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Interactions between parasite, host and host-associated microbiota are increasingly understood as important determinants of disease progression and morbidity. Salmon lice, including the parasitic copepod Lepeophtheirus salmonis and related species, are perhaps the most important problem facing Atlantic Salmon aquaculture after feed sustainability. Salmon lice parasitize the surface of the fish, feeding off mucus, scales and underlying tissue. Secondary bacterial infections are a major source of associated morbidity. In this study we tracked the diversity and composition of Salmo salar skin surface microbiota throughout a complete L. salmonis infection cycle among 800 post-smolts as compared to healthy controls. Among infected fish we observed a significant reduction in microbial richness (Chao1, P = 0.0136), raised diversity (Shannon, P < 7.86e-06) as well as highly significant destabilisation of microbial community composition (Pairwise Unifrac, beta-diversity, P < 1.86e-05; P = 0.0132) by comparison to controls. While undetectable on an individual level, network analysis of microbial taxa on infected fish revealed the association of multiple pathogenic genera (Vibrio, Flavobacterium, Tenacibaculum, Pseudomonas) with high louse burdens. We discuss our findings in the context of ecological theory and colonisation resistance, in addition to the role microbiota in driving primary and secondary pathology in the host.

Despite the importance of larval biology in the life histories of many marine animals, relatively little information exists on the dynamics and genetic composition of larval cohorts. The supply of megalopae larvae of the shore crab, Carcinus maenas, was measured on a daily basis during 8 months spread along two larval periods (2006 and 2007) at the Ria de Aveiro estuary, on the Portuguese northwest coast. A total of 10 microsatellite DNA loci were employed to explore the genetic structure, variability and relatedness of temporally distinct megalopal events, selected from the major pulses of supply. Larval variation was also compared genetically with that of a previously studied adult crabs sample, at the same loci, collected in 2006 and 2007 along the Iberian Peninsula. Results revealed a lack of genetic differentiation and identical diversity levels among larval events over time. No evidence of reduced genetic diversity between megalopae relative to the diversity assessed from the pooled sample of adults was found. Moreover, there was no evidence of any family relatedness among larvae from temporal events. The results obtained for C. maenas contradict predictions made by the sweepstakes reproduction hypothesis, in which large variance in reproductive success is expected, which is presumably detectable as sharp genetic discontinuities among separate larval events. Data here indicate conversely a high degree of temporal genetic stability among larval supply to a given estuary under variable oceanographic conditions, consistent with the hypothesis that sampled larvae were drawn from a large number of adults that do not differ in reproductive success.

In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.

The Atlantic Ocean-Mediterranean Sea junction has been proposed as an important phylogeographical area on the basis of concordance in genetic patterns observed at allozyme, mtDNA and microsatellite DNA markers in several marine species. This study presents microsatellite DNA data for a mobile invertebrate species in this area, the cuttlefish Sepia officinalis, allowing comparison of this relatively new class of DNA marker with previous allozyme results, and examination of the relative effects on gene flow of the Strait of Gibraltar and the Almería-Oran oceanographic front. Genetic variation at seven microsatellite loci screened in six samples from NE Atlantic and Mediterranean coasts of the Iberian Peninsula was high (mean Na = 9.6, mean H(e) = 0.725). Microsatellites detected highly significant subpopulation structuring (F(ST)= 0.061; R(ST) = 0.104), consistent with an isolation-by-distance model of low levels of gene flow. Distinct and significant clinal changes in allele frequencies between Atlantic and Mediterranean samples found at five out of seven loci, however indicate these results might be also consistent with an alternative model of secondary contact and introgression between previously isolated and divergent populations, as previously proposed for other marine species from the Atlantic-Mediterranean area. A pronounced 'step' change between SW Mediterranean samples associated with the Almería-Oran front suggests this oceanographic feature may represent a contemporary barrier to gene flow.

Two regions of the mtDNA of Atlantic herring (Clupea harengus), ND3/4 and ND5/6, were surveyed by RFLP analysis to assess the effects of marker variability on the power of statistical tests. Although haplotype diversity was similar, marked differences in the number of common haplotypes were observed between the two regions, with ND3/4 having a more even distribution of haplotype frequencies. ND3/4 also revealed higher differentiation among samples than ND5/6, similar to previously published microsatellite data of the same samples. The data suggested that the highly skewed haplotype distribution of many mtDNA markers may be one of the reasons for the less frequent detection of population differentiation compared to microsatellites. Pooling ('binning') of related haplotypes did not increase differentiation revealed by each mtDNA region individually, but greatly strengthened geographical patterns shown by both regions combined. The data provided evidence for genetic differentiation of Icelandic herring from other north-eastern Atlantic stocks, and indicated genetic differences between Baltic and Celtic Sea herring. However, mtDNA data failed to confirm previously reported differences between Barents Sea herring, Norwegian fjord populations and Norwegian spring spawners.

Previous attempts to test for small-scale stock structuring within Atlantic herring (Clupea harengus L.) with molecular markers have been hampered by uninformative levels of genetic variation. Here we report the first application of microsatellite DNA markers to investigate population subdivision in Atlantic herring from Norwegian waters and the Barents Sea, and also examine microsatellite differentiation between C. harengus and Pacific herring (C. pallasi). Results from four microsatellite loci indicate high, and informative, variation compared to molecular markers used previously: number of alleles per locus=18-41; mean expected heterozygosity within samples=0.90-0.93. Significant genetic differences were detected between almost all samples representing postulated Icelandic summer-spawner, Norwegian spring-spawner and Norwegian fjord stocks, using Fisher's exact test, FST and RST values. Levels of allele frequency differentiation between Atlantic and Pacific herring overlapped the range seen among Atlantic herring samples, indicating that microsatellites are poor indicators of the degree of species differentiation. Comparison with allozyme and mitochondrial DNA restriction fragment length polymorphism (RFLP) datasets from the same samples suggests that microsatellites may detect structuring at a finer scale, but are less informative at larger scales of divergence.