Saimaa Ringed Seal Research Articles

Re‐identification of patterned animals by multi‐image feature aggregation and geometric similarity

AbstractImage‐based re‐identification of animal individuals allows gathering of information such as population size and migration patterns of the animals over time. This, together with large image volumes collected using camera traps and crowdsourcing, opens novel possibilities to study animal populations. For many species, the re‐identification can be done by analysing the permanent fur, feather, or skin patterns that are unique to each individual. In this paper, the authors study pattern feature aggregation based re‐identification and consider two ways of improving accuracy: (1) aggregating pattern image features over multiple images and (2) combining the pattern appearance similarity obtained by feature aggregation and geometric pattern similarity. Aggregation over multiple database images of the same individual allows to obtain more comprehensive and robust descriptors while reducing the computation time. On the other hand, combining the two similarity measures allows to efficiently utilise both the local and global pattern features, providing a general re‐identification approach that can be applied to a wide variety of different pattern types. In the experimental part of the work, the authors demonstrate that the proposed method achieves promising re‐identification accuracies for Saimaa ringed seals and whale sharks without species‐specific training or fine‐tuning.

Resurrected analysis: Navigating time between two environmental projects in Finland

AbstractThis paper considers the ways in which research projects linger beyond their ‘official’ endings, and how to deal with this. Building on conversations in human geography and related disciplines on slow research, performed endings, and the practical and socio‐political complexities of data storage and analysis over time, I relate some experiences with my research on the Finnish Saimaa Ringed Seal, which resurfaced years later via a new project. Should I re‐engage or leave it as a discrete period of previous work? An end to funding or finishing the write‐up does not necessarily sever the connection between a researcher and their data. I argue that social research can be an ongoing, slow, and personal process. My aim is to encourage both new and more experienced researchers to reflect on how we think about data and analysis when projects may live on in our minds or in boxes in a cupboard.

Lack of differences in anatomical structures of the head associated with thermoregulation between Saimaa (Pusa hispida saimensis) and Baltic ringed seals (Pusa hispida botnica)

Lack of differences in anatomical structures of the head associated with thermoregulation between Saimaa (Pusa hispida saimensis) and Baltic ringed seals (Pusa hispida botnica)

Seal of approval: Public preferences for the conservation of endangered Saimaa ringed seal

Seal of approval: Public preferences for the conservation of endangered Saimaa ringed seal

Mercury exposure in ringed seals (Pusa hispida saimensis) in Lake Saimaa, Finland, and the placenta as a possible non-invasive biomonitoring tool

The Saimaa ringed seal (Pusa hispida saimensis) is a subspecies of ringed seal, landlocked in Lake Saimaa, Finland. The small population of less than 500 seals is facing many human-induced threats, including chemical contaminants. Mercury, in particular, has previously been suggested to be one of the chemicals affecting the viability of this endangered population. We analysed mercury concentrations from placentas and lanugo pup tissues (blubber, brain, kidney, liver, and muscle) to determine current prenatal exposure levels. These pups were found dead in or near birth lairs and were less than 3 months old. Additionally, we used threshold values available in the literature to estimate the potential mercury toxicity to the Saimaa ringed seal. We also determined selenium concentrations for its potential to alleviate the adverse effects of mercury. We further supplemented our study with brain samples collected from various seal age classes. These seals were found dead by either natural causes or by being caught in gillnets. The analysed chemicals were present in all tissues. For lanugo pups, mercury concentrations were the highest in the kidney and liver, whereas the highest selenium to mercury molar ratio was observed in placentas. The toxicity evaluation suggested that, in severe cases, mercury may cause adverse effects in lanugo and older pups. In these cases, the selenium concentrations were low and selenium to mercury ratio was below 1:1 threshold ratio and thus unlikely to provide adequate protection from the adverse effects of mercury. Furthermore, adverse effects are more likely to occur in adult seals, as mercury bioaccumulates, leading to higher concentrations in older individuals. Placental mercury concentrations correlated to those in the livers and muscle tissues of lanugo pups. This, together with the fact that placentas can be collected non-invasively and in good condition, provides a potential novel method for biomonitoring mercury exposure in Saimaa ringed seals.

Modelling climate change impacts on lake ice and snow demonstrates breeding habitat decline of the endangered Saimaa ringed seal

Snowdrifts on lake ice provide vital breeding habitats for the endangered Saimaa ringed seal. In this study, a lake ice model of Watershed Simulation and Forecasting System (WSFS-Ice) was developed for improved estimation of ice and snow conditions in Lake Saimaa during the pupping season of the Saimaa ringed seal. The WSFS-Ice model is based on energy balance, enabling reliable estimation of the ice cover evolution in current and future climate. In addition, a simple snowdrift model was used to simulate formation of snowdrifts, which are essential for the seals breeding success in Lake Saimaa. The model was calibrated against ice thickness, ice type and snow depth measurements. According to our results based on climate scenarios with intermediate representative concentration pathway (RCP4.5), the breeding habitat of the Saimaa ringed seal is significantly deteriorating during the twenty-first century. The mean depth of the snowdrifts is projected to decrease approximately to half from the 1981–2010 to 2070–99 period and at the same time the ice-covered period is reduced by one and a half months. During the mildest winters the ice cover is projected to melt even before the pupping season has ended. The results highlight the importance of climate change mitigation and active conservation measures to enhance seal population growth, enabling it to survive in a changing climate.

Morphology of sweat glands in the skin of Saimaa (Pusa hispida saimensis) and Baltic ringed (Pusa hispida botnica) seals.

The endangered Saimaa ringed seal (Pusa hispida saimensis) is an endemic freshwater subspecies inhabiting Lake Saimaa in Finland. The Baltic ringed seal (Pusa hispida botnica) inhabits the brackish Baltic Sea, which is almost entirely landlocked. Recent research shows that Saimaa and Baltic ringed seals may be genetically even further apart from each other than from other ringed seal subspecies. We documented histologically the integument microstructure of Saimaa and Baltic ringed seals to determine whether the geographic and genetic isolation was manifested as variation in the integument microstructure of these subspecies adapted to icy aquatic environments. The skin structures of these subspecies were similar to those of other phocids. The association of the sweat glands with hair follicles in both subspecies suggested that they were small apocrine sweat glands described previously in terrestrial or aquatic mammals. None of the apocrine glands had large lumina, and some of the ducts were relatively straight and short. Further studies analysing the mode of secretion, for example, apocrine versus eccrine, in the sweat glands are necessary to confirm the types of sweat glands in seals.

Effects of fishing restrictions on the recovery of the endangered Saimaa ringed seal (Pusa hispida saimensis) population.

Over the past three decades, incidental bycatch has been the single most frequent verified cause of death of the endangered Saimaa ringed seal (Pusa hispida saimensis). Spatial and temporal fishing closures have been enforced to mitigate bycatch, which is mainly caused by the gillnets of recreational fishers. In this study, we employed an array of statistical machine learning methods to recognize patterns of death and to evaluate the impacts of annual fishing closures (15th April-30th June) on the recovery of the Saimaa ringed seal population during 1991-2021. We additionally used the potential biological removal (PBR) procedure to assess bycatch sustainability. The study shows that gillnet restriction areas are reflected in the timing of juvenile bycatch mortality of the Saimaa ringed seal. In the 1990s, peak mortality occurred at the beginning of June, but as the restrictions expanded regionally in the 2000s, the peak shifted to the beginning of July. Longer temporal coverage of annual closures would have improved juvenile survival. The study also shows that estimated bycatch mortality is higher than observed: the estimated bycatch averaged approximately two unobserved bycatches per one observed bycatch. Despite the continuing bycatch mortality, a larger number of juveniles nowadays survive to the age of 15 months due to fishing closures, and the population (some 420 individuals) has increased an average 4% per year between 2017 and 2021. However, human-caused mortality limits (PBR) were exceeded by observed bycatch only, which could lead to population depletion in the long run.

Loss of species and genetic diversity during colonization: Insights from acanthocephalan parasites in northern European seals.

Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.

Anatomical variations in the cerebral arterial circle of the Saimaa (Pusa hispida saimensis) and Baltic ringed seals (Pusa hispida botnica).

The intracranial arterial vascularization of the Saimaa ringed seals (Pusa hispida saimensis; Nordquist, 1899) and Baltic ringed seals (Pusa hispida botnica; Gmelin, 1788) disclosed patterns of anatomical architecture comparable to that of other pinniped species. Arterial silicone casts on skull scaffolds, and magnetic resonance imaging (MRI) showed that the besides joining the caudal communicating arteries upon entering the cerebral arterial circle, the bilateral internal carotid arteries bifurcated as laterally oriented rostral choroidal arteries and rostral cerebral arteries. The latter arteries almost immediately gave off the laterally oriented middle cerebral arteries. Numerous individual variations were evident in differences in the exact branching sites of bilateral vessels or the size or number of arterial branches. Two Saimaa ringed seals had only a tiny foramen for the left internal carotid artery to enter the intracranial space, and the intracranial part of this vessel was short. It did not reach the cerebral arterial circle. The intracranial part of the right internal carotid artery is bifurcated and also supplied the left side of the cerebral arterial circle. Both specimens had aplasia of the left rostral cerebral artery. The intracranial arterial arrangement of Saimaa and Baltic ringed seals reflects the arterial architecture of this body region in terrestrial mammals with little evidence for aquatic adaptations or changes related to thermoregulation.

Seasonal changes in diel haul‐out patterns of a lacustrine ringed seal (Pusa hispida saimensis)

AbstractSeasonal changes in diel haul‐out patterns of the lacustrine Saimaa ringed seal (Pusa hispida saimensis) were studied using a combination of satellite telemetry and camera traps during 2007–2015. We found the haul‐out activity patterns to vary seasonally. Our results show that during the ice‐covered winter period before the seals start their annual molt, the peak in haul‐out generally occurs at midnight. Similarly, during the postmolt season of summer and autumn when the lake is free of ice, the haul‐out is concentrated in the early hours of the morning. In contrast, over the spring molting period, Saimaa ringed seals tend to haul out around the clock. The spring molt is also the only period when a slight difference in haul‐out behavior between the sexes is observed, with females having a haul‐out peak at nighttime while the males have a less visible diel pattern. According to our results, the diel haul‐out patterns of Saimaa ringed seals are similar to the ones of marine ringed seals. Gathering information on haul‐out activity is important in order to safeguard the natural patterns of Saimaa ringed seals in areas that are prone to disturbance from human activities.

Fragmented habitat compensates for the adverse effects of genetic bottleneck

In the face of the human-caused biodiversity crisis, understanding the theoretical basis of conservation efforts of endangered species and populations has become increasingly important. According to population genetics theory, population subdivision helps organisms retain genetic diversity, crucial for adaptation in a changing environment. Habitat topography is thought to be important for generating and maintaining population subdivision, but empirical cases are needed to test this assumption. We studied Saimaa ringed seals, landlocked in a labyrinthine lake and recovering from a drastic bottleneck, with additional samples from three other ringed seal subspecies. Using whole-genome sequences of 145 seals, we analyzed the distribution of variation and genetic relatedness among the individuals in relation to the habitat shape. Despite a severe history of genetic bottlenecks with prevalent homozygosity in Saimaa ringed seals, we found evidence for the population structure mirroring the subregions of the lake. Our genome-wide analyses showed that the subpopulations had retained unique variation and largely complementary patterns of homozygosity, highlighting the significance of habitat connectivity in conservation biology and the power of genomic tools in understanding its impact. The central role of the population substructure in preserving genetic diversity at the metapopulation level was confirmed by simulations. Integration of genetic analyses in conservation decisions gives hope to Saimaa ringed seals and other endangered species in fragmented habitats.

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

Fragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~ 400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1000 generations, is alarmingly low. We performed whole-genome sequencing on Saimaa ringed seals (N = 30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p < 0.001). There is also a tendency for stillborn seal pups to have more pronounced RoH. Since the population is divided into semi-isolated subpopulations within the Lake Saimaa exposing the population to deleterious genomic effects, our results support augmented gene flow as a genetic conservation action. Based on our results suggesting inbreeding depression in the population, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.

Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections.

The Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to postglacial bedrock rebound around 9000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. We sequenced sections of the mitochondrial control region from 60 up to 125-years-old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies and how it is phylogenetically related to other ringed seal populations from the Baltic Sea, Lake Ladoga, North America, Svalbard, and the White Sea. We observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation also shows affinities to North American ringed seals. Our results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seal is not representative of the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.

SealID: Saimaa Ringed Seal Re-Identification Dataset.

Wildlife camera traps and crowd-sourced image material provide novel possibilities to monitor endangered animal species. The massive data volumes call for automatic methods to solve various tasks related to population monitoring, such as the re-identification of individual animals. The Saimaa ringed seal (Pusa hispida saimensis) is an endangered subspecies only found in Lake Saimaa, Finland, and is one of the few existing freshwater seal species. Ringed seals have permanent pelage patterns that are unique to each individual and that can be used for the identification of individuals. A large variation in poses, further exacerbated by the deformable nature of seals, together with varying appearance and low contrast between the ring pattern and the rest of the pelage makes the Saimaa ringed seal re-identification task very challenging, providing a good benchmark by which to evaluate state-of-the-art re-identification methods. Therefore, we make our Saimaa ringed seal image (SealID) dataset (N = 57) publicly available for research purposes. In this paper, the dataset is described, the evaluation protocol for re-identification methods is proposed, and the results for two baseline methods—HotSpotter and NORPPA—are provided. The SealID dataset has been made publicly available.

Molting phenology of a lacustrine ringed seal, Pusa hispida saimensis

AbstractThe timing and effect of a range of environmental variables on the annual molt of ringed seals (Pusa hispida saimensis) in Lake Saimaa were studied in 2013–2019. Molting patterns were investigated by mixed models run on photoidentification data collected by camera trapping and digital camera surveys. Photoperiod was the predominant environmental variable affecting the molt but molting of females was also linked to air temperature and ice thickness. The cumulative proportion of molting seals peaked around the 18th–20th May, when day length reached 18 h. The main molting season, when most of the seals were hauled out at the same time, lasted on average for 16 days with considerable inter‐annual differences in the duration (range 11–22 days). The results provide important baseline information on Saimaa ringed seal molt. Continued monitoring is important as the molt is an energetically demanding period for the seals, and any changes in molting behavior may indicate changes in habitat or in environmental conditions.

High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal.

Host‐specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among‐host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly‐transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host‐specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among‐host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population‐genetic analyses of the seals themselves.

Developing artificial nest boxes for a large aquatic mammal

Abstract Nest boxes and other human‐made constructions have been widely and successfully used as conservation tools to increase nest‐availability for hollow‐dependent fauna, especially birds and some small and medium mammals. This study applies, for the first time, this recovery technique to a large aquatic mammal, aiming to improve resting, birthing and nursing sites of endangered Saimaa ringed seals (Pusa hispida saimensis) by developing artificial nest boxes. This landlocked subspecies' breeding habitat is severely affected by climate change. Because of mild winters, sufficient ice and snow habitat for subnivean lairs is lacking. In this study, floating nest boxes were developed. It was found that free‐ranging ringed seals accept nest boxes as sites for resting, birthing and nursing. Thirty‐four boxes in total were offered during six successive breeding seasons. Almost half (47%) of the available boxes were used by seals, and two pups were born and reared in the boxes during the 6‐year study. Our study indicates that this innovative technique can be a valuable tool for the Saimaa ringed seal conservation in the changing climate.

Extreme moulting site fidelity of the Saimaa ringed seal

Site fidelity is commonly observed in pinnipeds and has direct consequences for individual space use and population dynamics. Here, we used photo-identification recapture data to quantify site fidelity of the endangered Saimaa ringed seal (Pusa hispida saimensis) over four successive moulting seasons. We identified 337 seals based on their permanent fur patterns, and 192 of them were observed during at least 2 years. Over the study period, the median number of terrestrial haul-out sites used by an individual seal was four, and nearly 50% of the seals reused them over the years. Although eight seals performed movements (up to 48 km) between the different water basins of Lake Saimaa, most of the studied seals remained in the same water basin over the years. The median distance between successive moulting sites used by an individual seal was 643 m. While these distances were similar within years in both sexes, the distances between years were longer in females, suggesting post-nursing related behaviour. The extreme site fidelity of the Saimaa ringed seal has important implications for its conservation, especially in the land use management of the Lake Saimaa shoreline.

Hip and stifle joint anatomy of the Saimaa (Pusa hispida saimensis) and Baltic ringed seals (Pusa hispida botnica).

The anatomical architecture of the hip and stifle joints of the Saimaa ringed seal was determined by dissection to be similar to that of the Baltic ringed seal. There was no ligament of the femoral head in the hip joint. The lateral side of the stifle joint lacked a collateral ligament but the collateral ligament on the medial side was of considerable size. The medial meniscus was larger and thicker than the lateral meniscus. The asymmetrical anatomical architecture allows for much lateral movement during aquatic motion, but it is poorly adapted to terrestrial locomotion.