Sex, size, competition and escape-strategies of reproduction and dispersal in Lasallia pustulata (Umbilicariaceae, Ascomycetes)

Circadian clock- and temperature-associated genes contribute to overall genomic differentiation along elevation in lichenized fungi

Circadian regulation is linked to local environmental adaptation, and many species with broad climatic niches display variation in circadian genes. Here, we hypothesize that lichenizing fungi occupying different climate zones tune their metabolism to local environmental conditions with the help of their circadian systems. We study two species of the genus Umbilicaria occupying similar climatic niches (Mediterranean and the cold temperate) in different continents. Using homology to Neurospora crassa genes, we identify gene sets associated with circadian rhythms (11 core, 39 peripheral genes) as well as temperature response (37 genes). Nucleotide diversity of these genes is significantly correlated with mean annual temperature, minimum temperature of the coldest month and mean temperature of the coldest quarter. Furthermore, we identify altitudinal clines in allele frequencies in several non-synonymous substitutions in core clock components, for example, white collar-like, frh-like and various ccg-like genes. A dN/dS approach revealed a few significant peripheral clock- and temperature-associated genes (e.g. ras-1-like, gna-1-like) that may play a role in fine-tuning the circadian clock and temperature-response machinery. An analysis of allele frequency changes demonstrated the strongest evidence for differentiation above the genomic background in the clock-associated genes in U. pustulata. These results highlight the likely relevance of the circadian clock in environmental adaptation, particularly frost tolerance, of lichens. Whether or not the fungal clock modulates the symbiotic interaction within the lichen consortium remains to be investigated. We corroborate the finding of genetic variation in clock components along altitude-not only latitude-as has been reported in other species.

Regionally Varying Habitat Relationships in Lichens: The Concept and Evidence with an Emphasis on North-Temperate Ecosystems

Habitat ecology of lichens (lichen-forming fungi) involves diverse adaptations to stressful environments where lichens use specific habitat conditions. Field observations confirm that such habitat ‘preferences’ can vary significantly across species’ distribution ranges, sometimes revealing abrupt changes over short distances. We critically review and generalize such empirical evidence as broad ecological patterns, link these with the likely physiological mechanisms and evolutionary processes involved, and outline the implications for lichen conservation. Non-replicated correlative studies remain only suggestive because the data are frequently compromised by sampling bias and pervasive random errors; further noise is related to unrecognized cryptic species. Replicated evidence exists for three macroecological patterns: (a) regional limiting factors excluding a species from a part of its microhabitat range in suboptimal areas; (b) microhabitat shifts to buffer regionally adverse macroclimates; (c) substrate suitability changed by the chemical environment, notably air pollution. All these appear to be primarily buffering physiological challenges of the adverse conditions at the macrohabitat scale or, in favorable environments, coping with competition or predation. The roles of plasticity, adaptation, dispersal, and population-level stochasticity remain to be studied. Although lichens can inhabit various novel microhabitats, there is no evidence for a related adaptive change. A precautionary approach to lichen conservation is to maintain long-term structural heterogeneity in lichen habitats, and consider lichen ecotypes as potential evolutionarily significant units and a bet-hedging strategy for addressing the climate change-related challenges to biodiversity.

What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

Abandoning the ship using sex, dispersal or dormancy: multiple escape routes from challenging conditions

Natural populations often experience environments that vary across space and over time, leading to spatio-temporal variation of the fitness of a genotype. If local conditions are poor, organisms can disperse in space (physical movement) or time (dormancy, diapause). Facultatively sexual organisms can switch between asexual and sexual reproduction, and thus have a third option available to deal with maladaptedness: they can engage in sexual reproduction in unfavourable conditions (an 'abandon-ship' response). Sexual reproduction in facultatively sexual organisms is often coupled with dispersal and/or dormancy, while bet-hedging theory at first sight predicts sex, dispersal and dormancy to covary negatively, as they represent different escape mechanisms that could substitute for each other. Here we briefly review the observed links between sex, dormancy and dispersal, and model the expected covariation patterns of dispersal, dormancy and the reproductive mode in the context of local adaptation to spatio-temporally fluctuating environments. The correlations between sex, dormancy and dispersal evolve differently within species versus across species. Various risk-spreading strategies are not completely interchangeable, as each has dynamic consequences that can feed back into the profitability of others. Our results shed light on the discrepancy between previous theoretical predictions on covarying risk-spreading traits and help explain why sex often associates with other means of escaping unfavourable situations.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.

Whole-Genome Sequence Data Uncover Widespread Heterothallism in the Largest Group of Lichen-Forming Fungi

Fungal reproduction is regulated by the mating-type (MAT1) locus, which typically comprises two idiomorphic genes. The presence of one or both allelic variants at the locus determines the reproductive strategy in fungi—homothallism versus heterothallism. It has been hypothesized that self-fertility via homothallism is widespread in lichen-forming fungi. To test this hypothesis, we characterized the MAT1 locus of 41 genomes of lichen-forming fungi representing a wide range of growth forms and reproductive strategies in the class Lecanoromycetes, the largest group of lichen-forming fungi. Our results show the complete lack of genetic homothallism suggesting that lichens evolved from a heterothallic ancestor. We argue that this may be related to the symbiotic lifestyle of these fungi, and may be a key innovation that has contributed to the accelerated diversification rates in this fungal group.

Variation in the reproductive strategy of a lichenized fungus along a climatic gradient

BACKGROUND AND AIMS

Onset of reproduction and reproductive allocation patterns are key components of plant reproductive strategies. Life history theory predicts that plants in adverse environments for juvenile performance start reproduction at smaller sizes and exhibit higher reproductive allocation compared to their counterparts in favourable environments. Life history theory will gain in generality if its predictions are shown to apply to a broad range of organisms and modes of reproduction. This study tested whether the asexual reproductive strategy of a lichenized fungus changed along a climatic gradient.

METHODS

The variation in threshold size for asexual reproduction and asexual reproductive allocation of the lichen Lobarina scrobiculata was assessed in 18 populations (9665 individuals) along a climatic gradient spanning 800 km in latitude in Southern Europe. Using generalized linear models and standardized major axis regressions, the allometric relationships and the associated variation in climatic factors according to the changes in the threshold size for reproduction and reproductive allocation patterns were assessed.

KEY RESULTS

The onset of reproduction was size-dependent and the reproductive allocation increased with individual size. Both the threshold size for reproduction and the reproductive allocation varied along the rainfall gradient. A lower threshold size for reproduction and higher reproductive allocation in drier, adverse locations were found. Therefore, populations in drier locations fitted the predictions of life history theory for sexually reproducing organisms in adverse environments for juvenile performance.

CONCLUSIONS

This study highlights the applicability of the life history theory to fungi and to modes of reproduction other than sexual reproduction. Based on the intraspecific variation in the asexual reproductive strategy of a fungal organism with climatic factors, these findings expand the scope of life history theory predictions and increase our understanding of life history diversity and reproductive strategies across environments.

Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus

Background

Many fungal species occur across a variety of habitats. Particularly lichens, fungi forming symbioses with photosynthetic partners, have evolved remarkable tolerances for environmental extremes. Despite their ecological importance and ubiquity, little is known about the genetic basis of adaption in lichen populations. Here we studied patterns of genome-wide differentiation in the lichen-forming fungus Lasallia pustulata along an altitudinal gradient in the Mediterranean region. We resequenced six populations as pools and identified highly differentiated genomic regions. We then detected gene-environment correlations while controlling for shared population history and pooled sequencing bias, and performed ecophysiological experiments to assess fitness differences of individuals from different environments.

Results

We detected two strongly differentiated genetic clusters linked to Mediterranean and temperate-oceanic climate, and an admixture zone, which coincided with the transition between the two bioclimates. High altitude individuals showed ecophysiological adaptations to wetter and more shaded conditions. Highly differentiated genome regions contained a number of genes associated with stress response, local environmental adaptation, and sexual reproduction.

Conclusions

Taken together our results provide evidence for a complex interplay between demographic history and spatially varying selection acting on a number of key biological processes, suggesting a scenario of ecological speciation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0929-8) contains supplementary material, which is available to authorized users.

Multiple-scale environmental modulation of lichen reproduction

It is necessary to understand how environmental changes affect plant fitness to predict survival of a species, but this knowledge is scarce for lichens and complicated by their formation of sexual and asexual reproductive structures. Are the presence and number of reproductive structures in Lobaria pulmonaria, a threatened lichen, dependent on thallus size, and is their formation sequential? Does any size-dependence and sequential formation vary along a climate gradient? Generalized linear mixed models were used to explore the effect of environmental predictors on the size and presence/abundance of each reproductive structure and to determine the probability of a given-sized thallus to develop any reproductive structure. The largest individuals are more likely to develop reproductive structures, and the lichen uses a mixed strategy of early asexual reproduction and late sexual. Macro and microclimatic variables also influenced reproductive capacity. Relationships among climate conditions and lichen size and reproductive capacity can compromise the future viability of the species in the most southern populations of Europe.

Photosynthesis in chlorolichens: the influence of the habitat light regime

The hypothesis that CO(2) gas exchange and chlorophyll a fluorescence (ChlaF) of lichens vary according to the light regimes of their original habitat, as observed in vascular plants, was tested by analysing the photosynthetic performance of 12 populations of seven dorsoventral, foliose lichens collected from open, south-exposed rocks to densely shaded forests. Light response curves were induced at optimum thallus water content and ChlaF emission curves at the species-specific photon flux at which the quantum yield of CO(2) assimilation is the highest and is saturating the photosynthetic process. Photosynthetic pigments were quantified in crude extracts. The results confirm that the maximum rate of gross photosynthesis is correlated with the chlorophyll content of lichens, which is influenced by light as well as by nitrogen availability. Like leaves, shade tolerant lichens emit more ChlaF than sun-loving ones, whereas the photosynthetic quantum conversion is higher in the latter.

Mating systems in representatives of Parmeliaceae, Ramalinaceae and Physciaceae (Lecanoromycetes, lichen-forming ascomycetes)

The progeny of meiosis of eight Parmeliaceae, two Ramalinaceae and seven Physciaceae were subjected to fingerprint analysis using RAPD-PCR applied to single spore isolates. The sample set included common and widespread rarely fertile species (Parmelia sulcata, Pseudevernia furfuracea, Physcia tenella), local to common, infrequently fertile species (Melanelixia glabra, Parmelina tiliacea, Xanthoparmelia conspersa, X. stenophylla, Anaptychia runcinata, Diploicia canescen, Physconia distorta), local to rare, infrequently or regularly fertile species with declining distributions (Parmelina carporrhizans, P. quercina, Ramalina fastigiata, R. fraxinea, Anaptychia ciliaris), and local to common, regularly fertile species (Physcia aipolia, P. stellaris). All species turned out to be heterothallic, polymorphisms among RAPD markers ranging from 10-87%. The significance of these findings for population genetics and conservation biology, and potential reasons for infrequent ascoma formation in some of the species are discussed.

Breeding systems in the lichen-forming fungal genus Cladonia

The breeding systems of three species of the lichen-forming fungal genus Cladonia were investigated. Cladonia floerkeana, Cladonia galindezii, and Cladonia portentosa were selected due to their contrasting ecologies and reproductive strategies, and because they belong to the Lecanorales, the major lichen-forming order. Sibling single-spore progeny were collected from apothecia and used to establish axenic cultures. Two experimental approaches were used to determine breeding systems. First, RAPD-PCR and AFLP fingerprinting revealed that spores from the same apothecium were not genetically uniform, indicating heterothallism in each of these species. Second, segregation of a MAT-2 mating-type gene was assessed using degenerate PCR primers designed to amplify the high-mobility group region. A MAT-2 gene occurred in 40-60% of progeny, consistent with a heterothallic breeding system. The PCR product from C. galindezii was cloned and sequenced, and confirmed to have the characteristic motifs of a MAT-2 HMG gene. This is thought to be the first report of the use of segregation of a mating-type gene among ascospore progeny to determine the breeding system of a fungal species. The ecological significance of the results is discussed.

Growth, reproduction, and population structure in four alpine lichens during 240 years of primary colonization

The increase in thallus diameter and apothecium production, and the population size structure of the saxicolous lichens Umbilicaria cylindrica (L.) Del., Umbilicaria hyperborea (Ach.) Hoffm., Umbilicaria proboscidea (L.) Schrad, and Umbilicaria torrefacta (Lightf.) Schrad, were measured in a chronosequence of 240 years in a glacier foreland in the alpine Jotunheimen National Park in Norway. All four species exhibited a pattern of fast growth in the early decades of their life history, followed by a rapid decrease in growth, slowly approaching a maximum body size. There were clear interspecific differences in initial estimated growth rate, growth period, and maximum size. In all species, apothecium production is strongly correlated with thallus size, but in U. hyperborea the relationship approximates an exponential function, while in the other species the trend is more linear. In U. proboscidea, the slowest to mature, a fairly high proportion of sterile individuals also occur in the higher size classes. There was no observed trade off between growth and reproduction. Quite the contrary: the species that grow faster also start to reproduce abundantly and early. The relatively slow growth and reproductive maturation of the species implies that a population of 40- to 50-year-old individual thalli is still a population consisting mainly of immigrants. The population size structure of all four species remains strongly skewed during the entire chronosequence, with a predominance of small thalli.Key words: plant life histories, lichen growth rates, size structure, Umbilicaria.

Fungus-specific microsatellite primers of lichens: application for the assessment of genetic variation on different spatial scales in Lobaria pulmonaria

We isolated 12 microsatellite loci for the epiphytic lichen-forming ascomycete Lobaria pulmonaria and studied their patterns of variation within and among populations from Canada and Switzerland. Even though several microsatellites exhibited high levels of variability at different spatial scales, we did not find any evidence for intrathalline variation. Most of the genetic variation was attributed to differences among individuals within populations. High genetic variation was also detected among L. pulmonaria samples taken from individual trees, suggesting that either multiple colonization events had occurred or that local recombination is frequent. The geographically structured distribution of alleles from several microsatellites indicated that L. pulmonaria from Canada and Switzerland represent two distinct evolutionary lineages. The potential to identify multiple alleles, and their transferability to closely related species, make microsatellites an ideal tool to study dispersal, population differentiation, and microevolution in lichens.