Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene

Abstract

BackgroundIncreasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe.ResultsWe sequenced the homologues of the SlX1/Y1 genes in several Sileneae species. We demonstrate that different parts of the SlX1/Y1 region give different phylogenetic signals. The major discrepancy is that Silene vulgaris and S. sect. Conoimorpha (S. conica and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the Silene SlX1/Y1 gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict.ConclusionThe phylogenetic conflict in the Silene SlX1/Y1 gene cannot be explained by paralogy or artefacts, such as in vitro recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.

A New Lineage‐Based Tribal Classification of the Family Caryophyllaceae

“…1); just like Paronychia, Dianthus is a very large genus (;300 species; Bittrich 1993) that has not been broadly sampled. Our matK analysis identified a paraphyletic Silene with Lychnis nested within it, which is consistent with results of other studies, including Oxelman and Lidén (1995;ITS and 5.8S), Oxelman et al (1997;rps16), Erixon and Oxelman (2008), and Rautenberg et al (2008;SIX1 and YI). Our combined analysis showed that Silene and Lychnis were sister to each other, consistent with findings of Popp and Oxelman (2004; RNA polymerase gene family, ITS, and rps16), Oxelman et al (2001;ITS and rps16), and Fior et al (2006); this may be due to the more limited sampling in those analyses.…”

“…For most specimens, the matK, trnL-F, and rps16 chloroplast gene regions were analyzed; three independent regions were chosen to test for incongruence that may have resulted from chloroplast recombination, which was detected in the Sileneae by Erixon and Oxelman (2008), or from hybridization or lineage sorting, as hypothesized by Rautenberg et al (2008). To amplify matK, the entire matK coding exon was amplified, together with a portion of the 59 and 39 exons for trnK (and associated intronic regions), with the primers trnK1F and trnK2R (see table 2 for primer source information) under the following polymerase chain reaction (PCR) parameters: 94°C for 4 min, followed by 30 cycles of 94°C for 1 min, 50°C for 1 min, and 72°C for 2.5 min.…”

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

“…Although recombination can be seen simply as a confounding process, it can also be an opportunity to detect the footprint of ancient hybridisation (Wendel and Doyle 1998;Linder and Rieseberg 2004;Rautenberg et al 2008;Kelly et al 2010). Hybridisation has the potential to bring together divergent alleles into the same genome, where they can then be recombined.…”

“…However, competing explanations for the origins of chimaeric alleles need to be considered before hybridisation can be inferred (e.g. Rautenberg et al 2008;Frajman et al 2009). …”

“…Hybridisation has the potential to bring together divergent alleles into the same genome, where they can then be recombined. If a recombined allele becomes fixed and persists to be sampled, it may be possible to infer which lineages contributed to this allele, for example, by separate phylogenetic analysis of non-recombined parts of the locus (Rautenberg et al 2008;Kelly et al 2010;Schwartz et al 2015) combined with multi-labelling approaches (Visser et al 2012). However, competing explanations for the origins of chimaeric alleles need to be considered before hybridisation can be inferred (e.g.…”