Microsatellites are simple repetitive DNA sequences that are used as genetic markers throughout the biological sciences. The high levels of variation observed at microsatellite loci contribute to their utility in studies at the population and individual levels. This variation is a consequence of mutations that change the length of microsatellite repeat tracts. Current understanding suggests that most mutations are caused by polymerase slippage during DNA replication and lead to changes of a single repeat unit in length, but some changes involving multiple repeats can also occur. Despite this simplistic overview, there is evidence for considerable heterogeneity in mutation processes between species, loci and alleles. Such complex patterns suggest that other mechanisms, including those associated with DNA recombination, are also involved in the generation of microsatellite mutations. Understanding which mutational mechanisms are responsible for variation at microsatellite markers is essential to enable accurate data interpretation in genotyping projects, as many commonly used statistics assume specific mutation models. I developed microsatellite markers specific to the X and Y chromosomes and an autosome in the tammar wallaby, Macropus eugenii, and investigated their evolutionary properties using two approaches: indirectly, as inferred from population data, and directly, from observation of mutation events. First, I found that allelic richness increased with repeat length and that two popular mutation models, the stepwise mutation model and the infinite allele model, were poor at predicting the number of alleles per locus, particularly when gene diversity was high. These results suggest that neither model can account for all mutations at tammar wallaby microsatellites and hint at the involvement of more complex mechanisms than replication slippage. I also determined levels of variation at each locus in two tammar wallaby populations. I found that allelic richness was highest for chromosome 2, intermediate for the X chromosome and lowest for the Y chromosome in both populations. Thus, allelic richness varied between chromosomes in the manner predicted by their relative exposure to recombination, although these results may also be explained by the relative effective population sizes of the chromosomes studied. Second, I used small-pool PCR from sperm DNA to observe de novo mutation events at three of the most polymorphic autosomal markers. To determine the reliability of my observations I developed and applied strict criteria for scoring alleles and mutations at microsatellite loci. I observed mutations at all three markers, with rate variation between loci. Single step mutations could not be distinguished because of the limitations of the approach, but 24 multi-step mutations, involving changes of up to 35 repeat units, were recorded. Many of these mutations involved changes that could not be explained by the gain or loss of whole repeat units. These results imply that a large number of mutations at tammar wallaby microsatellites are caused by mechanisms other than replication slippage and are consistent with a role for recombination in the mutation process. Taken as a whole, my results provide evidence for complex mutation processes at tammar wallaby microsatellites. I conclude that careful characterisation of microsatellite mutation properties should be conducted on a case-by-case basis to determine the most appropriate mutation models and analysis tools for each locus. In addition, my work has provided a set of chromosome-specific markers for use in macropod genetic studies, which includes the first marsupial Y chromosome microsatellites. Sex chromosome microsatellites open a new range of possibilities for population studies, as they provide opportunities to investigate gene flow in a male context, to complement data from autosomal and maternally-inherited mitochondrial markers.

<p>Due to Ireland’s secluded geographical location, its genetic structure is a popular topic of study. The indigenous inhabitants of Ireland remained undisturbed for a long period time, allowing for a distinct genetic population to be created. This peace was disrupted by conflict with invading forces, such as the Nordic Vikings and Anglo-Norman forces. However, these historical events helped to shape both the culture of Ireland and the ancestry seen in the Irish population today. In Ireland, quite like many countries around the world, the male’s surname is passed from father to son, just as the Y-chromosome. The relationship between Irish surnames and their corresponding Y-haplogroups was examined to determine if common and rare Irish surnames can be genetically linked to the historical invasions listed above. The surnames chosen for this study were selected based on their prevalence in Ireland, rare or common, and their proposed historical origin, Irish, Norse or British. To discover any possible patterns in surnames and Y-chromosomal DNA, Y-haplogroups were generated from the DNA of 630 Irish male subjects using an assay specifically developed for the region. The assay contains twenty single-nucleotide polymorphisms (SNPs) that were selected to further resolve the R1b-L21 Y-haplogroup for Irish ancestry, the most prevalent haplogroup in Western Europe, and Ireland in particular. Additional Y-STR data was also generated to examine recent surname history within the collected individuals. Each surname was examined to determine whether one haplogroup occurred more frequently and with this method, distinct patterns in Irish surnames and geographical locations were discovered. In addition to resolving Y-surname history patterns, it is also believed that this assay may be beneficial in determining if an unknown DNA sample is of Western European origin and even in some cases, if a more specific Irish origin can be predicted.</p>

Conselho Nacional de Desenvolvimento Científico e Tecnológico / Preimplantation genetic diagnosis (PGD) is becoming a current issue in animal reproduction biotechnology due to economical reasons. Predetermining the sex of offspring is one example of PGD. This study aimed to determine the percentage of male and female bovine embryos in vitro produced after oocyte fertilization with Percoll density gradient centrifugation or with self-migration (swim-up) selected semen. In experiment 1, sperm selection was performed by 90%-45% discontinuous Percoll density gradient centrifugation (T1) and swim-up (T2). In experiment 2, along side the discontinuous gradient, a 67.5% continuous density gradient, and centrifugation time of 5 and 10 minutes were used. A total of 4 treatment groups was defined (TI = continuous, 5 minutes, TII = discontinuous, 5 minutes, TIII = continuous, 10 minutes and TIV = discontinuous, 10 minutes). Polymerase chain reaction (PCR) was used to determine the sex of the embryos. T1 (n=185) resulted in 48.65% (n=90) male embryos and 51.35% (n=95) female embryos and T2 (n=142) in 58.45% (n=83) male and 41.55% (n=59) female embryos. In experiment 2, the percentages of male and female embryos obtained in TI (n=93), TII (n=70), TIII (n=82) and TIV (n=82) were 49.46% (n=46) and 50.54% (n=47), 57.14% (n=40) and 42.86% (n=30), 36.59% (n=30) and 63.41% (n=52) and 48.78% (n=40) and 51.22% (n=42), respectively. There was no difference on the percentage of males and females in all treatment groups from experiments 1 and 2 when these were individually compared to the expected percentage of 50% of each sex. There was also no difference in male and female embryo percentage between treatment groups in experiments 1 and 2. / O diagnóstico genético pré-implantação (DGP) vem se destacando na área da biotecnologia da reprodução animal por motivos econômicos. Um exemplo de DGP é a predeterminação do sexo da prole. Neste estudo foi verificada a percentagem de embriões bovinos machos e fêmeas produzidos in vitro após a fertilização de oócitos com sêmen selecionado por centrifugação em gradiente de densidade de Percoll ou por migração ascendente (swim-up). No experimento 1 a seleção espermática foi realizada usando o gradiente descontínuo de Percoll de 90% e 45% (T1) e o swimup (T2). No experimento 2 foi utilizado, além do gradiente descontínuo, um gradiente contínuo de densidade de Percoll de 67,5%, e tempos de centrifugação de 5 e 10 minutos, totalizando 4 tratamentos (TI = contínuo 5 minutos, TII = descontínuo 5 minutos, TIII = contínuo 10 minutos e TIV = descontínuo 10 minutos). A sexagem dos embriões foi realizada através da técnica da reação em cadeia da polimerase (PCR). No T1 (n=185) foram obtidos 48,65% (n=90) de embriões masculinos e 51,35% (n=95) de femininos e no T2 (n=142) 58,45% (n=83) foram machos e 41,55% (n=59) fêmeas. No experimento 2, a percentagem de embriões masculinos e femininos no TI (n=93), TII (n=70), TIII (n=82) e TIV (n=82) foi de 49,46% (n=46) e 50,54% (n=47), 57,14% (n=40) e 42,86% (n=30), 36,59% (n=30) e 63,41% (n=52), e 48,78% (n=40) e 51,22% (n=42), respectivamente. Não houve alteração na percentagem de machos e fêmeas nos tratamentos dos experimentos 1 e 2 quando estes tratamentos foram comparados individualmente com a percentagem teoricamente esperada de 50% de cada sexo. Também não houve alteração na percentagem de machos e fêmeas na comparação entre os dois tratamentos do experimento 1 e entre os quatro tratamentos do experimento 2.