Unveiling cryptic species diversity of flowering plants: successful biological species identification of Asian Mitella using nuclear ribosomal DNA sequences

Yudai Okuyama,Makoto Kato

doi:10.1186/1471-2148-9-105

Yudai Okuyama, Makoto Kato

Open Access

https://doi.org/10.1186/1471-2148-9-105

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Abstract

BackgroundAlthough DNA sequence analysis is becoming a powerful tool for identifying species, it is not easy to assess whether the observed genetic disparity corresponds to reproductive isolation. Here, we compared the efficiency of biological species identification between nuclear ribosomal and chloroplast DNA sequences, focusing on an Asian endemic perennial lineage of Mitella (Asimitellaria; Saxifragaceae). We performed artificial cross experiments for 43 pairs of ten taxonomic species, and examined their F1 hybrid pollen fertility in vitro as a quantitative measure of postzygotic reproductive isolation.ResultsA nonlinear, multiple regression analysis indicated that the nuclear ribosomal DNA distances are sufficient to explain the observed pattern of F1 hybrid pollen fertility, and supplementation with chloroplast DNA distance data does not improve the explanatory power. Overall, with the exception of a recently diverged species complex with more than three biological species, nuclear ribosomal DNA sequences successfully circumscribed ten distinct biological species, of which two have not been described (and an additional one has not been regarded as a distinct taxonomic species) to date.ConclusionWe propose that nuclear ribosomal DNA sequences contribute to reliable identification of reproductively isolated and cryptic species of Mitella. More comparable studies for other plant groups are needed to generalize our findings to flowering plants.

Highlights

DNA sequence analysis is becoming a powerful tool for identifying species, it is not easy to assess whether the observed genetic disparity corresponds to reproductive isolation
Cladistic grouping of the nuclear ribosomal DNA sequences using maximum parsimony (MP), NJ, and BI all resulted in nearly identical topology, subdividing the entire ingroup into three subclades, A-C, in which two to five distinct genotypic clusters were consistently recognized (Figure 3)
The monophyly of M. acerina was not supported by BI, this was apparently due to genetic introgression of ITS sequences with sympatric M. furusei var. subramosa, which has been reported previously [20]

Summary

Introduction

DNA sequence analysis is becoming a powerful tool for identifying species, it is not easy to assess whether the observed genetic disparity corresponds to reproductive isolation. A recent survey of DNA sequences of a nuclear-encoded gene in the Pinus subgenus Strobus indicated that 58% of the taxonomic species studied did not form a monophyletic group [6]. These authors reported that many published studies that include multiple accessions per taxonomic species failed to reconstruct species monophyly for up to 100% of the species examined. If such species non-monophyly is common among plants, any attempt at DNA-based approaches for taxonomy would lose their relevance. Most of these studies examining the correspondence between supported clades in a phylogenetic tree and species rely heavily on traditional taxonomic species circumscriptions, obscuring whether such patterns of species non-monophyly, if observed, can be attributed to true non-monophyly or only to poor resolution of the present taxonomic system

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