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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.

Nostoc cyanobacteria are among the few organisms capable of fixing both carbon and nitrogen. These metabolic features are essential for the cyanolichen symbiosis, where Nostoc supplies both carbon (as glucose) and nitrogen (as ammonium) to a cyanolichen-forming fungal partner. This nutrient flow was established by seminal biochemical studies published in the 20th century. Since then, cyanolichen metabolism has received little attention, and the molecular mechanisms that underlie the physiology of lichenized Nostoc remain mostly unknown. Here, we aimed to elucidate the genomic and transcriptional changes that enable Nostoc’s metabolic role in cyanolichens. We used comparative genomics across 243 genomes of Nostoc s. lat. coupled with metatranscriptomic experiments using Peltigera cyanolichens. We found that genes for photoautotrophic carbon fixation are upregulated in lichenized Nostoc. This likely results in a higher rate of carbon fixation that allows Nostoc to provide carbon to the fungal partner while meeting its own metabolic needs. We also found that the transfer of ammonium from Nostoc to the lichen-forming fungus is facilitated by two molecular mechanisms: (i) transcriptional downregulation of glutamine synthetase, the key enzyme responsible for ammonium assimilation in Nostoc; and (ii) frequent losses of a putative high-affinity ammonium permease, which likely reduces Nostoc’s capacity to recapture leaked ammonium. Finally, we found that the development of motile hormogonia is downregulated in lichenized Nostoc, which resembles the repression of motility in Nostoc symbionts after they colonize symbiotic cavities of their plant hosts. Our results pave the way for a revival of cyanolichen ecophysiology in the omics era.

A new species belonging to the lichen genus Physconia is described from Alaska and the Canadian and American Rocky Mountains and adjacent forested regions. It is also reported from China, Nepal, India and Siberia. The new species, Physconia labrata, is superficially similar to P. perisidiosa, but can be distinguished by having a blackened, corticate lower surface and a paraplectenchymatous upper cortex.

Species conservation depends on accurate data, but for many lichens existing collections are geographically biased and contain many taxonomic errors. It is unclear whether ‘non-expert’, systematic monitoring schemes can address these sources of error, particularly for taxonomically challenging lichens (e.g. species requiring chemistry for accurate identification). In this case study we use the Alberta Biodiversity Monitoring Institute (ABMI), a large-scale, systematic, multi-taxon monitoring programme, to better understand the ecology and distribution of a putative rare species, Cladonia rei. Collections of C. rei from Alberta dating from 1947 suggested the species was broadly distributed but rare, with seven accessioned specimens. We used comparative morphology, thin-layer chromatography and habitat modelling to compare historical records against more recent material from ABMI surveys. Contrary to the historical collections, ABMI samples suggest C. rei is almost entirely limited to the dry mixed grassland, northern fescue grassland and aspen parkland natural regions, and that within these ecosystems it is relatively common. The typical ecotype exhibited included a persistent primary thallus, podetia with a persistent basal cortex, and secondary squamules; typically they lacked cups, well-developed apothecia and fumarprotocetraric acid, and ramifications were sparse. Cladonia rei was consistently found in pastures and undisturbed grasslands that hosted relatively rich communities of epigeic lichens, thus it does not appear to act as a pioneer in Alberta or to commonly occupy the anthropogenic niches documented elsewhere. In summary, large-scale, systematic, non-targeted monitoring employing novices redressed issues of sample bias through almost 300 C. rei collections, simultaneously improving the ecological understanding of a putative rare species.

There is a critical need for monitoring programmes to assess change or trends in species status to inform conservation. A key aspect in developing such programmes is evaluating their statistical power--the ability to detect a real change. Here we examine the capacity of a broad-scale biodiversity monitoring programme in Alberta, Canada to measure changes in species prevalence. Using observed variation in detectability and prevalence for 252 species monitored at 85 sites, we simulated 3% annual declines and evaluated sample size (6 different sizes) and length of monitoring (5 different durations) necessary to detect change with a 90% certainty (power) at an α of 0.1. Our results suggest that after four monitoring cycles (e.g., 20 years for a 5-year cycle) a power of 90% can be expected for 99% of species when monitoring 1,625 sites, 65% of species for 300 sites, 27% of species for 75 sites, and 8% of species for 25 sites. We found that 66% detectability and 50% prevalence were needed to ensure that 3% annual change is detected at 50 sites over a 20-year period. Our results demonstrate that broad-scale monitoring programmes cannot effectively detect trends in all species at all spatial scales. The time period and spatial scale necessary to detect a real change at a specified level needs to be provided to stakeholders to ensure the short-term success of biodiversity monitoring programmes and to ensure that the most robust indicators of biodiversity are selected.

1. Dispersers in heterogeneous habitat theoretically should target the habitat(s) where reproduction and survival (i.e. fitness) will be highest. However, the cues that dispersing animals respond to are not well understood: differences in habitat quality ultimately may be important, but whether animals respond to these differences may be influenced by their own familiarity with different habitats. 2. To determine if dispersers reacted to differences in habitat, we documented the exploratory movements, dispersal, and settlement patterns of juvenile North American red squirrels (Tamiasciurus hudsonicus) originating in adjacent patches of different habitats. 3. Dispersers originating in mature, closed-canopy forest (linked to higher female reproductive success and smaller territories) did not explore contrasting open forest with lower tree densities, and the magnitude of the dispersers' explorations was relatively similar. In contrast, dispersers from the open forest habitat made explorations that carried them into contrasting, mature forest habitat, and their explorations were more variable across individuals. 4. When settlement occurred, it was strongly philopatric in all groups of dispersers, although the distances and directions favoured during the exploratory phase of dispersal remained strong predictors of where settlement occurred. Overall, processes favouring philopatry (i.e. maternal influences, competitive advantages, etc.) appeared to dominate the dispersal of our study animals, even those that were exposed to higher quality habitat during their explorations. 5. Secondarily, annual stochasticity (or some correlate) affected the scale of exploration and timing of settlement more than the relative quality of habitat in which dispersers were born. 6. Studies such as this that seek to understand the relative importance of individual experience, habitat familiarity, and habitat quality are important to ultimately understanding how individual animals and populations react to habitat heterogeneity.

The Alberta Biodiversity Monitoring Institute (ABMI) monitors large-scale responses of biodiversity to environmental change in Alberta, Canada, based on standardized and ongoing data collection. In this case study, we show that such a standardized monitoring system has many data management challenges. In the almost 20 years since the conception of the Institute, we have identified 4 key characteristics that are required for large-scale, long-term biodiversity monitoring programs to be operational: 1) data must be publicly accessible; 2) methods and terminology must be standardized to facilitate consistency around data and information collection, analysis, and reporting; 3) the information system must be flexible so that components can be modified or added without compromising the functionality of the other components or the whole system; and 4) the system must be scalable so that it can support input, storage, and retrieval as data load increases. These characteristics are important to ensure that the products and tools generated from our monitoring program can support management at large spatial scales in the complex socio-ecological system of Alberta.

Because natal dispersal affects both individual fitness and population persistence, it is important to understand how dispersers are affected by habitat heterogeneity. To explore the effect of habitat on dispersal, we compared the ecology and natal dispersal of red squirrels (Tamiasciurus hudsonicus) originating from mature forest and adjacent commercially thinned forest. Because individuals living along the edge between the 2 forest types were more likely to have experience in both habitats, we classified squirrels according to habitat type (mature or thinned) and position (edge or deep within forest). Using livetrapping and radiotelemetry, we compared 4 habitats in terms of juvenile settlement patterns, surrogate measures of fitness, and population demography. Mature forest appeared to represent the highest quality habitat: mean density, mean overwinter survival, probability of surviving the field season, and success at raising ≥1 juveniles to emergence were higher in mature forest. However, the majority of juveniles from all habitats settled close to their natal territory, and with the exception of juveniles living along the edge of mature forest, juveniles settled within their habitat of origin. Juveniles living along mature edge biased their settlement for deep within mature forest. It appears that dispersal outcomes were affected by a combination of experience and opportunity. There are few, if any, other studies that have simultaneously compared demography, dispersal movements, and settlement patterns across contrasting habitats. While rare, studies such as this that link individual behavior and population theory are vital to effective population and landscape management.

Conservation of lichens is impeded by knowledge gaps on their distribution and habitat requirements. This is a significant issue in vast, isolated and harsh environment regions such as subarctic regions, where lichen communities remain under documented. Lichen biodiversity assessments provide useful insights to better understand the functions supported by these ecologically important and sensitive species. This study aims i) to describe the conservation status of lichen communities and their α- and β-diversity components across a subarctic region in Northern Quebec (190 km2), ii) to describe their functional traits across the habitat types found in this region, and iii) to identify habitat types constituting lichen biodiversity hotspots. Lichens were sampled in 45 plots in habitats ranging from coniferous and deciduous forests to bogs, fens and rocky outcrops. A total of 115 species of largely macrolichens, calicioid lichens and allied fungi were identified, of which 18% currently have ranks of conservation concern at the provincial level, and 38% are newly reported for the region (~124,000 km2 around our study area). Richness across plots averaged 36 ± 9 species and plots richer in microhabitats often harbored more species (R2 = 0.22). Differences in species composition were identified among plots and habitat types through NMDS and perMANOVA analyses (R2 = 0.35; p < 0.001), both being supported by differences in microhabitat composition (Mantel r = 0.22 and perMANOVA R2 = 0.29, respectively; p < 0.001). Thirty-five species showed significant preferences for a habitat based on the Pearson’s phi coefficient of association. Our analysis on functional traits revealed significant patterns of association with habitat types, including i) saxicolous species with rocky outcrops, ii) epiphytic/epixylic species and vegetative reproduction traits (soredia, isidia) with coniferous stands, and iii) species belonging to the Parmeliaceae family with fens. Rocky outcrops represented the main lichen biodiversity hotspots in the region, while other habitat types were also important for maintaining total and complementary biodiversity. We are confident that our methodological approach including systematic sampling, full habitat variability representation, and the evaluation of complementary biodiversity components, can be effectively applied to fill gaps on lichen biodiversity in other underexplored regions across the globe.