ETD

Archivio digitale delle tesi discusse presso l'Università di Pisa

Tesi etd-06272018-105858


Tipo di tesi
Tesi di laurea magistrale
Autore
BETTIN, JACOPO
URN
etd-06272018-105858
Titolo
Microsatellite genotyping with NGS to infer the population genetic structure of a murid species: approach suitability and implications for conservation in Doñana National Park
Dipartimento
BIOLOGIA
Corso di studi
CONSERVAZIONE ED EVOLUZIONE
Relatori
relatore Prof. Barbanera, Filippo
relatore Dott. Forcina, Giovanni
relatore Dott.ssa Leonard, Jennifer Ann
Parole chiave
  • NGS
  • Microsatellite
  • Mus spretus
  • Doñana
  • population genetics
Data inizio appello
16/07/2018
Consultabilità
Non consultabile
Data di rilascio
16/07/2088
Riassunto
Small mammals play key ecological roles in almost all terrestrial habitats acting as primary/secondary consumers, seed dispersers, or predators. With their relatively short lifespan and rapid life-history, small mammals are particularly suitable for genetic studies, as they quickly react to environmental factors and, as such, allow to understand ecological changes affecting animal population dynamics over time. The Algerian mouse (Mus spretus, Lataste 1883) and the wood mouse (Apodemus sylvaticus, Linnaeus 1758) are small-sized rodents belonging to the family of Muridae, subfamily Murinae, which live in the Palearctic regions. These species are sympatric in Doñana National Park, a UNESCO World Heritage Site located at the Guadalquivir River mouth in the southwest of Spain. Data collected during trapping campaigns carried out over the last 40 years indicate drastic changes in the abundance of both rodents, with a sharp increase of the Algerian mouse and a decrease in number of the wood mouse. Genetic diversity and structure of the two species were investigated by means of Next Generation Sequencing (NGS) technology, which is rapidly pervading all areas of molecular biology, improving speed and precision in parallel with rapidly declining costs. However, microsatellite genotyping through NGS sequencing is still challenging, and, as such, it is not yet widely. This thesis aims at testing the suitability of NGS technology to detect population genetic structure for both rodent species and to bring Park management plans for their long-term conservation into line with the fine-scale knowledge of their genetic structure. One-hundred seventy two samples (ear clips: M. spretus, n = 154 and A. sylvaticus, n = 18) were collected. Genomic DNA was extracted and a panel of 56 microsatellite loci, which were isolated from the genome of Mus musculus and Apodemus semotus, were selected for cross-amplification in our species. Then, sequencing was performed by NGS MiSeq® platform, IlluminaTM. However, complications in the amplification did not allow us to retrieve enough information from A. sylvaticus sequences, thus genotypic data of this species were not used in downstream analyses. Conversely, 10 loci provided a reliable dataset for M. spretus. Bayesian analysis of individual multilocus genotypes identified two main genetic clusters (A: n = 54; B: n = 54), with mice belonging to these divergent groups being uniformly distributed across the Park. The remaining 37 individuals turned out to be A x B genetic hybrids (sensu Short, 1969), hence, they held admixed genetic identity yet no spatial genetic structure was disclosed in much the same way as in the “parental” groups. We found that gene flow between A and B mice was half of that between hybrids and each parental group. Concordantly, pairwise FST distance values indicated that A and B were the most diverging groups, with mice from A being more closely related to those from AB than to those from B. The partition of the genetic diversity investigated by means of the Analysis of Molecular Variance showed that the very large majority of diversity was found within groups (98.8%; among groups, 1.2%) (FST = 0.012, P < 0.001). Overall, on the one hand, our findings suggest that crossing and reproductive success between A and B M. spretus groups does not hinder ongoing genetic divergence between them. On the other hand, a deeper investigation into how natural (e.g., ecological/behavioural) and/or anthropogenic selective factors possibly shaped the genetic structure of M. spretus is needed to better understand population dynamics of the species and run adequate management plans.
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