A retrotransposição de mRNAs como fator de variabilidade genética no genoma humano e de outros primatas / The retrotransposition of mRNAs as a factor of genetic variability in the human and other primates genomes

Duplicação genica é uma das principais forças levando a evolução dos genomas eucarioto. O impacto de duplicações gênicas/genômicas vem sendo investigado a muito tempo em humanos e outros primatas. Um segundo mecanismo de duplicação gênica, a retrotransposição baseada em RNA maduros, vem sendo menos estudada devido ao seu potencial menor de gerar cópias funcionais. No entanto, recentemente, publicações descreveram retrocópias funcionais em humanos, roedores e mosca de fruta. Nesta tese, para investigar sobre retrocópias causando variabilidade genética no genoma de primatas, nós desenvolvemos a implementamos os métodos para detectar estas inserções. Utilizando nove genomas e transcriptomas publicamente disponíveis (sete primatas e dois roedores) nós confirmamos um número similar, porém, com origem independente, de retrocópias em primatas e roedores. Nós também encontramos um enriquecimento de retrocópias no genoma de Platyrrhini, possivelmente explicado pela expansão de L1PA7 e L1P3 nestes genomas. Posteriormente, nós analisamos a ortologia de retrocópias no genoma de primatas e encontramos 127 eventos específicos à linhagem humana. Nós também exploramos dados do projeto 1000 Genomes para detectar retrocópias polimórficas (retroCNVs germinativos) e encontramos 17 eventos, presentes no genoma referência humano, mas ausentes em mais de um indivíduo. Similarmente, nós investigamos novas retroduplicações de mRNAs no genoma humano, detectando 21 eventos ausentes do genoma referência. Finalmente, investigamos a existência de retroCNVs somáticos e descrevemos sete possíveis retrocópias somáticas. Apesar de sua possível insignificância, nós encontramos que algumas retrocópias compartilhadas entre todos os primatas, espécie específicas, e polimórficas podem ser expressas per se ou como transcritos quiméricos com genes hospedeiros. Sobretudo, nós encontramos que retrocópias são um fator importante da variabilidade genética inter-espécie, intra-espécie e intra-indivíduo e podem estar influenciando a evolução de mamíferos ao criar reservatórios de duplicações potencialmente funcionais

Gene duplication is a major driving force of evolution in eukaryotic genome. The impact of gene/genomic duplication has long been investigated in human and other primates. A second mechanism of gene duplication, retrotransposition, which is based on mature RNA, has been traditionally less studied due to their lower potential to generate functional copies. Recently, however, publications described functional retrocopies in humans, murines and drosophila. Here, to gain insights of the genetic variability arising from retrocopies on primate genomes, we developed and implemented the methods to detect these insertions. Using nine publicly available reference genomes and transcriptomes (seven primates and two rodents) we described a similar number independently arisen retrocopies in primates and rodents. We also found an enrichment of retrocopies in Platyrhinni genomes, putatively explained by the expansion of L1PA7 and L1P3 in these genomes. Next, we evaluated the orthology of retrocopies in primate genomes and found 127 events specific to human lineage. We also explored 1000 Genomes Project data to detect polymorphic events (germinative retroCNVs) on human populations and found 17 events, present on the reference genome, absent in more than one individual. Conversely, we also investigated new insertions of mRNA retroduplications in the human genome, detecting 21 events absent to the human reference genome. Finally, we evaluated the existence of somatic retroCNVs and described seven putative somatic retrocopies. Despite their putative insignificance, we found that some of these shared, specie-specific and polymorphic events may be expressed per se and as chimeric transcripts within host genes. Taken together, we found that retrocopies are a great factor of genetic variation interspecie, intraspecie e intraindividual and may be affecting mammal evolution by creating reservoirs of potentially functional duplications

Comparative morphometry of the olfactory bulb, tract and stria in the human, dog and goat / Morfometría comparada del bulbo, tracto y estría olfatoria en el humano, perro y cabra

Morphometric parameters of olfactory brain components show species-dependent variations. However, the association of these parameters with olfactory function vis-à-vis ecological and evolutionary behaviors is poorly understood. In this study, a morphometric analysis of the olfactory bulb, tract and stria was carried out in three ecologically diverse animals comprising humans (primate), dogs (carnivore) and goats (herbivore) to elucidate differences in morphometry in relation to olfactory function. Using formalin-fixed brains, volumes and linear measurements of the olfactory structures were determined and correlated with those of cerebrum and the whole brain. The volume of the olfactory bulb was greatest in dogs, followed by goats and humans and constituted 0.31 percent, 0.18 percent and 0.01 percent, respectively, of the brain volume. Similarly, the ratio of volume of the bulb, tract and stria to that of brain was 1.95 percent in the dog, 0.77 percent in the goat and 0.03 percent in the human. The width of the bulb was greatest (p< 0.05) in dogs (10.80 +/- 1.64mm) compared to goats (8.25 +/- 0.96mm) and humans (5.50 +/- 0.71mm), and accounted for a hemisphere breadth of 42.91 percent, 29.73 percent and 8.94 percent respectively. Interestingly though, the total length of the olfactory bulb, tract and striae increased in the order of goat (34.5 +/- 1.30mm), human (36.25 +/- 1.70mm) and dog (48.20 +/- 1.92mm), and constituted 21.47 percent, 51.87 percent and 72.30 percent, respectively, of the hemisphere length. These results suggest that the morphometric adaptations of the olfactory components to olfactory function decline from the dog, to goat, to human, and this may be indicative of the varied olfactory functional needs in regard to the ecological diversity of these species.

Los parámetros morfométricos de los componentes del cerebro olfativo presentan variaciones que dependen de las especies. Sin embargo, la asociación de estos parámetros con la función olfativa vis-à-vis los comportamientos ecológicos y evolutivos es poco conocida. En este estudio se llevó a cabo un análisis morfométrico del bulbo, tracto y estría olfatoria en tres animales de diversidad ecológica que abarcan los seres humanos (primates), perros (carnívoros) y cabras (herbívoros) para dilucidar las diferencias en la morfometría en relación con la función olfatoria. El uso de cerebros fijados en formalina, los volúmenes y las medidas lineales de las estructuras olfativas se determinaron y se correlacionaron con el cerebro. El volumen del bulbo olfatorio fue mayor en los perros, seguidos por cabras y seres humanos y constituyeron un 0,31 por ciento, 0,18 por ciento y 0,01 por ciento, respectivamente, del volumen del cerebro. Del mismo modo, la relación entre el volumen del bulbo, vías y estrías al del cerebro fue de 1,95 por ciento en el perro, un 0,77 por ciento en la cabra y 0,03 por ciento en el ser humano. El ancho del bulbo fue mayor (p <0,05) en los perros (10,80 +/- 1.64mm) en comparación con cabras (8,25 +/- 0.96mm) y humanos (5,50 +/- 0.71mm), y representó una total hemisférico de 42,91 por ciento, 29,73 por ciento y 8,94 por ciento respectivamente. Sin embargo, curiosamente la longitud total del bulbo olfatorio, del tracto y estrías aumentaron en la cabra (34,5 +/- 1,30 mm), en humanos (36,25 +/- 1.70mm) y en el perro (48,20 +/- 1,92mm), y constituyeron 21,47 por ciento, 51,87 por ciento y 72,30 por ciento, respectivamente, del largo del hemisferio. Estos resultados sugieren que las adaptaciones morfométricas de los componentes olfativos de la función olfativa se van reduciendo de perro a cabra y al hombre y esto puede ser indicativo de las variadas necesidades funcionales olfativas en lo que respecta a la diversidad ecológica de estas especies.

An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping

The molecular clock theory has greatly enlightened our understanding of macroevolutionary events. Maximum likelihood (ML) estimation of divergence times involves the adoption of fixed calibration points, and the confidence intervals associated with the estimates are generally very narrow. The credibility intervals are inferred assuming that the estimates are normally distributed, which may not be the case. Moreover, calculation of standard errors is usually carried out by the curvature method and is complicated by the difficulty in approximating second derivatives of the likelihood function. In this study, a standard primate phylogeny was used to examine the standard errors of ML estimates via the bootstrap method. Confidence intervals were also assessed from the posterior distribution of divergence times inferred via Bayesian Markov Chain Monte Carlo. For the primate topology under evaluation, no significant differences were found between the bootstrap and the curvature methods. Also, Bayesian confidence intervals were always wider than those obtained by ML.

Noninvasive genetic sampling of endangered muriqui (Primates, Atelidae): efficiency of fecal DNA extraction

The muriqui (Brachyteles) is one of the most endangered primates in the world, however little is known about the viability of the remaining populations. We evaluated the technique of extracting DNA from wild muriqui feces for PCR applications. In order to determine the effect of the DNA in subsequent amplifications, we analyzed five different extracts. The importance of the recommended BSA and the HotStarTaq DNA polymerase was tested. The minimal conditions to successfully amplify highly degraded fecal DNA were determined, showing that the recommended reagents are not required. We envision that this method may be useful in further conservation management studies.