During the last twenty years, immense progress occurred in the area of analysis of DNA extracted from historical material. Considering the common level of preservation of tissue material, this analysis is usually executed on samples procured from bones and teeth. The analysis of soft mummified tissue is possible only in rare cases. Limiting factor of these analyses is a high degree of degradation and small amount of DNA extractable from this kind of material. First researches concentrated only on short sections of mainly mitochondrial DNA. Today, the analysis of the complete mitochondrial genome of both contemporary and extinct organisms was made possible. In case of analyses conducted on human remains, sections of nuclear DNA are far more valuable, because they can reveal information including not only subject's sex, but also possible kinship between subjects found e.g. in the same grave. Fundamental component of the whole analysis is the process of extracting DNA from cells. Probably every laboratory working with historical DNA uses a differently modified extract protocol. The main requirement for methods of extraction is to secure enough DNA with such a level of purity that would allow its use for following steps of the analysis. Taking in consideration high fragmentation of DNA, it is necessary...

The conservation biology field seeks to preserve biodiversity and the processes shaping that variation. Conservation biology is intimately tied to evolutionary research, in order to identify evolutionary distinct lineages that may be in danger of disappearing. Interestingly, patterns and processes of lineage divergence and persistence change with respect to spatial and temporal scale. I seek to evaluate biodiversity, the factors that have shaped this heterogeneity, and how this variability persists. To accomplish this I used a phylogeographic approach as well as niche and population modeling on the Peromyscus maniculatus species group found widely distributed in North America. My emphasis was on the southeastern U.S. species P. polionotus and its distinct beach forms. At a continental scale, I found that environmental niches are likely involved in generating and/or maintaining genetic lineages within the P. maniculatus species group. These findings add to a growing number of studies that have identified lineages occupying different environmental spaces. At a regional scale, I supported the hypothesis that barrier islands on the Atlantic coast of Florida were colonized by an ancestral form of P. polionotus by a single colonization, from the central Florida area. Subsequently, at least two distinct lineages diverged (P. p. phasma and P. p. niveiventris). I also found evidence that suggests that the extinct form of beach mouse (P. p. decoloratus) is part of the P. p. phasma lineage. At the population level, I evaluated changes in genetic diversity in historical samples compared to those that experienced recent human encroachment on natural habitat I used tissue preserved in natural history collections to compare with live-trapped specimens, and found that P. p. niveiventris has maintained historical genetic diversity levels. I suggest that the continuation of historical levels of genetic diversity is due to the presence of a single large area iv of continuous habitat in the central portion of the species’ current distribution. Finally, I evaluated the importance of scrub and beach habitat to the population dynamics of beach mice. Beach mice have traditionally have been associated with beach dunes rather than with the scrub habitat found more inland on barrier islands. Using almost three years of capture-recapture data from Cape Canaveral Air Force Station (CCAFS), I created a stochastic matrix model to assess the relative contribution of populations from the two different habitats to a variety of demographic measures. Both field data and model results provided evidence that the population dynamics of beach mice may rely much more on scrub habitat than formerly documented. Overall, my research emphasized a hierarchical approach to evaluate biodiversity and the processes shaping differentiation at different spatial and temporal scales. The methods and findings give insight into speciation at different scales, and can be applied to a wide range of taxa for questions related to evolutionary and conservation biology.

The mitochondrion is a tiny organelle that is the power supplier of the cell and vital to the functioning of the body organs. Additionally it contains a small circular genome of about 16 kb, present in many copies which makes the mitochondrial DNA more viable than nuclear DNA. Mitochondrial DNA is also maternally inherited and thus provides a direct link to maternal relatives. These two properties are of particular use for forensic samples, which only contain limited or degraded amounts of DNA, and for historical samples (ancient DNA). This thesis presents work on the mitochondrial DNA in the hypervariable regions (HV) I and II, in both contemporary and historical samples. Forensic genetics makes use of mitochondrial DNA analysis in court as circumstantial evidence, and population databases are used for the calculation of evidence value. Population samples (299) across Sweden have been analysed in order to enrich the EDNAP mtDNA database (EMPOP) (paper I). The application of mitochondrial DNA analysis allowed for analysis of historical skeletal remains: Copernicus, 1473-1543 (paper II), Karin Göring, 1888-1931 (paper III) and Medieval bones, 880-1000 AD, from a mass grave found in Sigtuna, Sweden (paper IV). The thesis also includes analyses of bones and teeth from the shipwrecked crew of the Vasa warship, 1628, samples from the Vasa museum, Stockholm, Sweden (paper V). Overall, the varying age of the samples and the different conservation environments (soil and water) accounted for variations in quality, but still allowed for successful DNA analysis.