Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity

Fungal-Algal Association Drives Lichens' Mutualistic Symbiosis: A Case Study with Trebouxia-Related Lichens

Biotic and abiotic factors influence the formation of fungal-algal pairings in lichen symbiosis. However, the specific determinants of these associations, particularly when distantly related fungi are involved, remain poorly understood. In this study, we investigated the impact of different drivers on the association patterns between taxonomically diverse lichenized fungi and their trebouxioid symbiotic partners. We collected 200 samples from four biomes and identified 41 species of lichenized fungi, associating them with 16 species of trebouxioid green algae, of which 62% were previously unreported. The species identity of both the fungal and algal partners had the most significant effect on the outcome of the symbiosis, compared to abiotic factors like climatic variables and geographic distance. Some obviously specific associations were observed in the temperate zone; however, the nestedness value was lower in arid regions than in cold, polar, and temperate regions according to interaction network analysis. Cophylogenetic analyses revealed congruent phylogenies between trebouxioid algae and associated fungi, indicating a tendency to reject random associations. The main evolutionary mechanisms contributing to the observed phylogenetic patterns were "loss" and "failure to diverge" of the algal partners. This study broadens our knowledge of fungal-algal symbiotic patterns in view of Trebouxia-associated fungi.

Phylogeography of Ramalina farinacea (Lichenized Fungi, Ascomycota) in the Mediterranean Basin, Europe, and Macaronesia

Ramalina farinacea is an epiphytic lichen-forming fungus with a broad geographic distribution, especially in the Northern Hemisphere. In the eighties of the last century, it was hypothesized that R. farinacea had originated in the Macaronesian–Mediterranean region, with the Canary Islands as its probable southernmost limit, and thereafter it would have increased its distribution area. In order to explore the phylogeography of this emblematic lichen, we analyzed 120 thalli of R. farinacea collected in 38 localities distributed in temperate and boreal Europe, the Western Mediterranean Basin, and several Macaronesian archipelagos in the Atlantic Ocean. Data from two nuclear markers (nrITS and uid70) of the mycobiont were obtained to calculate genetic diversity indices to infer the phylogenies and haplotype networks and to investigate population structure. In addition, dating analysis was conducted to provide a valuable hypothesis of the timing of the origin and diversification of R. farinacea and its close allies. Our results highlight that phylogenetic species circumscription in the “Ramalina farinacea group” is complex and suggests that incomplete lineage sorting is at the base of conflicting phylogenetic signals. The existence of a high number of haplotypes restricted to the Macaronesian region, together with the diversification of R. farinacea in the Pleistocene, suggests that this species and its closest relatives originated during relatively recent geological times and then expanded its range to higher latitudes. However, our data cannot rule out whether the species originated from the Macaronesian archipelagos exclusively or also from the Mediterranean Basin. In conclusion, the present work provides a valuable biogeographical hypothesis for disentangling the evolution of this epiphytic lichen in space and time.

Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids

The study of congruency between phylogenies of interacting species can provide a powerful approach for understanding the evolutionary history of symbiotic associations. Orchid mycorrhizal fungi can survive independently of orchids making cospeciation unlikely, leading us to predict that any congruence would arise from host-switches to closely related fungal species. The Australasian orchid subtribe Drakaeinae is an iconic group of sexually deceptive orchids that consists of approximately 66 species. In this study, we investigated the evolutionary relationships between representatives of all six Drakaeinae orchid genera (39 species) and their mycorrhizal fungi. We used an exome capture dataset to generate the first well-resolved phylogeny of the Drakaeinae genera. A total of 10 closely related Tulasnella Operational Taxonomic Units (OTUs) and previously described species were associated with the Drakaeinae orchids. Three of them were shared among orchid genera, with each genus associating with 1-6 Tulasnella lineages. Cophylogenetic analyses show Drakaeinae orchids and their Tulasnella associates exhibit significant congruence (p < 0.001) in the topology of their phylogenetic trees. An event-based method also revealed significant congruence in Drakaeinae-Tulasnella relationships, with duplications (35), losses (25), and failure to diverge (9) the most frequent events, with minimal evidence for cospeciation (1) and host-switches (2). The high number of duplications suggests that the orchids speciate independently from the fungi, and the fungal species association of the ancestral orchid species is typically maintained in the daughter species. For the Drakaeinae-Tulasnella interaction, a pattern of phylogenetic niche conservatism rather than coevolution likely explains the observed phylogenetic congruency in orchid and fungal phylogenies. Given that many orchid genera are characterized by sharing of fungal species between closely related orchid species, we predict that these findings may apply to a wide range of orchid lineages.

The Role of Photobionts as Drivers of Diversification in an Island Radiation of Lichen-Forming Fungi

Speciation in oceanic islands has attracted the interest of scientists since the 19th century. One of the most striking evolutionary phenomena that can be studied in islands is adaptive radiation, that is, when a lineage gives rise to different species by means of ecological speciation. Some of the best-known examples of adaptive radiation are charismatic organisms like the Darwin finches of the Galapagos and the cichlid fishes of the great African lakes. In these and many other examples, a segregation of the trophic niche has been shown to be an important diversification driver. Radiations are known in other groups of organisms, such as lichen-forming fungi. However, very few studies have investigated their adaptive nature, and none have focused on the trophic niche. In this study, we explore the role of the trophic niche in a putative radiation of endemic species from the Macaronesian Region, the Ramalina decipiens group. The photobiont diversity was studied by Illumina MiSeq sequencing of the ITS2 region of 197 specimens spanning the phylogenetic breadth and geographic range of the group. A total of 66 amplicon sequence variants belonging to the four main clades of the algal genus Trebouxia were found. Approximately half of the examined thalli showed algal coexistence, but in most of them, a single main photobiont amounted to more than 90% of the reads. However, there were no significant differences in photobiont identity and in the abundance of ITS2 reads across the species of the group. We conclude that a segregation of the trophic niche has not occurred in the R. decipiens radiation.

Global Biodiversity Patterns of the Photobionts Associated with the Genus Cladonia (Lecanorales, Ascomycota)

The diversity of lichen photobionts is not fully known. We studied here the diversity of the photobionts associated with Cladonia, a sub-cosmopolitan genus ecologically important, whose photobionts belong to the green algae genus Asterochloris. The genetic diversity of Asterochloris was screened by using the ITS rDNA and actin type I regions in 223 specimens and 135 species of Cladonia collected all over the world. These data, added to those available in GenBank, were compiled in a dataset of altogether 545 Asterochloris sequences occurring in 172 species of Cladonia. A high diversity of Asterochloris associated with Cladonia was found. The commonest photobiont lineages associated with this genus are A. glomerata, A. italiana, and A. mediterranea. Analyses of partitioned variation were carried out in order to elucidate the relative influence on the photobiont genetic variation of the following factors: mycobiont identity, geographic distribution, climate, and mycobiont phylogeny. The mycobiont identity and climate were found to be the main drivers for the genetic variation of Asterochloris. The geographical distribution of the different Asterochloris lineages was described. Some lineages showed a clear dominance in one or several climatic regions. In addition, the specificity and the selectivity were studied for 18 species of Cladonia. Potentially specialist and generalist species of Cladonia were identified. A correlation was found between the sexual reproduction frequency of the host and the frequency of certain Asterochloris OTUs. Some Asterochloris lineages co-occur with higher frequency than randomly expected in the Cladonia species.

Epiphytes in wooded pastures: Isolation matters for lichen but not for bryophyte species richness

Sylvo-pastoral systems are species-rich man-made landscapes that are currently often severely threatened by abandonment or management intensification. At low tree densities, single trees in these systems represent habitat islands for epiphytic cryptogams. Here, we focused on sycamore maple (Acer pseudoplatanus) wooded pastures in the northern European Alps. We assessed per tree species richness of bryophytes and lichens on 90 sycamore maple trees distributed across six study sites. We analysed the effects of a range of explanatory variables (tree characteristics, environmental variables and isolation measures) on the richness of epiphytic bryophytes and lichens and various functional subgroups (based on diaspore size, habitat preference and red list status). Furthermore, we estimated the effect of these variables on the occurrence of two specific bryophyte species (Tayloria rudolphiana, Orthotrichum rogeri) and one lichen species (Lobaria pulmonaria) of major conservation concern. Bryophytes and lichens, as well as their subgroups, were differently and sometimes contrastingly affected by the variables considered: tree diameter at breast height had no significant effect on bryophytes but negatively affected many lichen groups; tree phenological age positively affected red-listed lichens but not red-listed bryophytes; increasing isolation from neighbouring trees negatively affected lichens but not bryophytes. However, the high-priority bryophyte species T. rudolphiana was also negatively affected by increased isolation at small spatial scales. Orthotrichum rogeri was more frequent on young trees and L. pulmonaria was more frequent on trees with thin stems and large crowns. The results indicate that local dispersal is important for lichens, whereas long distance dispersal seems to be more important for colonisation by bryophytes. Furthermore, our study highlights that different conservation measures need to be taken depending on the taxonomic and functional species group or the individual species that is addressed. In practice, for the conservation of a high overall richness in sylvo-pastoral systems, it is crucial to sustain not only old and large trees but rather a wide range of tree sizes and ages.

Assembling the challenging puzzle of algal biodiversity: species delimitation within the genus Asterochloris (Trebouxiophyceae, Chlorophyta)

The genus Asterochloris represents one of the most common, widespread, and diverse taxa of lichen photobionts. In this report, we describe and characterize six new species (A. echinata, A. friedlii, A. gaertneri, A. leprarii, A. lobophora, and A. woessiae) that were identified during our recent investigation of photobiont diversity. We found that the species differed genetically, morphologically, ecologically, and with respect to their mycobiont partners. Statistical analyses revealed significant morphological differentiation of all six newly described species, as well as their separation from previously described Asterochloris species. Chloroplast morphology represented the best morphological marker for species delineation. In fact, each species can be recognized by the dominance and unique assemblage of particular chloroplast types. Although genetically well recognized by rapidly evolving internal transcribed spacer rDNA and actin intron markers, all 13 investigated Asterochloris species shared identical small subunit rDNA sequences. We therefore demonstrated that morphologically and ecologically diverse species can frequently be grouped into a single taxonomic unit in whole-transcriptome sequencing studies, considerably affecting the resulting estimates of species diversity. Finally, we demonstrated the presence of isogamous sexual reproduction in Asterochloris, disputing the current symbiotic dogma of the loss of sexual reproduction in algal symbionts.