Species assemblages of insular Caribbean Sticta (lichenized Ascomycota: Peltigerales) over ecological and evolutionary time scales.

Phylogenetic approaches to macroevolution have provided unique insight into evolutionary relationships, ancestral ranges, and diversification patterns for many taxa. Similar frameworks have also been developed to assess how environmental and/or spatial variables shape species diversity and distribution patterns at different spatial/temporal scales, but studies implementing these are still scarce for many groups, including lichens. Here, we combine phylogeny-based ancestral range reconstruction and diversification analysis with community phylogenetics to reconstruct evolutionary origins and assess patterns of taxonomic and phylogenetic relatedness between island communities of the lichenized fungal genus Sticta in the Caribbean. Sampling was carried out in the Greater Antilles (Cuba, Jamaica, Dominican Republic, and Puerto Rico) and Lesser Antilles (Dominica, Guadeloupe, and Martinique). Data for six molecular loci were obtained for 64 candidate Caribbean species and used to perform both macroevolutionary phylogenetics, which also included worldwide taxa, and phylobetadiversity analyses, which emphasized island-level communities. Our work uncovered high levels of island endemism (∼59%) in Caribbean Sticta. We estimate initial colonization of the region occurred about 19 Mya from a South American ancestor. Reverse migration events by Caribbean lineages to South America were also inferred. We found no evidence for increased diversification rates associated with range expansion into the Caribbean. Taxonomic and phylogenetic turnover between island-level communities was most strongly correlated with environmental variation rather than with geographic distance. We observed less dissimilarity among communities from the Dominican Republic and Jamaica than between these islands and the Lesser Antilles/Puerto Rico. High levels of hidden diversity and endemism in Caribbean Sticta reaffirm that islands are crucial for the maintenance of global biodiversity of lichenized fungi. Altogether, our findings suggest that strong evolutionary links exist between Caribbean and South American biotas but at regional scales, species assemblages exhibit complex taxonomic and phylogenetic relationships that are determined by local environments and shared evolutionary histories.

Cophylogenetic patterns in algal symbionts correlate with repeated symbiont switches during diversification and geographic expansion of lichen-forming fungi in the genus Sticta (Ascomycota, Peltigeraceae).

Species in the fungal genus Sticta form symbiotic associations primarily with either green algae or cyanobacteria, but tripartite associations or photosymbiodemes involving both types of photobionts occur in some species. Sticta is known to associate with green algae in the genus Symbiochloris. However, previous studies have shown that algae from other genera, such as Heveochlorella, may also be suitable partners for Sticta. We examined the diversity of green algal partners in the genus Sticta and assessed the patterns of association between the host fungus and its algal symbiont. We used multi-locus sequence data from multiple individuals collected in Australia, Cuba, Madagascar, Mauritius, New Zealand, Reunion and South America to infer phylogenies for fungal and algal partners and performed tests of congruence to assess coevolution between the partners. In addition, event-based methods were implemented to examine which cophylogenetic processes have led to the observed association patterns in Sticta and its green algal symbionts. Our results show that in addition to Symbiochloris, Sticta associates with green algae from the genera Chloroidium, Coccomyxa, Elliptochloris and Heveochlorella, the latter being the most common algal symbiont associated with Sticta in this study. Geography plays a strong role in shaping fungal-algal association patterns in Sticta as mycobionts associate with different algal lineages in different geographic locations. While fungal and algal phylogenies were mostly congruent, event-based methods did not find any evidence for cospeciation between the partners. Instead, the association patterns observed in Sticta and associated algae, were largely explained by other cophylogenetic events such as host-switches, losses of symbiont and failure of the symbiont to diverge with its host. Our results also show that tripartite associations with green algae evolved multiple times in Sticta.

Oligocene origin and drivers of diversification in the genus Sticta (Lobariaceae, Ascomycota).

A major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations but it is still not clear which have a significant impact and how drivers interact. To study diversification, we chose the lichen genus Sticta, by sampling through most of the global range and producing a time tree. We estimate that Sticta originated about 30 million years ago, but biogoegraphic analysis was unclear in estimating the origin of the genus. Furthermore, we investigated the effect of dispersal ability finding that Sticta has a high dispersal rate, as collections from Hawaii showed that divergent lineages colonized the islands at least four times. Symbiont interactions were investigated using BiSSE to understand if green-algal or cyanobacterial symbiont interactions influenced diversification, only to find that the positive results were driven almost completely by Type I error. On the other hand, another BiSSE analysis found that an association with Andean tectonic activity increases the speciation rate of species.

A new species of Megalaria (Ramalinaceae, Ascomycota) from Thailand, and recognition of subgenus Catillochroma.

Tropical regions harbor a substantial diversity of lichenized fungi, but face numerous threats to their persistence, often even before previously unknown species have been described and their evolutionary relationships have been elucidated. Megalaria (Ramalinaceae) is a lichen-forming genus of fungi that produces crustose thalli, and includes a number of lineages occupying tropical rain forests; however, taxonomic and phylogenetic work on this clade is limited. Here we leverage both morphological and sequence data to describe a new species from the tropics, M.pachaylenophila. This taxon forms a crustose thallus, lacks secondary metabolites, and occurs in mangrove forests of Thailand. We supplemented molecular data from this species with data from other species, including two genera related to and occasionally included in Megalaria, namely Catillochroma and Lopezaria. Our analyses revealed Catillochroma species form a monophyletic group embedded within Megalaria, and we therefore recognize this clade at the subgeneric level. Since we only included the type species of Lopezaria in this study, we refrain from proposing a taxonomic conclusion for that clade at the moment. Several taxonomic combinations are made to reflect phylogenetic evidence supporting the inclusion of these species in Megalaria.

Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota).

In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.