Journal articles: 'Phylogentic'

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Journal, Baghdad Science. "phylogentic study of cephalopharyngeal selerites." Baghdad Science Journal 3, no. 1 (March 5, 2006): 62–72. http://dx.doi.org/10.21123/bsj.3.1.62-72.

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Maharjan, Mahendra. "Characterization of Heat Shock Protein (HSP 70) Sequence in Leishmania donovani." Journal of Institute of Science and Technology 20, no. 1 (November 25, 2015): 82–86. http://dx.doi.org/10.3126/jist.v20i1.13914.

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Heat shock protein HSP70 is the highly conserved protein along the kinetoplastid phylogenetic spectrum. A full length hsp70 gene was amplified, cloned and sequenced. The protein sequence was aligned and phylogentic tree was constructed. The Leishmania donovani HSP70 protein sequence (653 amino acids) is slightly larger than the Human HSP70 protein sequence (641 amino acids) with 72% identity. The putative protein sequence is 98%, 97%, 96% and 92% identical to L. major, L. infantum, L. tarentolae and L. braziliensis respectively. Evolutionary relationship showed that kinetoplastid parasites are closely related to the human compared to prokaryotes, E. coli.Journal of Institute of Science and Technology, 2015, 20(1): 82-86

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Aravena-Román, M., T. J. J. Inglis, C. Siering, P. Schumann, and A. F. Yassin. "Canibacter oris gen. nov., sp. nov., isolated from an infected human wound." International Journal of Systematic and Evolutionary Microbiology 64, Pt_5 (May 1, 2014): 1635–40. http://dx.doi.org/10.1099/ijs.0.058859-0.

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A facultatively anaerobic, Gram-reaction-positive, catalase- and oxidase-negative, rod-shaped bacterium isolated from an infected human wound caused by a dog bite was characterized by phenotypic and molecular genetic methods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMMIB Q2029717T was a member of the order Micrococcales of the class Actinobacteria , displaying 91.6 % to 96 % sequence similarity with members of the family Microbacteriaceae . Phylogentic trees generated by different algorithms indicated that the strain forms an independent phylogenetic line of descent that consistently clustered proximal to the base of the genus Leucobacter . Chemical studies revealed the presence of a cell-wall murein based on l-lysine (type B1α), major menaquinone (MK-10) and a DNA G+C content of 56.9 mol%. The distinct phylogenetic position, ribotyping and matrix-assisted laser desorption/ionization time-of-flight MS profiles and the significant phenotypic differences clearly separate strain IMMIB Q2029717T from its nearest phylogenetic neighbour and support its classification as a representative of a novel genus and species, with the suggested name Canibacter oris gen. nov., sp. nov. The type strain is IMMIB Q2029717T ( = DSM 27064T = CCUG 64069T).

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Titov, V. N. "Phylogentic theory of pathology. Common phylogenetic features in the pathogenesis of essential arterial hyperntesion and insulin resistance syndrome." Systemic Hypertension 11, no. 3 (September 15, 2014): 53–60. http://dx.doi.org/10.26442/sg29045.

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Our phylogenetic theory of pathology (algorrhythm of a disease development) is based on 1) a theory of biological functions and biological reactions in vivo; 2) regulation of biological functions, reactions, and metabolic processes at three phylogenetically different levels: а) autocrine (cell level); b) paracrine (in paracrine-regulated cell communities) and c) total organism level; 3) conceptions on formation of physiological and aphysiological processes («civilization» diseases) at various stages of phylogenesis. Universal pathogenesis of essential arterial hypertension and insulin resistance syndrome is based on functional discrepancy between phylogenetically early regulatory mechanisms at the level of paracrine cell communities and phylogenetically late regulation at the organism level. Pathogenic factors of this discrepancy are impaired biological functions of homeostasis, trophology, endoecology and adaptation. An increase in the content of unesterified fatty acids in the intercellular medium results from activation of lipolysis in paracrine community cells which cannot inhibit phylogenetically late insulin, but not in insulin-dependent adipocytes. The formation of pathogenesis of each metabolic pandemia occurs dynamically at different stages of phylogenesis.

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Jin-Chan, Wang, Qi Wei-Wei, Zhang Long-Xian, Ning Chang-Shen, Jian Fu-Chun, Zhao Jin-Feng, and Wang Ming. "Phylogenetic analysis ofCryptosporidiumisolates in Henan." Chinese Journal of Agricultural Biotechnology 4, no. 3 (December 2007): 247–52. http://dx.doi.org/10.1017/s1479236207001957.

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AbstractThe functional mitochondrial protein alternative oxidase (AOX) gene was used as a marker to analyse the phylogenetic relationship betweenCryptosporidiumisolates. This gene was characterized, and the phylogentic tree was established fromCryptosporidiumisolates and compared to those generated from 18S rRNA and heat-shock protein 70 (HSP70) gene sequences. The present trial aimed at finding out whether the AOX gene is suitable for phylogenetic analysis of theCryptosporidiumgenus. The results revealed that the genusCryptosporidiumcontained the phylogenetically distinct speciesC. parvum,C. hominis,C. suisandC. baileyi, which were consistent with the biological characterization and host specificity reported earlier.Cryptosporidiumspecies formed two clades: one includedC. hominis,C. suis,C. parvumcattle genotypes andC. parvummouse genotype; and the other comprisedC. meleagridisandC. baileyiisolates. WithinC. parvum, both the mouse genotype and the pig genotype I (also known asC. suis) isolates differed from cattle and human (also known asC. hominis) genotypes, based on the aligned nucleotide sequences. The sequence identity of the AOX gene was higher betweenC. meleagridisandC. baileyithan betweenC. meleagridisandC. parvum. The phylogenetic trees showed thatC. meleagridiswas closer toC. baileyithan toC. parvum. This result was inconsistent with the phylogenetic analysis deduced from 18S rRNA and HSP70 gene sequences, respectively. The present results suggest that the AOX gene is not only equally suitable for the phylogenetic analysis ofCryptosporidium, but also provides an outstanding and new approach in determiningCryptosporidiumheredity.

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Day, J. Michael. "The diversity of the orthoreoviruses: Molecular taxonomy and phylogentic divides." Infection, Genetics and Evolution 9, no. 4 (July 2009): 390–400. http://dx.doi.org/10.1016/j.meegid.2009.01.011.

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Les, Donald, Michael Moody, and Connie Soros. "A Reappraisal of Phylogentic Relationships in the Monocotyledon Family Hydrocharitaceae (Alismatidae)." Aliso 22, no. 1 (2006): 211–30. http://dx.doi.org/10.5642/aliso.20062201.18.

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ABDELMAKSOUD, HESHAM M., AYMAN M. MANDOUR, and AHMED S. GAMAL ELDIN. "MOLECULAR IDENTIFICATION AND PHYLOGENTIC ANALYSIS OF POTATO LEAF ROLL VIRUS IN EGYPT." Egyptian Journal of Agricultural Research 91, no. 4 (December 1, 2013): 1259–69. http://dx.doi.org/10.21608/ejar.2013.165097.

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Price, Peter W. "Phylogentic constraints, adaptive syndromes, and emergent properties: From individuals to population dynamics." Researches on Population Ecology 36, no. 1 (June 1994): 3–14. http://dx.doi.org/10.1007/bf02515079.

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Achatz, Tyler J., Eric E. Pulis, Ethan T. Woodyard, Thomas G. Rosser, Jakson R. Martens, Sara B. Weinstein, Alan Fecchio, Chris T. McAllister, Carlos Carrión Bonilla, and Vasyl V. Tkach. "Molecular phylogenetic analysis of Neodiplostomum and Fibricola (Digenea, Diplostomidae) does not support host-based systematics." Parasitology 149, no. 4 (January 19, 2022): 542–54. http://dx.doi.org/10.1017/s003118202100216x.

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AbstractFibricola and Neodiplostomum are diplostomid genera with very similar morphology that are currently separated based on their definitive hosts. Fibricola spp. are normally found in mammals, while Neodiplostomum spp. typically parasitize birds. Previously, no DNA sequence data was available for any member of Fibricola. We generated nuclear ribosomal and mtDNA sequences of Fibricola cratera (type-species), Fibricola lucidum and 6 species of Neodiplostomum. DNA sequences were used to examine phylogenetic interrelationships among Fibricola and Neodiplostomum and re-evaluate their systematics. Molecular phylogenies and morphological study suggest that Fibricola should be considered a junior synonym of Neodiplostomum. Therefore, we synonymize the two genera and transfer all members of Fibricola into Neodiplostomum. Specimens morphologically identified as Neodiplostomum cratera belonged to 3 distinct phylogenetic clades based on mitochondrial data. One of those clades also included sequences of specimens identified morphologically as Neodiplostomum lucidum. Further study is necessary to resolve the situation regarding the morphology of N. cratera. Our results demonstrated that some DNA sequences of N. americanum available in GenBank originate from misidentified Neodiplostomum banghami. Molecular phylogentic data revealed at least 2 independent host-switching events between avian and mammalian hosts in the evolutionary history of Neodiplostomum; however, the directionality of these host-switching events remains unclear.

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Namiotko, Tadeusz, Dan L. Danielopol, Claude Meisch, Martin Gross, and Nataša Mori. "Redefinition of the genus Typhlocypris Vejdovský, 1882 (Ostracoda, Candonidae)." Crustaceana 87, no. 8-9 (2014): 952–84. http://dx.doi.org/10.1163/15685403-00003338.

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The taxonomy of the genusTyphlocyprisVejdovský, 1882 is reviewed. New morphological information onTyphlocypris eremita(Vejdovský, 1882), the type species of the genus, is provided, and a new reference material is presented. The generic diagnosis is emended with details derived from the developmental trajectory of the valves, from the juvenile stage A-3 to the adult. Those criteria clearly differentiateTyphlocyprisfrom the related genusPseudocandonaKaufmann, 1900. As here redefined,Typhlocyprisis a phylogentic lineage of the subfamily Candoninae containing extant species presently living in aquatic subterranean habitats and fossil species recovered from non-marine Late Palaeogene to Neogene and Quaternary deposits in Europe and western Asia. The type species ofTyphlocyprisis considered a metaspecies, taxonomically treated asT. eremita(sensu lato), which includes populations resembling the newly designated reference material. The homeomorphic triangular valve shape of the Candoninae is discussed. Careful examination of the valve morphology ofTyphlocypriscombined with the analysis of limb traits helps to distinguish representatives of this genus from unrelated phylogenetic groups presenting similar triangularly shaped valves. It is emphasised that for a useful description ofTyphlocypristaxa both transmitted light and scanning electron microscopy are necessary.

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Petrželová, Irena, and Michal Sochor. "How useful is the current species recognition concept for the determination of true morels? Insights from the Czech Republic." MycoKeys 52 (May 9, 2019): 17–43. http://dx.doi.org/10.3897/mycokeys.52.32335.

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The phylogentic diversity of the genus Morchella has only been sporadically studied in Central Europe. In this study, a molecular taxonomic revision of the Morchella species of the Czech Republic was performed using available fungarium specimens, fresh collections, and axenic cultures. Molecular phylogenetic analyses based on either ITS or five-locus (ITS, LSU, RPB1, RPB2, and EF-1α) sequencing and the application of principles of the genealogical concordance phylogenetic species recognition (GCPSR) have revealed the occurrence of 11 phylogenetic species in the region, but only six of them could be assigned unequivocally to the previously published phylospecies: Mel-3 (M.semilibera), Mel-10 (M.importuna), Mel-19 (M.eohespera), Mes-4 (M.americana), Mes-5 and Mes-8 (M.esculenta). One lineage was identified as a new phylospecies and is designated as Mel-39. Four lineages grouped together with two or more previously published phylospecies: Mel-13/26 (M.deliciosa), Mel-15/16 (M.angusticeps / M.eximioides), Mel-20/34 (M.purpurascens), and Mel-23/24/31/32 (M.pulchella). Our phylogenetic analyses and literature review shed light on the pitfalls of current molecular taxonomy of morels and highlight the ambiguities of present species recognition concepts. The main source of the problems seems to be rooted in the application of different methods (multigene vs single-gene sequencing, phenotypic determination) and approaches (monophyly vs paraphyly, the application or not of GCPSR, degree of differentiation between accepted species, etc.) by various authors for the delimitation of new phylospecies. Therefore, we propose five criteria for distinguishing new phylospecies in the genus Morchella based on molecular data, and recommend a more conservative approach in species delimitation.

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KAYA, SARP, and BATTAL CIPLAK. "Taxonomy of Anterastes and related genera: a new synonym and a new species of Anterastes." Zootaxa 2771, no. 1 (February 22, 2011): 41. http://dx.doi.org/10.11646/zootaxa.2771.1.4.

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Among the Anatolian Tettigoniinae (Orthoptera, Tettigoniidae) the genera Anterastes, Koroglus, Sureyaella and Rhacocleis are distinguishable from the others by presence of one pair of spurs on the apico-ventral end of hind tibiae. The last two can be easily distinguished from the others by several distinct features, but the separation of the first two from each other is problematic. A new species described here provided opportunity of re-evaluating their taxonomy. The new species Anterastes antecessor sp. n. is described based on morphology, male calling song and genetic data. The taxonomy of Anterastes and Koroglus is rectified based on phylogentic hypotheses obtained from representative 16S rDNA haplotypes. Sureyaella bella, Parapholidoptera signata and Bolua turkiyae are used as out groups in different combinations to obtain a more stable phylogeny. Although analyses with different outgroups suggested the same topology, the phylogenetic tree with outgroups Parapholidoptera signata and Bolua turkiyae resulted with the highest bootstrap supports to the branches. Phylogenetic trees suggested the following relationships for the ingroup species; (A. antecessor sp. n. + ((Koroglus disparalatus + A. uludaghensis) + (A. turcicus + (A. niger + (A. ucari + A. babadaghi))) + ((A. tolunayi + (A. serbicus + A. antitauricus + A. burri)))). Considering the phylogenetic hypotheses and characters used in previous publications, Koroglus is put in synonymy with Anterastes, and a new combination is suggested for the only species of the former Anterastes disparalatus comb. n. A short remark is given about the characters used in the generic taxonomy of the group.

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CHIRON, GUY R., ADAM P. KARREMANS, and CASSIO VAN DEN BERG. "Nomenclatural notes in the Pleurothallidinae (Orchidaceae): Phloeophila." Phytotaxa 270, no. 1 (August 12, 2016): 56. http://dx.doi.org/10.11646/phytotaxa.270.1.6.

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Two of us found some years ago that Phloeophila nummularia, type species of the genus Phloeophila, was placed in a molecular phylogentic study in Pabstiella. In this article, we show with the inclusion of new sequences of Phloeophila that this result was not correct. Phloeophila forms a unique clade in Pleurothallidinae and is not closely related to Pabstiella. In addition, the exclusion of three species, one transferred to Dryadella and two others to Acianthera, is proposed.

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Angert, Ester R., Diana E. Northup, Anna-Louise Reysenbach, Andrew S. Peek, Brett M. Goebel, and Norman R. Pace. "Molecular phylogentic analysis of a bacterial community in Sulphur River, Parker Cave, Kentucky." American Mineralogist 83, no. 11-12 Part 2 (December 1, 1998): 1583–92. http://dx.doi.org/10.2138/am-1997-11-1246.

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Angert, Ester R., Diana E. Northup, Anna-Louise Reysenbach, Andrew S. Peek, Brett M. Goebel, and Norman R. Pace. "Molecular phylogentic analysis of a bacterial community in Sulphur River, Parker Cave, Kentucky." American Mineralogist 83, no. 11-12 Part 2 (December 1, 1998): 1583–92. http://dx.doi.org/10.2138/am-1998-11-1246.

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Khairnar, K., I. Salit, D. Martin, and D. Pillai. "P209 Genotyping and phylogentic analysis of a hypervirulent outbreak strain of Entamoeba histolytica." International Journal of Antimicrobial Agents 34 (July 2009): S93. http://dx.doi.org/10.1016/s0924-8579(09)70428-5.

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CHEN, HONGLIANG, IHSAN A. AL-SHEHBAZ, JIPEI YUE, and HANG SUN. "Solms-laubachia tianbaoshanensis (Brassicaceae), a new species from NW Yunnan, China." Phytotaxa 379, no. 1 (November 27, 2018): 39. http://dx.doi.org/10.11646/phytotaxa.379.1.3.

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Solms-laubachia tianbaoshanensis, a new species from the scree slopes and alpine meadows of Hengduan Mountains of NW Yunnan, China, is described and illustrated. It resembles S. linearifolia and S. pulcherrima in gross morphology but differs in having crisped simple subhirsute trichomes to 2 mm long, persistent sepals, pink petals, and longer fruit. In addition, molecular phylogentic analyses based on sequences of nuclear ITS and chloroplast matK, petN-psbM, and trnL-F clearly showed that the new species is distinct from the other congeners.

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Akhtar, Naureen, Rahila Hafeez, and Waheed Anwar. "COMBRETUM INDICUM – A NEW HOST RECORD OF ALTERNARIA BRASSICAE LEAF SPOT DISEASE FROM PAKISTAN." Pakistan Journal of Phytopathology 29, no. 1 (July 12, 2017): 171. http://dx.doi.org/10.33866/phytopathol.029.01.0348.

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Combretum indicum leaf spot disease was observed during a survey of horticultural plants in Lahore. Isolation of causal organism was carried out from the disease leaves. The pathogen, Alternaria brassicae, was first identified considering morphological characters. The morphology based identification was confirmed by nucleotide sequence analysis of ITS region of rDNA and phylogentic analysis of this fungus with closely related other fungal species. Pathogenicity of A. brassicae was verified following the Koch’s pathogenicity postulates. This report represents the first record of leaf spot of Combretum indicum by Alternaria brassicae from Pakistan.

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THELL, Arne, Filip HÖGNABBA, John A. ELIX, Tassilo FEUERER, Ingvar KÄRNEFELT, Leena MYLLYS, Tiina RANDLANE, et al. "Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers." Lichenologist 41, no. 5 (August 6, 2009): 489–511. http://dx.doi.org/10.1017/s0024282909990090.

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AbstractFourteen genera belong to a monophyletic core of cetrarioid lichens, Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, Usnocetraria and Vulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, β-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the genera Allocetraria, Cetraria s. str., Cetrariella and Vulpicida. Arctocetraria, Cetreliopsis, Kaernefeltia and Tuckermanella are monophyletic genera, whereas Cetraria, Flavocetraria and Tuckermannopsis are polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known species Cetraria annae is analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy of Cetraria annae and Flavocetraria minuscula are also provided.

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Sun, Yan-Lin, In-Lee Choi, Yong-Beom Lee, Ki Young Choi, Soon-Kwan Hong, and Ho-Min Kang. "Molecular diversity and phylogentic analysis of Capsicum annuum varieties using the nrDNA ITS region." Scientia Horticulturae 165 (January 2014): 336–43. http://dx.doi.org/10.1016/j.scienta.2013.11.009.

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Hand, S. J. "New Miocene megadermatids (Chiroptera: Megadermatidae) from Australia with comments on megadermatid phylogenetics." Australian Mammalogy 8, no. 1 (January 1, 1985): 5–43. http://dx.doi.org/10.1071/am85001.

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Two new species of megadermatid bats (Macroderma godthelpi and an unnamed taxon) are described from middle Miocene limestone deposits on Riversleigh Station, northwestern Queensland and their probable phylogentic positions within the Megadermatidae are discussed. The new Riversleigh species appear to be representatives of two separate megadermatid lineages. Consideration is given to the significance of the Australian forms within a world context. The Riversleigh material has also prompted a re-evaluation of morphological characters used to determine limits for fossil megadermatids. To facilitate this assessment, size and morphological variation present in Australia's Recent megadermatid, Macroderma gigas, have been investigated.

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Pitt, Alexandra, Johanna Schmidt, Ulrike Koll, and Martin W. Hahn. "Rariglobus hedericola gen. nov., sp. nov., belonging to the Verrucomicrobia, isolated from a temperate freshwater habitat." International Journal of Systematic and Evolutionary Microbiology 70, no. 3 (March 1, 2020): 1830–36. http://dx.doi.org/10.1099/ijsem.0.003980.

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The bacterial strain 53C-WASEF was isolated from a small freshwater ditch located in Eugendorf, Austria. Phylogenetic reconstructions with 16S rRNA gene sequences and genome based, with amino acid sequences obtained from 105 single copy genes, suggested that the strain represents a new genus and a new species within the family Opitutaceae , which belongs to the class Opitutae of the phylum Verrucomicrobia . Comparisons of the 16S rRNA gene sequence of strain 53C-WASEF with those of related type strains revealed a highest sequence similarity of 93.5 % to Nibricoccus aquaticus and of 92.9 % to Geminisphaera colitermitum . Interestingly, phylogentic trees indicated the latter as being the closest known relative of the new strain. Phenotypic, chemotaxonomic and genomic traits were investigated. Cells were observed to be small, spherical, motile and unpigmented, and grew chemoorganotrophically and aerobically. The respiratory quinone was MK-7, the predominant fatty acids were anteiso-C15 : 0, C16 : 1ω5c and C16 : 0. The identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genome sequencing revealed genes putatively encoding for flagella synthesis and cellulose degradation. The genome size was 4.1 Mbp and the G+C content 60.6 mol%. For the new genus and the new species, we propose the name Rariglobus hedericola gen. nov., sp. nov. (=CIP 111665T=DSM 109123T).

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Kasem, Samy, Ali Abdel-Kader, Abdelnaby Tahoon, and Hanan Shaban. "Phylogentic analysis of recent infectious bronchitis virus isolates from broiler chicken farms in Kafrelsheikh, Egypt." Benha Veterinary Medical Journal 29, no. 1 (September 1, 2015): 189–95. http://dx.doi.org/10.21608/bvmj.2015.31817.

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Fatma, Y. Ahmad, M. Abd El Baky Rehab, F. M. Gad Gamal, and A. Soliman Youssef. "Sociodemographic, microbial and phylogentic studies of Mycobacterium tuberculosis cases diagnosed in El-Minia governorate, Egypt." African Journal of Microbiology Research 10, no. 7 (February 21, 2016): 191–202. http://dx.doi.org/10.5897/ajmr2015.7794.

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PUSEY, BRADLEY J., DAMIEN W. BURROWS, MARK J. KENNARD, COLTON N. PERNA, PETER J. UNMACK, QUENTIN ALLSOP, and MICHAEL P. HAMMER. "Freshwater fishes of northern Australia." Zootaxa 4253, no. 1 (April 11, 2017): 1. http://dx.doi.org/10.11646/zootaxa.4253.1.1.

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Northern Australia is biologically diverse and of national and global conservation signicance. Its ancient landscape contains the world’s largest area of savannah ecosystem in good ecological condition and its rivers are largely free-flowing. Agriculture, previously confined largely to open range-land grazing, is set to expand in extent and to focus much more on irrigated cropping and horticulture. Demands on the water resources of the region are thus, inevitably increasing. Reliable information is required to guide and inform development and help plan for a sustainable future for the region which includes healthy rivers that contain diverse fish assemblages. Based on a range of information sources, including the outcomes of recent and extensive new field surveys, this study maps the distribution of the 111 freshwater fishes (excluding elasmobranches) and 42 estuarine vagrants recorded from freshwater habitats of the region. We classify the habitat use and migratory biology of each species. This study provides a comprehensive assessment of the diversity and distribution of fishes of the region within a standardised nomenclatural framework. In addition, we summarise the outcomes of recent phylogeographic and phylogenetic research using molecular technologies to identify where issues of taxonomy may need further scrutiny. The study provides an informed basis for further research on the spatial arrangement of biodiversity and its relationship to environmental factors (e.g. hydrology), conservation planning and phylogentic variation within individual taxa.

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Coombs, J. M., and T. Barkay. "New Findings on Evolution of Metal Homeostasis Genes: Evidence from Comparative Genome Analysis of Bacteria and Archaea." Applied and Environmental Microbiology 71, no. 11 (November 2005): 7083–91. http://dx.doi.org/10.1128/aem.71.11.7083-7091.2005.

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ABSTRACT In order to examine the natural history of metal homeostasis genes in prokaryotes, open reading frames with homology to characterized PIB-type ATPases from the genomes of 188 bacteria and 22 archaea were investigated. Major findings were as follows. First, a high diversity in N-terminal metal binding motifs was observed. These motifs were distributed throughout bacterial and archaeal lineages, suggesting multiple loss and acquisition events. Second, the CopA locus separated into two distinct phylogenetic clusters, CopA1, which contained ATPases with documented Cu(I) influx activity, and CopA2, which contained both efflux and influx transporters and spanned the entire diversity of the bacterial domain, suggesting that CopA2 is the ancestral locus. Finally, phylogentic incongruences between 16S rRNA and PIB-type ATPase gene trees identified at least 14 instances of lateral gene transfer (LGT) that had occurred among diverse microbes. Results from bootstrapped supported nodes indicated that (i) a majority of the transfers occurred among proteobacteria, most likely due to the phylogenetic relatedness of these organisms, and (ii) gram-positive bacteria with low moles percent G+C were often involved in instances of LGT. These results, together with our earlier work on the occurrence of LGT in subsurface bacteria (J. M. Coombs and T. Barkay, Appl. Environ. Microbiol. 70:1698-1707, 2004), indicate that LGT has had a minor role in the evolution of PIB-type ATPases, unlike other genes that specify survival in metal-stressed environments. This study demonstrates how examination of a specific locus across microbial genomes can contribute to the understanding of phenotypes that are critical to the interactions of microbes with their environment.

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Liu, Guo-Qing, Lian Lian, and Wei Wang. "The Molecular Phylogeny of Land Plants: Progress and Future Prospects." Diversity 14, no. 10 (September 21, 2022): 782. http://dx.doi.org/10.3390/d14100782.

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Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas.

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LUO, Kun, Gui-ping DU, Zhi-xiang ZHAO, Bing-yan XIE, and Ding-jun LI. "Phylogentic analysis of typeⅠpolyketide synthase and nonribosomal peptide synthetase genes from Mila Mountain in Tibet plateau." JOURNAL OF HUNAN AGRICULTURAL UNIVERSITY 36, no. 5 (January 19, 2011): 506–11. http://dx.doi.org/10.3724/sp.j.1238.2010.00506.

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Psaroulaki, Anna, Dimosthenis Chochlakis, Vassilios Sandalakis, Iosif Vranakis, Ioannis Ioannou, and Yannis Tselentis. "Phylogentic analysis of Anaplasma ovis strains isolated from sheep and goats using groEL and mps4 genes." Veterinary Microbiology 138, no. 3-4 (September 2009): 394–400. http://dx.doi.org/10.1016/j.vetmic.2009.04.018.

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Yin, Yanqiang, Wei Jiang, Zhe Zhang, Yan Li, Bayaerta Twenke, Mardan Turghan, Weikang Yang, and Bin Liu. "The divergence of small mammals in Xinjiang, China, as revealed by phylogentic analyses of COI and Cytb." Animal Biology 64, no. 2 (2014): 163–76. http://dx.doi.org/10.1163/15707563-00002435.

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Changes in the palaeoenvironment and paleoclimate expedite the process of evolutionary divergence in animals. The evolutionary events of some small mammals distributed in Xinjiang Arid Region remain ambiguous. Thus, it is necessary to predict their evolutionary histories based on divergence estimates. Some museum specimens were involved in this analysis because of sampling limitation for threatened species in the arid region. A related problem is that some mutilated specimens without complete taxonomic data made it difficult to directly analyze species divergence. Here, sequences of cytochrome c oxydase I were used to identify museum specimens and combined with cytochrome b to estimate the recent divergence of extant small mammals constrained with eight fossil calibrations. The results showed that the massive species differentiation emerged during the Middle and Late Miocene periods. We inferred that differentiation of these small mammals might be associated with the retreat of the Tethys Sea from the Tarim Basin around the Eocene-Oligocene boundary and the global climate fluctuations during the Miocene period. Furthermore, the aridification and changes in the Taklimakan and Gurbantunggut Deserts might have driven the diversification of intraspecies and the emergence of cryptic species since the Late Pleistocene.

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C. More, Kamlakar, and Prashant A. Gawande. "Phylogeny of bamboos based on morphological key characters." YMER Digital 21, no. 05 (May 17, 2022): 818–24. http://dx.doi.org/10.37896/ymer21.05/94.

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Exploration of bamboos resources in a sustainable manner needs more emphasis on evaluation of morphological characters-based species discrimination. In a present work, fifty-two various qualitative morphological characters and seven quantitative characters were studied in ten bamboo species. The cluster analysis and principal component revealed highest similarity between Ochlandra travancorica and Ochlandra ebracteata followed by Bambusa nutan, Bambusa oliveriana and Gigantichola rostrata, Ochlandra ebracteata respectively, whereas, Bambusa wamin showing separate evolutionary branching. Conclusion: due to the long and irregular flowering in bamboos, it is essential to adopt the advance phylogentic clustering tools for generation of reliable and taxonomically supporting information for species discrimination, moreover, the time to time morphological characters studies are essential to trace the phenotypic plasticity and adaptability of bamboos with respect to non- predicted changing climatic conditions.

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Stout, Carla, Susana Schonhuth, Richard Mayden, Nicole L. Garrison, and Jonathan W. Armbruster. "Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups." PeerJ 10 (October 10, 2022): e14072. http://dx.doi.org/10.7717/peerj.14072.

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North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).

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Osman, Yehia A., Ahmed Abd Elrazak, Wesam Khater, EL-Shahat Nashy, and Attia Mohamadeen. "Molecular Characterization of a Poly-β-Hydroxybutyrate-Producing Microbacterium Isolate." International Journal of Applied Sciences and Biotechnology 3, no. 2 (June 25, 2015): 143–50. http://dx.doi.org/10.3126/ijasbt.v3i2.12277.

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Bacterial poly-β-hydroxybutyrate (PHB) is a natural, biodegradable polymer, which is accumulated in the cells as an energy reserve materialdue to depletion of nitrogen or phosphorous in the presence of excess carbon source. This polymer is foreseen to possess high industrialpotentiality and excellent alternative to the non-degradable petroleum-based plastics. In this study, we isolated and characterized a localbacterial strain WA81 which accumulated 18mg/L PHB after 72 h growth in mineral salt medium under nitrogen deficiency. The PHB granuleswere detected in the cells using TEM and the genes encode for this polymer were detected by oligonucleotide primers using PCR technology.The 16S rRNA gene nucleotide sequence for this isolate was used to construct a phylogentic tree against all available sequences in the GenBank.The phylogenetic tree data suggested that the closest type strain to the local bacterium is the Microbacterium paraoxydans CF36T and hencewe named it Microbacterium sp. strain WA81. Moreover, the set of enzymes responsible for the PHB biosynthetic pathway and their controllingelements were detected in this local isolate using PCR. The genes encode for the biosynthesis enzymes are phbA (β-ketothiolase), phbB(acetoacetly CoA reductase), phbC (PHB polymerase), while the genes encode for the controlling elements are phbP (phasin), phbZ (PHBdepolymerase). The novelty of this local bacterium lies in its ability to accumulate huge amounts of PHB in its cytoplasm and the presence ofa whole set of genes encode for the PHB biosynthetic and catabolic pathways of this polymer.Int J Appl Sci Biotechnol, Vol 3(2): 143-150 DOI: http://dx.doi.org/10.3126/ijasbt.v3i2.12277

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Aspöck, Ulrike, and Susanne Randolf. "Beaded lacewings – a pictorial identification key to the genera, their biogeographics and a phylogentic analysis (Insecta: Neuroptera: Berothidae)." Deutsche Entomologische Zeitschrift 61, no. 2 (December 2, 2014): 155–72. http://dx.doi.org/10.3897/dez.61.8850.

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PARK, JONG-WOO, JU HEE KIM, AE-RA CHO, YUN-DUK JUNG, PYOUNG JOONG KIM, HYUNG-SEOP KIM, and WONHO YIH. "Phylogentic Position, Pigment Content and Optimal Growth Condition of the Unicellular Hydrogen-Producing Cyanobacterial Strains from Korean Coasts." Sea 20, no. 3 (August 31, 2015): 131–40. http://dx.doi.org/10.7850/jkso.2015.20.3.131.

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Moser, Meinhard M., Heidi Ladurner, Ursula Peintner, and Martin Kirchmair. "Gymnopilus turficola (Agaricales), a new species from sub-arctic palsa mires and its phylogentic relationship based on ITS sequences." Nordic Journal of Botany 21, no. 3 (July 2001): 321–28. http://dx.doi.org/10.1111/j.1756-1051.2001.tb00773.x.

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Gryganskyi, Andrii P., Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, et al. "Phylogenetic and Phylogenomic Definition ofRhizopusSpecies." G3: Genes|Genomes|Genetics 8, no. 6 (April 19, 2018): 2007–18. http://dx.doi.org/10.1534/g3.118.200235.

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Blank, Miriam, Karl Jürss, and Ralf Bastrop. "A mitochondrial multigene approach contributing to the systematics of the brook and river lampreys and the phylogenetic position of Eudontomyzon mariae." Canadian Journal of Fisheries and Aquatic Sciences 65, no. 12 (December 2008): 2780–90. http://dx.doi.org/10.1139/f08-178.

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The evolution of nonparasitic brook lamprey forms and their relationship to the morphological similar parasitic river lampreys are long-standing questions in lamprey research. The present study examines the utility of 11 mitochondrial gene segments (a total of 3800 base pairs) to discriminate the closely related members of the European species pair Lampetra fluviatilis and Lampetra planeri . The intent was to identify fast-evolving genes in the mtDNA that might allow a discrimination of pair members. Therefore, the noncoding regions as the fastest evolving gene segments of animal mtDNA were also included. The results revealed that in all investigated loci, L. fluviatilis and L. planeri were genetically indistinguishable, indicating either a very recent divergence event or ongoing gene flow between both species. The position of the Ukrainian brook lamprey, Eudontomyzon mariae , and the phylogentic relationships within the Lampetrini was inferred from partial cytochrome b by adding available sequences from GenBank to the data set. Eudontomyzon mariae formed a monophyletic cluster with Lampetra aegyptera and the European species pair. A reintegration of E. mariae in the genus Lampetra is therefore recommended.

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Stewart, James Bruce, and Andrew T. Beckenbach. "Insect mitochondrial genomics 2: the complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements." Genome 49, no. 7 (July 1, 2006): 815–24. http://dx.doi.org/10.1139/g06-037.

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Mitochondrial (mt) genome sequences of insects are receiving renewed attention in molecular phylogentic studies, studies of mt-genome rearrangement, and other unusual molecular phenomena, such as translational frameshifting. At present, the basal neopteran lineages are poorly represented by mt-genome sequences. Complete mt-genome sequences are available in the databases for only the Orthoptera and Blatteria; 9 orders are unrepresented. Here, we present the complete mt-genome sequence of a giant stonefly, Pteronarcys princeps (Plecoptera; Pteronarcyidae). The 16 004 bp genome is typical in its genome content, gene organisation, and nucleotide composition. The genome shows evidence of strand-specific mutational biases, correlated with the time between the initiation of leading and the initiation of lagging strand replication. Comparisons with other insects reveal that this trend is seen in other insect groups, but is not universally consistent among sampled mt-genomes. The A+T region is compared with that of 2 stoneflies in the family Peltoperlidae. Conserved stem-loop structures and sequence blocks are noted between these distantly related families.Key words: mitochondrial genomics, directional mutation pressure, A+T-rich region, Plecoptera, stonefly.

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Bhowmick*, Rakesh, Sushma Tiwari, Vandana Rai, and Nagendra Kumar Singh. "Expression and co-location of prohibitin genes in salt-tolerance QTLs in rice (Oryza sativa)." Indian Journal of Agricultural Sciences 90, no. 3 (June 22, 2020): 610–15. http://dx.doi.org/10.56093/ijas.v90i3.101498.

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Prohibitin proteins are involved in diverse biological functions including cell cycle regulation, mitochondrial activity, apoptosis, hormonal signalling and so on. Prohibitin family genes are conserved across the life taxa in both eukaryotes and prokaryotes. An experiment was conducted at ICAR-National Institute for Plant Biotechnology, New Delhi (2018-19) in which we identified 19 prohibitin genes present on 10 different chromosomes of the ‘Nipponbare’ reference rice (Oryza sativa L.) genome and analysed their possible role in salt tolerance, as they are known to regulate ion channels in plant and animal cells. A protein sequence based neighbour joining phylogentic tree clustered these 19 genes into three groups. Digital gene expression analysis revealed the highest level of expression of the prohibitin genes in anthers and radicle tips. Nine of these prohibitin genes were co-located in the salt-tolerance QTL regions of the rice genome, three of which (LOC_Os01g40560, LOC_Os03g60000 and LOC_Os08g15600) were significantly upregulated in response to salt stress in the tolerant genotype. These prohibitin genes are strong candidates for improving salt-tolerance in rice through marker-assited rice breeding after validation.

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Dhawan, Sunita S., Anand Mishra, Pankhuri Gupta, J. R. Bahl, and R. P. Bansal. "Phylogentic relationship of cold tolerant Mentha arvensis variety ‘CIM Kranti’ with some released varieties as assessed through physiological and molecular analysis." Journal of Applied Research on Medicinal and Aromatic Plants 10 (September 2018): 67–74. http://dx.doi.org/10.1016/j.jarmap.2018.06.004.

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Singh, B., L. C. Chaudhary, Neeta Agarwal, and D. N. Kamra. "Phenotypic and phylogentic characterisation of tannin degrading/tolerating bacterial isolates from the rumen of goats fed on pakar (Ficus infectoria)leaves." Journal of Applied Animal Research 39, no. 2 (June 2011): 120–24. http://dx.doi.org/10.1080/09712119.2011.558682.

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Yoshida, Ruriko, Lillian Paul, and Peter Nesbitt. "Stochastic Safety Radius on UPGMA." Algorithms 15, no. 12 (December 18, 2022): 483. http://dx.doi.org/10.3390/a15120483.

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Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree from a distance matrix computed from an alignment of sequences. Since we use equidistant trees as gene trees for phylogenomic analyses under the multi-species coalescent model and since an input distance matrix computed from an alignment of each gene in a genome is estimated via the maximum likelihood estimators, it is important to conduct a robust analysis on UPGMA. Stochastic safety radius, introduced by Steel and Gascuel, provides a lower bound for the probability that a phylogenetic tree reconstruction method returns the true tree topology from a given distance matrix. In this article, we compute the stochastic safety radius of UPGMA for a phylogenetic tree with n leaves. Computational experiments show an improved gap between empirical probabilities estimated from random samples and the true tree topology from UPGMA, increasing confidence in phylogenic results.

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Hu, Xi Xia, An Chun Cheng, and Ming Shu Wang. "Characterization of Codon Usage Bias in UL13 Gene of the Duck Plague Virus." Advanced Materials Research 393-395 (November 2011): 641–50. http://dx.doi.org/10.4028/www.scientific.net/amr.393-395.641.

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A comprehensive analysis of codon usage bias of DPV UL13 gene (GenBank Accession No. EU195098) was performed to provide a basis for understanding the relevant mechanism for its biased usage of synonymous codons and for selecting suitable expression systems to improve the expression of UL13 genes. Our study showed that codon usage bias of DPV UL13 gene strongly prefered to the synonymous with A and T at the third codon position. And ENC value and GC3s contents of the codon usage bias of UL13 gene in DPV were significantly different compared with those in other 21 reference herpesviruses. The phylogentic analysis about the putative protein of DPV UL13 and the 21 reference herpesviruses revealed that DPV was evolutionarily closer to the AnHV-1. In addition, the codon usage bias of DPV UL13 gene was compared with those of E. coli, yeast and human. There are 23 codons showing distinct usage differences between DPV and E. coli, 12 codons between DPV and yeast, 21 codons between DPV and human. Therefore, the yeast expression system is more appropriate for heterologous expression of the DPV UL13 gene.

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Budd, Graham E. "Arthropods from North Greenland: exceptional data in the ‘Cambrian explosion’ debate." Paleontological Society Special Publications 6 (1992): 44. http://dx.doi.org/10.1017/s2475262200006043.

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'Sirius Passet’ fauna arthropods from the Lower Cambrian Buen Formation of North Greenland form the major component of this exceptionally preserved biota. Early mineralisation of body cavities led to internal anatomy being preserved more readily than external structures such as limbs. Musculature and gut are known in three dimensional form. Many of the taxa present are more easily compared to extant arthropods than to flattened fossil material such as from the Burgess Shale.The most common arthropod is represented by some 1600 specimens. Although widely differing in preservational style, these specimens may be reconciled to provide a coherent model of the three-dimensional anatomy of the arthropod. The affinities of this arthropod lie with the ‘Cheliceromorph’ rather than the Crustacean biramous-limbed arthropods, and may represent a fairly advanced lineage within the clade.Recent discussions of the patterns produced by the early metazoan radiations have concentrated on data available from the Burgess Shale. The continuing discovery and description of other Cambrian lagerstätten such as from North Greenland and Chengjiang has highlighted the degree to which the Burgess Shale fauna should be considered to be an aliquot taken from the foment of the ‘Cambrian Explosion’. The discovery of more taxa is tending to flesh out the bare bones of the Burgess fauna. Conclusions about phylogentic patterns drawn from the Burgess Shale alone may thus be premature.Body patterning in the arthropods, and the validity of the ‘Bauplan’ concept may be investigated by consideration of the actual mechanisms available for profound morphological change. One promising route is provided by the ‘homeotic’ and other hierarchically arranged developmental genes. When the mode of action of these genes is considered in conjunction with phylogenetic methods, it may prove possible to assess evolutionary pathways in terms of the feasibility of the morphological changes required by them rather than relying on what seems inherently reasonable or on marginal advantages in parsimony. Exceptionally preserved biotas also contain the evidence for the evolution of the developmental mechanisms themselves.

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Serbin, Giulia Melill, Rafael Barbosa Pinto, Raquel Moura Machado, Vidal de Freitas Mansano, Ana Maria Goulart de Azevedo Tozzi, and Eliana Regina Forni-Martins. "Cytogenetics studies in Hymenaea Clade (Leguminosae, Detarioideae)." Semina: Ciências Biológicas e da Saúde 38, no. 1supl (February 16, 2018): 142. http://dx.doi.org/10.5433/1679-0367.2017v38n1suplp142.

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The genera Hymenaea L., Guibourtia Benn. and Peltogyne Vog. belong to the Detarioideae subfamily (Leguminosae) and they are supported by phylogenetic studies as a clade which we call here the Hymenaea clade. Representatives of this clade are mainly recognized by their resin production capability and the bifoliolate leaves. Hymenaea and Guibourtia currently comprise about 23 and 14 species, distributed mainly in the Neotropical region and the African continent respectively. Peltogyne comprises ca. 24 species, all of them restricted to the New World. Even with this biogeographical pattern and an evident difficulty in the delimitation of taxa, especially at an infrageneric level, the knowledge on cytological characteristics for the group is scarce and restricted only to chromosome number. Thus, this work aims to provide karyotype data for taxa from the Hymenaea clade, helping further taxonomic and evolutionary studies that are being developed. After the cataloging of the data available in the literature we observed that apparently, the predominant chromosome number in the Detarioideae subfamily is 2n=24 but, within the Hymenaea clade this information is available only for 11 species of Hymenaea and two species of Guibourtia. Other cytogenetic approaches as CMA/DAPI and FISH analyses have never been applied for the clade. The seeds of 11 taxa (three Guibourtia, seven Hymenaea and one Peltogyne) were collected in several regions of Brazil. We observed some variations in numbers of chromosome, CMA+ bands and rDNA sites. Representatives of the Hymenaea clade presented predominantly 2n=24 (except G. coleosperma - 2n=48), two pairs of CMA+ bands (except G. coleosperma and G. conjugata with one pair, and H. altissima Ducke with three pairs), one pair of rDNA 5S (except P. pauciflora, with two pairs), and one pair of rDNA 45S. Despite the apparent karyotype stability among taxa from the three genera, some finds support important ideas as the possible non-monophyly of Guibourtia, since species as G. coleosperma and G. conjugata belong to different lineages as pointed by ongoing phylogentic studies. More taxa are being investigated to improve the support for clades and for taxonomic decisions.

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Zhang, Yanyun, Liuwang Nie, Yuqing Huang, Youguang Pu, and Li Zhang. "The mitochondrial DNA control region comparison studies of four hinged turtles and its phylogentic significance of the genusCuora sensu lato (Testudinata: Geoemydidae)." Genes & Genomics 31, no. 5 (October 2009): 349–59. http://dx.doi.org/10.1007/bf03191253.

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Vinh, Lê Sỹ. "Phylogenetic and Phylogenomic Analyses for Large Datasets." Journal of Research and Development on Information and Communication Technology 2019, no. 2 (December 31, 2019): 84–92. http://dx.doi.org/10.32913/mic-ict-research.v2019.n2.898.

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The phylogenetic tree is a main tool to study the evolutionary relationships among species. Computational methods for building phylogenetic trees from gene/protein sequences have been developed for decades and come of age. Efficient approaches, including distance-based methods, maximum likelihood methods, or classical maximum parsimony methods, are now able to analyze datasets with thousands of sequences. The advanced sequencing technologies have resulted in a huge amount of data including whole genomes. A number of methods have been proposed to analyze the wholegenome datasets, however, numerous challenges need to be addressed and solved to translate phylogenomic inferences into practices. In this paper, we will analyze widely-used methods to construct large phylogenetic trees, and available methods to build phylogenomic trees from whole-genome datasets. We will also give recommendations for best practices when performing phylogenetic and phylogenomic analyses. The paper will enable researchers to comprehend the state-ofthe-art methods and available software to efficiently study the evolutionary relationships among species from large datasets.

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Binder, Manfred, Alfredo Justo, Robert Riley, Asaf Salamov, Francesc Lopez-Giraldez, Elisabet Sjökvist, Alex Copeland, et al. "Phylogenetic and phylogenomic overview of the Polyporales." Mycologia 105, no. 6 (November 1, 2013): 1350–73. http://dx.doi.org/10.3852/13-003.

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Journal articles on the topic 'Phylogentic'

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