Rumbling Orchids: How To Assess Divergent Evolution Between Chloroplast Endosymbionts and the Nuclear Host

Abstract

Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provide valuable information on evolutionary processes such as chloroplast capture following hybridization, incomplete lineage sorting, and horizontal gene transfer. Statistical tools that to date have been used in cophylogenetic studies only also have the potential to test for the degree of topological congruence between organellar and nuclear data sets and reliably detect outlier associations. Two distance-based methods, namely ParaFit and Procrustean Approach to Cophylogeny (PACo), were used in conjunction to detect those outliers contributing to conflicting phylogenies independently derived from chloroplast and nuclear sequence data. We explored their efficiency of retrieving outlier associations, and the impact of input data (unit branch length and additive trees) between data sets, by using several simulation approaches. To test their performance using real data sets, we additionally inferred the phylogenetic relationships within Neotropical Catasetinae (Epidendroideae, Orchidaceae), which is a suitable group to investigate phylogenetic incongruence because of hybridization processes between some of its constituent species. A comparison between trees derived from chloroplast and nuclear sequence data reflected strong, well-supported incongruence within Catasetum, Cycnoches, and Mormodes. As a result, outliers among chloroplast and nuclear data sets, and in experimental simulations, were successfully detected by PACo when using patristic distance matrices obtained from phylograms, but not from unit branch length trees. The performance of ParaFit was overall inferior compared to PACo, using either phylograms or unit branch lengths as input data. Because workflows for applying cophylogenetic analyses are not standardized yet, we provide a pipeline for executing PACo and ParaFit as well as displaying outlier associations in plots and trees by using the software R. The pipeline renders a method to identify outliers with high reliability and to assess the combinability of the independently derived data sets by means of statistical analyses.

Phylogenetic relationships in Mormodes (Orchidaceae, Cymbidieae, Catasetinae) inferred from nuclear and plastid DNA sequences and morphology

“…The issue of more than one version of trnL-trnF in these orchids deserves further research, which is beyond the scope of this study. Phylogenetic analyses:-Both the MP and BI analyses of all datasets recovered Mormodes as monophyletic, in agreement with previous morphological (Romero-González 1990, Chase & Hills 1992) and molecular studies (Pridgeon & Chase 1998, Salazar et al 2009, Pérez-Escobar et al 2015. Both analyses also support monophyly of section Coryodes (BP 90, PP 0.84, respectively), but section Mormodes received low support from the MP analysis (BP 70) and was not recovered as monophyletic in the BI analysis (Fig.…”

Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics

“…Previous phylogenetic studies about Catasetinae have included not more than three species of Cycnoches 47, 48, 50, 51, 55 , hence keeping internal relationships (and corresponding conflicts, see below) of the lineages unresolved. Serious phylogenetic incongruence between nuclear and plastid tree topologies of Catasetinae has been firstly identified by Pérez-Escobar and colleagues 64 , but the plausibility of the trees were not discussed before.…”

“…We also sequenced a ~1500 bp fragment of the plastid gene ycf 1, as well as the trn S– trn G intergenic spacer. Amplification and sequencing settings, as well as sequencing primers used for ITS, ETS, Xdh , trn S– trn G, and ycf 1, are the same as previously reported 64, 81 (Tab. S2).…”

“…the -qINSi option). Congruence between nuclear and plastid datasets was assessed as previously done by Pérez-Escobar and colleagues 64 , and using PACo 83 . The procedure is available as a pipeline (http://www.uv.es/cophylpaco/) and was also employed to identify operational terminal units (OTUs) from the plastid dataset that are in conflict with the nuclear dataset (potential outliers detected by PACo are shown in Figs S1 and S2).…”

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

“…Many studies have used nuclear simple sequence repeat (SSR) chloroplast DNA makers to study phylogeny and population variation [2,3]. Previously, studies found a conflict (inconsistency) between the phylogeny of plastid data and nuclear data in Senecioneae and Neotropical Catasetinae [4,5]. Therefore, it is not sufficient to study Quercus simply by using plastid regions.…”