Evolutionary Insights from DNA Sequences from Chaetanthera Ruiz & Pav
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Hershkovitz Chaetanthera molecular systematics & evolution 1 Evolutionary Insights from DNA Sequences from Chaetanthera Ruiz & Pav. and Oriastrum Poepp. & Endl. (Asteraceae; Mutisieae). I. Of Molecules and Systematics Mark A. Hershkovitz Santiago, Chile [email protected] ABSTRACT Phylogenetic analysis of combined ribosomal DNA internal transcribed spacer (ITS) and chloroplast DNA rpl32-trnL intergenic spacer sequences greatly improves phylogenetic resolution within the central/southern Andean genera Chaetanthera Ruiz & Pav. and Oriastrum Poepp. & Endl. (Asteraceae; Mutisieae) over a previously published phylogeny based on ITS alone. The results support segregation of Chaetanthera subg. Liniphyllum Less. from C. subg. Chaetanthera. One sample with peculiar ITS and rpl32-trnL sequences may be of extraterrestrial origin. Fifteen of 16 nominal species sampled more than once for both loci were polymorphic for at least one of them, and only half of the polymorphic samples were demonstrably monophyletic in the combined data analysis. An additional five species sampled only for ITS all were polymorphic. These results underscore the ontological difference between gene trees and species trees and further discredit the notion of “species barcodes.” The gene trees for both loci manifest departures from all evolutionary models implemented for phylogenetic reconstruction. This result is explained as a consequence of evolutionary idiosyncraticity, in turn a function of the determinacy of biological organisms and processes consequent to autopoiesis. This determinacy implicates a chaotic evolutionary function that theoretically cannot be reconstructed or predicted by stochastic models. However, because phylogenetic history and clades are materially tangible entities, their reconstruction is within the realm of scientific inquiry. I discuss the phylogeny of Chaetanthera/Oriastrum in this epistemological framework. Key words: Chaetanthera, Oriastrum, Mutisieae, Asteraceae, rDNA-ITS, cpDNA rpl32-trnL, gene trees, species trees, molecular evolutionary models, phylogenetic methods, evolutionary idiosyncraticity, alien species CITATION: Hershkovitz, M. [A.]. 2021. Evolutionary insights from DNA sequences from Chaetanthera Ruiz & Pav. and Oriastrum Poepp. & Endl. (Asteraceae; Mutisieae). I. Of molecules and systematics. EcoEvoRxiv, 4 January 2021. https://doi.org/10.32942/osf.io/ak68m/ [Verify most recent version]. INTRODUCTION Hershkovitz et al. (2006a) published a phylogeny of the central/southern Andean genus Chaetanthera Ruiz & Pav. (sensu lato, including the later segregated Oriastrum Poepp. & Endl.; Davies, 2010; Asteraceae; Mutisieae) based on ribosomal DNA (rDNA) internal transcribed spacer region (ITS) sequences. These genera and their tribe and subfamily Mutisioideae pertain are among the earliest diverging members of the basal grade of extant Asteraceae (Susanna et al., 2020). Per a revised species taxonomy (Davies, 2010; see also Davies, 2013), Hershkovitz et al. (2006a) sampled, 24/30 and 13/18 (total, 37/48) nominal species of Chaetanthera and Oriastrum, respectively. A few taxonomic adjustments were proposed by Nicola et al. (2015), as elaborated later in the text. The principal conclusion of Hershkovitz et al. (2006a) was that the exclusively alpine genus Oriastrum originated millions of years before the development of their modern habitat, whereas alpine species of Chaetanthera s. str. are of relatively recent origin. Subsequent analysis of the same ITS data (Guerrero et al., 2013) did not challenge this conclusion. Likewise, a more limited analysis of some of the same and some additional ITS sequences of Chaetanthera s. str. (Cabezas Álvarez, 2015) did not alter significantly the phylogenetic conclusions of Hershkovitz et al. (2006a), except as discussed later. Hershkovitz Chaetanthera molecular systematics & evolution 2 The present work adds to Hershkovitz et al. (2006a) analysis of chloroplast DNA (cpDNA) intergenic spacer sequences between the Large Ribosomal Protein 32 and tRNA-Leucine (UAG) genes (rpl32-trnL; Shaw et al., 2007). The sequences are analyzed separately and in combination with the ITS sequences using maximum parsimony (MP) and maximum likelihood (ML) criteria. Addition of the rpl32-trnL sequences greatly enhances phylogenetic resolution among the samples, as evidenced by bootstrap analysis. The data support segregation of Chaetanthera subg. Liniphyllum Less. from C. subg. Chaetanthera sensu Davies (2010). However, the position of a sample identified in Hershkovitz et al. (2006a) as C. flabelleta D.Don is incongruent in the ITS and rpl32-trnL trees, and, consequently, this sample cannot be assigned to subgenus. It may have an extraterrestrial origin. While the data are consistent with the segregation of the monophyletic and presumed sister-groups Chaetanthera s. str. and Oriastrum, they also are axiomatically consistent with retention of the latter in the former. In fact, their remerging may be favored on morphological evidence and also in the interest of taxonomic stability. In particular, the 150 year-old concept of Chaetanthera s. l. readily distinguishes from other genera, whereas Chaetanthera s. str. and Oriastrum are distinguished only by less or not macroscopic traits that appear to intergrade more than proposed by Davies (2010). But the present work emphasizes more the epistemological basis of the relation between molecular evolution and systematics (Hershkovitz, 2018a, 2019a, b), here using Chaetanthera/Oriastrum as the “model.” For example, the ontological distinction between “gene trees” and “species trees” predicts incongruencies (as opposed to “conflicts”) between these, and this is what is observed. The explicit or subliminal effort to force congruence between these, as in the “species barcodes” paradigm, thus is misguided at best. The present data demonstrate strong incongruence between genetic haplotype diversity and nominal species taxonomy. This incongruence is theoretically predicted, hence its evidence should be sought, appreciated, and scientifically exploited rather than avoided or marginalized. The present work also emphasizes the theoretically well-articulated but usually ignored differences between molecular evolution and simplistic, erroneous, and mindlessly-applied reductionist phylogenetic reconstruction models/methods. But while the consequences of technically misspecified stochastic evolutionary models have been extensively studied, practically no attention has been paid to their epistemological misspecification. In particular, evolution is not stochastic, as commonly presumed or asserted, but, rather, idiosyncratic (Hershkovitz, 2018a, 2019a, b). This evolutionary idiosyncraticity is a function of the determinacy of biological organisms and processes, which is a function of the autopoietic character of life (Maturana and Mpodozis, 2000). This determinacy implicates a chaotic evolutionary function that theoretically cannot be reconstructed or predicted by stochastic models. However, because phylogenetic history and clades are materially tangible entities, their reconstruction is within the realm of scientific inquiry. Thus, I argue that methods based on unrealistic models/assumptions can have heuristic value in phylogenetic reconstruction, but only in the framework of reason and logic. I discuss the phylogeny of Chaetanthera/Oriastrum in this epistemological framework. MATERIALS AND METHODS 1. Samples and sequences Molecular and sequence analysis methods for rpl32-trnL were the same as described in Hershkovitz et al. (2006a) for ITS, but using the corresponding primers. The DNA samples are the same as in Hershkovitz et al. (2006a), but the most of the vouchers here are identified according to Davies Hershkovitz Chaetanthera molecular systematics & evolution 3 (2010; Table 1). Table 1 also notes taxonomic adjustments proposed by Nicola et al. (2015), and consequences on the present results are addressed in the Results and Discussion. Nicola et al. (2015) did not examine the collections sampled here. The present analysis includes 62/63 of the samples in the phylogeny of Hershkovitz et al. (2006a), these representing 24/30 and 13/18 of the nominal species of, respectively, Chaetanthera s. str. and Oriastrum as recognized by Davies (2010), plus one unidentified Chaetanthera sample. The vouchers of 12 samples analyzed here were not mentioned and presumably not seen by Davies (2010). Their species identification here is based on circumstantial evidence (morphology, geography, and DNA sequence), but one or more of the identifications might be “incorrect” per Davies’ (2010) taxonomy. The inclusion in the present analysis is, in any case, “informative,” just as the analysis of Hershkovitz et al. (2006a) was informative, even though many of the vouchers have been since identified differently by Davies (2010). “Ambiguous” identification in no way signifies no identity at all. Moreover, technically, the only absolutely unambiguously identified individuals are holotypes. All other identifications are relative. One sample identified in Hershkovitz et al. (2006a) as Chaetanthera flabellata is listed here as sp_indet_25161. This is because the ITS sequence apparently is highly divergent from that of a specimen of C. flabellata identified by Davies (2010) and analyzed by Cabezas Álvarez (2015). The latter unpublished sequence evidently is very similar to that from the same specimen of C. euphrasioides used in both analyses. In fact, Davies (2010) noted that C. flabellata and C. euphrasioides