Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usneaantarctica and Usneaaurantiacoatra.

Felix Grewe,Huini Wu,H Thorsten Lumbsch,Elisa Lagostina,Christian Printzen

doi:10.3897/mycokeys.43.29093

Abstract

Neuropogonoid species in the lichen-forming fungal genus Usnea exhibit great morphological variation that can be misleading for delimitation of species. We specifically focused on the species delimitation of two closely-related, predominantly Antarctic species differing in the reproductive mode and representing a so-called species pair: the asexual U.antarctica and the sexual U.aurantiacoatra. Previous studies have revealed contradicting results. While multi-locus studies based on DNA sequence data provided evidence that these two taxa might be conspecific, microsatellite data suggested they represent distinct lineages. By using RADseq, we generated thousands of homologous markers to build a robust phylogeny of the two species. Furthermore, we successfully implemented these data in fine-scale population genomic analyses such as DAPC and fineRADstructure. Both Usnea species are readily delimited in phylogenetic inferences and, therefore, the hypothesis that both species are conspecific was rejected. Population genomic analyses also strongly confirmed separated genomes and, additionally, showed different levels of co-ancestry and substructure within each species. Lower co-ancestry in the asexual U.antarctica than in the sexual U.aurantiacoatra may be derived from a wider distributional range of the former species. Our results demonstrate the utility of this RADseq method in tracing population dynamics of lichens in future analyses.

Highlights

Over the last decades, the use of DNA sequence data to delimit species and reconstruct phylogenetic relationships has become standard (Barraclough and Nee 2001; de Queiroz 2007; Holder and Lewis 2003; Huelsenbeck et al 2001; Taylor et al 2000; Wiens and Penkrot 2002)
We focused on the species delimitation of two closely-related, predominantly Antarctic species differing in the reproductive mode and representing a so-called species pair: the asexual U. antarctica and the sexual U. aurantiacoatra
As a reference sequence to filter for lichen-fungal loci of U. antarctica and U. aurantiacoatra during the restriction associated DNA sequencing (RADseq) processing, we sequenced a specimen of U. strigosa that was collected in Arkansas, U.S.A. (Suppl. material 1)

Summary

Introduction

The use of DNA sequence data to delimit species and reconstruct phylogenetic relationships has become standard (Barraclough and Nee 2001; de Queiroz 2007; Holder and Lewis 2003; Huelsenbeck et al 2001; Taylor et al 2000; Wiens and Penkrot 2002). Some studies demonstrated that morphologically distinct populations could not be separated using single- or multi-locus genetic data These results have been interpreted either as an indication of recent diversification and incomplete lineage sorting (Leavitt et al 2016a; Zhao et al 2017) or that the phenotypes represented populations of the same species (Articus et al 2002; Buschbom and Mueller 2006; Kotelko and Piercey-Normore 2010; Lohtander et al 1998; Myllys et al 2001; Velmala et al 2009). These are lichens that differ in forming either ascomata and reproducing sexually or forming asexual diaspores (soredia), which propagate the fungal and photosynthetic partner simultaneously (Mattsson and Lumbsch 1989; Poelt 1970; Tehler 1982) Otherwise, these species are morphologically identical, but were traditionally regarded as distinct species due to their different reproductive modes (Poelt 1972). A recent study suggests that the phylogenetic relationships between sexual and asexual populations might be more complex (Widhelm et al 2016)

Methods

Results

Discussion

Conclusion