233,937 results match your criteria phylogenetic tree


First mitogenome of subfamily Langiinae (Lepidoptera: Sphingidae) with its phylogenetic implications.

Gene 2021 Apr 18:145667. Epub 2021 Apr 18.

Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, China. Electronic address:

To date, a relatively complete classification of Sphingidae (Lepidoptera) has been generated, but the phylogeny of the family remains need to be fully resolved. Some phylogenetic relationships within Sphingidae still remains uncertain, especially the taxonomic status of the subfamily Langiinae and its sole included genus and species, Langia zenzeroides. To begin to address this problem, we generated nine new complete mitochondrial genomes, including that of Langia, and together with that of Theretra oldenlandiae from our previous study and 25 other Sphingidae mitogenomes downloaded from GenBank, analyzed the phylogenetic relationships of Sphingidae and investigated the mitogenomic differences among members of the Langiinae, Sphinginae, Smerinthinae and Macroglossinae. Read More

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Reclassification of as comb. nov. based on whole genome analysis.

Int J Syst Evol Microbiol 2021 Apr;71(4)

Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany.

The genera (family '') and (family ) are close relatives within the phylum . Members of these genera are strictly anaerobic, non-spore-forming and short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest that splits into a polyphyletic clade. Read More

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Cloning, Expression, Characterization, and Tissue Distribution of Cystatin C from Silver Carp ().

J Agric Food Chem 2021 Apr 21. Epub 2021 Apr 21.

Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki 00014, Finland.

Cystatins are proteins, which inhibit cysteine proteases, such as papain. In this study, the 336-bp gene (family II, Hm) of silver carp () was cloned and expressed in BL21 (DE3). Hm encodes the mature peptide of cystatin C (HmCystatin C), with 111 amino acids. Read More

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A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades.

Antonie Van Leeuwenhoek 2021 Apr 21. Epub 2021 Apr 21.

Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada.

The order Legionellales contains several clinically important microorganisms. Although members of this order are well-studied for their pathogenesis, there is a paucity of reliable characteristics distinguishing members of this order and its constituent genera. Genome sequences are now available for 73 Legionellales species encompassing ≈90% of known members from different genera. Read More

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Mining of the water hyssop (Bacopa monnieri) transcriptome reveals genome sequences of two putative novel rhabdoviruses and a solendovirus.

Arch Virol 2021 Apr 21. Epub 2021 Apr 21.

Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.

The genomes of three putative novel viruses, tentatively named "Bacopa monnieri virus 1" (BmV1), "Bacopa monnieri virus 2" (BmV2), and "Bacopa monnieri virus 3" (BmV3) were identified in the transcriptome dataset of a medicinally important herb - water hyssop (Bacopa monnieri (L.) Wettst.). Read More

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Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses.

J Helminthol 2021 Apr 21;95:e23. Epub 2021 Apr 21.

Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Street, 1113Sofia, Bulgaria.

The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1-D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. Read More

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Does the Dzungarian racerunner ( Orlova, Poyarkov, Chirikova, Nazarov, Munkhbaatar, Munkhbayar & Terbish, 2017) occur in China? Species delimitation and identification with DNA barcoding and morphometric analyses.

Zool Res 2021 May;42(3):287-293

Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.E-mail:

The species complex is a viviparous group in the genus , and a well-known representative of taxonomically complicated taxa. Within this complex, a new species - (Orlova et al., 2017) - has been described recently from western Mongolia and eastern Kazakhstan, with an apparent distribution gap in northwestern China. Read More

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Endocrine Influence on Cardiac Metabolism in Development and Regeneration.

Endocrinology 2021 Apr 21. Epub 2021 Apr 21.

Cardiovascular Research Institute & Department of Physiology, University of California San Francisco, San Francisco, CA, USA.

Mammalian cardiomyocytes mostly utilize oxidation of fatty acids to generate ATP. The fetal heart, in stark contrast, mostly uses anaerobic glycolysis. During perinatal development, thyroid hormone drives extensive metabolic remodeling in the heart for adaptation to extrauterine life. Read More

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Phylogeny, function and ecology in the deep evolutionary history of the mammalian forelimb.

Proc Biol Sci 2021 Apr 21;288(1949):20210494. Epub 2021 Apr 21.

Negaunee Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA.

Mammals are the only living members of the larger clade Synapsida, which has a fossil record spanning 320 Ma. Despite the fact that much of the ecological diversity of mammals has been considered in the light of limb morphology, the ecological comparability of mammals to their fossil forerunners has not been critically assessed. Because of the wide use of limb morphology in testing ecomorphological hypothesis about extinct tetrapods, we sought: (i) to estimate when in synapsid history, modern mammals become analogues for predicting fossil ecologies; (ii) to document examples of ecomorphological convergence; and (iii) to compare the functional solutions of distinct synapsid radiations. Read More

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Environmental genomics of Late Pleistocene black bears and giant short-faced bears.

Curr Biol 2021 Apr 16. Epub 2021 Apr 16.

Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany. Electronic address:

Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time, by allowing for parallel sequencing of DNA from all trophic levels. However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species, the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies. This is in contrast to data from fossils where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable. Read More

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Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning.

PLoS Pathog 2021 Apr 20;17(4):e1009149. Epub 2021 Apr 20.

Department of Health Data Science, University of Liverpool, Brownlow Street, Liverpool, United Kingdom.

The COVID-19 pandemic has demonstrated the serious potential for novel zoonotic coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the causative virus, SARS-CoV-2, remains unknown, a notoriously challenging task for emerging disease investigations. Coevolution with hosts leads to specific evolutionary signatures within viral genomes that can inform likely animal origins. Read More

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De Novo, Divergence, and Mixed Origin Contribute to the Emergence of Orphan Genes in Pristionchus Nematodes.

G3 (Bethesda) 2019 Jul;9(7):2277-2286

Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany.

Homology is a fundamental concept in comparative biology. It is extensively used at the sequence level to make phylogenetic hypotheses and functional inferences. Nonetheless, the majority of eukaryotic genomes contain large numbers of orphan genes lacking homologs in other taxa. Read More

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Identification, methylation profiling, and expression analysis of stress-responsive cytochrome P450 genes in rice under abiotic and phytohormones stresses.

GM Crops Food 2021 Apr 20:1-13. Epub 2021 Apr 20.

College of Economics and Management, Kunming University, Kunming China.

The cytochrome P450 (CYP) is a large and complex eukaryotic gene superfamily with enzymatic activities involved in several physiological and regulatory processes. As an objective, an genome-wide DNA methylation (5mC) analysis was performed in rice ( cv. Zhonghua11), and the epigenetic role of CYPs in two abiotic stresses was observed. Read More

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Primate phageomes are structured by superhost phylogeny and environment.

Proc Natl Acad Sci U S A 2021 Apr;118(15)

Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353 Berlin, Germany;

Humans harbor diverse communities of microorganisms, the majority of which are bacteria in the gastrointestinal tract. These gut bacterial communities in turn host diverse bacteriophage (hereafter phage) communities that have a major impact on their structure, function, and, ultimately, human health. However, the evolutionary and ecological origins of these human-associated phage communities are poorly understood. Read More

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Molecular markers in plant ecology.

Authors:
Konrad Bachmann

New Phytol 1994 Mar;126(3):403-418

Hugo de Vries Laboratory, University of Amsterdam, Kruislaan 318, NL-1098 SM Amsterdam, The Netherlands.

Various methods from molecular biology reveal sequence polymorphisms in organelle and nuclear DNA that can be used as highly informative markers for the structure and dynamics of genomes at the level of populations and individuals. Molecular markers that can be determined without regard to the phenotype permit an unbiased comparison of the adaptation of organisms to their environment, its genetic basis and its effect on evolution. Several marker types used in ecological research and their uses and limitations arc briefly discussed. Read More

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Comparison of hydraulic architecture of woody plants of differing phylogeny and growth form with special reference to freestanding and hemi-epiphytic Ficus species from Panama.

New Phytol 1995 Jan;129(1):125-134

Smithsonian Tropical Research Institute, P.O. Box 2072, Balboa, Republic of Panama.

Hydraulic parameters were measured in seven species of Fiats (three free-standing and four hemi-epiphytic) on stem segments of 3-35 mm in wood diameter. Parameters measured included K (water flux per unit pressure gradient), K (leaf specific conductivity =K per unit leaf area), K (specific conductivity =H per unit wood cross section), and H (Huber value = wood cross section per unit leaf area). The hemi-epiphytes tended to have less conductive stems per unit leaf area (lower K and invested less wood cross section per unit leaf area (lower H ) than free-standing species. Read More

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January 1995

The ultrastructure of the placenta in Sphagnum.

New Phytol 1989 Feb;111(2):197-201

Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee 37614, USA.

The placenta of two Sphagnum species was examined by electron microscopy. In contrast to all mosses so far investigated, neither sporophyte nor gametophyte placental cells of Sphagnum develop wall ingrowths. The sporophyte cells are highly vacuolate and the gametophyte cells close to them degenerate to produce a system of spaces filled with mucilage. Read More

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February 1989

Evolution and host specificity in the ectomycorrhizal genus Leccinum.

New Phytol 2004 Jul;163(1):201-215

National Herbarium of the Netherlands, University of Leiden Branch, PO Box 9514, NL-2300 RA Leiden, The Netherlands.

•  Species of the ectomycorrhizal genus Leccinum are generally considered to be host specialists. We determined the phylogenetic relationships between species of Leccinum from Europe and North America based on second internal transcribed spacer (ITS2) and glyceraldehyde 3-phosphate dehydrogenase (Gapdh). •  We plotted host associations onto the phylogenies using maximum likelihood and parsimony approaches. Read More

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Genetic diversity of Pisolithus in New Zealand indicates multiple long-distance dispersal from Australia.

New Phytol 2003 Dec 6;160(3):569-579. Epub 2003 Nov 6.

UMR INRA/UHP 1136 1aM, Centre INRA de Nancy, F-54280, France.

•  Pisolithus is a common ectomycorrhizal (EcM) associate of prostrate kanuka Kunzea ericoides var. microflora (Myrtaceae) in New Zealand geothermal areas. Here, we report the genetic diversity and phylogeny of Pisolithus and interpret the results in relation to the origin of this fungus in New Zealand. Read More

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December 2003

Calmodulins and related potential calcium sensors of Arabidopsis.

New Phytol 2003 Sep;159(3):585-598

Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005-1892, USA.

•   Calcium (Ca ) signaling is thought to orchestrate responses to cellular stimuli. The efficacy of Ca signaling requires mediation by Ca -binding proteins. •   The determination of the Arabidopsis genome sequence enables the identification of genes encoding potential Ca sensors. Read More

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September 2003

Evolutionary dynamics of nickel hyperaccumulation in Alyssum revealed by its nrDNA analysis.

New Phytol 2003 Sep;159(3):691-699

Dipartimento di Biologia Vegetale, Laboratorio di Fisiologia Vegetale, Università di Firenze, via Micheli 1, I-50121 Firenze, Italy.

•   Molecular phylogeny based on ribosomal internal transcribed spacer (ITS) sequences was studied to investigate the phyletic relationships among some nickel (Ni)-hyperaccumulating and nonhyperaccumulating species of the genus Alyssum in relation to their geographic distribution and Ni-hyperaccumulating phenotype. •   Thirty-seven samples belonging to 32 taxa were analysed by sequencing the polymerase chain reaction-amplified ITS region and performing neighbor joining, maximum parsimony and maximum likelihood phylogenetic analyses. •   The ITS region in the sampled species varied from 221 to 307 bp of ITS1 and from 194 to 251 bp of ITS2. Read More

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September 2003

Diversity in the distribution of polysaccharide and glycoprotein epitopes in the cell walls of bryophytes: new evidence for the multiple evolution of water-conducting cells.

New Phytol 2002 Dec;156(3):491-508

School of Biological Sciences, Queen Mary University of London, Mile End Road, London E3 4NS, UK.

•   Although histologically much simpler than higher plants, bryophytes display a considerable degree of tissue differentiation, notably in those groups that possess an internal system of specialized water-conducting cells (WCCs). Here, using a battery of monoclonal antibodies, we examined the distribution of cell wall polysaccharide and glycoprotein carbohydrate epitopes in the gametophyte of four hepatics and eight mosses, with special reference to water-conducting cells. •   CCRC-M7, an antibody against an arabinogalactan epitope, gave a highly consistent and generally specific labelling of WCCs; more variable results were obtained with other antibodies. Read More

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December 2002

Suillus bovinus glutamine synthetase gene organization, transcription and enzyme activities in the Scots pine mycorrhizosphere developed on forest humus.

New Phytol 2004 Nov;164(2):389-399

Department of Bio- and Environmental Sciences, General Microbiology, PO Box 56 (Viikinkaari 9), FI-00014 University of Helsinki, Finland.

•  Glutamine synthetase (GS) expression and activity is of central importance for cellular ammonium assimilation and recycling. Thus, a full characterization of this enzyme at the molecular level is of critical importance for a better understanding of nitrogen (N) assimilation in the mycorrhizal symbiosis. •  Genomic and cDNA libraries of Suillus bovinus were constructed to isolate the GS gene, glnA, and corresponding cDNAs. Read More

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November 2004

High functional diversity within species of arbuscular mycorrhizal fungi.

New Phytol 2004 Nov;164(2):357-364

Plant Research Department, Risø National Laboratory, PO Box 49, DK-4000 Roskilde, Denmark.

•  Species of arbuscular mycorrhizal fungi (AMF) differ markedly in their improvement of plant nutrition and health. However, it is not yet possible to relate the diversity of an AMF community to its functional properties due to the lack of information on the functional diversity at each taxonomic level. This study investigates the inter- and intraspecific functional diversity of four Glomus species in relation to a phylogenetic analysis of large ribosomal subunit (LSU) sequences. Read More

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November 2004

On the unreliability of published DNA sequences.

New Phytol 2003 Oct;160(1):43-48

School of Biological and Chemical Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.

•  Here, the reliability of published fungal nucleic acid sequences is tested by the critical re-evaluation of 206 named sequences obtained from public-access databases. •  Sequences from the ribosomal RNA (rRNA) gene cluster were examined as these are commonly used to establish fungal phylogeny and evolution, and are also increasingly employed in the identification of fungi from nonculture based studies. •  Fifty-one rRNA internal transcribed spacer (ITS) sequences were obtained for species of Amanita, 55 ITS sequences were obtained for species of Phoma and 100 rRNA small subunit sequences were obtained from representative genera of the order Helotiales. Read More

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October 2003

Molecular diversity of arbuscular mycorrhizal fungi in Prunus africana, an endangered medicinal tree species in dry Afromontane forests of Ethiopia.

New Phytol 2004 Feb 25;161(2):517-528. Epub 2003 Nov 25.

Universität Tübingen, Botanisches Institut, Spezielle Botanik & Mykologie, Auf der Morgenstelle 1, D-72076, Tübingen, Germany.

•  The molecular diversity of arbuscular mycorrhizal (AM) fungi colonizing roots of Prunus africana and of AM fungal spores obtained from baiting cultures of indigenous soils from two dry afromontane forests of Ethiopia was investigated. •  The internal transcribed spacer (ITS) rDNA region from colonized roots and single spores of three AM fungal spore types was amplified, cloned and sequenced using AM fungal specific primers. •  Phylogenetic analysis using the 5. Read More

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February 2004

Occurrence of N-acetylhexosaminidase-encoding genes in ectomycorrhizal basidiomycetes.

New Phytol 2004 Oct;164(1):193-199

Department of Forest Mycology and Pathology, SLU, Box 7026, SE-750 07 Uppsala, Sweden.

•  The genetic potential of ectomycorrhizal fungi to produce N-acetylhexosaminidases was investigated here. N-acetylhexosaminidases are enzymes that cleave monosaccharides from oligomers of N-acetylhexosamines and play an important role in the degradation of chitin. •  Degenerate PCR-primers were designed against genes coding for N-acetylhexosaminidases in basidiomycetes. Read More

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October 2004

Closely related MADS-box genes in club moss (Lycopodium) show broad expression patterns and are structurally similar to, but phylogenetically distinct from, typical seed plant MADS-box genes.

New Phytol 2002 May;154(2):439-450

Evolutionary Biology Centre, Department of Physiological Botany, Uppsala University, Villavägen 6, S-752 36 Uppsala, Sweden; Current address: Institut für Spezielle Zoologie und Evolutionsbiolog mit Phyletischem Museum, D-07743 Jena, Germany.

•  The relation between the duplication history of the MADS-box gene family of transcription factors and the evolution of plant development is investigated here. The lycopsids, for example the club mosses, constitute the sister group of all other vascular plants, and are therefore interesting from this perspective. •  PCR-based methods were used to isolate MADS-box genes from the club moss, Lycopodium annotinum. Read More

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Coevolution of roots and mycorrhizas of land plants.

Authors:
Mark C Brundrett

New Phytol 2002 May;154(2):275-304

Soil Science and Plant Nutrition, Faculty of Natural & Agricultural Sciences, The University of Western Australia, Nedlands WA 6097, Australia; Postal address: Kings Park and Botanic Garden, Botanic Gardens & Parks Authority, West Perth, 6005, Western Australia.

Here, the coevolution of mycorrhizal fungi and roots is assessed in the light of evidence now available, from palaeobotanical and morphological studies and the analysis of DNA-based phylogenies. The first bryophyte-like land plants, in the early Devonian (400 million years ago), had endophytic associations resembling vesicular-arbuscular mycorrhizas (VAM) even before roots evolved. Mycorrhizal evolution would have progressed from endophytic hyphae towards balanced associations where partners were interdependent due to the exchange of limiting energy and nutrient resources. Read More

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Nuclear ribosomal sequence analysis of Oidiodendron: towards a redefinition of ecologically relevant species.

New Phytol 2001 Mar;149(3):565-576

Dipartimento di Biologia Vegetale, Viale Mattioli 25, 10125 Torino, Italy.

• Nuclear ribosomal sequence analysis was performed to investigate delimitation of common Oidiodendron species comprising endomycorrhizal symbionts and close associates of ectomycorrhizal plants. • Neighbour-joining, maximum likelihood and parsimony analyses were used to compare 35 ribosomal DNA (internal transcribed spacer (ITS) and 5.8S) sequences (including sequences available in databases) from 15 putative species. Read More

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