Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on Paphiopedilum Pfitz. (Orchidaceae).

Dariusz L Szlachetko,Natalia Olędrzyńska,Aleksandra M Naczk,Marek S Ziętara,Marcin Górniak,Lidia Boss,Agata Mieszkowska

doi:10.3390/ijms222111393

Dariusz L Szlachetko, Natalia Olędrzyńska + Show 5 more

Open Access

https://doi.org/10.3390/ijms222111393

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Abstract

The phylogeny of the genus Paphiopedilum based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus Paphiopedilum. The low-copy nuclear protein-coding gene PHYC was obtained for 22 species representing all sections and subgenera of Paphiopedilum. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused by ancestral homoploid hybridization. We present a model for inferring the phylogeny of the species despite the incongruence of the different tree topologies. Our analysis, based on six low-copy nuclear genes, is congruent with plastome phylogeny and has been confirmed by phylogenetic network analysis.

Highlights

In recent years, nuclear genome data have shown discrepancies among phylogenetic trees based on various markers
Gene duplication and incomplete lineage sorting (ILS) cannot be rejected as the reason for phylogenetic tree topology incongruence among the XDH, LFY, RAD51, and PHYC genes (Figure 1a–d), where the subgenus Paphiopedilum is concerned, ancestral hybridization is a more probable explanation, as well as a parsimonious one
The first group (ACO, DEF4, plastid DNA trees; Figure 1g–i) strongly supports (PP 1.0) the subgenus Paphiopedilum in its current circumscription and shows a strong division into two groups corresponding to morphology

Summary

Introduction

Nuclear genome data (often obtained using new sequencing methods) have shown discrepancies among phylogenetic trees based on various markers. Tree topology conflicts can be explained either by hybridization or incomplete lineage sorting (ILS) [1] The latter stems from incomplete random sorting of alleles at many loci, independently, due to short intervals. In order to determine which of the aforementioned processes may be responsible for incongruence in tree topologies, analyses based on the molecular clock were applied [3], in addition to gene coalescence time analysis for a selected group [3,4]. Determining the coalescence time of a particular molecular marker, compared with species divergence time, enables the elimination of ILS as a factor influencing the topology of the phylogenetic tree [3]. Hybridization is not random, and it shortens the genetic distance between species within the introduced markers Differences between those processes have been used in order to identify them [5]. We explain the reason for the conflict in the phylogenetic tree topologies constructed on the basis of nuclear markers

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