Abstract

BackgroundIdentifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other “fast” evolving plastid markers.ResultsOur data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae).ConclusionsWhile nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0416-z) contains supplementary material, which is available to authorized users.

Highlights

  • Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade

  • The phylogenetic informativeness (PI) method does not account for potential phylogenetic noise, Townsend and collaborators [49] recently proposed an analytical solution for estimating the probabilities of correct, incorrect and polytomous resolutions given rates of evolution and a defined state space

  • Mined potential nuclear single-copy genes (NSCG) Our data mining process retrieved 4949 Cornales scaffolds that could be aligned to 546 A. thaliana single-copy gene orthologs

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Summary

Introduction

Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Plastid and nuclear ribosomal DNA loci (nrDNA) have predominantly been used in phylogenetic studies of flowering plants [2,3,4,5,6,7]. Their applicability for resolving shallow divergences is limited by several characteristics. Plastid markers show reduced sequence divergence at a low phylogenetic level in most plant lineages due to the slow and nearly constant rate of plastome evolution relative to the nuclear genome [3, 8]. Due to incomplete homogenization of nrDNA gene families (i.e. partial concerted evolution; [12, 13]), biparental inheritance might be traced inconsistently in hybrids [3, 10, 14, 15]

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