Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota).

Bruce Mccune,Steven Leavitt,Xinli Wei,Hui Li,Yoshikazu Yamamoto,H Thorsten Lumbsch,Jiangchun Wei,Tamás Papp,Svetlana Tchabanenko

doi:10.1371/journal.pone.0163664

Abstract

Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the “Automatic Barcode Gap Discovery” (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories.

Highlights

Molecular sequence data have had a pronounced effect on our understanding of species boundaries, especially in organisms with relatively simple morphologies and considerable variability of phenotypic characters, such as lichen-forming fungi
Soredia were present in all H. hypotrypa specimens, in many cases, the soredia were distributed along the cracks of the upper surface and could be overlooked (Fig 1C)
Note: Marginal-likelihood estimates and Bayes factor testing results (2lnBf)BF = 2 x; The model receiving the best marginal-likelihood score for each estimation method is indicated by a 2lnBf score = N/A, and its associated marginal likelihood is in bold

Summary

Introduction

Molecular sequence data have had a pronounced effect on our understanding of species boundaries, especially in organisms with relatively simple morphologies and considerable variability of phenotypic characters, such as lichen-forming fungi. Similar to most major biological groups, identifying the appropriate character sets is one of the greatest challenges with empirical species delimitation in lichen-forming fungi [1,2,3,4,5,6]. Cryptic species are often identified using molecular data, and in some cases cryptic species are corroborated by formerly overlooked phenotypic characters [7,8,9,10,11]. Some species-level lineages were shown to consist of chemically or morphologically polymorphic individuals that were previously regarded as separate taxa [12,13,14]

Methods

Results

Conclusion