (Pinnipedia, Phocidae).” Journal of Anatomy 228 (3): 396-413.Kleman, J., M. Hättestrand, I. Borgström, D. Fabel and F. Preusser (2021). ”Age and duration of a MIS 3 interstadial in the Fennoscandian Ice Sheet core area–Implications for ice sheet dynamics.” Quaternary Science Reviews 264 : 107011.Klingenberg, C. P. (2011). ”MorphoJ: an integrated software package for geometric morphometrics.” Molecular ecology resources 11 (2): 353-357.Klingenberg, C. P., M. Barluenga and A. Meyer (2002). ”Shape analysis of symmetric structures: quantifying variation among individuals and asymmetry.” Evolution 56 (10): 1909-1920.Kokko, H., E. Helle, J. Lindström, E. Ranta, T. Sipilä and F. Courchamp (1999). Backcasting population sizes of ringed and grey seals in the Baltic and Lake Saimaa during the 20th century. Annales Zoologici Fennici, JSTOR.Kovacs, K. M., J. Citta, T. Brown, R. Dietz, S. Ferguson, L. Harwood, M. Houde, E. V. Lea, L. Quakenbush and F. Riget (2021). ”Variation in body size of ringed seals (Pusa hispida hispida ) across the circumpolar Arctic: evidence of morphs, ecotypes or simply extreme plasticity?” Polar Research 40 .Kumar, S., M. Suleski, J. M. Craig, A. E. Kasprowicz, M. Sanderford, M. Li, G. Stecher and S. B. Hedges (2022). ”TimeTree 5: an expanded resource for species divergence times.” Molecular biology and evolution 39 (8): msac174.Kunnasranta, M., M. Niemi, M. Auttila, M. Valtonen, J. Kammonen and T. Nyman (2021). ”Sealed in a lake—Biology and conservation of the endangered Saimaa ringed seal: A review.” Biological Conservation 253 : 108908.Kvist, R. (1991). ”Sealing and sealing methods in the Bay of Bothnia 1551-70.” Polar Record 27 (163): 339-344.Lachenbruch, P. A. (1967). ”An almost unbiased method of obtaining confidence intervals for the probability of misclassification in discriminant analysis.” Biometrics: 639-645.Lang, J., T. Lauer and J. Winsemann (2018). ”New age constraints for the Saalian glaciation in northern central Europe: Implications for the extent of ice sheets and related proglacial lake systems.” Quaternary Science Reviews 180 : 240-259.Lebas, E., R. Gromig, S. Krastel, B. Wagner, G. Fedorov, C. Görtz, T. Averes, D. Subetto, M. Naumenko and M. Melles (2021). ”Pre-glacial and post-glacial history of the Scandinavian Ice Sheet in NW Russia–Evidence from Lake Ladoga.” Quaternary Science Reviews 251 : 106637.Leigh, J. W. and D. Bryant (2015). ”POPART: full-feature software for haplotype network construction.” Methods in Ecology and Evolution 6 (9): 1110-1116.Loseva, A., O. Chirkova and E. Akhatov (2022). ”Ladoga Ringed Seal (Pusa hispida ladogensis ) Can Breed on Land.” Arctic 75 (4): 480-490.Louis, M., M. Skovrind, J. A. Samaniego Castruita, C. Garilao, K. Kaschner, S. Gopalakrishnan, J. S. Haile, C. Lydersen, K. M. Kovacs and E. Garde (2020). ”Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros .” Proceedings of the Royal Society B 287 (1925): 20192964.Lydersen, C., J. Vaquie-Garcia, E. Lydersen, G. N. Christensen and K. M. Kovacs (2017). ”Novel terrestrial haul-out behaviour by ringed seals (Pusa hispida ) in Svalbard, in association with harbour seals (Phoca vitulina).” Polar Research 36 (1): 1374124.Löytynoja, A., P. Rastas, M. Valtonen, J. Kammonen, L. Holm, M. T. Olsen, L. Paulin, J. Jernvall and P. Auvinen (2023). ”Fragmented habitat compensates for the adverse effects of genetic bottleneck.” Current Biology 33 (6): 1009-1018. e1007.Madsen, M. L., R. J. Nelson, S.-E. Fevolden, J. S. Christiansen and K. Præbel (2016). ”Population genetic analysis of Euro-Arctic polar cod Boreogadus saida suggests fjord and oceanic structuring.” Polar Biology 39 (6): 969-980.Mangerud, J., M. Jakobsson, H. Alexanderson, V. Astakhov, G. K. Clarke, M. Henriksen, C. Hjort, G. Krinner, J.-P. Lunkka and P. Möller (2004). ”Ice-dammed lakes and rerouting of the drainage of northern Eurasia during the Last Glaciation.” Quaternary Science Reviews 23 (11-13): 1313-1332.Martinez-Bakker, M. E., S. K. Sell, B. J. Swanson, B. P. Kelly and D. A. Tallmon (2013). ”Combined genetic and telemetry data reveal high rates of gene flow, migration, and long-distance dispersal potential in Arctic ringed seals (Pusa hispida ).” PLoS One 8 (10): e77125.McLaren, I. (1993). ”Growth in pinnipeds.” Biological Reviews of the Cambridge Philosophical Society 68 (1): 1-79.McLaren, I. A. (1958). The biology of the ringed seal (Phoca hispida Schreber ) in the eastern Canadian Arctic, Fisheries Research Board of Canada Ottawa.Meier, H. M., M. Kniebusch, C. Dieterich, M. Gröger, E. Zorita, R. Elmgren, K. Myrberg, M. P. Ahola, A. Bartosova and E. Bonsdorff (2022). ”Climate change in the Baltic Sea region: a summary.” Earth System Dynamics 13 (1): 457-593.Melnikov, V. V. (2022). ”Observations of Ringed Seal (Phoca hispida) in the Nearshore Waters of the Chukotka Peninsula.” Arctic 75 (4): 431-448.Morin, P. A., K. K. Martien, A. R. Lang, B. L. Hancock-Hanser, V. L. Pease, K. M. Robertson, M. Sattler, E. Slikas, P. E. Rosel and C. S. Baker (2023). ”Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes.” Journal of Heredity 114 (6): 612-624.Nyman, T., M. Valtonen, J. Aspi, M. Ruokonen, M. Kunnasranta and J. U. Palo (2014). ”Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies.” Ecology and Evolution 4 (17): 3420-3434.Olsen, M. T., N. H. Nielsen, V. Biard, J. Teilmann, M. C. Ngô, G. Víkingsson, T. Gunnlaugsson, G. Stenson, J. Lawson and L. Lah (2022). ”Genetic and behavioural data confirm the existence of a distinct harbour porpoise ecotype in West Greenland.” Ecological Genetics and Genomics 22 : 100108.Palo, J. U., H. Hyvärinen, E. Helle, H. S. Mäkinen and R. Väinölä (2003). ”Postglacial loss of microsatellite variation in the landlocked Lake Saimaa ringed seal.” Conservation Genetics 4 (2): 117-128.Palo, J. U., H. S. Mäkinen, E. Helle, O. Stenman and R. Väinola (2001). ”Microsatellite variation in ringed seals (Phoca hispida ): genetic structure and history of the Baltic Sea population.” Heredity 86 (5): 609-617.Palo, J. U. and R. Väinölä (2006). ”The enigma of the landlocked Baikal and Caspian seals addressed through phylogeny of phocine mitochondrial sequences.” Biological Journal of the Linnean Society 88 (1): 61-72.Panin, A. V., V. I. Astakhov, E. Lotsari, G. Komatsu, J. Lang and J. Winsemann (2020). ”Middle and Late Quaternary glacial lake-outburst floods, drainage diversions and reorganization of fluvial systems in northwestern Eurasia.” Earth-Science Reviews 201 : 103069.Patton, H., A. Hubbard, K. Andreassen, A. Auriac, P. L. Whitehouse, A. P. Stroeven, C. Shackleton, M. Winsborrow, J. Heyman and A. M. Hall (2017). ”Deglaciation of the Eurasian ice sheet complex.” Quaternary Science Reviews 169 : 148-172.Rambaut, A. (2006-2018). FigTree: Tree Figure Drawing Tool, v.1.4.4.Rambaut, A., A. J. Drummond, D. Xie, G. Baele and M. A. Suchard (2018). ”Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.” Systematic Biology 67 (5): 901-904.Reusch, T. B., J. Dierking, H. C. Andersson, E. Bonsdorff, J. Carstensen, M. Casini, M. Czajkowski, B. Hasler, K. Hinsby and K. Hyytiäinen (2018). ”The Baltic Sea as a time machine for the future coastal ocean.” Science advances 4 (5): eaar8195.Roffe, T. J. and B. R. Mate (1984). ”Abundances and feeding habits of pinnipeds in the Rogue River, Oregon.” The Journal of Wildlife Management: 1262-1274.Rohlf, F. J. and D. Slice (1990). ”Extensions of the Procrustes Method for the Optimal Superimposition of Landmarks.” Systematic Biology 39 (1): 40-59.Rosing‐Asvid, A., A. Löytynoja, P. Momigliano, R. G. Hansen, C. H. Scharff‐Olsen, M. Valtonen, J. Kammonen, R. Dietz, F. F. Rigét and S. H. Ferguson (2023). ”An evolutionarily distinct ringed seal in the Ilulissat Icefjord.” Molecular Ecology.Rozas, J., A. Ferrer-Mata, J. C. Sánchez-DelBarrio, S. Guirao-Rico, P. Librado, S. E. Ramos-Onsins and A. Sánchez-Gracia (2017). ”DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.” Molecular Biology and Evolution 34 (12): 3299-3302.Ruiz-Puerta, E. J., X. Keighley, S. P. Desjardins, A. B. Gotfredsen, S. E. Pan, B. Star, S. Boessenkool, J. H. Barrett, M. L. McCarthy and L. W. Andersen (2023). ”Holocene deglaciation drove rapid genetic diversification of Atlantic walrus.” Proceedings of the Royal Society B 290 (2007): 20231349.Sasaki, H., K. Numachi and M. A. Grachev (2003). ”The origin and genetic relationships of the Baikal seal, Phoca sibirica, by restriction analysis of mitochondrial DNA.” Zoological Science 20 (11): 1417-1422.Savriama, Y., M. Valtonen, J. I. Kammonen, P. Rastas, O.-P. Smolander, A. Lyyski, T. J. Häkkinen, I. J. Corfe, S. Gerber, I. Salazar-Ciudad, L. Paulin, L. Holm, A. Löytynoja, P. Auvinen and J. Jernvall (2018). ”Bracketing phenogenotypic limits of mammalian hybridization.” Royal Society Open Science 5 (11): 180903.Scharff-Olsen, C. H., A. Galatius, J. Teilmann, R. Dietz, S. M. Andersen, S. Jarnit, A.-M. Kroner, A. B. Botnen, K. Lundström, P. R. Møller, M. T. Olsen and N. Handling editor: Simon (2018). ”Diet of seals in the Baltic Sea region: a synthesis of published and new data from 1968 to 2013.” ICES Journal of Marine Science: fsy159-fsy159.Schreber, J. C. D. (1775). Die Säugetiere in Abbildungen nach der Natur mit Beschreibungen.Sejrup, H., A. Nygård, A. Hall and H. Haflidason (2009). ”Middle and Late Weichselian (Devensian) glaciation history of south-western Norway, North Sea and eastern UK.” Quaternary Science Reviews 28 (3-4): 370-380.Siegstad, H., P. B. Neve, M. P. Heide-Jorgensen and T. Harkonen (1998). ”Diet of the ringed seal (Phoca hispida ) in Greenland.” NAMMCO Scientific Publications 1 : 229-241.Sipilä, T. and H. Hyvärinen (1998). ”Status and biology of Saimaa (Phoca hispida saimensis ) and Ladoga (Phoca hispida ladogensis ) ringed seals.” NAMMCO Scientific Publications 1 : 83-99.Skovrind, M., M. Louis, M. V. Westbury, C. Garilao, K. Kaschner, J. A. S. Castruita, S. Gopalakrishnan, S. W. Knudsen, J. S. Haile and L. Dalén (2021). ”Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations.” Molecular Ecology 30 (11): 2543-2559.Smith, R. J., D. M. Lavigne and W. R. Leonard (1994). ”Subspecific status of the freshwater harbor seal (Phoca vitulina mellonae): A re‐assessment.” Marine mammal science 10 (1): 105-110.Smith, T. G. and C. Lydersen (1991). ”Availability of suitable land-fast ice and predation as factors limiting ringed seal populations, Phoca hispida, in Svalbard.” Polar Research 10 (2): 585-594.Sommer, R. and N. Benecke (2003). ”Post-glacial history of the European seal fauna on the basis of sub-fossil records.” Beitraege zur Archaeozoologie und Praehistorischen Anthropologie 4 : 16-28.Sonne, C., J. Lakemeyer, J.-P. Desforges, I. Eulaers, S. Persson, I. Stokholm, A. Galatius, S. Gross, K. Gonnsen and K. Lehnert (2020). ”A review of pathogens in selected Baltic Sea indicator species.” Environment international 137 : 105565.Sonne, C., U. Siebert, K. Gonnsen, J.-P. Desforges, I. Eulaers, S. Persson, A. Roos, B.-M. Bäcklin, K. Kauhala and M. T. Olsen (2020). ”Health effects from contaminant exposure in Baltic Sea birds and marine mammals: A review.” Environment international 139 : 105725.Sromek, L., K. P. Johnson, M. Kunnasranta, E. Ylinen, S. Virrueta Herrera, E. Andrievskaya, V. Alexeev, O. Rusinek, A. Rosing‐Asvid and T. Nyman (2024). ”Population genomics of seal lice provides insights into the postglacial history of northern European seals.” Molecular ecology: e17523.Sundell, T., J. I. Kammonen, E. Mustanoja, V. Biard, M. Kunnasranta, M. Niemi, M. Nykänen, T. Nyman, J. U. Palo and M. Valtonen (2023). ”Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population.” Conservation Genetics 24 (2): 155-165.Svendsen, J. I., H. Alexanderson, V. I. Astakhov, I. Demidov, J. A. Dowdeswell, S. Funder, V. Gataullin, M. Henriksen, C. Hjort, M. Houmark-Nielsen, H. W. Hubberten, Ó. Ingólfsson, M. Jakobsson, K. H. Kjær, E. Larsen, H. Lokrantz, J. P. Lunkka, A. Lyså, J. Mangerud, A. Matiouchkov, A. Murray, P. Möller, F. Niessen, O. Nikolskaya, L. Polyak, M. Saarnisto, C. Siegert, M. J. Siegert, R. F. Spielhagen and R. Stein (2004). ”Late Quaternary ice sheet history of northern Eurasia.” Quaternary Science Reviews 23 (11): 1229-1271.Svetochev, V. N., N. N. Kavtsevich and O. N. Svetocheva (2022). ”Seasonal distribution of ringed seal in the White Sea monitored by satellite tagging.” Czech Polar Reports 12 (2): 160–171-160–171.Taylor, B. L., F. I. Archer, K. K. Martien, P. E. Rosel, B. L. Hancock-Hanser, A. R. Lang, M. S. Leslie, S. L. Mesnick, P. A. Morin, V. L. Pease, W. F. Perrin, K. M. Robertson, K. M. Parsons, A. Viricel, N. L. Vollmer, F. Cipriano, R. R. Reeves, M. Krützen and C. S. Baker (2017). ”Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data.” Marine Mammal Science 33 (S1): 132-155.Tempestini, A., A. I. Pinchuk and F. Dufresne (2020). ”Spatial genetic structure in Themisto libellula (Amphipoda: Hyperiidae) from the coastal Gulf of Alaska, Bering and Chukchi seas.” Polar Biology 43 (11): 1795-1804.Toucanne, S., T. Rodrigues, G. Menot, G. Soulet, S. Cheron, I. Billy, F. Eynaud, P. Antoine, J. S. S. Damste and E. Bard (2023). ”Marine Isotope Stage 4 (71–57 ka) on the Western European margin: Insights to the drainage and dynamics of the Western European Ice Sheet.” Global and Planetary Change 229 : 104221.Toucanne, S., S. Zaragosi, J.-F. Bourillet, P. Gibbard, F. Eynaud, J. Giraudeau, J. Turon, M. Cremer, E. Cortijo and P. Martinez (2009). ”A 1.2 Ma record of glaciation and fluvial discharge from the West European Atlantic margin.” Quaternary Science Reviews 28 (25-26): 2974-2981.Trukhanova, I. S., E. M. Andrievskaya and V. A. Alekseev (2021). ”Bycatch in Lake Ladoga Fisheries Remains a Threat to Ladoga Ringed Seal (Pusa hispida ladogensis ) Population.” Aquatic Mammals 47 (5).Trukhanova, I. S., P. M. Bakunovich and M. V. Sokolovskaya (2024). ”Haul-out site use by Ladoga ringed seal (Pusa hispida ladogensis ) on the islands of the Valaam Archipelago.” Limnology 25 (1): 25-36.Trukhanova, I. S., E. Gurarie and R. A. Sagitov (2013). ”Distribution of hauled-out Ladoga ringed seals (Pusa hispida ladogensis ) in spring 2012.” Arctic: 417-428.Ukkonen, P., K. Aaris-Sørensen, L. Arppe, L. Daugnora, A. Halkka, L. Lõugas, M. J. Oinonen, M. Pilot and J. Storå (2014). ”An Arctic seal in temperate waters: History of the ringed seal (Pusa hispida ) in the Baltic Sea and its adaptation to the changing environment.” The Holocene.Valtonen, M., J. Palo, M. Ruokonen, M. Kunnasranta and T. Nyman (2012). ”Spatial and temporal variation in genetic diversity of an endangered freshwater seal.” Conservation Genetics 13 (5): 1231-1245.Vassiljev, J., L. Saarse and A. Rosentau (2011). ”Palaeoreconstruction of the Baltic Ice Lake in the Eastern Baltic.” The Baltic Sea Basin: 189-202. FIGURES AND TABLES Figure 1 Fennoscandian and Arctic ringed seal sampling localities. The study included 246 mitogenomes from 11 localities (circles) and 180 skulls from five regions (asterisk), representing most of the species’ range in Canada, Greenland, Svalbard and northern Europe. Sample sizes for each locality are listed for mitogenomes and skulls, when applicable. The skulls representing the “High Arctic” are listed under Qaanaaq, but originate from multiple distinct localities in the region of northwest Greenland and the Canadian High Arctic. Ringed seal illustration courtesy of NOAA Fisheries. Figure 2 Ringed seal mitogenome median-joining haplotype network illustrating the eight major lineages (A-H) found in the Atlantic Arctic, Baltic Sea, Lake Ladoga and Lake Saimaa. Colour and size of circles reflect sampling locality and relative abundance of each haplotype, respectively. Black bars on the branches denote segregating sites and inferred haplotypes not present in the data are represented by black circles. Note that Lake Saimaa has been down-sampled from 112 animals to only include the 7 unique haplotypes detected in this subspecies. Figure 3 Bayesian phylogenetic tree based on 141 ringed seal mitogenomes, inferred under a strict clock model, and the root rescaled to 1000 kya. The analyses indicate the existence of eight evolutionary lineages (A-H). Most lineages have shallow internal branch lengths, except C and F. Vertical grey bars outline marine isotope stages (MIS) characterised by relatively warm climatic periods. Sample IDs, branch support values and 95%HPD intervals on branch divergence time estimates are provided in Supplementary Figure S3. Figure 4 Morphospace representation of ringed seal cranial shapes using the first eight Residual Shape Components (RSCs), representing 58.7% of the residual variation after correcting for allometry. Symbol and convex hull polygon colour codes: Red=Baltic; orange=Saimaa; yellow=Ladoga; blue=East Greenland; and green=High Arctic. Figure 5 Size and shape variation in ringed seal skulls measured in terms of A) centroid sizes and B) Procrustes distances of specimens to the mean of the relevant sample. The bold horizontal line shows the median and the bottom and top of the box show the 25th and 75th percentiles, respectively. The vertical dashed lines (whiskers) show one of two things; either the maximum value or 1.5 times the interquartile range (roughly 2 standard deviations) of the data, whichever is the smaller. Points are outliers, defined as more than 1.5 times the interquartile range above the third quartile (below the first quartile). Red letters signify regions that are not statistically significantly different from each other. Red=Baltic; orange=Saimaa; yellow=Ladoga; blue=East Greenland; and green=High Arctic. Figure 6 Conceptual map illustrating the hypothesizd complex origins of Fennoscandian ringed seals through several colonisation events, routes and glacial refugia. Pre-LGM (1.) and LGM (2.) events are hypothesized based on genetic and geological data presented here and/or in previous studies (see Discussion), whereas late Pleistocene (3.), early Holocene (4.) and present day (5.) events are well-supported by zooarchaeological and genetic data. Table 1 Genetic summary statistics for the four ringed seal subspecies, as well as each Arctic locality separately. The mitogenome diversity of Baltic and Arctic ringed seals is extremely high, whereas in particular Lake Saimaa ringed seals are characterised low levels of mitogenome diversity. | Subspecies | ||||||| | Atlantic Arctic | 84 | 83 | 0.000 | 1.000 | 0.938 | 972 | 100.5 | | Baltic Sea | 29 | 26 | 0.109 | 0.995 | 0.847 | 286 | 90.7 | | Lake Ladoga | 21 | 15 | 0.074 | 0.962 | 0.313 | 168 | 33.6 | | Lake Saimaa | 112 | 7 | 0.070 | 0.697 | 0.044 | 14 | 4.7 | | Atlantic Arctic localities | ||||||| | Ittoqqortoormiit | 20 | 20 | - | 1.00 | 0.969 | 577 | 103.8 | | Qaanaaq | 16 | 16 | - | 1.00 | 0.905 | 441 | 97.0 | | Qeqertarsuaq | 9 | 9 | - | 1.00 | 1.015 | 335 | 108.7 | | Kangia | 15 | 15 | - | 1.00 | 0.949 | 396 | 101.6 | | Ulukhaktok | 7 | 7 | - | 1.00 | 1.074 | 294 | 115.1 | | Arviat | 5 | 5 | - | 1.00 | 0.894 | 178 | 95.8 | | Svalbard | 11 | 11 | - | 1.00 | 0.865 | 361 | 92.7 | | White Sea | 1 | - | - | - | - | - | - | | Total | 246 | 131 | 0.937 | 0.762 | 1054 | 81.6 | N = Number of sequences; h = haplotypes; P = probably of h given H and theta, based on Ewens 1972; H d = haplotype diversity; π = nucleotide diversity; S = segregating sites; K = Average number of differences Table 2 Mitogenomic differentiation between Fennoscandian and Arctic ringed seal subspecies estimated by K ST (above diagonal) and d A (below diagonal). | Atlantic Arctic | 0.054 | 0.137 | 0.290 | | | Baltic Sea | 0.0013 | 0.151 | 0.513 | | | Lake Ladoga | 0.0040 | 0.0023 | 0.754 | | | Lake Saimaa | 0.0036 | 0.0066 | 0.0099 | All K ST estimates are statistically significant at P<0.001. Table 3 Ringed seal skull geometric morphometric distances among the five sampling regions estimated by Procrustes (above diagonal) and Mahalanobis (below diagonal). | High Arctic | 0.017 | 0.020 | 0.032 | 0.031 | | | East Greenland | 1.940 | 0.017 | 0.025 | 0.031 | | | Baltic Sea | 5.040 | 3.570 | 0.028 | 0.030 | | | Lake Ladoga | 9.460 | 7.030 | 7.120 | 0.036 | | | Lake Saimaa | 9.800 | 8.590 | 8.120 | 11.300 | Table 4 Number and proportion of ringed seal specimens correctly assigned to each geographical area by canonical variates analysis of skull geometric morphometric shape using Jackknife cross-validation. | Origin | High Arctic | East Greenland | Baltic Sea | Lake Ladoga | Lake Saimaa | Total | | High Arctic | 10 (0.53) | 4 (0.21) | 2 (0.11) | 3 (0.16) | 0 (0.00) | 19 | | East Greenland | 13 (0.22) | 29 (0.48) | 11 (0.18) | 3 (0.05) | 4 (0.07) | 60 | | Baltic Sea | 7 (0.14) | 4 (0.08) | 29 (0.59) | 6 (0.12) | 3 (0.06) | 49 | | Lake Ladoga | 1 (0.04) | 1 (0.04) | 0 (0.00) | 23 (0.82) | 3 (0.11) | 28 | | Lake Saimaa | 1 (0.04) | 2 (0.08) | 0 (0.00) | 0 (0.00) | 21 (0.88) | 24 | | Total | 32 | 40 | 42 | 35 | 31 | 180 | Table 5 Proportion of ringed seal specimens that was correctly assigned to geographical area (subspecies) by linear discriminant analysis of skull geometric morphometric shape using jackknife cross-validation in pairwise comparisons of subspecies. Assignment success was between 78.9% and 90.3% for all comparisons. | Arctic-Baltic | 78.9% | | Arctic-Ladoga | 88.8% | | Arctic-Saimaa | 90.3% | | Baltic-Ladoga | 88.1% | | Baltic-Saimaa | 86.3% | | Ladoga-Saimaa | 84.6% | SUPPLEMENTARY MATERIAL Supplementary Figure S1 Landmarks used for the geometric morphometric analyses Supplementary Figure S2 Multispecies time-calibrated Bayesian phylogenetic tree based on mitogenomes from 36 ringed seals representing major lineages in Figure 2 and Figure 3 with eight related phocid seal species included to time the tree and provide an estimate of ringed seal crown age at 0.5385 Mya (95% HPD interval 0.3217-0.741 Mya). The tree includes sample IDs, 95%HPD intervals on branch divergence time estimates, and node posterior support values above 0.90 illustrated by black circles. All nodes with posterior support <0.5 have been collapsed. A high resolution pdf is available as separate file. Supplementary Figure S3 Time-calibrated Bayesian phylogenetic tree based on 141 ringed seal mitogenomes, representing populations the Atlantic Arctic, Lake Saimaa, Lake Ladoga and the Baltic Sea. The tree includes sample IDs, 95%HPD intervals on branch divergence time estimates, and node posterior support values above 0.90 illustrated by black circles. A high resolution pdf is available as separate file. not-yet-known not-yet-known not-yet-known unknown Supplementary Figure S4 PhyML phylogenetic tree based on 141 ringed seal mitogenomes. The tree includes sample IDs and node support values. A high resolution pdf is available as separate file. Supplementary Figure S5 Mean area-specific shapes of ringed seal skulls from Baffin Bay, East Greenland, Baltic Sea, Lake Ladoga and Lake Saimaa (blue outline and markers) compared to the grand mean shape of all areas (red outline and markers). In general, Lake Ladoga ringed seals seem to have slightly longer snouts and more flattened skull, whereas Lake Saimaa ringed seals have shorter snouts, larger eye sockets and more compact skulls. Correction for allometric effects has been performed. Supplementary Table S1 Genetic differentiation between Arctic ringed seals estimated by K ST (above diagonal) and D A (below diagonal). None of the K ST estimates were statistically significant at P<0.05. | Ittoqqortoormiit | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0222 | 0.0000 | | | Qaanaaq | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0284 | 0.0000 | | | Qeqertarsuaq | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | | | Kangia | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | | | Ulukhaktok | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0103 | 0.0057 | | | Arviat | 0.0007 | 0.0007 | 0.0000 | 0.0000 | 0.0002 | 0.0348 | | | Svalbard | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0001 | 0.0007 | Supplementary Table S2 Summary statistics for the multi-species BEAST2 analysis | posterior | -31586 | 0.200 | 10.2 | 103.8 | -31586.9 | [-31605, -31565] | 3471 | 2593 | | likelihood | -31541 | 0.193 | 6.0 | 36.4 | -31540.7 | [-31553, -31529] | 9261 | 972 | | prior | -45 | 0.096 | 8.3 | 68.2 | -45.9 | [-60, -28] | 1217 | 7397 | ACT = Auto-correlation time ESS = Effective sample size Supplementary Table S3 Summary statistics for the ringed seal BEAST2 analysis | posterior | -23201 | 0.435 | 16.6 | 276.4 | -23201.0 | [-23233, -23168] | 24617 | 1463 | | likelihood | -23806 | 0.338 | 14.2 | 200.8 | -23805.2 | [-23834, -23779] | 20436 | 1762 | | prior | 604 | 0.293 | 11.7 | 137.1 | 604.5 | [580, 625] | 22498 | 1600 | ACT = Auto-correlation time ESS = Effective sample size Supplementary File S1 Nexus file with 246 ringed seal mitogenomes Supplementary File S1 Nexus file with 36 ringed seal and 8 related phocid seal mitogenomes Supplementary File S3 Txt file with ringed seal geometric morphometric data Supplementary Material File (image7.emf) - Download - 2.19 MB Information & Authors Information Version history Copyright This work is licensed under a Non Exclusive No Reuse License. Collection

Authors Metrics & Citations Metrics Article Usage 609views 247downloads Citations Download citation Morten Tange Olsen, Ari Löytynoja, Mia Valtonen, et al. Complex origins and history of the relict Fennoscandian ringed seals. Authorea. 01 February 2025. DOI: https://doi.org/10.22541/au.173841332.26158034/v1 DOI: https://doi.org/10.22541/au.173841332.26158034/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu.