Cryptic diversity and speciation in an endemic copepod crustacean Harpacticella inopinata within Lake Baikal.

Ancient lakes are hotspots of species diversity, posing challenges and opportunities for exploration of the dynamics of endemic diversification. Lake Baikal in Siberia, the oldest lake in the world, hosts a particularly rich crustacean fauna, including the largest known species flock of harpacticoid copepods with some 70 species. Here, we focused on exploring the diversity and evolution within a single nominal species, Harpacticella inopinata Sars, 1908, using molecular markers (mitochondrial COI, nuclear ITS1 and 28S rRNA) and a set of qualitative and quantitative morphological traits. Five major mitochondrial lineages were recognized, with model-corrected COI distances of 0.20-0.37. A concordant pattern was seen in the nuclear data set, and qualitative morphological traits also distinguish a part of the lineages. All this suggests the presence of several hitherto unrecognized cryptic taxa within the baikalian H. inopinata, with long independent histories. The abundances, distributions and inferred demographic histories were different among taxa. Two taxa, H. inopinata CE and H. inopinata CW, were widespread on the eastern and western coasts, respectively, and were largely allopatric. Patterns in mitochondrial variation, that is, shallow star-like haplotype networks, suggest these taxa have spread through the lake relatively recently. Three other taxa, H. inopinata RE, RW and RW2, instead were rare and had more localized distributions on either coast, but showed deeper intraspecies genealogies, suggesting older regional presence. The rare taxa were often found in sympatry with the others and occasionally introgressed by mtDNA from the common ones. The mitochondrial divergence between and within the H. inopinata lineages is still unexpectedly deep, suggesting an unusually high molecular rate. The recognition of true systematic diversity in the evaluation and management of ecosystems is important in hotspots, as it is everywhere else, while the translation of the diversity into a formal taxonomy remains a challenge.

Patterns in antipredator armature reduction and maintenance in isolated spring populations of an amphipod crustacean.

Organisms colonizing new habitats can undergo adaptive change due to novel selective landscapes encountered in the new environment. Examples in nature where the development of the same traits has repeatedly occurred on multiple independent occasions upon colonizing a novel habitat represent instances of parallel evolution. Here we test whether the colonization of spring habitat by the principally lacustrine amphipod crustacean Pallaseopsis quadrispinosa has resulted in parallel evolution in armature traits using empirical data on morphology and mitochondrial DNA and through a breeding experiment. Analysis of mtDNA CO1 sequences shows that the spring populations share no common history and have evolved in isolation from each other and from their neighbouring lake populations since deglaciation approximately 12,000 years ago and are now fixed for different haplogroups. Dorsal spines and lateral projections were absent or less developed in all spring populations than in lake populations. Variation in armature development also could be explained by predator presence as populations with fish predators exhibited more developed spines than those without fish. In a laboratory breeding experiment, hybrid Spring × Lake F1 offspring had intermediate development of armature compared to offspring of Lake × Lake and Spring × Spring matings. The results support the hypothesis that armature reduction has independently evolved on multiple occasions in P. quadrispinosa. Recent research has questioned the degree to which parallel evolution actually explains variance in traits. Taking into account the predation regime, sexual dimorphism and mineral composition of the trait, a more precise understanding of the factors influencing parallel evolution emerges.

A Long-Standing Hybrid Population Between Pacific and Atlantic Herring in a Subarctic Fjord of Norway.

Atlantic herring (Clupea harengus) and Pacific herring (C. pallasii) are sister species that split from a common ancestor about 2 million years ago. Balsfjord, a subarctic fjord in Northern Norway, harbors an outpost population of Pacific herring within the range of the Atlantic herring. We used whole genome sequencing to show that gene flow from Atlantic herring into the Balsfjord population has generated a stable hybrid population that has persisted for thousands of generations. The Atlantic herring ancestry in Balsfjord was estimated in the range 25-26%. The old age and large proportion of introgressed regions suggest there are no obvious genetic incompatibilities between species. Introgressed regions were widespread in the genome and large, with some in excess of 1 Mb, and they were overrepresented in low-recombination regions. We show that the distribution of introgressed material is non-random; introgressed sequence blocks in different individuals are shared more often than expected by chance. Furthermore, introgressed regions tend to show elevated divergence (FST) between Atlantic and Pacific herring. Together, our results suggest that introgression of genetic material has facilitated adaptation in the Balsfjord population. The Balsfjord population provides a rare example of a stable interspecies hybrid population that has persisted over thousands of years.

Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections.

The Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to postglacial bedrock rebound around 9000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. We sequenced sections of the mitochondrial control region from 60 up to 125-years-old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies and how it is phylogenetically related to other ringed seal populations from the Baltic Sea, Lake Ladoga, North America, Svalbard, and the White Sea. We observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation also shows affinities to North American ringed seals. Our results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seal is not representative of the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.

Species identification based on a semi-diagnostic marker: Evaluation of a simple conchological test for distinguishing blue mussels Mytilus edulis L. and M. trossulus Gould.

Cryptic and hybridizing species may lack diagnostic taxonomic characters leaving researchers with semi-diagnostic ones. Identification based on such characters is probabilistic, the probability of correct identification depending on the species composition in a mixed population. Here we test the possibilities of applying a semi-diagnostic conchological character for distinguishing two cryptic species of blue mussels, Mytilus edulis and M. trossulus. These ecologically, stratigraphically and economically important molluscs co-occur and hybridize in many areas of the North Atlantic and the neighboring Arctic. Any cues for distinguishing them in sympatry without genotyping would save much research effort. Recently these species have been shown to statistically differ in the White Sea, where a simple character of the shell was used to distinguish two mussel morphotypes. In this paper, we analyzed the associations between morphotypes and species-specific genotypes based on an abundant material from the waters of the Kola Peninsula (White Sea, Barents Sea) and a more limited material from Norway, the Baltic Sea, Scotland and the Gulf of Maine. The performance of the "morphotype test" for species identification was formally evaluated using approaches from evidence-based medicine. Interspecific differences in the morphotype frequencies were ubiquitous and unidirectional, but their scale varied geographically (from 75% in the White Sea to 15% in the Baltic Sea). In addition, salinity-related variation of this character within M. edulis was revealed in the Arctic Barents Sea. For every studied region, we established relationships between the proportions of the morphotypes in the populations as well as between the proportions of the morphotypes in samples and the probabilities of mussels of different morphotypes being M. trossulus and M. edulis. We provide recommendations for the application of the morphotype test to mussels from unstudied contact zones and note that they may apply equally well to other taxa identified by semi-diagnostic traits.

First description of a widespread Mytilus trossulus-derived bivalve transmissible cancer lineage in M. trossulus itself.

Two lineages of bivalve transmissible neoplasia (BTN), BTN1 and BTN2, are known in blue mussels Mytilus. Both lineages derive from the Pacific mussel M. trossulus and are identified primarily by their unique genotypes of the nuclear gene EF1α. BTN1 is found in populations of M. trossulus from the Northeast Pacific, while BTN2 has been detected in populations of other Mytilus species worldwide but not in M. trossulus itself. Here we examined M. trossulus from the Sea of Japan (Northwest Pacific) for the presence of BTN. Using hemocytology and flow cytometry of the hemolymph, we confirmed the presence of disseminated neoplasia in our specimens. Cancerous mussels possessed the BTN2 EF1α genotype and two mitochondrial haplotypes with different recombinant control regions, similar to that of common BTN2 lineages. This is the first report of BTN2 in its original host species M. trossulus. A comparison of all available BTN and M. trossulus COI sequences suggests a common and recent origin of BTN2 diversity in populations of M. trossulus outside the Northeast Pacific, possibly in the Northwest Pacific.

Cycles of trans-Arctic dispersal and vicariance, and diversification of the amphi-boreal marine fauna.

The amphi-boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans-Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent inter-oceanic vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further trans-Arctic dispersal have risen at times, however, and molecular data now expose more complex patterns of inter-oceanic affinities and dispersal histories. For a general view on the trans-Arctic dynamics and of the roles of potential dispersal-vicariance cycles in generating systematic diversity, we produced new phylogeographic data sets for amphi-boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 inter-oceanic comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond to a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene-Pleistocene-Holocene time frame. Repeated inter-oceanic exchange was inferred for 23 taxa, and the latest connection was usually post-glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late- or post-glacial exchange was inferred in 46% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the North Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter-oceanic vicariance scenario underlying amphi-boreal speciation, the data expose complex patterns of reinvasion and reticulation that complicate the interpretation of taxon boundaries in the region.

Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae).

Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.

Genetic, Ecological and Morphological Distinctness of the Blue Mussels Mytilus trossulus Gould and M. edulis L. in the White Sea.

Two blue mussel lineages of Pliocene origin, Mytilus edulis (ME) and M. trossulus (MT), co-occur and hybridize in several regions on the shores of the North Atlantic. The two species were distinguished from each other by molecular methods in the 1980s, and a large amount of comparative data on them has been accumulated since that time. However, while ME and MT are now routinely distinguished by various genetic markers, they tend to be overlooked in ecological studies since morphological characters for taxonomic identification have been lacking, and no consistent habitat differences between lineages have been reported. Surveying a recently discovered area of ME and MT co-occurrence in the White Sea and employing a set of allozyme markers for identification, we address the issue whether ME and MT are true biological species with distinct ecological characteristics or just virtual genetic entities with no matching morphological and ecological identities. We find that: (1) in the White Sea, the occurrence of MT is largely concentrated in harbors, in line with observations from other subarctic regions of Europe; (2) mixed populations of ME and MT are always dominated by purebred individuals, animals classified as hybrids constituting only ca. 18%; (3) in terms of shell morphology, 80% of MT bear a distinct uninterrupted dark prismatic strip under the ligament while 97% of ME lack this character; (4) at sites of sympatry MT is more common on algal substrates while ME mostly lives directly on the bottom. This segregation by the substrate may contribute to maintaining reproductive isolation and decreasing competition between taxa. We conclude that while ME and MT are not fully reproductively isolated, they do represent clearly distinguishable biological, ecological and morphological entities in the White Sea. It remains to be documented whether the observed morphological and ecological differences are of a local character, or whether they have simply been overlooked in other contact zones.

Migration and isolation during the turbulent Ponto-Caspian Pleistocene create high diversity in the crustacean Paramysis lacustris.

The Ponto-Caspian brackish-water fauna inhabits estuaries and rivers of the Black, Azov and Caspian seas and is fragmented by higher salinity waters and a major interbasin watershed. The fauna is known for the high levels of endemism, complex zoogeographic histories, and as a recent source of successful invasive species. It remains debated whether the Black and Azov Sea brackish-water populations survived unfavourable Pleistocene conditions in multiple separate refugia or whether the two seas were (repeatedly) recolonized from the Caspian. Using microsatellite and mtDNA markers, we demonstrate deep among- and within-basin subdivisions in a widespread Ponto-Caspian mysid crustacean Paramysis lacustris. Five genetic clusters were identified, but their relationships did not reflect the geography of the region. The Azov cluster was the most distinct (4-5% COI divergence), despite its geographic position in the corridor between Black and Caspian seas, and may represent a new species. In the northern Black Sea area, the Dnieper cluster was closer to the Caspian cluster than to the neighbouring Danube-Dniester-Bug populations, suggesting separate colonizations of the Black Sea. Overall, the data implied a predominant gene flow from the east to the Black Sea and highlight the importance of Caspian Sea transgressions in facilitating dispersal. Yet, the presence of distinct lineages in the Black Sea points to the persistence of isolated refugial populations that have gained diagnostic differences under presumably high mutation rates and large population sizes. The unfavourable Pleistocene periods in the Black Sea therefore appear to have promoted diversification of the brackish-water lineages, rather than extirpated them.

The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa.

The acanthocephalan genus Echinorhynchus Zoega in Müller, 1776 (sensuYamaguti 1963) is a large and widespread group of parasites of teleost fish and malacostracan crustaceans, distributed from the Arctic to the Antarctic in habitats ranging from freshwaters to the deep-sea. A total of 52 species are currently recognised based on the conventional morphological species concept; however, the true diversity in the genus is masked by cryptic speciation. The considerable diversity within Echinorhynchus is an argument for subdividing the genus if monophyletic groups with supporting morphological characters can be identified. With this objective in mind, partial sequences of two genes with different rates of evolution and patterns of inheritance (nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I) were used to infer the phylogenetic relationships among eight taxa of Echinorhynchus. These included representatives of each of three genus group taxa proposed in a controversial revision of the genus based on cement gland pattern, namely Echinorhynchus (sensu stricto), Metechinorhynchus Petrochenko, 1956 and Pseudoechinorhynchus Petrochenko, 1956. These groupings have previously been rejected by some authorities, because the diagnostic character is poorly defined; this study shows that Echinorhynchus (sensu stricto) and Metechinorhynchus are not natural, monophyletic groups. A revision of Echinorhynchus will require tandem molecular phylogenetic and morphological analyses of a larger sample of taxa, but this study has identified two morhological characters that might potentially be used to define new genera. The estimated phylogeny also provides insight into the zoogeographical history of Echinorhynchus spp. We postulate that the ancestral Echinorhynchus had a freshwater origin and the genus subsequently invaded the sea, probably several times. The freshwater taxa of the Echinorhynchusbothniensis Zdzitowiecki & Valtonen, 1987 clade may represent a reinvasion of freshwater by one or more ancestral marine species.

Phylogeography of amphi-boreal fish: tracing the history of the Pacific herring Clupea pallasii in North-East European seas.

BACKGROUND: The relationships between North Atlantic and North Pacific faunas through times have been controlled by the variation of hydrographic circumstances in the intervening Arctic Ocean and Bering Strait. We address the history of trans-Arctic connections in a clade of amphi-boreal pelagic fishes using genealogical information from mitochondrial DNA sequence data. The Pacific and Atlantic herrings (Clupea pallasii and C. harengus) have basically vicarious distributions in the two oceans since pre-Pleistocene times. However, remote populations of C. pallasii are also present in the border waters of the North-East Atlantic in Europe. These populations show considerable regional and life history differentiation and have been recognized in subspecies classification. The chronology of the inter-oceanic invasions and genetic basis of the phenotypic structuring however remain unclear. RESULTS: The Atlantic and Pacific herrings both feature high mtDNA diversities (large long-term population sizes) in their native basins, but an ocean-wide homogeneity of C. harengus is contrasted by deep east-west Pacific subdivision within Pacific C. pallasii. The outpost populations of C. pallasii in NE Europe are identified as members of the western Pacific C. pallasii clade, with some retained inter-oceanic haplotype sharing. They have lost diversity in colonization bottlenecks, but have also thereafter accumulated abundant new variation. The data delineate three phylogeographic groups within the European C. pallasii: herring from the inner White Sea; herring from the Mezen and Chesha Bays; and a strongly bottlenecked peripheral population in Balsfjord of the Norwegian Sea. CONCLUSIONS: The NE European outposts of C. pallasii are judged to be early post-glacial colonists from the NW Pacific. A strong regional substructure has evolved since that time, in contrast to the apparent broad-scale uniformity maintained by herrings in their native basins. The structure only partly matches the previous biological concepts based on seasonal breeding stocks or geographical subspecies designations. The trans-Arctic herring phylogeography is notably similar to those of the amphi-boreal mollusk taxa Macoma and Mytilus, suggesting similar histories of inter-oceanic connections. We also considered the time dependency of molecular rates, critical for interpreting timing of relatively recent biogeographical events, by comparing the estimates from coding and non-coding mitochondrial regions of presumably different mutation dynamics.

Opsin gene sequence variation across phylogenetic and population histories in Mysis (Crustacea: Mysida) does not match current light environments or visual-pigment absorbance spectra.

The hypothesis that selection on the opsin gene is efficient in tuning vision to the ambient light environment of an organism was assessed in 49 populations of 12 Mysis crustacean species, inhabiting arctic marine waters, coastal littoral habitats, freshwater lakes ('glacial relicts') and the deep Caspian Sea. Extensive sequence variation was found within and among taxa, but its patterns did not match expectations based on light environments, spectral sensitivity of the visual pigment measured by microspectrophotometry or the history of species and populations. The main split in the opsin gene tree was between lineages I and II, differing in six amino acids. Lineage I was present in marine and Caspian Sea species and in the North American freshwater Mysis diluviana, whereas lineage II was found in the European and circumarctic fresh- and brackish-water Mysis relicta, Mysis salemaai and Mysis segerstralei. Both lineages were present in some populations of M. salemaai and M. segerstralei. Absorbance spectra of the visual pigment in nine populations of the latter three species showed a dichotomy between lake (λ(max) =554-562 nm) and brackish-water (Baltic Sea) populations (λ(max) = 521-535 nm). Judged by the shape of spectra, this difference was not because of different chromophores (A2 vs. A1), but neither did it coincide with the split in the opsin tree (lineages I/II), species identity or current light environments. In all, adaptive evolution of the opsin gene in Mysis could not be demonstrated, but its sequence variation did not conform to a neutral expectation either, suggesting evolutionary constraints and/or unidentified mechanisms of spectral tuning.

Mytilus trossulus in Northern Europe.

From data on allozyme, nuclear DNA and mitochondrial DNA markers, we show that the originally North Pacific/Northwest Atlantic mussel Mytilus trossulus is widespread on North European coasts, earliM. trossuluser thought to be inhabited only by Mytilus edulis. Several local occurrences of , interspersed with a dominant M. edulis, were recorded on the North Sea, Norwegian Sea and Barents Sea coasts of Norway and the Barents and White Sea coasts of Kola Peninsula in Russia. The proportion of M. trossulus genetic background observed at any one site varied from 0 to 95%. These new occurrences are not related to the previously known, introgressed M. trossulus population that occupies the Baltic Sea. The new northern occurrences retain both the F and M M. trossulus mitochondria, which have been lost from the Baltic stock. While hybridization takes place wherever M. trossulus and M. edulis meet, the extent of hybrization varies between the different contact areas. Hybrids are rare, and the hybrid zones are bimodal in the northern areas; more interbreeding has taken place further south in Norway, but even there genotypic disequilibria are higher than those in the steep transition zone between the Baltic mussel and M. edulis: there is no evidence of a collapse toward a hybrid swarm unlike in the Baltic. The Barents and White Sea M. trossulus are genetically slightly closer to the NW Atlantic than NE Pacific populations, while the Baltic mussel has unique features distinguishing it from the others. We postulate that the presence of M. trossulus in Northern Europe is a result of repeated independent inter- or transoceanic cryptic invasions of various ages, up to recent times.

Evaluating signatures of glacial refugia for North Atlantic benthic marine taxa.

A goal of phylogeography is to relate patterns of genetic differentiation to potential historical geographic isolating events. Quaternary glaciations, particularly the one culminating in the Last Glacial Maximum approximately 21 ka (thousands of years ago), greatly affected the distributions and population sizes of temperate marine species as their ranges retreated southward to escape ice sheets. Traditional genetic models of glacial refugia and routes of recolonization include these predictions: low genetic diversity in formerly glaciated areas, with a small number of alleles/haplotypes dominating disproportionately large areas, and high diversity including "private" alleles in glacial refugia. In the Northern Hemisphere, low diversity in the north and high diversity in the south are expected. This simple model does not account for the possibility of populations surviving in relatively small northern periglacial refugia. If these periglacial populations experienced extreme bottlenecks, they could have the low genetic diversity expected in recolonized areas with no refugia, but should have more endemic diversity (private alleles) than recently recolonized areas. This review examines evidence of putative glacial refugia for eight benthic marine taxa in the temperate North Atlantic. All data sets were reanalyzed to allow direct comparisons between geographic patterns of genetic diversity and distribution of particular clades and haplotypes including private alleles. We contend that for marine organisms the genetic signatures of northern periglacial and southern refugia can be distinguished from one another. There is evidence for several periglacial refugia in northern latitudes, giving credence to recent climatic reconstructions with less extensive glaciation.

A broad transition zone between an inner Baltic hybrid swarm and a pure North Sea subspecies of Macoma balthica (Mollusca, Bivalvia).

The populations of the bivalve clam Macoma balthica in the low-salinity Northern Baltic Sea represent an admixture of two strongly diverged genomic origins, the Pacific Macoma balthica balthica (approx. 60% genomic contribution) and Atlantic Macoma balthica rubra (40%). Using allozyme and mtDNA characters, we describe the broad transition from this hybrid swarm to the pure M. b. rubra in the saline North Sea waters, spanning hundreds of kilometre distance. The zone is centred in the strong salinity gradient of the narrow Oresund strait and in the adjacent Western Baltic. Yet the multilocus clines show no simple and smoothly monotonic gradation: they involve local reversals and strong differences between neighbouring populations. The transitions in different characters are not strictly coincident, and the extent of introgression varies among loci. The Atlantic influence extends further into the Baltic in samples from the southern and eastern Baltic coasts than on the western coast, and further in deeper bottoms than at shallow (< 1 m) sites. This fits with the counterclockwise net circulation pattern and with a presumably weaker salinity barrier for invading Atlantic type larvae in saline deeper water, and corresponding facilitation of outwards drift of Baltic larvae in diluted surface waters. Genotypic disequilibria were strong particularly in the shallow-water samples of the steepest transition zone. This suggests larval mixing from different sources and limited interbreeding in that area, which makes a stark contrast to the evidence of thorough amalgamation of the distinct genomic origins in the inner Baltic hybrid swarm of equilibrium structure.

Phylogeny of Paramysis (Crustacea: Mysida) and the origin of Ponto-Caspian endemic diversity: resolving power from nuclear protein-coding genes.

The Ponto-Caspian (Black and Caspian seas) brackish-water fauna represents a special case of the endemic diversification in world's ancient lakes; it also involves a hotspot of continental diversity in the predominantly marine mysid crustaceans. We explored the origins and history of the mysid diversification in a phylogenetic analysis of some 20 endemic Ponto-Caspian species mainly of the genus Paramysis and their marine congeners, using sequences of two nuclear protein-coding genes, two nuclear rRNA genes, the mitochondrial COI gene and morphological data. A nearly completely resolved phylogeny was recovered, with no indication of rapid diversification bursts. Deep divergences were found among the main endemic clades, attesting to a long independent faunal history in the continental Paratethys waters. The current marine Paramysis species make a monophyletic cluster secondarily derived from the continental Paratethyan (Ponto-Caspian) Paramysis ancestors. The good phylogenetic resolution was mainly due to the two nuclear protein-coding genes, opsin and EPRS, here for the first time applied to peracarid systematics. In contrast, 'conventional' mtDNA and nuclear rRNA genes provided poor topological resolution and weak congruence of divergence rates. The two nuclear protein-coding genes had more congruent rates of evolution, and were about 10-15 times slower than the mitochondrial COI gene.

Macoma balthica in the White and Barents Seas: properties of a widespread marine hybrid swarm (Mollusca: Bivalvia).

A main molecular subdivision in the circumpolar Macoma balthica complex has been described between Atlantic and Pacific taxa. In NE Europe, the clams of the White and Barents Seas, however, show deviant genetic structures. Using allozyme and mitochondrial DNA data, we explore the hypothesis that these deviations result from hybridization between an Atlantic (M. b. rubra) and an invading Pacific (M. b. balthica) lineage. A practically pure Atlantic Macoma extends from France north to the Varanger Peninsula (NE Norway), whereas populations farther east have genetic compositions intermediate between true Atlantic and true Pacific. Admixture estimates range from 32 to 90% Pacific contribution, with a notable deviation in a nearly pure Atlantic outpost in the Mezen Bay (NE White Sea). The pattern of variation is not one of a simple collinear mixing however. Different characters exhibit different degrees of introgression, and the relative introgression varies regionally. Yet, there are practically no interlocus genotypic disequilibria between the diverged loci, which brings out the White Sea-Barents Sea M. balthica as the best-documented marine animal hybrid swarms so far, arisen through amalgamation of genomes previously isolated since pre-Pleistocene times. On top of the main admixture pattern, strong geographical structuring is also seen in characters unrelated to the principal systematic distinction. The persistence of the regional patterns indicates restricted gene flow at the present time, despite the high dispersal potential of the species. The causes of this structuring could be in a complex history of colonization events and features of local hydrography enhancing isolation and divergence of populations.

Diversity and trans-arctic invasion history of mitochondrial lineages in the North Atlantic Macoma balthica complex (Bivalvia: Tellinidae).

The history of repeated inter- or transoceanic invasions in bivalve mollusks of the circumpolar Macoma balthica complex was assessed from mtDNA COIII sequences. The data suggest that four independent trans-Arctic invasions, from the Pacific, gave rise to the current lineage diversity in the North Atlantic. Unlike in many other prominent North Atlantic littoral taxa, no evidence for (postinvasion) trans-Atlantic connections was found in the M. balthica complex. The earliest branch of the mtDNA tree is represented by the temperate-boreal North American populations (=Macoma petalum), separated from the M. balthica complex proper in the Early Pliocene at latest. The ensuing trans-Arctic invasions established the North European M. b. rubra, which now prevails on the North Sea and northeast Atlantic coasts, about two million years ago, and the currently northwest Atlantic M. balthica lineage in the Canadian Maritimes, in the Middle Pleistocene. The final reinvasion(s) introduced a lineage that now prevails in a number of North European marginal seas and is still hardly distinguishable from North Pacific mtDNA (M. b. balthica). We used coalescence simulation analyses to assess the age of the latest invasion from the Pacific to the northeast Atlantic. The results refute the hypothesis of recent, human-mediated reintroductions between northeast Pacific and the North European marginal seas in historical times. Yet they also poorly fit the alternative hypotheses of an early postglacial trans-Arctic invasion (< 11 thousand years ago), or an invasion during the previous Eemian interglacial (120 thousand years ago). Divergence time estimates rather fall in the Middle Weichselian before the Last Glacial Maximum, in conflict with the conventional thinking of trans-Arctic biogeographical connections; an early Holocene reinvasion may still be regarded as the most plausible scenario. Today, the most recently invaded Pacific mtDNA lineage is found admixed with the earlier established European Atlantic "rubra" lineage in the Baltic Sea and in Barents Sea populations east of the Varanger peninsula, and it is practically exclusive in the White and Pechora seas. Yet mtDNA does not always constitute an unequivocal taxonomic marker at individual level; the marginal populations represent hybrid swarms of the Atlantic and Pacific lineages in their nuclear genes.

Phylogeographic analyses of a circumarctic coastal and a boreal lacustrine mysid crustacean, and evidence of fast postglacial mtDNA rates.

Phylogeographic structures of two weakly dispersing Mysis sibling species, one with a circumarctic coastal, the other with a boreal lacustrine-Baltic distribution, were studied from mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Mysis segerstralei showed high overall diversity and little phylogeographic structure across the Arctic, indicating late-glacial dispersal among coastal and lake populations from Alaska, Siberia and the north of Europe. A strongly divergent refugial lineage was however identified in Beringia. The boreal 'glacial relict'Mysis salemaai in turn displayed clear structuring among postglacially isolated Scandinavian lake populations. The inferred pattern of intralake mitochondrial DNA (mtDNA) monophyly in Scandinavia suggested relatively small population sizes and a remarkably fast postglacial mtDNA divergence rate (0.27% per 10 000 years). Nevertheless, the broader phylogeographic pattern did not support distinct eastern and western glacial refugia in Northern Europe, unlike in some other aquatic taxa. In all, the two species comprised three equidistant mitochondrial lineages (approximately 2% divergence), corresponding to M. salemaai, to the bulk of M. segerstralei, and to the Beringian M. segerstralei lineage. The lack of reciprocal monophyly of the two species in respect to their mitochondrial genealogy could indicate postspeciation mitochondrial introgression, also exemplified by an evidently more recent capture of M. segerstralei mitochondria in a Karelian population of M. salemaai. Overall, the data suggest that the continental boreal M. salemaai has a relatively recent ancestry in arctic coastal waters, whereas two other boreal 'glacial relict'Mysis sibling species in Europe (Mysis relicta) and North America (Mysis diluviana) have colonized inland waters much earlier (approximately 8% COI divergence).