1,721,003 research outputs found
Locomotor activity pattern of two recently introduced non-native ungulate species in a Mediterranean habitat
No full textVariations in random encounter model density estimates of European mouflon island population
No full textEstimating wildlife density is challenging, and various methods have been developed to account for imperfect detection probability. In this study, we applied the Random encounter model (REM) to estimate the population density of the European mouflon Ovis aries on the Mediterranean island of Dugi Otok, Croatia. Our goal was to test if density estimations vary throughout the year in a closed population. We systematically placed 27 camera traps over an area of 35 km2 at the intersections of 1.5-km grid cells and kept them active for 12 months (March 2022 – March 2023). All REM parameters (i.e., average movement speed, angle and radius) were estimated from the camera trap data. To explore potential correlations of mean temperature and humidity with REM parameters, six data loggers were placed systematically. The mouflon was recorded at 21 locations in 1,227 independent events on 6,719 camera-trapping days. The lowest density was recorded in winter while the highest density was observed in autumn. Our findings indicate that mouflon changed activity patterns between July and October, with trap rates increasing during the rut, which led to a fluctuation in density estimates. Correlations of temperature and humidity with the trapping rate were statistically non-significant. The trend in density estimates from two-month data subsets suggests that the largest variation in density estimation occurred between June and November, coinciding with high temperatures and the rut season. This research suggests that density estimation using REM may be influenced by sampling bias driven by seasonal variation in animal behaviour. Consequently, integrating behavioural ecology into survey design is critical to an appropriate study planning and interpretation of results
Estimation of golden jackal (Canis aureus) abundance with random encounter model
No full textU posljednjih nekoliko desetljeća u Hrvatskoj i Europi je zabilježen porast brojnosti i širenje populacija zlatnog čaglja (Canis aureus) zbog čega su potrebne sofisticirane metode praćenja te vrste. Cilj ovog rada bio je procijeniti gustoću i veličinu populacije zlatnog čaglja koristeći kamere s pasivnim infracrvenim senzorom i model nasumičnih susreta (eng. random encounter model; REM) za kojeg nije potrebna identifikacija životinja na razini jedinke. Istraživanje je provedeno u državnom otvorenom lovištu IX/13 "Senj". Procijenjena gustoća populacije bila je 1.47 ± 0.41 čagljeva/km2 i brojnost c. 90–160 čagljeva. Model nasumičnih susreta doprinos je razvoju metodologije za monitoring čaglja i korisna je metoda za procjenu populacijskih parametara čaglja.In the last several decades in Croatia and Europe, an increase in abundance and expansion of golden jackal (Canis aureus) populations have been observed, making sophisticated methods for monitoring of this species necessary. The aim of this study was to estimate population density and size of golden jackal using passive infrared sensor cameras and random encounter model (REM) that does not require individual identification of animals. Survey was conducted in state open hunting ground IX/13 "Senj". Estimated population density was 1.47 ± 0.41 jackals/km2 and abundance c. 90–160 jackals. The random encounter model adds to the methodological development of jackal monitoring and is a useful method for estimation of jackal population parameters
Effect of weather factors on growth and development of European Mouflon (Ovis aries musimon Pall.) horns in continental Croatia
Full text linkRogovi kod porodice Bovidae predstavljaju sekundarno spolno obilježje jednog ili oba spola. Kod muflonske divljači rogovi se uglavnom pojavljuju kod muškog spola, a u iznimnim slučajevima mogu se pojaviti i kod ženki, ali mnogo manji nego kod mužjaka. Analizom rogova mogu se dobiti važne informacije o životu jedinke i populacije. U istraživanjima opisanim u analiziranoj literaturi klima i okolišni čimbenici pokazali su se značajnim za rast rogova uz ostale čimbenike poput selekcije, trofejnog lova, veličine populacije, dobne strukture unutar populacija, i drugih. Cilj ovog istraživanja je testirati može li se ovisnost duljine drugog segmenta, odnosno godišnjeg prirasta rogova muflona (Ovis aries musimon Pall.) iz lovišta Garjevica objasniti okolišnim čimbenicima (temperaturom i padalinama). U istraživanju su kao prediktori za model prirasta roga korištene minimalna i maksimalna proljetna temperatura (ožujak, travanj, svibanj) te prosječna količina padalina za proljetni period. U modelu su analizirane duljine drugog segmenta roga, a uzorkovane su 83 trofeje muflona, stečenih u državnom otvorenom lovištu broj: VII/15 – „ZAPADNA GARJEVICA“, u periodu od 1992. do 2002. godine. Velika varijabilnost prirasta roga unutar istih kalendarskih godina, uz iste okolišne uvjete, te nedovoljan broj prediktora rasta uključenih u model, ukazuju na neadekvatnost ovakvog pojednostavljenog modela za opis rasta rogova muflona na ovom području.Horns in the Bovidae family represent the secondary sex characteristic of one or both sexes. At wild mouflons, horns usually occurs in male sex, but in exceptional cases they may occur in female sex but much less often than in males. By analyzing horns, important information about the life of the individual and the population can be obtained. In the studies described in the analyzed literature, climate and environmental factors have proved to be significant for the growth of horns along with other factors such as selection, trophy hunting, population size, age structure in the population and others. The objective of this study is to test whether the dependence of the length of the second segment, or the annual growth of mouflons horns (Ovis aries musimon Pall.) from the Garjevica hunting ground can be explained by environmental factors (temperature and precipitation). In the study, the minimum and maximum spring temperatures (March, April, May) and the average rainfall for the spring period were used as predictors for the horn growth model. In the model it was analyzed the lengths of the second horn segment, and 83 trophies of mouflon were sampled, obtained in the state open hunting ground number: VII / 15 - "ZAPADNA GARJEVICA", in the period from 1992 to 2002. The high variability of horn growth within the same calendar years, with the same environmental conditions, and the insufficient number of growth predictors involved in the model, indicate the inadequacy of such a simplified model for describing the growth of mouflons horns in this area
Estimation of golden jackal (Canis aureus) abundance with random encounter model
No full textU posljednjih nekoliko desetljeća u Hrvatskoj i Europi je zabilježen porast brojnosti i širenje populacija zlatnog čaglja (Canis aureus) zbog čega su potrebne sofisticirane metode praćenja te vrste. Cilj ovog rada bio je procijeniti gustoću i veličinu populacije zlatnog čaglja koristeći kamere s pasivnim infracrvenim senzorom i model nasumičnih susreta (eng. random encounter model; REM) za kojeg nije potrebna identifikacija životinja na razini jedinke. Istraživanje je provedeno u državnom otvorenom lovištu IX/13 "Senj". Procijenjena gustoća populacije bila je 1.47 ± 0.41 čagljeva/km2 i brojnost c. 90–160 čagljeva. Model nasumičnih susreta doprinos je razvoju metodologije za monitoring čaglja i korisna je metoda za procjenu populacijskih parametara čaglja.In the last several decades in Croatia and Europe, an increase in abundance and expansion of golden jackal (Canis aureus) populations have been observed, making sophisticated methods for monitoring of this species necessary. The aim of this study was to estimate population density and size of golden jackal using passive infrared sensor cameras and random encounter model (REM) that does not require individual identification of animals. Survey was conducted in state open hunting ground IX/13 "Senj". Estimated population density was 1.47 ± 0.41 jackals/km2 and abundance c. 90–160 jackals. The random encounter model adds to the methodological development of jackal monitoring and is a useful method for estimation of jackal population parameters
Estimation of golden jackal (Canis aureus) abundance with random encounter model
No full textU posljednjih nekoliko desetljeća u Hrvatskoj i Europi je zabilježen porast brojnosti i širenje populacija zlatnog čaglja (Canis aureus) zbog čega su potrebne sofisticirane metode praćenja te vrste. Cilj ovog rada bio je procijeniti gustoću i veličinu populacije zlatnog čaglja koristeći kamere s pasivnim infracrvenim senzorom i model nasumičnih susreta (eng. random encounter model; REM) za kojeg nije potrebna identifikacija životinja na razini jedinke. Istraživanje je provedeno u državnom otvorenom lovištu IX/13 "Senj". Procijenjena gustoća populacije bila je 1.47 ± 0.41 čagljeva/km2 i brojnost c. 90–160 čagljeva. Model nasumičnih susreta doprinos je razvoju metodologije za monitoring čaglja i korisna je metoda za procjenu populacijskih parametara čaglja.In the last several decades in Croatia and Europe, an increase in abundance and expansion of golden jackal (Canis aureus) populations have been observed, making sophisticated methods for monitoring of this species necessary. The aim of this study was to estimate population density and size of golden jackal using passive infrared sensor cameras and random encounter model (REM) that does not require individual identification of animals. Survey was conducted in state open hunting ground IX/13 "Senj". Estimated population density was 1.47 ± 0.41 jackals/km2 and abundance c. 90–160 jackals. The random encounter model adds to the methodological development of jackal monitoring and is a useful method for estimation of jackal population parameters
The impact of environmental factors on the development and horn growth of the european muflon (Ovis gmelini musimon Pall.)
No full textNa rast rogova divljih populacija goveda Bovidea mogu utjecati različiti čimbenici, a njihovom analizom se mogu dobiti važne informacije o životu jedinke i populacije. U istraživanjima opisanim u analiziranoj literaturi su se klima i okolišni faktori pokazali kao neki od značajnih faktora za rast rogova (uz veličinu populacije, trofejni lov, gustoća i omjer spolova u populaciji). Cilj ovog istraživanja je testirati može li se ovisnost godišnjeg prirasta rogova muflona (Ovis gmelini musimon Pall.) objasniti samo okolišnim faktorima (temperaturom i padalinama). U istraživanju su kao prediktori za model prirasta roga korištene minimalna i maksimalna temperatura te prosječna količina oborina za proljetni period (ožujak, travanj i svibanj). Analizirane su duljine prirasta 2. godine od ukupno 332 rogova muflona iz senjskog lovišta Sv. Juraj od 1995. - 2007. godine. Proljetna minimalna temperatura je jedini testirani okolišni faktor koji se pokazao značajnim (p=4.67%) za rast rogova muflona. Velika varijabilnost prirasta roga unutar istih kalendarskih godina, uz iste okolišne uvjete, te nedovoljan broj prediktora rasta uključenih u model, ukazuju na neadekvatnost ovakvog pojednostavnjenog modela za opis rasta rogova muflona.Horn growth of wild populations of Bovidae, can be influenced by various factors, and their analysis can provide important information on the life history of the individual and the population. In the studies described in the analyzed literature, climate and environmental factors have been shown as important factors for horn growth (also with population size, trophy hunting, density and sex ratio in the population). The aim of this study is to test whether the dependence of annual growth of mouflon (Ovis gmelini musimon Pall.) can be explained only by environmental factors (temperature and precipitation). In this study, the minimum and maximum temperature and average rainfall for the spring period (March, April and May) were used as predictors for horn growth model. Length of the 2nd year growth of the total of 332 horns from hunting ground Sv. Juraj in Senj, from 1995 to 2007 was analyzed. The spring minimum temperature is the only tested environmental factor that proved to be significant (p = 4.67%) for horn growth. The high variability of horn growth within the same calendar years, with the same environmental conditions, and the inadequate number of growth predictors involved in the model, indicate the inadequacy of such a simplified model for describing the horn growth
The origin analysis of croatian Barbary sheep (Ammotragus lervia PALLAS,1777) population using mitochondrial DNA sequences
No full textGrivasti skakač (Ammotragus lervia Pallas, 1777) životinjska je vrsta kojoj je izvorno stanište usko geografsko područje Sjeverne Afrike. Pripada porodici Bovidae i brojnost u Republici Hrvatskoj se procjenjuje na 200 jedinki. S obzirom da je objavljeno vrlo malo znanstvenih podataka o hrvatskoj populaciji grivastog skakača, cilj ovog diplomskog rada bio je analizirati raznolikost kontrolne regije mitohondrijske DNA grivastog skakača na području Hrvatske i usporediti dobivene sekvence sa sekvencama iz NCBI baze sekvenci. Istraživanje je provedeno na uzorcima prikupljenim s područja Mosora i analiziran je slijed kontrolne regije duljine 1075 parova baza. Pronađeno je jedno polimorfno mjesto koje čini dva haplotipa. Haplotipska raznolikost analiziranih slijedova iznosila je 0,530, dok je nukleotidna raznolikost iznosila 0,00050. Na temelju dobivenih rezultata zaključujem da je genetička raznolikost kontrolne regije mitohondrijske DNA grivastog skakača iz Hrvatske relativno niska.The barbary sheep (Ammotragus lervia Pallas, 1777) is an animal species originally inhabited by the narrow geographic region of North Africa. It belongs to the family Bovidae and the population in Croatia is estimated at 200 individuals. Considering that a very little scientific data on Croatian population was published, the aim of this graduate thesis was to analyze the diversity of the control region of the mitochondrial DNA in barbary sheep in Croatia and to compare identified sequences with sequences from NCBI base of sequences. The study was carried out on samples collected from the Mosor area and a sequence of control regions 1075 base pairs long was analysed. One polymorphic site was found which makes two haplotypes. The haplotype diversity of the analyzed sequences was 0.530, while the nucleotide diversity was 0.00050. Based on these results, I can conclude that the genetic diversity of the control region of the mitochondrial DNA of the barbary sheep from Croatia is relatively low
Comparison of methods for assembly and annotation of mitochondrial and nuclear genomes for application of chamois (Rupicapra spp.) phylogeny
No full textGenomi su sve češće korišteni podaci u proučavanju biologije i evolucije organizama, a broj dostupnih genoma u Banci gena se u posljednih nekoliko godina udvostručio kao posljedica razvoja tehnologije sekvenciranja. Razvoj ovih tehnologija utjecao je na populariziranje područja genomike i to prvenstveno zbog značajnog pada cijene sekvenciranja.
Rekonstrukcija genoma provodi se u tri koraka: sekvenciranje, sastavljanje i anotacija, a za svaki korak postoji više različitih pristupa. Sastavljanje genoma je računalno i vremenski nazahtjevniji korak te je jedan od glavnih fokusa istraživanja u području genomike. Tri su trenutno dostupne metode za sastavljanje genoma (mapiranje, de novo i hibridna metoda), a odabir metode ovisi o nekoliko glavnih parametara koji uključuju: vrstu organizma koji se proučava, pokrivenost genomskih podataka, dostupnost referentne sekvence, broj uzoraka, dostupnost računalnog servera za provođenje analiza i sl. Prema tome, svaki genomski projekt je jedinstven i teško je odabrati samo jednu metodu koja će dati najbolje rezultate, pogotovo kada se proučavaju nemodelne vrste.
Divokoza (Rupicapra spp.) je zbog svoje rasprostranjenosti i predložene sistematike dobar model za proučavanje utjecaja povijesnih i evolucijskih događaja. U ovoj se disertaciji koristilo nekoliko metoda za sastavljanje i anotaciju mitohondrijskih i jezgrinih genoma divokoze, a dobiveni su se rezultati usporedili. Na temelju usporedbi rezultata metoda za sastavljanje mitohondrijske i jezgrine DNA, procijenile su se pogodnosti različitih metoda za sastavljanje i anotaciju genoma, uspoređen je utjecaj korištenja osam genoma divokozi srodnih vrsta kao referenci u metodi mapiranja te su se rekonstruirali filogenetski odnosi s ciljem boljeg razumijevanja povezanosti taksonomskih jedinica roda Caprini i vrste Rupicapra. Uz navedeno, testirana je točnost novosastavljenih genoma divokoze usporedbom izoliranih fragmenata introna s intronskim sekvencama divokoza dostupnih u Banci gena.
Rezultati ovog istraživanja pridonijet će boljem poznavanju raznolikosti i evolucije genoma divokoze, razjašnjavanju taksonomskih odnosa podvrsta, a sastavljeni genomi pružit će dobru referentnu osnovu za buduće populacijske i genomske analize divokoze i njenih srodnika.The genome is a collection of all biological information necessary for the functioning of an organism, and in humans and animals consists of the mitochondrial genome (mtDNA) and the nuclear genome (nDNA). With the development of genomic technologies, the genome data are increasingly being used to study the biology and evolution of organisms, which is confirmed by the fact that the number of available genomes in the Gene bank has doubled in recent years. In addition, the development of these technologies has influenced the popularization of the field of genomics, mainly due to the significant decrease in the cost of sequencing. Genomic analysis can be used: to identify genes responsible for inherited diseases or adaptations to the environment, to study structural changes, to identify common conserved sites, to find genes specific to a group of organisms, etc. To perform any of these analyzes, the genome of the species under study must be reconstructed.
Reconstruction of a genome involves three steps: sequencing, assembly, and annotation. There are different approaches for each step, and the choice of method depends primarily on whether the reconstruction is of the mitochondrial or nuclear genome. Genome assembly is a computationally intensive and time-consuming step, and there are currently three available methods for genome assembly (mapping, de novo, and hybrid methods). The choice of method depends on several key parameters that include: the type of organism studied, the coverage of genomic data, the availability of reference sequences, the number of samples, the availability of a computer server for analysis, etc. Therefore, each genome project is unique and it is difficult to determine the method that will be most successful, especially when studying non-model species.
The chamois (Rupicapra spp.) is a good model for studying the effects of historical and evolutionary events because of its wide distribution and proposed systematics. In this dissertation, 12 completely sequenced chamois samples were used and their genome reconstruction was performed using different methods for assembling and annotating mtDNA and nDNA. Mapping and de novo methods were used for mtDNA assembly, while GeSeq and MITOS annotators were used for annotation. All sequences obtained with both assembly methods were compared and validated with the web application BLAST. In this process, each sequence was compared to the chamois mtDNA reference sequences. For nDNA assembly, eight available genomes of closely related species were used as references for the mapping method, followed by SNP calling procedure. Based on the filtered SNPs and references, 56 combinations were identified (newly assembled chamois genomes) that were validated and annotated using BUSCO tools. Then, three smaller sets of genes were defined from the common set of annotated genes, based on which distance matrices were calculated and the relationships were visualized using the multidimensional scaling (MDS) method. Newly assembled genomes generated by mapping chamois samples against the domestic goat genome were used to verify structure by comparing them with the chamois genome sequences (23 sets of introns) available in Gene bank. Phylogenetic analyses of mtDNA (maximum likelihood and Bayesian methods) were performed using a dataset containing 10 mtDNA sequences from this dissertation, 5 chamois mtDNA sequences from Gene bank, and two related sequences as outgroup. Phylogenetic analyses (maximum likelihood and Bayesian methods) of the genus Caprinae were performed on a data set containing 40 sequences of the genus Caprinae and 5 sequences of Bovidae as outgroup. The final phylogenetic analysis of chamois was performed using the program BEAST on a common
alignment of an intron data set consisting of 21 chamois sequences and three sequences representing an outgroup.
After performing two methods for reconstructing complete mtDNA sequences (mapping and de novo) and comparing the obtained mtDNA sequences, it was clearly determined that both methods were suitable for reconstruction. The de novo method proved to be the better choice because of its speed and simpler procedure. In addition, the de novo methods successfully isolated complete mtDNA sequences from samples that had failed quality control (Gams53, Gams85, OSIL-06). For this reason, all mtDNA analyses were performed on a larger number of samples. In other words, if only the mapping method had been used, these three samples could not have been included in the further analysis.
The mtDNA annotation tools MITOS and GeSEQ gave very similar results for all 10 samples, and variations in START and STOP codons were detected in four genes (ND1, ND2, ND3, ND5). The variations found refer to two or three bases found in the START and STOP codons. Their occurrence can be interpreted as a consequence of the different algorithms used by the annotators in the analyzes and as a consequence of the larger variation in these genes.
Phylogenetic analyses (maximum likelihood and Bayesian methods) performed on ten mtDNA sequences from chamois reconstructed in this dissertation, in combination with five mtDNA sequences from Gene bank, yielded identical phylogenetic trees for the genus Rupicapra. These results confirmed previous research on chamois in which they were divided into three mtDNA clusters (W, C, and E). Performed phylogenetic analyses (maximum likelihood and Bayesian method) on 40 mtDNA sequences of the genus Caprinae (including the four sequences obtained in this dissertation) and five sequences of the genus Bovidae also revealed the same topology as presented in previous studies.
From the comparison of the newly assembled chamois genomes with the genomes of related species, it was concluded that almost all of the related genomes used can serve as good references. Although all the species used were non-model species, the best results were obtained with the genomes of domestic goats and domestic sheep, which was to be expected since these species are extremely important species in agriculture and are often the focus of research. The number of genes found for most combinations of chamois and related species was very high, confirming that these genomes can be used for mapping processes. However, during the mapping processes it was found that some of the genomes used were of low quality, while some genomes were found to have irregularities in the information available in the Gene bank. This confirms once again that not all available genomes are of good quality. In other words, any sequence available in the Gene bank should be verified before use.
From the similarity analyses, it can be concluded that the relationships between all combinations depend primarily on the gene or genome fragments used for these analyses. Although the number of polymorphisms found had a greater impact on the results when single gene fragments were used, this number was negligible when longer portions of the genome (100 and 500 genes) were used, with differences between samples of approximately 1 %. In other words, larger distances were calculated between combinations from shorter alignments. The results of the MDS for a set of 100 and 500 genes clearly showed that samples from chamois samples mapped to different references were more similar to each other, while still exhibiting some differences in amino acid composition. Smaller differences between samples were found for combinations with domestic sheep and American mountain goat (about 1 % and 000,5 %, respectively).
The comparisons of the intron regions of the newly assembled chamois genomes with the introns available in the Gene bank suggest that the intron sequences obtained from the newly assembled genomes are of satisfactory quality and have been grouped with other chamois samples at the species and subspecies level.
The results of this research will contribute to a better knowledge of the diversity and evolution of the chamois genome, elucidate the taxonomic relationships among subspecies, and assembled genomes will provide a good reference base for future population and genome analyses of chamois and its relatives
MedUng – Uloga lova i lovnog gospodarenja u širenju novonastalih populacija divljih papkara na Mediteranu
No full textPlan upravljanja istraživačkim podatcima za projekt HRZZ MedUng – Uloga lova i lovnog gospodarenja u širenju novonastalih populacija divljih papkara na
Mediteran
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