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.     

Micro- and macrogeographical genetic structure of colonies of naked mole-rats Heterocephalus glaber

Patterns of genetic structure in eusocial naked mole-rat populations were quantified within and among geographically distant populations using multilocus DNA fingerprinting and mitochondrial DNA (mtDNA) sequence analysis. Individuals within colonies were genetically almost monomorphic, sharing the same mtDNA control region haplotype and having coefficients of band sharing estimated from DNA fingerprints ranging from 0.93 to 0.99. Family analysis of a hybrid captive colony of naked mole-rats with increased levels of genetic variability using multilocus DNA fingerprinting gave results consistent with Mendelian inheritance, and has revealed for the first time that multiple paternity can occur. In a survey of wild colonies from Ethiopia, Somalia and locations in northern and southern Kenya, we have examined mtDNA control region sequence variation in 42 individuals from 15 colonies, and together with multilocus DNA fingerprinting and mtDNA cytochrome- b sequence analysis in selected individuals have shown that these populations show considerable genetic divergence. Most of the variance in sequence divergence was found to be between geographical locations (Φ_ct= 0.68) and there was a significant correlation between sequence divergence and geographical separation of haplotypes. Six colonies from Mtito Andei in southern Kenya shared the same control region haplotype, suggesting a recent common maternal ancestor. In contrast, out of four colonies at Lerata in north Kenya, three haplotypes were identified, and phylogenetic analysis suggests that this area may be a zone where two distinct lineages are in close proximity. Genetic distances were maximal between Ethiopian and southern Kenyan populations at 5.8% for cytochrome- b , and are approaching interspecific values seen between other Bathyergids.     

Mitochondrial DNA haplotypes indicate two postglacial re‐colonization routes of the spruce bark beetle Ips typographus through northern Europe to Scandinavia

Species in northern Europe re‐colonized the region after the last glacial maximum via several routes, which could have lingering signatures in current intraspecific trait variation. The spruce bark beetle, Ips typographus, occurs across Europe, and biological differences have been found between southern and northern Scandinavian populations. However, the postglacial history of I. typographus in Scandinavia has not been previously studied at a fine geographical scale. Therefore, we collected specimens across northern Europe and analysed the genetic variation in a quite large mitochondrial fragment (698 bp). A high genetic diversity was found in some of the most northern populations, in the Baltic States, Gotland and central Europe. Detected genetic and phylogeographic structures suggest that I. typographus re‐colonized Scandinavia via two pathways, one from the northeast and one from the south. These findings are consistent with the re‐colonization history of its host plant, Picea abies. However, we observed low haplotype and nucleotide diversity in southern Scandinavian populations of I. typographus, indicating that (unlike P. abies) it did not disperse across the Baltic Sea in multiple events. Further, the divergence among Scandinavian populations was shallow, conflicting with a scenario where I. typographus expanded concurrently with its host plant from a ‘cryptic refugium’ in the northwest.     

Dispersal routes and species identification of freshwater animals in Northern Europe: A review of molecular evidence

According to genetic data, North European freshwater areas were colonized from refugia along the eastern Atlantic coast, in southern and eastern basins of Baltic Sea, in Siberia, North America, and areas of the Caspian and Black seas. Probably, a refugium also existed in Southern Norway. Colonization from the sea also took place. The taxonomic position of some forms, such as members of the complex groups of Arctic chars and coregonids, was refined in the course of combined studies including morphological analysis and molecular markers.     

Plastid DNA haplotype variation in Dactylorhiza incarnata (Orchidaceae): evidence for multiple independent colonization events into Scandinavia

The early marsh orchid, Dactylorhiza incarnata (L.) Soó s. l., grows in medium-rich to rich fens and marshes over much of Europe and parts of Asia. The species is highly polymorphic and different forms may grow together at the same site. In the present study, I tested the hypothesis that these forms represent different migrant populations that have colonized Scandinavia independently of each other, possibly from different source areas. Accessions from Scandinavia and elsewhere were screened for variation at three size-variable plastid marker loci, one polyA repeat, one polyA-polyTA-polyT repeat and one 9 bp indel. Ten haplotypes were defined on basis on the combined variation pattern. The common occurrence of several haplotypes in southern Scandinavia and adjacent areas to the south and the east of the Baltic Sea suggests that D. incarnata has been dispersed on repeated occasions across the Baltic. Also, there was some correlation between haplotype composition and morphological form on the island of Gotland, in agreement with the independent colonization hypothesis. Material from northernmost Sweden, Finland and northwest Russia was fixed for a single widespread haplotype, indicating that populations in this area are located farther away from the Pleistocene refugia. Dactylorhiza incarnata ssp. lobelii from southwest Norway was characterized by a haplotype that was not encountered elsewhere in Scandinavia. Given its proximity to British populations dominated by the same haplotype, it is suggested that D. incarnata ssp. lobelii was established independently of the other Scandinavian populations, from coastal refugia located in western Europe.     

Coastal and freshwater pikeperch (Sander lucioperca) populations differ genetically in the Baltic Sea basin

Microsatellite DNA based analysis of the pattern of genetic diversity among three coastal and five freshwater populations of pikeperch Sander lucioperca in the northern part of the Baltic Sea drainage basin indicated marked genetic differentiation between the coastal and lake populations. The F(st) between these population groups was as high as 0.25 and R(st) =0.32. In general, the lake populations showed higher genetic diversity than the coastal ones. In terms of genetic distance, the three coastal populations (Vanhankaupunginlahti, V?stanfj?rd and Taivassalo) grouped tightly together. The freshwater samples formed a looser group, in which the northern Lake Kemij?rvi showed greater distance from the southern lakes than these did from each other. The two lake populations originally established through stockings (Lakes Painio and Averia) grouped near to their source population of Lake Lohjanj?rvi and their diversity level was nearly the same. Safeguarding the unique Baltic coastal populations of S. lucioperca against gene flow from increasing hatchery releases using freshwater S. lucioperca should be a high management priority.     

The ghost of hybrids past: fixation of arctic charr (Salvelinus alpinus) mitochondrial DNA in an introgressed population of lake trout (S. namaycush)

Complete fixation of arctic charr ( Salvelinus alpinus ) mitochondrial DNA (mtDNA) was observed in a southern Québec population of lake trout ( S. namaycush ). This introgressed population otherwise appeared to be normal with regard to lake trout morphology and three species-diagnostic microsatellite loci. Arctic charr do not occur in the area, suggesting that the hybridization event was prehistoric. Of several possible hypotheses, the most plausible explanation for this aberrant population is that hybridization occurred in situ soon after deglaciation, with repeated backcrossing of hybrids with lake trout. Fixation of S. alpinus mtDNA in the population may have occurred either by chance (drift) or selection, although indirect evidence and data from similarly introgressed brook trout ( S. fontinalis ) populations in the region suggest that selection favouring the S. alpinus mitochondrial type and/or associated nuclear genes may have been involved.     

Dispersal of the Ponto-Caspian amphipod Echinogammarus ischnus: invasion waves from the Pleistocene to the present

The geographical range of the amphipod crustacean Echinogammarus ischnus has expanded over the past century from the Ponto-Caspian region to Western Europe, the Baltic Sea, and the Great Lakes of North America. The present study explores the phylogeographic patterns of this amphipod across its current distribution, based on an examination of nucleotide diversity in the mitochondrial cytochrome c oxidase subunit I (COI) gene. Marked genetic divergence exists among populations of E. ischnus from the Black and Caspian Seas, as well as those from the drainage system of the Black Sea. This divergence suggests the prolonged geographic isolation of these native populations, reflecting the limited dispersal capability of E. ischnus. By contrast, invading populations are characterized by a lack of genetic variation; a single mitochondrial genotype of Black Sea origin has colonized sites from the Rhine River to North America. The dispersal pattern in E. ischnus is very similar to that in the Ponto-Caspian cladoceran Cercopagis pengoi. Despite their contrasting life history strategies, these invading species followed the same route of invasion from the northern Black Sea to the Baltic Sea region, and subsequently to North America.     

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”.     

Multilocus DNA fingerprinting detects population differentiation in the outbred and abundant fish species Poecilia latipinna

Several workers have suggested that multilocus multilocus variable number of tandem repeat (VNTR) based 'DNA fingerprints' are not useful in detecting differentiation among outbred populations. They suggest that the extremely high mutation rates and complexity associated with multilocus VNTR fragments make detection of interpopulation differences against a background of extremely high intrapopulation variation unlikely. This paper shows that DNA fingerprinting with the multilocus VNTR probes (GACA)₄ and (CT)₉ reveal significant population differences in VNTR frequencies between Florida and Georgia populations of the outbred, abundant and vagile fish species Poecilia latipinna. Differences in mutation rates among some VNTR loci may account for the ability to detect interpopulation differentiation with these probes. These results suggest that appropriate species/probe combinations would allow investigations of population structure on a microgeographical scale even in outbred species with multilocus VNTR probes where less-sensitive techniques have failed.     

Geographical patterns in the population genetics of Atlantic salmon, Salmo salar L., on U.S.S.R. territory, as evidence for colonization routes

From data on interpopulation genetic structure of the Atlantic salmon from the rivers of the Barents, White and Baltic Sea basins on U.S.S.R. territory, it is suggested that salmon colonized the Onega and Pechora River basins from the Baltic drainage as the last ice-sheet receded, and that the Kola Peninsula rivers were colonized separately from the Barents Sea area.     

Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology

Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction‐site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare‐cutting restriction enzymes and strict size selection of the library allowing sequencing of a relatively small number of genomic fragments with high sequencing depth. We applied this approach to a common freshwater fish species, the Eurasian perch (Perca fluviatilis L.), and generated over 2.2 MB of novel sequence data consisting of ~17 000 contigs, identified 1259 single nucleotide polymorphisms (SNPs). We also estimated genetic differentiation between the DNA pools from freshwater (Lake Peipus) and brackish water (the Baltic Sea) populations and identified SNPs with the strongest signal of differentiation that could be used for robust individual assignment in the future. This work represents an important step towards developing genomic resources and genetic tools for the Eurasian perch. We expect that our ddRAD sequencing protocol for semiconductor sequencing technology will be useful alternative for currently available RAD protocols.     

Postglacial colonization of Northern Europe by distinct phylogeographic lineages of the bullhead, Cottus gobio

Three major phylogeographic lineages of the cottid fish Cottus gobio (bullhead) were identified in northern Europe from mitochondrial DNA sequences and allozyme data. The largely separate freshwater distributions of the lineages demonstrate distinct postglacial colonization histories. West of the Baltic Sea, Swedish lakes were invaded from the southwest (Germany). Another, eastern lineage has colonized the inland waters northeast and east of the Baltic, from refugia in northwest Russia; this lineage comprises a distinct subgroup found only from Estonia. The third lineage, found south and southeast of the Baltic, probably descended from rivers draining to the Black Sea from the north (e.g. Dnepr). In coastal waters of the Baltic Sea, and in near-coast inland waters, the lineages are now found intermixed in various combinations. The alternating fresh- and saltwater phases of the Baltic basin have variously enabled and disabled the use of coastal waters as colonization routes. Hypotheses on the chronology of dispersal and lineage mixing can be based on the distribution of the marker genes and the paleohydrographical record. The diversity of the Fennoscandian bullhead thus comprises anciently diverged (probably mid-Pleistocene) refugial lineages that in their freshwater range constitute distinct evolutionarily significant units. The thorough mixing of the various genomic origins in and around the Baltic, however, refutes the controversial view of distinct species status for the western and eastern ('Cottus koshewnikowi') bullheads. The postglacial contact of the lineages has created new diversity that cannot be interpreted in a conventional hierarchical framework of taxonomic or conservation units.     

Locomotory capacity of Baltic Sea and freshwater populations of the threespine stickleback (Gasterosteus aculeatus)

Two freshwater populations and one marine population (Baltic Sea) of threespine stickeback (Gasterosteus aculeatus) from Northeastern Germany were studied with regard to locomotory capacity: sustained swimming performance, activities of key enzymes in axial muscle, pectoral fin muscle and heart, and morphology. We postulated that life history differences between migratory Baltic Sea and resident freshwater populations could have led to a divergence in their locomotory capacity. The activity of citrate synthase (CS) in pectoral muscle correlated with critical swimming speed. Critical swimming speed, aerobic and anaerobic capacity of the pectoral fin muscle were population-specific. The Baltic Sea sticklebacks had a higher locomotory capacity (activity of CS in pectoral muscle, critical swimming speed) than sticklebacks of one freshwater population. However, another freshwater population expressed a similar locomotory capacity as the Baltic Sea population. In addition, Baltic Sea sticklebacks had a greater mass and lower anaerobic capacity of the pectoral fin muscle than the freshwater sticklebacks. The results are interpreted as an indication of a proceeding divergence between marine and resident freshwater populations and between freshwater populations of G. aculeatus originating from marine ancestors. The migratory Baltic Sea sticklebacks had better morphological prerequisites for sustained swimming than both freshwater populations, but there was no general difference in the locomotory capacity between marine and freshwater sticklebacks. However, their morphology could favour a more effective locomotion in the Baltic Sea sticklebacks.     

Microsatellite data resolve phylogeographic patterns in European grayling, Thymallus thymallus, Salmonidae

The phylogeography of an endangered salmonid, European grayling (Thymallus thymallus), was studied based on analysis of 17 nuclear microsatellite DNA loci. In agreement with earlier mitochondrial DNA (mtDNA) studies, phylogenetic relationships of the populations suggested that northern Europe was colonized from two distinct Pleistocene refugia. Furthermore, microsatellites revealed highly supported grouping of mainland Swedish, Norwegian, Danish, German and Slovenian populations, suggesting that grayling from the northwestern and central Europe have descended from their southern conspecifics. The level of divergence between populations was substantial, even across short geographical distances. Although this was in part due to postglacial colonization patterns and contemporary barriers for gene flow, the high divergence estimates between hydrologically connected sampling locations implied efficient interpopulation reproductive isolation. Microsatellites revealed that the populations exhibited, on average, only 3.5 (+/-2.2) alleles per locus, indicating that T. thymallus has strikingly low levels of intrapopulation genetic diversity as compared with other freshwater fish species. Accordingly, as indicated by analysis of molecular variance (AMOVA), only 49.1-58.0% of the total grayling microsatellite diversity resided within populations. A latitudinal genetic diversity gradient, potentially resulting from glaciation-mediated founder events, was not evident. Alternatively, it is possible that grayling display limited dispersal behaviour/capability, leading to low long-term effective population sizes and, consequently, depauperate intrapopulation polymorphism. These findings have implications for conservation of T. thymallus. Importantly, they exemplify that microsatellites can be highly informative for intraspecific phylogeography studies dealing with substantial divergence scales.     

MORPHOLOGICAL AND MOLECULAR VARIATION ACROSS A MIGRATORY DIVIDE IN WILLOW WARBLERS,PHYLLOSCOPUS TROCHILUS

A migratory divide is a narrow region in which two populations showing different migratory directions meet arid presumably also mate and hybridize. Banding of willow warblers, Phylloscopus trochilus, in Europe has demonstrated a migratory divide latitudinally across central Scandinavia. In autumn, southern birds migrate southwest to tropical West Africa, whereas northern birds migrate southeast to East and South Africa. The migratory divide is associated with concordant differences in size and plumage coloration. Based on morphology, we estimate the width of the transition zone between northern and southern willow warblers to be less than 350 km. We found indication of linkage disequilibria around the migratory divide, in that measures of body size were correlated with plumage coloration within the contact zone, but uncorrelated within the populations south or north of the contact zone. The presence of linkage disequilibria and the fact that several morphological clines occur together suggest that the hybrid zone is a result of secondary contact between populations that have differentiated in allopatry. This interpretation is in accord with the knowledge of the recolonization pattern of the Scandinavian peninsula after the last glaciation; animals and plants appeared to have colonized either from the south or from the north around the northern bay of the Baltic Sea. If northern and southern willow warblers resided in allopatric populations during late Pleistocene glaciations and the hybrid zone is a result of postglacial range expansions, we would expect some degree of genetic differentiation accumulated during the period in isolation. In contrast, northern and southern willow warblers are near panmictic in the frequencies of alleles of mitochondrial DNA and at two microsatellite loci. The observed pattern, clear morphological and behavioral differentiation without genetic differentiation at neutral loci, suggests either that the differences are maintained by strong selection on the expressed genes in combination with high levels of current gene flow or, in the case of weak gene flow, that the divergence in morphology and behavior is very recent.     

Northern refugia and recent expansion in the North Sea: the case of the wrasse Symphodus melops (Linnaeus, 1758)

Pleistocene climate changes have imposed extreme conditions to intertidal rocky marine communities, forcing many species to significant range shifts in their geographical distributions. Phylogeographic analyses based on both mitochondrial and nuclear genetic markers provide a useful approach to unravel phylogeographic patterns and processes of species after this time period, to gain general knowledge of how climatic changes affect shifts in species distributions. We analyzed these patterns on the corkwing wrasse (Symphodus melops, Labridae), a rocky shore species inhabiting North Sea waters and temperate northeastern Atlantic Ocean from Norway to Morocco including the Azores, using a fragment of the mitochondrial control region and the first intron of the nuclear S7 ribosomal protein gene. We found that S. melops shows a clear differentiation between the Atlantic and the Scandinavian populations and a sharp contrast in the genetic diversity, high in the south and low in the north. Within each of these main geographic areas there is little or no genetic differentiation. The species may have persisted throughout the last glacial maximum in the southern areas as paleotemperatures were not lower than they are today in North Scandinavia. The North Sea recolonization most likely took place during the current interglacial and is dominated by a haplotype absent from the south of the study area, but present in Plymouth and Belfast. The possibility of a glacial refugium in or near the English Channel is discussed.     

Invasion phylogeography of the Ponto-Caspian crustacean Limnomysis benedeni dispersing across Europe

Aim  Limnomysis benedeni Czerniavsky, 1882 is a mysid crustacean native to the Ponto-Caspian (Black and Caspian Sea) rivers and estuaries, and has recently spread across Europe through intentional and unintentional introductions. We explored the structuring of genetic variation in native and non-native populations with an aim to trace the sources of the invasions, and to infer whether the spread has occurred through a single or multiple invasion waves.
Location  Native estuaries in the Ponto-Caspian basin (Volga, Don, Dnieper, Dniester, Danube) and the recently colonized range along the Danube–Rhine river systems and Lithuania.
Methods  A fragment of the mitochondrial COI gene was sequenced to assess genetic affinities and diversity in native and recently established populations.
Results  The genetic diversity in the native regions is organized into several strongly diverged haplotype groups or lineages, partly allopatric, partly sympatric. All these lineages have also spread beyond the native range. Even the recent rapid dispersal across Europe along the Danube–Rhine system towards the North Sea basin involved several lineages from the Danube delta sector. The structuring of genetic diversity among invaded sites suggests multiple invasion events to the Danube–Rhine drainage. This contrasts with data from some other Ponto-Caspian species, where a single haplotype seems to have occupied most invaded areas. There is no evidence that intentionally stocked reservoirs in the Baltic Sea basin would have contributed to further unintentional spread of L. benedeni.
Main conclusions  Limnomysis benedeni is spreading across Europe using the southern invasion corridor. The invasion most likely involved several waves from differentiated sources in the native Danube delta area.     

Genetic structure of Eurasian badgers Meles meles (Carnivora: Mustelidae) and the colonization history of Ireland

The present study examined the contemporary genetic composition of the Eurasian badger, Meles meles, in Ireland, Britain and Western Europe, using six nuclear microsatellite loci and a 215‐bp fragment of the mitochondrial DNA control region. Significant population structure was evident within Europe (global multilocus microsatellite F_ST = 0.205, P < 0.001; global mitochondrial control region Φ_ST = 0.399, P < 0.001). Microsatellite‐based cluster analyses detected one population in Ireland, whereas badgers from Britain could be subdivided into several populations. Excluding the island populations of Ireland and Britain, badgers from Western Europe showed further structuring, with evidence of discrete Scandinavian, Central European, and Spanish populations. Mitochondrial DNA cluster analysis grouped the Irish population with Scandinavia and Spain, whereas the majority of British haplotypes grouped with those from Central Europe. The findings of the present study suggest that British and Irish badger populations colonized from different refugial areas, or that there were different waves of colonization from the source population. There are indications for the presence of an Atlantic fringe element, which has been seen in other Irish species. We discuss the results in light of the controversy about natural versus human‐mediated introductions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Diet,stable isotopes and morphology of Eurasian perch (Perca fluviatilis) in littoral and pelagic habitats in the northern Baltic Proper

We present morphology, stable isotope signals and stomach contents of Eurasian perch (Perca fluviatilis) from littoral and pelagic habitats in a brackish water embayment in the northern Baltic Proper. Studies conducted in freshwater habitats repeatedly state that littoral perch have deeper bodies than the pelagic ones. In this study we observed the opposite; the perch from the pelagic study site had deeper bodies than the littoral ones, indicating that more factors than habitat structure affect the perch morphology. A possible explanation to this discrepancy is the diet choice; the pelagic perch in this study were more benthivorous than freshwater pelagic perch. Our results on stable isotope signals combined with the stomach contents also shed new light on the dietary preferences of perch. Perch is known to be a generalist predatory fish, but our results indicate that perch have individual diet preferences. Based on our results, it seems that at some point in their lives the perch in brackish water choose between the littoral and pelagic habitats and also specialise in a certain diet. This study shows that the perch morphology and diet in the Baltic Sea coast differ among habitats, but the patterns are not similar to those observed in freshwater studies.