Search results for: phylogenetic tree

Authors: G. Sava, I. Popa, T. Sava, A. Ion, M. Ilie, C. Manailescu, A. Robu

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At the RoAMS laboratory in Bucharest we have looked for a head-to-head meeting between AMS radiocarbon dating and dendrochronology dating, aiming to point out and explain any differences or similarities that might appear between their output results. As a subject of this investigation, we have fixed our attention on a sequence of tree rings spanning on a period of 700 years, starting with 1000 AD. The samples were collected from the northern Romanian territory within Moldavia region, and were provided by the ‘Marin Dracea - National Institute for Research and Development in Forestry’. All the 23 single ring wood samples were radiocarbon dated using alpha-cellulose extraction, followed by graphitization in an AGE3 installation. A wiggle matching procedure was applied to reduce the radiocarbon uncertainties for the calibrated ages. The results showed a good agreement on 3 out of 4 wood cores, the age-shifting of one of the wood cores being interpreted as an uncertain dendrochronology matching, which was further corrected.

Keywords: wiggle matching, tree-ring radiocarbon dating, dendrochronology, AMS radiocarbon dating, radiocarbon dating in Romania

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Authors: Sofia F. Franco, Jacob Macdonald

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This paper estimates the value of urban public street trees and their complementary and substitution value with other broader urban amenities and dis-amenities via the residential housing market. We estimate a lower bound value on a city’s tree amenities under instrumental variable and geographic regression discontinuity approaches with an application to Lisbon, Portugal. For completeness, we also explore how urban trees and in particular public street trees impact house prices across the city. Finally, we jointly analyze the planting and maintenance costs and benefits of urban street trees. The estimated value of all public trees in Lisbon is €8.84M. When considering specifically trees planted alongside roads and in public squares, the value is €6.06M or €126.64 per tree. This value is conditional on the distribution of trees in terms of their broader density, with higher effects coming from the overall greening of larger areas of the city compared to the greening of the direct neighborhood. Detrimental impacts are found when the number of trees is higher near street canyons, where they may exacerbate the stagnation of air pollution from traffic. Urban street trees also have important spillover benefits due to pollution mitigation around €6.21 million, or an additional €129.93 per tree. There are added benefits of €26.32 and €28.58 per tree in terms of flooding and heat mitigation, respectively. With significant resources and policies aimed at urban greening, the value obtained is shown to be important for discussions on the benefits of urban trees as compared to mitigation and abatement costs undertaken by a municipality.

Keywords: urban public goods, urban street trees, spatial boundary discontinuities, geospatial and remote sensing methods

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Authors: Jacob Lewis Watts, Adam F. A. Pellegrini

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Prairies, grasslands, and forests cover an expansive portion of the world’s surface and contribute significantly to Earth’s carbon cycle. The largest driver of carbon dynamics in some of these ecosystems is fire. As the global climate changes, most fire-dominated ecosystems will experience increased fire frequency and intensity, leading to increased carbon flux into the atmosphere and soil nutrient depletion. The plant communities associated with different fire regimes are important for reassimilation of carbon lost during fire and soil recovery. More frequent fires promote conservative plant functional traits aboveground; however, belowground fine root traits are poorly explored and arguably more important drivers of ecosystem function as the primary interface between the soil and plant. The root economic spectrum (RES) hypothesis describes single-dimensional covariation between important fine-root traits along a range of plant strategies from acquisitive to conservative – parallel to the well-established leaf economic spectrum (LES). However, because of the paucity of root trait data, the complex nature of the rhizosphere, and the phylogenetic conservatism of root traits, it is unknown whether the RES hypothesis accurately describes plant nutrient and water acquisition strategies. This project utilizesplants grown in common garden conditions in the Cambridge University Botanic Garden and a meta-analysis of long-term fire manipulation experiments to examine the belowground physiological traits of fire-adapted and non-fire-adapted herbaceous species to 1) test the RES hypothesis and 2) describe the effect of fire regimes on fine root functional traits – which in turn affect carbon and nutrient cycling. A suite of morphological, chemical, and biological root traits (e.g. root diameter, specific root length, percent N, percent mycorrhizal colonization, etc.) of 50 herbaceous species were measuredand tested for phylogenetic conservatism and RES dimensionality. Fire-adapted and non-fire-adapted plants traits were compared using phylogenetic PCA techniques. Preliminary evidence suggests that phylogenetic conservatism may weaken the single-dimensionality of the RES, suggesting that there may not be a single way that plants optimize nutrient and water acquisition and storage in the complex rhizosphere; additionally, fire-adapted species are expected to be more conservative than non-fire-adapted species, which may be indicative of slower carbon cycling with increasing fire frequency and intensity.

Keywords: climate change, fire regimes, root economic spectrum, fine roots

Procedia PDF Downloads 88

Authors: Kaomud Tyagi, Rajasree Chakraborty, Shantanu Kundu, Devkant Singha, Kailash Chandra, Vikas Kumar

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The melon thrips, Thrips palmi is a serious pest of a wide range of agriculture crops and also act as vectors for plant viruses (genus Tospovirus, family Bunyaviridae). More molecular data on this species is required to understand the cryptic speciation and evolutionary affiliations. Mitochondrial genomes have been widely used in phylogenetic and evolutionary studies in insect. So far, mitogenomes of five thrips species (Anaphothrips obscurus, Frankliniella intonsa, Frankliniella occidentalis, Scirtothrips dorsalis and Thrips imaginis) is available in the GenBank database. In this study, we sequenced the first complete mitogenome T. palmi and compared it with available thrips mitogenomes. We assembled the mitogenome from the whole genome sequencing data generated using Illumina Hiseq2500. Annotation was performed using MITOS web-server to estimate the location of protein coding genes (PCGs), transfer RNA (tRNAs), ribosomal RNAs (rRNAs) and their secondary structures. The boundaries of PCGs and rRNAs was confirmed manually in NCBI. Phylogenetic analyses were performed using the 13 PCGs data using maximum likelihood (ML) in PAUP, and Bayesian inference (BI) in MrBayes 3.2. The complete mitogenome of T. palmi was 15,333 base pairs (bp), which was greater than the genomes of A. obscurus (14,890bp), F. intonsa (15,215 bp), F. occidentalis (14,889 bp) and S. dorsalis South Asia strain (SA1) (14,283 bp), but smaller than the genomes of T. imaginis (15,407 bp) and S. dorsalis East Asia strain (EA1) (15,343bp). Like in other thrips species, the mitochondrial genome of T. palmi was represented by 37 genes, including 13 PCGs, large and small ribosomal RNA (rrnL and rrnS) genes, 22 transfer RNA (tRNAs) genes (with one extra gene for trn-Serine) and two A+T-rich control regions (CR1 and CR2). Thirty one genes were observed on heavy (H) strand and six genes on the light (L) strand. The six tRNA genes (trnG,trnK, trnY, trnW, trnF, and trnH) were found to be conserved in all thrips species mitogenomes in their locations relative to a protein-coding or rRNA gene upstream or downstream. The gene arrangements of T. palmi is very close to T. imaginis except the rearrangements in tRNAs genes: trnR (arginine), and trnE (glutamic acid) were found to be located between cox3 and CR2 in T. imaginis which were translocated between atp6 and CR1 in T. palmi; trnL1 (Leucine) and trnS1(Serine) were located between atp6 and CR1 in T. imaginis which were translocated between cox3 and CR2 in T. palmi. The location of CR1 upstream of nad5 gene was suggested to be ancestral condition of the thrips species in subfamily Thripinae, was also observed in T. palmi. Both the Maximum likelihood (ML) and Bayesian Inference (BI) phylogenetic trees generated resulted in similar topologies. The T. palmi was clustered with T. imaginis. We concluded that more molecular data on the diverse thrips species from different hierarchical level is needed, to understand the phylogenetic and evolutionary relationships among them.

Keywords: thrips, comparative mitogenomics, gene rearrangements, phylogenetic analysis

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Authors: Kang Woobang

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The base of the column is not only a support but also the embodiment of profound symbolism full of cosmic energy. Finding the full jars from which various energy emanate at the Notre Dame of Paris and Saint-Germain-des-Pres in France, the author was so shocked. As the column is cosmic tree, from the Full Jar full with cosmic energy emerges the cosmic tree composed of shaft and capital.

Keywords: full picher or jar, transcendental or supernatural birth from yonggi, yonggimun, yonggissak

Procedia PDF Downloads 387

Authors: Yassine Messaoud, Gordon Nigh, Faouzi Messaoud, Han Chen

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The effect of climate change on tree growth in boreal and temperate forests has received increased interest in the context of global warming. However, most studies were conducted in small areas and with a limited number of tree species. Here, we examined the height growth responses of seventeen tree species to climate change in Western North America. 37009 stands from forest inventory databases in Canada and USA with varying establishment date were selected. Dominant and co-dominant trees from each stand were sampled to determine top tree height at 50 years breast height age. Height was related to historical mean annual and summer temperatures, annual and summer Palmer Drought Severity Index, tree establishment date, slope, aspect, soil fertility as determined by the rate of carbon organic matter decomposition (carbon/nitrogen), geographic locations (latitude, longitude, and elevation), species range (coastal, interior, and both ranges), shade tolerance and leaf form (needle leaves, deciduous needle leaves, and broadleaves). Climate change had mostly a positive effect on tree height growth. The results explained 62.4% of the height growth variance. Since 1880, height growth increase was greater for coastal, high shade tolerant, and broadleaf species. Height growth increased more on steep slopes and high soil fertility soils. Greater height growth was mostly observed at the leading range and upward. Conversely, some species showed the opposite pattern probably due to the increase of drought (coastal Mediterranean area), precipitation and cloudiness (Alaska and British Columbia) and peculiarity (higher latitudes-lower elevations and vice versa) of western North America topography. This study highlights the role of the species ecological amplitude and traits, and geographic locations as the main factors determining the growth response and its magnitude to the recent global climate change.

Keywords: Height growth, global climate change, species range, species characteristics, species ecological amplitude, geographic locations, western North America

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Authors: Siwapech Silapaprayoon, Januluk Khanobdee, Sompid Samipak

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Chili peppers are the fruits of Capsicum pepper plants well known for their fiery burning sensation on the tongue after consumption. They are members of the Solanaceae or common nightshade family along with potato, tomato and eggplant. Thai cuisine has gained popularity for its distinct flavors due to usages of various spices and its heat from the addition of chili pepper. Though being used in little quantity for each dish, chili pepper holds a special place in Thai cuisine. There are many varieties of chili peppers in Thailand, and thirty accessions were collected at Rajamangala University of Technology Lanna, Lampang, Thailand. To effectively manage any germplasm it is essential to know the diversity and relationships among members. Thirty-six Inter Simple Sequence Repeat (ISSRs) DNA markers were used to analyze the germplasm. Total of 335 polymorphic bands was obtained giving the average of 9.3 alleles per marker. Unweighted pair-group mean arithmetic method (UPGMA) clustering of data using NTSYS-pc software indicated that the accessions showed varied levels of genetic similarity ranging from 0.57-1.00 similarity coefficient index indicating significant levels of variation. At SM coefficient of 0.81, the germplasm was separated into four groups. Phenotypic variation was discussed in context of phylogenetic tree clustering.

Keywords: diversity, germplasm, Chili pepper, ISSR

Procedia PDF Downloads 127

Authors: Muna A. Eissawi, Safaa Abed Elfataah, Haytham Hago, Fatima E Abukunna, Ibtisam Amin Goreish, Nahid Gornas

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The study examined and analyzed the genetic diversity of DRB1locus of exon 2 of major histocompatibility complex of Sudanese desert sheep using PCR-RFLP and DNA sequencing. Five hundred samples belonging to five ecotypes of Desert Sudanese sheep (Abrag (Ab), Ashgar (Ash), Hamari (H), Kabashi (K) and Watish (W) were included. Amplification of exon 2 of the DRB1 gene yielded (300bp) amplified product in different ecotypes. Nine different digestion patterns corresponding to Five distinct alleles were observed with Rsa1 digestion. Genotype (ag) was the most common among all ecotypes, with a percentage comprised (40.4 %). The Hardy-Weinberg equilibrium (HWE) test showed that the studied ecotypes have significantly deviated from the theoretical proportions of Rsa1 patterns; probability values of the Chi-square test for HWE for MHC-DRB1 gene in SDS were 0.00 in all ecotypes. The constructed phylogenetic tree revealed the relation of 22 Sudanese isolates with each other and showed the shared sequences with 47 published foreign sequences randomly selected from different geographic regions. The results of this study highlight the effect of heterozygosity of MHC genes of the Desert sheep of Sudan which may clarify some of genetic back ground of their disease resistance and adaptation to environment.

Keywords: desert sheep, MHC, Ovar-DRB1, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP)

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Authors: Elham Serkani, Hossein Gharaee Garakani, Naser Mohammadzadeh, Elaheh Vaezpour

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Intrusion detection systems (IDS) are the main components of network security. These systems analyze the network events for intrusion detection. The design of an IDS is through the training of normal traffic data or attack. The methods of machine learning are the best ways to design IDSs. In the method presented in this article, the pruning algorithm of C5.0 decision tree is being used to reduce the features of traffic data used and training IDS by the least square vector algorithm (LS-SVM). Then, the remaining features are arranged according to the predictor importance criterion. The least important features are eliminated in the order. The remaining features of this stage, which have created the highest level of accuracy in LS-SVM, are selected as the final features. The features obtained, compared to other similar articles which have examined the selected features in the least squared support vector machine model, are better in the accuracy, true positive rate, and false positive. The results are tested by the UNSW-NB15 dataset.

Keywords: decision tree, feature selection, intrusion detection system, support vector machine

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Authors: Ghazanfar Ali, Fahad N Almajhdi

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This study provides data on the viral diagnosis and molecular epidemiology of influenza A(H3N2) virus isolated in Riyadh, Saudi Arabia. Nasopharyngeal aspirates from 80 clinically infected patients in the peak of the 2010-2011 winter seasons were processed for viral diagnosis by RT-PCR. Sequencing of entire HA and NA genes of representative isolates and molecular epidemiological analysis were performed. A total of 06 patients were positive for influenza A, B and respiratory syncytial viruses by RT-PCR assays; out of these only one sample was positive for influenza A(H3N2) by RT-PCR. Phylogenetic analysis of the HA and NA gene sequences showed identities higher than 99-98.8 % in both genes. They were also similar to reference isolates in HA sequences (99 % identity) and in NA sequences (99 % identity). Amino acid sequences predicted for the HA gene were highly identical to reference strains. The NA amino acid substitutions identified did not include the oseltamivir-resistant H275Y substitution. Conclusion: Viral isolation and RT-PCR together were useful for diagnosis of the influenza A (H3N2) virus. Variations in HA and NA sequences are similar to those identified in worldwide reference isolates and no drug resistance was found.

Keywords: influenza A (H3N2), genetic characterization, viral isolation, RT-PCR, Saudi Arabia

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Authors: Haifa Ben Saber, Mourad Elloumi

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In a number of domains, like in DNA microarray data analysis, we need to cluster simultaneously rows (genes) and columns (conditions) of a data matrix to identify groups of constant rows with a group of columns. This kind of clustering is called biclustering. Biclustering algorithms are extensively used in DNA microarray data analysis. More effective biclustering algorithms are highly desirable and needed. We introduce a new algorithm called, Enumerative tree (EnumTree) for biclustering of binary microarray data. is an algorithm adopting the approach of enumerating biclusters. This algorithm extracts all biclusters consistent good quality. The main idea of ​​EnumLat is the construction of a new tree structure to represent adequately different biclusters discovered during the process of enumeration. This algorithm adopts the strategy of all biclusters at a time. The performance of the proposed algorithm is assessed using both synthetic and real DNA micryarray data, our algorithm outperforms other biclustering algorithms for binary microarray data. Biclusters with different numbers of rows. Moreover, we test the biological significance using a gene annotation web tool to show that our proposed method is able to produce biologically relevent biclusters.

Keywords: DNA microarray, biclustering, gene expression data, tree, datamining.

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Authors: Masoud Sheidaei, Melica Tabasi, Fahimeh Koohdar, Mona Sheidaei

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Juglans regia L. is an economically important species of edible nuts. Iran is known as a center of origin of genetically rich walnut germplasm and expected to be found a large diversity within Iranian walnut populations. A detailed population genetic of local populations is useful for developing an optimal strategy for in situ conservation and can assist the breeders in crop improvement programs. Different phylogenetic studies have been carried out in this genus, but none has been concerned with genetic changes associated with geographical divergence and the identification of adaptive SNPs. Therefore, we carried out the present study to identify discriminating ITS nucleotides among Juglans species and also reveal association between ITS SNPs and geographical variables. We used different computations approaches like DAPC, CCA, and RDA analyses for the above-mentioned tasks. We also performed population genetics analyses for population effective size changes associated with the species expansion. The results obtained suggest that latitudinal distribution has a more profound effect on the species genetic changes. Similarly, multiple analytical approaches utilized for the identification of both discriminating DNA nucleotides/ SNPs almost produced congruent results. The SNPs with different phylogenetic importance were also identified by using a parsimony approach.

Keywords: Persian walnut, adaptive SNPs, data analyses, genetic diversity

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Authors: Mark Joseph Quinto, Roan Beronilla, Guiller Damian, Eliza Camaso, Ronaldo Alberto

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Forest inventories are essential to assess the composition, structure and distribution of forest vegetation that can be used as baseline information for management decisions. Classical forest inventory is labor intensive and time-consuming and sometimes even dangerous. The use of Light Detection and Ranging (LiDAR) in forest inventory would improve and overcome these restrictions. This study was conducted to determine the possibility of using LiDAR derived data in extracting high accuracy forest biophysical parameters and as a non-destructive method for forest status analysis of San Manual, Pangasinan. Forest resources extraction was carried out using LAS tools, GIS, Envi and .bat scripts with the available LiDAR data. The process includes the generation of derivatives such as Digital Terrain Model (DTM), Canopy Height Model (CHM) and Canopy Cover Model (CCM) in .bat scripts followed by the generation of 17 composite bands to be used in the extraction of forest classification covers using ENVI 4.8 and GIS software. The Diameter in Breast Height (DBH), Above Ground Biomass (AGB) and Carbon Stock (CS) were estimated for each classified forest cover and Tree Count Extraction was carried out using GIS. Subsequently, field validation was conducted for accuracy assessment. Results showed that the forest of San Manuel has 73% Forest Cover, which is relatively much higher as compared to the 10% canopy cover requirement. On the extracted canopy height, 80% of the tree’s height ranges from 12 m to 17 m. CS of the three forest covers based on the AGB were: 20819.59 kg/20x20 m for closed broadleaf, 8609.82 kg/20x20 m for broadleaf plantation and 15545.57 kg/20x20m for open broadleaf. Average tree counts for the tree forest plantation was 413 trees/ha. As such, the forest of San Manuel has high percent forest cover and high CS.

Keywords: carbon stock, forest inventory, LiDAR, tree count

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Authors: Mina Jafari, Kobra Hamraee, Saied Hossein Hosseini

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The prediction of breast cancer disease is one of the challenges in medicine. In this paper we collected 528 records of women’s information who live in Kabul including demographic, life style, diet and pregnancy data. There are many classification algorithm in breast cancer prediction and tried to find the best model with most accurate result and lowest error rate. We evaluated some other common supervised algorithms in data mining to find the best model in prediction of breast cancer disease among afghan women living in Kabul regarding to momography result as target variable. For evaluating these algorithms we used Cross Validation which is an assured method for measuring the performance of models. After comparing error rate and accuracy of three models: Decision Tree, Naive Bays and Rule Induction, Decision Tree with accuracy of 94.06% and error rate of %15 is found the best model to predicting breast cancer disease based on the health care records.

Keywords: decision tree, breast cancer, probability, data mining

Procedia PDF Downloads 108

Authors: Meixia Zhang, Chengjun Ji, Wenxuan Han

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Many wood traits are important functional attributes for tree species, connected with resource competition among species, community dynamics, and ecosystem functions. Large variations in these traits exist among taxonomic categories, but variation in these traits between gymnosperms and angiosperms is still poorly documented. This paper explores the systematic differences in 12 traits between the two tree categories and the potential effects of environmental factors and life form. Based on a database of wood traits for major gymnosperm and angiosperm tree species across China, the values of 12 wood traits and their driving factors in gymnosperms vs. angiosperms were compared. The results are summarized below: i) Means of wood traits were all significantly lower in gymnosperms than in angiosperms. ii) Air-dried density (ADD) and tangential shrinkage coefficient (TSC) reflect the basic information of wood traits for gymnosperms, while ADD and radial shrinkage coefficient (RSC) represent those for angiosperms, providing higher explanation power when used as the evaluation index of wood traits. iii) For both gymnosperm and angiosperm species, life form exhibits the largest explanation rate for large-scale spatial patterns of ADD, TSC (RSC), climatic factors the next, and edaphic factors have the least effect, suggesting that life form is the dominant factor controlling spatial patterns of wood traits. Variations in the magnitude and key traits between gymnosperms and angiosperms and the same dominant factors might indicate the evolutionary divergence and convergence in key functional traits among woody plants.

Keywords: allometry, functional traits, phylogeny, shrinkage coefficient, wood density

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Authors: Hilal Naimi, Amelbahahouda Adamou-Mitiche, Lahcene Mitiche

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The main problem in the area of medical imaging has been image denoising. The most defying for image denoising is to secure data carrying structures like surfaces and edges in order to achieve good visual quality. Different algorithms with different denoising performances have been proposed in previous decades. More recently, models focused on deep learning have shown a great promise to outperform all traditional approaches. However, these techniques are limited to the necessity of large sample size training and high computational costs. This research proposes a denoising approach basing on LDTCWT (Lifting Dual Tree Complex Wavelet Transform) using Hybrid Thresholding with Wiener filter to enhance the quality image. This research describes the LDTCWT as a type of lifting wavelets remodeling that produce complex coefficients by employing a dual tree of lifting wavelets filters to get its real part and imaginary part. Permits the remodel to produce approximate shift invariance, directionally selective filters and reduces the computation time (properties lacking within the classical wavelets transform). To develop this approach, a hybrid thresholding function is modeled by integrating the Wiener filter into the thresholding function.

Keywords: lifting wavelet transform, image denoising, dual tree complex wavelet transform, wavelet shrinkage, wiener filter

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Authors: Muhammad Awais

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Study on the nesting biology of the House Crow Corvus splendens was conducted at Hazara University, Garden Campus (125 acres), Mansehra during the 2013 breeding season (June to September). Details about nest locations, tree characteristics, nest and egg characteristics were recorded. Mean nest density of House Crow was 2.4 nests/ acre. Mean tree and nest height were 14.8±6.30 and 11.8±5.42m. Mean tree canopy spread 9.5±2.48m. Mean maximum and minimum nest diameters were 42.3±2.08 and 39.0±1.73cm respectively while maximum and minimum diameters of nest cup were 15.6±1.52 and 13.3±1.15cm respectively. Nest depth and nest cup depth were measured 19.3±2.08 and 8.3±1.15cm respectively. Mean nest weight was 1.4±0.24 kg. Mean clutch size was 4.0 (ranged 1–6). Mean egg length was 38.6±0.69mm, breadth 26.0±0.69mm, egg volume 13.3±0.83cm3 and egg shape index 1.42±0.83. Mean egg weight was 12.3±0.70g. Egg and nest success was calculated 55.1% and 69.0%. Hatchlings and fledglings produced per nest were 2.20 and 1.44 respectively. Main reasons for reproductive failures were unhatched eggs, poor nest construction, bad weather conditions and observer’s disturbance.

Keywords: breeding, Corvus splendens, fledglings, Hazara university, house crow, Mansehra, populus orientalis

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Authors: Yi Xiong, Tao Kong

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Traditional safety, risk and reliability analysis approaches are problem-oriented, which make it great workload when analyzing complicated and huge system, besides, too much repetitive work would to do if the analyzed system composed by many similar components. It is pressing need an object and function oriented approach to maintain high consistency with problem domain. A new approach is proposed to overcome these shortcomings of traditional approaches, the concepts: class, abstract, inheritance, polymorphism and encapsulation are introduced into FTA and establish the professional class library that the abstractions of physical objects in real word, four areas relevant information also be proposed as the establish help guide. The interaction between classes is completed by the inside or external methods that mapping the attributes to base events through fully search the knowledge base, which forms good encapsulation. The object oriented fault tree analysis system that analyze and evaluate the system safety and reliability according to the original appearance of the problem is set up, where could mapped directly from the class and object to the problem domain of the fault tree analysis. All the system failure situations can be analyzed through this bottom-up fault tree construction approach. Under this approach architecture, FTA approach is developed, which avoids the human influence of the analyst on analysis results. It reveals the inherent safety problems of analyzed system itself and provides a new way of thinking and development for safety analysis. So that object oriented technology in the field of safety applications and development, safety theory is conducive to innovation.

Keywords: FTA, knowledge base, object-oriented technology, reliability analysis

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Authors: Arturo J. Anci Alméstar, Jose D. Fernandez Huapaya, David Mauricio

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Companies make erroneous decisions by not evaluating the inherent difficulties of entering electronic commerce without a prior review of current digital and alternate means of payment. For this reason, it is very important for businesses to have reliable, complete and integrated information on the means of current digital and alternate payments that allow decisions to be made about which of these to use. However, there is no such consolidated information or criteria that companies use to make decisions about the means of payment according to their needs. In this paper, we propose a decision tree model based on a taxonomy that presents us with a categorization of digital and alternative means of payment, as well as the visualization of the flow of information at a high level from the company to obtain a recommendation. This will allow the company to make the most appropriate decision about the implementation of the digital means of payment or alternative ideal for their needs, which allows a reduction in costs and complexity of the payment process. Likewise, the efficiency of the proposed model was evaluated through a satisfaction survey presented to company personnel, confirming the satisfactory quality level of the recommendations obtained by the model.

Keywords: digital payment medium, decision tree, decision making, digital payments taxonomy

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Authors: S.K. Bhandari, E. Veneklaas, L. McCaw, R. Mazanec, K. Whitford, M. Renton

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Eucalyptus marginata, E. diversicolor and Corymbia calophylla form widespread forests in south-west Western Australia (SWWA). These forests have economic and ecological importance, and therefore, tree growth and sustainable management are of high priority. This paper aimed to analyse and model the growth of these species at both stand and individual levels, but this presentation will focus on predicting the growth of E. Marginata at the individual tree level. More specifically, the study wanted to investigate how well individual E. marginata tree growth could be predicted by considering the diameter and height of the tree at the start of the growth period, and whether this prediction could be improved by also accounting for the competition from neighbouring trees in different ways. The study also wanted to investigate how many neighbouring trees or what neighbourhood distance needed to be considered when accounting for competition. To achieve this aim, the Pearson correlation coefficient was examined among competition indices (CIs), between CIs and dbh growth, and selected the competition index that can best predict the diameter growth of individual trees of E. marginata forest managed under different thinning regimes at Inglehope in SWWA. Furthermore, individual tree growth models were developed using simple linear regression, multiple linear regression, and linear mixed effect modelling approaches. Individual tree growth models were developed for thinned and unthinned stand separately. The developed models were validated using two approaches. In the first approach, models were validated using a subset of data that was not used in model fitting. In the second approach, the model of the one growth period was validated with the data of another growth period. Tree size (diameter and height) was a significant predictor of growth. This prediction was improved when the competition was included in the model. The fit statistic (coefficient of determination) of the model ranged from 0.31 to 0.68. The model with spatial competition indices validated as being more accurate than with non-spatial indices. The model prediction can be optimized if 10 to 15 competitors (by number) or competitors within ~10 m (by distance) from the base of the subject tree are included in the model, which can reduce the time and cost of collecting the information about the competitors. As competition from neighbours was a significant predictor with a negative effect on growth, it is recommended including neighbourhood competition when predicting growth and considering thinning treatments to minimize the effect of competition on growth. These model approaches are likely to be useful tools for the conservations and sustainable management of forests of E. marginata in SWWA. As a next step in optimizing the number and distance of competitors, further studies in larger size plots and with a larger number of plots than those used in the present study are recommended.

Keywords: competition, growth, model, thinning

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Authors: Roza Dzierzak, Waldemar Wojcik, Piotr Kacejko

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Analysis of the texture of medical images consists of determining the parameters and characteristics of the examined tissue. The main goal is to assign the analyzed area to one of two basic groups: as a healthy tissue or a tissue with pathological changes. The CT images of the thoracic lumbar spine from 15 healthy patients and 15 with confirmed osteoporosis were used for the analysis. As a result, 120 samples with dimensions of 50x50 pixels were obtained. The set of features has been obtained based on the histogram, gradient, run-length matrix, co-occurrence matrix, autoregressive model, and Haar wavelet. As a result of the image analysis, 290 descriptors of textural features were obtained. The dimension of the space of features was reduced by the use of three selection methods: Fisher coefficient (FC), mutual information (MI), minimization of the classification error probability and average correlation coefficients between the chosen features minimization of classification error probability (POE) and average correlation coefficients (ACC). Each of them returned ten features occupying the initial place in the ranking devised according to its own coefficient. As a result of the Fisher coefficient and mutual information selections, the same features arranged in a different order were obtained. In both rankings, the 50% percentile (Perc.50%) was found in the first place. The next selected features come from the co-occurrence matrix. The sets of features selected in the selection process were evaluated using six classification tree methods. These were: decision stump (DS), Hoeffding tree (HT), logistic model trees (LMT), random forest (RF), random tree (RT) and reduced error pruning tree (REPT). In order to assess the accuracy of classifiers, the following parameters were used: overall classification accuracy (ACC), true positive rate (TPR, classification sensitivity), true negative rate (TNR, classification specificity), positive predictive value (PPV) and negative predictive value (NPV). Taking into account the classification results, it should be stated that the best results were obtained for the Hoeffding tree and logistic model trees classifiers, using the set of features selected by the POE + ACC method. In the case of the Hoeffding tree classifier, the highest values of three parameters were obtained: ACC = 90%, TPR = 93.3% and PPV = 93.3%. Additionally, the values of the other two parameters, i.e., TNR = 86.7% and NPV = 86.6% were close to the maximum values obtained for the LMT classifier. In the case of logistic model trees classifier, the same ACC value was obtained ACC=90% and the highest values for TNR=88.3% and NPV= 88.3%. The values of the other two parameters remained at a level close to the highest TPR = 91.7% and PPV = 91.6%. The results obtained in the experiment show that the use of classification trees is an effective method of classification of texture features. This allows identifying the conditions of the spongy tissue for healthy cases and those with the porosis.

Keywords: classification, feature selection, texture analysis, tree algorithms

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Authors: Boyun Lee

Abstract:

This study aims to discuss whether anthropomorphism some scientists tend to use in cross-species comparison can be justified epistemologically, especially in the primate mind-reading debate. Concretely, this study critically analyzes Elliott Sober’s argument about mind-reading hypothesis (MRH), an anthropomorphic hypothesis which states that nonhuman primates (e.g., chimpanzee) are mind-readers like humans. Although many scientists consider anthropomorphism as an error and choosing anthropomorphic hypothesis like MRH without any definite evidence invalid, Sober advocates that anthropomorphism is supported by cladistic parsimony that suggests choosing the simplest hypothesis postulating the minimum number of evolutionary changes, which can be justified epistemologically in the mind-reading debate. However, his argument has several problems. First, Reichenbach’s theorem which Sober uses in process of showing that MRH has the higher likelihood than its competing hypothesis, behavior-reading hypothesis (BRH), does not fit in the context of inferring the evolutionary relationship. Second, the phylogenetic tree Sober supports is one of the possible scenarios of MRH, and even without this problem, it is difficult to prove that the possibility nonhuman primate species and human share mind-reading ability is higher than the possibility of the other case, considering how evolution occurs. Consequently, it seems hard to justify anthropomorphism of MRH under Sober’s argument. Some scientists and philosophers say that anthropomorphism sometimes helps observe interesting phenomena or make hypotheses in comparative biology. Nonetheless, we cannot determine that it provides answers about why and how the interesting phenomena appear or which of the hypotheses is better, at least the mind-reading debate, under the current state.

Keywords: anthropomorphism, cladistic parsimony, comparative biology, mind-reading debate

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Authors: Irene Capecchi, Tommaso Borghini, Iacopo Bernetti

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One of the most common pieces of equipment still used today for pruning, felling, and processing trees is the chainsaw in forestry. However, chainsaw use highlights dangers and one of the highest rates of accidents in both professional and non-professional work. Felling is proportionally the most dangerous phase, both in severity and frequency, because of the risk of being hit by the plant the operator wants to cut down. To avoid this, a correct sequence of chainsaw cuts must be taught concerning the different conditions of the tree. Virtual reality (VR) makes it possible to virtually simulate chainsaw use without danger of injury. The limitations of the existing applications are as follow. The existing platforms are not symmetrical collaborative because the trainee is only in virtual reality, and the trainer can only see the virtual environment on a laptop or PC, and this results in an inefficient teacher-learner relationship. Therefore, most applications only involve the use of a virtual chainsaw, and the trainee thus cannot feel the real weight and inertia of a real chainsaw. Finally, existing applications simulate only a few cases of tree felling. The objectives of this research were to implement and test a symmetrical collaborative training application based on VR and mixed reality (MR) with the overlap between real and virtual chainsaws in MR. The research and training platform was developed for the Meta quest 2 head-mounted display. The research and training platform application is based on the Unity 3D engine, and Present Platform Interaction SDK (PPI-SDK) developed by Meta. PPI-SDK avoids the use of controllers and enables hand tracking and MR. With the combination of these two technologies, it was possible to overlay a virtual chainsaw with a real chainsaw in MR and synchronize their movements in VR. This ensures that the user feels the weight of the actual chainsaw, tightens the muscles, and performs the appropriate movements during the test allowing the user to learn the correct body posture. The chainsaw works only if the right sequence of cuts is made to felling the tree. Contact detection is done by Unity's physics system, which allows the interaction of objects that simulate real-world behavior. Each cut of the chainsaw is defined by a so-called collider, and the felling of the tree can only occur if the colliders are activated in the right order simulating a safe technique felling. In this way, the user can learn how to use the chainsaw safely. The system is also multiplayer, so the student and the instructor can experience VR together in a symmetrical and collaborative way. The platform simulates the following tree-felling situations with safe techniques: cutting the tree tilted forward, cutting the medium-sized tree tilted backward, cutting the large tree tilted backward, sectioning the trunk on the ground, and cutting branches. The application is being evaluated on a sample of university students through a special questionnaire. The results are expected to test both the increase in learning compared to a theoretical lecture and the immersive and telepresence of the platform.

Keywords: chainsaw, collaborative symmetric virtual reality, mixed reality, operator training

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Authors: Endrick Barnacin, Jean-Luc Henry, Jack Molinié, Jimmy Nagau, Hélène Delatte, Gérard Lebreton

Abstract:

Palynology is a field of interest for many disciplines. It has multiple applications such as chronological dating, climatology, allergy treatment, and even honey characterization. Unfortunately, the analysis of a pollen slide is a complicated and time-consuming task that requires the intervention of experts in the field, which is becoming increasingly rare due to economic and social conditions. So, the automation of this task is a necessity. Pollen slides analysis is mainly a visual process as it is carried out with the naked eye. That is the reason why a primary method to automate palynology is the use of digital image processing. This method presents the lowest cost and has relatively good accuracy in pollen retrieval. In this work, we propose a system combining recognition and grouping of pollen. It consists of using a Logistic Model Tree to classify pollen already known by the proposed system while detecting any unknown species. Then, the unknown pollen species are divided using a cluster-based approach. Success rates for the recognition of known species have been achieved, and automated clustering seems to be a promising approach.

Keywords: pollen recognition, logistic model tree, expectation-maximization, local binary pattern

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Authors: Othman E. Othman, Agnés Germot, Daniel Petit, Abderrahman Maftah

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Threats to the biodiversity are increasing due to the loss of genetic diversity within the species utilized in agriculture. Due to the progressive substitution of the less productive, locally adapted and native breeds by highly productive breeds, the number of threatened breeds is increased. In these conditions, it is more strategically important than ever to preserve as much the farm animal diversity as possible, to ensure a prompt and proper response to the needs of future generations. Mitochondrial (mtDNA) sequencing has been used to explain the origins of many modern domestic livestock species. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. Because of the eastern location of Egypt in the Mediterranean basin and the presence of fat-tailed sheep breeds- character quite common in Turkey and Syria- where genotypes that seem quite primitive, the phylogenetic studies of Egyptian sheep breeds become particularly attractive. We aimed in this work to clarify the genetic affinities, biodiversity and phylogeny of five Egyptian sheep breeds using cytochrome B sequencing. Blood samples were collected from 63 animals belonging to the five tested breeds; Barki, Rahmani, Ossimi, Saidi and Sohagi. The total DNA was extracted and the specific primer allowed the conventional PCR amplification of the cytochrome B region of mtDNA (approximately 1272 bp). PCR amplified products were purified and sequenced. The alignment of Sixty-three samples was done using BioEdit software. DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 34 polymorphic sites leading to the formation of 18 haplotypes. The haplotype diversity in five tested breeds ranged from 0.676 in Rahmani breed to 0.894 in Sohagi breed. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Rahmani and Saidi (D: 1.674 and Dxy: 0.00150) while the highest distance was observed between Ossimi and Sohagi (D: 5.233 and Dxy: 0.00475). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of the 63 analyzed samples were aligned with references sequences of different haplogroups. The phylogeny result showed the presence of three haplogroups (HapA, HapB and HapC) in the 63 examined samples. The other two haplogroups described in literature (HapD and HapE) were not found. The result showed that 50 out of 63 tested animals cluster with haplogroup B (79.37%) whereas 7 tested animals cluster with haplogroup A (11.11%) and 6 animals cluster with haplogroup C (9.52%). In conclusion, the phylogenetic reconstructions showed that the majority of Egyptian sheep breeds belonging to haplogroup B which is the dominant haplogroup in Eastern Mediterranean countries like Syria and Turkey. Some individuals are belonging to haplogroups A and C, suggesting that the crosses were done with other breeds for characteristic selection for growth and wool quality.

Keywords: cytochrome B, diversity, phylogheny, Egyptian sheep breeds

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Authors: M. Nakkuntod, S. Srinarang, K.W. Hilu

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Water lily (Nymphaea L.) is the largest genus of Nymphaeaceae. This family is composed of six genera (Nuphar, Ondinea, Euryale, Victoria, Barclaya, Nymphaea). Its members are nearly worldwide in tropical and temperate regions. The classification of some species in Nymphaea is ambiguous due to high variation in leaf and flower parts such as leaf margin, stamen appendage. Therefore, the phylogenetic relationships based on 18S rDNA were constructed to delimit this genus. DNAs of 52 specimens belonging to water lily family were extracted using modified conventional method containing cetyltrimethyl ammonium bromide (CTAB). The results showed that the amplified fragment is about 1600 base pairs in size. After analysis, the aligned sequences presented 9.36% for variable characters comprising 2.66% of parsimonious informative sites and 6.70% of singleton sites. Moreover, there are 6 regions of 1-2 base(s) for insertion/deletion. The phylogenetic trees based on maximum parsimony and maximum likelihood with high bootstrap support indicated that genus Nymphaea was a paraphyletic group because of Ondinea, Victoria and Euryale disruption. Within genus Nymphaea, subgenus Nymphaea is a basal lineage group which cooperated with Euryale and Victoria. The other four subgenera, namely Lotos, Hydrocallis, Brachyceras and Anecphya were included the same large clade which Ondinea was placed within Anecphya clade due to geographical sharing.

Keywords: nrDNA, phylogeny, taxonomy, waterlily

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Authors: Funmilayo Sarah Eguakun, Peter Oluremi Adesoye

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One of the major problems being faced by human society is that the global temperature is believed to be rising due to human activity that releases carbon IV oxide (CO2) to the atmosphere. Carbon IV oxide is the most important greenhouse gas influencing global warming and possible climate change. With climate change becoming alarming, reducing CO2 in our atmosphere has become a primary goal of international efforts. Forest landsare major sink and could absorb large quantities of carbon if the trees are judiciously managed. The study aims at estimating the carbon sequestration capacity of Pinus caribaea (pine)and Tectona grandis (Teak) under the prevailing environmental conditions and exploring tree growth variables that influencesthe carbon sequestration capacity in Omo Forest Reserve, Ogun State, Nigeria. Improving forest management by manipulating growth characteristics that influences carbon sequestration could be an adaptive strategy of forestry to climate change. Random sampling was used to select Temporary Sample Plots (TSPs) in the study area from where complete enumeration of growth variables was carried out within the plots. The data collected were subjected to descriptive and correlational analyses. The results showed that average carbon stored by Pine and Teak are 994.4±188.3 Kg and 1350.7±180.6 Kg respectively. The difference in carbon stored in the species is significant enough to consider choice of species relevant in climate change adaptation strategy. Tree growth variables influence the capacity of the tree to sequester carbon. Height, diameter, volume, wood density and age are positively correlated to carbon sequestration. These tree growth variables could be manipulated by the forest manager as an adaptive strategy for climate change while plantations of high wood density speciescould be relevant for management strategy to increase carbon storage.

Keywords: adaptation, carbon sequestration, climate change, growth variables, wood density

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Authors: Lien Gysens, Bert Vanmechelen, Maarten Haspeslagh, Piet Maes, Ann Martens

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Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in a clinical presentation on the one hand and the host-dependent clinical outcome of BPV-1 infection, on the other hand, indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of the cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. By generating a significant amount of complete-length BPV genomes, we succeeded in introducing next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

Keywords: Bovine papillomavirus, equine sarcoid, horse, nanopore sequencing, phylogenetic analysis

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Authors: Mohammad Ali Al-Deeb, Hamda Ateeq Al Dhaheri

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Insects cause major damage to crops and fruit trees worldwide. In the United Arab Emirates, the date palm tree is the most economically important tree which is used for date production as well as an ornamental tree. In 2002, the number of date palm trees in UAE was 40,700,000 and it is increasing over time. The longhorn stem borer (Jebusaea hammerschmidtii) and the lesser date month (Batrachedra amydraula) are important insect pests causing damage to date palm trees in UAE. Population dynamics of the Jebusaea hammerschmidtii and Batrachedra amydraula were studied by using light and pheromons traps, respectively in Al-Ain, UAE. The first trap catch of B. amydraula adults occurred on 19 April and the insect population peaked up on 26 April 2014. The first trap catch of J. hammerschmidtii occurred in April 2014. The numbers increased over time and the population peak occurred in June. The trapping was also done in 2015. The changes in insect numbers in relation to weather parameters are discussed. Also, the importance of the results on the management of these two pests is highlighted.

Keywords: date palm, integrated pest management, UAE, light trap, pheromone trap

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Authors: Niloofar Fariborzi, Hamzeh Alipour, Kourosh Azizi, Neda Eskandarzade, Abozar Ghorbani

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The family Parvoviridae consists of a large diversity of single-stranded DNA viruses, which cause mild to severe diseases in both vertebrates and invertebrates. The Parvoviridae are classified into three subfamilies: Parvovirinae infect vertebrates, Densovirinae infects invertebrates, while Hamaparovirinae infects both vertebrates and invertebrates. Except for the NS1 region, which is the prime criterion for phylogeny analysis, other parts of the parvoviruses genome, such as UTRs, are diverse even among closely related viruses or within the same genus. It is believed that host switching in parvoviruses may be related to genetic changes in regions other than NS1; therefore, whole-genome screening is valuable for studying parvoviruses' host-virus interactions. The aim of this study was to analyze genome organization and phylogeny of the complete genome sequence of the 132 Paroviridae family members, focusing on viruses that infect invertebrates. The maximum and minimum divergence within each subfamily belonged to Densovirinae and Parvovirinae, respectively. The greatest evolutionary divergence was between Hamaparovirinae and Parvovirinae. Unclassified viruses were mostly from Parovirinae and had the highest divergence to densoviruses and the lowest divergence to Parovirinae viruses. In a phylogenetic tree, all hamparoviruses were found in the center of densoviruses, with the exception of Syngnathid Ichthamaparvovirus 1 (NC_055527), which was positioned between two Parvovirinae members (NC _022089 and NC_038544). The proximity of hamparoviruses members to some densoviruses strengthens the possibility that densoviruses may be the ancestors of hamaparoviruses or vice versa. Therefore, examination and phylogeny analysis of the whole genome is necessary to understand Parvoviridae family host selection.

Keywords: densoviruses, parvoviridae, bioinformatics, phylogeny

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