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The Balkan terrapin (Mauremys rivulata) is an endangered species protected by the Habitats Directive. Its range in Croatia is restricted to the southernmost karstic aquatic habitats. Most of these habitats are antropogenic modifications of lentic and lotic water used historically for agriculture. The aim of this study was to investigate the available genetic tools for conservation management of the species and to conduct a preliminary analysis of the genetic diversity of M. rivulata in Croatia. The survey of literature and openly accessible genetic repositories revealed the knowledge on complete and incomplete genes, microsatellite markers, rRNA and complete mtDNA for the species. Ampliffication of all 18 microsatellite markers available for the species on 56 samples resulted in 15 successfully amplified markers. Nine of them were estimated to have high probability of null alleles and were excluded. Preliminary genetic diversity analysis of two populations from Croatia (Majkovi and Konavle) and one from Montenegro (Sutorina) based on six microsatellite markers revealed a high level of polymorphism (24 alleles per locus on average). The values of expected heterozygosity ranged from 0.85 (Sutorina) to 0.93 (both Majkovi and Konavle populations). Bayesian analysis of population structure revealed the existence of three gene pools, the first dominant in the Suturina population, and the second in both Croatian populations, while the third was present to a lesser extent in all populations. Although they provide insights into the population genetics of M. rivulata, the available microsatellite markers are limited due to the high proportion of null aleles, especially for parentage analysis. SNP markers developed using the ddRAD method would provide a more precise and cost-effective estimate of effective population size and efficient population management of this threatened species.

Barbary sheep (Ammotragus lervia) is a non- native ungulate from North Africa which has been established in the wild beyond its natural range due to intentional introductions and illegal releases. In Europe, four countries are inhabited with free-ranging Barbary sheep population: Croatia, Czech Republic, Italy and Spain. While being threatened in their native area, the majority of its exotic populations have showed high adaptability and formidable capacity to settle and expand their ranges. Non-native species cause changes to the ecosystems in which they are introduced. To understand their potential to establish and spread in the novel range, it is crucial to study their genetic diversity and population genetic structure. Population genetic parameters affect population viability and adaptive potential under environmental change. Here, we report the first genetic study of European Barbary sheep populations. We used ten microsatellite loci previously published to characterize and compare the genetic diversity and spatial pattern of genetic structure among study populations. We aimed to understand how current levels of genetic diversity and structuring vary among Barbary sheep populations that differ with regard to the time and source of introduction. Our results present important knowledge about origins of these populations and are the basis for further management.

Brown bears in Croatia are a game species and through the hunting management since the 1950s the population grew from less than 100 bears to the current estimate of 600 to 1000. According to the management plan, hunting of bears is dane through yearly quotas. However, presently, the decision of quota size is made with out the necessary knowledge on the scientifically based population estimate and it's genetic status. This is the source of various complains: same believe that the quota should be much higher, believing that there are too many bears, and the others are against any quota fearing the population can not sustain such losses. As the bear range is also inhabited by humans, typically the capacity of the habitat is above the social capacity, i.e. above the point when the conflict (damages and threats to human safety) is perceived as unacceptably high. Hence, knowledge about the actual population size of the brown bear population is a prerequisite for the gaining and maintaining of pu blic acceptance of the bear in Croatia. To investigate the genetic diversity of Croatian brown bear population, we surveyed 13 polymorphic microsatellite loci for 90 bears and obtained partial mitochondrial DNA control region. sequences (267 bp) for 71 bears that had been hunted or accidentally killed during 2005/06 and whose muscle tissue samples we had received. The mean allelic diversity per microsatellite locus was 6.54, ranging from three to 10 alleles, which is relatively high. The analysis of mtDNA control region sequences revealed only two haplotypes that differ by two nucleotides, and whose frequencies were 0.18 and 0.82. This extremely law mtDNA haplotype and nucleotide diversity may indicate pop.ulation bottleneck in the recent past by severe hunting and should be explored further. Genotyping of bear scat samples using six microsatellite loci for individual identification is now in progress with DNA extracted from over 500 samples. The procedure will be followed with statistical elaboration and population viability modeling. With more sam ples coming in and further analysis, genetic data shali provide scientific guidelines for brown bear management in the future. Traditionally bear managers counted the animals at feeding sites. That method suffered of biases but the genetic method and standardization of hunter's counts will allow the calibration of traditional methods and the continuous insight in the population trend. On the internationallevel the results of this study will help conserve the brown bear on the European level, and will help Croatia to comply with conventions signed (Bern, Habitat directive, CITES).

Plavobijeli dupin, Stenella coeruleoalba (Meyen, 1833), je najučestalija vrsta kita u Sredozemnom moru. Populacija koja nastanjuje Sredozemno more klasificirana je prema IUCN-u kao osjetljiva. Smatra se da nije rezidentna vrsta Jadrana te je ovo istraživanje tek drugo na temu plavobijelih dupina Jadrana. U radu su analizirane kraniometrijske osobitosti plavobijelih dupina iz hrvatskog dijela Jadrana i uspoređene s plavobijelim dupinima drugih mora. Napravljena je analiza haplotipova kontrolne regije mitohondrijske DNA plavobijelih dupina Jadrana, 17 po prvi puta analiziranih i deset iz prijašnjeg istraživanja, te šest iz Ligurskog mora za usporedbu. Analizom 37 kraniometrijskih mjera 30 lubanja utvrđeno je da mužjaci imaju dulji rostrum, veći broj zubiju, šire zube te veće posttemporalne jame od ženki, dok ženke imaju veći neurokranij, očnice i hoane. Prema kraniometrijskim vrijednostima plavobijeli dupini iz hrvatskog dijela Jadrana slični su onima iz talijanskih voda i manji od onih iz japanskog dijela Tihog oceana. Na 27 uzoraka mtDNA iz Jadrana utvrđeno je devet haplotipova koji se razlikuju u 32 polimorfna mjesta. Haplotipska raznolikost iznosi 0,832, a nukleotidna 0,00729, što ukazuje na veliku genetičku raznolikost plavobijelih dupina Jadrana. Jedan uzorak iz Ligurskog mora pripadao je haplotipu pronađenom u Jadranskom moru, dok je svaki od preostalih pet pripao jednom od pet novo-utvrđenih haplotipova. Striped dolphin, Stenella coeruleoalba (Meyen, 1833), is the most abundant cetacean species in the Mediterranean Sea. The population that inhabits the Mediterranean is classified as vulnerable by IUCN. It is considered a nonresident species in the Adriatic Sea and this is the second research on striped dolphins from the Adriatic. In this thesis we analyze the craniometric characteristics of striped dolphins from the Croatian part of the Adriatic and compares them to striped dolphins of other seas. An analysis of haplotypes of the control region of mitochondrial DNA of striped dolphins from the Adriatic was conducted, 17 samples were analyzed for the first time and ten were added from a previous research. Six samples from the Ligurian Sea were analyzed for comparison. Analysis of 37 craniometrical features on 30 skulls revealed that males have a longer rostrum, greater number of teeth, wider teeth and bigger temporal fossae than females, while females have a greater neurocranium, orbital bones and internal nares. When compared by craniometrical values, striped dolphins from the Croatian part of Adriatic are similar to those from Italian waters and smaller than those from the Japanese part of the Pacific Ocean. Nine haplotypes were found among 27 mtDNA samples from the Adriatic, differing in 32 polymorphic sites. Haplotype and nucleotide diversity were 0,832 and 0,00723, respectively, which indicates great genetic diversity of striped dolphins from the Adriatic. One sample from the Ligurian Sea belongs to a haplotype found in the Adriatic, while each of the other five belong to one of the five newly-found haplotypes.

Crvenokljuna čigra (Sterna hirundo) je ptičja vrsta čija je aktivnost usko vezana uz vodena staništa. Prirodna gnjezdilišta kopnenih populacija čine šljunčani otoci na kojima im veliku prijetnju čini ljudska aktivnost. Iz tog razloga, određivanje genetičke raznolikosti i strukture ključno je jer nam može ukazati na eventualno potrebne mjere za njezinu zaštitu. Cilj ovog diplomskog rada bio je analizirati nukleotidne sljedove kontrolne regije mitohondrijske DNA populacije crvenokljune čigre iz Njemačke, utvrditi distribuciju i učestalost haplotipova te usporediti haplotipove i razinu raznolikosti dobivene u ovom istraživanju s onima utvrđenim u populacijama Slovenije i Hrvatske. U istraživanom uzorku od 95 jedinki utvrđena je prisutnost od ukupno 23 haplotipa od čega je njih 13 zabilježeno samo kod jedne jedinke. Nađena je mala, ali statistički značajna diferencijacija između populacija jezera Neuwarper i jezera Lieps, dok je diferencijacija između grupe populacija iz Njemačke i grupe populacija iz Slovenije i Hrvatske izuzetno niska, što ukazuje na međusobnu povezanost tih skupina populacija. Rezultati dobiveni ovim istraživanjem bit će dobra podloga za daljnje stvaranje baze podataka o raznolikosti crvenokljune čigre. Na taj način bi se stekla bolja cjelokupna slika ugroženosti ove vrste. Common Tern (Sterna hirundo) is a bird whose activity is closely related to water habitats. Natural freshwater tern habitats include river and lake islands in which the main threat for them is human activity. Studies on genetic diversity and structure provide a basis for protection actions that are potentially needed. The aim of this thesis was to analyse nucleotide sequences of the mitochondrial DNA control region of common tern population from Germany, to determine haplotype frequency and distribution, and to compare the levels of genetic diversity among populations from Germany and those from Croatia and Slovenia. In the sample of 95 individuals, 23 haplotypes were found, while 13 of them were found in only one individual. The results indicate that there is low, but statistically significant level of differentiation between populations from lake Nuwarper and lake Lieps. In addition, we found that level of differentiation between Common Terns from Germany and examined individuals from Croatia and Slovenia is low indicating connectivity between the studied population groups. Results of this investigation will be useful for creation of the mitochondrial DNA control region diversity database for Common Terns, which will contribute to better understanding of the threats for this species.

Divlja mačka (Felis silvestris) autohtona je i strogo zaštićena vrsta u Hrvatskoj, međutim objavljeno je vrlo malo znanstvenih podataka o hrvatskoj populaciji divlje mačke. Cilj ovog istraživanja bio je analizirati raznolikost kontrolne regije mitohondrijske DNA divlje mačke na području Hrvatske te usporediti dobivene haplotipove s haplotipovima domaće mačke (Felis catus). Istraživanje je provedeno na 41 uzorku divljih, te 38 uzoraka domaćih mačaka. Analiziran je slijed kontrolne regije mitohondrijske DNA duljine 814 parova baza, te je kod divlje mačke utvrđena prisutnost 22 polimorfna mjesta koji čine 11 različitih haplotipova. Haplotipska raznolikost analiziranih sljedova iznosila je 0,857 +/- 0,036, dok je nukleotidna raznolikost 0,017 +/- 0,009. Kod 38 uzoraka domaće mačke utvrđeno je 21 polimorfno mjesto koji čine 11 haplotipova. Haplotipska raznolikost analiziranih sljedova domaće mačke iznosila je 0,758 +/- 0,067, a nukleotidna 0,011 +/- 0,006. Među haplotipovima divlje i domaće mačke nema podudaranja. Na temelju dobivenih rezultata zaključujem da je genetička raznolikost kontrolne regije mitohondrijske DNA divlje mačke iz Hrvatske relativno visoka. Wildcat (Felis silvestris) is autochthonous and strictly protected species in Croatia; however there is almost none scientific data on Croatian wildcat population. The goal of this research was to investigate diversity of mitochondrial DNA control region of wildcat from Croatia and to compare identified haplotypes with haplotypes of domestic cat (Felis catus). A total of 41 samples of wildcats and 38 domestic cat samples were included in the research. I analysed 814 base pairs long control region sequences and in wildcat samples 22 polymorphic sites were identified yielding 11 different haplotypes. Haplotype diversity of analysed sequences was 0,857 +/- 0,036, while nucleotide diversity was 0,017 +/- 0,009. Among 38 domestic cats samples 21 polymorphic sites were identified yielding 11 haplotypes. Haplotype diversity of analysed sequences of domestic cats was 0,758 +/- 0,067, while nucleotide diversity was 0,011 +/- 0,006. There were no matches between wildcat and domestic cat haplotypes. Based on these results I conclude that mitochondrial DNA control region diversity of wildcat from Croatia is fairly high.

Dobri dupin - Tursiops truncatus (Montagu, 1821) jedini je stalni morski sisavac Jadranskog mora te se pretpostavlja da u hrvatskom dijelu živi između 220 do 250 jedinki. Korišteni su uzorci dobrih dupina uginulih u hrvatskom dijelu Jadranskog mora i dva uzorka iz talijanskog dijela Jadrana. Cilj je utvrditi kraniometrijske značajke i raznolikost sljedova dijela kontrolne regije mtDNA dobrog dupina iz Jadranskog mora. Unutar 108 jedinki postoji 11 različitih haplotipova. Najučestaliji je haplotip DD01. Genska raznolikost iznosi 0,6108, a nukleotidna 0,010452. Haplotip DD07 je jedinstven. U 96 lubanja odraslih jedinki nađeno je da se mužjaci i ženke jadranske populacije razlikuju u 19 kraniometrijskih mjera, u mužjaka je lubanja robusnija. Lubanje dupina izraelskih, crnomorskih, kineskih te istočno floridskih populacija su kraće, a u populacija iz istočnog Atlantika, Sjevernog mora, mora oko Mauritanije, mora oko Južnoafričke Republike i iz mora oko Australije znatno su dulje su od lubanja jadranskih dobrih dupina. Bottlenose dolphin - Tursiops truncatus (Montagu, 1821) is the only resident marine mammal in the Adriatic Sea, and it is assumed that in the Croatian part live between 220-250 individuals. Carcasses of bottlenose dolphins from the Croatian part and two samples from the Italian part of the Adriatic were used. The goal is to determine craniometrical features and diversity of the mtDNA control region of bottlenose dolphins from the Adriatic Sea. Among 108 individuals, there are 11 different haplotypes. The most common haplotype is DD01. Genetic diversity was 0.6108, and nucleotide 0.010452. Haplotype DD07 is unique. Males and females of Adriatic population differ in 19 skull variables, in males the skull is more robust. Skulls of Israeli, Black Sea, Chinese and Eastern Florida populations are shorter, while skulls of populations from the Eastern Atlantic, North Sea, the seas around Mauritania, South Africa and Australia are considerably longer than the skulls of Adriatic bottlenose dolphins.

Bakterijska vrsta Coxiella burnetii je vrlo infektivna bakterija i obvezatni unutarstanični parazit. U ljudi i životinja uzrokuje Q-groznicu koja je raširena po cijelom svijetu. U ovom radu su po prvi put genotipizirani sojevi vrste C. burnetii u Hrvatskoj metodom MLVA (Multi Locus VNTR Analysis, Variable Number of Tandem Repeats) koja se u svijetu tek uvodi kao metoda za genotipizaciju bakterije C. burnetii. Metoda je primijenjena na 49 uzoraka podrijetlom od domaćih životinja, 15 uzoraka je u potpunosti tipizirano, a njih 14 svrstano je u jedan od 10 dobivenih genotipova. Dva genotipa srodnija su s genotipovima u svijetu nego s hrvatskim genotipovima, a karakteristični su za kontinentalni dio Hrvatske. Ostali genotipovi srodniji su međusobno nego sa stranim genotipovima, a karakteristični su za primorski dio Hrvatske. Metoda MLVA uvedena je kao rutinski dijagnostički postupak čime je omogućeno utvrđivanje izvora i puteva širenja infekcije što će pridonijeti kontroli i suzbijanju bolesti u domaćih životinja koje su ujedno primarni izvor zaraze za ljude. Coxiella burnetii is very infectious intracellular bacterium. In humans and animals it causes Q-fever which is spread all around the world. This study was the first time of genotyping C. burnetii strains in Croatia. The strains were genotyped using MLVA (Multi Locus VNTR Analysis, Variable Number of Tandem Repeats) method, a method recently introduced for the C. burnetii genotyping in the world. The 49 domestic animals' samples were genotyped, 15 samples were typed completely and 14 of them were assigned to one of 10 obtained genotypes. Two genotypes are more similar to the genotypes in the world than to other genotypes in Croatia and they are typical for continental part of Croatia. All other genotypes are more similar to each other than to foreign genotypes. These genotypes are typical for the coastal part of Croatia. The MLVA was implemented as tool for locating the source of the infection and the route of transmission which is essential in prevention and controlling the disease.