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Detection of positive selection in reproductive genes of songbirds
Cakl, Lukáš ; Reifová, Radka (advisor) ; Těšický, Martin (referee)
Reproductive genes are assumed to play an important role in adaptive evolution and speciation, yet little is known about the patterns of molecular evolution in these genes within avian species. This thesis is focused on identifying reproductive genes under positive selection and analyzing their function in songbirds, the largest and most diverse suborder of modern birds. Using existing bioinformatic approaches and published genomic data of 14 songbird species, we have first constructed 12000 groups of orthologous genes and detected significant traces of recurrent positive selection within 385 of them. Using proteomic data, this genome wide set of genes was then filtered to obtain genes expressed within songbird spermatozoa and fluids from the female reproductive tract. Within spermatozoa 22 out of 940 expressed genes were positively selected, while female fluids were found to be more conserved, as only 6 out of 529 expressed genes have shown traces of positive selection. We have then computed the enrichment of gene ontology terms within the positively selected genes. The enriched terms suggest evolutionary pres- sures acting on spermatozoa cytoskeleton, molecular motors and energetic metabolism, highlighting the importance of sperm morphology and swimming speed. Furthermore, the enrichment results...
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A neural network for reconstruction of extinct animals
Pešek, David ; Bilík, Šimon (referee) ; Jirsík, Václav (advisor)
This work was focused on designing, learning and evaluating an artificial neural network for reconstructing extinct species. First, the main element of the proposed artificial neural network, i.e., the generative model, was selected. Given their excellent performance in the field of image generation, the class of diffusion models reasonably seemed to be the right choice. Specifically, the Stable diffusion model was chosen. One of the initial steps of the work was to create a training set for the proposed model. The animal images needed to be paired with some labels that could be used to identify the animal. For this purpose, the cytochrome c oxidase subunit I genes of the given animals were used. Furthermore, the sequential transformer model GPT-2, which is learned on the training set of human natural language, was used. This model was used to encode the DNA sequences into a vector form in which the semantics and context between the different parts of the DNA sequence were captured. The models would be very difficult to learn from scratch due to the large training set size required and the computational and time requirements. Thus, the GPT-2 model was only learned on the training set of DNA sequences of the passeriformes order, and the diffusion model itself was learned on pairs of images of these animals and DNA sequences encoded by the GPT-2 model. To generate the images, the original DNA sequences that resembled the sequences from the training set were generated using GPT-2. The encoding of these sequences was then passed to the diffusion model, which generated the images itself. The method of generating new DNA sequences using the GPT-2 model is based on the idea that the generated DNA sequence partially resembles the DNA sequences from the training set. Such experimentally generated DNA sequences may resemble DNA sequences of extinct ancestors or relatives of the passeriformes order. The model was in some cases able to generate images that could be considered as animal species , but it should be noted that often the generated images could not be considered as animal reconstructions. The success rate of generating a decent animal image was approximately 10%. The functionality of the model was also tested on a test set of DNA sequences of animals of several orders that fall under the class of birds as well as the order of passeriformes. The success rate of generating a reconstruction that could be compared to a photograph was around 5%.
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Functions of different song types and song structures in songbirds
Pišvejcová, Iveta ; Petrusková, Tereza (advisor) ; Linhart, Otomar (referee)
In this review I summarize information about different types of song and its structures in which has been well documented their context of use. I have tried to find out, if there are some generally valid rules. The work is aimed at Passerines (Passeriformes) males living in the temperate zone. They sing the most intensively after their arrival on breeding grounds in early spring. Depending on a species and moreover an individual, the song might differ in structure, time and frequency parameters. Some species use complex songs, and change the way of its production according to attending audience. In such cases, the length and versatility of the song (the number and variability of syllables) may reflect the quality of a male. On the other hand some species with a simple song use different criteria to assess the singer quality. The individuals then differ in the way of song production or just in use of particular structures. For example, wide frequency range and length are considered to be energy-demanding for production, and so it could be a suitable indicator for a male quality. Short syllables produced at a faster rate can be not only production-demanding but can also indicate aggression. In general, we can estimate the function of a produced song according to "mating status" (before and after pairing) and...
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Inter-population variability of the bird song
Bílková, Jana ; Petrusková, Tereza (advisor) ; Musilová, Zuzana (referee)
Inter-population variability of the song is widespread phenomenon among birds. Populations of same species from different geographical areas might differ in vocalization. In case of dialects there are even no transitions between particular song forms, but clearly demarcated boundaries. Although the majority of studied cases concerns songbirds, it is possible to find examples in other orders as well. Studies showed that individuals inhabiting forests sing shorter and simpler songs with a lower frequency than their relatives from open landscapes. Changes in temporal and frequency characteristics can also be found in populations living in noisy cities. Different songs, however, are also produced by individuals from populations whose habitats do not show any significant differences. If these groups also differ genetically, then the different variants of song could be caused by heredity, especially in species with innate song. However, this variability may be the consequence instead of the cause of assortative mating, which might be the result of interpopulation variability in some cases. In species where the song is at least partially learned it is more likely that social interactions will play the key role - particularly if females prefer males singing local dialect or if sharing the song with neighbors...
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Functions of different song types and song structures in songbirds
Pišvejcová, Iveta ; Petrusková, Tereza (advisor) ; Linhart, Otomar (referee)
In this review I summarize information about different types of song and its structures in which has been well documented their context of use. I have tried to find out, if there are some generally valid rules. The work is aimed at Passerines (Passeriformes) males living in the temperate zone. They sing the most intensively after their arrival on breeding grounds in early spring. Depending on a species and moreover an individual, the song might differ in structure, time and frequency parameters. Some species use complex songs, and change the way of its production according to attending audience. In such cases, the length and versatility of the song (the number and variability of syllables) may reflect the quality of a male. On the other hand some species with a simple song use different criteria to assess the singer quality. The individuals then differ in the way of song production or just in use of particular structures. For example, wide frequency range and length are considered to be energy-demanding for production, and so it could be a suitable indicator for a male quality. Short syllables produced at a faster rate can be not only production-demanding but can also indicate aggression. In general, we can estimate the function of a produced song according to "mating status" (before and after pairing) and...
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