Population genetic structure in the Temminck’s stint <Emphasis Type="Italic">Calidris temminckii</Emphasis>, with an emphasis on Fennoscandian populations

Temminck’s stint breeds in Eurasian arctic tundra and subarctic and temperate boreal zones in a range extending from Fennoscandia to easternmost Siberia. In contrast to the favourable global conservation status of the species, it has been classified as vulnerable in Finland and near threatened in Sweden. A fragment of the control region of mtDNA was sequenced from 127 individuals from breeding areas in Fennoscandia in the west (three populations) and in the eastern end of the range. The mtDNA variability and structuring were among the lowest values reported for waders (F _ST −0.02616). The mtDNA sequences revealed seven haplotypes, of which four were present in single individuals. The most common haplotype occurred in 81% of all individuals and in all birds in the Siberian sample. There was evidence of two maternal lineages. The most common lineage occurred in 95% of the individuals and was the only one present in the Siberian sample. The lineages coexisted in all three Fennoscandian populations, indicating a secondary contact of two previously isolated populations. The mtDNA variation and the mitochondrial nucleotide and haplotype diversities indicated panmixis of the populations. However, a higher degree of population differentiation was detected in microsatellite allele frequencies (125 birds, six loci) in Fennoscandia between the Bothnian Bay population and the two inland populations (Lapland and southern Norway). The difference may be caused by the female-biased dispersal pattern of the species. In addition, the Bothnian Bay population appeared to be genetically bottlenecked, an observation in concordance with the recent decimation of the population.     

High survival rate and site fidelity in the Siberian Tit Parus cinctus, a focal species of the taiga

The Siberian Tit Parus cinctus population of Finland, and probably of the whole of Fennoscandia, has declined dramatically during this century. Understanding its population dynamics is essential for its conservation. We studied annual survival rate and dispersal distance of both breeding and fledgling Siberian Tits during 1989-97 in a moderately managed forest habitat near the southern border of its range in Kuusamo, northeastern Finland. Breeding density was low, averaging 0.51 pairs/km in a nestbox area of about 42 km². This was probably an underestimate, because we did not search for nests in natural holes. However, following its population decline, overall densities at the southern border of the range are low. The study area was, however, suitable breeding habitat as reflected by their high nesting success. Brood size at fledging averaged 7.45 young, and reproductive output was 6.16 young per breeding pair, including failed nests. Clutch size adjustment was successful among pairs producing fledglings because, on average, 92.6% of the eggs laid produced young in successful broods. Median distance between consecutive breeding attempts was 100 m for both males and females (range 0–2500 m and 0–6000 m, respectively). Natal dispersal distance was significantly longer in females than in males. We applied Cormack-Jolly-Seber modelling to estimate survival and recapture probabilities separately. Survival of breeding birds was not sex-related, averaging 0.69 annually. Some of the ringed fledglings (3.0%) were later captured as breeders in the area. This is an underestimate of local survival rate due to incomplete recapturing of breeding birds. The implications of these results with respect to the conservation status of the species are discussed.     

Genetic diversity in the Siberian jay Perisoreus infaustus in fragmented old-growth forests of Fennoscandia

The Siberian jay Perisoreus infaustus is a bird inhabiting old-growth coniferous taiga forests. It has recently declined in numbers in Finland mainly because of habitat fragmentation. Distant mtDNA lineages from Taimyrian Peninsula (subspecies P. i. monjerensis ) and middle Yenisei valley ( P. i. rogosovi ) have diverged from Fennoseandian ( P. i. infaustus ) lineage ca 610000 yr ago. The estimated time to the most recent common ancestor for Fennoscandian population (78000 yr) coincides with the beginning of the Weichselian ice age. Within Fennoscandia, the observed distribution of pairwise genetic distances followed the expected distribution of an expanding population reflecting the postglacial history rather than the present day situation of the Siberian jay. Mitochondrial control region sequences showed that among 65 Fennoseandian individuals the most common baplotype (40%) was found in all but two populations. Genetic structuring (φ_ST= 0.111) was clear within the Fennoseandian population. This may be attributable to low intrinsic natal dispersal. In an isolate of western Finland, nucleotide diversity was significantly lower than in P. i. infaustus populations of the continuous distribution area. We suggest that isolation by habitat fragmentation in modern landscapes may effectively reduce gene flow below the level occurring in natural conditions. Thus, Siberian jay isolates with limited number of individuals would be highly vulnerable to loss of genetic variation or even to extinction by demographic or environmental stochasticity.     

Colonization history of north European field voles (Microtus agrestis) revealed by mitochondrial DNA

The genetic structure of field vole (Microtus agrestis) populations from northern Europe was examined by restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in 150 individuals from 67 localities. A total of 83 haplotypes was observed, most of which were rare and highly localized geographically. Overall nucleotide diversity was high (134%), but showed a tendency to decrease with higher latitude. Two major mtDNA lineages differing by 2% in nucleotide sequence were identified. A southern mtDNA lineage was observed in field voles from Britain, Denmark and southern and central Sweden, whereas voles from Finland and northern Sweden belonged to a northern lineage. The strict phylogeographic pattern suggests that the present population generic structure in field voles reflects glacial history: the two groups are derived from different glacial refugia, and recolonized Fennoscandia from two directions. A 150–200-km-wide secondary contact zone between the two mtDNA groups was found in northern Sweden. Distinct phylogeographic substructuring was observed within both major mtDNA groups.     

Indo-Pacific population structure and evolutionary history of the coconut crab Birgus latro

Mitochondrial DNA variation was used to examine population structure in a widespread, marine-dispersed species, Birgus latro . Crabs were collected from eight locations throughout the species' Indo-Pacific distribution. Purified mtDNA from 160 individuals was cut with five restriction enzymes, revealing high haplotype diversity (0.96) and moderate nucleotide diversity (0.75%). Island populations from the Indian Ocean (Christmas I.) and Pacific Ocean were significantly different ( G _ST= 0.37) and had distinct mtDNA lineages with a net sequence divergence of 1.4%. Pacific island populations had diverged in a manner consistent with isolation by distance, with only the most peripheral populations being significantly different. The results for mtDNA are largely concordant with those from allozymes, although estimates of gene flow between the Indian and Pacific Oceans were much lower when based on mtDNA. The mtDNA phylogeny also permitted a deeper examination of the evolutionary and demographic history of Birgus latro . Long-term separation of populations is evident in the complete phylogenetic subdivision of mtDNA lineages between the Indian and Pacific Ocean populations sampled. The starlike phylogeny of alleles from the Pacific suggests a rapid population expansion in the Pacific during the Pleistocene. Including information about allele phylogeny, as well as distribution and frequency, obscured contemporary population structure, but provided unique insights into the evolutionary history of the species.     

Autosomal, mitochondrial, and Y chromosome DNA variation in Finland: evidence for a male-specific bottleneck

The high prevalence of rare genetic diseases in Finland has been attributed to a founder effect some 2,000 years ago. However, this hypothesis has not been supported from mtDNA sequence and autosomal microsatellite data which indicate high levels of gene diversity. Here we have identified genetic evidence for a population bottleneck by examining variable microsatellite loci on the nonrecombining portion of Y chromosomes from Finland and four populations from Europe and the Americas. Sequence data from segment I of the control region (HVS-1) of mtDNA (360 bases) and 20 autosomal dinucleotide repeat markers were also analyzed. Partitions of genetic variance within and between populations revealed significant levels of Y-chromosome differentiation between populations. Phylogenetic and diversity analyses revealed divergent Finnish Y-haplotype clades and significantly lower Y-haplotype diversity among Finns as compared to other populations. Surprisingly, Finnish Y-haplotype diversity was even lower than the Native American populations. These results provide support for the Finnish bottleneck hypothesis. Evidence for two separate founding Finnish Y-chromosome lineages was also observed from the Y-chromosome phylogeny. A limited number of closely related founding males may have contributed to the low number of paternal lineages in the Finnish population. In contrast, high levels of genetic diversity for mtDNA and autosomal STRs may be the result of sex-biased gene flow and recent immigration to urban areas from established internal isolates within Finland.     

Temporal increase in mtDNA diversity in a declining population

In small and declining populations levels of genetic variability are expected to be reduced due to effects of inbreeding and random genetic drift. As a result, both individual fitness and populations’ adaptability can be compromised, and the probability of extinction increased. Therefore, maintenance of genetic variability is a crucial goal in conservation biology. Here we show that although the level of genetic variability in mtDNA of the endangered Fennoscandian lesser white‐fronted goose Anser erythropus population is currently lower than in the neigbouring populations, it has increased six‐fold during the past 140 years despite the precipitously declining population. The explanation for increased genetic diversity in Fennoscandia appears to be recent spontaneous increase in male immigration rate equalling 0.56 per generation. This inference is supported by data on nuclear microsatellite markers, the latter of which show that the current and the historical Fennoscandian populations are significantly differentiated (F_ST = 0.046, P = 0) due to changes in allele frequencies. The effect of male‐mediated gene flow is potentially dichotomous. On the one hand it may rescue the Fennoscandian lesser white‐fronted goose from loss of genetic variability, but on the other hand, it eradicates the original genetic characteristics of this population.     

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 phiST 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.     

Fennoscandian phylogeography of the common shrew <Emphasis Type="Italic">Sorex araneus</Emphasis>. Postglacial recolonisation—combining information from chromosomal variation with mitochondrial DNA data

We examine mtDNA variation of the common shrew in Fennoscandia to explore the incongruence found in previous studies using chromosomal and mitochondrial markers, aiming to reveal post-glacial recolonisation patterns. A total of 241 common shrews from 51 localities in Fennoscandia were analysed. This area includes a secondary contact zone between two groups (the Northern group and the Western group) showing distinct karyotypes. All individuals were sequenced for 447 bp of the mitochondrial control region. No significant differentiation in the mtDNA variation was observed between the two major chromosomal groups in Fennoscandia. The star-like shape of the sequence network for the entire study area shows the most common haplotype A as ancestral in all regions but one, in situ formation of most haplotypes and population expansion. The only significant mtDNA structure observed occurs between south Finland and the rest of Fennoscandia. We propose that the Northern and Western group shared a common refugium during the Last Glacial Maximum but recolonised Fennoscandia via two routes. Karyotypic differences between south and north Finland has led researchers to suggest that both regions originate from the same ancestral population east of Finland. The observed divergence of mtDNA variation between these two regions supports this hypothesis.     

Evolutionary history of the European whitefish Coregonus lavaretus (L.) species complex as inferred from mtDNA phylogeography and gill-raker numbers

We compared mitochondrial DNA and gill-raker number variation in populations of the European whitefish Coregonus lavaretus (L.) species complex to illuminate their evolutionary history, and discuss mechanisms behind diversification. Using single-strand conformation polymorphism (SSCP) and sequencing 528 bp of combined parts of the cytochrome oxidase b (cyt b) and NADH dehydrogenase subunit 3 (ND3) mithochondrial DNA (mtDNA) regions, we documented phylogeographic relationships among populations and phylogeny of mtDNA haplotypes. Demographic events behind geographical distribution of haplotypes were inferred using nested clade analysis (NCA) and mismatch distribution. Concordance between operational taxonomical groups, based on gill-raker numbers, and mtDNA patterns was tested. Three major mtDNA clades were resolved in Europe: a North European clade from northwest Russia to Denmark, a Siberian clade from the Arctic Sea to southwest Norway, and a South European clade from Denmark to the European Alps, reflecting occupation in different glacial refugia. Demographic events inferred from NCA were isolation by distance, range expansion, and fragmentation. Mismatch analysis suggested that clades which colonized Fennoscandia and the Alps expanded in population size 24 500-5800 years before present, with minute female effective population sizes, implying small founder populations during colonization. Gill-raker counts did not commensurate with hierarchical mtDNA clades, and poorly with haplotypes, suggesting recent origin of gill-raker variation. Whitefish designations based on gill-raker numbers were not associated with ancient clades. Lack of congruence in morphology and evolutionary lineages implies that the taxonomy of this species complex should be reconsidered.     

Low mitochondrial DNA variation and recent colonization of Scandinavia by the wood lemming Myopus schisticolor

The population genetic structure of wood lemmings ( Myopus schisticolor ) from Scandinavia, Finland and western Siberia was examined by restriction fragment length polymorphism of mitochondrial DNA (mtDNA) in 45 individuals from six localities. The 12 observed mtDNA haplotypes demonstrated a distinct phylogeographic pattern, suggesting that the postglacial colonization of Scandinavia by wood lemmings occurred from north-east. However, a very low level of haplotype and nucleotide diversity and a lack of geographical structure were found within Scandinavia. The limited mtDNA diversity in the Scandinavian populations probably reflects recent divergence in situ after colonization by a limited number of founders. Allozyme data support this scenario.     

Different population structures in northern and southern populations of the European blue tit (Parus caeruleus)

We sequenced the control region of the mitochondrial DNA from a sample of six European blue tit populations to investigate the phylogeography of Parus species. Along a transect from Barcelona, Spain to Oulu, Finland, the blue tit showed a different phylogeographic structure than the great tit and the willow tit. The southernmost sample from Barcelona consisted of two widely divergent maternal lineages (nucleotide divergence, π = 0.30%), a situation also found earlier in the French Alps. The more northern populations had a relatively uniform structure (π = 0.19%) with distinctive marks of a growing population, thus resembling the great tit populations (π = 0.19%). The amount of genetic variation among blue tits is lower than in the willow tit (π = 0.53%). This probably reflects a smaller long-term effective population size in the great tit and the blue tit than in the willow tit. The different genetic structure of the Barcelona population vs. the rest had an influence on the estimated population parameters, which are calculated based on the assumptions of genetic equilibrium of the populations.     

Characterization of MHC-I in the blue tit (Cyanistes caeruleus) reveals low levels of genetic diversity and trans-population evolution across European populations

The major histcompatibility complex (MHC) is a vital component of the adaptive immune system in all vertebrates. This study is the first to characterize MHC class I (MHC-I) in blue tits (Cyanistes caeruleus), and we use MHC-I exon 3 sequence data from individuals originating from three locations across Europe: Spain, the Netherlands to Sweden. Our phylogeny of the 17 blue tit MHC-I alleles contains one allele cluster with low nucleotide diversity compared to the remaining more diverse alleles. We found a significant evidence for balancing selection in the peptide-binding region in the diverse allele group only. No separation according to geographic location was found in the phylogeny of alleles. Although the number of MHC-I loci of the blue tit is comparable to that of other passerine species, the nucleotide diversity of MHC-I appears to be much lower than that of other passerine species, including the closely related great tit (Parus major) and the severely inbred Seychelles warbler (Acrocephalus sechellensis). We believe that this initial MHC-I characterization in blue tits provides an important step towards understanding the mechanisms shaping MHC-I diversity in natural populations.     

The evolutionary history of Afrocanarian blue tits inferred from genomewide SNPs

A common challenge in phylogenetic reconstruction is to find enough suitable genomic markers to reliably trace splitting events with short internodes. Here, we present phylogenetic analyses based on genomewide single‐nucleotide polymorphisms (SNPs) of an enigmatic avian radiation, the subspecies complex of Afrocanarian blue tits (Cyanistes teneriffae). The two sister species, the Eurasian blue tit (Cyanistes caeruleus) and the azure tit (Cyanistes cyanus), constituted the out‐group. We generated a large data set of SNPs for analysis of population structure and phylogeny. We also adapted our protocol to utilize degraded DNA from old museum skins from Libya. We found strong population structuring that largely confirmed subspecies monophyly and constructed a coalescent‐based phylogeny with full support at all major nodes. The results are consistent with a recent hypothesis that La Palma and Libya are relic populations of an ancient Afrocanarian blue tit, although a small data set for Libya could not resolve its position relative to La Palma. The birds on the eastern islands of Fuerteventura and Lanzarote are similar to those in Morocco. Together they constitute the sister group to the clade containing the other Canary Islands (except La Palma), in which El Hierro is sister to the three central islands. Hence, extant Canary Islands populations seem to originate from multiple independent colonization events. We also found population divergences in a key reproductive trait, viz. sperm length, which may constitute reproductive barriers between certain populations. We recommend a taxonomic revision of this polytypic species, where several subspecies should qualify for species rank.     

Mitochondrial DNA diversity in Siberian Tatars of the Tobol-Irtysh basin

Data on the variation of the nucleotide sequence of hypervariable segment I (HVSI) and restriction fragment length polymorphism (RFLP) of the coding region of mitochondrial DNA (mtDNA) have been used to characterize the mitochondrial gene pool of Siberian Tatars of the Tobol-Irtysh basin (N = 218), one of three geographic/linguistic groups of Siberian Tatars. The gene pool of Siberian Tatars has been shown to contain both Asian and European mtDNA lineages at a ratio of 1.0 : 1.5. The mtDNA diversity of Siberian Tatars is substantially higher than that of other Turkic-speaking populations of North and Central Asia. The position of the mitochondrial gene pool of Tatars of the Tobol-Irtysh basin in the genetic space of northern Eurasia populations has been determined.     

Large-scale geographic patterns of genetic variation in Melica nutans, a widespread Eurasian woodland grass

 The geographic distribution of allozyme variation within the Eurasian boreo-nemoreal woodland grass Melica nutans L. has been investigated together with a minor subset of other Melica species. Twenty alleles were found at nine polymorphic loci in M. nutans. Allelic richness was highest in areas central in the species' European distribution, i.e. in southern Fennoscandia. High population densities, reducing the effects of genetic drift, as well as accumulation of variation through long-distance gene-flow from different marginal populations, is proposed to explain high allelic richness in this area. Several alleles showed geographic patterns in distribution and frequency variation. However, these patterns were not congruent, e.g. some alleles appear to have migrated to northern Europe from the south-west whereas others may have spread from the east. Genetic distances between geographic regions, each consisting of 2–6 populations, were generally low between all Fennoscandian, Russian and Siberian regions, but much higher between western and continental European regions. On the population level, cluster analysis grouped populations from Siberia, Russia, coastal and lowland areas in Fennoscandia and British Cumbria into one subcluster whereas other subclusters contained mainly south-west European populations or populations from almost throughout the distribution range. A scenario with several independent glacial refugia in central Europe, south-western Siberia and possibly western Norway, and subsequent colonisation of Fennoscandia mainly from the east, but with some long-distance gene-flow from central Europe, is proposed. Received April 3, 2002; accepted September 17, 2002 Published online: December 11, 2002     

Mitochondrial DNA diversity in Siberian Tatars of the Tobol-Irtysh basin

Data on the variation of the nucleotide sequence of hypervariable segment I (HVSI) and restriction fragment length polymorphism (RFLP) of the coding region of mitochondrial DNA (mtDNA) have been used to characterize the mitochondrial gene pool of Siberian Tatars of the Tobol-Irtysh basin (N = 218), one of three geographic/linguistic groups of Siberian Tatars. The gene pool of Siberian Tatars has been shown to contain both Asian and European mtDNA lineages at a ratio of 1 : 1.5. The mtDNA diversity of Siberian Tatars is substantially higher than that of other Turkic-speaking populations of North and Central Asia. The position of the mitochondrial gene pool of Tatars of the Tobol-Irtysh basin in the genetic space of northern Eurasia populations has been determined.     

Phylogeographic differentiation in the mitochondrial control region in the koala, Phascolarctos cinereus (Goldfuss 1817)

The koala, Phascolarctos cinereus, is a geographically widespread species endemic to Australia, with three currently recognized subspecies: P.c. adustus, P.c. cinereus, and P.c. victor. Intraspecific variation in the mitochondrial DNA (mtDNA) control region was examined in over 200 animals from 16 representative populations throughout the species’ range. Eighteen different haplotypes were defined in the ≈ 860 bp mtDNA control region, as determined by heteroduplex analysis/temperature gradient gel electrophoresis (HDA/TGGE). Any single population typically possessed only one or two haplotypes yielding an average within-population haplotypic diversity of 0.180 ± 0.003, and nucleotide diversity of 0.16%. Overall, mtDNA control region sequence diversity between populations averaged 0.67%, and ranged from 0% to 1.56%. Nucleotide divergence between populations averaged 0.51%, and ranged from 0% to 1.53%. Neighbour-joining methods revealed limited phylogenetic distinction between geographically distant populations of koalas, and tentative support for a single evolutionarily significant unit (ESU). This is consistent with previous suggestions that the morphological differences formalized by subspecific taxonomy may be interpreted as clinal variation. Significant differentiation in mtDNA-haplotype frequencies between localities suggested that little gene flow currently exists among populations. When combined with microsatellite analysis, which has revealed substantial differentiation among koala populations, we conclude that the appropriate short-term management unit (MU) for koalas is the local population.     

Genetic passportization and identification of Siberian cranes (Grus leucogeranus Pallas) in captivity

The genetic diversity of the founders of an artificial population of the Siberian crane Grus leucogeranus Pallas (rare species of cranes) was characterized using 10 microsatellite loci. It was established that the allelic diversity (on average, 5.9 alleles per locus) and genic (H _O = 0.739) diversity of the Siberian crane is rather high and comparable with the estimations for natural populations of different crane species. Genetic passportization of the birds (119 individuals) from the register of the Siberian crane International Studbook was carried out at the initial stage. The efficiency of genetic passportization for individual identification, identification of the origin, paternity analysis, and exclusion of inbreeding was demonstrated in Siberian cranes under natural mating and artificial insemination. Cases of natural reproduction in pairs of Siberian cranes imprinted to the human and continuous storage of spermatozoa in the female reproductive ducts were registered.     

Hierarchical analyses of genetic variation of samples from breeding and feeding grounds confirm the genetic partitioning of northwest Atlantic and South Atlantic populations of swordfish (Xiphias gladius L.)

In species with high migratory potential, the genetic signal revealing population differentiation is often obscured by population admixture. To our knowledge, the explicit comparison of genetic samples from known spawning and feeding areas has not been conducted for any highly migratory pelagic fish species. This study examines the geographic heterogeneity of swordfish mitochondrial DNA (mtDNA) lineages within the Atlantic Ocean using 330 base pairs of sequence of the control region from 480 individuals. Hierarchical analyses of sequence variation were conducted to test whether samples from areas identified as the corresponding spawning and feeding grounds for the northwest (NW) Atlantic (Caribbean and Georges Banks-US northeast) and the South Atlantic (Brazil-Uruguay and Gulf of Guinea), were more closely related to each other than to samples from any other region, including the Mediterranean Sea, the Indian Ocean, and the Pacific Ocean. Phylogeographic analyses reveal that swordfish mtDNA phylogeny is characterized by incomplete lineage sorting and secondary contact of two highly divergent clades. However, despite this complex phylogenetic signature, results from an analysis of nucleotide diversity and from an analysis of molecular variance (AMOVA) were for the most part concordant and indicate that NW Atlantic and South Atlantic swordfish belong to separate populations. The mtDNA distinctiveness of NW Atlantic and South Atlantic swordfish populations is indicative of philopatric behavior in swordfish towards breeding and feeding areas.