DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe

The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EUWater Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel ecogenomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a DNAqua-Net: Developing new genetic tools for bioassessment and monitoring ... 3 conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments

Genetic variability of Chilean and Peruvian surfclams (Donax marincovichi and Donax obesulus)

Exposed intertidal sandy beaches are commonly dominated by surf clams of the genus Donax. In Peru and Chile these bivalves play an important role for artisanal fisheries. Beside that, little is known about the taxonomy, biology, and the clams susceptibility to climatically induced changes. The taxonomic status of the two Donax species Donax marincovichi and Donax obesulus, distributed along the Peruvian coastline, is controversially discussed. As morphometric comparisons reveal no significant differences we possibly deal with a single rather than with two species. Furthermore, our knowledge on larval dispersal allowing gene flow among populations is scarce. Therefore, both putative Donax species were sampled at ten beaches along the coastline from northern Chile to northern Peru. Partial cytochrome oxidase I sequences were analysed in order to estimate the genetic distances between both putative species and to estimate the intraspecific gene flow along the coastline. Region specific patterns and the dependence on recruitment of local stocks are discussed

Relación filogenética de los Cumacea (Crustacea: Peracarida) y variabilidad genética de dos especies antárticas de la familia Leuconidae

Phylogenetic hypotheses for the peracarid order Cumacea are scarce and have not provided a solution to the full extent. In the present study, a fragment of the mitochondrial 16S rDNA was used to erect a phylogenetic hypothesis for three cumacean families, Diastylidae, Bodotriidae and Leuconidae, along with intra-family relationships of the latter. The Cumacea resolved monophyletic with tanaids and isopods as outgroup taxa. The Diastylidae were the only family with good support for monophyly. The genus Leucon resolved paraphyletic, whereas the subgenus Crymoleucon was monophyletic. Furthermore, the genetic structure was analysed for two leuconid species, Leucon antarcticus Zimmer, 1907 and L. intermedius Mühlenhardt-Siegel, 1996, from the Weddell Sea and the Ross Sea. The two species showed different patterns of intraspecific genetic variability. In contrast to L. intermedius, a bimodal distribution of pairwise genetic distances was observed for L. antarcticus, which is correlated with geographical and depth distributions between the Ross Sea and the Weddell Sea. Although a clear evaluation of cryptic speciation in these species requires additional work on more specimens from more geographic regions and broader depth ranges, differences shown in the sequences of 16S rDNA can only be explained by genetic separation of populations between the Weddell Sea and the Ross Sea for an extended period of time.Las hipótesis filogenéticas para los peracáridos del orden Cumacea son escasas y no han proporcionado una solución definitiva. En el presente estudio se utilizó un fragmento del rDNA 16S mitocondrial para formular una hipótesis filogenética para tres familias de cumáceos, Diastylidae, Bodotriidae y Leuconidae. Además se han analizado las relaciones intrafamiliares de esta última. Los cumáceos es un grupo monofilético con tanaidáceos e isópodos como taxones externos. De las tres familias analizadas, los Diastylidae fueron la única con buen apoyo para la monofilia. El género Leucon se resolvió parafilético mientras que el subgénero Crymoleucon fue monofilético. Además, se analizó la estructura genética de dos especies de leucónidos Leucon antarcticus Zimmer, 1907 y L. intermedius Mühlenhardt-Siegel, 1996 del mar de Weddell y el mar de Ross respectivamente. Ambas especies mostraron diferentes patrones de variabilidad genética intraespecífica. A diferencia de L. intermedius, para L. antarcticus se observó una distribución bimodal del mismatch distribution, que se correlaciona con las distribuciones geográficas y de profundidad entre el mar de Ross y el mar de Weddell. Aunque una evaluación clara de la especiación críptica en estas especies requiere trabajo adicional con más especímenes de más regiones geográficas y rangos de profundidad más amplios, las diferencias que se muestran en las secuencias del rDNA 16S solo pueden explicarse por la separación genética de poblaciones entre el mar de Weddell y el mar de Ross durante un período de tiempo prolongad

Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini).

BackgroundInsects rely more on chemical signals (semiochemicals) than on any other sensory modality to find, identify, and choose mates. In most insects, pheromone production is typically regulated through biosynthetic pathways, whereas pheromone sensory detection is controlled by the olfactory system. Orchid bees are exceptional in that their semiochemicals are not produced metabolically, but instead male bees collect odoriferous compounds (perfumes) from the environment and store them in specialized hind-leg pockets to subsequently expose during courtship display. Thus, the olfactory sensory system of orchid bees simultaneously controls male perfume traits (sender components) and female preferences (receiver components). This functional linkage increases the opportunities for parallel evolution of male traits and female preferences, particularly in response to genetic changes of chemosensory detection (e.g. Odorant Receptor genes). To identify whether shifts in pheromone composition among related lineages of orchid bees are associated with divergence in chemosensory genes of the olfactory periphery, we searched for patterns of divergent selection across the antennal transcriptomes of two recently diverged sibling species Euglossa dilemma and E. viridissima.ResultsWe identified 3185 orthologous genes including 94 chemosensory loci from five different gene families (Odorant Receptors, Ionotropic Receptors, Gustatory Receptors, Odorant Binding Proteins, and Chemosensory Proteins). Our results revealed that orthologs with signatures of divergent selection between E. dilemma and E. viridissima were significantly enriched for chemosensory genes. Notably, elevated signals of divergent selection were almost exclusively observed among chemosensory receptors (i.e. Odorant Receptors).ConclusionsOur results suggest that rapid changes in the chemosensory gene family occurred among closely related species of orchid bees. These findings are consistent with the hypothesis that strong divergent selection acting on chemosensory receptor genes plays an important role in the evolution and diversification of insect pheromone systems

Cryptic speciation in a benthic isopod from Patagonian and Falkland Island waters and the impact of glaciations on its population structure

<p>Abstract</p> <p>Background</p> <p>The Falkland Islands and Patagonia are traditionally assigned to the Magellan Biogeographic Province. Most marine species in Falkland waters are also reported from southern Patagonia. It remains unclear if relatively immobile, marine benthic, shallow-water species maintain gene flow, and by what mechanism. Recurrent fluctuations in sea level during glacial cycles are regarded as a possible mechanism that might have allowed genetic exchange between the regions. However, the realized genetic exchange between the Falkland Islands and Patagonia has never been estimated.</p> <p>Results</p> <p>This study analyses the genetic structure of three populations of the marine shallow-water isopod <it>Serolis paradoxa </it>(Fabricius, 1775) from the Falkland Islands and southern Patagonia (central Strait of Magellan and the Atlantic opening) applying seven nuclear microsatellites and a fragment of the mitochondrial 16S rRNA gene. Both marker systems report highest genetic diversity for the population from the central Strait of Magellan and lowest for the Falkland Islands. The estimated effective population sizes were large for all populations studied. Significant differentiation was observed among all three populations. The magnitude of differentiation between Patagonia and the Falkland Islands (16S: uncorrected p-distance 2.1%; microsatellites: standardized F'_ST> 0.86) was an order of magnitude higher than between populations from within Patagonia. This indicates that there is currently no effective gene flow for nominal <it>S. paradoxa </it>between these two regions and it has been absent for time exceeding the last glacial maximum. We argue that specimens from the Strait of Magellan and the Falkland Islands very likely represent two distinct species that separated in the mid-Pleistocene (about 1 MY BP).</p> <p>Conclusion</p> <p>The results of this study indicate limited gene flow between distant populations of the brooding isopod <it>Serolis paradoxa</it>. The patterns of genetic diversity suggest that the only recently inundated Strait of Magellan was colonized by different source populations, most likely from Atlantic and Pacific coastal waters. Our results demonstrate that more systematic testing of shared faunal inventory and realized genetic exchange between Patagonia and the Falkland Islands is needed before a consensus concerning the position of the Falkland Islands relative to the Magellan zoogeographic province can be reached.</p

Genetic data support independent glacial refugia and open ocean barriers to dispersal for the Southern Ocean sea spider Austropallene cornigera (Möbius, 1902)

The diversity and distribution of Antarctic life has been strongly influenced by climatic events, in particular by large scale extension of ice sheets onto the continental shelf during repeated glacial cycles. It has been suggested that populations of benthic marine biota in the Antarctic were limited to very few refugia because the Antarctic shelf was covered with ice. Using the broadly-distributed pycnogonid Austropallene cornigeraas a model, in this study we tested different hypotheses for possible locations of glacial refugia ( ex situon the peri-Antarctic islands or in situon the Antarctic shelf). We sampled 64 individuals of A. cornigerafrom peri-Antarctic islands, the Weddell Sea and East Antarctica. The phylogeographic structure was analysed using partial sequences of the nuclear ribolomal genes 18S and 28S and the mitochondrial cytochrome coxidase subunit I gene (COI). The 18S and 28S sequences were highly conserved. Sequences of the COI were variable and revealed highest haplotype diversity for populations on the Antarctic shelf and lowest for the population from the remote island of Bouvetøya. In addition, the data showed clear genetic distances between the island and shelf populations. Our data are consistent with the hypothesis of survival in situ. The results also suggest that gene flow within A. cornigerais limited, hinting at possible speciation processes acting independently on the Antarctic continental shelf and the peri-Antarctic islands