phylogenetics Concept

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research area of

• Anglin, Noelle, Leader for Conserving Biodiversity for The Future So6, CIP, CIP
• Cenci, Alberto, Associate Scientist, The Alliance of Bioversity International and CIAT, The Alliance of Bioversity and CIAT
• Coyne, Danny, Soil Health Scientist, IITA, IITA
• Cuellar, Wilmer, Project Leader, The Alliance of Bioversity International and CIAT, The Alliance of Bioversity and CIAT
• Debouck, Daniel, Visiting Researcher, The Alliance of Bioversity International and CIAT, The Alliance of Bioversity and CIAT
• Dionora, Jacqueline, Senior Associate Scientist, IRRI, IRRI
• Ellis, David, CIP, CIP
• Fuentes, Segundo, Senior Research Associate, CIP, CIP
• Hanotte, Olivier, Principal Scientist - Quantitative Geneticist, ILRI, ILRI
• Harrison, Rhett, Tropical forest ecologist and conservation biologist, ICRAF, ICRAF
• Jianlin, Han, Senior Scientist - Population Geneticist, ILRI, ILRI
• Kemp, Steve, Program Leader, Livestock Genetics, ILRI, ILRI
• Kreuze, Jan, Leader, Crop and Systems Sciences Division, CIP, CIP
• Kumar, Lava, Head of Germplasm Health Unit/Virologist, IITA, ICRISAT
• McNally, Kenneth, Senior Scientist II, IRRI, IRRI
• Mortimer, Peter, Soil Ecophysiology Specialist, ICRAF, ICRAF
• Mwacharo, Joram, ICARDA, ICARDA
• Mwanga, Robert, Consultant, CIP, CIP
• Oliva, Ricardo Francisco, Scientist II, IRRI, CIP
• Quick, William Paul, Principal Scientist, IRRI, IRRI
• Rossel, Genoveva, Curator, CIP, CIP
• Rouard, Mathieu, Senior Scientist, Bioinformatics, The Alliance of Bioversity International and CIAT, The Alliance of Bioversity and CIAT
• SINGH, Abhay Kumar, Field Research Technician, CIMMYT, CIMMYT
• Tripathi, Leena, Plant Biotechnologist, IITA, IITA
• Vera Cruz, Casiana, IRRI
• Xu, Jianchu, Regional Coordinator-East and Central Asia, ICRAF, ICRAF
• Yazbek, Mariana, Genebank Manager - Scientist, ICARDA, ICARDA

subject area of

• A Natural Language Processing Pipeline to Extract Phenotypic Data from Formal Taxonomic Descriptions with a Focus on Flagellate Plants.
• A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds
• A new record of Ganoderma tropicum (Basidiomycota, Polyporales) for Thailand and first assessment of optimum conditions for mycelia production
• A taxonomic monograph of Ipomoea integrated across phylogenetic scales.
• Adaptive evolution of Mediterranean pines
• Alternative oxidase (AOX) genes of African trypanosomes: phylogeny and evolution of AOX and plastid terminal oxidase families.
• An analysis of interspecific hybrids and phylogenetic implications inCucumis (Cucurbitaceae)
• An overview of evolution in plant 5S DNA
• Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation
• Aquapteridospora lignicola gen. et sp. nov., a New Hyphomycetous Taxon (Sordariomycetes) from Wood Submerged in a Freshwater Stream
• Biochemical and molecular tools reveal two diverse Xanthomonas groups in bananas.
• CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea
• COMPLETE GENOMIC SEQUENCE OF VIRULENT PIGEON PARAMYXOVIRUS IN LAUGHING DOVES (STREPTOPELIA SENEGALENSIS) IN KENYA
• Cloning and characterization of a putative GS3 ortholog involved in maize kernel development
• Cloning and phylogenetic analysis of polyphenol oxidase genes in common wheat and related species
• Combining conservative and variable markers to infer the evolutionary history of Prunus subgen. Amygdalus s.l. under domestication
• Comparative analysis of the complete genome sequences of Kenyan African swine fever virus isolates within p72 genotypes IX and X.
• Comparative genomic analysis and phylogenetic position of Theileria equi
• Complete genome sequence of bean leaf crumple virus, a novel begomovirus infecting common bean in Colombia.
• Complete plastome assemblies from a panel of 13 diverse potato taxa.
• Conservation and variability of sequence-tagged microsatellite sites (STMSs) from chickpea (Cicer aerietinum L.) within the genus Cicer
• Coryneum heveanum sp. nov. (Coryneaceae, Diaporthales) on twigs of Para rubber in Thailand
• Cryptic Diversity Hidden within the Leafminer Genus Liriomyza (Diptera: Agromyzidae)
• Deinbollia mosaic virus: a novel begomovirus infecting the sapindaceous weed Deinbollia borbonica in Kenya and Tanzania.
• Diaporthe diversity and pathogenicity revealed from a broad survey of grapevine diseases in europe
• Diatrypella tectonae and Peroneutypa mackenziei spp. nov. (Diatrypaceae) from northern Thailand
• Discordances between morphological systematics and molecular taxonomy in the stem line of equids: A review of the case of taxonomy of genus Equus
• Distinct cavemoviruses interact synergistically with sweet potato chlorotic stunt virus (genus Crinivirus) in cultivated sweet potato
• Diversity of aflatoxin-producing fungi and their impact on food safety in sub-Saharan Africa
• Dominant Allele Phylogeny and Constitutive Subgenome Haplotype Inference in Bananas Using Mitochondrial and Nuclear Markers.
• Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution.
• Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes.
• Epitypification of Broomella vitalbae and Introduction of a Novel Species of Hyalotiella
• Epitypification of Two Bambusicolous Fungi from Thailand
• Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae).
• Evolution of GOLDEN2 - LIKE gene function in C 3 and C 4 plants
• Evolution of plant genome architecture
• Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification
• Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)
• Extensive polymorphism of Ra86 genes in field populations of Rhipicephalus appendiculatus from Kenya.
• First Report of a 16SrIII-L Phytoplasma Associated with Frogskin Disease in Cassava (Manihot esculenta Crantz) in Brazil
• Genetic Diversity and Origin of Gansu Indigenous Sheep Breeds Determined by Mitochondrial DNA D-loop Sequence
• Genetic Diversity and Phylogeny Analysis of Anabaena-azollae Based On Rflps Detected in Azolla-anabaena Azollae Dna Complexes Using Nif Gene Probes
• Genetic Diversity and Phylogeny Analysis of Azolla Based On Dna Amplification By Arbitrary Primers
• Genetic Profiling of Aspergillus Isolates with Varying Aflatoxin Production Potential from Different Maize-Growing Regions of Kenya.
• Genetic divergence of Chikungunya virus plaque variants from the Comoros Island (2005).
• Genetic diversity and origin of timopheevi wheat inferred by chloroplast DNA fingerprinting
• Genetic diversity and phylogenetic relationships among the annual Cicer species as revealed by isozyme polymorphism
• Genetic diversity of Bursaphelenchus cocophilus in South America
• Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection
• Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement.
• Genome sequencing data for wild and cultivated bananas, plantains and abacá.
• Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis
• Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
• Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench)
• Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
• Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria.
• Genomic evidence of intraspecific recombination in sugarcane mosaic virus.
• Geographical variation of gene diversity of Pinus pinaster Ait. in the Iberian Peninsula
• Global phylogenetic relationships, population structure and gene flow estimation of Trialeurodes vaporariorum (Greenhouse whitefly).
• Global versus Chinese perspectives on the phylogeny of the N-fixing clade
• Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria
• Glycosyltransferase Family 61 in Liliopsida (Monocot): The Story of a Gene Family Expansion.
• Greatly reduced phylogenetic structure in the cultivated potato clade (Solanum section Petota pro parte).
• Horizontal gene transfer from a flowering plant to the insular pine Pinus canariensis (Chr. Sm. Ex DC in Buch).
• ICTV Virus Taxonomy Profile: Potyviridae.
• Identification of ERF genes in peanuts and functional analysis of AhERF008 and AhERF019 in abiotic stress response
• Inhabiting plant roots, nematodes, and truffles-Polyphilus, a new helotialean genus with two globally distributed species.
• Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes.
• Isolation and Characterization of Intestinal Escherichia coli Clones from Wild Boars in Germany
• Jatropha curcas oil body proteome and oleosins: L-form JcOle3 as a potential phylogenetic marker ☆
• Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata.
• Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change.
• Lateral transfers of large DNA fragments spread functional genes among grasses.
• Lentil (Lens culinaris Medik.) nodulates with genotypically and phenotypically diverse rhizobia in Ethiopian soils.
• Machine Learning Reveals Spatiotemporal Genome Evolution in Asian Rice Domestication
• Molecular Characterization of the 3′‐Terminal Region of Turnip mosaic virus Isolates from Eastern China
• Molecular Phylogeny of Daucus (Apiaceae)
• Molecular characterisation of Solanum melongena L. and the crop wild relatives, S. violaceum Ortega and S. torvum Sw., using phylogenetic/DNA barcoding markers
• Molecular characterisation of a putative new polerovirus infecting pumpkin (Cucurbita pepo) in Kenya.
• Molecular taxonomy and morphological characterization reveal new species and new host records of Torula species (Torulaceae, Pleosporales)
• Molecular taxonomy of five species of microfungi on Alnus spp. from Italy
• Morphological and molecular characterisation of Aporcelaimellus nigeriensis sp. n. (Dorylaimida: Aporcelaimidae), a remarkable dorylaim from Nigeria
• Morphological and molecular characterisation of Scutellonema species from yam (Dioscorea spp.) and a key to the species of the genus
• Morphophylogenetic study of Sydowiellaceae reveals several new genera
• Multigene phylogeny and taxonomy of Dendryphion hydei and Torula hydei spp. nov. from herbaceous litter in northern Thailand.
• Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico.
• Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor.
• New species of Thozetella and Chaetosphaeria and new records of Chaetosphaeria and Tainosphaeria from Thailand
• Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors
• Orthostichellaceae fam. nov. and other novelties in pleurocarpous mosses revealed by phylogenetic analyses
• Overexpression of two ATNAC3-related genes improves drought and salt tolerance in tomato (Solanum lycopersicum L.)
• Patellariopsidaceae Fam. Nov. With Sexual-Asexual Connection and a New Host Record for Cheirospora botryospora (Vibrisseaceae, Ascomycota).
• Phylogenetic Revision of Savoryellaceae and Evidence for Its Ranking as a Subclass
• Phylogenetic and pathotypic analysis of rice bacterial blight Race 3
• Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from analyses of nuclear and chloroplast DNA regions
• Phylogenetic relationships among Oryza species revealed by AFLP markers.
• Phylogenetic relationships in the genus Arachis based on seed protein profiles
• Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans
• Phylogenetic relationships of graminicolous downy mildews based on cox2 sequence data
• Plastid phylogenetics of Oceania yams (Dioscorea spp., Dioscoreaceae) reveals natural interspecific hybridization of the greater yam (D. alata)
• Ploidy levels of Dioscorea alata L. germplasm determined by flow cytometry
• Population genetic structure and cladistic analysis of Trypanosoma brucei isolates
• Potato systematics and germplasm collecting, 1989–2000
• Potato virus A isolates from three continents: their biological properties, phylogenetics and prehistory.
• Potato virus Y; the Andean connection.
• Prevalence and Genome Characterization of Field Isolates of Sugarcane Mosaic Virus (SCMV) in Nigeria.
• Pseudostanjehughesia aquitropica gen. et sp. nov. and Sporidesmium sensu lato species from freshwater habitats
• Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia
• Relationship between Phylogeny and Pathotype for the Bacterial Blight Pathogen of Rice
• Ribosomal and Protein Gene Phylogeny Reveals Novel Saprobic Fungal Species From Juglans regia and Urtica dioica.
• Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.
• Roussoellaceae , a new pleosporalean family to accommodate the genera Neoroussoella gen. nov., Roussoella and Roussoellopsis
• SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza
• Screening of Phosphate-Solubilizing Fungi From Air and Soil in Yunnan, China: Four Novel Species in Aspergillus, Gongronella, Penicillium, and Talaromyces.
• Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage.
• Sectional relationships in the genus Musa L. inferred from the PCR-RFLP of organelle DNA sequences.
• Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships.
• Sequence diversity among badnavirus isolates infecting yam ( Dioscorea spp.) in Ghana, Togo, Benin and Nigeria
• Single copy nuclear gene analysis of polyploidy in wild potatoes ( Solanum section Petota )
• Spatio-temporal patterns of genetic change amongst populations of cassava Bemisia tabaci whiteflies driving virus pandemics in East and Central Africa
• Species-diagnostic markers in the genus Pinus: evaluation of the chloroplast regions matK and ycf1
• Taxonomic and phylogenetic characterizations reveal two new species and two new records of Roussoella (Roussoellaceae, Pleosporales) from Yunnan, China
• Taxonomy and phylogeny of hyaline-spored coelomycetes
• The CD45 locus in cattle: allelic polymorphism and evidence for exceptional positive natural selection.
• The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy
• The Gene Pool Concept Applied to Crop Wild Relatives: An Evolutionary Perspective
• The Generation Challenge Programme comparative plant stress-responsive gene catalogue
• The Genome of Caenorhabditis bovis
• The Horn of Africa as a centre of barley diversification and a potential domestication site.
• The Oryza BAC resource : a genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives
• The Plant Pathogen Phytophthora andina Emerged via Hybridization of an Unknown Phytophthora Species and the Irish Potato Famine Pathogen, P. infestans
• The Prehistoric Indian Ayurvedic Rice Shashtika Is an Extant Early Domesticate With a Distinct Selection History.
• The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
• The complete genome sequences of a Peruvian and a Colombian isolate of Andean potato latent virus and partial sequences of further isolates suggest the existence of two distinct potato-infecting tymovirus species
• The complete mitochondrial genome of Mong Cai pig (Sus scrofa) in Vietnam
• The complete mitochondrial genome of a Pabdah catfish, Ompok pabda (Hamilton, 1822)
• The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms
• The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato.
• The wild species genome ancestry of domestic chickens
• Three FLOWERING LOCUS T‐like genes function as potential florigens and mediate photoperiod response in sorghum
• Towards unraveling relationships in Xylariomycetidae (Sordariomycetes)
• Use of chloroplast DNA polymorphisms for the phylogenetic study of seven Phaseolus taxa including P. vulgaris and P. coccineus.
• Using Plant Functional Traits and Phylogenies to Understand Patterns of Plant Community Assembly in a Seasonal Tropical Forest in Lao PDR.
• Vamsapriya (Xylariaceae) Re-Described, with Two New Species and Molecular Sequence Data
• Variation for aggressiveness within and between lineages of Xanthomonas oryzae pv. oryzae
• Viruses representing two new genomovirus species identified in citrus from Tunisia
• Wide sampling of natural diversity identifies novel molecular signatures of C4 photosynthesis
• Wild almonds gone wild: revisiting Darwin's statement on the origin of peaches
• Zeloasperisporiales ord. nov., and two new species of Zeloasperisporium