scholarly journals Identification and Characterization of a Novel Etiological Agent of Mango Malformation Disease in Mexico, Fusarium mexicanum sp. nov.

2010 ◽  
Vol 100 (11) ◽  
pp. 1176-1184 ◽  
Author(s):  
Gabriel Otero-Colina ◽  
Gerardo Rodríguez-Alvarado ◽  
Sylvia Fernández-Pavía ◽  
Marcel Maymon ◽  
Randy C. Ploetz ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Species Recognition ◽  
Gibberella Fujikuroi ◽  
Fusarium Spp ◽  
Data Set ◽  
Dna Sequence Data ◽  
Mango Malformation ◽  
American Clade

The primary objective of this study was to characterize Fusarium spp. associated with the economically devastating mango malformation disease (MMD) in Mexico. In all, 142 Fusarium strains were isolated from symptomatic mango inflorescences and vegetative tissues in eight geographically diverse Mexican states from 2002 through 2007. Initially, all the Mexican isolates were screened for genetic diversity using appolymerase chain reaction and random amplified polymorphic DNA markers and were grouped into seven distinct genotypes. Based on results of these analyses, evolutionary relationships and species limits of the genetically diverse MMD-associated Fusarium spp. were investigated using multilocus DNA sequence data and phylogenetic species recognition. Maximum parsimony analyses of a five-locus data set comprising 5.8 kb of aligned DNA sequence data indicated that at least nine phylogenetically distinct Fusarium spp. within the Gibberella fujikuroi species complex are associated with MMD, including one species within the African clade (Fusarium pseudocircinatum), two species within the Asian clade (F. mangiferae and F. proliferatum), and at least six species within the American clade (F. sterilihyphosum and five undescribed Fusarium spp.). Molecular phylogenetic analyses indicate that a novel genealogically exclusive lineage within the American clade was the predominant MMD associate in Mexico. This new Fusarium sp. caused MMD and could be distinguished from all other known species morphologically by the production of mostly sterile, coiled hyphae which are typically associated with sporodochial conidiophores together with unbranched or sparsely branched aerial conidiophores. Koch's postulates were completed for isolates of the new species on nucellar seedlings of mango cv. Ataulfo. This pathogen is formally described herein as F. mexicanum.

scholarly journals Analysis of Genetic Diversity of Fusarium tupiense, the Main Causal Agent of Mango Malformation Disease in Southern Spain

Plant Disease ◽  
2016 ◽  
Vol 100 (2) ◽  
pp. 276-286 ◽  
Author(s):  
M. Crespo ◽  
F. M. Cazorla ◽  
A. de Vicente ◽  
E. Arrebola ◽  
J. A. Torés ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Southern Spain ◽  
Fusarium Fujikuroi ◽  
Dna Sequence Data ◽  
Fusarium Fujikuroi Species Complex ◽  
Polymerase Chain ◽  
Mango Malformation

Mango malformation disease (MMD) has become an important global disease affecting this crop. The aim of this study was to identify the main causal agents of MMD in the Axarquía region of southern Spain and determine their genetic diversity. Fusarium mangiferae was previously described in the Axarquía region but it represented only one-third of the fusaria recovered from malformed trees. In the present work, fusaria associated with MMD were analyzed by arbitrary primed polymerase chain reaction (ap-PCR), random amplified polymorphic DNA (RAPD), vegetative compatibility grouping (VCG), a PCR screen for mating type idiomorph, and phylogenetic analyses of multilocus DNA sequence data to identify and characterize the genetic diversity of the MMD pathogens. These analyses confirmed that 92 of the isolates were F. tupiense, which was previously only known from Brazil and Senegal. In addition, two isolates of a putatively novel MMD pathogen were discovered, nested within the African clade of the Fusarium fujikuroi species complex. The F. tupiense isolates all belonged to VCG I, which was first described in Brazil, and the 11 isolates tested showed pathogenicity on mango seedlings. Including the prior discovery of F. mangiferae, three exotic MMD pathogenic species have been found in southern Spain, which suggests multiple independent introductions of MMD pathogens in the Axarquía region.

scholarly journals The Estimation of the Number and the Length Distribution of Gene Conversion Tracts From Population DNA Sequence Data

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 89-99 ◽  
Author(s):  
Esther Betrán ◽  
Julio Rozas ◽  
Arcadio Navarro ◽  
Antonio Barbadilla
Keyword(s):  
Maximum Likelihood ◽  
Gene Conversion ◽  
Dna Sequence ◽  
Geometric Distribution ◽  
Sequence Data ◽  
Length Distribution ◽  
Data Set ◽  
Tract Length ◽  
Dna Sequence Data ◽  
Basic Parameters

DNA sequence variation studies report the transfer of small segments of DNA among different sequences caused by gene conversion events. Here, we provide an algorithm to detect gene conversion tracts and a statistical model to estimate the number and the length distribution of conversion tracts for population DNA sequence data. Two length distributions are defined in the model: (1) that of the observed tract lengths and (2) that of the true tract lengths. If the latter follows a geometric distribution, the relationship between both distributions depends on two basic parameters: ψ, which measures the probability of detecting a converted site, and φ the parameter of the geometric distribution, from which the average true tract length, 1 / (1 – φ), can be estimated. Expressions are provided for estimating φ by the method of the moments and that of the maximum likelihood. The robustness of the model is examined by computer simulation. The present methods have been applied to the published rp49 sequences of Drosophila subobscura. Maximum likelihood estimate of φ for this data set is 0.9918, which represents an average conversion tract length of 122 bp. Only a small percentage of extant conversion events is detected.

scholarly journals Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated?

2019 ◽  
Vol 69 (4) ◽  
pp. 708-721 ◽  
Author(s):  
Luke C Campillo ◽  
Anthony J Barley ◽  
Robert C Thomson
Keyword(s):  
Reproductive Isolation ◽  
Dna Sequence ◽  
Sequence Data ◽  
Species Recognition ◽  
Species Boundaries ◽  
Simultaneous Estimation ◽  
Dna Sequence Data ◽  
Multispecies Coalescent ◽  
Species Pairs ◽  
History Of

Abstract A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here, we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation-based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed. [BPP; Drosophila speciation; genetic distance; multispecies coalescent.]

A cladistic analysis of Diopsidae (Diptera) based on morphological and DNA sequence data

2002 ◽  
Vol 33 (3) ◽  
pp. 325-336 ◽  
Author(s):  
Richard Baker ◽  
Rudolf Meier
Keyword(s):  
Sensitivity Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Dna Sequence Data ◽  
Character Weighting ◽  
Character Matrix

AbstractThe results of a cladistic analysis based on a combined character matrix consisting of the morphological data set of Meier & Hilger (2000) and the molecular data set of Baker & al. (2001) is presented. The data set is subjected to an extensive sensitivity analysis and equal character weighting is found to perform best according to character incongruence and tree support. The sensitivity analysis also reveals a remarkable stability of the preferred tree with 25 of the 36 tree nodes supported under 16 different analysis conditions. Cyrtodiopsis is synonymized with Teleopsis and Shillito's (1971) synonymization of Trichodiopsis and Chaetodiopsis with Diasemopsis is confirmed. Morphological and DNA sequence data agree on all major clades and conflict is restricted to the placement of two species within their respective genera. Only in one case can the conflict be confidently resolved. Partitioned Bremer Support values reveal that 90% of the tree support is generated by the DNA sequence characters, although the average morphological character contributes twice the support of an average molecular character. The evolution of eye-stalk morphology and of a meiotic drive chromosome system in Teleopsis is briefly discussed in the light of the phylogenetic tree.

scholarly journals The Age of a Unique Event Polymorphism

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 401-409
Author(s):  
Lada Markovtsova ◽  
Paul Marjoram ◽  
Simon Tavaré
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Hypervariable Region ◽  
Data Set ◽  
Dna Sequence Data ◽  
Unique Event ◽  
Mitochondrial Data ◽  
Region I ◽  
History Of ◽  
Hypervariable Region I

Abstract We develop a Markov chain Monte Carlo approach for estimating the distribution of the age of a mutation that is assumed to have arisen just once in the history of the population of interest. We assume that in addition to the presence or absence of this mutation in a sample of chromosomes, we have DNA sequence data from a region completely linked to the mutant site. We apply our method to a mitochondrial data set in which the DNA sequence data come from hypervariable region I and the mutation of interest is the 9-bp region V deletion.

scholarly journals Model-based species delimitation: are coalescent species reproductively isolated?

2019 ◽  
Author(s):  
Luke C. Campillo ◽  
Anthony J. Barley ◽  
Robert C. Thomson
Keyword(s):  
Reproductive Isolation ◽  
Dna Sequence ◽  
Sequence Data ◽  
Species Recognition ◽  
Species Boundaries ◽  
Simultaneous Estimation ◽  
Dna Sequence Data ◽  
Multispecies Coalescent ◽  
Species Pairs ◽  
History Of

ABSTRACTA large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question, and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.

scholarly journals DNA sonification for public engagement in bioinformatics

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Heleen Plaisier ◽  
Thomas R. Meagher ◽  
Daniel Barker
Keyword(s):  
Dna Sequence ◽  
Public Engagement ◽  
Sequence Data ◽  
Sensory Perception ◽  
Data Representation ◽  
Sequence Information ◽  
Dna Sequence Data ◽  
Public Events ◽  
Dna Base ◽  
Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia

Zootaxa ◽  
2020 ◽  
Vol 4766 (3) ◽  
pp. 472-484
Author(s):  
HANNAH E. SOM ◽  
L. LEE GRISMER ◽  
PERRY L. JR. WOOD ◽  
EVAN S. H. QUAH ◽  
RAFE M. BROWN ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Dna Sequence ◽  
Rare Species ◽  
Sequence Data ◽  
Peninsular Malaysia ◽  
Tropical Asia ◽  
Dna Sequence Data ◽  
A New Species ◽  
Lines Of Evidence

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12. 

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