Unidirectional response to bidirectional selection on body size II. Quantitative genetics

Evolutionary implications of size-selective mortality on the ontogenetic development of shoal cohesion: a neurochemical approach using a zebrafish, Danio rerio, harvest selection experiment

Abstract

Size-selective mortality may evolutionarily alter life-history as well as individual behavioral and physiological traits. Moreover, size-selective mortality can affect group behavioral traits, such as shoaling and collective properties (e.g., shoal cohesion), which are relevant for finding food and reducing risk of predation. Here, we present experimental evidence using selection lines of zebrafish (Danio rerio) that were exposed to positive (large-harvested), negative (small-harvested), and random (control) size-selective mortality for five generations, followed by eight generations during which harvesting was halted to remove maternal effects and to study evolutionarily fixed outcomes. We investigated changes in shoal cohesion and turnover in monoamines in zebrafish through ontogeny. To that end, we repeatedly measured inter-individual distance in groups of eight fish and the turnovers of dopamine and serotonin in brains of fish from juvenile to the adult stage at 40-day intervals. We, firstly, found that shoal cohesion was overall consistent through ontogeny at group levels suggesting the presence of collective personality. Secondly, we found a decrease in shoal cohesion through ontogeny in the small-harvested and control lines, while the large-harvested line did not show any ontogenetic change. Thirdly, the selection lines did not differ among each other in shoal cohesion at any ontogenetic stage. Fourthly, dopamine turnover increased through ontogeny in a similar way for all lines while the serotonin turnover decreased in the large-harvested and control lines, but not in the small-harvested line. The large-harvested line also had higher serotonin turnover than controls at specific time periods. In conclusion, intensive size-selective mortality left an evolutionary legacy of asymmetric selection responses in the ontogeny of shoal cohesion and the underlying physiological mechanisms in experimentally harvested zebrafish in the laboratory.

Significant statement

The evolution of animal behavior can be affected by human activities both at behavioral and physiological levels, but causal evidence is scarce and mostly focusing on single life-stages. We studied whether and to what extent size-selective harvesting, a common selection pattern in fisheries, can be an evolutionary driver of the development of shoal cohesion during ontogeny. We used a multi-generation experiment with zebrafish to study cause-and-effects of opposing size-selection patterns. We quantified shoal cohesion, and serotonin and dopamine turnover in the brain. We found that shoal cohesion emerged as a collective personality trait and that behavioral and physiological responses were asymmetrical with respect to the opposing selection patterns.

A method to predict the response to directional selection using a Kalman filter

Predicting evolution remains challenging. The field of quantitative genetics provides predictions for the response to directional selection through the breeder's equation, but these predictions can have errors. The sources of these errors include omission of traits under selection, inaccurate estimates of genetic variance, and nonlinearities in the relationship between genetic and phenotypic variation. Previous research showed that the expected value of these prediction errors is often not zero, so predictions are systematically biased. Here, we propose that this bias, rather than being a nuisance, can be used to improve the predictions. We use this to develop a method to predict evolution, which is built on three key innovations. First, the method predicts change as the breeder's equation plus a bias term. Second, the method combines information from the breeder's equation and from the record of past changes in the mean to predict change using a Kalman filter. Third, the parameters of the filter are fitted in each generation using a learning algorithm on the record of past changes. We compare the method to the breeder's equation in two artificial selection experiments, one using the wing of the fruit fly and another using simulations that include a complex mapping of genotypes to phenotypes. The proposed method outperforms the breeder's equation, particularly when traits under selection are omitted from the analysis, when data are noisy, and when additive genetic variance is estimated inaccurately or not estimated at all. The proposed method is easy to apply, requiring only the trait means over past generations.

Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)

Growth is one of the most important traits of an organism. For exploited species, this trait has ecological and evolutionary consequences as well as economical and conservation significance. Rapid changes in growth rate associated with anthropogenic stressors have been reported for several marine fishes, but little is known about the genetic basis of growth traits in teleosts. We used reduced genome representation data and genome-wide association approaches to identify growth-related genetic variation in the commercially, recreationally, and culturally important Australian snapper (Chrysophrys auratus, Sparidae). Based on 17,490 high-quality single-nucleotide polymorphisms and 363 individuals representing extreme growth phenotypes from 15,000 fish of the same age and reared under identical conditions in a sea pen, we identified 100 unique candidates that were annotated to 51 proteins. We documented a complex polygenic nature of growth in the species that included several loci with small effects and a few loci with larger effects. Overall heritability was high (75.7%), reflected in the high accuracy of the genomic prediction for the phenotype (small vs large). Although the single-nucleotide polymorphisms were distributed across the genome, most candidates (60%) clustered on chromosome 16, which also explains the largest proportion of heritability (16.4%). This study demonstrates that reduced genome representation single-nucleotide polymorphisms and the right bioinformatic tools provide a cost-efficient approach to identify growth-related loci and to describe genomic architectures of complex quantitative traits. Our results help to inform captive aquaculture breeding programs and are of relevance to monitor growth-related evolutionary shifts in wild populations in response to anthropogenic pressures.

Ecological ramifications of adaptation to size-selective mortality

Size-selective mortality due to harvesting is a threat to numerous exploited species, but how it affects the ecosystem remains largely unexplored. Here, we used a pond mesocosm experiment to assess how evolutionary responses to opposite size-selective mortality interacted with the environment (fish density and light intensity used as a proxy of resource availability) to modulate fish populations, prey community composition and ecosystem functions. We used medaka (Oryzias latipes) previously selected over 10 generations for small size (harvest-like selection; small-breeder line) or large size (large-breeder line), which displayed slow somatic growth and early maturity or fast somatic growth and late maturity, respectively. Large-breeder medaka produced more juveniles, which seemed to grow faster than small-breeder ones but only under high fish density. Additionally, large-breeder medaka had an increased impact on some benthic prey, suggesting expanded diet breadth and/or enhanced foraging abilities. As a consequence, increased light stimulated benthic algae biomass only in presence of large-breeder medaka, which were presumably better at controlling benthic grazers. Aggregated effect sizes at the community and ecosystem levels revealed that the ecological effects of medaka evolution were of similar magnitude to those induced by the environment and fish introduction. These findings indicate the important environmental dependency of evolutionary response to opposite size-selective mortality on higher levels of biological organizations.

Density-dependent natural selection mediates harvest-induced trait changes

Rapid life-history changes caused by size-selective harvesting are often interpreted as a response to direct harvest selection against a large body size. However, similar trait changes may result from a harvest-induced relaxation of natural selection for a large body size via density-dependent selection. Here, we show evidence of such density-dependent selection favouring large-bodied individuals at high population densities, in replicated pond populations of medaka fish. Harvesting, in contrast, selected medaka directly against a large body size and, in parallel, decreased medaka population densities. Five years of harvesting were enough for harvested and unharvested medaka populations to inherit the classically predicted trait differences, whereby harvested medaka grew slower and matured earlier than unharvested medaka. We show that this life-history divergence was not driven by direct harvest selection for a smaller body size in harvested populations, but by density-dependent natural selection for a larger body size in unharvested populations.