Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci

Abstract

Plant molecular systematic studies of closely related taxa have relied heavily on sequence data from nuclear ITS and cpDNA. Positive attributes of using ITS sequence data include the rapid rate of evolution compared to most plastid loci and availability of universal primers for amplification and sequencing. On the other hand, ITS sequence data may not adequately track organismal phylogeny if concerted evolution and high rDNA array copy number do not permit identification of orthologous copies. Shaw et al. (American Journal of Botany 92: 142-166) recently identified nine plastid regions that appear to provide more potentially informative characters than many other plastid loci. In the present study, sequences of these loci and ITS were obtained for six taxonomic groups in which phylogenetic relationships have been difficult to establish using other data. The relative utility of these regions was compared by assessing the number of parsimony informative characters, character congruence, resolution of inferred trees, clade support, and accuracy. No single locus emerged as the best in all lineages for any of these measures of utility. Results further indicated that in preliminary studies, sampling strategy should include at least four exemplar taxa. The importance of sampling data from independent distributions is also discussed.

Survey of endophytic Alternaria species isolated from plants in the Brazilian restinga biome

“…Genetic variability was observed among these isolates, which may show that some of them may be novel Alternaria species. However trees using the ITS region do not give strong support, as these regions are ribosomal and highly conserved [63]. The coding regions of proteins (TEF1-α) may confirm distinct and new species of Alternaria sp.…”

Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding

“…The higher overall variation in nuclear genomes can be explained by the different modes of inheritance for cp (uniparental) and nc (biparental) genomes, and the much higher mutation rates in nuclear genomes [35,36].…”

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“…DOI: 10.31862/2500-2961-2018-1- [9][10][11][12][13][14][15][16][17][18][19][20][21][22] Preliminary results of the molecular genetic investigation of the poplar hybridization naturally and in the urban beautification 2…”