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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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Proteomic architecture of sperm-egg interactions
Otčenášková, Tereza ; Stopka, Pavel (advisor) ; Petr, Jaroslav (referee) ; Vrbacký, Marek (referee)
Recent advances in proteomic methods provide new insights for biological research including the field of reproductive biology. Determination of the proteomic basis of spermatozoa is pivotal for understanding the complex process of gamete interactions during fertilization such as acrosome reaction. Great differences imposed by postcopulatory sexual selection and phylogeny can be observed regarding the size, shape, and molecular composition of sperm across animal taxa. The first objective of this doctoral thesis is to characterize the protein contents of the acrosome to ascertain its further functional significance in sperm-egg interaction. Also, we aim to investigate the potential relationships between sperm protein composition and sperm morphology diversification, risk of sperm competition, and species phylogenetic background. Wild-caught males from natural populations of species of Mus musculus musculus, Apodemus flavicollis, Microtus arvalis (order Rodentia), Acrocephalus palustris, Chloris chloris, Phylloscopus collybita, Cinclus cinclus, Hirundo rustica, and Taeniopygia guttata from a captive population (order Passeriformes) were subject to the analyses. Nano-liquid chromatography with tandem mass spectrometry was applied as the main methodological approach in this thesis. Our data implicate...
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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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Host-microbiota, pro-inflammatory immunity and physiological senescence in wild birds
Těšický, Martin
Triggered by microbial ligands, inflammation serves as a "double-edged sword" to fight infections on the one hand, but on the other hand causing tissue damage due to oxidative stress if it is dysregulated. For example, chronic inflammation can contribute to inflammaging, which is now widely regarded as one of the causes of ageing. In my interdisciplinary dissertation, my colleagues and I investigated three interrelated aspects of inflammation, using an evolutionary framework and various free-living birds as models: (1) ecological and evolutionary determinants of gut microbiota (GM) composition and diversity, a driver of wild bird immunity, (2) diversity in immune genes affecting inflammatory responses in wild birds and (3) inflammation-related physiological senescence in a free-living passerine bird, the great tit (Parus major). Firstly, using 16S rRNA gene metabarcoding, we revealed high intra- and interspecific variation in passerine gut microbiota (GM) dominated by the major phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Although in mammals GM depends strongly on host phylogeny and diet, in birds we found only moderate effects of phylogeny and very limited effects of host geography and ecology on GM composition. While microbiota diverged between the upper and lower...
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Yellowhammer dialects and citizen science
Diblíková, Lucie ; Petrusková, Tereza (advisor) ; Linhart, Pavel (referee) ; Osiejuk, Tomasz S. (referee)
Bird dialects, the cultural phenomena that can be linked to migration, gene flow, speciation and cultural evolution, have been studied extensively. The yellowhammer Emberiza citrinella, a common European bird with a simple song and long singing season, has been a model species for studying dialects for decades. In this thesis, I collate several studies that benefited from citizen science approaches to push this field forward. First, we have compiled and unified information on yellowhammer dialect distribution scattered in numerous publications, and unified different dialect nomenclatures used in the past. We supplemented this with data available thanks to volunteers contributing to public databases and other online sources, and demonstrated that the continental distribution patterns of yellowhammer dialects do not support the existence of broad, geographically distinct macrodialect groups as previously believed. In 2011, as part of the Bird of the Year campaign of the Czech Society of Ornithology, we launched a year-long public awareness project "Dialects of Czech Yellowhammers". Its first year's results exceeded expectations in quality and quantity, so a one-year, conservation-focused citizen science project became a long-term, investigative one. In subsequent years, improvements to the web user...
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Host-microbiota, pro-inflammatory immunity and physiological senescence in wild birds
Těšický, Martin ; Vinkler, Michal (advisor) ; Tschirren, Barbara (referee) ; Štěpánek, Ondřej (referee)
Triggered by microbial ligands, inflammation serves as a "double-edged sword" to fight infections on the one hand, but on the other hand causing tissue damage due to oxidative stress if it is dysregulated. For example, chronic inflammation can contribute to inflammaging, which is now widely regarded as one of the causes of ageing. In my interdisciplinary dissertation, my colleagues and I investigated three interrelated aspects of inflammation, using an evolutionary framework and various free-living birds as models: (1) ecological and evolutionary determinants of gut microbiota (GM) composition and diversity, a driver of wild bird immunity, (2) diversity in immune genes affecting inflammatory responses in wild birds and (3) inflammation-related physiological senescence in a free-living passerine bird, the great tit (Parus major). Firstly, using 16S rRNA gene metabarcoding, we revealed high intra- and interspecific variation in passerine gut microbiota (GM) dominated by the major phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Although in mammals GM depends strongly on host phylogeny and diet, in birds we found only moderate effects of phylogeny and very limited effects of host geography and ecology on GM composition. While microbiota diverged between the upper and lower...
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Evolution of brain complexity and processing capacity in birds: Cracking the problem using isotropic fractionator technique
Kocourek, Martin ; Němec, Pavel (advisor) ; Sedláček, František (referee) ; Kratochvíl, Lukáš (referee)
The most fundamental principle of comparative sciences has always been and still is the search for similarities and differences. Maybe that is why people are fascinated by the cognitive abilities of birds like corvids and parrots and their similarities to those of humans. For a long time, the prevailing explanation for the unique abilities of these species was their high relative brain size. However, the brain's processing capacity is not based on its size but on its internal architecture and the number of neurons and synapses. Today, we already have data on the numbers of neurons for hundreds of mammalian, avian, and reptilian species, obtained with the isotropic fractionator. In this thesis, I analyse cellular scaling rules for brains of birds and compare them between avian clades. Bird brains are characterized by large numbers of neurons and high neuron densities, which are comparable to those of mammals in gallinaceous birds (Galliformes) and in passerine birds (Passeriformes) and parrots (Psittaciformes) even exceed those observed in primates. The distribution of neurons is also different. In songbirds and parrots, the majority of neurons are typically located in the telencephalon, specifically in the pallium. The latest data suggest that this is a common feature of core land birds...
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Sperm competition in birds and causes for its intra- and iterspecific variation
Šplíchalová, Petra ; Albrecht, Tomáš (advisor) ; Poláková, Radka (referee)
This bachelor thesis focuses on describing the occurrence and within- and between species variation of extra-pair paternity (EPP) in socially monogamous birds. In the first part of thesis I discribe variation in EPP levels among birds - I identify species with no EPP ever recorded, and species with extreme values of EPP. Extra-pair paternity seems to be more common in passerines than non-passerines. In the second part of my thesis, the most influential correlates of EPP levels in passerine birds are discussed. I summarize contemporary knowledge of the effect of these (mostly ecological) factors on EPP. These include breeding density and synchrony, population genetic diversity, adult mortality and longevity and male contribution to parental care. Key words: promiscuity, extar-pair paternity, extra-pair copulations, sperm competition
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Mechanisms enabling individual recognition of passerine birds
Caha, Ondřej ; Petrusková, Tereza (advisor) ; Vokurková, Jana (referee)
Vocalization allows birds to communicate over long distances or in environments, where can be difficult to detect visual signals. Vocalization can be divided into songs and calls. Song may inform a listener of signal about species, sex, male quality, aggressive motivation and also about singer's identity. Recognition of different individuals is very valuable ability that is commonly used during territorial interactions among males. Correct identification of males, that pose different threat, enable to respond adequately to the situation and save energy or to avoid injury in potential conflict. The ability of individual distinguishing based on song was demonstrated by using playback experiments for many passerines, but it was rarely revealed the way of such identification. This review deals with the issue of neighbour-stranger experiments that confirm the ability of passerines to discriminate between neighbours and strangers. Further, it focus on structures or characteristics of birdsong enabling individual recognition of passerines and their possibly use for individual acoustic monitoring.
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