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Made available in DSpace on 2022-04-28T19:44:05Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-02-01 Biotechnology and Biological Sciences Research Council H2020 European Research Council Natural Environment Research Council 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. School of Biological Sciences University of East Anglia Department of Structural and Functional Biology Institute of Biosciences/UNESP Rua Doutor Antonio Celso Wagner Zanin Department of Cell and Developmental Biology John Innes Centre Future Food Beacon of Excellence and the School of Life Sciences University of Nottingham Department of Structural and Functional Biology Institute of Biosciences/UNESP Rua Doutor Antonio Celso Wagner Zanin Biotechnology and Biological Sciences Research Council: BB/P013511/1 Biotechnology and Biological Sciences Research Council: BB/R017174/1 H2020 European Research Council: ERC-StG 679056 HOTSPOT Natural Environment Research Council: NE/L002582/1

Crustaceans are notoriously difficult to age because of their indeterminate growth and the moulting of their exoskeleton throughout life. The poor knowledge of population age structure in crustaceans therefore hampers accurate assessment of population dynamics and consequently sustainable fisheries management. Quantification of DNA methylation of the evolutionarily conserved ribosomal DNA (rDNA) may allow for age prediction across diverse species. However, the rDNA epigenetic clock remains to be tested in crustaceans, despite its potential to inform both ecological and evolutionary understanding, as well as conservation and management practices. Here, patterns of rDNA methylation with age were measured across 5154 bp of rDNA corresponding to 355 quality‐filtered loci in the economically important European lobster (Homarus gammarus). Across 0‐ to 51‐month‐old lobsters (n = 155), there was a significant linear relationship between age and percentage rDNA methylation in claw tissue at 60% of quality‐filtered loci (n = 214). An Elastic Net regression model using 46 loci allowed for the accurate and precise age estimation of individuals (R 2 = 0.98; standard deviation = 1.6 months). Applying this ageing model to antennal DNA from wild lobsters of unknown age (n = 38) resulted in predicted ages that are concordant with estimates of minimum size at age in the wild (mean estimated age = 40.1 months; range 32.8–55.7 months). Overall, the rDNA epigenetic clock shows potential as a novel, nonlethal ageing technique for European lobsters. However, further validation is required across a wider range of known‐age individuals and tissue types before the model can be used in fisheries management.

Background Transposable elements are significant components of most organism’s genomes, yet the reasons why their abundances vary significantly among species is poorly understood. A recent study has suggested that even in the absence of traditional molecular evolutionary explanations, transposon proliferation may occur through a process known as ‘transposon engineering’. However, their model used a fixed beneficial transposon insertion frequency of 20%, which we believe to be unrealistically high. Results Reducing this beneficial insertion frequency, while keeping all other parameters identical, prevented transposon proliferation. Conclusions We conclude that the author’s original findings are better explained through the action of positive selection rather than ‘transposon engineering’, with beneficial insertion effects remaining important during transposon proliferation events.

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., Seminal Fluid Proteins (Sfps) are transferred with the ejacuate during mating, conferring a variety of post‐mating effects on females. We found asymmetries in the strength and effects of these Sfps in reciprocal cross‐species comparisons between closely related Drosophila species.

Aim: We compare the performance of habitat suitability models using climate data only or climate data together with water chemistry, land cover and predation pressure data to model the distribution of European grayling (Thymallus thymallus). From these models, we (a) investigate the relationship between habitat suitability and genetic diversity; (b) project the distribution of grayling under future climate change; and (c) model the effects of habitat mitigation on future distributions. Location: United Kingdom. Methods: Maxent species distribution modelling was implemented using a Simple model (only climate parameters) or a Full model (climate, water chemistry, land use and predation pressure parameters). Areas of high and low habitat suitability were designated. Associations between habitat suitability and genetic diversity for both neutral and adaptive markers were examined. Distribution under minimal and maximal future climate change scenarios was modelled for 2050, incorporating projections of future flow scenarios obtained from the Centre for Ecology and Hydrology. To examine potential mitigation effects within habitats, models were run with manipulation of orthophosphate, nitrite and copper concentrations. Results: We mapped suitable habitat for grayling in the present and the future. The Full model achieved substantially higher discriminative power than the Simple model. For low suitability habitat, higher levels of inbreeding were observed for adaptive, but not neutral, loci. Future projections predict a significant contraction of highly suitable areas. Under habitat mitigation, modelling suggests that recovery of suitable habitat of up to 10% is possible. Main conclusions: Extending the climate-only model improves estimates of habitat suitability. Significantly higher inbreeding coefficients were found at immune genes, but not neutral markers in low suitability habitat, indicating a possible impact of environmental stress on evolutionary potential. The potential for habitat mitigation to alleviate distributional changes under future climate change is demonstrated, and specific recommendations are made for habitat recovery on a regional basis.

Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits. However, the impact of domestication on eye size has not been studied. We measured body size corrected eye size in 4000 salmon from six common garden experiments conducted under artificial and natural conditions, in freshwater and saltwater environments, in two countries. Within these common gardens, offspring of domesticated and wild parents were crossed to produce 11 strains, with varying genetic backgrounds (wild, domesticated, F1 hybrids, F2 hybrids and backcrosses). Size-adjusted eye size was influenced by both genetic and environmental factors. Domesticated fish reared under artificial conditions had smaller adjusted eye size when compared to wild fish reared under identical conditions, in both the freshwater and marine environments, and in both Irish and Norwegian experiments. However, in parr that had been introduced into a river environment shortly after hatching and sampled at the end of their first summer, differences in adjusted eye size observed among genetic groups were of a reduced magnitude and were nonsignificant in 2-year-old sea migrating smolts sampled in the river immediately prior to sea entry. Collectively, our findings could suggest that where natural selection is present, individuals with reduced eye size are maladapted and consequently have reduced fitness, building on our understanding of the mechanisms that underlie a well-documented reduction in the fitness of the progeny of domesticated salmon, including hybrid progeny, in the wild. publishedVersion

Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p

Genetic bottlenecks can limit the success of populations colonizing new ranges. However, successful colonizations can occur despite bottlenecks, a phenomenon known as the genetic paradox of invasion. Eusocial Hymenoptera such as bumblebees (Bombusspp.) should be particularly vulnerable to genetic bottlenecks, since homozygosity at the sex-determining locus leads to costly diploid male production (DMP). The Tree Bumblebee (Bombus hypnorum) has rapidly colonized the UK since 2001 and has been highlighted as exemplifying the genetic paradox of invasion. Using microsatellite genotyping, combined with the first genetic estimates of DMP in UKB. hypnorum, we tested two alternative genetic hypotheses (‘bottleneck’ and ‘gene flow’ hypotheses) forB. hypnorum's colonization of the UK. We found that the UK population has not undergone a recent severe genetic bottleneck and exhibits levels of genetic diversity falling between those of widespread and range-restrictedBombusspecies. Diploid males occurred in 15.4% of reared colonies, leading to an estimate of 21.5 alleles at the sex-determining locus. Overall, the findings show that this population is not bottlenecked, instead suggesting that it is experiencing continued gene flow from the continental European source population with only moderate loss of genetic diversity, and does not exemplify the genetic paradox of invasion.

Understanding trade‐offs in wild populations is difficult, but important if we are to understand the evolution of life histories and the impact of ecological variables upon them. Markers that reflect physiological state and predict future survival would be of considerable benefit to unraveling such trade‐offs and could provide insight into individual variation in senescence. However, currently used markers often yield inconsistent results. One underutilized measure is hematocrit, the proportion of blood comprising erythrocytes, which relates to the blood's oxygen‐carrying capacity and viscosity, and to individual endurance. Hematocrit has been shown to decline with age in cross‐sectional studies (which may be confounded by selective appearance/disappearance). However, few studies have tested whether hematocrit declines within individuals or whether low hematocrit impacts survival in wild taxa. Using longitudinal data from the Seychelles warbler (Acrocephalus sechellensis), we demonstrated that hematocrit increases with age in young individuals (, Using long‐term data we investigated the association between haematocrit, longitudinal age and survival in a wild vertebrate population—the Seychelles warbler (Acrocephalus sechellensis). Haematocrit exhibited a distinctive age‐dependent pattern within‐individuals, and young individuals with high haematocrit had poorer survival prospects. This study highlights a novel physiological change with age that is indicative of individual condition in wild populations.

Livestock domestication has long been a part of agriculture, estimated to have first occurred approximately 10 000 years ago. Despite the plethora of traits studied, there is little understanding of the possible impacts domestication has had on internal organs, which are key determinants of survival. Moreover, the genetic basis of observed associated changes in artificial environments is still puzzling. Here we examine impacts of captivity on two organs in Atlantic salmon ( Salar salar ) that have been domesticated for approximately 50 years: heart and liver, in addition to growth. We studied multiple families of wild, domesticated, F 1 and F 2 hybrid, and backcrossed strains of S. salar in replicated common garden tanks during the freshwater and marine stages of development. Heart and liver weight were investigated, along with heart morphology metrics examined in just the wild, domesticated and F 1 hybrid strains (heart height and width). Growth was positively linked with the proportion of the domesticated strain, and recombination in F 2 hybrids (and the potential disruption of co-adapted gene complexes) did not influence growth. Despite the influence of domestication on growth, we found no evidence for domestication-driven divergence in heart or liver morphology. However, sexual dimorphism was detected in heart morphology, and after controlling for body size, females exhibited significantly larger heart weight and heart width when compared with males. Wild females also had an increased heart height when compared with wild males, and this was not observed in any other strain. Females sampled in saltwater showed significantly larger heart height with rounder hearts, than saltwater males. Collectively, these results demonstrate an additive basis of growth and, despite a strong influence of domestication on growth, no clear evidence of changes in heart or liver morphology associated with domestication was identified.

BackgroundQuantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations.ResultsAfter rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets.DiscussionThe observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.

The tendency of predators to preferentially attack phenotypically odd prey in groups (the oddity effect) is a clear example of how predator cognition can impact behaviour and morphology in prey. Through targeting phenotypically odd prey, predators are thought to avoid the cognitive constraints that delay and limit the success of attacks on homogenous prey groups (the confusion effect). In addition to influencing which prey a predator will attack, the confusion and oddity effects would also predict that attacks on odd prey can occur more rapidly than attacking the majority prey type, as odd prey are more easily targeted, but this prediction has yet to be tested. Here, we used kerri tetra fish, Inpaichthys kerri, presented with mixed phenotypic groups of Daphnia dyed red or black to investigate whether odd prey in groups are preferentially attacked and whether these attacks were faster than those on the majority prey type. In agreement with previous work, odd prey were targeted and attacked more often than expected from their frequency in the prey groups, regardless of whether the odd prey was red in a group of black prey or vice versa. However, no difference was found in the time taken to attack odd vs. majority prey items, contrary to our predictions. Our results suggest that the time taken to make an attack is determined by a wider range of factors or is subject to greater variance than the choice of which prey is selectively targeted in a group.

Additional co-authors: G. Peirson, K. K. Richter, M. I. Taylor,C. N. Trueman, B. Hayden, J. R. Stevens

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A review of the functional role of jellyfish in Ecopath with Ecosim (EwE) models by Pauly et al. [Pauly, D., Graham, W., Libralato, S., Morissette, L., and Deng Palomares, M. L. 2009. Jellyfish in ecosystems, online databases, and ecosystem models. Hydrobiologia, 616: 67–85.] a decade ago concluded that recreation of jellyfish population dynamics in models required additional ecological research and the careful consideration of their unique biology during model construction. Here, amidst calls for ecosystem-based management and the growing recognition of jellyfishes' role in foodwebs, we investigate how jellyfish are implemented in EwE models and identify areas requiring improvement. Over time, an increasing percentage of models have included jellyfish. Jellyfish were often linked to the wider ecosystem, with many predators and prey included in models. However, ecotrophic efficiency, a measure of the extent to which they are used by higher trophic levels, was frequently set at low values, suggesting that jellyfish are still perceived as under-utilized components of the ecosystem. Moving forward, greater care should be taken to differentiate the functional roles played by ctenophores, cnidarians, and pelagic tunicates. Additionally, when feasible, early life stages should be incorporated as multi-stanza groups to more accurately depict jellyfishes' complex life cycle.

To establish if fishes’ consumption of jellyfish changes through the year, we conducted a molecular gut‐content assessment on opportunistically sampled species from the Celtic Sea in October and compared these with samples previously collected in February and March from the Irish Sea. Mackerel Scomber scombrus were found to feed on hydrozoan jellyfish relatively frequently in autumn, with rare consumption also detected in sardine Sardina pilchardus and sprat Sprattus sprattus. By October, moon jellyfish Aurelia aurita appeared to have escaped predation, potentially through somatic growth and the development of stinging tentacles. This is in contrast with sampling in February and March where A. aurita ephyrae were heavily preyed upon. No significant change in predation rate was observed in S. sprattus, but jellyfish predation by S. scombrus feeding in autumn was significantly higher than that seen during winter. This increase in consumption appears to be driven by the consumption of different, smaller jellyfish species than were targeted during the winter.

The diversity of reproduction and associated mating patterns in Atlantic salmon (Salmo salar) has long captivated evolutionary biologists.Salmo salarexhibit strategies involving migration, bold mating behaviours and radical morphological and physiological change. One such radical change is the elongation and curvature of the lower jaw in sexually mature males into a hook-like appendage called the kype. The kype is a secondary sexual characteristic used in mating hierarchies and a prime candidate for sexual selection. As one of the core global aquaculture fish species, however, mate choice, and thus sexual selection, has been replaced by industrial artificial fertilization seeking to develop more commercially viable strains. Removal of mate choice provides a unique opportunity to examine the kype over successive generations in the absence of sexual selection. Here we use a large-scale common-garden experiment, incorporating six experimental strains (wild, farmed and wild × farmed hybrids), experiencing one to three sea winters, to assess the impact of age and genetic background. After controlling for allometry, fork length-adjusted kype height (AKH) was significantly reduced in the domesticated strain in comparison to two wild strains. Furthermore, genetic variation at a locus on linkage group SSA1 was associated with kype height, and a locus on linkage group SSA23 was associated with fork length-adjusted kype length (AKL). The reduction in fork length-AKH in domesticated salmon suggests that the kype is of importance in mate choice and that it has decreased due to relaxation of sexual selection. Fork length-AKL showed an increase in domesticated individuals, highlighting that it may not be an important cue in mate choice. These results give us insight into the evolutionary significance of the kype, as well as implications of genetic induced phenotypic change caused by domesticated individuals escaping into the natural environment.

Growth of farmed, wild and F1 hybrid Atlantic salmon parr Salmo salar was investigated under three contrasting feeding regimes in order to understand how varying levels of food availability affects relative growth. Treatments consisted of standard hatchery feeding (ad libitum), access to feed for 4 h every day, and access to feed for 24 h on three alternate days weekly. Mortality was low in all treatments, and food availability had no effect on survival of all groups. The offspring of farmed S. salar significantly outgrew the wild S. salar, while hybrids displayed intermediate growth. Furthermore, the relative growth differences between the farmed and wild S. salar did not change across feeding treatments, indicating a similar plasticity in response to feed availability. Although undertaken in a hatchery setting, these results suggest that food availability may not be the sole driver behind the observed reduced growth differences found between farmed and wild fishes under natural conditions.

The global trade in ornamental fish involves c. 125 countries worldwide and is worth c. US $15-30 billion each year. This total is dominated (90%) by freshwater fishes, most of which are sourced from breeding facilities located in developing countries, typically in Asia or South America, but also in Israel, USA and Europe. Some fish are obtained from natural (wild) sources in Asia and South America, but the exact percentage of wild-caught fish is difficult to quantify given a lack of reliable data. Although c. 1000 species of freshwater fishes are widely available (from a total of > 5300 on sale), the most dominant freshwater fishes in the market comprise only 30 species from the orders Cyprinodontiformes, Perciformes, Characiformes and Siluriformes. In this perspectives review, illustrative example case studies of wild-fish collecting (Barcelos and Rio Xingu, Brazil) and breeding projects (Java, Indonesia) are described. In addition, wild-collecting expeditions to West Papua, Indonesia are discussed, focused on discovering novel species of rainbowfish (Melanotaeniidae) for breeding in captivity. Sustainability of the aquarium industry is considered in its broadest sense. The aquarium industry has been portrayed as both a major threat to natural ecosystems, but also as being part of the solution in terms of helping to maintain species when they have gone extinct in the wild or offering an income to impoverished citizens who might otherwise engage in much more destructive practices.

Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.

Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this article, we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short. Our method is based on representing introgression in terms of a certain “overlay” of the allele tree over the lineage trees, called an overlaid species forest (OSF). OSFs are similar to phylogenetic networks although a key difference is that they typically have multiple roots because each monophyletic group in the species tree has a different point of origin. Employing a new model for introgression, we derive an efficient algorithm for building OSFs called OSF-Builder that is guaranteed to return an optimal OSF in the sense that the number of potential introgression events is minimized. As well as using simulations to assess the performance of OSF-Builder, we illustrate its use on a butterfly data set in which introgression has been previously inferred. The OSF-Builder software is available for download from https://www.uea.ac.uk/computing/software/OSF-Builder.

Preservation of genetic diversity is critical to successful conservation, and there is increasing demand for the inclusion of ecologically meaningful genetic information in management decisions. Supportive breeding programmes are increasingly implemented to combat declines in many species, yet their effect on adaptive genetic variation is understudied. This is despite the fact that supportive breeding may interfere with natural evolutionary processes. Here, we assessed the performance of neutral and adaptive markers (major histocompatibility complex; MHC) to inform management of European grayling (Thymallus thymallus), which routinely involves supplementation of natural populations with hatchery-reared fish (stocking). This study is the first to characterize MH II DAA and DAB loci in grayling and to investigate immune genetic variation in relation to management practice in this species. High-throughput Illumina sequencing of "introduced," "stocked native" and "non-stocked native" populations revealed significantly higher levels of allelic richness and heterozygosity for MH markers than microsatellites exclusively in non-stocked native populations. Likewise, significantly lower differentiation at the MH II than for microsatellites was apparent when considering non-stocked native populations, but not stocked populations. We developed a simulation model to test the effects of relaxation of selection during the early life stage within captivity. Dependent on the census population size and stocking intensity, there may be long-term effects of stocking on MH II, but not neutral genetic diversity. This is consistent with our empirical results. This study highlights the necessity for considering adaptive genetic variation in conservation decisions and raises concerns about the efficiency of stocking as a management practice.

Venomous teeth are rare in fishes, which typically utilise spines for defence. A new study reveals the evolutionary origins of fangs and venom in the Nemophini blennies and shows that, in contrast to snakes and lizards, the fangs pre-date the venom.

Localized outbreaks of jellyfish, known as blooms, cause a variety of adverse ecological and economic effects. However, fundamental aspects of their ecology remain unknown. Notably, there is scant information on the role jellyfish occupy in food webs: in many ecosystems, few or no predators are known. To identify jellyfish consumers in the Irish Sea, we conducted a molecular gut content assessment of 50 potential predators using cnidarian-specific mtDNA primers and sequencing. We show that jellyfish predation may be more common than previously acknowledged: uncovering many previously unknown jellyfish predators. A substantial proportion of herring and whiting were found to have consumed jellyfish. Rare ingestion was also detected in a variety of other species. Given the phenology of jellyfish in the region, we suggest that the predation was probably targeting juvenile stages of the jellyfish life cycle.

Size-selective harvesting in commercial fisheries can induce rapid changes in biological traits. While experimental and wild harvested populations often exhibit clear shifts in body size and maturation associated with fishing pressure, the relative contributions of genetic and environmental factors to these shifts remain uncertain and have been much debated. To date, observations of so-called fisheries-induced evolution (FIE) have been based solely on phenotypic measures, such as size data. Genetic data are hitherto lacking. Here, we quantify genetic versus environmental change in response to size-selective harvesting for small and large body size in guppies (Poecilia reticulata) across three generations of selection. We document for the first time significant changes at individual genetic loci, some of which have previously been associated with body size. In contrast, variation at neutral microsatellite markers was unaffected by selection, providing direct genetic evidence for rapid evolution induced by size-selective harvesting. These findings demonstrate FIE in an experimental system, with major implications for the sustainability of harvested populations, as well as impacts on size-structured communities and ecosystem processes. These findings highlight the need for scientists and managers to reconsider the capacity of harvested stocks to adapt to, and recover from, harvesting and predation. © 2013 The Ecological Society of America.

Twelve microsatellite markers were developed for the scallop Pecten maximus. The markers were tested in three geographically diverse populations and all markers were polymorphic in all three populations. The mean number of alleles per locus ranged from 2 to 10.67 and the observed and expected heterozygosity ranged from 0.05 to 0.67 and 0.05 to 0.81 respectively. Some loci showed evidence of null alleles and an excess of homozygotes in some populations but 9 loci conformed to Hardy–Weinberg expectations. These new loci can be combined with previously published microsatellites to create a powerful suite of markers for genetic analyses.

Severe impacts on biodiversity are predicted to arise from climate change. These impacts may not be adequately addressed by conventional approaches to conservation. As a result, additional management actions are now being considered. However, there is currently limited guidance to help decision makers choose which set of actions (and in what order) is most appropriate for species that are considered to be vulnerable. Here, we provide a decision framework for the full complement of actions aimed at conserving species under climate change from ongoing conservation in existing refugia through various forms of mobility enhancement to ex situ conservation outside the natural environment. We explicitly recognize that allocation of conservation resources toward particular actions may be governed by factors such as the likelihood of success, cost and likely co-benefits to non-target species in addition to perceived vulnerability of individual species. As such, we use expert judgment of probable tradeoffs in resource allocation to inform the sequential evaluation of proposed management interventions.

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 (Nb) of the hatchery scallops was estimated at 32.4 (95% CI: 24.4–44.9). The confidence intervals for the estimates of Nbfor the IOM included infinity. When Nbbecomes large the genetic signal is weak compared with the sampling noise; therefore, while we can be confident that the Nbof 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.

Released individuals can have negative impacts on native populations through various mechanisms, including competition, disease transfer and introduction of maladapted gene complexes. Previous studies indicate that the level of farmed Atlantic salmon introgression in native populations is population specific. However, few studies have explored the potential role of population diversity or river characteristics, such as temperature, on the consequences of hybridization. We compared freshwater growth of multiple families derived from two farmed, five wild and two F1 hybrid salmon populations at three contrasting temperatures (7°C, 12°C and 16°C) in a common garden experiment. As expected, farmed salmon outgrew wild salmon at all temperatures, with hybrids displaying intermediate growth. However, differences in growth were population specific and some wild populations performed better than others relative to the hybrid and farmed populations at certain temperatures. Therefore, the competitive balance between farmed and wild salmon may depend both on the thermal profile of the river and on the genetic characteristics of the respective farmed and wild strains. While limited to F1 hybridization, this study shows the merits in adopting a more complex spatially resolved approach to risk management of local populations.

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method.

High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5‐12 � C) and two salinity clines (5‐35&). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic‐North Sea transition area, North Sea ⁄British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea ⁄North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.

Stomach contents of potential predators from a flatfish nursery ground on the Scot- tish west coast were examined visually and probed using a TaqMan real-time PCR based assay designed to detect plaice Pleuronectes platessa DNA. Stomachs from 1137 brown shrimp Crangon crangon, along with a lesser number of shore crab Carcinus maenas, grey gurnard Eutrigla gurnardus and Gobiidae were analysed. Overall 45% of shrimp tested positive for plaice DNA, a proportion considerably higher than in stomachs containing visually identifiable flatfish remains. When scaled to the population level, predation by shrimp generated an estimated mortality of ~9% d -1 , which compares with a decline in plaice abundance from mid-May to mid-June of ~4.4% d −1 . The discrepancy between mortality estimates based on molecular and catch-curve analysis might be due to sampling being conducted at low water between dusk and dawn, which would concentrate predators and prey at times coincident with peaks of shrimp feeding. In addition, the sensitivity of the TaqMan assay could have led to some over-estimation because non-fatal interac- tions may also have been detected, e.g. shrimp are known to nibble the fins of flatfish, that might result in a positive TaqMan result but not necessarily in mortality for the fish. The percentage of shrimp testing positive for presence of plaice DNA in their stomachs was also related to plaice density in a positive, linear manner. For less abundant predators, stomachs of 6% of shore crabs, 40% of gurnards and 11% of large gobies also tested positive.

Whole genome duplication (leading to polyploidy) is widely accepted as an important evolutionary force in plants, but it is less recognized as a driver of animal diversification. Nevertheless, it occurs across a wide range of animals; this review investigates why it is particularly common in fish and amphibians, while rare among other vertebrates. We review the current geographic, ecological and phylogenetic distributions of sexually reproducing polyploid taxa before focusing more specifically on what factors drive polyploid formation and establishment. In summary, (1) polyploidy is phylogenetically restricted in both amphibians and fishes, although entire fish, but not amphibian, lineages are derived from polyploid ancestors. (2) Although mechanisms such as polyspermy are feasible, polyploid formation appears to occur principally through unreduced gamete formation, which can be experimentally induced by temperature or pressure shock in both groups. (3) External reproduction and fertilization in primarily temperate freshwater environments potentially exposes zygotes to temperature stress, which can promote increased production of unreduced gametes. (4) Large numbers of gametes and group breeding in relatively confined areas could increase the probability of compatible gamete combinations in both groups. (5) Both fish and amphibians have a propensity to form reproductively successful hybrids; although the relative frequency of autopolyploidy versus allopolyploidy is difficult to ascertain, multiple origins involving hybridization have been confirmed for a number of species in both groups. (6) Problems with establishment of polyploid lineages associated with minority cytotype exclusion could be overcome in amphibians via assortative mating by acoustic recognition of the same ploidy level, but less attention has been given to chemical or acoustic mechanisms that might operate in fish. (7) There is no strong evidence that polyploid fish or amphibians currently exist in more extreme environments than their diploid progenitors or have broader ecological ranges. (8) Although pathogens could play a role in the relative fitness of polyploid species, particularly given duplication of genes involved in immunity, this remains an understudied field in both fish and amphibians. (9) As in plants, many duplicate copies of genes are retained for long periods of time, indicative of selective maintenance of the duplicate copies, but we find no physiological or other reasons that could explain an advantage for allelic or genetic complexity. (10) Extant polyploid species do not appear to be more or less prone to extinction than related diploids in either group. We conclude that, while polyploid fish and amphibians share a number of attributes facilitating polyploidy, clear drivers of genome duplication do not emerge from the comparison. The lack of a clear association of sexually reproducing polyploids with range expansion, harsh environments, or risk of extinction could suggest that stronger correlations in plants may be driven by shifts in mating system more than ploidy. However, insufficient data currently exist to provide rigorous tests of these hypotheses and we make a plea for zoologists to also consider polyploidy as a possibility in continuing taxonomic surveys.

Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.

While currently in a state of recovery in the United Kingdom (UK), the grayling (Thymallus thymallus) remains of conservation interest due to its historical decline, socio-economic value and the potential impact of hatchery-reared stock fish on the genetic structure and diversity of wild populations. However, little is known about the levels and distribution of genetic diversity among UK grayling populations. To this end, 27 UK populations of grayling were genotyped across 10 microsatellite loci and sequenced at the mtDNA D-Loop. All populations clustered into four higher-level groups: Northern England, Southern England, Wales, and group consisting of a mixture of native and introduced populations. Ten populations showed evidence of bottleneck or founder effects, and the effective population size (Ne) was low in all populations. In most cases, historical stocking records agreed with the genetic relationships revealed in the study. A D-Loop haplotype network supported the groupings observed in the nuclear data, while phylogenetic inference places the UK populations amongst Central European samples. The combined datasets demonstrate that many of the UK populations can be treated as separate Management Units and we recommend that to preserve population specific genetic diversity, that stocking should be an intervention of last resort. However, if stocking is deemed essential, brood stock should originate from the river to be stocked.

Until recently, the study of negative and antagonistic interactions (for example, competition and predation) has dominated our understanding of community structure, maintenance and assembly1. Nevertheless, a recent theoretical model suggests that positive interactions (for example, mutualisms) may counterbalance competition, facilitating long-term coexistence even among ecologically undifferentiated species2. Mullerian mimics are mutualists that share the costs of predator education3 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 overlap4 (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.

We describe a protocol for the preservation, extraction, and detection of plaice (Pleuronectes platessa) DNA from the stomach contents of the brown shrimp, Crangon crangon and the shore crab, Carcinus maenas. These two predatory species are thought to be important sources of mortality of small juvenile plaice on inshore nursery grounds. Previous studies of predation on juvenile plaice have used visual examination of stomach contents but this is time consuming and may under-estimate true predation levels as remains may become unidentifiable due to maceration and digestion. Molecular based tools for detecting the presence of prey tissue in predator stomachs and scat are becoming increasingly used in marine ecology and provide an alternative or complementary approach to visual identification. We sequenced a part of the cytochrome-b region of plaice mitochondrial DNA and designed a species-specific, TaqMan real-time Polymerase Chain Reaction (PCR) based assay which was successfully tested for intra- and inter-species-specificity. For application to predator stomach contents, two tissue preservation and two DNA extraction methods were tested followed by a set of aquarium experiments to determine the effect of digestion time on detectability. The quality of the extracted DNA was comparable for the two preservation and two extraction methods tested and the detectability remained similar for all of them. However, levels of PCR inhibition were significant for samples from both predators but could be overcome using serial dilution and 1.25 μg/μl Bovine Serum Albumin to reduce the incidence of false negatives. Successful amplification and detection of plaice DNA from stomach contents was possible up to 24 h after ingestion for both predator species. For extracts of C. crangon stomachs the half-life detection rate (T50) was ~ 10 h at water temperatures of 14–16 °C. The effects of a wider range of temperatures were tested for stomach contents of C. maenas where the T50s were ~ 7 h at 6–10 °C and ~ 6 h at 14–16 °C but only 2 h at 19–20 °C. Our results indicate that the TaqMan method is applicable in field studies providing species-specific T50s, PCR inhibition and water temperatures are taken into account.

Dab (Limanda limanda) are the principal target fish species in offshore biomonitoring programmes in the UK; however, detailed knowledge of genetic structure and connectivity among sampling locations is unavailable. Here, the isolation and characterization of 30 polymorphic microsatellite loci for dab is described. The number of alleles per locus ranged from 2 to 42, with observed heterozygosities ranging from 0.089 to 1. These loci will enable high resolution of genetic population structure and dynamics of dab around the British Isles.

The European flounder (Platichthys flesus L.) is used in ecotoxicological studies to provide detailed information on the effects of pollution on individual fish. Data on population and evolutionary level effects are, however, limited. Here, the isolation and characterization of 28 novel species specific microsatellite loci are presented. The number of alleles ranged from 8 to 38, and observed heterozygosity from 0.542 to 1.