Jenni Harmoinen

Genetic monitoring is an essential tool for managing threatened or commercially valuable wildlife species. Ideally, genetic monitoring relies on straightforward protocols for genotyping and data handling, accommodates varying sample volumes, applies to non-invasive samples such as scat and hair, produces reliable and repeatable genotypes, and is cost-effective. Moreover, the marker panel itself should be tailored to specific species and/or population management information needs. We describe the development of a microarray-based 96-SNP panel specifically designed for non-invasive genetic monitoring of the Finnish wolf population. The panel was developed to meet four specific needs for this population: identification of wolf genotypes from the non-target species (fox, raccoon dog, golden jackal), sexing, individual identification, and kinship resolution. We demonstrate the utility of the SNP panel using a subset of the genetic monitoring data collected in 2022–2023, including an overview of the data analysis workflow. The development and successful application of this SNP panel, along with a comparison with similar studies in the field, provide valuable insights for researchers and conservationists aiming to implement similar strategies for other species.

One of the most fascinating mammalian range expansions in Europe involves an opportunistic mesocarnivore―the golden jackal (Canis aureus). However, key questions about the origins and dispersal strategies of pioneering individuals, likely the first to establish new populations, remain unanswered. We analyzed genetic data from three golden jackals found at the forefront of the expansion, reaching the Iberian Peninsula (Spain) and Fennoscandia (Finland and Norway, beyond the Arctic Circle). We genotyped two tissue samples and one fecal sample using 15 microsatellites and compared results with an extensive reference dataset. Additionally, we analyzed the mtDNA control region (HVR1) for two individuals. All individuals were males, identified as pure jackals and first-generation migrants. Our results suggested either western Pannonia (1650 km distance) or, less probably, the Adriatic region (1300 km) as the region of origin for the Spanish individual, also western Pannonia for the Finnish individual (2500 km), and the Baltics or the Caucasus for the Norwegian individual (1400 km to 3400 km). These sources represent abundant core populations or relatively recent and successfully colonized areas. Both the Spanish and Finnish individuals carried the prevalent H1 HVR1 haplotype in Europe, confirming matrilineal genetic uniformity on the continent. The recent expansion of C. aureus is fueled by several sources, showcasing the golden jackals’ remarkable ability for long-distance dispersal as they extend their range to northernmost and westernmost Europe. Our findings highlight the dynamic nature of wildlife distribution, providing insights into species movement across vast distances amidst climatic, environmental, and anthropogenic pressures.

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.

Aim: 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 post-glacial bedrock rebound around 9,000 years ago. During the 20 ^th 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. Our main aim was to evaluate the role of the 20 ^th century bottleneck in the erosion of genetic diversity in the Saimaa seal population. We also evaluated connections with other ringed seals from the Baltic Sea, Lake Ladoga, North America, Svalbard and the White Sea. Location: Lake Saimaa, Finland, together with the Baltic Sea and the Arctic Ocean. Methods: 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. Results: 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 shows also affinities to North American ringed seals. Main conclusions: 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 seals do not represent well the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.

Sociality in animal populations is a continuum, and interactions between conspecifics are meaningful for all vertebrates. Ignorance of social structures can lead to misunderstanding their ecology and, consequently, to unsuccessful species management. Here, we combined genetic and spatial data on radio-collared brown bears (Ursus arctos) to investigate kin-related home range overlap and kin-related centroid distance within central and eastern Finland. We found that the extent of home range overlap was positively correlated with relatedness among adult females. In addition, home range centroid distance decreased as relatedness increased. Moreover, there were significant differences between the two studied regions: female brown bears in central Finland were more closely related to each other, and the sizes of their home ranges were larger than those in eastern Finland. The smaller home ranges and lower degree of relatedness among bears in eastern Finland might be a result of the substantially higher hunting pressure in the area, combined with immigration of new unrelated individuals from Russia.

Sociality in animal populations is a continuum, and interactions between conspecifics are meaningful for all vertebrates. Ignorance of social structures can lead to misunderstanding their ecology and, consequently, to unsuccessful species management. Here, we combined genetic and spatial data on radio-collated brown bears (Ursus arctos) to investigate kin-related home range overlap and kin-related centroid distance within central and eastern Finland. We found that the extent of overlap of home ranges was positively linked with relatedness among adult females. A similar positive correlation could be detected between home range centroid distance and relatedness among adult females. Moreover, there were significant differences between the two studied regions: female brown bears in central Finland were more closely related to each other, and the sizes of their home ranges were larger than those in eastern Finland. The smaller home ranges and lower degree of relatedness among bears in eastern Finland might be a result of the substantially higher hunting pressure in the area, combined with immigration of new unrelated individuals from Russia.

Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results: Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions: We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.

BackgroundUnderstanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. ResultsGenotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the status of individuals regarded as wolves to be wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations, as migrants are increasingly more common.ConclusionsCompared to microsatellites, this method is faster to implement, economically more feasible and results are directly comparable across laboratories. The new panel is thus suitable as a new tool for wolf-dog hybrid assessments and monitoring on a continental scale.

Carnivores are re-establishing in many human-populated areas, where their presence is often contentious. Reaching consensus on management decisions is often hampered by a dispute over the size of the local carnivore population. Understanding the reproductive dynamics and individual movements of the carnivores can provide support for management decisions, but individual-level information can be difficult to obtain from elusive, wide-ranging species. Non-invasive genetic sampling can yield such information, but makes subsequent reconstruction of population history challenging due to incomplete population coverage and error-prone data. Here, we combine a collaborative, volunteer-based sampling scheme with Bayesian pedigree reconstruction to describe the pack dynamics of an establishing grey wolf (Canis lupus) population in south-west Finland, where wolf breeding was recorded in 2006 for the first time in over a century. Using DNA extracted mainly from faeces collected since 2008, we identified 81 individual wolves and assigned credible full parentages to 70 of these and partial parentages to a further 9, revealing 7 breeding pairs. Individuals used a range of strategies to obtain breeding opportunities, including dispersal to established or new packs, long-distance migration and inheriting breeding roles. Gene flow occurred between all packs but inbreeding events were rare. These findings demonstrate that characterizing ongoing pack dynamics can provide detailed, locally-relevant insight into the ecology of contentious species such as the wolf. Involving various stakeholders in data collection makes these results more likely to be accepted as unbiased and hence reliable grounds for management decisions.

Many western European carnivore populations became almost or completely eradicated during the last ~200 years, but are now recovering. Extirpation of wolves started in Finland in the 19th century, and for more than 150 years the population size of wolves has remained small. To investigate historical patterns of genetic variation, we extracted DNA from 114 wolf samples collected in zoological museums over the last ~150 years. Fifteen microsatellite loci were used to look at genotypic variation in this historical sample. Additionally, we amplified a 430 bp sequence of mtDNA control region from the same samples. Contemporary wolf samples (N = 298) obtained after the population recovery in the mid-1990s, were used as a reference.