Evidence of genetic selection for growth in new recruits of a marine fish

Genomic basis for early-life mortality in sharpsnout seabream

Mortality at early life stages of fishes is common in nature and can be shaped by stochastic and selective processes. Selective mortality has rarely been assessed in natural conditions but can now be studied by combining genomic data with information on different life stages that realates to fitness. Here we investigate selective mortality between settlers and six-month survivors of the sharpsnout seabream by genotype-phenotype/environmental association studies in three localities along a geographic gradient. We gathered information on 105 individuals at 85,031 SNPs, obtained from individual based 2b-RAD libraries, as well as 9 phenotypic and environmental variables derived from individual otolith readings. We found common signals across localities for potential selection, such as lower survival rates for individuals hatching earlier, growing faster and experiencing higher temperatures during their planktonic phase. We identified 122 loci with parallel significant association to phenotypic and environmental variables. Importantly, one of these loci mapped to the exonic region of the il20rb, a gene involved in immune response, in the phylogenetically closest reference genome, showing parallel frequency changes in non-synonymous mutations in the three studied populations. Further temporal assessments are needed to understand how polymorphisms that are key to selective mortality are maintained.

Stage-specific influence of temperature on the growth rate of Japanese Spanish mackerel (Scomberomorus niphonius) in early life

Since 1850, each successive decade has been warmer than any preceding one. Warming could make a major contribution to the growth of fish larvae. To evaluate the influence of water temperature on the growth of larvae who spawned in later spring and early summer, we selected Scomberomorus niphonius, which has important ecological and economic value as a sample fish species. We conducted high-resolution spatiotemporal surveys during the 2015 spawning season at an important spawning ground in China. We found that the temperature required for larval survival was stricter than that for spawning. Within the appropriate temperature range, a rapid rise in water temperature was favourable for larval hatching, but S. niphonius hatched at relatively low temperature exhibited a faster growth rate in the yolk-sac and pre-flexion stages. The accumulated temperature and hatching temperature significantly affected the growth rate of S. niphonius larvae. The model that considered developmental stages provided a better explanation of the data than the model that only considered the temperature effect. The model improvement in terms of variance explained was higher for the early developmental stages than for the later developmental stages, suggesting that stage-specific temperature influences were prominent in the earlier stages, like the yolk-sac stage, and then reduced. Our results implied that water temperature anomalies could be hazardous to fish larvae, especially for fish spawning in late spring and early summer. Given that early-life stage fish are highly sensitive to water temperature, it is imperative to incorporate the potential effects of climate change into fisheries management.

Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure

Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3-5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only 1 year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects population genetics. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment-related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.

Ontogenetic shift in the energy allocation strategy and physiological condition of larval plaice (Pleuronectes platessa)

Condition indices aim to evaluate the physiological status of fish larvae by estimating both the level of starvation and potential of survival. Histological indices reveal direct effects of starvation whereas biochemical indices such as lipid classes or RNA:DNA ratios are used as proxies of condition, giving information on the amount of energy reserves and growth rate, respectively. We combined these three indices to evaluate ontogenetic variations of growth performance, lipid dynamics and nutritional condition of plaice larvae caught in the field during winter 2017 in the eastern English Channel and the Southern Bight of the North Sea. RNA:DNA ratios showed that larvae at the beginning of metamorphosis (stage 4) had a lower growth rate than younger individuals (stages 2 and 3). A significant increase in the proportion of triglycerides also occurred at stage 4, indicating energy storage. Histological indices indicated that most of the larvae were in good condition, even younger ones with low lipid reserves. There was, however, an increase in the proportion of healthy individuals over ontogeny, especially with respect to liver vacuoles which were larger and more numerous for stage 4 larvae. Combined together, these condition indices revealed the ontogenetic shift in the energy allocation strategy of plaice larvae. Young larvae (stages 2 and 3) primarily allocate energy towards somatic growth. The decrease in growth performance for stage 4 was not related to poor condition, but linked to a higher proportion of energy stored as lipids. Since the quantity of lipid reserves is particularly important for plaice larvae to withstand starvation during metamorphosis, this could be considered as a second critical period after the one of exogenous feeding for larval survival and recruitment success.

Within-generation consequences of postsettlement mortality for trait composition in wild populations: An experimental test

There is a critical need to understand patterns and causes of intraspecific variation in physiological performance in order to predict the distribution and dynamics of wild populations under natural and human-induced environmental change. However, the usual explanation for trait differences, local adaptation, fails to account for the small-scale phenotypic and genetic divergence observed in fishes and other species with dispersive early life stages. We tested the hypothesis that local-scale variation in the strength of selective mortality in early life mediates the trait composition in later life stages. Through in situ experiments, we manipulated exposure to predators in the coral reef damselfish Dascyllus aruanus and examined consequences for subsequent growth performance under common garden conditions. Groups of 20 recently settled D. aruanus were outplanted to experimental coral colonies in Moorea lagoon and either exposed to natural predation mortality (52% mortality in three days) or protected from predators with cages for three days. After postsettlement mortality, predator-exposed groups were shorter than predator-protected ones, while groups with lower survival were in better condition, suggesting that predators removed the longer, thinner individuals. Growth of both treatment groups was subsequently compared under common conditions. We did not detect consequences of predator exposure for subsequent growth performance: Growth over the following 37 days was not affected by the prior predator treatment or survival. Genotyping at 10 microsatellite loci did indicate, however, that predator exposure significantly influenced the genetic composition of groups. We conclude that postsettlement mortality did not have carryover effects on the subsequent growth performance of cohorts in this instance, despite evidence for directional selection during the initial mortality phase.

Differential Survival among Batches of Atlantic Cod (Gadus morhua L.) from Fertilisation through to Post-Metamorphosis

Aquaculture production of cod has decreased from over 20,000 tonnes in 2009 to less than 2,000 tonnes in 2014 and the industry faces many challenges, one of which is high and unpredictably variable mortality rates in the early life stages. Hence, full-cycle farming with hatchery produced juveniles is still considered unprofitable compared to fisheries and on-growing of wild cod. In the present study, potential batch differences in progeny survival of wild-caught, hatchery-spawned Faroe Bank cod (Gadus morhua L.) were investigated at two defined periods during early life history; i) the embryo stage (60 day degrees post fertilisation) and ii) the fry stage (110 days post hatch), post metamorphosis. The fry stage experiment was conducted in three replicates (N = 300 per replicate), and a panel of three polymorphic microsatellite markers was used for parental analysis. Mean survival rate at the embryo stage was 69% (± 20% SD). Survival was positively associated with egg diameter (P < 0.01), explaining 90% of the variation in egg survival rates. The data were too scarce to conclude either way concerning a possible correlation between survival rates between the two periods (P < 0.10). Offspring from three batches (from a total of eight) dominated in the fry stage, contributing over 90% of the progeny, and results were consistent over all three replicate tanks. The skewed batch representation observed may be of relevance to the effective management of selective breeding programmes for cod.

Elevated CO2 affects predator-prey interactions through altered performance

Recent research has shown that exposure to elevated carbon dioxide (CO2) affects how fishes perceive their environment, affecting behavioral and cognitive processes leading to increased prey mortality. However, it is unclear if increased mortality results from changes in the dynamics of predator-prey interactions or due to prey increasing activity levels. Here we demonstrate that ocean pCO2 projected to occur by 2100 significantly effects the interactions of a predator-prey pair of common reef fish: the planktivorous damselfish Pomacentrus amboinensis and the piscivorous dottyback Pseudochromis fuscus. Prey exposed to elevated CO2 (880 µatm) or a present-day control (440 µatm) interacted with similarly exposed predators in a cross-factored design. Predators had the lowest capture success when exposed to elevated CO2 and interacting with prey exposed to present-day CO2. Prey exposed to elevated CO2 had reduced escape distances and longer reaction distances compared to prey exposed to present-day CO2 conditions, but this was dependent on whether the prey was paired with a CO2 exposed predator or not. This suggests that the dynamics of predator-prey interactions under future CO2 environments will depend on the extent to which the interacting species are affected and can adapt to the adverse effects of elevated CO2.

Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata

The genetic basis and evolutionary implications of local adaptation in high gene flow marine organisms are still poorly understood. In several Mediterranean fish species, alternative migration patterns exist between individuals entering coastal lagoons that offer favourable conditions for growth and those staying in the sea where environmental conditions are less subject to rapid and stressful change. Whether these coexisting strategies are phenotypically plastic or include a role for local adaptation through differential survival needs to be determined. Here, we explore the genetic basis of alternate habitat use in western Mediterranean populations of the gilthead sea bream (Sparus aurata). Samples from lagoonal and open-sea habitats were typed for three candidate gene microsatellite loci, seven anonymous microsatellites and 44 amplified fragment length polymorphism markers to test for genotype-environment associations. While anonymous markers globally indicated high levels of gene flow across geographic locations and habitats, non-neutral differentiation patterns correlated with habitat type were found at two candidate microsatellite loci located in the promoter region of the growth hormone and prolactin genes. Further analysis of these two genes revealed that a mechanism based on habitat choice alone could not explain the distribution of genotype frequencies at a regional scale, thus implying a role for differential survival between habitats. We also found an association between allele size and habitat type, which, in the light of previous studies, suggests that polymorphisms in the proximal promoter region could influence gene expression by modulating transcription factor binding, thus providing a potential explanatory link between genotype and growth phenotype in nature.

The relationship between dispersal ability and geographic range size

There are a variety of proposed evolutionary and ecological explanations for why some species have more extensive geographical ranges than others. One of the most common explanations is variation in species' dispersal ability. However, the purported relationship between dispersal distance and range size has been subjected to few theoretical investigations, and empirical tests reach conflicting conclusions. We attempt to reconcile the equivocal results of previous studies by reviewing and synthesizing quantitative dispersal data, examining the relationship between average dispersal ability and range size for different spatial scales, regions and taxonomic groups. We use extensive data from marine taxa whose average dispersal varies by seven orders of magnitude. Our results suggest dispersal is not a general determinant of range size, but can play an important role in some circumstances. We also review the mechanistic theories proposed to explain a positive relationship between range size and dispersal and explore their underlying rationales and supporting or refuting evidence. Despite numerous studies assuming a priori that dispersal influences range size, this is the first comprehensive conceptual evaluation of these ideas. Overall, our results indicate that although dispersal can be an important process moderating species' distributions, increased attention should be paid to other processes responsible for range size variation.

Social facilitation of selective mortality

Territorial defense by breeders influences access to resources near defended nest sites by intruder species and may have indirect effects on other species within the territory, leading to local patchiness in distribution patterns. The present study demonstrates that adult males of a damselfish, Pomacentrus amboinensis, indirectly facilitate the increased survival of conspecific juveniles through the territorial defense of their nesting site from potential egg predators. Moreover, male territoriality results in a shift in the selectivity of predation on newly settled juveniles. We monitored the fate of pairs of predator-naive, newly settled P. amboinensis placed inside and outside nesting territories. Individuals within a pair differed in size by approximately 1 mm and were tagged for individual identification. Away from male territories larger juveniles had greater survival, while within territories, larger juveniles suffered higher mortality. Behavioral observations indicated that the moonwrasse Thalassoma lunare, a predator of benthic eggs and small fishes, had reduced access to juveniles within male territories, while another predator on small fishes, the dottyback Pseudochromis fuscus, had unobstructed access to male territories. Experimental removal of P. fuscus indicated that the shift in the direction of phenotypic selection on newly settled juveniles was the indirect effect of aggression by nest-guarding male damselfish, which resulted in differential access to male territories by these two predators of small fishes. Evidence suggests that behavioral interactions between the resident community and intruders will influence patchiness in selective pressures imposed on benthic prey by influencing both the composition of predator types that can access the prey resource and their relative abundance. How this spatial and temporal patchiness in predator pressure interacts with spatial patchiness of recruiting prey will have a major influence on the resulting distribution of juveniles and their phenotypic traits.

GENETIC IDENTITY DETERMINES RISK OF POST-SETTLEMENT MORTALITY OF A MARINE FISH

Longitudinal sampling of four cohorts of Neopomacentrus filamentosus, a common tropical damselfish from Dampier Archipelago, Western Australia, revealed the evolution of size structure after settlement. Light traps collected premetamorphic individuals from the water column ("settlers") to establish a baseline for each cohort. Subsequently, divers collected benthic juveniles ("recruits") at 1-3-month intervals to determine the relative impacts of post-settlement mortality during the first three months. Growth trajectories for individual fish were back-calculated from otolith records and compared with nonlinear mixed-effects models. Size-selective mortality was detected in all cohorts with the loss of smaller, slower growing individuals. Three months after settlement, recruits showed significantly faster growth as juveniles, faster growth as larvae, and larger sizes as hatchlings. The timing and intensity of post-settlement selection differed among cohorts and was correlated with density at settlement. The cohort with the greatest initial abundance experienced the strongest selective mortality, with most of this mortality occurring between one and two months after settlement when juveniles began foraging at higher positions in the water column. Significant genetic structure was found between settlers and three-month-old recruits in this cohort as a result of natural selection that changed the frequency of mtDNA haplotypes measured at the control region. The extent of this genetic difference was enlarged or reduced by artificially manipulating the intensity of size-based selection, thus establishing a link between phenotype and haplotype. Sequence variation in the control region of the mitochondrial genome has been linked to mitochondrial efficiency and weight gain in other studies, which provides a plausible explanation for the patterns observed here.

QTL Analysis of Behavioral and Morphological Differentiation Between Wild and Laboratory Zebrafish (Danio rerio)

The zebrafish is an important model organism for neuro-anatomy and developmental genetics. It also offers opportunities for investigating the functional and evolutionary genetics of behaviour but these have yet to be exploited. The ecology of anti-predator behaviour has been widely studied in fish and has been shown to vary among populations and between wild and domesticated (laboratory) fish. Here, we utilise the strong behavioural differences present between a wild-derived strain of fish from Bangladesh and the laboratory strain AB. In total, 184 F2 fish were generated and tested for shoaling tendency and willingness to approach an unfamiliar object ('boldness'). Our results indicate the existence of QTL for boldness on chromosomes 9 and 16 and suggest another genomic region that influences anti-predator behaviour on chromosome 21. QTL for growth rate, weight and fat content, all of which are elevated in laboratory fish, were detected on chromosome 23. These initial results confirm the potential for QTL mapping of behavioural traits in zebrafish and also for dissecting the consequences of selection during domestication.

Genetic Clines in the Bay of Biscay Provide Estimates of Migration for Sardina pilchardus

Nine allozymic loci in 1,635 individuals of Sardina pilchardus obtained at 33 sites ranging from the North to the South limits of the Bay of Biscay were analyzed to provide a description of the genetic structure of the sardine population. Individual body size and age were also recorded and analyzed. In the study population, weak but significant genetic differences were found, and a cline was observed between multilocus heterozygosity and longitude. The cline was predominantly driven by allelic frequencies of two loci, PGM-1* and PEP-lt*, and using a cline model, we estimated a migration rate of 103.1 km/gen (dispersal distance per generation). In addition, we observed that the cline was linked to biological data such as mean length and mean age of the fish. Two hypotheses may explain this cline: mixing of two different populations in the Bay of Biscay or a selective process. The weak genetic differences, the important dispersal distance per generation, and the link between genetic and biological data suggest that selection is likely to be the primary factor that maintains the cline.

The Atlantic-Mediterranean transition: discordant genetic patterns in two seabream species, Diplodus puntazzo (Cetti) and Diplodus sargus (L.)

Sparids are a group of demersal perciform fish of high commercial value, which have experienced an extensive radiation, particularly in the Mediterranean, where they occupy a variety of different niches. The present study focuses on two species: Diplodus sargus and D. puntazzo, presenting a wide distribution from the Mediterranean to the eastern Atlantic coasts. They display similar ecological behaviour and are evolutionary closely related. Both are highly appreciated in fisheries and D. puntazzo is currently under domestication process. However, little is know on their population structure and it is an open question whether any genetic differentiation exists at the geographic level. To address this issue we examined sequence variation of a portion of the mitochondrial DNA (mtDNA) control region in population samples of each of the two species collected over a wide geographic range. In addition to the mtDNA, analysis of nuclear loci (allozymes) was included in the study to compare patterns revealed by nuclear and mitochondrial markers. The studied samples covered an area from the eastern Mediterranean to the Portuguese coasts immediately outside the Gibraltar Strait. The two species revealed a level of sequence polymorphism remarkably different for the control region with the D. puntazzo and D. sargus showing 111 and 28 haplotypes, respectively. Such a difference was not detected with allozyme markers. The two species also showed large differences in their population structure. While D. puntazzo presented a marked genetic divergence between the Atlantic and Mediterranean samples, D. sargus showed little intraspecific differentiation. These results were supported using both mtDNA and allozyme markers, and were interpreted as the consequence of differences in the history of the two species such as fluctuations in the effective population size due to bottlenecks and expansions, possibly combined with present-day differences in levels of gene flow.

Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies

Strategies for the identification of functional genetic variation underlying phenotypic traits of ecological and evolutionary importance have received considerable attention in the literature recently. This paper aims to bring together and compare the relative strengths and limitations of various potentially useful research strategies for dissecting functionally important genetic variation in a wide range of organisms. We briefly explore the relative strengths and limitations of traditional and emerging approaches and evaluate their potential use in free-living populations. While it is likely that much of the progress in functional genetic analyses will rely on progress in traditional model species, it is clear that with prudent choices of methods and appropriate sampling designs, much headway can be also made in a diverse range of species. We suggest that combining research approaches targeting different functional and biological levels can potentially increase understanding the genetic basis of ecological and evolutionary processes both in model and non-model organisms.