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Abstract Species are a fundamental unit of biodiversity. Yet, the existence of clear species boundaries among bacteria has long been a subject of debate. Here, we studied species boundaries in the context of the phylogenetic history of Nostoc, a widespread genus of photoautotrophic and nitrogen-fixing cyanobacteria that includes many lineages that form symbiotic associations with plants (e.g. cycads and bryophytes) and fungi (e.g. cyanolichens). We found that the evolution of Nostoc was characterized by eight rapid radiations, many of which were associated with major events in the evolution of plants. In addition, incomplete lineage sorting associated with these rapid radiations outweighed reticulations during Nostoc evolution. We then show that the pattern of diversification of Nostoc shapes the distribution of average nucleotide identities (ANIs) into a complex mosaic, wherein some closely related clades are clearly isolated from each other by gaps in genomic similarity, while others form a continuum where genomic species boundaries are expected. Nevertheless, recently diverged Nostoc lineages often form cohesive clades that are maintained by within-clade gene flow. Boundaries to homologous recombination between these cohesive clades persist even when the potential for gene flow is high, i.e. when closely related clades of Nostoc co-occur or are locally found in symbiotic associations with the same lichen-forming fungal species. Our results demonstrate that rapid radiations are major contributors to the complex speciation history of Nostoc. This underscores the need to consider evolutionary information beyond thresholds of genomic similarity to delimit biologically meaningful units of biodiversity for bacteria. 

Abstract PremiseSouthern Africa is a biodiversity hotspot rich in endemic plants and lichen‐forming fungi. However, species‐level data about lichen photobionts in this region are minimal. We focused onTrebouxia(Chlorophyta), the most common lichen photobiont, to understand how southern African species fit into the global biodiversity of this genus and are distributed across biomes and mycobiont partners. MethodsWe sequencedTrebouxianuclear ribosomal ITS andrbcLof 139 lichen thalli from diverse biomes in South Africa and Namibia. GlobalTrebouxiaphylogenies incorporating these new data were inferred with a maximum likelihood approach.Trebouxiabiodiversity, biogeography, and mycobiont–photobiont associations were assessed in phylogenetic and ecological network frameworks. ResultsAn estimated 43 putativeTrebouxiaspecies were found across the region, including seven potentially endemic species. Only five clades represent formally described species:T. arboricolas.l. (A13),T. cf.cretacea(A01),T. incrustata(A06),T. lynniae(A39), andT. maresiae(A46). Potential endemic species were not significantly associated with the Greater Cape Floristic Region or desert.Trebouxiaspecies occurred frequently across multiple biomes. Annual precipitation, but not precipitation seasonality, was significant in explaining variation inTrebouxiacommunities. Consistent with other studies of lichen photobionts, theTrebouxia–mycobiont network had an anti‐nested structure. ConclusionsDepending on the metric used, ca. 20–30% of globalTrebouxiabiodiversity occurs in southern Africa, including many species yet to be described. With a classification scheme forTrebouxianow well established, tree‐based approaches are preferable over “barcode gap” methods for delimiting new species. 

Abstract Peltigera globulata Miadl. & Magain, a new species in the P. ponojensis/monticola species complex of section Peltigera , is formally described. This clade was previously given the interim designation Peltigera sp. 17. It is found in sun-exposed and xeric habitats at high altitudes in Peru and Ecuador. Peltigera globulata can be easily recognized by its irregularly globulated margins covered mostly by thick, white pruina, somewhat resembling the sorediate thallus margins of P. soredians , another South American species from section Peltigera . The hypervariable region of ITS1 (ITS1-HR), which is in general highly variable among species of section Peltigera , does not have diagnostic value for species identification within the P. ponojensis/monticola complex. Nevertheless, no significant level of gene flow was detected among eight lineages representing a clade of putative species (including P. globulata ) within this complex. ITS sequences from the holotype specimens of P. monticola Vitik. (collected in 1979) and P. soredians Vitik. (collected in 1981) and lectotype specimens of P. antarctica C. W. Dodge (collected in 1941) and P. aubertii C. W. Dodge (collected in 1952) were successfully obtained through Sanger and Illumina metagenomic sequencing. BLAST results of these sequences revealed that the type specimen of P. monticola falls within the P. monticola/ponojensis 7 clade, which represents P. monticola s. str., and confirmed that the type specimen of P. aubertii falls within a clade identified previously as P. aubertii based on morphology. The ITS sequence from the type specimen of P. soredians , which superficially resembles P. globulata , confirms its placement in the P. rufescens clade. Finally, we discovered that the name P. antarctica was erroneously applied to a lineage in the P. ponojensis/monticola clade. The ITS sequence from the type specimen of P. antarctica represents a lineage within the P. rufescens clade, which is sister to the P. ponojensis/monticola clade. 

Abstract Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package athttps://github.com/cjpardodelahoz/pss.