Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae

Sidonie Bellot,Hanno Schaefer,Thomas C Mitchell

doi:10.1038/s41598-019-57249-2

Sidonie Bellot, Hanno Schaefer + Show 1 more

Open Access

https://doi.org/10.1038/s41598-019-57249-2

Copy DOI

Abstract

Phylogenomic studies have so far mostly relied on genome skimming or target sequence capture, which suffer from representation bias and can fail to resolve relationships even with hundreds of loci. Here, we explored the potential of phylogenetic informativeness and tree confidence analyses to interpret phylogenomic datasets. We studied Cucurbitaceae because their small genome size allows cost-efficient genome skimming, and many relationships in the family remain controversial, preventing inferences on the evolution of characters such as sexual system or floral morphology. Genome skimming and PCR allowed us to retrieve the plastome, 57 single copy nuclear genes, and the nuclear ribosomal ITS from 29 species representing all but one tribe of Cucurbitaceae. Node support analyses revealed few inter-locus conflicts but a pervasive lack of phylogenetic signal among plastid loci, suggesting a fast divergence of Cucurbitaceae tribes. Data filtering based on phylogenetic informativeness and risk of homoplasy clarified tribe-level relationships, which support two independent evolutions of fringed petals in the family. Our study illustrates how formal analysis of phylogenomic data can increase our understanding of past diversification processes. Our data and results will facilitate the design of well-sampled phylogenomic studies in Cucurbitaceae and related families.

Highlights

Rapid advances in generation sequencing techniques continue to make it easier and more affordable to produce large amounts of sequence data from fresh material as well as from old herbarium collections[1]
Each plastome could be assembled in a circular molecule consisting of a large and a small single-copy (LSC and SSC) region separated by an inverted repeat (IR)
In all species the IR started with the gene rpl[2] and ended inside the gene ycf[1], except for L. amara, where it started before trnV-GAC and ended in ndhG, so that part of what was the SSC in other Cucurbitaceae was in the IR in L. amara (Fig. 1b)

Summary

Introduction

Rapid advances in generation sequencing techniques continue to make it easier and more affordable to produce large amounts of sequence data from fresh material as well as from old herbarium collections[1]. Due to the large number of crop species in the family, the group has been well classified in the past decades both morphologically[19,20] and through the analysis of a small set of chloroplast (rbcL, matK, trnL, rpl20-rps12) and nuclear (ITS) DNA regions, the latter for more than 60% of the cucurbit species worldwide[21,22,23] In combination, these data have resulted in a reasonably resolved phylogeny estimate for the family, which is largely compatible with biogeographical data[16], but several key relationships remain unresolved so far. We demonstrate the potential of genome skimming data and phylogenetic informativeness methods to resolve divergence events at different epochs of the Cucurbitaceae history and provide new insights on their diversification

Methods

Results

Conclusion