<p>Management of wolves is a complex issue, and molecular genetics is an important tool in this work. Molecular genetics can provide important information at the species, population and individual level, which can be essential for the development of management programs aiming at the long term survival of wolf populations.</p><p>In this thesis I developed new genetic markers on the canine Y chromosome to estimate the number of founders of the Scandinavian wolf population. This knowledge is important to reconstruct the history of the population and to design the most appropriate conservation strategies. Next, genetic markers with different pattern of inheritance have been used to identify hybrids between wolves and dogs. This allowed us to determine the direction of hybridization and to evaluate its possible impact on the gene pool of a wolf population. Furthermore, I also developed a method for a more reliable identification of the predator responsible of an attack by using saliva remains left on the prey. Since predation on livestock is perhaps the main reason for the negative opinions about the predator, the correct identification of the responsible for an attack (wolf, dog or hybrid) is essential. </p><p>Finally, this thesis has also been focusing on the domestication of dogs. By using Y chromosome markers (paternally inherited), it has been possible to complement previous studies based on mtDNA sequences (maternally inherited) and autosomal markers (inherited from both parents). In this way I have obtained a more complete picture of the domestication process and of the origin of breeds. This has shown that there has been a bias in the contribution of the two sexes in the origin of dog breeds (fewer males then females contributing to each breed) and that the origin of dogs was not marked by extensive backcrosses with male wolves over the entire species range.</p>

The phylogeography of a wide ranging temperate species, the adder, Vipera berus, was investigated using several genetic tools, with special emphasis on the post-glacial colonisation pattern of Fennoscandia. The area was colonised from two directions by adder populations representing different glacial refugia. The two populations meet in three places and the main contact zone is situated in Northern Finland. The two other contact zones are the result of dispersal across the Baltic Sea to the Umeå archepelago and South-Western Finland. Asymmetrically distributed nuclear genetic variation compared to mitochondrial DNA in the northern contact zone suggests a skewed gene flow from the east to the west across the zone. This pattern might reflect differences in dispersal among sexes and lineages, or may be accounted for by a selective advantage for nuclear variation of eastern origin among Fennoscandian adders. The phylogeographic pattern for adders across the entire species range was addressed by sequencing part of the mitochondrial genome and scoring microsatellite markers. The adder can be divided into three major genetic groups. One group is confined to the Balkan peninsula harbouring the distribution range of V. b. bosniensis. A second, well differentiated group is restricted to the Southern Alps. These two areas have probably served as refugia for adders during a number of ice ages for the adders. The third group is distributed across the remainder of the species’ range, from extreme Western Europe to Pacific Russia and can be further divided into one ancestral group inhabiting the Carpathians refugial area, and three more recent groups inhabiting areas west, north and east of the Alps. The adder provides an example of a species where the Mediterranean areas are housing endemic populations, rather than the sources for post-glacial continental colonisation. Continent-wide colonisation has instead occurred from up to three cryptic northern refugia.

The white-tailed eagle is a formerly threatened raptor that is commonly used as a flagship and indicator species in conservation work. This thesis uses molecular genetic methods to study sex determination of nestlings, genetic variability, population structure and phylogeography of the white-tailed eagle. Fourteen microsatellite markers were developed and tested for the white-tailed eagle. A method to sex white-tailed eagle nestlings in the field is presented. The method is based on just one tarsus measure, and is suitable for situations where a single person is handling the nestlings alone in a treetop. Most European white-tailed eagle populations underwent extreme declines during the 20th century. The results presented here show that bottlenecked populations have maintained significant levels of genetic diversity. Gene flow between regions is not a main explanation for this, as indicated by both genetic and ringing data. Instead, the long generation time of white-tailed eagles has acted as an intrinsic buffer against rapid loss of genetic diversity. Additionally, local conservation led to protection of more genetic diversity than if conservation had focused on the large remnant population in Norway. Mitochondrial DNA of white-tailed eagles is structured in two main clades with a predominantly eastern and western Eurasian distribution. The clades likely correspond to separate Ice Age refugia but do not grant classification as evolutionary significant units given their current extensive overlap across large parts of Eurasia. Microsatellite variation was studied in populations across Eurasia. Variability was rather constant across the continent, but clearly lower on Iceland and Greenland. This is best explained by founder effects during their colonisation, but only weak bottlenecks during colonisation of and persistence on the continent. Current population differentiation between Europe and eastern Eurasia is not compatible with a zero gene flow model but requires some amount of gene flow over evolutionary time scales.

Management of wolves is a complex issue, and molecular genetics is an important tool in this work. Molecular genetics can provide important information at the species, population and individual level, which can be essential for the development of management programs aiming at the long term survival of wolf populations. In this thesis I developed new genetic markers on the canine Y chromosome to estimate the number of founders of the Scandinavian wolf population. This knowledge is important to reconstruct the history of the population and to design the most appropriate conservation strategies. Next, genetic markers with different pattern of inheritance have been used to identify hybrids between wolves and dogs. This allowed us to determine the direction of hybridization and to evaluate its possible impact on the gene pool of a wolf population. Furthermore, I also developed a method for a more reliable identification of the predator responsible of an attack by using saliva remains left on the prey. Since predation on livestock is perhaps the main reason for the negative opinions about the predator, the correct identification of the responsible for an attack (wolf, dog or hybrid) is essential. Finally, this thesis has also been focusing on the domestication of dogs. By using Y chromosome markers (paternally inherited), it has been possible to complement previous studies based on mtDNA sequences (maternally inherited) and autosomal markers (inherited from both parents). In this way I have obtained a more complete picture of the domestication process and of the origin of breeds. This has shown that there has been a bias in the contribution of the two sexes in the origin of dog breeds (fewer males then females contributing to each breed) and that the origin of dogs was not marked by extensive backcrosses with male wolves over the entire species range.

The genetic diversity and phylogeography of brown bear maternal lineages have been studied extensively over the last two decades. In this study the genetic diversity and maternal phylogeography of non-invasively sampled 35 brown bears, including 5 captive individuals were reported from Turkey. In addition to the optimization of DNA extraction from hair, faeces and old skin samples and their PCRs, Bayesian phylogenetic analyses based on a 269 bp long piece of bear mitochondrial DNA were conducted and 14 novel haplotypes belonging to three major lineages were revealed. The most widespread lineage was found to be the &ldquo / Eastern&rdquo / clade 3a, while geographically more restricted &ldquo / Western&rdquo / and &ldquo / Middle Eastern&rdquo / lineages were reported for the country for the first time. A specimen from the Taurus range (southern Turkey) was shown to be closely related to the presumably extinct bears in Lebanon. Moreover, a unique novel lineage that appears to have split early within the Middle Eastern clade was defined. Despite limited sampling, this study demonstrates a high level of mitochondrial diversity in Turkish brown bears, extends the ranges of both European and Middle Eastern clades into Turkey, and identifies a new divergent lineage of possibly wider historical occurrence while demonstrating the significance of non-invasive genetic sampling for such analysis.

The island of Gotland houses a number of terrestrial mammalian species even though it was covered with ice during the last glacial period. The purpose of this study is to genetically analyse the mountain hare (Lepus timidus) to deduce its origin and genetic structure during different time periods, and also to discuss how it reached the island. A 130 base pair sequence of mitochondrial DNA from 38 prehistoric hares was analysed and compared to modern hares from different locations in Europe. The result shows a discrepancy among the samples creating two populations with different origin.

Water frogs are one of the most interesting vertebrate groups, showing great diversity and complexity in their reproductive modes, ecology and evolutionary relationships, and with many cryptic species due to high morphological similarity. For many decades, a single species, Rana ridibunda, has been suggested to exist in Turkey. However, the application of new morphometric, molecular and bioacoustic techniques has recently revealed the occurrence of several distinct water frog taxa in Turkey. In this study, 340 bp long mtDNA ND3 region in 195 specimens was sequenced and subjected to phylogenetic analyses to detect geographical structure and species boundaries. Neighbor joining tree, minimum spanning network, SAMOVA and AMOVA were used to understand relationship within and among clades. Population demography was studied through mismatch distribution and neutrality tests. Results indicated that populations in southwestern Turkey show high diversity and strong geographic structuring. In Turkey there are four major maternal lineages, each probably representing a species: Thrace lineage represents Rana ridibunda Pallas 1771 in European Turkey / Ceyhan lineage indicates an unnamed taxon in Cilicia plain / South-central lineage occurs at the Lake District, Antalya, Konya and Karaman provinces and represents Rana caralitana Arikan, 1988 / Anatoliaca lineage (occuring in Asiatic Turkey except for central southern Turkey, Rhodes &amp / Karpathos, northeastern Syria, and probably also Iraq and Transcaucasia) is designated either as Rana cerigensis Beerli, Hotz, Tunner, Heppich, and Uzzell 1994 or as a new subspecies of R. caralitana, based on the degree of reproductive isolation present between the last two lineages.

In the present study, history of domestic sheep were investigated by mitochondrial DNA (mtDNA) based haplogroups (HPG) of 628 samples and mtDNA control region (CR) sequences of 240 samples from 13 Turkish sheep breeds which were located in the hearth of the first domestication center. Also, 30 Anatolian wild sheep (Ovis gmelinii anatolica) mtDNA CR sequences were obtained to contribute to the scenarios on initial domestication stages of sheep. Haplogroup compositions of breeds were identified with SSCP method by using mtDNA ND2 region. The genetic diversity and relationship between haplogroups were calculated. Phylogenetic analyses of haplogroups such as median joining networks and neighbor joining trees were constructed for mtDNA CR, cytochrome B (cytB) and combined CR-cytB sequences with sequences from the present study together with sequences retrieved from NCBI (http://www.ncbi.nlm.nih.gov/). Results of the present study showed that all previously observed haplogroups (HPG A-E) were present in Turkish sheep breeds. Two individuals from rare HPG D and eleven individuals from rare HPG E were detected and sequenced. With increased sample size, for HPG E, past population expansion was observed as was the case of HPG A, B and C with mismatch distributions and neutrality tests. Spatial autocorrelation analyses and synthetic map with respect to mtDNA (maternal) pattern revealed that Turkey was separated into two regions which may be attributed to the imprints of third migration of sheep associated with the arrivals of nomadic Turks to Anatolia nearly 1000 years before present. Finally, Ovis gmelinii anatolica samples exhibited two haplotypes / one of them belongs to HPG A (possibly feral domesticate), and the other one shows a distinct haplotype (close to HPG E and C) that was not observed before. Observed, low mtDNA diversity might be the result of isolation, fragmentation, extinction of fragments and bottlenecks. Ovis gmelinii anatolica can be part of the evolved descendants of the wild sheep which gave birth to the domestic sheep.

Abstract MtDNA D-loop sequences and cranial morphometrics were used to analyze the phylogenetic relationships of bharal (Pseudois nayaur szechuanensis) populations. The habitat preferences of bharal were also investigated in Helanshan, Ningxia. The results from the analysis of mtDNA D-loop sequences and cranial morphometrics were in accordance. Among all populations analyzed, the phylogenetic relationships between populations in Lixian, Sichuan and Helanshan, Ningxia were most distantly related, while populations in Dulan, Qinghai and Subei, Gansu were close to one another. No matter in summer or winter, bharal generally prefer to stay in meadows, but they would appear in forests and shrubs as well.

<p>The first method for DNA analysis in forensics was presented in 1985. Since then, the introduction of the polymerase chain reaction (PCR) has rendered possible the analysis of small amounts of DNA and automated sequencing and fragment analysis techniques have facilitated the analyses. In most cases short tandemly repeated regions (STRs) of nuclear DNA are analysed in forensic investigations, but all samples cannot be successfully analysed using this method. For samples containing minute amounts of DNA or degraded DNA, such as shed hairs, analysis of mitochondrial DNA (mtDNA) is generally more successful due to the presence of thousands of copies of mtDNA molecules per cell.</p><p>In Sweden, ~40 % of all households have cats or dogs. With ~9 million humans shedding ~100 scalp hairs per day, and ~1.6 million cats and ~1 million dogs shedding hairs it is not surprising that shed hairs are one of the most common biological evidence found at crime scenes. However, the match probability for domestic dog mtDNA analysis has only been investigated in a few minor studies. Furthermore, although breed –sequence correlations of the noncoding mtDNA control region (CR) have been analysed in a few studies, showing limited correlations, no largescale studies have been performed previously. Thus, there have not been any comprehensive studies of forensic informativity of dog mtDNA. In the two papers presented in this thesis we have tried to lay a foundation for forensic use of analysis of domestic dog mtDNA. In the first paper, CR sequences were analysed and the exclusion capacity was investigated for a number of different populations. This is also the first comprehensive study of the correlation between mtDNA CR type and breed, type, and geographic origin of domestic dogs. Since the exclusion capacity for analysis of domestic dog CR sequences is relatively low, it was investigated in the second paper to what extent the discrimination power is improved by analysis of coding sequence. The exclusion capacity improved considerably when 3,000 base pairs of coding sequences where analysed in addition to CR sequences. This study will hopefully work as a basis for future development of analysis of dog mtDNA for forensic purposes.</p>