Recombination provides evidence for ancient hybridisation in the Silene aegyptiaca (Caryophyllaceae) complex
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ORIGINAL ARTICLE
Recombination provides evidence for ancient hybridisation in the Silene aegyptiaca (Caryophyllaceae) complex Bernard E. Pfeil 1 & Zeynep Toprak 1,2 & Bengt Oxelman 1
Received: 10 July 2016 / Accepted: 24 May 2017 # The Author(s) 2017. This article is an open access publication
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. Bernard E. Pfeil and Zeynep Toprak are equal contributors. Electronic supplementary material The online version of this article (doi:10.1007/s13127-017-0331-9) contains supplementary material, which is available to authorized users. * Bernard E. Pfeil [email protected]
1
Department of Biological and Environmental Sciences, University of Gothenburg, 40530 Gothenburg, Sweden
2
Department of Biology, Faculty of Sciences, University of Dicle, 21280 Diyarbakir, Turkey
Keywords Recombination . Hybridisation . Phylogenetics . Paralogy . Silene aegyptiaca . Cryptic species
Introduction Recombination among distinct allele lineages can pose a challenge for phylogenetic inference of gene trees (Sanderson and Doyle 1992; Posada and Crandall 2002). In vivo recombination occurs during meiosis when a chromatid of each homologous chromosome crosses over and is exchanged, thus potentially forming chimaeric alleles. The presence of chimaeric alleles has the potential to introduce additional homoplasy into a dataset if non-monophyletic alleles contributed to the chimaera (Sanderson and Doyle 1992). The result can be the disruption of the historical signal, which in turn can lead to incorrect gene tree inference (Sanderson and Doyle 1992; Posada and Crandall 2002), biased branch length (Penny et al. 2008) and node age (Pfeil 2009) estimation. Although recombination can be seen simply as a confounding process, it can also be an opportunity to detect the footprint o
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