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Parental care has evolved across the animal kingdom to increase the probability of offspring surviving in an environment fraught with danger. While parental care is common among mammals and birds, it is relatively rare in fish with the vast majority of fish showing no form of parental care at all, whilst those that do, often just provide parental care to developing eggs pre-hatch. The provision of parental care in discus fish (Symphysodon spp.) is, therefore, interesting in that parents provide mucus to offspring as a source of nutrition during the first few weeks of care. In mammals this post-birth provision of parental care can lead to the development of the parent offspring conflict. It is, however, possible that this conflict is also present in discus fish. This thesis examines both the interesting parental care strategy of discus fish along with the potential for the parent offspring conflict to develop. To examine the dynamics of parental care in discus fish, a range of behavioural and mucus composition studies were carried out. The analysis of mucus revealed that similar to mammals, parents provided offspring with an initial high quantity of nutritional and non-nutritional factors including antibodies (IgM), essential ions and hormones. Behavioural studies also revealed that initially parents were highly diligent in providing care to offspring but that after two weeks of care, the behaviour of parents changed making it harder for offspring to obtain mucus. At this point a weaning period was initiated where offspring began spending less time with parents and more time foraging for external food sources. The initiation of this weaning period suggests the presence of the parent offspring conflict and indicates that a point is reached where the energetic demands of offspring are too great and that energy is better invested in to future offspring. Research into the bite size and feeding rate of fry suggest that during the weaning period fry could demand excessive amounts of mucus, which may be energetically unsustainable leading to the observed offspring avoiding behaviour of parents. As parental care behaviour is known to be intimately associated with mate choice, mate choice behaviour was also assessed in discus fish with the hypothesis that the ability to provide mucus would be selected for by prospective mates. While my dietary experiment did not influence mucus quality, the mate choice experiment did reveal the importance of hierarchies in discus fish, indicating that dominant individuals were significantly more likely to pair than subordinates. This is similar to that observed in closely related cichlids where the ability to be dominant and protect a territory was indicative of the ability to successfully raise offspring. In conclusion, the parental care behaviour of discus fish appears to share more similarities with that seen in mammals than that observed in fish. The implications of these findings indicate that parental care in discus fish could be a new model of parent offspring conflict hitherto unseen in fish which could ultimately help our understanding of the evolution of parental care in fish.

Neotropical cichlid fishes are highly diverse and occupy diverse environments. Visual pigment evolution has been important in the diversification of African rift lake cichlids, but little is known of Neotropical cichlid visual systems. This thesis addresses the molecular evolution of rhodopsin in the Geophagini tribe of Neotropical cichlids. We use likelihood-based codon models of molecular evolution and newly isolated sequences for Neotropical cichlid rhodopsin to compare patterns of selective constraint among Neotropical, African rift lake, and African riverine cichlid rhodopsin. We provide evidence for differences in selective constraint among clades, with positive selection occurring in the Neotropical and African rift lake clades. Further, we find variation in selective constraint within geophagine cichlids. Our results suggest that Clade model C may be more appropriate than branch-site models for investigating variation in selective constraint among clades. Neotropical cichlids are emerging as an excellent system for investigating molecular evolution in visual pigments.

Neotropical cichlid fishes are highly diverse and occupy diverse environments. Visual pigment evolution has been important in the diversification of African rift lake cichlids, but little is known of Neotropical cichlid visual systems. This thesis addresses the molecular evolution of rhodopsin in the Geophagini tribe of Neotropical cichlids. We use likelihood-based codon models of molecular evolution and newly isolated sequences for Neotropical cichlid rhodopsin to compare patterns of selective constraint among Neotropical, African rift lake, and African riverine cichlid rhodopsin. We provide evidence for differences in selective constraint among clades, with positive selection occurring in the Neotropical and African rift lake clades. Further, we find variation in selective constraint within geophagine cichlids. Our results suggest that Clade model C may be more appropriate than branch-site models for investigating variation in selective constraint among clades. Neotropical cichlids are emerging as an excellent system for investigating molecular evolution in visual pigments.

Epidermal appendages are found on every vertebrate this world has to offer. In fish, these are commonly represented by scales. While we have a solid grasp of how scales develop, little is known about the underlying genetic mechanisms behind these phenotypic changes. Using two species of African cichlids (Labeotropheus fuelleborni and Tropheops “red cheek”) with varying scale phenotypes, we sought to examine their F2 hybrid offspring and statistically link the responsible genetic elements to their respective parental phenotypes through Quantitative Loci Trait (QTL) analysis. Scales were removed from six different locations across the midline of each individual. Then, numerous traits on each scale were measured, and these values were used in the QTL analysis. 42 significant QTL were identified, with multiple QTL intervals possessing promising candidate genes. These genes include: fgfr1b, efna5a, TGIF1, eIF6, and col1a1a. Previous studies have implicated these particular genes and gene families to play important roles in scale and placode development. However, they represent the minority of QTL intervals discovered, providing direction for future research towards the other QTL intervals represented by this study.

Sexual selection and the maintenance of species diversity in Lake Malawi cichlid fishes are greatly dependent on optical communication, which is influenced by environmental, physiological and endocrinological factors. The diversity in spectral sensitivity of cichlids has been partially attributed to differences in opsin gene expression, with each species preferentially expressing a subset of seven possible genes. Hormones such as gonadotropin releasing hormone (GnRH) can mediate changes in gene expression and the presence of GnRH immunoreactive fibers and GnRH receptors throughout the retinal layers make it an excellent candidate for mediating changes in visual processes. Effects of exogenous GnRH administration on the visual system of zebra cichlids (Metriaclima zebra) via prolonged release cholesterol implants and intubation was investigated using electroretinogram (ERG) recordings, quantitative real-time RT-PCR and in situ hybridization. Three week and ten week sampling periods were used in the intubation study. No obvious differences in spectral sensitivity were evident when looking at a-wave, b-wave and d-wave components of the ERG waveform in any of the treatment groups. A multiple mechanism model was used to describe the cone mechanisms mediating spectral sensitivity and this analysis showed that the activity of cones was shaped by opponent and non opponent cone interactions based on subsets of five opsin genes previously described in cichlids (SWS1, SWS2b, RH2b, RH2aβ, and RH2aα). Although differences in the spectral sensitivity between control and GnRH-treated fish were not evident on a functional level, there were changes in the gonadosomatic index in the intubation group. Quantitative real-time RT-PCR (qRT-PCR) and in situ hybridization demonstrated that treatment with a synthetic GnRH3 analogue using the oral intubation delivery system resulted in statistically significant changes in opsin gene expression in both three week and ten week treatment groups, specifically the upregulation of RH2b and the downregulation of RH2a opsin genes. Moreover, in situ hybridization analysis showed that the pattern of labeling for the RH2a and RH2b riboprobes corroborated the changes in opsin gene expression found in the qRT-PCR data. In contrast, GnRH treatment using the cholesterol implant delivery system did not result in significant changes in spectral sensitivity or opsin gene expression. / Thesis (Master, Biology) -- Queen's University, 2011-01-05 22:57:11.308

Orientador: Cesar Martins / Resumo: B chromosomes (Bs) are additional to the standard regular chromosome set (As), and present in all groups of eukaryotes. A reference genome is key to understand genomics aspects of an organism. Here, we present the de novo genome assembly of the cichlid fish A. latifasciata: a well known model to study Bs. The assembly of A. latifasciata genome has not been performed so far. The main focus of this study is to analyze and assemble the A. latifasciata genome with no B (B-) and with B (B+) chromosomes. The assembled draft B- and B+ genomes comprised of 774 Mb and 781 Mb with 1.8 Mb and 2.5Mb of N50 value of scaffolds respectively, and spanning 23,391 number of genes. High coverage data with Illumina sequencing was obtained for males and females with 0B, 1B and 2B chromosomes to provide information regarding the population polymorphism of these genomes. We observed a high scale genomic diversity in all analyzed genomes showing a high rate/frequency of population polymorphism with no evident effect of B chromosome presence. However, the B specific single nucleotide polymorphisms were found in the sequences that were located on B chromosome. While, the whole-genome rearrangements (inter chromosomal translocations) were detected in B+ genome, and structural variations including insertions, deletions, inversions and duplications were predicted in a representative genomic region of B chromosome. These results bring an evidence that existence of Bs in a genome should favour the accumu... (Resumo completo, clicar acesso eletrônico abaixo) / Mestre

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Brain size varies greatly among vertebrates. It has been proposed that the diversity of brain size is produced and maintained through a balance of adaptations to different types and levels of cognitive ability and constraints for adaptive evolution. Phylogenetic comparative studies have made major contributions to our understanding of brain size evolution. However, previous studies have nearly exclusively focused on mammalian and avian taxa and almost no attempts have been made to investigate brain size evolution in ectothermic vertebrates. In my thesis, I studied brain size evolution in two groups of fish with extreme diversity in ecology, morphology and life history, Cichlidae and Syngnathidae. Using phylogenetic comparative methods, I investigated four key questions in vertebrate brain size evolution; cognitive adaptation, sexual selection, phenotypic integration and energetic constraints. I have demonstrated i) that phenotypic integration can link functionally unrelated traits, and this may constrain independent evolution of each part involved or promote concerted evolution of an integrated whole, ii) that brain-body static allometry constrains the direction of brain size evolution, even though the static-allometry showed ability to evolve, allowing evolution of relative brain size under allometric constraints, iii) that the energetic constraints of development and maintenance of brain tissue is an important factor in forming the diversity in brain size in cichlids and syngnathids, both at macroevolutionary and microevolutionary time scales, and iv) that adaptation for feeding and female mating competition may have played key roles in the adaptive evolution of brain size in pipefishes and seahorses. To conclude, my thesis shows the strong benefit of using fish as a model system to study brain size evolution with a phylogenetic comparative framework.

Perissodus microlepis is a species of cichlid fish endemic to Lake Tanganyika (Africa). Adult P. microlepis are lepidophages, feeding on the scales of other living fish. As an adaptation for this feeding behavior P. microlepis exhibit lateral asymmetry with respect to jaw morphology: the mouth either opens to the right or left side of the body. Field data illustrate a temporal phenotypic oscillation in the mouth-handedness, and this oscillation is maintained by frequency-dependent selection. To better understand the oscillation, Takahashi and Hori model frequency-dependent selection in P. microlepis using a population genetic model. Their results are intriguing, and the purpose of this dissertation is to improve and extend their model, which fails to account for important biological aspects.We model P. microlepis with a novel approach that fuses the disparate modeling traditions of population genetics and population dynamics; we account for both processes since, in the case of P. microlepis, they occur on the same time scale (a case of microevolution). We construct our models using systems of difference equations. We prove the existence and uniqueness of a positive equilibrium, which corresponds to a 1 : 1 phenotypic ratio. Using a local stability and bifurcation analysis, we show that the equilibrium becomes unstable when frequency-dependent selection is sufficiently strong. We determine necessary and sufficient conditions for onset of oscillation. Local bifurcation analysis indicates key features of the oscillation that may suggest critical experiments.We determine the role of stage structure and the role of strong and weak intraspecific competition. We show that stage-structure is not necessary for, but enhances, oscillatory behavior. Finally we demonstrate the complicated interplay between population dynamic and population genetic processes. Our findings indicate that classical population genetic models can fail to elucidate complex dynamics.