Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers.

Ingrid Toresen,Heidi Lie Andersen,Torsten Eriksson,Jenny E E Smedmark,Nannie L Persson,Jeremy Beaulieu

doi:10.1093/aobpla/plaa017

Abstract

The genus Potentilla (Rosaceae) has been subjected to several phylogenetic studies, but resolving its evolutionary history has proven challenging. Previous analyses recovered six, informally named, groups: the Argentea, Ivesioid, Fragarioides, Reptans, Alba and Anserina clades, but the relationships among some of these clades differ between data sets. The Reptans clade, which includes the type species of Potentilla, has been noticed to shift position between plastid and nuclear ribosomal data sets. We studied this incongruence by analysing four low-copy nuclear markers, in addition to chloroplast and nuclear ribosomal data, with a set of Bayesian phylogenetic and Multispecies Coalescent (MSC) analyses. A selective taxon removal strategy demonstrated that the included representatives from the Fragarioides clade, P. dickinsii and P. fragarioides, were the main sources of the instability seen in the trees. The Fragarioides species showed different relationships in each gene tree, and were only supported as a monophyletic group in a single marker when the Reptans clade was excluded from the analysis. The incongruences could not be explained by allopolyploidy, but rather by homoploid hybridization, incomplete lineage sorting or taxon sampling effects. When P. dickinsii and P. fragarioides were removed from the data set, a fully resolved, supported backbone phylogeny of Potentilla was obtained in the MSC analysis. Additionally, indications of autopolyploid origins of the Reptans and Ivesioid clades were discovered in the low-copy gene trees.

Highlights

Polyploidy is a well-known and common phenomenon in plants, defined as having three or more complete sets of chromosomes
The Alba species are in unresolved positions to the rest of the ingroup, in which the Reptans clade is sister to a clade that consists of P. dickinsii, P. fragarioides, the Argentea clade and the Ivesioid clade
When P. fragarioides is excluded [see Supporting Information—Fig. S2], there are only small changes in the posterior probabilities of the tree, and the same is true in the tree in which the Reptans clade is excluded [see Supporting Information—Fig. S4]

Summary

Introduction

Polyploidy is a well-known and common phenomenon in plants, defined as having three or more complete sets of chromosomes. Through a number of different processes resulting in genomic reorganizations, many species with polyploidy in their ancestry function as diploids (Leitch and Bennett 2004; Bento et al 2011; Mandáková et al 2017). There are diploid as well as polyploid species (Index to Plant Chromosome Numbers, IPCN 1979; Kurtto et al 2004), with ploidy levels of up to hexadecaploid (16x) (Kalkman 2004), and a base chromosome. Received: 13 December 2019; Editorial decision: 13 March 2020; Accepted: 4 May 2020. Polyploidization as well as hybridization are considered important processes in the evolution of Potentilla (Potter et al 2007; Dobeš and Paule 2010; Paule et al 2011, 2012)

Objectives

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Results

Discussion

Conclusion