Search results for: phylogenetic analysis

Authors: M. Y. Abubakar, Ipinjolu J. K., Yuzine B. Esa, Magawata I., Hassan W. A., Turaki A. A.

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Catfish (Heterobranchus spp.) is a major freshwater fish that are widely distributed in Nigeria waters and are gaining rapid aquaculture expansion. However, indiscriminate artificial crossbreeding of the species with others poses a threat to their biodiversity. There is a paucity of information about the genetic variability, hence this insight on the genetic variability is badly needed, not only for the species conservation but for aquaculture expansion. In this study, we tested the level of Genetic diversity, population differentiation and phylogenetic relationship analysis on 35 individuals of two populations of Heterobranchus bidorsalis and 29 individuals of three populations of Heterobranchus longifilis using the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene sequence. Nucleotide sequences of 650 bp fragment of the COI gene of the two species were compared. In the whole 4 and 5 haplotypes were distinguished in the populations of H. bidorsalis & H. longifilis with accession numbers (MG334168 - MG334171 & MG334172 to MG334176) respectively. Haplotypes diversity indices revealed a range of 0.59 ± 0.08 to 0.57 ± 0.09 in H. bidorsalis and 0.000 to 0.001051 ± 0.000945 in H. longifilis population, respectively. Analysis of molecular variance (AMOVA) revealed no significant variation among H. bidorsalis population of the Niger & Benue Rivers, detected significant genetic variation was between the Rivers of Niger, Kaduna and Benue population of H. longifilis. Two main clades were recovered, showing a clear separation between H. bidorsalis and H. longifilis in the phylogenetic tree. The mtDNA COI genes studied revealed high gene flow between populations with no distinct genetic differentiation between the populations as measured by the fixation index (FST) statistic. However, a proportion of population-specific haplotypes was observed in the two species studied, suggesting a substantial degree of genetic distinctiveness for each of the population investigated. These findings present the description of the species character and accessions of the fish’s genetic resources, through gene sequence submitted in Genetic database. The data will help to protect their valuable wild resource and contribute to their recovery and selective breeding in Nigeria.

Keywords: AMOVA, genetic diversity, Heterobranchus spp., mtDNA COI, phylogenetic tree

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Authors: Shantanu Prakash, Suruchi Shukla, Amita Jain

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Introduction: The hepatitis C virus (HCV) is a major public health problem and a leading cause of chronic liver disease. Injection drug use and individuals receiving blood and blood products are the primary modes of HCV transmission. Our study aims to establish the prevalent genotypes/ subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. Methods: It is a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital during September 2014 to April 2017. The study was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried on stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger’s sequencing of the core region. The phylogenetic analysis of 179 HCV strains with high -quality sequencing data was performed. Results: The distribution of prevalent genotypes/ subtypes as noted in the present study was; Genotype (GT)1a [n-101(25%)], GT1b [n-12(2.9%)], GT1c [1(0.25%)], GT3a [275(68.07%)], GT3b [9(2.2%)], GT3g [2(0.49%)], GT3i [3(0.74%)], and GT4a [1(0.24%)]. HCV genotypes GT2, GT5 and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. Conclusions: HCV genotypes 3a and 1a are commonest circulating genotypes in Uttar Pradesh (UP), India.

Keywords: Hepatitis C virus, genetic variation, bioinformatics, genotype, HCV

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Authors: Masoud Soltanialvar, Ali Bagherpour

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Documented cases of human infection with H9N2 avian influenza viruses, first detected in 1999 in Hong Kong and China, indicate that these viruses can be directly transmitted from birds to humans. In this study, we characterized the mutation in the Hemagglutinin (HA) genes and proteins that correlates with a shift in affinity of the Hemagglutinin (HA) protein from the “avian” type sialic receptors to the “human” type in 10 Iranian isolates. We delineated the genomes and receptor binding profile of HA gene of some field isolates and established their phylogenetic relationship to the other Asian H9N2 sub lineages. A total of 1200 tissue samples collected from 40 farms located in various states of Iran during 2008 – 2010 as part of a program to monitor Avian Influenza Viruses (AIV) infection. To determine the genetic relationship of Iranian viruses, the Hemagglutinin (HA) genes from ten isolates were amplified and sequenced (by RT-PCR method). Nucleotide sequences (orf) of the (HA) genes were used for phylogenetic tree construction. Deduced amino acid sequences showed the presence of L226 (234 in H9 numbering) in all ten Iranian isolates which indicates a preference to binding of α (2–6) sialic acid receptors, so these Iranian H9N2 viruses have the potential to infect human beings. These isolates showed high degree of homology with 2 human H9N2 isolates A/HK/1073/99, A/HK/1074/99. Phylogenetic analysis of showed that all the HA genes of the Iranian H9N2 viruses fall into a single group within a G1-like sublineage which had contributed as donor of six internal genes to H5N1 highly pathogenic avian influenza. The results of this study indicated that all Iranian viruses have the potential to emerge as highly pathogenic influenza virus, and considering the homology of these isolates with human H9N2 strains, it seems that the potential of these avian influenza isolates to infect human should not be overlooked.

Keywords: influenza virus, hemagglutinin, neuraminidase, Iran

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Authors: Waqas Shafqat Chattha, Muhammad Iqbal, Amir Shakeel

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Transcriptional factors are proteins that play a vital role in regulating the transcription of target genes in different biological processes and are being widely studied in different plant species. In the current era of genomics, plant genomes sequencing has directed to the genome-wide identification, analyses and categorization of diverse transcription factor families and hence provide key insights into their structural as well as functional diversity. The DNA-binding with One Finger (DOF) proteins belongs to C2-C2-type zinc finger protein family. DOF proteins are plant-specific transcription factors implicated in diverse functions including seed maturation and germination, phytohormone signalling, light-mediated gene regulation, cotton-fiber elongation and responses of the plant to biotic as well as abiotic stresses. In this context, a genome-wide in-silico analysis of DOF TF family in diploid cotton species i.e. Gossypium raimondii has enabled us to identify 55 non-redundant genes encoding DOF proteins renamed as GrDofs (Gossypium raimondii Dof). Gene distribution studies have shown that all of the GrDof genes are unevenly distributed across 12 out of 13 G. raimondii chromosomes. The gene structure analysis illustrated that 34 out of 55 GrDof genes are intron-less while remaining 21 genes have a single intron. Protein sequence-based phylogenetic analysis of putative 55 GrDOFs has divided these proteins into 5 major groups with various paralogous gene pairs. Molecular evolutionary studies aided with the conserved domain as well as gene structure analysis suggested that segmental duplications were the principal contributors for the expansion of Dof genes in G. raimondii.

Keywords: diploid cotton , G. raimondii, phylogenetic analysis, transcription factor

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Authors: Gerardo Arias, Richard Wall, Jamie Stevens

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Lucilia bufonivora Moniez, is an obligate parasite of toads and frogs widely distributed in Europe. Its sister taxon Lucilia silvarum Meigen behaves mainly as a carrion breeder in Europe, however it has been reported as a facultative parasite of amphibians. These two closely related species are morphologically almost identical, which has led to misidentification, and in fact, it has been suggested that the amphibian myiasis cases by L. silvarum reported in Europe should be attributed to L. bufonivora. Both species remain poorly studied and their taxonomic relationships are still unclear. The identification of the larval specimens involved in amphibian myiasis with molecular tools and phylogenetic analysis of these two closely related species may resolve this problem. In this work seventeen unidentified larval specimens extracted from toad myiasis cases of the UK, the Netherlands and Switzerland were obtained, their COX1 (mtDNA) and EF1-α (Nuclear DNA) gene regions were amplified and then sequenced. The 17 larval samples were identified with both molecular markers as L. bufonivora. Phylogenetic analysis was carried out with 10 other blowfly species, including L. silvarum samples from the UK and USA. Bayesian Inference trees of COX1 and a combined-gene dataset suggested that L. silvarum and L. bufonivora are separate sister species. However, the nuclear gene EF1-α does not appear to resolve their relationships, suggesting that the rates of evolution of the mtDNA are much faster than those of the nuclear DNA. This work provides the molecular evidence for successful identification of L. bufonivora and a molecular analysis of the populations of this obligate parasite from different locations across Europe. The relationships with L. silvarum are discussed.

Keywords: calliphoridae, molecular evolution, myiasis, obligate parasitism

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Authors: Alexander A. Stakheev, Larisa V. Samokhvalova, Sergey K. Zavriev

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Fusarium fungi are among the most devastating plant pathogens distributed all over the world. Significant reduction of grain yield and quality caused by Fusarium leads to multi-billion dollar annual losses to the world agricultural production. These organisms can also cause infections in immunocompromised persons and produce the wide range of mycotoxins, such as trichothecenes, fumonisins, and zearalenone, which are hazardous to human and animal health. Identification of Fusarium fungi based on the morphology of spores and spore-forming structures, colony color and appearance on specific culture media is often very complicated due to the high similarity of these features for closely related species. Modern Fusarium taxonomy increasingly uses data of crossing experiments (biological species concept) and genetic polymorphism analysis (phylogenetic species concept). A number of novel Fusarium sibling species has been established using DNA barcoding techniques. Species recognition is best made with the combined phylogeny of intron-rich protein coding genes and ribosomal DNA sequences. However, the internal transcribed spacer of (ITS), which is considered to be universal DNA barcode for Fungi, is not suitable for genus Fusarium, because of its insufficient variability between closely related species and the presence of non-orthologous copies in the genome. Nowadays, the translation elongation factor 1 alpha (TEF1α) gene is the “gold standard” of Fusarium taxonomy, but the search for novel informative markers is still needed. In this study, we used two novel DNA markers, frataxin (FXN) and heat shock protein 90 (HSP90) to discover phylogenetic relationships between Fusarium species. Multilocus phylogenetic analysis based on partial sequences of TEF1α, FXN, HSP90, as well as intergenic spacer of ribosomal DNA (IGS), beta-tubulin (β-TUB) and phosphate permease (PHO) genes has been conducted for 120 isolates of 19 Fusarium species from different climatic zones of Russia and neighboring countries using maximum likelihood (ML) and maximum parsimony (MP) algorithms. Our analyses revealed that FXN and HSP90 genes could be considered as informative phylogenetic markers, suitable for evolutionary and taxonomic studies of Fusarium genus. It has been shown that PHO gene possesses more variable (22 %) and parsimony informative (19 %) characters than other markers, including TEF1α (12 % and 9 %, correspondingly) when used for elucidating phylogenetic relationships between F. avenaceum and its closest relatives – F. tricinctum, F. acuminatum, F. torulosum. Application of novel DNA barcodes confirmed the fact that F. arthrosporioides do not represent a separate species but only a subspecies of F. avenaceum. Phylogeny based on partial PHO and FXN sequences revealed the presence of separate cluster of four F. avenaceum strains which were closer to F. torulosum than to major F. avenaceum clade. The strain F-846 from Moldova, morphologically identified as F. poae, formed a separate lineage in all the constructed dendrograms, and could potentially be considered as a separate species, but more information is needed to confirm this conclusion. Variable sites in PHO sequences were used for the first-time development of specific qPCR-based diagnostic assays for F. acuminatum and F. torulosum. This work was supported by Russian Foundation for Basic Research (grant № 15-29-02527).

Keywords: DNA barcode, fusarium, identification, phylogenetics, taxonomy

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Authors: Maryam Beiranvand, Sajad Yaghoubi

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Background: Some microbes can colonize plants’ inner tissues without causing obvious damage and can even produce useful bioactive substances. In the present study, the diversity of the endophytic bacteria associated with medicinal plants from Iran was investigated by culturing techniques, molecular gene identification, as well as measuring them for antibacterial activity. Results: In the spring season from 2013 to 2014, 35 herb pharmacology samples were collected, sterilized, meshed, and then cultured on selective media culture. A total of 199 endophytic bacteria were successfully isolated from 35 tissue cultures of medical plants, and sixty-seven out of 199 bacterial isolates were subjected to identification by the 16S rRNA gene sequence analysis method. Based on the sequence similarity gene and phylogenetic analyses, these isolates were grouped into five classes, fourteen orders, seventeen families, twenty-one genera, and forty strains. The most abundant group of endophytic bacteria was actinobacterial, consisting of thirty-two (47%) out of 67 bacterial isolates. Ten (22.3%) out of 67 bacterial isolates remained unidentified and classified at the genus level. The signature of the 16S rRNA gene formed a distinct line in a phylogenetic tree showing that they might be new species of bacteria. One (5.2%) out of 67 bacterial isolates was still not well categorized. Forty-two out of 67 strains were candidates for antimicrobial activity tests. Nineteen (45%) out of 42 strains showed antimicrobial activity multidrug resistance (MDR); thirteen (68%) out of 19 strains were allocated to classes actinobacteria. Four (21%) out of 19 strains belonged to the Bacillaceae family, one (5.2%) out of 19 strains was the Paenibacillaceae family, and one (5.2%) out of 19 strains belonged to the Pseudomonadaceae family. The other twenty-three strains did not show inhibitory activities. Conclusions: Our research showed a high-level phylogenetic diversity and the intoxicating antibiotic activity of endophytic bacteria in the herb pharmacology of Iran.

Keywords: Antibacterial activity, endophytic bacteria, multidrug-resistant bacteria, whole genom sequencing

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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: Asma Karim

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Fish taxonomy plays a fundamental role in the study of biodiversity. However, traditional methods of fish taxonomy rely on morphological features, which can lead to confusion due to great similarities between closely related species. To overcome this limitation, modern taxonomy employs DNA barcoding as a species identification method. This involves using a short standardized mitochondrial DNA region as a barcode, specifically a 658 base pair fragment near the 5′ ends of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, to exploit the diversity in this region for identification of species. To test the effectiveness and reliability of DNA barcoding, 25 fish specimens from nine different fish species found in various rivers of Pakistan were identified morphologically using a dichotomous key at the start of the study. Comprising nine freshwater fish species, including Mystus cavasius, Mystus bleekeri, Osteobrama cotio, Labeo rohita, Labeo culbasu, Labeo gonius, Cyprinus carpio, Catla catla and Cirrhinus mrigala from different rivers of Pakistan were used in the present study. DNA was extracted from one of the pectoral fins and a partial sequence of CO1 gene was amplified using the conventional PCR method. Analysis of the barcodes confirmed that genetically identified fishes were the same as those identified morphologically at the beginning of the study. The sequences were also analyzed for biodiversity and phylogenetic studies. Based on the results of the study, it can be concluded that DNA barcoding is an effective and reliable method for studying biodiversity and conducting phylogenetic analysis of different fish species in Pakistan.

Keywords: DNA barcoding, fresh water fishes, taxonomy, biodiversity, Pakistan

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Authors: Faisal Nouroz, Mukaramin Mukaramin

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Of the transposable elements (TEs), the retrotransposons are the most copious elements identified from many sequenced genomes. They have played a major role in genome evolution, rearrangement, and expansions based on their copy and paste mode of proliferation. They are further divided into LTR and Non-LTR retrotransposons. The purpose of the current study was to identify the LTR REs in sequenced Phoenix dactylifera genome and to study their structural diversity. A total of 150 P. dactylifera BAC sequences with > 60kb sizes were randomly retrieved from National Center for Biotechnology Information (NCBI) database and screened for the presence of LTR retrotransposons. Seven bacterial artificial chromosomes (BAC) sequences showed full-length LTR Retrotransposons with 4 Copia and 3 Gypsy families having variable copy numbers in respective families. Reverse transcriptase (RT) domain was found as the most conserved domain among Copia and Gypsy superfamilies and was used to deduce evolutionary analysis. The amino acid residues among various RT sequences showed variability in their percentages indicating post divergence evolution. Amino acid Leucine was found in highest proportions followed by Lysine, while Methionine and Tryptophan were in lowest percentages. The phylogenetic analysis based on RT domains confirmed that although having most conserved RT regions, several evolutionary events occurred causing nucleotide polymorphisms and hence clustering of Gypsy and Copia superfamilies into their respective lineages. The study will be helpful in identification and annotation of these elements in other species and genera and their distribution patterns on chromosomes by fluorescent in situ hybridization techniques.

Keywords: transposable elements, Phoenix dactylifera, retrotransposons, phylogenetic analysis

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Authors: Catherine K. Derow

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Possibly a slime mold somehow mutated or already was mutated at progeniture and so stayed as a metazoan when it developed into the fruiting stage and so the slime mold(s) we are evolved and similar to are genetically differ from the slime molds in existence now. This may be why there are genetic links between humans and other metazoa now alive and slime molds now alive but we are now divergent branches of the evolutionary tree compared to the original slime mold, or perhaps slime mold-like organisms, that gave rise to metazoan animalia and perhaps algae and plantae as slime molds were undifferentiated enough in many ways that could allow their descendants to evolve into these three separate phylogenetic categories. Or it may be a slime mold was born or somehow progenated as multicellular, as the particular organism was mutated enough to have say divided in a a 'pseudo-embryonic' stage, and this could have happened for algae, plantae as well as animalia or all the branches may be from the same line but the missing link might be covered in 'phylogenetic sequence comparison noise'.

Keywords: metazoan evolution, unicellular bridge to metazoans, evolution, slime mold

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Authors: Suganiya Rama Rao, Yoon-Yen Yow, Thor-Seng Liew, Shyamala Ratnayeke

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Invasive snails in the genus Pomacea have spread across Southeast Asia including Peninsular Malaysia. Apart from significant economic costs to wetland crops, very little is known about the snails’ effects on native species, and wetland function through their alteration of macrophyte communities. This study was conducted to establish diagnostic characteristics of Pomacea species in the Malaysian environment using genetic and morphological criteria. Snails were collected from eight localities in northern and central regions of Peninsular Malaysia. The mitochondrial COI gene of 52 adult snails was amplified and sequenced. Maximum likelihood analysis was used to analyse species identity and assess phylogenetic relationships among snails from different geographic locations. Shells of the two species were compared using geometric morphometric analysis and covariance analyses. Shell height accounted for most of the observed variation between P. canaliculata and P. maculata, with the latter possessing a smaller mean ratio of shell height: aperture height (p < 0.0001) and shell height to shell width (give p < 0.0001). Genomic and phylogenetic analysis demonstrated the presence of two monophyletic taxa, P. canaliculata and P. maculata, in Peninsular Malaysia samples. P. maculata co-occurred with P. canaliculata in 5 localities, but samples from 3 localities contained only P. canaliculata. This study is the first to confirm the presence of two of the most invasive species of Pomacea in Peninsular Malaysia using a genomic approach. P. canaliculata appears to be the more widespread species. Despite statistical differences, both quantitative and qualitative morphological characteristics demonstrate much interspecific overlap and intraspecific variability; thus morphology alone cannot reliably verify species identity. Molecular techniques for distinguishing between these two highly invasive Pomacea species are needed to understand their specific ecological niches and develop effective protocols for their management.

Keywords: Pomacea canaliculata, Pomacea maculata, invasive species, phylog enetic analysis, geometric morphometric analysis

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to reassess the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high gene support confidence with confidence intervals exceeding 95%, high internode certainty, and high gene concordance factor. The evidence stems from two datasets containing recently deciphered whole genomes of two lungfish species, as well as five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa diminishes the number of orthologues and leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction (LBA) and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: gene support confidence (GSC), origin of land vertebrates, coelacanth, two whole genomes of lungfishes, confidence intervals

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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: Amr A. El Hanafy, Muhammad I. Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek

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β-Lactoglobulin (β-LG) is the dominant non-casein whey protein found in bovine milk and of most ruminants. The amino acid sequence of β-LG along with its 3-dimensional structure illustrates linkage with the lipocalin superfamily. Preliminary studies in goats indicated that milk yield can be influenced by polymorphism in genes coding for whey proteins. The aim of this study is to identify and evaluate the incidence of functional polymorphisms in the exonic and intronic portions of β-LG gene in native Saudi goat breeds (Ardi, Habsi, and Harri). Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted using QIAamp DNA extraction Kit. A fragment of the β-LG gene from exon 7 to 3’ flanking region was amplified with pairs of specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Two already established SNPs in exon 7 (+4601 and +4603) and one fresh SNP in the 3’ UTR region were detected in the β-LG fragments with designated AA genotype. The polymorphisms in exon 7 did not produce any amino acid change. Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus.

Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, functional polymorphism, nucleotide sequencing, phylogenetic analysis

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

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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

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Authors: Ayesha Imtiaz, Darlina Md. Naim

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Family Nemipteridae is among the most abundantly distributed family in Malaysian fish markets due to its high contribution to landing sites of Malaysia. Using an advanced molecular approach that used two mitochondrial (Cytochrome oxidase c I and Cytochrome oxidase b) and one nuclear gene (Recombination activating gene, RAGI) to expose cryptic diversity and phylogenetic relationships among commercially important species of family Nemipteridae. Our research covered all genera (including 31 species out total 45 species) of family Nemipteridae, distributed in Malaysia. We also found certain type of geographical barriers in the South China sea that reduces dispersal and stops a few species to intermix. Northside of the South China Sea (near Vietnam) does not allow genetic diversity to mix with the Southern side of the South China sea (Sarawak) and reduces dispersal. Straits of Malacca reduce the intermixing genetic diversity of South China Sea and the Indian Ocean.

Keywords: Nemipteridae, RAG I, south east Asia, Malaysia

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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: Hyppolite Aignon, Souleymane Yorou, Martin Ryberg, Anneli Svanholm

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Climate change and human actions cause the extinction of wild mushrooms. In Benin, the diversity of fungi is large and may still contain species new to science but the inventory effort remains low and focuses on particularly edible species (Russula, Lactarius, Lactifluus, and also Amanita). In addition, inventories have started recently and some groups of fungi are not sufficiently sampled, however, the degradation of fungal habitat continues to increase and some species are already disappearing. (Yorou and De Kesel, 2011), however, the degradation of fungi habitat continues to increase and some species may disappear without being known. This genus (Inocybe) overlooked has a worldwide distribution and includes more than 700 species with many undiscovered or poorly known species worldwide and particularly in tropical Africa. It is therefore important to orient the inventory to other genera or important families such as Inocybe (Fungi, Agaricales) in order to highlight their diversity and also to know their phylogenetic positions with a combined approach of gene regions. This study aims to evaluate the species richness and phylogenetic position of Inocybe species and affiliated taxa in West Africa. Thus, in North Benin, we visited the Forest Reserve of Ouémé Supérieur, the Okpara forest and the Alibori Supérieur Forest Reserve. In the center, we targeted the Forest Reserve of Toui-Kilibo. The surveys have been carried during the raining season in the study area meaning from June to October. A total of 24 taxa were collected, photographed and described. The DNA was extracted, the Polymerase Chain Reaction was carried out using primers (ITS1-F, ITS4-B) for Internal transcribed spacer (ITS), (LROR, LWRB, LR7, LR5) for nuclear ribosomal (LSU), (RPB2-f5F, RPB2-b6F, RPB2- b6R2, RPB2-b7R) for RNA polymerase II gene (RPB2) and sequenced. The ITS sequences of the 24 collections of Inocybaceae were edited in Staden and all the sequences were aligned and edited with Aliview v1.17. The sequences were examined by eye for sufficient similarity to be considered the same species. 13 different species were present in the collections. In addition, sequences similar to the ITS sequences of the thirteen final species were searched using BLAST. The nLSU and RPB2 markers for these species have been inserted in a complete alignment, where species from all major Inocybaceae clades as well as from all continents except Antarctica are present. Our new sequences for nLSU and RPB2 have been manually aligned in this dataset. Phylogenetic analysis was performed using the RAxML v7.2.6 maximum likelihood software. Bootstrap replications have been set to 100 and no partitioning of the dataset has been performed. The resulting tree was viewed and edited with FigTree v1.4.3. The preliminary tree resulting from the analysis of maximum likelihood shows us that these species coming from Benin are much diversified and are distributed in four different clades (Inosperma, Inocybe, Mallocybe and Pseudosperma) on the seven clades of Inocybaceae but the phylogeny position of 7 is currently known. This study marks the diversity of Inocybe in Benin and the investigations will continue and a protection plan will be developed in the coming years.

Keywords: Benin, diversity, Inocybe, phylogeny placement

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Authors: Luciana Salomon

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The Andes hold one of the highest plant species diversity in the world. How such diversity originated is one of the most intriguing questions in studies addressing the pattern of plant diversity worldwide. Recently, the explosive adaptive radiations found in high Andean groups have been pointed as major triggers of this spectacular diversity. The Andes are one of the most species-rich area for the largest genus from the Asteraceae family, Senecio. There, the genus presents an incredible variation in growth form and ecological niche space. If this diversity of Andean Senecio can be explained by a monophyletic origin and subsequent radiation has not been tested up to now. Previous studies trying to disentangle the evolutionary history of some Andean Senecio struggled with the relatively low resolution and support of the phylogenies, which is indicative of recently radiated groups. Using Hyb-Seq, a powerful approach is available to address phylogenetic questions in groups whose evolutionary histories are recent and rapid. This approach was used for Senecio to build a phylogenetic backbone on which to study the mechanisms shaping its hyper-diversity in the Andes, focusing on Senecio ser. Culcitium, an exclusively Andean and well circumscribed group presenting large morphological variation and which is widely distributed across the Andes. Hyb-Seq data for about 130 accessions of Seneciowas generated. Using standard data analysis work flows and a newly developed tool to utilize paralogs for phylogenetic reconstruction, robustness of the species treewas investigated. Fully resolved and moderately supported species trees were obtained, showing Senecio ser. Culcitium as monophyletic. Within this group, some species formed well-supported clades congruent with morphology, while some species would not have exclusive ancestry, in concordance with previous studies showing a geographic differentiation. Additionally, paralogs were detected for a high number of loci, indicating duplication events and hybridization, known to be common in Senecio ser. Culcitium might have lead to hybrid speciation. The rapid diversification of the group seems to have followed a south-north distribution throughout the Andes, having accelerated in the conquest of new habitats more recently available: i.e., Montane forest, Paramo, and Superparamo.

Keywords: evolutionary radiations, andes, paralogy, hybridization, senecio

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Authors: Nidhi S. Chandra, Veena Agrawal, Debprasad Chattopadhyay

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Background: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in developing countries. It spreads feco orally mainly due to contamination of drinking water by sewage. There is limited data on the genotypic comparison of HEV isolates from sewage water and humans. The aim of this study was to identify genotype and conduct phylogenetic analysis of HEV isolates from sewage water and humans. Materials and Methods: 14 sewage water and 60 serum samples from acute sporadic hepatitis E cases (negative for hepatitis A, B, C) were tested for HEV-RNA by nested polymerase chain reaction (RTnPCR) using primers designed with in RdRp (RNA dependent RNA polymerase) region of open reading frame-1 (ORF-1). Sequencing was done by ABI prism 310. The sequences (343 nucleotides) were compared with each other and were aligned with previously reported HEV sequences obtained from GeneBank, using Clustal W software. A Phylogenetic tree was constructed by using PHYLIP version 3.67 software. Results: HEV-RNA was detected in 49/ 60 (81.67%) serum and 5/14 (35.71%) sewage samples. The sequences obtained from 17 serums and 2 sewage specimens belonged to genotype I with 85% similarity and clustering with previously reported human HEV sequences from India. HEV isolates from human and sewage in North West India are genetically closely related to each other. Conclusion: These finding suggest that sewage acts as reservoir of HEV. Therefore it is important that measures are taken for proper waste disposal and treatment of drinking water to prevent outbreaks and epidemics due to HEV.

Keywords: hepatitis E virus, nested polymerase chain reaction, open reading frame-1, nucleotidies

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Authors: Anupama Sekhar, Preeti Saryan, Vinita Gowda

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Plants, due to their sedentary lifestyle, have evolved mechanisms to synthesize a huge diversity of complex, specialized chemical metabolites, a majority of them being volatile organic compounds (VOCs). These VOCs are heavily involved in their biotic and abiotic interactions. Since chemical composition could be under the same selection processes as other morphological characters, we test if VOCs can be used to taxonomically distinguish species in the well-studied, fragrant ginger genus -Hedychium (Zingiberaceae). We propose that variations in the volatile profiles are suggestive of adaptation to divergent environments, and their presence could be explained by either phylogenetic conservatism or ecological factors. In this study, we investigate the volatile chemistry within Hedychium, which is endemic to Asian palaeotropics. We used an unsupervised clustering approach which clearly distinguished most taxa, and we used ancestral state reconstruction to estimate phylogenetic signals and chemical trait evolution in the genus. We propose that taxonomically, the chemical composition could aid in species identification, especially in species complexes where taxa are not morphologically distinguishable, and extensive, targeted chemical libraries will help in this effort.

Keywords: chemotaxonomy, dynamic headspace sampling, floral fragrance, floral volatile evolution, gingers, Hedychium

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Authors: Ricardo Godoy, Herbert Venthur, Hector Jimenez, Andres Quiroz, Ana Mutis

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In agriculture, grape production has great economic importance at global level, considering that in 2013 it reached 7.4 million hectares (ha) covered by plantations of this fruit worldwide. Chile is the number one exporter in the world with 800,000 tons. However, these values have been threatened by the attack of the grapevine moth, Lobesia botrana (Denis & Schiffermuller) (Lepidoptera: Tortricidae), since its detection in 2008. Nowadays, the use of semiochemicals, in particular the major component of the sex pheromone, (E,Z)-7.9-dodecadienil acetate, are part of mating disruption methods to control L. botrana. How insect pests can recognize these molecules, is being part of huge efforts to deorphanize their olfactory mechanism at molecular level. Thus, an interesting group of proteins has been identified in the antennae of insects, where odorant-binding proteins (OBPs) are known by transporting molecules to odorant receptors (ORs) and a co-receptor (ORCO) causing a behavioral change in the insect. Other proteins such as chemosensory proteins (CSPs), ionotropic receptors (IRs), odorant degrading enzymes (ODEs) and sensory neuron membrane proteins (SNMPs) seem to be involved, but few studies have been performed so far. The above has led to an increasing interest in insect communication at a molecular level, which has contributed to both a better understanding of the olfaction process and the design of new pest management strategies. To date, it has been reported that the ORs can detect one or a small group of odorants in a specific way. Therefore, the objective of this study is the identification of genes that encode these ORs using the antennal transcriptome of L. botrana. Total RNA was extracted for females and males of L. botrana, and the antennal transcriptome sequenced by Next Generation Sequencing service using an Illumina HiSeq2500 platform with 50 million reads per sample. Unigenes were assembled using Trinity v2.4.0 package and transcript abundance was obtained using edgeR. Genes were identified using BLASTN and BLASTX locally installed in a Unix system and based on our own Tortricidae database. Those Unigenes related to ORs were characterized using ORFfinder and protein Blastp server. Finally, a phylogenetic analysis was performed with the candidate amino acid sequences for LbotORs including amino acid sequences of other moths ORs, such as Bombyx mori, Cydia pomonella, among others. Our findings suggest 61 genes encoding ORs and one gene encoding an ORCO in both sexes, where the greatest difference was found in the OR6 because of the transcript abundance according to the value of FPKM in females and males was 1.48 versus 324.00. In addition, according to phylogenetic analysis OR6 is closely related to OR1 in Cydia pomonella and OR6, OR7 in Epiphyas postvittana, which have been described as pheromonal receptors (PRs). These results represent the first evidence of ORs present in the antennae of L. botrana and a suitable starting point for further functional studies with selected ORs, such as OR6, which is potentially related to pheromonal recognition.

Keywords: antennal transcriptome, lobesia botrana, odorant receptors (ORs), phylogenetic analysis

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Authors: Dang Thuy Binh, Truong Thi Oanh, Le Phan Khanh Hung, Luong thi Tuong Vy

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One of the greatest environmental challenges facing Asia is the management and conservation of the marine biodiversity threaten by fisheries overexploitation, pollution, habitat destruction, and climate change. To date, a few molecular taxonomical studies has been conducted on marine fauna in Vietnam. The purpose of this study was to clarify the phylogeny of economic and ecological reef fish species in Vietnam Reef fish species covering Labridae, Scaridae, Nemipteridae, Serranidae, Acanthuridae, Lutjanidae, Lethrinidae, Mullidae, Balistidae, Pseudochromidae, Pinguipedidae, Fistulariidae, Holocentridae, Synodontidae, and Pomacentridae representing 28 genera were collected from South and Center, Vietnam. Combine with Genbank sequences, a phylogenetic tree was constructed based on 16S gene of mitochondrial DNA using maximum parsimony, maximum likelihood, and Bayesian inference approaches. The phylogram showed the well-resolved clades at genus and family level. Perciformes is the major order of reef fish species in Vietnam. The monophyly of Perciformes is not strongly supported as it was clustered in the same clade with Tetraodontiformes syngnathiformes and Beryciformes. Continue sampling of commercial fish species and classification based on morphology and genetics to build DNA barcoding of fish species in Vietnam is really necessary.

Keywords: reef fish, 16s rDNA, Vietnam, phylogeny

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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: Mohamed El-Shikh

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Phaseolus vulgaris L. is the world’s second most important bean after soybeans; used for human food and animal feed. It has generally been linked to reduced risk of cardiovascular disease, diabetes mellitus, obesity, cancer and diseases of digestive tract. The effectiveness of ISSR in achievement of the genetic diversity among 60 common bean accessions; represent various germplasms around the world was investigated. In general, the studied Phaseolus vulgaris accessions were divided into 2 major groups. All of the South-American accessions were separated into the second major group. These accessions may have different genetic features that are distinct from the rest of the accessions clustered in the major group. Asia and Europe accessions (1-20) seem to be more genetically similar (99%) to each other as they clustered in the same sub-group. The American and African varieties showed similarities as well and clustered in the same sub-tree group. In contrast, Asian and American accessions No. 22 and 23 showed a high level of genetic similarities, although these were isolated from different regions. The phylogenetic tree showed that all the Asian accessions (along with Australian No. 59 and 60) were similar except Indian and Yemen accessions No. 9 and 20. Only Netherlands accession No. 3 was different from the rest of European accessions. Morocco accession No. 52 was genetically different from the rest of the African accessions. Canadian accession No. 44 seems to be different from the other North American accessions including Guatemala, Mexico and USA.

Keywords: phylogenetic tree, Phaseolus vulgaris, ISSR technique, genetics

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Authors: Laura Mclean

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A recurring point of interest in computational phylogenetic analysis of Indo-European family trees is the inference of a Germano-Italo-Celtic clade in some versions of the trees produced. The presence of this clade in the models is intriguing as there is little evidence for innovations shared among Germanic, Italic, and Celtic, the evidence generally used in the traditional method to construct a subgroup. One source of this unexpected outcome could be the input to the models. The datasets in the various models used so far, for the most part, take as their basis the Swadesh list, a list compiled by Morris Swadesh and then revised several times, containing up to 207 words that he believed were resistant to change among languages. The judgments made by Swadesh for this list, however, were subjective and based on his intuition rather than rigorous analysis. Some scholars used the Swadesh 200 list as the basis for their Indo-European dataset and made cognacy judgements for each of the words on the list. Another dataset is largely based on the Swadesh 207 list as well although the authors include additional lexical and non-lexical data, and they implement ‘split coding’ to deal with cases of polymorphic characters. A different team of scholars uses a different dataset, IECoR, which combines several different lists, one of which is the Swadesh 200 list. In fact, the Swadesh list is used in some form in every study surveyed and each dataset has three words that, when they are coded as cognates, seemingly contribute to the inference of a Germano-Italo-Celtic clade which could happen due to these clades sharing three words among only themselves. These three words are ‘fish’, ‘flower’, and ‘man’ (in the case of ‘man’, one dataset includes Lithuanian in the cognacy coding and removes the word ‘man’ from the screened data). This collection of cognates shared among Germanic, Italic, and Celtic that were deemed important enough to be included on the Swadesh list, without the ability to account for possible reasons for shared cognates that are not shared innovations, gives an impression of affinity between the Germanic, Celtic, and Italic branches without adequate methodological support. However, by changing how cognacy is defined (ie. root cognates, borrowings vs inherited cognates etc.), we will be able to identify whether these three cognates are significant enough to infer a clade for Germanic, Celtic, and Italic. This paper examines the question of what definition of cognacy should be used for phylogenetic datasets by examining the Germano-Italo-Celtic clade as a case study and offers insights into the reconstruction of a Germano-Italo-Celtic clade.

Keywords: historical, computational, Italo-Celtic, Germanic

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Authors: Najat El-Kurdi, Sherif Hammad, Mohamed Ghazi, Sahar El-Shatoury, Khaled Zakaria

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The increasing number of plastic production and its importance to humanity in daily life made it a headache to the planet earth. The persistence of plastic wastes in the environment formed a serious problem. They are prominent with their capability to resist microbial degradation for decades. Thus, it was crucial to find ways to eliminate the plastics without depending on conventional recycling methods, which causes the formation of more hazardous compounds and doubles the problem. In this paper, mealworms were fed with a mixture of plastic wastes such as plastic bags, Styrofoam, PE foam, and plastic tarpaulins film as the sole food source for a month. Frass was collected at the end of the test and examined using FTIR analysis. Also, the gut bacteria were isolated and identified using 16S rRNA. The results show the mineralization of plastic in the frass of plastic-fed worms when compared to control. The 16S rRNA and the BLAST analysis showed that the obtained isolate belongs to the genus Bacillus Sp especially Bacillus subtilis. Phylogenetic analysis showed their relatedness to the other Bacillus species in the NCBI database.

Keywords: mealworm, waste management, plastic-degrading bacteria, gut microbiome, Bacillus sp

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Authors: Ghada Badr, Manar Hosny, Nuha Bintayyash, Eman Albilali, Souad Larabi Marie-Sainte

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The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms.

Keywords: median problem, phylogenetic tree, permutation, genetic algorithm, beam search, genome rearrangement distance

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