Analyses of Wild Ungulates Mitogenome

In the last two decades, mitochondrial DNA (mtDNA) has become one of the most used genetic markers for studying evolution and phylogeny. Understanding mitochondrial genome (mitogenome) structure, gene arrangements, base compositions and noncoding regions can reveal valuable information on various organisms, including wild ungulates. A huge number of sequenced mammalian mitogenomes are available on GenBank, including 8074 mitogenome sequences of wild ungulates. The Next-Generation Sequencing (NGS) approach can reveal mitogenome regions that can explain the variation in populations. Such variations could show ungulates’ resistance to pathogens or processes of their adaptation. Despite the extensive number of new sequenced mitogenomes, there is still a lot of ambiguity around the mitogenome architecture. Methods for NGS, genome assembly and annotation are still in the process of development, aiming to make these tools powerful enough to reveal enormous knowledge crucial for assessing wild ungulate species’ conservation status, and their ecological status. In this review paper, we describe the methods and principles derived from mtDNA studies on wild ungulate species. We outline basic sequence preparation methods and specialized software for mitogenome assembly and annotation. Additionally, we present several different approaches of mitogenome comparison

Analyses of Wild Ungulates Mitogenome

In the last two decades, mitochondrial DNA (mtDNA) has become one of the most used genetic markers for studying evolution and phylogeny. Understanding mitochondrial genome (mitogenome) structure, gene arrangements, base compositions and noncoding regions can reveal valuable information on various organisms, including wild ungulates. A huge number of sequenced mammalian mitogenomes are available on GenBank, including 8074 mitogenome sequences of wild ungulates. The Next-Generation Sequencing (NGS) approach can reveal mitogenome regions that can explain the variation in populations. Such variations could show ungulates’ resistance to pathogens or processes of their adaptation. Despite the extensive number of new sequenced mitogenomes, there is still a lot of ambiguity around the mitogenome architecture. Methods for NGS, genome assembly and annotation are still in the process of development, aiming to make these tools powerful enough to reveal enormous knowledge crucial for assessing wild ungulate species’ conservation status, and their ecological status. In this review paper, we describe the methods and principles derived from mtDNA studies on wild ungulate species. We outline basic sequence preparation methods and specialized software for mitogenome assembly and annotation. Additionally, we present several different approaches of mitogenome comparison

Prediction of bulk density in Croatian forest Pseudogleys based on contents of soil organic matter and clay

Soil bulk density (BD) is often used to assess soil properties related to soil structure and general soil quality, or to convert weight units to volume/area units. Because collecting undisturbed soil samples (cores) and directly measuring BD is laborious and time-consuming, data on BD are often lacking. Pedotransfer functions (PTFs) can be used to predict BD from more readily available (easily measured) properties. However, specific PTFs for specific range of soils should be developed. In this study, soil organic matter (SOM) and clay contents of 90 forest Pseudogleys horizons, distributed across 11 locations in continental Croatia, were used to develop a multiple linear regression equation that predicts BD. The results have shown that the increase in BD due to the unit increase in clay content is lower than the decrease in BD due to the unit decrease in SOM content. PTF performance was relatively high (R2adj=77.5%, RMSE=0.10 g cm-3, MAE=0.08 g cm-3), showing that missing data on soil BD of Croatian Pseudogleys (or other similar soils, formed on similar parent materials) can be estimated reasonably well by using it. However, care should be taken when dealing with arable soils, which have different properties, compared with the natural soils considered herein

Traces of past reintroduction in genetic diversity:The case of the Balkan chamois (Mammalia, Artiodactyla)

The translocation of wild animal species became a common practice worldwide to re-establish local populations threatened with extinction. Archaeological data confirm that chamois once lived in the Biokovo Mountain but, prior to their reintroduction in the 1960s, there was no written evidence of their recent existence in the area. The population was reintroduced in the period 1964–1969, when 48 individuals of Balkan chamois from the neighbouring mountains in Bosnia and Herzegovina were released. The main objective of this study was to determine the accuracy of the existing historical data on the origin of the Balkan chamois population from the Biokovo Mountain and to assess the genetic diversity and population structure of the source and translocated populations 56 years after reintroduction. Sixteen microsatellite loci were used to analyse the genetic structure of three source chamois populations from Prenj, Čvrsnica and Čabulja Mountains and from Biokovo Mountain. Both STRUCTURE and GENELAND analyses showed a clear separation of the reintroduced population on Biokovo from Prenj's chamois and considerable genetic similarity between the Biokovo population and the Čvrsnica-Čabulja population. This suggests that the current genetic composition of the Biokovo population does not derive exclusively from Prenj, as suggested by the available literature and personal interviews, but also from Čvrsnica and Čabulja. GENELAND analysis recognised the Balkan chamois from Prenj as a separate cluster, distinct from the populations of Čvrsnica and Čabulja. Our results thus highlight the need to implement genetic monitoring of both reintroduced and source populations of endangered Balkan chamois to inform sustainable management and conservation strategies in order to maximise the chances of population persistence

Effect of slope position on soil properties and soil moisture regime of Stagnosol in the vineyard

Hillslope hydrology in agricultural landscapes is complex due to a variety of hydropedological processes and field management possibilities. The aim was to test if there are any differences in soil properties and water regime along the hillslope and to compare vineyard rows (vine) with inter-rows (grass) area for those properties. The study determined that there are significant differences in the contents of soil particle fractions, pH, and humus content along the slope ( < 0.0001), with lower confidence level in bulk density < 0.05). Differences between row and inter-row space were significant for the pH, humus, and silt content, but for sand and clay content, and bulk density differences were not determined. The study determined differences in soil water content among five slope positions ( < 0.0001), and between row and inter-row vineyard space (all with < 0.05). Where in the upper slope positions (e. g., P1) soil water content was higher than on lower slope positions. Higher soil water content was observed at higher slope positions, associated with clay content. However, it can be concluded that the retention of moisture on the slope is more influenced by local-scale soil properties (primarily soil texture) and variability of the crop (row/inter-row) than the position on the slope

Utvrđivanje simptoma nedostatka hranjiva u grahu multispektralnom analizom i klorofilnom fluorescencijom

Crop production might suffer severe economic losses due to insufficient fertiliser availability. Specific signs of nutrient shortage influence plant morphology and physiology. This study pioneers the non-destructive tracking and characterization of nutrient deficiency symptoms in common beans using multispectral and chlorophyll fluorescence imaging, offering novel insights into the dynamic responses of plant morphology and physiology to specific nutrient shortages. Plants were cultivated in nutrient solutions with and without nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), iron (Fe) and control solution. Measurements were taken every three days for 12 days (MT1-MT4) of growth. K and N deficit plants had the earliest symptoms and most noticeable changes, whereas Fe deficiency plants had the slowest and least noticeable symptoms. Except for Fe, the most responsive chlorophyll fluorescence parameter was electron transport rate, which was reduced in plants from all nutrient deprivation treatments compared to control. All nutrient deficit treatments reduced leaf area at MT2, which was the most affected morphological parameter. The green leaf index, reflection in blue, and specific green were the most affected multispectral traits by nutritional deprivation. These findings demonstrate that plant nutrient deficit can be recognized and tracked non-destructively utilizing multispectral and chlorophyll fluorescence analysis. Overall, our work not only sheds light on the dynamics of nutrient deficiency in common bean plants but also offers practical implications for improving crop management strategies using non-destructive digital technology.Zbog nedovoljne dostupnosti gnojiva uzgoj poljoprivrednih usjeva mogao bi pretrpjeti ozbiljne ekonomske gubitke. Specifični znakovi nedostatka hranjiva utječu na morfologiju i fiziologiju biljke. Koristeći multispektralne analize i klorofilnu fluorescenciju u ovom je radu opisan i kvantificiran razvoj simptoma nedostatka hranjiva (dušik (N), fosfor (P), kalij (K), magnezij (Mg) i željezo (Fe)) kod graha (Phaseolus vulgaris L.). Biljke su uzgajane u hranjivim otopinama sa i bez N, P, K, Mg ili Fe. Mjerenja su provođena svaka tri dana tijekom 12 dana (MT1-MT4) rasta. Biljke s deficitom K i N su prve razvile simptome nedostatka hranjiva i imale su najizraženije fiziološke promjene, dok su biljke s nedostatkom Fe zadnje razvile simptome nedostatka hranjiva i imale najmanje izražene simptome. Od parametara klorofilne fluorescencije, u odnosu na kontrolu smanjenje transporta elektrona je najviše reagirao u svim tretmanima sa nedostatkom hranjiva, osim u slučaju tretmana s nedostatkom Fe. Svi tretmani s nedostatkom hranjivih tvari smanjili su lisnu površinu u MT2, Što predstavlja morfološki parametar koji je bio najviše pod utjecajem nedostatka hranjiva. Indeks zelenila lišća, refleksija u plavom spektru svjetlosti i refleksija u specifičnom zelenom spektru svjetlosti bila su multispektralna svojstva koja su najviše bila pod utjecajem nedostatka hranjiva. Ovi rezultati pokazuju da se nedostatak hranjiva može prepoznati i pratiti nedestruktivno korištenjem multispektralnih analiza i klorofilnom fluorescencijom

Reaction of cocksfoot (Dactylis glomerata L.) in grass-clover mixture on N fertilization and grazing

Napasivanje je najčešći način korištenja poljoprivrednih površina u brdsko-planinskim područjima zbog specifičnih agroekoloških uvjeta. Klupčasta oštrica (Dactylis glomerata L.) je trava visoke produktivnosti i kvalitete i preporučuje se sijati u tratine za napasivanje i košnju. Zahvaljujući dobroj adaptibilnosti na različite uzgojne uvjete, posebice na sušne uvjete i niske temperature, izvrsno se uklapa u agroekološke uvjete nepogodne za uzgoj većine kvalitetnih trava. Cilj istraživanja bio je utvrditi utjecaj gnojidbe sa 150 kg dušika ha-1(N150) i napasivanja (govedima i ovcama) te njihova međusobnog djelovanja na razvoj klupčaste oštrice u travno djetelinskoj smjesi zasnovanoj u brdsko-planinskim uvjetima. Gnojidbom sa 150 kg ha-1 N u odnosu na kontrolnu parcelu (N0) ostvarena je 51,4 % veća gustoća populacije klupčaste oštrice (broj izbojaka m-2) u odnosu na utvrđenu prije početka sezone napasivanja (P<0,05) i 42,2 % nakon sezone napasivanja (P<0,01). To je rezultiralo 38,6% većim prosječnim trogodišnjim prinosom suhe tvari (ST) klupčaste oštrice u odnosu na N0 (P<0,01). Osim toga, utvrđen je veći udio klupčaste oštrice u ukupnoj ST smjese 15,3 % u odnosu na N0 (P<0,01). Način napasivanja te interakcija napasivanja i razine dodanoga mineralnog dušika nisu utjecali na gustoću populacije klupčaste oštrice. Međutim, utvrđen je statistički značajan (P<0,01) utjecaj napasivanja na prinos ST klupčaste oštrice i njezin udio u ST travno-djetelinske smjese (P<0,01). Napasivanje govedima rezultiralo je 9,9 % većim prinosom ST klupčaste oštrice i 15,2 % povećanim udjelom klupčaste oštrice na pašnjaku u odnosu na napasivanje ovcama. Najveći udio klupčaste oštrice u ukupnoj ST travnjaka utvrđen je na pregonima napasivanima govedima i gnojenima sa 150 kg/ha dušika (74,1 %), a najmanji na pregonima napasivanim ovcama i bez dušične gnojidbe (55,1 %). Zaključeno je da razvoju klupčaste oštrice više odgovara napasivanje govedima u odnosu na napasivanje ovcama. Također, ako se žele postići veći prinosi klupčaste oštrice treba osigurati opskrbu dušikom.Grazing is the most common way of using a hill and mountain areas because of their specific agro-ecological conditions. Cocksfoot is a grass with high productivity and quality, and it is very good for sowing in the sward for grazing. Because of its good adaptability to different growing conditions, especially in very dry and cold areas, it is excellent in relation to some other good grasses, which can not be raised in such areas. The aim of the experiment was to determine effect of N application (0-N0 and 150 kg ha-1 year-1-N150) and rotational grazing by cattle (C) and sheep (S), and their interaction on the cocksfoot sown in a mixture of smooth-stalked meadow grass (Poa pratensis L.) and white clover (Trifolium repens L.) in hill mountain areas. In a three-year average, the application of 150 kg ha-1 N had significant impact on cocksfoot population density (number of tillers m-2), and it was 51.4 % higher than the recorded one before grazing (P<0.05) and 42.2 % higher after grazing (P<0.01) in comparison to N0. The application of 150 kg ha-1 N resulted in significantly higher cocksfoot dry matter (DM) yield for 38.6 % (P<0.01) and 15.3 % higher cocksfoot share in the total mixture in relation to N0 (P<0.01). Grazing management and grazing management interaction with N rate did not significantly affect the population density of individual years. However, in the three-year average, grazing management significantly affected cocksfoot DM (P<0.01) and its percentage in the total DM mixture (P<0.01). Cattle grazing resulted in 9.9 % higher cocksfoot DM yield and 15.2 % higher cocksfoot percentage in pasture. Interaction of grazing management and N-level had significant influence on the percentage of cocksfoot DM in grass-clover mixture. On cattle grazed areas fertilized with 150 kg ha-1 N, the percentage of cocksfoot DM was the highest (74. 07%), while the lowest percentage of cocksfoot DM was recorded on the sheep grazed areas without N (55.12%)

is chamois hybridization in the northern dinaric mountains an important factor for horn development

The Dinaric region is the natural habitat of the Alpine chamois Rupicapra rupicapra rupicapra and Balkan chamois Rupicapra rupicapra balcanica. Recently confirmed, these two subspecies hybridize in the contact zone on Mts Velebit, coastal Croatia. Patterns of horn development in chamois can differ within populations and subspecies, and are mostly influenced by genetic structure, sex and resource availability. These factors control the direct ability of energy allocation to secondary sexual traits with diverse outcomes. This is the first study to investigate the horn growth patterns of Alpine and Balkan chamois populations and their admixed progeny. We explored the differences in horn growth and compensatory patterns among populations as a function of genetic background, separately for females and males. A significantly different pattern of horn development was detected in the hybrid population showing higher rates of initial horn growth – until 2.5 years, and much lower compensation rates in the first 4.5 years of life in both sexes in comparison to other chamois populations. Interestingly, differences in growth patterns were more expressed among males. Higher initial horn growth and low compensation rates in the hybrid population can be explained by both non-genetic and genetic factors, but may suggest an effect of heterosis, i.e. the occurrence of hybrid vigour. Therefore, this situation could reveal the extent to which life history patterns and evolutionary consequences can shape important traits of population outlook/vigour, such as horn size, in different chamois populations