Evolutionary history of two Iberian Soricomorpha: genomics, phyligeography and dispersal patterns = Historia evolutiva de dos soricomorfos ibéricos genómica, filogeografía y patrones de dispersión

Abstract

The study of intraspecific diversity is essential in ecology and evolution as they reveal fine-scale patterns and it is crucial in conservation planning. The main aim of this thesis is to study the evolutionary history of two Iberian Soricomorpha: The Pyrenean desman (Galemys pyrenaicus) and the Mediterranean water shrew (Neomys anomalus). Both mammals are semi-aquatic and endemic to the Iberian Peninsula. To this end, different approaches were applied, such as genomics, phylogeography and species distribution modelling (SDM), in the three chapters of this thesis. In Chapter 1, the main aim was to study the population structure of the Pyrenean desman using genomic markers. In order to achieve this objective, we optimized a genomic reduction protocol, double-digestion RAD sequencing (ddRAD), for the low DNA quantities needed when working with endangered species, like the Pyrenean desman. Moreover, we filtered and evaluated the library and determined the sex of the specimens used. Then, we estimated the heterozygosity rate and we determined population structure and evolutionary units performing a Principal Component Analysis (PCA), a Structure analysis and a genomic phylogenetic tree. As result, the heterozygosity rate turned out to be one of the lowest in mammals and five clades were delimited in the population structure. These results have important conservation implications. In Chapter 2, our main aim was to infer the mitochondrial genetic structure and the postglacial dispersal patterns of the north-western clade of the Pyrenean desman, using non-invasive samples. We delimited a contact zone in the Cantabrian Mountains and we studied the structure of nucleotide diversity through an interpolation map, the genetic structure through an Analysis of Molecular Variance (AMOVA) and the dispersal patterns through an Isolation-by-Distance approach. The results revealed areas of very high genetic diversity and areas of extremely low genetic diversity. Moreover, half of the genetic structure can be explained by the isolation of river basin, meaning that the desmans were not completely isolated in these basins, which is consistent with postglacial overland dispersal between the basins. This result was confirmed by the Isolation-by-Distance approach, which also revealed a high relative importance of overland dispersal during the Holocene but a

similiar relative importance of overland and river dispersal for short distances. This study has also conservation implications, as it suggests that terrestrial corridors within the desman distribution range should also be restored and preserved. Finally, in Chapter 3, we studied the phylogeography of the Mediterranean water shrew, which was recently delimited as a species. We studied its phylogenetic structure using a Maximum Likelihood and Bayesian Inference phylogenetic trees. Moreover, we interpolated the nucleotide diversity and performed a species distribution modelling. The results revealed two main clades correlated with geographic structure. Moreover, the study suggests certain coincidence of high genetic diversity areas with optimal areas in the Last Glacial Maximum, which is consistent with the location of the glacial refugia.

La diversidad dentro de especies es clave desde el punto de vista ecológico y evolutivo y, además, para la conservación. El principal objetivo de esta tesis es estudiar la historia evolutiva de dos mamíferos ibéricos: el Desmán de los Pirineos (Galemys pyrenaicus) y el Musgaño de Cabrera (Neomys anomalus). Para ello, se han utilizado diversas metodologías, entre ellas genómica, filogeografía y modelos de distribución de especies, a lo largo de los tres capítulos que conforman esta tesis. En el capítulo 1, se busca estudiar la estructura genética del desmán usando marcadores genómicos. Para ello, se optimizó un protocolo de reducción genómica (ddRADSeq) y se realizaron análisis genómicos con los datos resultantes de la librería. Los resultados revelaron una heterozigosidad extremadamente baja y cinco clados como unidades evolutivas. Estos resultados tienen repercusión en la conservación de la especie. En el capítulo 2, se estudia la estructura genética mitocondrial y los patrones de dispersión postglacial del desmán en el clado nor-occidental. Los resultados sugieren que los desmanes no estuvieron completamente aislados en las cuencas de los ríos y se dispersaron durante el Holoceno por tierra para realizar desplazamientos largos. Por el contrario, para desplazamientos cortos, los resultados sugieren que se pudieron desplazar tanto por el río como por tierra. Finalmente, en el capítulo 3, se estudia la filogeografía e historia evolutiva del Musgaño de Cabrera y se ha descubierto una estructura genética dividida en dos clados correlacionados con la estructura geográfica. Además, los resultados sugieren la existencia de refugios glaciares y una compleja historia postglacial.