Data from: Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.

包括真菌在内的微生物物种的分布格局，长期以来被视作广布性分布（cosmopolitan）。近年来，历史生物地理学、系统发育学与种群遗传学领域的分子研究，对这一认知提出了挑战。本研究以真菌形态学物种（morphological species）Thelonectria discophora为研究对象探讨该问题，该菌是丛赤壳科（Nectriaceae）最常见的真菌类群之一，几乎在所有地理区域均有发现，被视为广布类群（cosmopolitan taxon）。为明确T. discophora究竟是单一广布物种还是姊妹物种复合体，我们对采集自广泛地理范围的菌株开展了多项系统发育分析，包括标准基因串联分析、贝叶斯一致性分析法（Bayesian concordance methods）以及基于溯祖理论（coalescent theory）的物种树重建。研究结果显示，被归为T. discophora的菌株其物种多样性被严重低估，该类群实际为一个物种复合体（species complex）；在此复合体中，我们共获得16个具有高支持度的独立演化支，每一支均具有局限的地理分布范围与生态特性。本研究重新审视了被归为T. discophora的菌株的分类学地位，并否定了该物种曾被假定的广布分布格局；我们还探讨了地理广布物种的相关假设对其分类学研究、真实物种多样性评估、生物多样性保护以及生态功能研究的启示。