ITS secondary structure reconstruction to resolve taxonomy and phylogeny of the Betula L. genus

Abstract

The taxonomy and phylogeny of the Betula L. genus remain unresolved and are very difficult to assess due to several factors, especially because of frequent hybridization among different species. In the current study, we used nucleotide sequences of two internal transcribed spacer regions (ITS1 and ITS2), which are commonly used as phylogenetic markers. In addition to their nucleotide variation we reconstructed their secondary structure and used it to resolve phylogenetic relationships of some birch species. We explored whether consideration of secondary structure in phylogenetic analyses based on neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods would help us obtain more solid support of the reconstructed phylogenetic trees. The results were not unambiguous. There were only a few clades with higher support when secondary structure was included into analysis. The phylogenetic trees generated using different methods were mostly in agreement with each other. However, the resolving power of these markers is still insufficient to reliably discriminate some closely related species. To achieve this aim more reliably there is a need for application of modern genomic approaches in combination with traditional ones.

Betula mcallisteri sp. nov. (sect. Acuminatae, Betulaceae), a new diploid species overlooked in the wild and in cultivation, and its relation to the widespread B. luminifera

“…Seventy additional ITS sequences from Betulaceae ( Wang et al., 2016 ; Wang et al., 2022 ) were included to infer the phylogenetic position of the “unidentified sample”. A total of 95 ITS sequences and their secondary structure (ITS1 and ITS2), as previously used by Tarieiev et al. (2021) , were aligned separately using BioEdit v.7.0.9.0 ( Hall, 1999 ) with default parameters.…”

A cryptic syngameon withinBetulashrubs revealed: Implications for conservation in changing subarctic environments

“…exilis (Sukaczev) Hultén as two distinct taxa (Cody, 2000;de Groot et al, 1997;Elven et al, 2011;Furlow, 1997;Hultén, 1968), while others suggest that they represent the same taxon (Ashburner & McAllister, 2013;Hultén & Fries, 1986;Moss & Packer, 1983;Porsild & Cody, 1980;Saarela et al, 2017). To date, the phylogenetic relationship between B. glandulosa and other birch species remains relatively unknown (Li et al, 2005;Tarieiev et al, 2021;Wang et al, 2016Wang et al, , 2021.…”