Theodore L. Esslinger

Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea(Parmeliaceae, Ascomycota) and Pleistocene population expansions

BackgroundFactors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescent-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies.ResultsWe found that divergence estimates, from both concatenated gene tree and coalescent-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages.ConclusionsOur results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

Multilocus phylogeny of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota): Insights on diversity, distributions, and a comparison of species tree and concatenated topologies

Accurate species circumscriptions are central for many biological disciplines and have critical implications for ecological and conservation studies. An increasing body of evidence suggests that in some cases traditional morphology-based taxonomy have underestimated diversity in lichen-forming fungi. Therefore, genetic data play an increasing role for recognizing distinct lineages of lichenized fungi that it would otherwise be improbable to recognize using classical phenotypic characters. Melanohalea (Parmeliaceae, Ascomycota) is one of the most widespread and common lichen-forming genera in the northern Hemisphere. In this study, we assess traditional phenotype-based species boundaries, identify previously unrecognized species-level lineages and discuss biogeographic patterns in Melanohalea. We sampled 487 individuals worldwide, representing 18 of the 22 described Melanohalea species, and generated DNA sequence data from mitochondrial, nuclear ribosomal, and protein-coding markers. Diversity previously hidden within traditional species was identified using a genealogical concordance approach. We inferred relationships among sampled species-level lineages within Melanohalea using both concatenated phylogenetic methods and a coalescent-based multilocus species tree approach. Although lineages identified from genetic data are largely congruent with traditional taxonomy, we found strong evidence supporting the presence of previously unrecognized species in six of the 18 sampled taxa. Strong nodal support and overall congruence among independent loci suggest long-term reproductive isolation among most species-level lineages. While some Melanohalea taxa are truly widespread, a limited number of clades appear to have much more restricted distributional ranges. In most instances the concatenated gene tree and multilocus species tree approaches provided similar estimates of relationships. However, nodal support was generally higher in the phylogeny estimated from concatenated data, and relationships among taxa within one major clade were largely unresolved in the species tree. This study contributes to our understanding of diversity and evolution in common lichen-forming fungi by incorporating multiple locus sequence data to circumscribe morphologicallly cryptic lineages and infer relationships within a coalescent-based species tree approach.

Diversification of the newly recognized lichen-forming fungal lineage Montanelia (Parmeliaceae, Ascomycota) and its relation to key geological and climatic events

UNLABELLED PREMISE OF THE STUDY In spite of the recent advances in generic and species circumscriptions and in recognizing species diversity in lichen-forming fungi, the timing of speciation and the factors that promote diversification in lichens remain largely unexplored. We used brown parmelioids as a model to assess the timing of divergence and explore the impact of geological and climatic events on lineage divergence and diversification in lichenized fungi. Additionally, to clarify the phylogenetic position of the species currently placed in Melanelia disjuncta group, we evaluated the taxonomic status and phylogenetic relationships within Parmeliaceae. • METHODS Phylogenetic relationships and divergence time estimates were inferred from a four-loci data set. Alternative hypotheses were tested using Shimodaira-Hasegawa and expected likelihood weights tests. • KEY RESULTS The M. disjuncta group forms a strongly supported, monophyletic lineage independent from Melanelia s.s. The M. disjuncta clade arose ca. 23.1 million years ago (Ma). Our results suggest that most of the lineages within the clade diversified during the Miocene (17.6 to 11.2 Ma). The split of other brown parmelioids, such as Emodomelanelia-Melanelixia occurred ca. 41.70 Ma, and the radiation of Melanelixia began during the Eocene-Oligocene transition (ca. 33.75 Ma). • CONCLUSIONS Montanelia is described here as a new genus to accommodate species of the Melanelia disjuncta group. Further, the study indicates that the current species delimitation within the newly described genus requires revision. We provide evidence of lineage divergence of Montanelia at the Oligocene-Miocene boundary. Our results indicate that the diversification during Miocene would have happened during major mountain uplifts.

Recent Literature on Lichens—192*

ABBAS, A., A. TUMUR, H. MIJIT & JI-NONG WU. 2002. Contribution to the knowledge of lichens from Xinjiang, China, including a preliminary checklist. Chenia 7: 173–186. 1 fig. 1 tab. [Lists 282 species, of which 182 are new records for the province and 36 are said to be new to China (not detailed).] AGHAMIRI, R. & D. W. SCHWARTZMAN. 2002. Weathering rates of bedrock by lichens: a mini watershed study. Chemical Geology 188: 249–259. 1 fig. 8 tab. AHMAN, B. 1996. Effect of bentonite and ammonium-ferric(III)-hexacyanoferrate (II) on uptake and elimination of radiocaesium in reindeer. Journal of Environmental Radioactivity 31: 29–50. 5 fig. 6 tab. AHMAN, B. 1998. Contaminants in food chains of Arctic ungulates: what have we learned from the Chernobyl accident. Rangifer 18: 119–126. 2 fig. AHMAN, B. 1999. Transfer of radiocaesium via reindeer meat to man—effects of countermeasures applied in Sweden. Journal of Environmental Radioactivity 46: 113–120. 1 fig. 1 tab. AHMAN, B., A. NILSSON, E. ELORANTA & K. OLSSON. 2002. Wet belly in reindeer (Rangifer tarandus tarandus) in relation to body condition, body temperature and blood constituents. Acta Veterinaria Scandinavica 43: 85–97. 4 fig. 2 tab. [Includes study of lichen fed reindeer.] AHMAN, B., A. RYDBERG & G. AHMAN. 1986. Macrominerals in free-ranging Swedish reindeer during winter. Rangifer, Special Issue 1986: 31–38. 3 fig. 4 tab. AHMAN, B., S. M. WRIGHT & B. J. HOWARD. 2002. Effect of origin of radiocaesium on the transfer from fallout to reindeer meat. Science of the Total Environment 278: 171–181. 3 fig. 5 tab. ALVERDIYEVA, S. 2003. Lichens of Azerbaijan. International Lichenological Newsletter 36: 15–16. [Brief note on progress studying the flora.] ANTIPIN, V. K. & T. Y. DYACHKOVA. 2001. Mire flora and vegetation in the eastern part of Onega Peninsula. Botanicheskii Zhurnal 86: 89–94. 1 fig. [A few lichens mentioned.] ANTONIN, V. 2002. The floras and identification keys of fungi and lichens in the Central European region: past and present, p. 12. In R. M. Mlezivova (ed.), Floras, Distribution Atlases and Vegetation Surveys in Central Europe. Abstracts from the IXth Congress of the Czech Botanical Society, Lednice, August 19–23, 2002 [Flory, atlasy rozsiřeni a vegetacni přehledy ve středni Evropř. Sbornik abstraktů z IX. Sjezdu Ceske botanicke spolesnosti, Lednice 19.–23. srpna 2002]. Czech Botanical Society [seska botanicka spolesnost], Praha. [Brief abstract.]

Neogene-dominated diversification in neotropical montane lichens: dating divergence events in the lichen-forming fungal genus Oropogon (Parmeliaceae).

PREMISE OF THE STUDY Diversification in neotropical regions has been attributed to both Tertiary geological events and Pleistocene climatic fluctuations. However, the timing and processes driving speciation in these regions remain unexplored in many important groups. Here, we address the timing of diversification in the neotropical lichenized fungal genus Oropogon (Ascomycota) and assess traditional species boundaries. METHODS We analyzed sequence data from three loci to assess phenotypically circumscribed Oropogon species from the Oaxacan Highlands, Mexico. We provide a comparison of dated divergence estimates between concatenated gene trees and a calibrated multilocus species-tree using substitution rates for two DNA regions. We also compare estimates from a data set excluding ambiguously aligned regions and a data set including the hyper-variable regions in two ribosomal markers. KEY RESULTS Phylogenetic reconstructions were characterized by well-supported monophyletic clades corresponding to traditionally circumscribed species, with the exception of a single taxon. Divergence estimates indicate that most diversification of the sampled Oropogon species occurred throughout the Oligocene and Miocene, although diversification of a single closely related clade appears to have occurred during the late Pliocene and into the Pleistocene. Divergence estimates calculated from a data set with ambiguously aligned regions removed were much more recent than those from the full data set. CONCLUSIONS Overall, our analyses place the majority of divergence events of Oropogon species from the Oaxacan Highlands within the Neogene and provide strong evidence that climatic changes during the Pleistocene were not a major factor driving speciation in the lichenized genus Oropogon in neotropical highlands.

Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae (Ascomycota).

Microbial symbionts are instrumental to the ecological and long‐term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species‐rich lichen‐forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.

Molecular phylogeny of the genus Physconia (Ascomycota, Lecanorales) inferred from a Bayesian analysis of nuclear ITS rDNA sequences

A Bayesian analysis of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences was used to infer phylogenetic relationships of 14 Physconia species. The analysis supports the monophyly of the genus. Three well supported clades can be distinguished within Physconia: the series griseae, venustae and pulverulentae. The relationships of these clades, however, is not resolved with confidence. Cortical characters are re-evaluated on the basis of the phylogenetic hypothesis. Anatomical features of the upper cortex are only diagnostic above the species level for two special forms of two-layered cortices, while morphological characters, such as lower surface and rhizine-type are characteristic for distinct clades. P. venusta and P. perisidiosa are not separated in this analysis, but populations of P. muscigena, and European and North American samples of P. americana are clearly distinct and the monophyly of both P. americana and P. muscigena s. lat. is rejected on the basis of a Bayesian hypothesis testing.

Chemosyndromic Variation in the Parmelia pulla Group

Eighteen species or races of the widespread and variable Parmelia pulla group provide the second example of chemosyndromic variation in lichens, a pattern first discovered in Cetrelia. The chemistry of the P. pulla group involves biogenetically related orcinol derivatives including the new depside oxostenosporic acid, for which the structure is determined microchemically, and two other new depsides tentatively identified as the 4-O-demethyl derivatives of divaricatic and stenosporic acids. Although the total chemistry of the P. pulla group is more com- plex than that of Cetrelia, the patterns of joint occurrences of orcinol-type dep- sides are similar and in both may involve partial enzyme specificities related to hy- drophobic side chains on the phenolic secondary products. Four new species from the southern hemisphere are described: P. scabrella Essl. (South Africa), P. pictada Essl. (New Zealand), P. verrucella Essl. (South Africa, Australia, New Zealand) and P. subverrucella Essl. (Australia). Chemosyndromic variation, a new type of chemical variation in the lichen-forming fungi, was recently described in Cetrelia (Culberson & Culberson, 1976), a genus of 15 species segregated from Parmelia (Culberson & Culberson, 1968). Chemosyndromic variation in the lichens differs sharply from classical chemical variation in which con- generic chemotypes show simple replacements of one or a few substances. From the relatively large number of biogenetically related secondary compounds in Cetrelia, in- dividual species produce characteristic sets of products, or chemosyndromes, that ap- pear to show progressive chemical changes. The chemosyndromes of the 15 species of Cetrelia can be ordinated by side-chain length of substituents on phenolic acid units. Most Cetrelia species, especially those having compounds with side chains of moderate length, produce a relatively large number of substances of which one or two are in ap- preciably higher concentration than the rest. Analysis of the total chemical variation in Cetrelia suggested an explanation involving partial enzyme specificities. For example, depsidases with hydrophobic binding sites could accommodate with differing degrees of efficiency the phenolic units having different hydrophobic side chains. The chemistry

DNA barcoding of brown Parmeliae (Parmeliaceae) species: a molecular approach for accurate specimen identification, emphasizing species in Greenland

Warming of Arctic and alpine regions has a substantial impact on high-altitude/-latitude ecosystems. Shifting biomes due to climate change may lead to adjustments in species distributions and potential extinctions. Therefore, detailed monitoring is requisite to assess biologically meaningful shifts in community composition and species distributions. Some Arctic-alpine lichens have been shown to be particularly sensitive to climatic shifts associated with global change. However, accurate identification of lichenized fungal species remains challenging and may limit the effective use of lichens in climate change research. Given the inherent difficulties in accurate identification of lichenized fungi and the potential value of efficient identifications for bio-monitoring research, we investigated the utility of DNA barcode identification of the 13 brown Parmeliae (Ascomycota) species occurring in Greenland. For these species, we assessed monophyly and genetic distances using the nuclear ribosomal internal transcribed spacer region (ITS), the standard DNA barcode for fungi. We also compared intraspecific distance values to a proposed intra-interspecific threshold value for Parmeliaceae to identify nominal taxa potentially masking previously unrecognized diversity. Our results indicated that the 13 brown Parmeliae species occurring in Greenland can be successfully discriminated using the ITS region. All phenotypically circumscribed species were recovered as well-supported, monophyletic clades. Furthermore, our data supported a barcode gap among congeners for all brown Parmeliae species investigated here. However, high intraspecific genetic distances suggest the potential for previously unrecognized species-lineages in at least five species: Melanelia agnata, M. hepatizon, Montanelia disjuncta, M. panniformis, and M. tominii. Our research facilitates effective, long-term bio-monitoring of climate change in Greenland using lichens by providing accurate molecular identification of brown Parmeliae specimens.