Molecular Mycology and Emerging Fungal Pathogens
Johan A. Maertens, Kieren A. Marr in Diagnosis of Fungal Infections, 2007
What makes a gene useful for molecular phylogeny? First, the gene should be present in all organisms under study, and this requirement forces one to select genes with essential cellular functions, such as ribosomal RNA genes. Second, the gene should serve as a molecular clock, with increasing evolutionary time since two organisms shared a common ancestor ticked off as accumulated nucleotide changes in the gene. If two organisms are close evolutionary cousins, then their genes should share a high degree of sequence similarity. If two organisms are distant evolutionary kin, then their genes should have been subjected to additional mutation and selection over this time period, witha resulting lower rate of sequence similarity noted. The application of molecular phylogenetic methods to some long-standing problems in mycology helps to illustrate this point.
Molecular Analysis of Plant DNA Genomes: Conserved and Diverged DNA Sequences
S. K. Dutta in DNA Systematics, 2019
It is known that many plant proteins are coded by gene families. A detailed study of the nucleotide sequences of individual genes from such families is of particular significance for molecular phylogenetics. These families have proved to be heterogenous, e.g., the soya leghemoglobin gene family includes normal, pseudo, and truncated genes.50,72 For the most part, gene families were formed as a result of repeated duplication-amplification events of the ancestor gene.73–75 Subsequent substitution accumulation rates in individual genes of the family could have been different; at times, gene “subfamilies” were formed. For this reason, attempts to use the nucleotide sequence of a fortuitously cloned gene of a family for interspecific comparisons may lead to erroneous conclusions (a quite different situation emerges by comparison of rRNA sequences; here we deal with the “mean statistical sequence” reflecting the properties of the entire family).
An Overview of Parasite Diversity
Eric S. Loker, Bruce V. Hofkin in Parasitology, 2015
Other examples of the disparity between existing taxonomy and the revelations of molecular phylogenetics are more glaring. For example, in the phylum Myxozoa, spore structure is a major feature differentiating taxonomic groups. The existing taxonomic scheme does not match the relationships derived from phylogenetic studies of either SSU rRNA or elongation factor 2 (EF-2) genes. This disparity is probably because relatively few characters are available to describe the myxozoan spore and because some spore configurations are just more successful than others. The result is that species that differ genetically have converged to the same spore morphology; that is, they exhibit homoplasy. Homoplasy refers to similarities that result from convergent evolution rather than common ancestry.
Identification, characterization, and molecular phylogeny of scorpion enolase (Androctonus crassicauda and Hemiscorpius lepturus)
Published in Toxin Reviews, 2023
Elham Pondehnezhadan, Atefeh Chamani, Fatemeh Salabi, Reihaneh Soleimani
The evolutionary origin and relevance of scorpions have been the subject of many studies in recent decades, especially recent pan-genome studies that support the Arachnopulmonata hypothesis: a sister-group relationship between scorpions and tetrapulmonates (i.e. spiders and allied orders) (Regier et al. 2010, Sharma et al. 2014, 2015). Previous morphological-based phylogenetic approaches are restricted to those scorpions exemplifying morphological stasis (Prendini and Wheeler 2005, Prendini et al. 2006). To address this challenge, however, phylogenetic relationships can be inferred more precisely using both molecular and morphological methods (Chippaux and Goyffon 2008). Molecular phylogeny compares homologous DNA or protein sequences to decide the relationships among organisms or genes. It constructs a hierarchical phylogenetic tree based on the genetic divergences of the similarity or dissimilarity of homologous molecules from different organisms, resulting from molecular evolution over time (Patwardhan et al. 2014).
Evolution of antifungals for invasive mold infections in immunocompromised hosts, then and now
Published in Expert Review of Anti-infective Therapy, 2023
Zoe Freeman Weiss, Jessica Little, Sarah Hammond
S. apiospermum complex includes a number of closely related species (eg. S. apiospermum, S. boydii). Of note S. apiospermum is the asexual stage (anamorph) of Pseudallescheria boydii. Lomentospora prolificans (formery S. prolificans) has no known teleomorph [101]. Classification based on sexual stage and morphology has been replaced with species identification by molecular phylogeny, but knowledge of prior taxonomical schemas can help reduce confusion when reading older literature.
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