Comparative phylogenies and host specialization in the alder ectomycorrhizal fungi Alnicola, Alpova and Lactarius (Basidiomycota) in Europe

<p>Abstract</p> <p>Background</p> <p>Mycorrhizal fungi form intimate associations with their host plants that constitute their carbon resource and habitat. <it>Alnus </it>spp. (Betulaceae) are known to host an exceptional species-poor and specialized ectomycorrhizal (ECM) fungal community compared to other tree species, but the host-specificity pattern and its significance in terms of fungal diversification and speciation remain poorly documented. The degree of parallel speciation, host switching, and patterns of biogeography were explored in the historical associations between alders and three ECM taxa of Basidiomycetes: <it>Alnicola </it>(Agaricales), <it>Alpova </it>(Boletales), and <it>Lactarius </it>(Russulales). The aim was to develop an evolutionary framework on host specificity and diversification of Basidiomycetes in this highly specialized plant-fungus symbiosis.</p> <p>Results</p> <p>Sporocarps of <it>Alnicola </it>(220), <it>Lactarius </it>(61) and <it>Alpova </it>(29) were collected from stands of the four European alder species (<it>A. alnobetula </it>including the endemic subsp. <it>suaveolens </it>in Corsica, <it>A. cordata</it>, <it>A. glutinosa</it>, <it>A. incana</it>) in Western Europe (mainly in France and Austria), from 1995 to 2009. Specimens were morphologically identified to the species level. From these, 402 sequences of four DNA regions (ITS, rpb2, gpd, and the V9 domain of the mit-SSU rDNA) were successfully obtained and analyzed in addition with 89 sequences available in GenBank and UNITE databases. Phylogenetic analyses were conducted on all sequence data sets (individual and combined) using maximum likelihood reconstruction and Bayesian inference. Fungal phylogenies are compared and discussed in relation to the host, with a focus on species boundaries by associating taxonomic, systematic and molecular information.</p> <p>Conclusions</p> <p>Patterns of host specificity and phylogenies of <it>Alnicola </it>and <it>Lactarius </it>suggest coevolution as a basal factor of speciation in relation with the subgeneric diversification of <it>Alnus</it>, possibly due to the very selective pressure of the host. A second element of the historical associations between <it>Alnus </it>and its fungal symbionts is a host-dependent speciation (radiation without host change), here observed in <it>Alnicola </it>and <it>Alpova </it>in relation with <it>Alnus </it>subgen. <it>Alnus</it>. Finally host shifts from <it>Alnus </it>subgen. <it>Alnus </it>to <it>A. alnobetula </it>are found in most lineages of <it>Alnicola </it>(at least four times), <it>Alpova </it>(twice) and <it>Lactarius </it>(once), but they do not represent such a common event as could be expected by geographic proximity of trees from the two subgenera. However, active or very recent host extensions clearly occurred in Corsica, where some fungi usually associated with <it>Alnus glutinosa </it>on mainland Europe locally extend there to <it>A. alnobetula </it>subsp. <it>suaveolens </it>without significant genetic or morphological deviation.</p

Facilitation of Balsam Fir by Trembling Aspen in the Boreal Forest: Do Ectomycorrhizal Communities Matter?

Succession is generally well described above-ground in the boreal forest, and several studies have demonstrated the role of interspecific facilitation in tree species establishment. However, the role of mycorrhizal communities for tree establishment and interspecific facilitation, has been little explored. At the ecotone between the mixed boreal forest, dominated by balsam fir and hardwood species, and the boreal forest, dominated by black spruce, several stands of trembling aspen can be found, surrounded by black spruce forest. Regeneration of balsam fir seems to have increased in the recent decades within the boreal forest, and it seems better adapted to grow in trembling aspen stands than in black spruce stands, even when located in similar abiotic conditions. As black spruce stands are also covered by ericaceous shrubs, we investigated if differences in soil fungal communities and ericaceous shrubs abundance could explain the differences observed in balsam fir growth and nutrition. We conducted a study centered on individual saplings to link growth and foliar nutrient concentrations to local vegetation cover, mycorrhization rate, and mycorrhizal communities associated with balsam fir roots. We found that foliar nutrient concentrations and ramification indices (colonization by mycorrhiza per length of root) were greater in trembling aspen stands and were positively correlated to apical and lateral growth of balsam fir saplings. In black spruce stands, the presence of ericaceous shrubs near balsam fir saplings affected ectomycorrhizal communities associated with tree roots which in turn negatively correlated with N foliar concentrations. Our results reveal that fungal communities observed under aspen are drivers of balsam fir early growth and nutrition in boreal forest stands and may facilitate ecotone migration in a context of climate change

Fungi of French Guiana gathered in a taxonomic, environmental and molecular dataset

International audienceIn Amazonia, the knowledge about Fungi remains patchy and biased towards accessible sites. This is particularly the case in French Guiana where the existing collections have been confined to few coastal localities. Here, we aimed at filling the gaps of knowledge in indersampled areas of this region, particularly focusing on the Basidiomycota. From 2011, we comprehensively collected fruiting-bodies with a stratified and reproducible sampling scheme in 126 plots. Sites of sampling reflected the main forest habitats of French Guiana in terms of soil fertility and topography. The dataset of 5219 specimens gathers 245 genera belonging to 75 families, 642 specimens are barcoded. The dataset is not a checklist as only 27% of the specimens are identified at the species level but 96% are identified at the genus level. We found an extraordinary diversity distributed across forest habitats. The dataset is an unprecedented and original collection of Basidiomycota for the region, making specimens available for taxonomists and ecologists. The database is publicly available in the GBIF repository (https://doi.org/10.15468/ymvlrp)

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species: Intraspecific dispersal of C4 physiology

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.This study was funded by the European Research Council (grant no. ERC-2014-STG-638333), the Royal Society (grant no. RGF\EA\181050) and has benefited from ‘Investissements d'Avenir' grants managed by the Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-25-01 and TULIP, ref. ANR-10-LABX-41). Edinburgh Genomics, which contributed to the sequencing, is partly supported through core grants from the NERC (grant no. R8/H10/ 56), MRC (grant no. MR/K001744/1) and BBSRC (grant no. BB/ J004243/1). P.A.C. is funded by a Royal Society University Research Fellowship (grant no. URF\R\180022).Abstract 1. Introduction 2. Materials and methods (a) Sampling, sequencing and data filtering (b) Genome sizing and carbon isotope analyses (c) Assembly of organelle genomes and molecular dating (d) Phylogenetic analyses of the nuclear genome (e) Genetic structure (f) Genome composition 3. Results (a) Genome sizes (b) Time-calibrated organelle phylogenies (c) Nuclear phylogeny (d) Population structure and genome composition 4. Discussion (a) Limited seed dispersal in the region of origin (b) Widespread pollen flow and sweep of the C4 nuclear genome (c) Recurrent hybridization and polyploidization 5. Concluding remarks Data accessibility Authors' contributions Competing interests Funding Acknowledgements Footnote

Species diversity and biogeography of an ancient frog clade from the Guiana Shield (Anura: Microhylidae: Adelastes, Otophryne, Synapturanus) exhibiting spectacular phenotypic diversification

The outstanding biodiversity of the Guiana Shield has raised many questions about its origins and evolution. Frogs of the genera Adelastes, Otophryne and Synapturanus form an ancient lineage distributed mostly across this region. These genera display strikingly disparate morphologies and life-history traits. Notably, Synapturanus is conspicuously adapted to fossoriality and is the only genus within this group to have dispersed further into Amazonia. Moreover, morphological differences among Synapturanus species suggest different degrees of fossoriality that might be linked to their biogeographical history. Through integrative analysis of genetic, morphometric and acoustic data, we delimited 25 species in this clade, representing a fourfold increase. We found that the entire clade started to diversify ~55 Mya and Synapturanus ~30 Mya. Members of this genus probably dispersed three times out of the Guiana Shield both before and after the Pebas system, a wetland ecosystem occupying most of Western Amazonia during the Miocene. Using a three-dimensional osteological dataset, we characterized a high morphological disparity across the three genera. Within Synapturanus, we further characterized distinct phenotypes that emerged concomitantly with dispersals during the Miocene and possibly represent adaptations to different habitats, such as soils with different physical properties.Peer reviewe

The complete mitochondrial genome of Iphisa elegans (Reptilia: Squamata: Gymnophthalmidae)

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How tectonic, volcanic and climatic processes in Andean ‘sky islands’ shaped the diversification of endemic ground beetles

International audienceAim: The Andean superpáramo ecosystem, above c. 4200 m a.s.l., currently forms an archipelago of isolated "sky islands" which provides a unique setting to study biogeography. However, there is still a poor understanding of how past geological events and climatic changes have shaped the distribution of life in this ecosystem. Our aim was to investigate the importance of biogeographic barriers in local diversifications and to analyze how populations have become isolated on current "sky islands"

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Environmental variables measured around each balsam fir saplin