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The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

The present study investigated the genetic efficiency of enhancing populations of wild scallops using hatchery-produced seed scallops. Scallops from the Isle of Man (IOM), Irish Sea, and from a scallop hatchery were genotyped using 15 microsatellite markers. Hatchery scallops had equivalent heterozygosity to wild scallops, but rare alleles were likely to be lost in hatchery scallops as represented by lower allelic richness. The effective number of breeders ([N.sub.b]) of the hatchery scallops was estimated at 32.4 (95% CI: 24.4-44.9). The confidence intervals for the estimates of [N.sub.b] for the IOM included infinity. When [N.sub.b] becomes large the genetic signal is weak compared with the sampling noise; therefore, while we can be confident that the [N.sub.b] of IOM scallops is larger than that of the hatchery, the precise difference is uncertain. Simulations showed it is possible, in some scenarios, that stock enhancement with hatchery seed can lead to an increase in the wild population's effective size; however, in the majority of scenarios a decrease in the effective size of the wild population is more likely. A precautionary approach to stock enhancement with hatchery seed is advised. La presente etude se penche sur l'efficacite genetique de la mise en valeur de populations de petoncles sauvages a l'aide de petoncles reproducteurs produits en ecloserie. Des petoncles de l'ile de Man (IOM), dans la mer d'Irlande, et d'une ecloserie de petoncles ont ete genotypes sur la base de 15 marqueurs microsatellites. Si les petoncles d'ecloserie presentaient une heterozygotie equivalente a celle des petoncles sauvages, la plus faible richesse allelique des petoncles d'ecloserie temoignait vraisemblablement de la disparition d'alleles rares. Le nombre effectif de geniteurs ([N.sub.b]) parmi les petoncles d'ecloserie a ete estime a 32,4 % (IC a 95 %: 24,4-44,9). Les intervalles de confiance pour les estimations du [N.sub.b] pour l'IOM comprenaient l'infinite; quand [N.sub.b] est grand, le signal genetique est faible par rapport au bruit d'echantillonnage de sorte que, s'il est permis de conclure que le [N.sub.b] des petoncles de l'IOM est plus eleve que celui des petoncles d'ecloserie, la difference exacte ne peut etre etablie avec certitude. Des simulations ont demontre qu'il est possible, dans certains scenarios, que la mise en valeur des stocks avec des petoncles producteurs provenant d'ecloserie puisse mener a une augmentation de la taille effective de la population sauvage. Cela dit, dans la majorite des scenarios, une diminution de la taille effective de la population sauvage est plus probable. Une approche prudente est donc a privilegier en ce qui concerne la mise en valeur des stocks a l'aide de petoncles reproducteurs issus d'ecloserie. [Traduit par la Redaction], Introduction Global scallop (Pectinid) capture production has risen from 500 000 tonnes in the 1980s to 840 000 tonnes in 2010 (FAO 2012), and these scallop fisheries are highly valuable. [...]

Until recently, the study of negative and antagonistic interactions (for example, competition and predation) has dominated our understanding of community structure, maintenance and assembly (1). Nevertheless, a recent theoretical model suggests that positive interactions (for example, mutualisms) may counterbalance competition, facilitating long-term coexistence even among ecologically undifferentiated species (2). Mullerian mimics are mutualists that share the costs of predator education (3) and are therefore ideally suited for the investigation of positive and negative interactions in community dynamics. The sole empirical test of this model in a Mullerian mimetic community supports the prediction that positive interactions outweigh the negative effects of spatial overlap (4) (without quantifying resource acquisition). Understanding the role of trophic niche partitioning in facilitating the evolution and stability of Mullerian mimetic communities is now of critical importance, but has yet to be formally investigated. Here we show that resource partitioning and phylogeny determine community structure and outweigh the positive effects of Mullerian mimicry in a species-rich group of neotropical catfishes. From multiple, independent reproductively isolated allopatric communities displaying convergently evolved colour patterns, 92% consist of species that do not compete for resources. Significant differences in phylogenetically conserved traits (snout morphology and body size) were consistently linked to trait-specific resource acquisition. Thus, we report the first evidence, to our knowledge, that competition for trophic resources and phylogeny are pivotal factors in the stable evolution of Mullerian mimicry rings. More generally, our work demonstrates that competition for resources is likely to have a dominant role in the structuring of communities that are simultaneously subject to the effects of both positive and negative interactions., Positive interactions, such as mutualistic associations, can have important roles in the maintenance of community structure, potentially outweighing the negative effects of competition for niche space (2). The empirical evidence [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.anbehav.2004.09.016 Byline: Suzanne C. Mills, Martin I. Taylor, John D. Reynolds Abstract: Two major hypotheses of host-parasite interactions have been proposed to explain cases where hosts do not defend themselves against parasites. The evolutionary lag hypothesis suggests that there has been insufficient time for a host response to evolve, whereas the evolutionary equilibrium hypothesis proposes that host defence does not evolve because it carries costs that outweigh the benefits. We tested potential benefits and costs of host defence in an unusual interaction, between a freshwater fish, the European bitterling, Rhodeus sericeus, and live unionid mussels that are used as hosts for the fish's eggs. We found a significant reduction in ventilation rate of mussels that were incubating bitterling embryos, which became more severe with an increasing number of embryos. We tested the hypothesis that the risk of ejecting a mussel's own larvae while ejecting bitterling embryos has constrained the evolution of a host response. This predicts that brooding female mussels would retain more bitterling larvae than males or nonbrooding females. This prediction was not supported: brooding female mussels contained as many larvae per accessible gill as, and fewer in total than, males or nonbrooding females. In summary, based on the costs and benefits of ejection that we measured, we found no evidence in support of the evolutionary equilibrium hypothesis. However, other differences between mussel species, such as gill structure as measured in this study, ventilation rates and differences in the distance eggs are lodged into the gills, may contribute to differences in egg ejection rates. Author Affiliation: Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, U.K. Article History: Received 1 July 2004; Revised 19 August 2004; Accepted 12 September 2004 Article Note: (miscellaneous) MS. number: 8184

Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi‐automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non‐model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE‐based estimates in non‐model species. [ABSTRACT FROM AUTHOR]

The relationship between spawning success and courtship was examined in bower-building cichlid fish from Lake Malawi, Africa. The results showed that the structure of a phenotypic character was inversely proportional to the male parasitic load, with spawning males having substantially fewer dilepipid cestodes in their livers compared to non-spawning males. Moreover, spawning males have substantially heavier gonads compared to unsuccessful males. Results also revealed a correlation between reproductive success and relative liver weight.

Abstract Background Research on the evolution of reproductive isolation in African cichlid fishes has largely focussed on the role of male colours and female mate choice. Here, we tested predictions from the hypothesis that allopatric divergence in male colour is associated with corresponding divergence in preference. Methods We studied four populations of the Lake Malawi Pseudotropheus zebra complex. We predicted that more distantly-related populations that independently evolved similar colours would interbreed freely while more closely-related populations with different colours mate assortatively. We used microsatellite genotypes or mesh false-floors to assign paternity. Fisher's exact tests as well as Binomial and Wilcoxon tests were used to detect if mating departed from random expectations. Results Surprisingly, laboratory mate choice experiments revealed significant assortative mating not only between population pairs with differently coloured males, but between population pairs with similarly-coloured males too. This suggested that assortative mating could be based on non-visual cues, so we further examined the sensory basis of assortative mating between two populations with different male colour. Conducting trials under monochromatic (orange) light, intended to mask the distinctive male dorsal fin hues (blue v orange) of these populations, did not significantly affect the assortative mating by female P. emmiltos observed under control conditions. By contrast, assortative mating broke down when direct contact between female and male was prevented. Conclusion We suggest that non-visual cues, such as olfactory signals, may play an important role in mate choice and behavioural isolation in these and perhaps other African cichlid fish. Future speciation models aimed at explaining African cichlid radiations may therefore consider incorporating such mating cues in mate choice scenarios.

The satyr of Greek mythology was half‐man, half‐goat, with an animal persona signifying immoderate sexual appetites. In biology, satyrization is the disruption of reproduction in matings between closely related species. Interestingly, its effects are often reciprocally asymmetric, manifesting more strongly in one direction of heterospecific mating than the other. Heterospecific matings are well known to result in female fitness costs due to the production of sterile or inviable hybrid offspring and can also occur due to reduced female sexual receptivity, lowering the likelihood of any subsequent conspecific matings. Here we investigated the costs and mechanisms of satyrization in the Drosophila melanogaster species subgroup of fruitflies. The results showed that D. simulans females experienced higher fitness costs from a loss of remating opportunities due to significantly reduced post‐mating sexual receptivity than did D. melanogaster females, as a result of reciprocal heterospecific matings. Reciprocal tests of the effects of male reproductive accessory gland protein (Acp) injections on female receptivity in pairwise comparisons between D. melanogaster and five other species within the melanogaster species subgroup revealed significant post‐mating receptivity asymmetries. This was due to variation in the effects of heterospecific Acps within species with which D. melanogaster can mate, and significant but nonasymmetric Acp effects in species with which it cannot. We conclude that asymmetric satyrization due to post‐mating effects of Acps may be common among diverging and hybridising species. The findings are of interest in understanding the evolution of reproductive isolation and species divergence. [ABSTRACT FROM AUTHOR]

We examine genetic structuring in three commercially important species of the teleost family Carangidae from Malaysian waters: yellowtail scad Atule mate, bigeye scad Selar crumenophthalmus and yellowstripe scad Selaroides leptolepis, from the Indo‐Malay Archipelago. In view of their distribution across contrasting habitats, we tested the hypothesis that pelagic species display less genetic divergence compared with demersal species, due to their potential to undertake long‐distance migrations in oceanic waters. To evaluate population genetic structure, we sequenced two mitochondrial (mt)DNA [650 bp of cytochrome oxidase I (coI), 450 bp of control region (CR)] and one nuclear gene (910 bp of rag1) in each species. One hundred and eighty samples from four geographical regions within the Indo‐Malay Archipelago including a population of yellowtail from Kuwait were examined. Findings revealed that the extent of genetic structuring among populations in the semi‐pelagic and pelagic, yellowtail and bigeye were lower than demersal yellowstripe, consistent with the hypothesis that pelagic species display less genetic divergence compared with demersal species. The yellowtail phylogeny identified three distinct clades with bootstrap values of 86%–99% in mtDNA and 63%–67% in rag1. However, in bigeye, three clades were also observed from mtDNA data while only one clade was identified in rag1 dataset. In yellowstripe, the mtDNA tree was split into three closely related clades and two clades in rag1 tree with bootstraps value of 73%–99% and 56% respectively. However, no geographic structure appears in both mtDNA and rag1 datasets. Hierarchical molecular variance analysis (AMOVA), pair wise FST comparisons and the nearest‐neighbour statistic (Snn) showed significant genetic differences among Kuwait and Indo‐Malay yellowtail. Within the Indo‐Malay Archipelago itself, two distinct mitochondrial lineages were detected in yellowtail suggesting potential cryptic species. Findings suggests varying degrees of genetic structuring, key information relevant to management of exploited stocks, though more rapidly evolving genetic markers should be used in future to better delimit the nature and dynamics of putative stock boundaries. [ABSTRACT FROM AUTHOR]