Genetic Analysis of the prehistoic peopling of Western Europe: Ancient DNA the role of contamination

In this thesis we have addressed three different although related topics. First, we studied the post-mortem mutation damage rate of contaminated DNA sequences in ancient human remains focusing on the development of strategies to avoid pre-laboratory derived contaminations. We proposed a guideline to control them consisting in typing every single person involved on the manipulation of the remains, especially when they have not been excavated and washed under controlled conditions. Second, we successfully develop a non-invasive technique to sequence ancient remains but preserving it from the destruction. And third, we sequenced ancient human remains from different evolutionary times (from Paleolithic to post-Neolithic) to make inferences about the peopling of Western Europe focusing mainly in the Iberia peninsula. We found that there is a long term genetic continuity at least since the Neolithic. The only clear genetic discontinuity found is that involving two different human species, H. sapiens and H. neanderthalensis.En la presente tesis hemos tratado tres temas diferentes aunque muy relacionados. Primero, hemos estudiado la tasa de mutación post-mortem de secuencias de ADN contaminante en restos humanos antiguos centrándonos en el desarrollo de estrategias para evitar que las muestras se contaminen antes de llegar al laboratorio. Proponemos una guía que consiste en el tipado genético de cada persona implicada en la manipulación de los restos, especialmente cuando estos han sido excavados y lavados bajo condiciones no controladas. Segundo, hemos desarrollado una técnica no invasiva para secuenciar DNA de restos humanos antiguos pero sin destruirlos. Y por ultimo, hemos secuenciado restos humanos antiguos pertenecientes a diferentes periodos evolutivos (desde el Paleolitico hasta el post-Neolitico) que nos han permitido hacer inferencias sobre el poblamiento Europeo centrándonos básicamente en la Península Ibérica. Hemos encontrado que ha habido una continuidad genética desde el Neolítico. La única clara discontinuidad genética encontrada es entre dos especies distintas: H. Sapiens y H.neanderthalensis

Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal

Background: Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs. Results: We have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs), plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 ± 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 ± 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought. Conclusion: Since there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree.This research was supported by the Dirección General de Investigación, Ministerio de Ciencia y Tecnología of Spain (grants BFU2004-02002 and BOS2003-08070), by Departament d'Universitats, Recerca i Societat de la Informació, Generalitat de Catalunya (grant 2001SGR00285) and a fellowship to LS