A Comprehensive Study of Genic Variation in Natural Populations of Drosophila Melanogaster. IV. Mitochondrial DNA Variation and the Role of History Vs. Selection in the Genetic Structure of Geographic Populations

Preliminary studies with restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in natural populations of Drosophila melanogaster revealed considerable variation in terms of nucleotide sequence and overall size. In this report we present data from more isofemale lines and more restriction enzymes, and explore the utility of the data in inferring a colonization history of this species. Size variation in the noncoding A + T-rich region is particularly plentiful, with size variants occurring in all restriction site haplotypes in all populations. We report here classes of small-scale mobility polymorphisms (apparent range of 20 bp) in specific restriction fragments in the coding region. The variation in one such fragment appears to be generated even more rapidly than in the noncoding region. On the basis of the distribution of restriction site haplotypes, the species range can be divided into three major regions along longitudinal lines: Euro-African populations are the most diverse and are taken to be oldest; Far East populations have a complex distribution of haplotypes; Western Hemisphere populations are the least diverse and are interpreted to be the youngest. The history inferred from mtDNA alone is remarkably similar to one based on several nuclear markers. The mtDNA haplotype distribution is also very different from that of allozymes in these same populations. We interpret this as further evidence that natural selection is still the most parsimonious explanation for the parallel latitudinal allozyme clines in this species.     

Present and past depth distribution of bladderwrack (Fucus vesiculosus) in the Baltic Sea

This study aimed to (1) assess the present depth distribution of Fucus vesiculosus in the Baltic Sea and evaluate differences between districts and (2) assess long-term and recent changes in depth distribution and evaluate reasons for such changes. This was done through compilation and analysis of existing data (3356 obs.). Depth limits were shallowest in the Kattegat, the Danish Belts and the Øresund (∼1.5 m on average), located at the entrance of the Baltic Sea and markedly deeper in the central and inner parts of the Baltic (up to ∼4.5 m on average). This increase in depth limits to some extent matched the decline in salinity and may in part be explained by reduced competition when species diversity decreases successively along the Baltic salinity gradient. In the central and inner Baltic Sea, Secchi depths explained part of the variation (16%) in depth limits and the majority (85%) of the variation in maximum attainable depth limits whereas at the entrance of the Baltic Secchi depths explained a negligible part of the variation (∼1%). In most districts, depth limits moved upwards during the 20th century. In many cases this happened during or shortly after the 1960s/1970s, and was most likely due to eutrophication.     

Haplotype Frequency Distribution in Northeastern European Saduria entomon (Crustacea: Isopoda) Populations. A Phylogeographic Approach

The distribution pattern of mtDNA haplotypes in distinct populations of the glacial relict crustacean Saduria entomon was examined to assess phylogeographic relationships among them. Populations from the Baltic, the White Sea and the Barents Sea were screened for mtDNA variation using PCR‐based RFLP analysis of a 1150 bp fragment containing part of the CO I and CO II genes. Five mtDNA haplotypes were recorded. An analysis of geographical heterogeneity in haplotype frequency distributions revealed significant differences among populations. The isolated populations of S. entomon have diverged since the retreat of the last glaciation. The geographical pattern of variation is most likely the result of stochastic (founder effect, genetic drift) mechanisms and suggests that the haplotype differentiation observed is probably older than the isolation of the Baltic and Arctic seas.     

Population structure of flounder (Platichthys flesus) in the Baltic Sea: differences among demersal and pelagic spawners

We found significant population structure and isolation by distance among samples of flounder (Platichthys flesus) in the Baltic, Kattegat and Skagerrak seas using microsatellite genetic markers. This pattern was almost entirely due to a difference between flounder that have demersal spawning in the northern Baltic, as compared to pelagic spawners in the southern Baltic and on the west coast of Sweden. Among demersal spawners we found neither genetic differentiation nor any isolation by distance among sampling sites. We speculate that demersal flounder are descendants of a population that colonized the Baltic previous to pelagic spawners. The demersal flounder may thus have had longer time to adapt to the low salinity in the Baltic, and accordingly display egg characteristics that make it possible to reproduce at the low salinity levels in the northern Baltic. Among pelagic spawners significant isolation by distance was detected. Pelagic spawners have previously been shown to display clinal variation in egg size, which allows them to float also at the moderate salinity levels up to the region north of the island Bornholm. Management units for harvesting should ideally be based on true biological populations, and for the commercially important flounder up to 15 different management stocks in the Baltic have been suggested. We could not find a population genetic foundation for such a high number of management units, and our data suggest three management units: the northern Baltic (demersal populations), southern Baltic with the Oresund straits and the most northwestern sampling sites (Skagerrak, Kattegat and North Sea).     

Salinity gradient of the Baltic Sea limits the reproduction and population expansion of the newly invaded comb jelly Mnemiopsis leidyi

The recent invasion of the comb jelly Mnemiopsis leidyi into northern European waters is of major public and scientific concern. One of the key features making M. leidyi a successful invader is its high fecundity combined with fast growth rates. However, little is known about physiological limitations to its reproduction and consequent possible abiotic restrictions to its dispersal. To evaluate the invasion potential of M. leidyi into the brackish Baltic Sea we studied in situ egg production rates in different regions and at different salinities in the laboratory, representing the salinity gradient of the Baltic Sea. During October 2009 M. leidyi actively reproduced over large areas of the Baltic Sea. Egg production rates scaled with animal size but decreased significantly with decreasing salinity, both in the field (7-29) and in laboratory experiments (6-33). Temperature and zooplankton, i.e. food abundance, could not explain the observed differences. Reproduction rates at conditions representing the Kattegat, south western and central Baltic Sea, respectively, were 2.8 fold higher at the highest salinities (33 and 25) than at intermediate salinities (10 and 15) and 21 times higher compared from intermediate to the lowest salinity tested (6). Higher salinity areas such as the Kattegat, and to a lower extent the south western Baltic, seem to act as source regions for the M. leidyi population in the central Baltic Sea where a self-sustaining population, due to the low salinity, cannot be maintained.     

Maternal and paternal genetic variation in Estonian local horse breeds in the context of geographically adjacent and distant Eurasian breeds

The maternal and paternal genetic variation of horse breeds from the Baltic Sea region, including three local Estonian breeds, was assessed and compared with that of Altai and Yakutian horses. In the mtDNA D‐loop region, 72 haplotypes assigned to 20 haplogroups in the nine breeds were detected. In Estonian local breeds, 38 mtDNA haplotypes were found, and five of them were shared by the three breeds. More than 60% of all identified haplotypes were rare. Compared with the Estonian Native and Estonian Heavy Draught breeds, a higher haplotypic diversity was found in the Tori breed (h = 0.969). Moreover, four haplotypes shared among Finnish and Estonian local horse breeds indicated ancient ancestry, and of these, H30 (haplogroup D3) showed global sharing and genetic links between modern Baltic Sea region and Siberian horses, specifically. The studied breed set showed high variability in maternal inheritance and mixed patterns of the international and native breeds of the Siberian and Baltic regions. No variation was found in paternally inherited markers among horse breeds in the Baltic Sea region.     

Absence of population structure of turbot (Psetta maxima) in the Baltic Sea

We found low, albeit significant, genetic differentiation among turbot (Psetta maxima) in the Baltic Sea but in contrast to earlier findings we found no evidence of isolation by distance. In fact temporal variation among years in one locality exceeded spatial variation among localities. This is an unexpected result since adult turbot are sedentary and eggs are demersal at the salinities occurring in the Baltic. Our findings are most likely explained by the fact that we sampled fish that were born after/during a large influx of water to the Baltic Sea, which may have had the consequence that previously locally and relatively sedentary populations became admixed. These results suggest that populations that colonize relatively variable habitats, like the Baltic, face problems. Any adaptations to local conditions that may build up during stable periods may quickly become eroded when conditions change and/or when populations become admixed. Our results indicate that the ability of turbot to survive and reproduce at the low salinity in the Baltic is more likely due to phenotypic plasticity than a strict genetic adaptation to low salinity.     

Mitochondrial Control Region and microsatellite analyses on harbour porpoise (Phocoena phocoena) unravel population differentiation in the Baltic Sea and adjacent waters

The population status of the harbour porpoise (Phocoena phocoena) in the Baltic area has been a continuous matter of debate. Here we present the by far most comprehensive genetic population structure assessment to date for this region, both with regard to geographic coverage and sample size: 497 porpoise samples from North Sea, Skagerrak, Kattegat, Belt Sea, and Inner Baltic Sea were sequenced at the mitochondrial Control Region and 305 of these specimens were typed at 15 polymorphic microsatellite loci. Samples were stratified according to sample type (stranding vs. by-caught), sex, and season (breeding vs. non-breeding season). Our data provide ample evidence for a population split between the Skagerrak and the Belt Sea, with a transition zone in the Kattegat area. Among other measures, this was particularly visible in significant frequency shifts of the most abundant mitochondrial haplotypes. A particular haplotype almost absent in the North Sea was the most abundant in Belt Sea and Inner Baltic Sea. Microsatellites yielded a similar pattern (i.e., turnover in occurrence of clusters identified by STRUCTURE). Moreover, a highly significant association between microsatellite assignment and unlinked mitochondrial haplotypes further indicates a split between North Sea and Baltic porpoises. For the Inner Baltic Sea, we consistently recovered a small, but significant separation from the Belt Sea population. Despite recent arguments that separation should exceed a predefined threshold before populations shall be managed separately, we argue in favour of precautionary acknowledging the Inner Baltic porpoises as a separate management unit, which should receive particular attention, as it is threatened by various factors, in particular local fishery measures.     

Diversity of Aphanizomenon flos-aquae (cyanobacterium) populations along a Baltic Sea salinity gradient

Colony-forming cyanobacteria of the genus Aphanizomenon form massive blooms in the brackish water of the Baltic Sea during the warmest summer months. There have been recent suggestions claiming that the Baltic Sea Aphanizomenon species may be different from Aphanizomenon flos-aquae found in lakes. In this study, we examined variability in the morphology and 16S-23S rRNA internal transcribed spacer (ITS) sequences of A. flos-aquae populations along a salinity gradient from a string of lakes to a fjord-like extension of the Baltic Sea to the open Baltic Sea. Morphological differences among the populations were negligible. We found that the Baltic Sea was dominated (25 out of 27 sequences) by one ITS1-S (shorter band of ITS 1 [ITS1]) genotype, which also was found in the lakes. The lake populations of A. flos-aquae tended to be genetically more diverse than the Baltic Sea populations. Since the lake ITS1-S genotypes of A. flos-aquae are continuously introduced to the Baltic Sea via inflowing waters, it seems that only one ITS1 genotype is able to persist in the Baltic Sea populations. The results suggest that one of the ITS1-S genotypes found in the lakes is better adapted to the conditions of the Baltic Sea and that natural selection removes most of the lake genotypes from the Baltic Sea A. flos-aquae populations.     

Population genetic structure of mussels from the Baltic Sea

In a macrogeographic survey, the population genetic structure of mussels from various regions of the Baltic Sea, a large semi-enclosed brackish-water basin, was examined with reference toMytilus edulis andM. galloprovincialis samples from the North Sea, Irish coast and southern Portugal. Electrophoretically detectable variation was analysed at 6 polymorphic enzyme loci (Ap, Est-D, Lap-2, Odh, Pgi andPgm). Evidence was provided of a remarkably large amount of biochemical genetic differentiation among ecologically and morphologically divergent mussel populations in the Baltic. Patterns of allele frequencies in low-salinity populations from the area of the Baltic Proper were demonstrated to be widely homogeneous but contrast strongly with those of the western Baltic, the latter resembling populations from marine habitats of the North Sea. Associated with a pronounced salinity gradient, the spatial heterogeneity in gene-pool structure is indicated by steep clines of allele frequency changes in the area of the eastern Danish isles. The adaptive significance of the observed allozymic variation is suggested. From genetic distance estimates, the subdivision of population structure is discussed in relation to the significant amount of differentiation detected withinMytilus populations to date and to the evolutionary time required for the divergence of Baltic mussel populations. The allozymic data provide evidence for the genetic distinctiveness of mussels from the low-salinity areas of the Baltic. Their position at the specific or subspecific level of classification requires further consideration.     

What is the effect of climate change on marine fish biodiversity in an area of low connectivity,the Baltic Sea?

Aim Climate change could result in an increase in species richness because large‐scale biogeography suggests that more species could be gained from equatorial regions than may be lost pole‐ward. However, the colonization of newly available habitat may lag behind the rate dictated by climatic warming if there exists of a lack of connectivity between ‘donor’ and receiving areas. The objective of this study was to compare how regional warming affected the biodiversity of marine fish in areas that differed in their connectivity in the Baltic Sea. Location North‐east Atlantic, Kattegat and Baltic Sea. Methods The total species richness and the mean species richness from scientific surveys were related to changes in temperature and salinity. Changes in the extent of the distribution of individual fish species were related to the latitudinal distribution, salinity tolerance, maximum body size and exploitation status to assess to what extent climate change and fishing impacts could explain changes in species richness in the Baltic. Results Rising temperatures in the well‐connected Kattegat correlated to an increase in the species richness of fish, due to an increase in low‐latitude species. Unexpectedly, species richness in the poorly connected Baltic Sea also increased. However, the increase seems to be related to higher salinity rather than temperature and there was no influx of low‐latitude species. Main conclusions These results do not support the hypothesis that low‐connectivity areas are less likely to see increases in species richness in response to warming. This indicates that the effect of climate change on biodiversity may be more difficult to predict in areas of low connectivity than in well‐connected areas.     

Genetic variation within and among North Atlantic and Baltic populations of the benthic alga Phycodrys rubens (Rhodophyta)

Genetic variation was examined within and among North Atlantic, North Sea and Baltic populations of the benthic red alga Phycodrys rubens using allozymes and random amplified polymorphic DNA (RAPD) markers. On western and eastern North Atlantic coasts distinct allozyme types were found, with the exception of western Newfoundland where East and West Atlantic types co-occur. Along the European coasts, two genetic groups were distinguished by fixed allelic differences: an outer oceanic group and a North Sea/Baltic group. The two genetic types co-occur in the Skagerrak and Kattegat region. Reproductive isolation between the two types is suggested by the lack of hybrids in the overlap zones, and they may therefore represent sibling species. Unexpectedly, an analysis of RAPD variation was unable to recover the two cryptic species identified using allozymes. Within-population RAPD variation was similar to or greater than between-population variation. The lack of structure in the RAPD data cannot be attributed solely to technical artefacts of the method but appears to reflect real biological variability. Within-population genomic polymorphisms caused by frequent mutational events are discussed, as are high amounts of genetic drift and possible disruptive selection brought about by stressed habitats. Finally, Baltic and extra-Baltic salinity ecotypes are known to exist in P. rubens. However, no correlation between ecotypic variation and allozyme groups was detected.     

Microsatellite and mtDNA analysis of the population structure of grey seals (Halichoerus grypus) from three breeding areas in the Baltic Sea

The growing number of grey seals in the Baltic Sea has led to a dramatic increase in interactions between seals and fisheries. The conflict has become such a problem that hunting was introduced in Finland in 1998 and the Swedish Environment Protection Agency recommended a cull of grey seals starting in 2001. Culling has been implemented despite the lack of data on population structure. Low levels of migration between regions would mean that intensive culling in specific geographic areas would have disproportionate effects on local population structure and genetic diversity. We used eight microsatellite loci and a 489 bp section of the mtDNA control region to examine the genetic variability and differentiation between three breeding sites in the Baltic Sea and two in the UK. We found high levels of genetic variability in all sampled Baltic groups for both the microsatellites and the control region. There were highly significant differences in microsatellite allele frequencies between all three Baltic breeding sites and between the Baltic sites and the UK sites. However, there were no significant differences in mtDNA control region haplotypes between the Baltic sites. This genetic substructure of the Baltic grey seal populations should be taken into consideration when managing the seal population to prevent the hunting regime from having an adverse effect on genetic diversity by setting hunting quotas separately for the different subpopulations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Biodiversity gradient in the Baltic Sea: a comprehensive inventory of macrozoobenthos data

In the Helsinki Commission Red List project 2009–2012, taxonomic and distributional data of benthic (macro) invertebrates were compiled by the present authors in a comprehensive checklist of the Baltic Sea fauna. Based on the most recent and comprehensive data, this paper presents the diversity patterns observed among benthic invertebrates in the Baltic Sea. As expected, the total number of species per sub-region generally declined along the salinity gradient from the Danish Straits to the northern Baltic Sea. This relationship is well known from the Baltic Sea and has resulted in a general assumption of an exponentially positive relationship between species richness and salinity for marine species, and a negative relationship for freshwater species. In 1934, Remane produced a diagram to describe the hypothetical distribution of benthic invertebrate diversity along a marine–freshwater salinity gradient. Our results clearly indicated the validity of this theory for the macrozoobenthic diversity pattern within the Baltic Sea. Categorisation of sub-regions according to species composition showed both separation and grouping of some sub-regions and a strong alignment of similarity patterns of zoobenthic species composition along the salinity gradient.     

Local adaptation and oceanographic connectivity patterns explain genetic differentiation of a marine diatom across the North Sea–Baltic Sea salinity gradient

Drivers of population genetic structure are still poorly understood in marine micro‐organisms. We exploited the North Sea–Baltic Sea transition for investigating the seascape genetics of a marine diatom, Skeletonema marinoi. Eight polymorphic microsatellite loci were analysed in 354 individuals from ten locations to analyse population structure of the species along a 1500‐km‐long salinity gradient ranging from 3 to 30 psu. To test for salinity adaptation, salinity reaction norms were determined for sets of strains originating from three different salinity regimes of the gradient. Modelled oceanographic connectivity was compared to directional relative migration by correlation analyses to examine oceanographic drivers. Population genetic analyses showed distinct genetic divergence of a low‐salinity Baltic Sea population and a high‐salinity North Sea population, coinciding with the most evident physical dispersal barrier in the area, the Danish Straits. Baltic Sea populations displayed reduced genetic diversity compared to North Sea populations. Growth optima of low salinity isolates were significantly lower than those of strains from higher native salinities, indicating local salinity adaptation. Although the North Sea–Baltic Sea transition was identified as a barrier to gene flow, migration between Baltic Sea and North Sea populations occurred. However, the presence of differentiated neutral markers on each side of the transition zone suggests that migrants are maladapted. It is concluded that local salinity adaptation, supported by oceanographic connectivity patterns creating an asymmetric migration pattern between the Baltic Sea and the North Sea, determines genetic differentiation patterns in the transition zone.     

An environmental gradient dominates ecological and genetic differentiation of marine invertebrates between the North and Baltic Sea

Environmental gradients have emerged as important barriers to structuring populations and species distributions. We set out to test whether the strong salinity gradient from the marine North Sea to the brackish Baltic Sea in northern Europe represents an ecological and genetic break, and to identify life history traits that correlate with the strength of this break. We accumulated mitochondrial cytochrome oxidase subunit 1 sequence data, and data on the distribution, salinity tolerance, and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta, and Gastrotricha. We included seven non‐native species covering a broad range of times since introduction, in order to gain insight into the pace of adaptation and differentiation. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times, and migration rates between North and Baltic Sea populations, and analyzed correlations between genetic and life history data. The majority of investigated species is either genetically differentiated and/or adapted to the lower salinity conditions of the Baltic Sea. Species exhibiting population structure have a range of patterns of genetic diversity in comparison with the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea. Two of the non‐native species showed signs of genetic differentiation, their times since introduction to the Baltic Sea being about 80 and >700 years, respectively. Our results indicate that the transition from North Sea to Baltic Sea represents a genetic and ecological break: The diversity of genetic patterns points toward independent trajectories in the Baltic compared with the North Sea, and ecological differences with regard to salinity tolerance are common. The North Sea–Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non‐native species.     

Postglacial recolonization patterns and genetic relationships among whitefish (Coregonus sp.) populations in Denmark, inferred from mitochondrial DNA and microsatellite markers

The genetic relationships among morphologically and geographically divergent populations of whitefish (genus: Coregonus ) from Denmark and the Baltic Sea region were studied by analysis of microsatellites and polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis of mitochondrial DNA (mtDNA) segments. The endangered North Sea houting (classified as C. oxyrhynchus ) differs morphologically and physiologically from other Danish whitefish ( C. lavaretus ). However, limited divergence of North Sea houting was observed both at the level of mtDNA and microsatellites. The implications of these results for the conservation status of North Sea houting are discussed in the light of current definitions of evolutionary significant units. Both mtDNA and microsatellite data indicated that postglacial recolonization by C. lavaretus in Denmark was less likely to have taken place from the Baltic Sea. Instead, the data suggested a recent common origin of all Danish whitefish populations, including North Sea houting, probably by recolonization via the postglacial Elbe River system. Estimates of genetic differentiation among populations based on mtDNA and microsatellites were qualitatively different. In addition, for both classes of markers analyses of genetic differentiation yielded different results, depending on whether molecular distances between alleles or haplotypes were included.     

Genetic divergence and phylogeographic relationships among european perch (Perca fluviatilis) populations reflect glacial refugia and postglacial colonization

We used the widely distributed freshwater fish, perch (Perca fluviatilis), to investigate the postglacial colonization routes of freshwater fishes in Europe. Genetic variability within and among drainages was assessed using mitochondrial DNA (mtDNA) D-loop sequencing and RAPD markers from 55 populations all over Europe as well as one Siberian population. High level of structuring for both markers was observed among drainages and regions, while little differentiation was seen within drainages and regions. Phylogeographic relationships among European perch were determined from the distribution of 35 mtDNA haplotypes detected in the samples. In addition to a distinct southern European group, which includes a Greek and a southern Danubian population, three major groups of perch are observed: the western European drainages, the eastern European drainages including the Siberian population, and Norwegian populations from northern Norway, and western side of Oslofjord. Our data suggest that present perch populations in western and northern Europe were colonized from three main refugia, located in southeastern, northeastern and western Europe. In support of this, nested cladistic analysis of mtDNA clade and nested clade distances suggested historical range expansion as the main factor determining geographical distribution of haplotypes. The Baltic Sea has been colonized from all three refugia, and northeastern Europe harbours descendants from both eastern European refugia. In the upper part of the Danube lineages from the western European and the southern European refugia meet. The southern European refugium probably did not contribute to the recolonization of other western and northern European drainages after the last glaciation. However, phylogenetic analyses suggest that the southern European mtDNA lineage is the most ancient, and therefore likely to be the founder of all present perch lineages. The colonization routes used by perch probably also apply to other freshwater species with similar distribution patterns.     

Adaptive and Neutral Genetic Variation and Colonization History of Atlantic Salmon, Salmo salar

Synopsis I combined neutral microsatellite markers with the major histocompatibility complex (MHC) class IIB to study genetic differentiation and colonization history in Atlantic salmon, Salmo salar, in the Baltic Sea and in the north-eastern Atlantic. Baltic salmon populations have lower levels of microsatellite genetic variation, in terms of heterozygosity and allelic richness than Atlantic populations, confirming earlier findings with other genetic markers, suggesting that the Baltic Sea populations have been exposed to genetic bottlenecks, most likely at a founding event. On the other hand, the level of MHC variation was similar in the Baltic and in the north-eastern Atlantic, indicating that positive balancing selection has increased the level of MHC-variation. Both microsatellite and MHC class IIB genetic variation give strong support to the hypothesis that the Baltic salmon are of a biphyletic origin, the southern population in this study is strongly differentiated from both the northern Baltic salmon populations and from the north-eastern Atlantic populations. Salmon may have colonized the northern Baltic Sea either from the south, via the so called “N?rke strait” or from the north, via a proposed historical connection between the White Sea and the northern Baltic. At microsatellites, no significant isolation-by distance was found at either colonization route. At the MHC, populations were significantly isolated by distance when assuming that colonization occurred via the “N?rke strait”.