Behavioral Differences Among Rainbow Trout Clonal Lines

Social experience influences thermal sensitivity: lessons from an amphibious mangrove fish

Understanding the factors affecting the capacity of ectothermic fishes to cope with warming temperature is critical given predicted climate change scenarios. We know that a fish's social environment introduces plasticity in how it responds to high temperature. However, the magnitude of this plasticity and the mechanisms underlying socially modulated thermal responses are unknown. Using the amphibious hermaphroditic mangrove rivulus fish Kryptolebias marmoratus as a model, we tested three hypotheses: (1) social stimulation affects physiological and behavioural thermal responses of isogenic lineages of fish; (2) social experience and acute social stimulation result in distinct physiological and behavioural responses; and (3) a desensitization of thermal receptors is responsible for socially modulated thermal responses. To test the first two hypotheses, we measured the temperature at which fish emerged from the water (i.e. pejus temperature) upon acute warming with socially naive isolated fish and with fish that were raised alone and then given a short social experience prior to exposure to increasing temperature (i.e. socially experienced fish). Our results did not support our first hypothesis as fish socially stimulated by mirrors during warming (i.e. acute social stimulation) emerged at similar temperatures to isolated fish. However, in support of our second hypothesis, a short period of prior social experience resulted in fish emerging at a higher temperature than socially naive fish suggesting an increase in pejus temperature with social experience. To test our third hypothesis, we exposed fish that had been allowed a brief social interaction and naive fish to capsaicin, an agonist of TRPV1 thermal receptors. Socially experienced fish emerged at significantly higher capsaicin concentrations than socially naive fish suggesting a desensitization of their TRPV1 thermal receptors. Collectively, our data indicate that past and present social experiences impact the behavioural response of fish to high temperature. We also provide novel data suggesting that brief periods of social experience affect the capacity of fish to perceive warm temperature.

Agonistic behaviour of wild eels and depressed survival and growth of farmed eels in mixed rearing experiments

To contribute to improving eel stocking procedures, the survival, growth and behaviour of farmed Japanese eels reared together with wild individuals were evaluated to learn about possible encounters of farmed- and stocked eels with wild eels. Two experiments were conducted to evaluate the (a) effect of the presence of wild eels on survival and growth of farmed eels in experimental ponds and (b) behavioural differences between wild and farmed eels placed in a small tank. In the survival and growth experiment, significantly lower survival and growth rates of farmed eels reared with wild eels were observed compared with farmed eels reared without wild eels (control). In the behavioural observations, the authors observed significantly higher occupation rates of a refuge and more frequent biting for wild eels, indicating a dominance of wild eels over farmed eels. Because wild and farmed eels used in the current experiments belong to the same genetic population, these differences resulted within one generation through the aquaculture rearing process.

Temporal Patterns in Interactions Across Same- and Mixed-Sex Wild Zebrafish Dyads

Animals communicate with each other through a variety of behavioral interactions, many of which are often complex due to the interplay of several ecological factors. Observations on dyadic interactions can help throw light on the more complex interactions observed among group living organisms and can help in understanding mechanisms of behaviors related to mating strategies, dominance hierarchies, and decision-making. This study focused on the assessment of several generally observed interactions among dyads of different sexes (female-female, male-male, and male-female) in wild zebrafish (Danio rerio). Temporal dynamics of these interactive behaviors were observed in 45 dyads across 3 time intervals of the day. We used generalized linear mixed models to investigate the effect of time, sex of dyad, and their interaction on specific behaviors. While the frequency of occurrence of some behaviors showed clear variation across time intervals of the day, these were further found to depend on the composition of the dyad. Contrary to previous reports, we found that same-sex dyads are equally aggressive and aggressive interactions did not vary temporally. Mating-associated interactions, as expected, were significantly higher in mixed-sex dyads and declined significantly from early morning to afternoon. Interestingly, we also found some mating-associated interactions in same-sex dyads. A fine line exists between social and mating-associated interactions in many organisms and so we speculate that these interactions could also be social interactions and not mating-related behavior. Our findings shed light on complex interactive behaviors among zebrafish, that are likely to be affected by time as well as sex composition of interacting individuals and thus has important implications for groups varying in sex ratios in the wild.

Genomic architecture and repertoire of the rainbow trout immunoglobulin light chain genes

The genomic loci encoding the four immunoglobulin light chains (IgL1, IgL2, IgL3, and IgL4) in the Swanson trout genome assembly were annotated in order to provide a measurement of the potential IgL repertoire. IgL1 and IgL3 gene segments are co-localized on chromosomes 21, 18, 15, and 7 while IgL2 and IgL4 were found on chromosomes 13 and 17, respectively. In total, 48 constant (C_L), 87 variable (V_L), and 59 joining (J_L) productive genes are described. Pairwise alignment of the V_L segments revealed that they belong to nine different families, three of which (kappa IV, V, and VI) are described for the first time in this study. V_L and C_L sequences on chromosome 15 and 21 and those on chromosomes 7 and 18 clustered together in phylogenetic analysis. PCR was used to examine IgL C_L and V_L genes in 9 lines of rainbow trout. IgL4 in the Hot Creek and Golden trout lines was missing 42 nucleotides resulting in a loss of 14 amino acids. The sigma IV variable family was completely absent from the Swanson, Arlee, Hot Creek, and wild type lines and silenced in the Skamania line with the addition of 176 bp mini-satellite insert. Similarly, the Whale Rock, Arlee, and wild type lines were all found to encode two sigma II products, a functional 252 bp product and a larger 425 bp product that contained a 172 bp insert. Results from this study indicate that there are genomic differences in IgL repertoire between different lines of trout that could affect humoral immune responses post vaccination and during disease.

The structural variation landscape in 492 Atlantic salmon genomes

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.

This study presents and validates a novel approach to reliably identify structural variations (SVs) in non-model genomes using whole genome sequencing, which was used to detect 15,483 SVs in 492 Atlantic salmon, shedding light on their roles in genome evolution and the genetic architecture of domestication.

Rainbow trout personality: individual behavioural variation in juvenile Oncorhynchus mykiss

We evaluated the variation in dispersal, exploration, and aggression across time in juvenile progeny produced from wild caught rainbow trout (Oncorhynchus mykiss) at a critical developmental shift associated with the highest mortality in fish. By testing multiple ecologically relevant behaviours repeatedly in the same individuals, we simultaneously tested multiple hypotheses regarding personality, plasticity, and behavioural syndromes to better understand the innate behavioural variation in a population containing both migratory and resident life histories. There were consistent behavioural differences, or personality, between individuals across time, for dispersal, aggression, and exploration, unrelated to size or sex. The significant repeatabilities (0.10–0.46) indicate that these traits are potentially heritable. Also, we found both habituation in all behaviours and significant differences between individuals in the rate of that habituation, despite no evidence of a behavioural syndrome. The identification of this individual level variation is a step towards understanding which heritable traits selection could influence.

Aggressive behavior, brain size and domestication in clonal rainbow trout lines

Domestication causes behavior and brain size changes in many species. We addressed three questions using clonal rainbow trout lines: What are the mirror-elicited aggressive tendencies in lines with varying degrees of domestication? How does brain size relate to genotype and domestication level? Finally, is there a relationship between aggressive behavior and brain size? Clonal lines, although sampling a limited subset of the species variation, provide us with a reproducible experimental system with which we can develop hypotheses for further research. We performed principal component analyses on 12 continuous behavior and brain/body size variables and one discrete behavioral variable ("yawn") and detected several aggression syndromes. Two behaviors, "freeze" and "escape", associated with high domestication; "display" and "yawn" behavior associated with wild lines and "swim against the mirror" behavior associated with semi-wild and domestic lines. Two brain size traits, total brain and olfactory volume, were significantly related to domestication level when taking total body size into account, with domesticated lines having larger total brain volume and olfactory regions. The aggression syndromes identified indicate that future QTL mapping studies on domestication-related traits would likely be fruitful.

Genetic inactivation of European sea bass (Dicentrarchus labrax L.) eggs using UV-irradiation: observations and perspectives

Androgenesis is a form of uniparental reproduction leading to progenies inheriting only the paternal set of chromosomes. It has been achieved with variable success in a number of freshwater species and can be attained by artificial fertilization of genetically inactivated eggs following exposure to gamma (γ), X-ray or UV irradiation (haploid androgenesis) and by restoration of diploidy by suppression of mitosis using a pressure or thermal shock. The conditions for the genetic inactivation of the maternal genome in the European sea bass (Dicentrarchus labrax L.) were explored using different combinations of UV irradiation levels and durations. UV treatments significantly affected embryo survival and generated a wide range of developmental abnormalities. Despite the wide range of UV doses tested (from 7.2 to 720 mJ x cm(-2)), only one dose (60 mJ x cm(-2) x min(-1) with 1 min irradiation) resulted in a small percentage (14%) of haploid larvae at hatching in the initial trials as verified by flow cytometry. Microsatellite marker analyses of three further batches of larvae produced by using this UV treatment showed a majority of larvae with variable levels of paternal and maternal contributions and only one larva displaying pure paternal inheritance. The results are discussed also in the context of an assessment of the UV-absorbance characteristics of egg extracts in this species that revealed the presence of gadusol, a compound structurally related to mycosporine-like amino acids (MAAs) with known UV-screening properties.

Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in channel catfish (Ictalurus punctatus)

Domestication and selection for important performance traits can impact the genome, which is most often reflected by reduced heterozygosity in and surrounding genes related to traits affected by selection. In this study, analysis of the genomic impact caused by domestication and artificial selection was conducted by investigating the signatures of selection using single nucleotide polymorphisms (SNPs) in channel catfish (Ictalurus punctatus). A total of 8.4 million candidate SNPs were identified by using next generation sequencing. On average, the channel catfish genome harbors one SNP per 116 bp. Approximately 6.6 million, 5.3 million, 4.9 million, 7.1 million and 6.7 million SNPs were detected in the Marion, Thompson, USDA103, Hatchery strain, and wild population, respectively. The allele frequencies of 407,861 SNPs differed significantly between the domestic and wild populations. With these SNPs, 23 genomic regions with putative selective sweeps were identified that included 11 genes. Although the function for the majority of the genes remain unknown in catfish, several genes with known function related to aquaculture performance traits were included in the regions with selective sweeps. These included hypoxia-inducible factor 1β· HIFιβ ¨ and the transporter gene ATP-binding cassette sub-family B member 5 (ABCB5). HIF1β· is important for response to hypoxia and tolerance to low oxygen levels is a critical aquaculture trait. The large numbers of SNPs identified from this study are valuable for the development of high-density SNP arrays for genetic and genomic studies of performance traits in catfish.

Assessment of genetic variability of fish personality traits using rainbow trout isogenic lines

The study of inter-individual variability of personality in fish is a growing field of interest but the genetic basis of this complex trait is still poorly investigated due to the difficulty in controlling fish genetic origin and life history. When available, isogenic lines that allow performing independent tests on different individuals having identical genotype constitute a very relevant experimental material to disentangle the genetic and environmental components of behavioural individuality. We took advantage of heterozygous isogenic lines to investigate the personality in rainbow trout through the analysis of their reactions to different experimental situations. To this end, seven to ten rainbow trout isogenic lines were screened for their spatial exploratory behaviour, their flight response toward a stressor and their risk taking behaviour. Results showed that some lines seemed less sensitive to new events or environmental changes and could be defined as low responsive, while others were very sensitive and defined as high responsive. The use of isogenic lines highlighted the importance of genetic factors, in combination with life history, in the expression of personality in domesticated fish.

Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing

Understanding how organisms interact with their environments is increasingly important for conservation efforts in many species, especially in light of highly anticipated climate changes. One method for understanding this relationship is to use genetic maps and QTL mapping to detect genomic regions linked to phenotypic traits of importance for adaptation. We used high-throughput genotyping by sequencing (GBS) to both detect and map thousands of SNPs in haploid Chinook salmon (Oncorhynchus tshawytscha). We next applied this map to detect QTL related to temperature tolerance and body size in families of diploid Chinook salmon. Using these techniques, we mapped 3534 SNPs in 34 linkage groups which is consistent with the haploid chromosome number for Chinook salmon. We successfully detected three QTL for temperature tolerance and one QTL for body size at the experiment-wide level, as well as additional QTL significant at the chromosome-wide level. The use of haploids coupled with GBS provides a robust pathway to rapidly develop genomic resources in nonmodel organisms; these QTL represent preliminary progress toward linking traits of conservation interest to regions in the Chinook salmon genome.

Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)

BACKGROUND

Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation.

RESULTS

Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4).

CONCLUSIONS

Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies.

A multivariate comparison of the stress response in three salmonid and three cyprinid species: evidence for inter-family differences

The response of six species of freshwater fishes, from the families Cyprinidae (common carp Cyprinus carpio, roach Rutilus rutilus and chub Leuciscus cephalus) and Salmonidae (rainbow trout Oncorhynchus mykiss, brown trout Salmo trutta and Arctic charr Salvelinus alpinus), to a standardized stressor was evaluated. A 6 h period of confinement resulted in changes to plasma cortisol, glucose, amino acid and lactate levels compared with unconfined controls. There were significant differences in the response profiles both within and between families. The cyprinid species exhibited higher and more sustained stress-induced increases in plasma cortisol and glucose than the salmonid species. In cyprinids, plasma lactate and plasma amino acid concentration showed less disturbance following stress than in salmonids. The results of the study, together with an evaluation of previously published data for eight salmonid species and six cyprinid species, support the hypothesis that differences in core elements of the stress response exist between species of fishes, and that this variation may have a systematic basis.

Behavioural and morphological differences between feral and domesticated strains of common carp Cyprinus carpio

Morphological and behavioural traits of a feral strain of the common carp Cyprinus carpio from Lake Biwa in Japan were compared with those of two domesticated strains reared in Japan (one commercial strain and one ornamental koi). To compare genetically inherited traits, all fish were reared from eggs under similar environmental conditions. Using these fish, the following five traits were compared among the three strains: body shape, consumption rate of two types of free-swimming shrimp, medaka Oryzias latipes and bottom-dwelling chironomid larvae prey items, preference for a bottom habitat, feeding skills in detecting prey and escape response to predator attack. The feral strain of fish had more streamlined bodies, higher consumption rates for free-swimming prey, a greater preference for a bottom habitat, possessed greater skill in detecting prey and were more cautious of predator attacks, compared with the fish of the two domesticated strains. These characteristics shown by the feral fish are probably adaptive to the natural environment. A genetic analysis based on five nuclear single nucleotide polymorphism markers, however, suggested that the feral strain was relatively recently derived from domesticated stocks. Considering this, the present results appear to indicate the possibility that domesticated C. carpio could re-adapt to the wild environment during a short evolutionary period, although further research using more feral strains is required.

HETEROSPECIFIC AGGRESSION AND ADAPTIVE DIVERGENCE IN BROOK STICKLEBACK (CULAEA INCONSTANS)

Agonistic behavior between heterospecifics, in which individuals of one species attack another, may cause a subordinate species to shift resource or habitat use. Subsequent evolutionary responses to selection may mimic shifts expected under ecological character displacement, but with no role played by exploitative competition. Alternatively, aggressive behavior can evolve when fitness is improved by excluding members of a coexisting species from a defendable resource through interference. We tested whether heterospecific agonistic behavior has evolved in brook stickleback (Culaea inconstans) by comparing replicate allopatric populations to those sympatric with ninespine stickleback (Pungitius pungitius). We also tested for heritable variation in heterospecific aggressive behavior by rearing family groups in a common environment. Allopatric populations of brook stickleback were more aggressive than ninespine stickleback, suggesting that pre-existing aggression in brook stickleback contributed to niche shifts by ninespine stickleback. In addition, sympatric adult brook stickleback were more aggressive toward ninespine stickleback than brook stickleback from allopatric populations. Overt heterospecific aggressive behaviors were heritable, and aggression in juvenile brook stickleback increased with age in sympatric but not in allopatric populations reared in a common environment. Brook stickleback have evolved increased aggression when they coexist with ninespine stickleback. These stickleback communities have been structured by both evolved and pre-existing variation in heterospecific aggressive behavior in brook stickleback.

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.