Minna Ruokonen

Structure and evolution of the avian mitochondrial control region

The structural and evolutionary characteristics of the mitochondrial control region were studied by using control region sequences of 68 avian species. The distribution of the variable nucleotide positions within the control region was found to be genus specific and not dependant on the level of divergence, as suggested before. Saturation was shown to occur at the level of divergence of 10% in pairwise comparisons of the control region sequences, as has also been reported for the third codon positions in ND2 and cytochrome b genes of mtDNA. The ratio of control region vs cytochrome b divergence in pairwise comparisons of the sequences was shown to vary from 0.13 to 21.65, indicating that the control region is not always the most variable region of the mtDNA, but also that there are differences in the rate of divergence among the lineages. Only two of the conserved sequence blocks localized earlier for other species, D box and CSB-1, were found to show a considerable amount of sequence conservation across the avian and mammalian sequences. Additionally, a novel avian-specific sequence block was found.

Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population

The Finnish wolf population (Canis lupus) was sampled during three different periods (1996–1998, 1999–2001 and 2002–2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long‐term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.

The colonization history and present-day population structure of the european great tit (Parus major major)

The colonization history and present-day population structure of the European subspecies of the great tit Parus major major were studied using mitochondrial control region sequences. One major haplotype was found in all but one of the eight sampled populations from Spain to northern Finland. The other haplotypes differed from the common one by just a few substitutions; the overall nucleotide diversity was 0.00187 and haplotype diversity 0.8633. No population structuring was detected. The mismatch distribution followed the expected distribution of an expanding population. The estimated time to the most recent common ancestor coincides with the last glacial period. The results suggest that P. m. major survived the last glacial period in a single isolated refuge probably by the Mediterranean Sea. This was followed by rapid colonization of the European continent and population growth. The most recent range expansion northwards is still occurring. Gene flow between the sampled populations is extensive. It is aided by juvenile dispersal, long-distance movements of juvenile flocks and partial migration in the northern parts of the great tit’s range.

Rise and fall of a wolf population: genetic diversity and structure during recovery, rapid expansion and drastic decline

The grey wolves (Canis lupus) of Finland have had a varied history, with a period of rapid population expansion after the mid‐1990s followed by a decline with a current census size of about 140 wolves. Here, we investigate the impact of unstable population size and connectivity on genetic diversity and structure in a long‐term genetic study of 298 Finnish wolves born in 1995–2009 and genotyped for 17 microsatellite loci. During the initial recovery and prior to population expansion, genetic diversity was high (1995–1997: LD‐Ne = 67.2; Ho = 0.749; He = 0.709) despite a small census size and low number of breeders (Nc < 100; Nb < 10) likely reflecting the status of the Russian source population. Surprisingly, observed heterozygosity decreased significantly during the study period (t = −2.643, P = 0.021) despite population expansion, likely a result of an increase in inbreeding (FIS = 0.108 in 2007–2009) owing to a low degree of connectivity with adjacent Russian wolf population (m = 0.016–0.090; FST = 0.086, P < 0.001) and population crash after 2006. However, population growth had a temporary positive impact on Ne and number of family lines. This study shows that even strong population growth alone might not be adequate to retain genetic diversity, especially when accompanied with low amount of subsequent gene flow and population decline.

Population Genetic Structure and Conservation of the Lesser White-Fronted GooseAnser erythropus

The lesser white-fronted goose is a sub-Arctic species with a currently fragmented breeding range, which extends from Fennoscandia to easternmost Siberia. The population started to decline at the beginning of the last century and, with a current world population estimate of 25,000 individuals, it is the most threatened of the Palearctic goose species. Of these, only 30–50 pairs breed in Fennoscandia. A fragment of the control region of mtDNA was sequenced from 110 individuals from four breeding, one staging and two wintering areas to study geographic subdivisions and gene flow. Sequences defined 15 mtDNA haplotypes that were assigned to two mtDNA lineages. Both the mtDNA lineages were found from all sampled localities indicating a common ancestry and/or some level of gene flow. Analyses of molecular variance showed significant structuring among populations (φST 0.220, P < 0.001). The results presented here together with ecological data indicate that the lesser white-fronted goose is fragmented into three distinctive subpopulations, and thus, the conservation status of the species should be reconsidered.

Balancing selection and heterozygote advantage in major histocompatibility complex loci of the bottlenecked Finnish wolf population

Maintaining effective immune response is an essential factor in the survival of small populations. One of the most important immune gene regions is the highly polymorphic major histocompatibility complex (MHC). We investigated how a population bottleneck and recovery have influenced the diversity and selection in three MHC class II loci, DLA‐DRB1, DLA‐DQA1 and DLA‐DQB1, in the Finnish wolf population. We studied the larger Russian Karelian wolf population for comparison and used 17 microsatellite markers as reference loci. The Finnish and Karelian wolf populations did not differ substantially in their MHC diversities ( GST″ = 0.047, P = 0.377), but differed in neutral microsatellite diversities ( GST″ = 0.148, P = 0.008). MHC allele frequency distributions in the Finnish population were more even than expected under neutrality, implying balancing selection. In addition, an excess of nonsynonymous compared to synonymous polymorphisms indicated historical balancing selection. We also studied association between helminth (Trichinella spp. and Echinococcus canadensis) prevalence and MHC diversity at allele and SNP level. MHC‐heterozygous wolves were less often infected by Trichinella spp. and carriers of specific MHC alleles, SNP haplotypes and SNP alleles had less helminth infections. The associated SNP haplotypes and alleles were shared by different MHC alleles, which emphasizes the necessity of single‐nucleotide‐level association studies also in MHC. Here, we show that strong balancing selection has had similar effect on MHC diversities in the Finnish and Russian Karelian wolf populations despite significant genetic differentiation at neutral markers and small population size in the Finnish population.

Limited gene flow among brown bear populations in far Northern Europe? Genetic analysis of the east–west border population in the Pasvik Valley

Noninvasively collected genetic data can be used to analyse large‐scale connectivity patterns among populations of large predators without disturbing them, which may contribute to unravel the species’ roles in natural ecosystems and their requirements for long‐term survival. The demographic history of brown bears (Ursus arctos) in Northern Europe indicates several extinction and recolonization events, but little is known about present gene flow between populations of the east and west. We used 12 validated microsatellite markers to analyse 1580 hair and faecal samples collected during six consecutive years (2005–2010) in the Pasvik Valley at 70°N on the border of Norway, Finland and Russia. Our results showed an overall high correlation between the annual estimates of population size (Nc), density (D), effective size (Ne) and Ne/Nc ratio. Furthermore, we observed a genetic heterogeneity of ∼0.8 and high Ne/Nc ratios of ∼0.6, which suggests gene flow from the east. Thus, we expanded the population genetic study to include Karelia (Russia, Finland), Västerbotten (Sweden) and Troms (Norway) (477 individuals in total) and detected four distinct genetic clusters with low migration rates among the regions. More specifically, we found that differentiation was relatively low from the Pasvik Valley towards the south and east, whereas, in contrast, moderately high pairwise FST values (0.91–0.12) were detected between the east and the west. Our results indicate ongoing limits to gene flow towards the west, and the existence of barriers to migration between eastern and western brown bear populations in Northern Europe.

Colonization history of the high-arctic pink-footed goose Anser brachyrhynchus.

Population structure and phylogeography of the pink‐footed goose, Anser brachyrhynchus Baillon 1833, was studied using mtDNA control region sequences (221 bp) from 142 individuals. Present breeding areas of the species in Greenland, Iceland, and Svalbard were largely covered by ice during the late Pleistocene. In pairwise comparisons φST estimates showed significant differentiation among eastern and western populations, whereas sampling localities within both areas were not differentiated. The mtDNA data indicate that the populations have separated recently (less than 10 000 years ago) and present breeding areas were colonized from one refugial population. The levels of haplotype and nucleotide diversity were approximately five times higher for the eastern population compared to the western population and suggest that the latter was colonized by a subset of eastern birds. Time to the most recent common ancestor of the species is 32 000–46 000 years, i.e. the present mtDNA variation of the pink‐footed goose has accumulated during the last 0.1 My. Estimates of the long‐term female effective population size (5400–7700 for the eastern population) imply that the refugial population of the pink‐footed goose has been large. Tundra habitats were more extensive in cold periods of the late Pleistocene than today and may have sustained population sizes that allowed the accumulation of extant genetic polymorphism. It is not probable that the postulated small refugial areas in the high latitudes had a significant role in maintaining this diversity.

Goose hybrids, captive breeding and restocking of the Fennoscandian populations of the Lesser White-fronted goose (Anser erythropus)

The lesser white-fronted goose (Anser erythropus) isthe most threatened of the Palearctic goose species with a decliningpopulation trend throughout its distributional range. The currentestimate of the Fennoscandian subpopulation size is 30–50 breedingpairs, whereas it still numbered more than 10000 individuals at thebeginning of the last century. Reintroduction and restocking have beencarried out in Sweden and Finland using captive lesser white-frontedgoose stock with unknown origins. We have carried out a study of thegenetic composition of captive-bred stock by sequencing a 221 bphypervariable fragment of the mitochondrial DNA (mtDNA) control regionfrom 15 individuals from the Hailuoto farm, Finland. Two out of thethree maternal lineages detected in the captive stock are also presentin wild populations. The third maternal lineage among the captive lesserwhite-fronted geese originates from the closely related greaterwhite-fronted goose (Anser albifrons). None of the investigatedwild lesser white-fronted goose individuals carried the mtDNA of thegreater white-fronted goose. The presence of greater white-fronted goosemtDNA in the lesser white-fronted goose captive stock suggests thathybridization has occurred during captive propagation.

Taxonomy of the bean goose–pink-footed goose

The bean goose Anser fabalis and the pink-footed goose A. brachyrhynchus breed in the tundra and taiga zones of Eurasia and eastern Greenland, and the taxonomy of the group based on morphology has been controversial. We investigated the phylogenetic relationships within the bean goose-the pink-footed goose complex using mitochondrial control region sequences of 199 individuals collected from the breeding areas in the Palaearctic and Eastern Nearctic. We found three mitochondrial clades geographically distributed to (1) Greenland, Iceland and Svalbard (A. brachyrhynchus), (2) the eastern taiga zone (former subspecies A. fabalis middendorffii), and (3) the western taiga and the tundra zone (subspecies A. fabalisrossicus, serrirostris and fabalis). MtDNA phylogeny suggests that morphological affinities between the taxa, e.g. in the bill structure, result from convergent evolution due to adaptation to similar habitats. Although a latitudinal cline in morphology was observed, clear phylogenetic discontinuities exist in the taiga and tundra zones supporting a species status for brachyrhynchus and middendorffii.