BackgroundThe Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam.ResultsA normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring.ConclusionsThe transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.

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1 Stable isotopes signatures ( ␦ 13 C and ␦ 15 N) of the most important tree-dwelling ants in an olive orchard were examined, together with the signatures of the most common herbivores, predators and sap-sucking insects. The olive orchard consists of separate subunits (trees) surrounded by a matrix of grasses or bare ground, and the role of ants in such a system is not fully understood. 2 None of the selected ant species was exclusive to the olive trees because they were also observed foraging on vegetation (mainly thistle) under the tree crowns. Hence, the relative contributions of these two sources of energy (olive trees versus herbs/grasses) were assessed by comparing the ␦ 13 C of ants with the signatures of plants and those of other arthropods collected on the trees and on nearby thistles. Next, the trophic level occupied by the ants and their ecological role within the olive food web were determined by examining the ␦ 15 N values and their relationship with indices of ecological performance measuring the potential pressure exerted by each species on the ecosystem. 3 The analysis of 13 C signatures revealed a different contribution of the two energy sources, olive trees versus herbs and grasses, with the former being more important for ants. The analysis of 15 N signatures suggested separate roles for different ant species: some ( Crematogaster scutellaris , Lasius lasioides ) occupied a higher trophic level, mostly involved in predation, whereas others ( Camponotus piceus , Camponotus lateralis ) occupied a lower level, probably involved more in homopteran tending. A fifth species ( Camponotus aethiops ) was in an intermediate position. Finally, the ␦ 15 N levels of the species were significantly correlated with indices of ecological performance.

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There is increasing evidence that most parapatric cryptic/sister taxa are reproductively compatible across their areas of contact. Consequently, the biological species concept, which assumes absence of interbreeding, is becoming a not so effective criterion in evolutionary ecology. Nevertheless, the few parapatric sister taxa showing complete reproductive barriers represent interesting models to study speciation processes and the evolution of reproductive isolation. In this study, we examined contact populations in northwestern Italy of two butterfly species, Zerynthia polyxena and Z. cassandra, characterized by different genitalic morphotypes. We studied levels of divergence among 21 populations distributed from Sicily to France using three genetic markers (the mitochondrial COI and ND1 genes and the nuclear wingless gene) and genitalic geometric morphometrics. Moreover, we performed species distribution modelling to estimate different climatic requirements of Z. polyxena and Z. cassandra. We projected climatic data into glacial maximum scenarios in order to verify if and to which extent glacial cycles could have contributed to speciation processes. Genetic and morphometric analyses identified two main groups. All specimens showed a concordant pattern of diversification, including those individuals sampled in the contact area. Haplotype distribution and climatic models showed that during glacial maxima both species experienced a strong range contraction and presumably remained separated into different microrefugia in southern France, in the Italian Peninsula and on the islands of Elba and Sicily. Long term separation was probably favoured by reduced dispersal ability and high phylopatry, while genitalic diversification probably favoured interbreeding avoidance. Conversely, the aposematic wing pattern remained almost identical. We compared our results with those obtained in other species and concluded that Z. polyxena and Z. cassandra represent a valuable model in the study of speciation.

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Habitat diversity plays a significant role in shaping the genetic structure of cetacean populations. However, the processes involved in defining the genetic differentiation of these highly mobile marine mammals are still largely unknown. Levels of genetic differentiation and dispersal patterns of common bottlenose dolphins (Tursiops truncatus) were assessed in the north‐eastern Mediterranean Sea, with a focus on the Adriatic Sea. This is a region characterized by diverse marine ecosystems and high levels of human‐induced habitat degradation. Although this species seems almost uniformly distributed throughout the Adriatic Basin, genetic evidence rejected the hypothesis of a single stock. Pairwise estimates of genetic differentiation at 12 microsatellite loci, and mitochondrial DNA (entire control region, 920bp), revealed diverse levels of genetic differentiation among five putative populations from the Tyrrhenian Sea to the Aegean Sea. A fine‐scale genetic structure was recorded within the Adriatic Sea, where females appear to be the principal gene flow mediators. The assessment of recent migration rates indicates a relatively high level of gene flow from the North Adriatic towards adjacent areas. Indication of a fine‐scale population structure across the Adriatic Sea is a factor to be carefully considered in the emerging marine management scenario set by the implementation of the EU Marine Strategy Framework Directive (2008/56/CE), particularly when it comes to assessing and managing direct mortality caused by human activities (e.g. fisheries or maritime traffic). A good knowledge of population structure at the basin level is also fundamental for the identification of potential Adriatic Special Areas of Conservation for the bottlenose dolphin under the Habitats Directive (Council Directive 92/43/EEC). Copyright © 2013 John Wiley & Sons, Ltd.

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