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See detailThe fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history
Spjut, Richard; Simon, Antoine ULiege; Guissard, Martin et al

in MycoKeys (2020), 73

We present phylogenetic analyses of the fruticose Ramalinaceae based on extensive collections from many parts of the world, with a special focus on the Vizcaíno deserts in northwestern Mexico and the ... [more ▼]

We present phylogenetic analyses of the fruticose Ramalinaceae based on extensive collections from many parts of the world, with a special focus on the Vizcaíno deserts in northwestern Mexico and the coastal desert in Namibia. We generate a four-locus DNA sequence dataset for accessions of Ramalina and two additional loci for Niebla and Vermilacinia. Four genera are strongly supported: the subcosmopolitan Ramalina, the new genus Namibialina endemic to SW Africa, and a duo formed by Niebla and Vermilacinia, endemic to the New World except the sorediate V. zebrina that disjunctly occurs in Namibia. The latter three genera are restricted to coastal desert and chaparral where vegetation depends on moisture from ocean fog. Ramalina is subcosmopolitan and much more diverse in its ecology. We show that Ramalina and its sister genus Namibialina diverged from each other at c. 48 Myrs, whereas Vermilacinia and Niebla split at c. 30 Myrs. The phylogeny of the fruticose genera remains unresolved to their ancestral crustose genera. Species delimitation within Namibialina and Ramalina is rather straightforward. The phylogeny and taxonomy of Vermilacinia are fully resolved, except for the two youngest clades of corticolous taxa, and support current taxonomy, including four new taxa described here. Secondary metabolite variation in Niebla generally coincides with major clades which are comprised of species complexes with still unresolved phylogenetic relationships. A micro-endemism pattern of allopatric species is strongly suspected for both genera, except for the corticolous taxa within Vermilacinia. Both Niebla and saxicolous Vermilacinia have chemotypes unique to species clades that are largely endemic to the Vizcaíno deserts. The following new taxa are described: Namibialina gen. nov. with N. melanothrix (comb. nov.) as type species, a single new species of Ramalina (R. krogiae) and four new species of Vermilacinia (V. breviloba, V. lacunosa, V. pustulata and V. reticulata). The new combination V. granulans is introduced. Two epithets are reintroduced for European Ramalina species: R. crispans (= R. peruviana auct. eur.) and R. rosacea (= R. bourgeana auct. p.p). A lectotype is designated for Vermilacinia procera. A key to saxicolous species of Vermilacinia is presented. [less ▲]

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See detailAscospore size declines with elevation in two tropical parmelioid lichens
Masson, Didier; Magain, Nicolas ULiege

in Plant and Fungal Systematics (2020), 65(1), 227237

Spore size and shape are biometric parameters frequently used in lichen taxonomy, especially in species characterization. However, the influence of environmental factors on the intraspecific variability ... [more ▼]

Spore size and shape are biometric parameters frequently used in lichen taxonomy, especially in species characterization. However, the influence of environmental factors on the intraspecific variability of these characters remains very little investigated in lichenology. The elevational variation in spore length, width, volume and shape (length/ width ratio) of two species of the genus Hypotrachyna (H. aff. damaziana et H. altorum) occurring on Réunion Island (Indian Ocean) were studied. Spore length, width and volume significantly decrease with elevation in H. aff. damaziana, and spore width and volume also significantly decrease with elevation in H. altorum. There is no relation between spore shape and elevation in either of the two species. A significant correlation was further observed between the intra-individual variability in spore size of H. aff. damaziana and elevation. For this species, inter-individual variability in spore volume is also correlated with mean annual temperature and mean annual precipitation of the sampling locations, and spore width and length are correlated with mean annual temperature. [less ▲]

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See detailPeltigera serusiauxii (Lecanoromycetes, Ascomycota), a new species from Papua New Guinea and Malaysia
Magain, Nicolas ULiege; Goffinet, Bernard; Simon, Antoine ULiege et al

in Plant and Fungal Systematics (2020)

Peltigera serusiauxii is proposed here as a new species from Papua New Guinea and Sabah, northern Borneo (Malaysia). The species belongs to the polydactyloid clade of section Polydactylon. Because of its ... [more ▼]

Peltigera serusiauxii is proposed here as a new species from Papua New Guinea and Sabah, northern Borneo (Malaysia). The species belongs to the polydactyloid clade of section Polydactylon. Because of its large thalli with a glabrous upper surface, this species was previously identified as P. dolichorhiza, but it differs by its polydactylon-type lower surface and the high amount of dolichorrhizin. It appears to be a strict specialist in its association with Nostoc phylogroup IX throughout its known distribution. This is one of many undescribed species remaining to be formally described within the genus Peltigera, especially in Asia and Australasia. [less ▲]

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See detailPeltigera hydrophila (Lecanoromycetes, Ascomycota), a new semi-aquatic cyanolichen species from Chile
Miadlikowska, Jolanta; Magain, Nicolas ULiege; Buck, William R et al

in Plant and Fungal Systematics (2020), 65(1), 210218

Peltigera hydrophila, a new species from Chile tentatively distinguished based on phylogenetic evidence but not yet named, is formally described here. Morphological differences (e.g., non-tomentose ... [more ▼]

Peltigera hydrophila, a new species from Chile tentatively distinguished based on phylogenetic evidence but not yet named, is formally described here. Morphological differences (e.g., non-tomentose thallus) and habitat preferences (semi-aquatic) corroborate molecular and phylogenetic distinctiveness of this early diverging lineage in section Peltigera. Due to overlapping ecological ranges, P. hydrophila shares some morphological traits with aquatic species from the phylogenetically unrelated section Hydrothyriae. [less ▲]

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See detailThree new lichen species from Macaronesia belonging in Ramalinaceae, with the description of a new genus
Van den Boom, Pieter; Magain, Nicolas ULiege

in Plant and Fungal Systematics (2020)

Tylocliostomum is described as a new genus and T. viridifarinosum as a new species. Two Bacidina species, B. pallidocarpa and B. violacea, are also described as new to science. They all occur in ... [more ▼]

Tylocliostomum is described as a new genus and T. viridifarinosum as a new species. Two Bacidina species, B. pallidocarpa and B. violacea, are also described as new to science. They all occur in Macaronesia (Azores, Madeira). [less ▲]

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See detailCophylogenetic patterns in algal symbionts correlate with repeated symbiont switches during diversification and geographic expansion of lichen-forming fungi in the genus Sticta (Ascomycota: Peltigeraceae)
Lindgren, Hanna; Moncada, Bibiana; Lucking, Robert et al

in Molecular Phylogenetics and Evolution (2020)

Highlights • We explored cophylogenetic patterns of fungal and algal partners in the genus Sticta. • Sticta associates with green algae from five genera in Trebouxiophyceae. • Sticta are selective towards ... [more ▼]

Highlights • We explored cophylogenetic patterns of fungal and algal partners in the genus Sticta. • Sticta associates with green algae from five genera in Trebouxiophyceae. • Sticta are selective towards their algal symbionts. • Photosymbiodemes with green algae evolved multiple times in Sticta. Abstract 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. [less ▲]

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See detailPhylogenetic evidence for an expanded circumscription of Gabura (Arctomiaceae)
Magain, Nicolas ULiege; Spribille, Toby; DiMeglio, Joseph et al

in Lichenologist (2020), 52(1), 3-15

Since the advent of molecular taxonomy, numerous lichen-forming fungi with homoiomerous thalli initially classified in the family Collemataceae Zenker have been transferred to other families, highlighting ... [more ▼]

Since the advent of molecular taxonomy, numerous lichen-forming fungi with homoiomerous thalli initially classified in the family Collemataceae Zenker have been transferred to other families, highlighting the extent of morphological convergence within Lecanoromycetes O. E. Erikss. & Winka. While the higher level classification of these fungi might be clarified by such transfers, numerous specific and generic classifications remain to be addressed. We examined the relationships within the broadly circumscribed genus Arctomia Th. Fr., which has been the recipient of several transfers from Collemataceae. We demonstrated that Arctomia insignis (P. M. Jørg. & Tønsberg) Ertz does not belong to Arctomia s. str. but forms a strong monophyletic group with Gabura fascicularis (L.) P. M. Jørg. We also confirmed that Arctomia borbonica Magain & Sérus. and the closely related Arctomia insignis represent two species. We formally transferred A. insignis and A. borbonica to the genus Gabura Adans. and introduced two new combinations: Gabura insignis and Gabura borbonica. We reported Gabura insignis from Europe (Scotland and Ireland) for the first time. While material from Europe and North America is genetically almost identical, specimens from Madagascar, South Africa and Reunion Island belong to three distinct phylogenetic lineages, all of which are present in the latter area and may represent distinct species. In its current circumscription, the genus Gabura may contain up to six species, whereas Arctomia s. str. includes only two species (A. delicatula Th. Fr. and A. teretiuscula P. M. Jørg.). The Gabura insignis group is shown to have an unexpectedly large, subcosmopolitan distribution. With the extended sampling from Arctomiaceae Th. Fr., the placement of Steinera sorediata P. James & Henssen in the genus Steinera Zahlbr. is confirmed and the presence of a new Steinera species from Chile is highlighted. [less ▲]

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See detailUnderstanding the lichen symbiosis through metagenomics
Magain, Nicolas ULiege

Scientific conference (2019, December 11)

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See detailMolybdenum threshold for ecosystem scale alternative vanadium nitrogenase activity in boreal forests
Darnajoux, Romain; Magain, Nicolas ULiege; Renaudin, Marie et al

in Proceedings of the National Academy of Sciences of the United States of America (2019)

Biological nitrogen fixation (BNF) by microorganisms associated with cryptogamic covers, such as cyanolichens and bryophytes, is a primary source of fixed nitrogen in pristine, high-latitude ecosystems ... [more ▼]

Biological nitrogen fixation (BNF) by microorganisms associated with cryptogamic covers, such as cyanolichens and bryophytes, is a primary source of fixed nitrogen in pristine, high-latitude ecosystems. On land, low molybdenum (Mo) availability has been shown to limit BNF by the most common form of nitrogenase (Nase), which requires Mo in its active site. Vanadium (V) and iron-only Nases have been suggested as viable alternatives to countering Mo limitation of BNF; however, field data supporting this long-standing hypothesis have been lacking. Here, we elucidate the contribution of vanadium nitrogenase (V-Nase) to BNF by cyanolichens across a 600-km latitudinal transect in eastern boreal forests of North America. Widespread V-Nase activity was detected (∼15–50% of total BNF rates), with most of the activity found in the northern part of the transect. We observed a 3-fold increase of V-Nase contribution during the 20-wk growing season. By including the contribution of V-Nase to BNF, estimates of new N input by cyanolichens increase by up to 30%. We find that variability in V-based BNF is strongly related to Mo availability, and we identify a Mo threshold of ∼250 ng·glichen−1 for the onset of V-based BNF. Our results provide compelling ecosystem-scale evidence for the use of the V-Nase as a surrogate enzyme that contributes to BNF when Mo is limiting. Given widespread findings of terrestrial Mo limitation, including the carbon-rich circumboreal belt where global change is most rapid, additional consideration of V-based BNF is required in experimental and modeling studies of terrestrial biogeochemistry. [less ▲]

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See detailT-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees
Carbone, Ignazio; White, James B; Miadlikowska, Jolanta et al

in Microbiology resource announcements (2019), 8(29), 00328-19

The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing ... [more ▼]

The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata. [less ▲]

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See detailSpecies diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera
Chagnon, Pierre-Luc; Magain, Nicolas ULiege; Miadlikowska, Jolanta et al

in Journal of Ecology (2019)

Ecological interactions range from purely specialized to extremely generalized in nature. Recent research has showed very high levels of specialization in the cyanolichens involving Peltigera (mycobionts ... [more ▼]

Ecological interactions range from purely specialized to extremely generalized in nature. Recent research has showed very high levels of specialization in the cyanolichens involving Peltigera (mycobionts) and their Nostoc photosynthetic partners (cyanobionts). Yet, little is known about the mechanisms contributing to the establishment and maintenance of such high specialization levels. Here, we characterized interactions between Peltigera and Nostoc partners at a global scale, using more than one thousand thalli. We used tools from network theory, community phylogenetics and biogeographical history reconstruction to evaluate how these symbiotic interactions may have evolved. After splitting the interaction matrix into modules of preferentially interacting partners, we evaluated how module membership might have evolved along the mycobionts’ phylogeny. We also teased apart the contributions of geographical overlap vs phylogeny in driving interaction establishment between Peltigera and Nostoc taxa. Module affiliation rarely evolves through the splitting of large ancestral modules. Instead, new modules appear to emerge independently, which is often associated with a fungal speciation event. We also found strong phylogenetic signal in these interactions, which suggests that partner switching is constrained by conserved traits. Therefore, it seems that a high rate of fungal diversification following a switch to a new cyanobiont can lead to the formation of large modules, with cyanobionts associating with multiple closely retated Peltigera species. Finally, when restricting our analyses to Peltigera sister species, the latter differed more through partner acquisition/loss than replacement (i.e., switching). This pattern vanishes as we look at sister species that have diverged longer ago. This suggests that fungal speciation may be accompanied by a stepwise process of (1) novel partner acquisition and (2) loss of the ancestral partner. This could explain the maintenance of high specialization levels in this symbiotic system where the transmission of the cyanobiont to the next generation is assumed to be predominantly horizontal. Synthesis. Overall, our study suggests that oscillation between generalization and ancestral partner loss may maintain high specialization within the lichen genus Peltigera, and that partner selection is not only driven by partners’ geographical overlap, but also by their phylogenetically conserved traits. [less ▲]

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See detailSpecies in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision
Miadlikowska, Jolanta; Magain, Nicolas ULiege; Pardo de la Hoz, Carlos et al

in Plant and Fungal Systematics (2018), 63(2), 4564

Closely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data ... [more ▼]

Closely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea [less ▲]

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See detailContrasting Symbiotic Patterns in Two Closely Related Lineages of Trimembered Lichens of the Genus Peltigera
Pardo De la Hoz, Carlos; Magain, Nicolas ULiege; Lutzoni, Francois et al

in Frontiers in Microbiology (2018), 9

Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the ... [more ▼]

Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus Peltigera, section Chloropeltigera. We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries. Single locus phylogenies were used to establish the identity of both photobionts, Nostoc (cyanobacterium) and Coccomyxa (green alga). Distribution and specificity patterns were compared to the closely related clade, section Peltidea, which includes mainly Peltigera species with trimembered thalli. For section Chloropeltigera, eight fungal species (including five newly delimited putative species) were found in association with nine Nostoc phylogroups and two Coccomyxa species. In contrast, eight fungal species (including three newly delimited putative species) in section Peltidea were found in association with only four Nostoc phylogroups and the same two Coccomyxa species as for section Chloropeltigera. This difference in cyanobiont biodiversity between these two sections can potentially be explained by a significantly higher frequency of sexual reproductive structures in species from section Chloropeltigera compared to section Peltidea. Therefore, horizontal transmission of the cyanobiont might be more prevalent in Chloropeltigera species, while vertical transmission might be more common in Peltidea species. All Peltigera species in section Chloropeltigera are generalists in their association with Nostoc compared to more specialized Peltigera species in section Peltidea. Constrained distributions of Peltigera species that associate strictly with one species of green algae (Coccomyxa subellipsoidea) indicate that the availability of the green alga and the specificity of the interaction might be important factors limiting geographic ranges of trimembered Peltigera, in addition to constraints imposed by their interaction with Nostoc partners and by climatic factors. [less ▲]

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See detailSpecies delimitation at a global scale reveals high species richness with complex biogeography and patterns of symbiont association in Peltigera section Peltigera (lichenized Ascomycota: Lecanoromycetes)
Magain, Nicolas ULiege; Truong, Camille; Goward, Trevor et al

in Taxon (2018), 67(5), 836-870

This comprehensive phylogenetic revision of sections Peltigera and Retifoveatae of the cyanolichen genus Peltigera is based on DNA sequences from more than 500 specimens from five continents. We amplified ... [more ▼]

This comprehensive phylogenetic revision of sections Peltigera and Retifoveatae of the cyanolichen genus Peltigera is based on DNA sequences from more than 500 specimens from five continents. We amplified five loci (nrITS, β-tubulin and three intergenic spacers part of colinear orthologous regions [COR]) for the mycobiont, and the rbcLX locus for the cyanobacterial partner Nostoc. Phylogenetic inferences (RAxML, BEAST) and species delimitation methods (bGMYC, bPTP, bPP) suggest the presence of 88 species in section Peltigera, including 50 species new to science, hence uncovering a surprisingly high proportion of previously unnoticed biodiversity. The hypervariable region in ITS1 (ITS1-HR) is a powerful marker to identify species within sections Peltigera and Retifoveatae. Most newly delimited species are restricted to a single biogeographic region, however, up to ten species have a nearly cosmopolitan distribution. The specificity of mycobionts in their association with Nostoc cyanobionts ranges from strict specialists (associate with only one Nostoc phylogroup) to broad generalists (up to eight Nostoc phylogroups uncovered), with widespread species recruiting a broader selection of Nostoc phylogroups than species with limited distributions. In contrast, species from the P. didactyla clade characterized by small thalli and asexual vegetative propagules (soredia) associate with fewer Nostoc phylogroups (i.e., are more specialized) despite their broad distributions, and show significantly higher rates of nucleotide substitutions. [less ▲]

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See detailOligocene origin and drivers of diversification in the genus Sticta (Lobariaceae, Ascomycota)
Widhelm, Todd J.; Bertolettiq, Francesca R.; Asztalos, Matt J. et al

in Molecular Phylogenetics and Evolution (2018), 126

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 ... [more ▼]

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. [less ▲]

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See detailBioclimatic factors at an intrabiome scale are more limiting than cyanobiont availability for the lichen‐forming genus Peltigera
Lu, Jade; Magain, Nicolas ULiege; Miadlikowska, Jolanta et al

in American Journal of Botany (2018), 105(7), 1198-1211

Premise of the Study Factors shaping spatiotemporal patterns of associations in mutualistic systems are poorly understood. We used the lichen‐forming fungi Peltigera and their cyanobacterial partners ... [more ▼]

Premise of the Study Factors shaping spatiotemporal patterns of associations in mutualistic systems are poorly understood. We used the lichen‐forming fungi Peltigera and their cyanobacterial partners Nostoc to investigate the spatial structure of this symbiosis at an intrabiome scale and to identify potential factors shaping these associations. Methods Ninety‐three thalli were sampled in Québec, Canada, along a south–north and an east–west transect of ~1300 km each. We identified the two main partners (Peltigera species and Nostoc phylogroups) using molecular markers and modeled the effects of environmental variables and partner occurrence on Peltigera–Nostoc distributions. Key Results Peltigera species showed a high degree of specialization toward cyanobionts, whereas two Nostoc phylogroups dominated both transects by associating with several Peltigera species. Peltigera species had narrower ranges than these two main cyanobionts. Distributions of three Peltigera species were highly associated with precipitation and temperature variables, which was not detected for Nostoc phylogroups at this spatial scale. Conclusions For these cyanolichens, factors driving patterns of symbiotic associations are scale dependent. Contrary to global‐scale findings, generalist Peltigera species were not more widespread within the boreal biome than specialists. Nostoc availability was not the only driver of Peltigera species’ geographic ranges; environmental factors also contributed to their intrabiome distributions. Climatic conditions (especially precipitation) limited the range of some Peltigera species more than the range of their cyanobacterial partners at an intrabiome (boreal) scale. [less ▲]

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See detailWorldwide eco-evolutionary dynamics of the Peltigera-Nostoc symbiosis
Magain, Nicolas ULiege

Poster (2018, July)

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