Impact of Gene Molecular Evolution on Phylogenetic Reconstruction: A Case Study in the Rosids (Superorder Rosanae, Angiosperms)

Abstract

Rate of substitution of genomic regions is among the most debated intrinsic features that impact phylogenetic informativeness. However, this variable is also coupled with rates of nonsynonymous substitutions that underscore the nature and degree of selection on the selected genes. To empirically address these variables, we constructed four completely overlapping data sets of plastid matK, atpB, rbcL, and mitochondrial matR genes and used the rosid lineage (angiosperms) as a working platform. The genes differ in combinations of overall rates of nucleotide and amino acid substitutions. Tree robustness, homoplasy, accuracy in contrast to a reference tree, and phylogenetic informativeness are evaluated. The rapidly evolving/unconstrained matK faired best, whereas remaining genes varied in degrees of contribution to rosid phylogenetics across the lineage's 108 million years evolutionary history. Phylogenetic accuracy was low with the slowly evolving/unconstrained matR despite least amount of homoplasy. Third codon positions contributed the highest amount of parsimony informative sites, resolution and informativeness, but magnitude varied with gene mode of evolution. These findings are in clear contrast with the views that rapidly evolving regions and the 3rd codon position have inevitable negative impact on phylogenetic reconstruction at deep historic level due to accumulation of multiple hits and subsequent elevation in homoplasy and saturation. Relaxed evolutionary constraint in rapidly evolving genes distributes substitutions across codon positions, an evolutionary mode expected to reduce the frequency of multiple hits. These findings should be tested at deeper evolutionary histories.

Molecular phylogeny of bark and ambrosia beetles (Curculionidae: Scolytinae) based on 18 molecular markers

“…Rates are not always inversely correlated with phylogenetic resolution and clade support [80] and only the implementation in large taxonomic samples represents the ultimate test of a phylogenetic marker performance. Our gene classification based on phylogenetic utility that was assessed according to clade congruence and phylogenetic informativeness (PI) must therefore be taken as a preliminary proxy for a marker's phylogenetic signal [81,82,83]. It will be particularly interesting to observe the contribution of Iap2 in a larger data set given its much higher PI compared with other markers.…”

Sequence analysis of Maturase K (matK): A chloroplast-encoding gene in some selected pulses

“…Importantly, analyses of the DNA sequences of various species provide valuable information about their taxonomy, gene make up as well as utilizations. Undoubtedly, genomic regions vary considerably in their potential phylogenetic informativeness and their contributions in resolving a given set of taxa over specified time (Hilu et al, 2014). Specifically, there are two schools of thought regarding the utilization of rapidly evolving regions as against slowly evolving regions of the genome.…”

“…Their argument was premised on the fact that multiple hits confounded by extended time scale could be significant enough to conceal phylogenetic signals and elevate homoplasy, with saturation reaching levels that can negatively impact tree structure (Graybeal, 1994;Wenzel and Siddal, 1999;Klopfstein et al, 2010;Townsend et al, 2012). The accumulation of multiple hits in rapidly evolving regions is capable of obscuring potential synapomorphies as well as results in long branch alteration (Townsend, 2007;Magallon and Sanderson, 2002).On the contrary, however, the opposing school of thought opined that rapidly evolving regions promotes effectiveness and less constrained genomic regions in deep level phylogenetics (Yang, 1998;Hilu et al, 2008;Hilu and Liang, 1997;Worberg et al, 2007).According to Hilu et al (2014), phylogenetic signal from rapidly evolving and un-constrained matK provides by far the most structure and accuracy, whereas slowly evolving, constrained and un-constrained genes display decreasing degrees of informativeness and tree structure. This was also the same position that had earlier posited that matK gene is very informative in plant systematics owing to its high phylogenetic signal when compared with other genes such as rbcL.…”

Diversity Assessment and Cultivar Identification in Date Palm through Molecular Markers- A Review

“…The resolution power of matK is better than other regions like rpoC, trnH-psbA, rbcL and atpF-atpH (Burgess et al, 2011). Overall the informativeness of matK was found to be 2.6 times greater than that of atpB and rcbL (Hilu et al, 2014). Chloroplast DNA sequence of rpoB and psbA-trnH can be used as molecular signature in date palm at seedling stage as there are 173 variable sites in the combined matrix of 1147 characters (Al-Qurainy et al, 2011).…”