Population genetic structure, parasite infection and somatic condition of pumpkinseed Lepomis gibbosus (Actinopterygii: Centrarchidae) in the Oder river basin.

In Poland, distribution of non-native pumpkinseed Lepomis gibbosus (Centrarchidae) is strictly limited to the Oder river basin, where it was introduced in the early 20th century. Recently, several populations have been found in waterbodies adjacent to the Oder, particularly in its lower reaches. In this study, we compare the genetic relatedness of populations in the Oder basin with other European populations using nuclear (microsatellite) and mitochondrial (partial cytochrome c oxidase subunit I; cox1) markers. Microsatellite analysis indicated that four populations in the lower Oder form a separate cluster, while one in the middle Oder clustered with Danubian populations, from where probably having been introduced. Microsatellite data suggested that the lower Oder populations differ from other non-native European populations, making it impossible to estimate the source of introduction. Nevertheless, analysis of cox1 indicated that Oder pumpkinseeds belong to the same haplotype as the vast majority of European populations. Parasitological examination confirmed the presence of two North American species, the monogenean Onchocleidus dispar and trematode Posthodiplostomum centrarchi, in the lower Oder, both previously unknown in the region. Fifteen other parasite species were acquired, including glochidia of invasive Sinanodonta woodiana. In the middle Oder, parasite infection was more limited. Fish from the Gryfino Canal, considered one of the most invasive populations in Europe, showed the highest parasite abundance and diversity, and the highest somatic condition and growth rate due to warm water released from the Dolna Odra power plant. Our results highlight significant differences in somatic condition and parasite infection in long-established non-native pumpkinseed populations in the same river system, reflecting mainly environmental conditions.

Low-level pathogen transmission from wild to farmed salmonids in a flow-through fish farm.

While the potential effects of pathogens spread from farmed fish to wild populations have frequently been studied, evidence for the transmission of parasites from wild to farmed fish is scarce. In the present study, we evaluated natural bacterial and parasitic infections in brown trout (Salmo trutta m. fario) collected from the Cerná Opava river (Czech Republic) as a potential source of infections for rainbow trout (Oncorhynchus mykiss) reared in a flow-through farm system fed by the same river. The prevalence of bacterial and protozoan infections in farmed fish was comparable, or higher, than for riverine fish. Despite this, none of the infected farmed fish showed any signs of severe diseases. Substantial differences in metazoan parasite infections were observed between wild and farmed fish regarding monogeneans, adult trematodes, nematodes, the myxozoan Tetracapsuloides bryosalmonae found in riverine fish only, and larval eye-fluke trematodes sporadically found in farmed fish. The different distribution of metazoan parasites between brown and rainbow trout most probably reflects the availability of infected intermediate hosts in the two habitats. Despite the river being the main water source for the farm, there was no significant threat of parasite infection to the farmed fish from naturally infected riverine fish.

The role of the non-indigenous pumpkinseed Lepomis gibbosus (Actinopterygii: Centrarchidae) in the life cycle of Bothriocephalus claviceps (Cestoda: Bothriocephalidae) in Europe.

Infection of non-indigenous pumpkinseed (Lepomis gibbosus, Centrarchidae) with the bothriocephalidean cestode Bothriocephalus claviceps (Cestoda: Bothriocephalidae) was confirmed at several sites in the lower Oder river basin in Poland. The preferred host for this cestode species is the European eel (Anguilla anguilla), with a wide range of other fish species serving as paratenic hosts. The pumpkinseed showed a relatively high prevalence and abundance of larvae, along with several mature and gravid specimens, thereby confirming development of B. claviceps to the adult stage in an alternative host. As such, the pumpkinseed may represent an additional definitive host for this cestode, in addition to its role as a paratenic host, as previously recorded in other European regions. Our results indicate that inclusion of pumpkinseed as an additional definitive host in the cestode's life cycle, high infection of pumpkinseed with B. claviceps larvae and inclusion of pumpkinseed in the eel's diet could potentially lead to increased parasite pressure on native fish hosts. Further comparative studies or experimental testing will be required to confirm this.

Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera.

The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.

Mitogenomics of the endemic Ethiopian rats: looking for footprints of adaptive evolution in sky islands.

Organisms living in high altitude must adapt to environmental conditions with hypoxia and low temperature, e.g. by changes in the structure and function of proteins associated with oxidative phosphorylation in mitochondria. Here we analysed the signs of adaptive evolution in 27 mitogenomes of endemic Ethiopian rats (Stenocephalemys), where individual species adapted to different elevation. Significant signals of positive selection were detected in 10 of the 13 mitochondrial protein-coding genes, with a majority of functional substitutions in the NADH dehydrogenase complex. Higher frequency of positively selected sites was found in phylogenetic lineages corresponding to Afroalpine specialists.

Genetic diversity of a widespread annual killifish from coastal Tanzania.

BACKGROUND: African annual killifishes (Nothobranchius spp.) are adapted to seasonally desiccating habitats (ephemeral pools), surviving dry periods as dormant eggs. Given their peculiar life history, geographic aspects of their diversity uniquely combine patterns typical for freshwater taxa (river basin structure and elevation gradient) and terrestrial animals (rivers acting as major dispersal barriers). However, our current knowledge on fine-scale inter-specific and intra-specific genetic diversity of African annual fish is limited to a single, particularly dry region of their distribution (subtropical Mozambique). Using a widespread annual killifish from coastal Tanzania and Kenya, we tested whether the same pattern of genetic divergence pertains to a wet equatorial region in the centre of Nothobranchius distribution. RESULTS: In populations of Nothobranchius melanospilus species group across its range, we genotyped a part of mitochondrial cytochrome oxidase subunit 1 (COI) gene (83 individuals from 22 populations) and 10 nuclear microsatellite markers (251 individuals from 16 populations). We found five lineages with a clear phylogeographic structure but frequent secondary contact. Mitochondrial lineages were largely congruent with main population genetic clusters identified on microsatellite markers. In the upper Wami basin, populations are isolated as a putative Nothobranchius prognathus, but include also a population from a periphery of the middle Ruvu basin. Other four lineages (including putative Nothobranchius kwalensis) coexisted in secondary contact zones, but possessed clear spatial pattern. Main river channels did not form apparent barriers to dispersal. The most widespread lineage had strong signal of recent population expansion. CONCLUSIONS: We conclude that dispersal of a Nothobranchius species from a wet part of the genus distribution (tropical lowland) is not constrained by main river channels and closely related lineages frequently coexist in secondary contact zones. We also demonstrate contemporary connection between the Ruvu and Rufiji river basins. Our data do not provide genetic support for existence of recently described cryptic species from N. melanospilus complex, but cannot resolve this issue.

High cryptic diversity of bitterling fish in the southern West Palearctic.

South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. We used mtDNA sequences to infer phylogenetic relationships and historical demography, and microsatellite markers to describe fine-scale genetic variability and structure. Our mtDNA analysis revealed six well-supported lineages, with limited local co-occurrence. Two lineages are distributed throughout central and western Europe (lineages "A" and "B"), with two zones of secondary contact. Another two lineages were restricted to the Ponto-Aegean region of Greece (lineages "C" and "D") and the final two lineages were restricted south of the Caucasus mountains (lineage "E" from the Black Sea watershed and lineage "F" from the Caspian watershed). A signal of recent expansion was revealed in the two widespread lineages and the Ponto-Aegean lineage "C". The geographic distribution of clusters detected by nuclear microsatellites corresponded well with mitochondrial lineages and demonstrated finely sub-structured populations. A profound population structure suggested a significant role of genetic drift in differentiation among lineages. Lineage divergence in the Ponto-Aegean and Caspian regions are substantial, supporting the validity of two described endemic species (Rhodeus meridionalis as lineage "D" and Rhodeus colchicus as lineage "E") and invite taxonomic evaluation of the other two southern lineages (Thracean "C" and Caspian "F").

Modelling the invasion history of Sinanodonta woodiana in Europe: Tracking the routes of a sedentary aquatic invader with mobile parasitic larvae.

Understanding the invasive potential of species outside their native range is one of the most pressing questions in applied evolutionary and ecological research. Admixture of genotypes of invasive species from multiple sources has been implicated in successful invasions, by generating novel genetic combinations that facilitate rapid adaptation to new environments. Alternatively, adaptive evolution on standing genetic variation, exposed by phenotypic plasticity and selected by genetic accommodation, can facilitate invasion success. We investigated the population genetic structure of an Asian freshwater mussel with a parasitic dispersal stage, Sinanodonta woodiana, which has been present in Europe since 1979 but which has expanded rapidly in the last decade. Data from a mitochondrial marker and nuclear microsatellites have suggested that all European populations of S. woodiana originate from the River Yangtze basin in China. Only a single haplotype was detected in Europe, in contrast to substantial mitochondrial diversity in native Asian populations. Analysis of microsatellite markers indicated intensive gene flow and confirmed a lower genetic diversity of European populations compared to those from the Yangtze basin, though that difference was not large. Using an Approximate Bayesian Modelling approach, we identified two areas as the probable source of the spread of S. woodiana in Europe, which matched historical records for its establishment. Their populations originated from a single colonization event. Our data do not support alternative explanations for the rapid recent spread of S. woodiana; recent arrival of a novel (cold-tolerant) genotype or continuous propagule pressure. Instead, in situ adaptation, facilitated by repeated admixture, appears to drive the ongoing expansion of S. woodiana. We discuss management consequences of our results.

Fine-scale genetic structure of the European bitterling at the intersection of three major European watersheds.

BACKGROUND: Anthropogenic factors can have a major impact on the contemporary distribution of intraspecific genetic diversity. Many freshwater fishes have finely structured and locally adapted populations, but their natural genetic structure can be affected by river engineering schemes across river basins, fish transfers in aquaculture industry and conservation management. The European bitterling (Rhodeus amarus) is a small fish that is a brood parasite of freshwater mussels and is widespread across continental Europe. Its range recently expanded, following sharp declines in the 1970s and 1980s. We investigated its genetic variability and spatial structure at the centre of its distribution at the boundary of three watersheds, testing the role of natural and anthropogenic factors in its genetic structure. RESULTS: Sequences of mitochondrial cytochrome B (CYTB) revealed that bitterling colonised central Europe from two Ponto-Caspian refugia, which partly defines its contemporary genetic structure. Twelve polymorphic microsatellite loci revealed pronounced interpopulation differentiation, with significant small-scale differentiation within the same river basins. At a large scale, populations from the Baltic Sea watershed (middle Oder and Vistula basins) were distinct from those from the Black Sea watershed (Danube basin), while populations from rivers of the North Sea watershed (Rhine, Elbe) originated from the admixture of both original sources. Notable exceptions demonstrated the potential role of human translocations across watersheds, with the upper River Oder (Baltic watershed) inhabited by fish from the Danube basin (Black Sea watershed) and a population in the southern part of the River Elbe (North Sea watershed) basin possessing a signal of admixture from the Danube basin. CONCLUSIONS: Hydrography and physical barriers to dispersal are only partly reflected in the genetic structure of the European bitterling at the intersection of three major watersheds in central Europe. Drainage boundaries have been obscured by human-mediated translocations, likely related to common carp, Cyprinus carpio, cultivation and game-fish management. Despite these translocations, populations of bitterling are significantly structured by genetic drift, possibly reinforced by its low dispersal ability. Overall, the impact of anthropogenic factors on the genetic structure of the bitterling populations in central Europe is limited.

Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique.

BACKGROUND: Intraspecific genetic variation of African fauna has been significantly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. RESULTS: Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary contact between Chefu and Limpopo populations. CONCLUSIONS: We demonstrated: (1) ancient (pre-Pleistocene) divergence between the two main N. furzeri lineages, their recent secondary contact and lack of reproductive isolation; (2) important genetic structuring attributed to the fragmented nature of their environment and isolation-by-distance, suggesting that dispersal is limited, occurs over short distances and is not directly associated with river routes; (3) an apparent role of the River Limpopo as a barrier to dispersal and gene flow.