Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)

Abstract

Background and Aims Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models. Methods We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing. Key Results Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models. Conclusions Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.

Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint

“…Compensatory base change (CBC) or compensatory mutation, wherein a base substitution on one side (hemi-CBC) is compensated by a substitution on the other side of that base pair, is expected to restore base-pairing and maintain the structure [ 42 ]. From an evolutionary perspective, such CBCs can be reserved in an ancestral ITS2 structure and are inherited by its descendant, making structural states include unique phylogenetic information not found in the nucleotide sequence [ 43 ].…”

“…Based on the above evidence, wherein CBCs occur between rather than within species, Wolf et al proposed a generalized “CBC species concept” [ 55 ]. Further development of Coleman’s hypothesis showed that CBC should expand to all four helices and even hemi-CBC rather than being restricted to helix II and III as Coleman originally suggested [ 43 , 56 , 57 ]. In practice, rapid identification of the ITS2 CBC among the potential parental species and assessing their fertility before their actual cross experiment could reduce the incompatible mating pairs and save time.…”

“…For example, only 25 out of 98 morphological species of foliar endophytic fungi were differentiated by CBC characters [ 58 ]. Likewise, only two CBCs are present among ten closely related species of Corydalis [ 43 ]. These results are consistent with some previous findings that CBC occurrence primarily corresponds to higher supra-specific lineages rather than species level distinction [ 57 , 59 ].…”

“…At present, there is no evidence of functional correlation between ITS2 sequence and gamete fusion and ITS2-CBC by itself is not related to speciation. The molecular dating of Corydalis showed that ITS2-CBC substitutions were separated by ~10.4–15.5 million years, within which several species have occurred [ 43 ]. This result indicates that CBC can provide a scale for measuring whether sufficient evolutionary time has elapsed for a speciation event in certain lineages.…”

Compensatory Base Changes Reveal Sexual Incompatibility among Members of the Anopheles subpictus Sensu Lato (Diptera: Culicidae) Species Complex in Sri Lanka

“…The occurrence of CBCs can be the underlying reason that ITS2 has appeared to be an effective indicator of species identification, accumulating mutations in reproductively isolated populations [ 39 ]. Thus, it has been shown that determining the presence of CBCs in ITS2 rRNA secondary structures is a reliable diagnostic tool of taxon analysis in prokaryotes placozoans [ 40 ] as well as higher eukaryotic lineages such as tick Paramacrobiotus [ 41 ], Altica beetles [ 42 ] and flowering plant Corydalis [ 43 ]. Furthermore, CBC analysis has been shown to play a supportive role in uncovering cryptic species in taxa including the marine protist Amoebophrya ceratii [ 44 ], marine diatom genus Pseudo-nitzschia [ 45 ] and skipper butterfly Urbanus belli [ 46 ].…”