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The process of evolution is of both scientific and medical interest. This thesis presents several studies using complete genomic reference sequences, comparative genomic data, and intraspecific diversity data to study the two key processes of evolution: mutation and selection. Large duplications, deletions, inversions, and translocations of DNA contribute to genomic variation both between and within species. Human chromosomes 15 and 17 contain a high percentage of dispersed, recently duplicated sequences. Examination of the relationships between these sequences showed that the majority of all duplications within each chromosome could be linked through core sequences that are prone to duplication. Comparison to orthologous sequences in other mammals allowed a reconstruction of the ancestral state of the human chromosomes, revealing that regions of rearrangement specific to the human lineage are highly enriched in chromosome-specific duplications. Comparison to copy number variation data from other studies also shows that these regions are enriched in current human structural variation. One specific region, the MAPT locus at 17q21.31, known to contain an inversion polymorphism in Europeans, was resequenced completely across both human orientation haplotypes and in chimpanzee and orangutan, revealing complex duplication structures at the inversion breakpoints, with the human region being more complex than chimpanzee or orangutan. Fluorescent in-situ hybridization analysis of human, chimpanzee, and orangutan chromosomes showed inversion polymorphisms of independent origin in all three species, demonstrating that this region has been a hotspot of genomic rearrangement for at least twelve million years. These results reveal a mechanistic relationship between sequence duplication and rearrangement in the great apes. We also generated a draft sequence of the chimpanzee genome and compared it to that of the human. Among other findings, this showed that CpG dinucleotides contribute 25% of all single base mutations, with a rate of mutation ~10-fold that of other bases, and that the male mutation rate in great apes is ~5-6 times the female rate, a higher ratio than had been observed in comparisons of primates and rodents. We detected six regions of probable recent positive selection in humans with a statistical method relying on chimpanzee sequence to control for regional variation in mutation rates. Finally, resequencing of several lines of domestic chicken and comparison to the reference chicken genome identified a number of gene deletions fixed in domestic lines and also several potential selective sweeps. Of particular interest are a missense mutation in TSHR nearly fixed in all domestic chickens and a partial deletion of SH3RF2 fixed in a high growth line. The TSHR mutation may play a role in relaxation of seasonal reproduction. A high-resolution QTL mapping experiment showed that the SH3RF2 deletion is significantly associated with increased growth. This work provides important new insights into the mechanics of evolutionary change at both the single nucleotide and structural level and identifies potential targets of natural and artificial selection in humans and chickens.

En la presente tesis doctoral se ha realizado un estudio de investigación encaminado a definir los genes responsables que causan hipercrecimiento en humanos, así como la identificación y caracterización de las mutaciones de pacientes españoles con síndromes de hipercrecimiento, con especial atención a los afectos de síndrome de Sotos. Los resultados obtenidos han permitido definir el espectro mutacional en un considerable número de pacientes con síndrome de Sotos, caracterizar en detalle estas mutaciones así como muchos polimorfismos intragénicos, en ambos casos, algunos cambios no han sido previamente descritos y otros son recurrentes. Se ha verificado la escasez de microdeleciones en población española, como en otros estudios europeos, y en los casos en los que se han identificado, se han caracterizado en detalle el tamaño y origen parental de las mismas. Se ha corroborado la validez de los criterios clínicos como indicación para estudio molecular. Se han diseñado estudios para buscar grandes reordenamientos genómicos en pacientes sin mutación previamente identificada, llegándose a caracterizar de estar manera varios reordenamientos genómicos en pacientes con sobrecremiento. / This doctoral thesis presents a research study designed to identify genes causing overgrowth in humans. The indentification and the characterization of mutations in spanish patients with overgrowth syndromes, mainly focusing on the patients with Sotos syndrome, were permormed. The obtained results helped to define the mutational spectrum in considerable amount of patients with Sotos syndrome, the detailed characterization of these mutations and, also, many intragenic polymorphisms. In both cases some of the identified changes were not previously reported and others were recurrent. It was verified that in spanish population the ratio of microdeletions is low, being similar to those previously reported in other european studies. In the cases that were identified, the detailed analysis of the size and the parental origin of mutations was carried out. The validity of clinical criteria as indicators for molecular study was confirmed. For the patients without known mutations, the experiments exploring large genomic rearrangements were designed and, consiquently, several genomic rearrangements in the patients with overgrowth were discovered.