Recombination provides evidence for ancient hybridisation in the Silene aegyptiaca (Caryophyllaceae) complex

Abstract

Recombination events among distinct alleles complicate phylogenetic estimation. Various in vivo and in vitro processes can bring distinct alleles into the same genome to then undergo recombination, which may subsequently mislead phylogenetic inference if not assessed properly. Among the processes bringing divergent alleles together, hybridisation is perhaps the simplest and most likely, but alternatives need to be considered before hybridisation can be accepted as the underlying cause. Such alternatives include the presence of paralogues or deeply coalescing alleles, as well as amplification artefacts. Here, we document a recombination event that apparently took place between two divergent lineages of the Silene aegyptiaca complex in the flowering plant family Caryophyllaceae. We evaluate several possible mechanisms that might be responsible for the observed pattern. An ancient introgressive hybridisation event was the simplest explanation for the observations, compatible with geographic proximity of the affected lineages, whereas paralogy and deep coalescence are difficult to reconcile with the evidence obtained from a species tree of the group based on six different, nonrecombinant genes and gene trees inferred using two partitions of the recombinant locus.

Speciation and periodic restricted environments. The case of genus Ononis L. (subsections Natrix and Viscosae)

“…The gene flow associated with those environmental variations explains coalescence and introgression phenomena between the complex O. natrix, O. ramosissima, O. pubescens, and O. breviflora and the other taxa. A similar possibility has been suggested by several authors for other Leguminosae genera (Byrne et al 2002;Ramos et al 2009;Yoder et al 2013;Liu et al 2017) and other botanic families (Guti errez-Larena et al 2002, Palme et al 2004Molins et al 2011;Blanco-Pastor et al 2012;Tamaki and Okada, 2014;Valc arcel et al 2017) as a gradual speciation (Pfeil et al 2017). In the case analyzed here, the low haplotype sharing between O. natrix or O. ramosissima with the species of subsection Viscosae (only three, 23% of haplotypes detected for this subsection), as well as the huge percentage of exclusive haplotypes for the other subspecies of O. viscosa (more specially O. subcordata, O. crotalarioides, O. brachycarpa and O. porrigens, 77% of haplotypes), better explains the restrictive environmental conditions for most of the subspecies of O. viscosa, and the strong current PRE that they are subject to.…”

A new taxonomic backbone for the infrageneric classification of the species‐rich genus Silene (Caryophyllaceae)

“…Therefore, we chose to analyse them in a species tree under the multispecies coalescent framework, which efficiently handles the problem of incomplete lineage sorting (Jones & al., 2015;Jones, 2016). There may be other reasons for the discrepancies between the gene trees, e.g., stochasticity, hybridization and paralogy Petri & Oxelman, 2011;Jones & al., 2013;Pfeil & al., 2017). Careful interpretation of support may reduce the impact of stochasticity, but support can be quantified in many different ways.…”

Phylogeography and population genetics ofAcanthophyllum squarrosumcomplex (Caryophyllaceae) in the Irano-Turanian region

“…In this study, phylogenetic trees and haplotype networks provided no evidence for distinct genetic groups in the A. squarrosum complex, possibly because of incomplete lineage sorting and/or introgression following secondary contacts after speciation. Introgression and hybridization in Caryophyllaceae have been described previously in a number of studies (Fior, Karis, Casazza, Minuto, & Sala, 2006;Petri, Pfeil, & Oxelman, 2013;Pfeil, Toprak, & Oxelman, 2017;Pirani et al, 2014), and had important roles in diversification of Acanthophyllum species (Ghaffari, 2004).…”