Estimation of phylogeographic patterns and divergence times of populations of small mammals from the iberian peninsula using genomic data
- Autores: Alfonso Balmori de la Puente
- Directores de la Tesis: José Castresana Villamor (dir. tes.)
- Lectura: En la Universitat de Barcelona ( España ) en 2020
- Idioma: español
- Tribunal Calificador de la Tesis: Marta Pascual Berniola (presid.), Salvador Carranza Gil-Dolz del Castellar (secret.), Carles Lalueza Fox (voc.)
- Programa de doctorado: Programa de Doctorado en Genética por la Universidad de Barcelona
- Materias:
- Enlaces
- Tesis en acceso abierto en: TESEO
- Resumen
The optimization of the work with minimally invasive samples has allowed us to obtain genetic and genomic data from them, contributing to the study of the phylogeography of two Eurosiberian species, Neomys fodiens and Arvicola scherman, in the Iberian Peninsula. In chapter 1, a subspecies of the Eurasian water shrew, Neomys fodiens niethammeri, which is found in a narrow strip of the northern Iberian Peninsula, was studied. This subspecies presents an abrupt increase in skull size when compared to the rest of the Eurasian population, which has led to the suggestion that it is actually a different species. Skulls obtained from owl pellets allowed us to perform a morphometric analysis in addition to an extensive multilocus analysis based on short intron fragments successfully amplified from these degraded samples. Interestingly, no genetic divergence was detected using either mitochondrial or nuclear data.
Additionally, an allele frequency analysis revealed no significant genetic differentiation.
The absence of genetic divergence and differentiation revealed here indicated that the large form of N. fodiens does not correspond to a different species and instead represents an extreme case of size increase, of possible adaptive value, which deserves further investigation. In chapter 2, the divergence time between two Iberian populations of the Montane water vole (Arvicola scherman) was estimated using double-digest restriction site-associated DNA (ddRAD) obtained through nextgeneration sequencing (NGS), including skulls from barn owl pellets among the samples, and applying an isolation-with-migration (IM) analysis. The Cantabrian and Pyrenean populations of A. scherman are geographically isolated and have subtle morphological differences between them. Thousands of single nucleotide polymorphisms (SNPs) derived from the ddRAD were used to study their genetic structure. In addition, a bioinformatic pipeline was developed to find orthologues of the ddRAD loci in other rodents and estimate specific mutation rates using a fossil calibration point (the mouse-rat split). The IMa3 software was then used together with the specific mutation rates of the calibrated loci in order to estimate divergence times and other demographic parameters (population sizes and migration rates). The results of using 300 ddRAD loci (including 85 with estimated mutation rates) revealed that the two Iberian populations of A. scherman diverged 39 thousand years (Kyr) ago with a small amount of migration between both populations, suggesting that they have been present in isolated Iberian refugia at least since the last glaciation and are not the product of a recent colonization. Estimating divergence times with this approach can be of great help to understand the generation of diversity and determine whether the populations have differentiated for enough time to deserve separate taxonomic or conservation status.
