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Morphological and genetic diversification of Russula floriformis, sp. nov., along the Isthmus of Panama
Abstract
Species of Russula are ubiquitous members of ectomycorrhizal fungal communities in tropical ecosystems. However, an important part of the total tropical diversity of this genus and its biogeo-graphic patterns is unknown due to the lack of studies on Russula in tropical ecosystems. We combined molecular, morphological, ecological, and biogeographic data to elaborate concepts for two new subspecies of R. floriformis (subsection Substriatinae). Russula floriformis subsp. floriformis and R. floriformis subsp. symphoniae are described as new from montane forest dominated by Quercus and/or Oreomunnea (Fagales) from Colombia and Panama, respectively. Phylogenies were constructed using nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), D1-D2 domains of nuc 28S rDNA (28S), and partial regions of the second largest subunit of RNA polymerase II (rpb2) and translation elongation factor 1-alpha (tef1). Similar environmental conditions, similar morphology, and an ITS sequence similarity higher than 99% with only three different positions indicate that these two subspecies are closely related. Detailed observations of microscopic structures and analyses of further DNA loci, however, revealed morphological and molecular characteristics that allow distinguishing the two subspecies of R. floriformis. Spatial distribution and phylogenetic proximity of the two Russula subspecies and their ectomycorrhizal hosts, i.e., species of Quercus, suggest that their diversification is a result of comigration, adaptation, and geographic isolation along the Isthmus of Panama during the Pliocene and Pleistocene. ARTICLE HISTORY
Supplementary resource (1)
... floriformis and R. floriformis subsp. symphoniae were recently described as new from montane forest dominated by Quercus and/or Oreomunnea (Fagales) from Colombia and Panama, respectively (Vera et al., 2021) ( Figure 4a). These two subspecies' morphological and phylogenetic proximities supported their diversification due to a co-immigration, adaptation and geographic isolation of Quercus and their symbionts along the Isthmus of Panama during the Pleistocene (Vera et al., 2021). ...
... symphoniae were recently described as new from montane forest dominated by Quercus and/or Oreomunnea (Fagales) from Colombia and Panama, respectively (Vera et al., 2021) ( Figure 4a). These two subspecies' morphological and phylogenetic proximities supported their diversification due to a co-immigration, adaptation and geographic isolation of Quercus and their symbionts along the Isthmus of Panama during the Pleistocene (Vera et al., 2021). While there are some specific examples, in general there is a big gap in the knowledge of EcM fungi, particularly those associated with Fagaceae. ...
This chapter attempts to assess the distribution patterns of three selected groups of fungi, namely polypores, ectomycorrhizal fungi (EcM), and lichenised fungi in Colombia. Assessing the biogeography of fungi is difficult because of two key issues:
1. information gaps on their distribution and biology in biodiversity-rich countries, such as Colombia, and 2. the traditional, phenotype-based species concepts, which make it difficult to recognise cryptic species or species complexes. This latter aspect is very frequent in fungi, as currently revealed by advanced molecular biology and phylogenetic analysis techniques. For instance, Polyporus is a widespread genus, commonly found in Colombia with numerous species recorded as cosmopolitan. However, detailed studies in some Polyporus sensu lato in Brazil and Argentina showed a hidden diversity now accommodated in different genera such as Atroporus, Neodictyopus, and Bresadolia. On the other hand, the various fungal lineages show different distribution patterns depending on their biology. This fact evidences how the biogeographic distribution of ectomycorrhizal symbiont fungi (EcM) is closely linked with the distribution patterns of their host plants, but due to information gaps, their real distribution ranges are unknown. It has been observed that the EcM fungi associated with Fagaceae in the Andean region belong to Holarctic lineages, while the species associated with the Fabaceae or Dipterocarpaceae in the Colombian Amazonia Region come from tropical lineages of Gondwanan origin. Finally, for lichenised fungi, we looked at eight genera in four families and two classes and phyla: Bunodophoron (Sphaerophoraceae), Neoprotoparmelia (Parmeliaceae), Crocodia, Lobariella, Podostictina, Pseudocyphellaria, Sticta (Peltigeraceae, all Ascomycota), and Cora (Hygrophoraceae, Basidiomycota). Comparing traditional taxonomy with modern taxon concepts derived from integrative approaches using molecular and phenotype data revealed that the proportion of distribution types assessed from the data changed substantially. When using a traditional taxon concept, 45% of the species were inferred to have a broad, intercontinental distribution, 39% neotropical, and 12% endemic. On the other hand, using the modern taxon concept indicated that only 4% of them were widespread, 20% neotropical, and 76% potentially endemic. These findings underline the importance of accurate taxon concepts and proper knowledge of evolutionary relationships when performing biogeographical analyses of Colombian fungi. As mycologists, we must then continue to generating information that allows us to understand the historical processes responsible for the geographical distributions of the different lineages of fungi present in the national territory.
... Approximately 3100 species of fungi are known from Panama [8,9]. Among these species, there are nine species of Russula recorded for the entire country [6,[10][11][12]. In contrast to this, a high number of 31 OTUs of Russula spp. ...
... In other lineages of the genus, it is much more complicated to identify undescribed species from Latin America, because recent molecular studies are lacking, the taxonomic concept of oreomunneae (holotype FH- species described only by morphology is unclear and because distribution areas and ecological amplitudes of Russula species in the tropics are unknown. Up to now, 77 Russula species are described from the region [12]. A larger part of these taxa is unlikely to occur in tropical montane forests of the Chiriquí region in Western Panama though, because they are either limited to lowland tropical habitats or associated with Nothofagus spp. in temperate regions of South America. ...
Species of the genus Russula are key components of ectomycorrhizal ecosystems worldwide.
Nevertheless, their diversity in the tropics is still poorly known. This study aims to contribute
to the knowledge of the diversity of Russula species classified in subsection
Roseinae based on specimens recently collected in tropical montane rainforests in western
Panama. A five gene multilocus phylogeny based on the nuclear markers ITS nrDNA,
MCM7, RPB1, RPB2 and TEF-1α was constructed to identify the systematic position of 22
collections from Panama. Four new species, Russula cornicolor, Russula cynorhodon, Russula
oreomunneae and Russula zephyrovelutipes are formally described and illustrated.
None of the four species are sister species and they are more closely related to North American
or Asian species. Two of the newly described species were associated with the ectomycorrhizal
tree species Oreomunnea mexicana, while the other two species were associated
with Quercus species. All four species are so far only known from mountains in western
Panama.
... 1), even when several reference sequences contained additional loci (LSU and rpb1). This result is also evident in earlier studies that used one or a few gene regions where support is lacking for deep nodes (Miller and Buyck 2002;Buyck et al. 2008); this emphasizes the importance of building complete, multilocus phylogenies for studying the evolutionary relationships within Russula, as was done in Looney et al. (2016) and Vera et al. (2021). Our work uncovered apparent misidentifications in public databases such as GenBank and UNITE. ...
... floriforms Vera & Corrales and subsp. symphoniae Manz, F. Hampe & Corrales (Vera et al. 2021), climactic disjunction led to speciation in the R. globispora lineage , and host and ecological differences led to speciation between R. clavipes and R. pascua (Adamčík et al. 2016). In this study, the heterozygous position found in collections of R. altaica from the Rocky Mountains and in collections of R. nana from the Rocky Mountains and Europe were phylogenetically informative and separated these species from the closely related R. gracillima and R. montana, respectively. ...
Russula (Russulales) is an important ectomycorrhizal fungal genus in Arctic and alpine regions where it occurs with Salix, Betula, Dryas, and Polygonum, yet a complex phylogenetic analysis of the genus in these habitats is lacking. This research compared collections of Russula from the Rocky Mountain alpine (Colorado, Montana, Wyoming) with reference specimens from Arctic and alpine habitats, mostly in Europe, using an in-depth morphological study and a phylogenetic analysis of the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and the second largest subunit of the RNA polymerase II gene (rpb2). One hundred thirty-nine Russula collections were sequenced, including type material. Ten species are reported from alpine or treeline habitats in the Rocky Mountains. This is the first formal report of R. cf. altaica, R. saliceticola, and R. subrubens from the Rocky Mountains and of R. purpureofusca in North America. Russula laevis is reported for the first time under this name with a voucher, and not as an environmental sample. Previous reports of R. nana and R. laccata are molecularly confirmed. Two species are reported from subalpine habitats at treeline: R. montana with conifers and R. cf. altaica with Betula. In this study, R. laccata, R. subrubens, and R. laevis were collected in alpine habitats but have been reported below treeline in Europe; these species may also be present at lower elevations in North America. Most species have an intercontinental distribution and have been reported in other alpine or Arctic habitats. Two unidentified and potentially new species were only found in North America and are discussed. A key to the alpine Russulas of North America is provided.
... The challenge of sequencing effectiveness touches on how well a technology can produce DNA barcode sequence data of sufficient quality. The Sanger sequencing approach to DNA barcoding fungal specimens has been used for over three decades (White et al., 1990), and many systematic and taxonomic studies currently rely on its effectiveness and practicality (Noffsinger and Cripps, 2021;Vera et al., 2021). Despite Sanger sequencing's long and productive history, there are some significant limitations to its effectiveness. ...
Premise:
Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor-efficient and cost-effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once.
Methods:
We applied a two-step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 Lactarius specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de-noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens.
Results:
The taxonomic identities derived from the nrITS2 sequence data were >90% accurate across all specimens sampled. A phylogenetic analysis of the Lactarius sequences identified 20 MOTUs.
Discussion:
The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.
... However, a tropical African origin has long been posited for Russulaceae based on endemism and morphological distinctiveness (Pirozynski, 1983;Buyck et al., 1996). In the wider Neotropics, Russulaceae occur in all highland and lowland regions where ECM vegetation is found, and modern work has revealed a plethora of new species (Buyck & Ovrebo, 2002;Miller et al., 2002Miller et al., , 2012Wartchow & Cavalcanti, 2010;Cheype & Campo, 2012;S a & Wartchow, , 2016Wartchow et al., 2013;Montoya et al., 2014;Trierveiler-Pereira et al., 2014;Crous et al., 2017;Delgat et al., 2020;Duque Barbosa et al., 2020;Silva-Filho et al., 2020;Manz et al., 2021;Vera et al., 2021). Several lowland neotropical Russulaceae have affinities with tropical African species (Buyck, 1990;Buyck & Ovrebo, 2002;De Crop et al., 2017). ...
The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae.
We inferred a supertree of 3285 operational taxonomic units, representing worldwide internal transcribed spacer sequences. We reconstructed biogeographic history and diversification and identified lineages in the Neotropics and adjacent Patagonia.
The ectomycorrhizal Russulaceae have a tropical African origin. The oldest lineages in tropical South America, most with African sister groups, date to the mid‐Eocene, possibly coinciding with a boreotropical migration corridor. There were several transatlantic dispersal events from Africa more recently. Andean and Central American lineages mostly have north‐temperate origins and are associated with North Andean uplift and the general north–south biotic interchange across the Panama isthmus, respectively. Patagonian lineages have Australasian affinities. Diversification rates in tropical South America and other tropical areas are lower than in temperate areas.
Neotropical Russulaceae have multiple biogeographic origins since the mid‐Eocene involving dispersal and co‐migration. Discontinuous distributions of host plants may explain low diversification rates of tropical lowland ectomycorrhizal fungi. Deeply diverging neotropical fungal lineages need to be better documented.
Trois nouvelles espèces du genre Russula Pers. provenant de forêts dominées par le Sal en Inde tropicale, décrites d'après la morphotaxonomie et l'analyse phylogénétique multigénique. Depuis 2013, des expéditions macrofongiques de routine ont été menées dans plusieurs zones forestières dominées par Shorea robusta C.F.Gaertn. dans l'est tropical de l'Inde (Bihar, Jharkhand et Bengale occidental). Trois nouvelles espèces de Russula Pers. collectées récemment dans ces états de l'Inde, Russula boddingii Hembrom, D.Chakr., A.Ghosh & K.Das, sp. nov. dans le subg. Compactae (Fr.) Bon, emend. Buyck & V.Hofst., R. pseudoflavida A.Ghosh, Hembrom, I.Bera & Buyck, sp. nov. dans le subg. Russula emend. Buyck & V.Hofst., et R. shoreae D.Chakr., A.Ghosh, K.Das & Buyck, sp. nov. dans le subg. Heterophyllidiae Romagnesi, emend. Buyck & V.Hofst., sont décrites sur la base de la morphotaxonomie et des données moléculaires. Russula boddingii Hembrom, D.Chakr., A.Ghosh & K.Das, sp. nov. se caractérise par un pileus de taille moyenne à grande (30-160 mm), un noircissement plus intense de la chair après une coupe ou une blessure, des lames inégales en plusieurs séries et avec des bifurcations présentes à différentes distances du stipe, l'absence de pileocystidia, une réticulation plus forte de l'ornementation des spores, des terminaisons hyphales plus fines dans le pileipellis et sa présence sous des diptérocarpes en Asie. Russula pseudoflavida A.Ghosh, Hembrom, I.Bera & Buyck, sp. nov. est unique par son pileus de taille réduite (10-45 mm), ses « hyphes primordiales» très longues, généralement avec de fortes incrustations couvrant la plupart de la surface, ses spores nettement plus petites et sa présence sous Shorea robusta. D'autre part, R. shoreae D.Chakr., A.Ghosh, K.Das & Buyck, sp. nov. se caractérise par sa chair insipide et inodore, et est ectomycorhizien avec Shorea robusta. Des descriptions morphologiques détaillées et illustrées pour ces trois espèces sont fournies. Leurs positions systématiques précises sont déterminées sur les bases d'une analyse phylogénétique de l'ITS et une analyse combinée multigénique (nrLSU-mtSSU-rpb2).
Heterophyllidiae , one of the main subgenus of Russula (Russulaceae, Russulales), is both ecologically and economically important. Although many studies have focused on subgenus Heterophyllidiae in China, the diversity, taxonomy, and molecular phylogeny still remained incompletely understood. In the present study, two new species, R. discoidea and R. niveopicta , and two known taxa, R. xanthovirens and R. subatropurpurea, were described based on morphology and molecular phylogenetic analyses of ITS and 28S DNA sequences with new collections of subgenus Heterophyllidiae from southern China. Both morphological and phylogenetic analyses consistently confirmed that R. niveopicta and R. xanthovirens belong to the subsect. Virescentinae , R. discoidea and R. subatropurpurea come under subsect. Heterophyllae , and R. prasina is synonymized with R. xanthovirens .
Two new species, Russula pseudopunicea C.L.Hou, G.Q.Cheng & H.Zhou sp. nov. and R. wulingshanensis C.L.Hou, G.Q.Cheng & H.Zhou sp. nov., from Yanshan mountains in North China are described herein based on morphological and phylogenetic analyses of nrITS, and nrLSU-rpb2-mtSSU gene regions. Morphologically, R. pseudopunicea sp. nov. is characterised by a reddish brown, light brown to brownish orange pileus with a greyish yellow margin, subglobose to broadly ellipsoid basidiospores with warts forming a partial reticulum and pleurocystidia turning grey to purplish red in sulfovanillin. Russula wulingshanensis sp. nov. is characterised by a purple pinkish pileus with a grey-white to greypurple margin, subglobose to broadly ellipsoid basidiospores with isolated warts, and pileocystidia turning black in sulfovanillin. Phylogenetic and morphological analyses resolved the two species in Russula subg. Heterophyllidia. Russula pseudopunicea sp. nov. and R. wulingshanensis sp. nov. were placed in the lineages of subsect. Virescentinae and subsect. Griseinae, respectively.
The harvesting, processing, and sale of wild edible mushrooms (WEM) is a relevant economic activity in Angola and a good example of the use of non-wood forest products for food. Although there is deep traditional knowledge about the general properties of WEMs, a huge gap remains in detailed scientific knowledge. Thus, this study aimed to investigate the socio-economic importance of the species sold at local markets in Huila, Angola, from their molecular identification to the assessment of their nutritional, chemical, and bioactive profiles. From the eight WEM morphotypes studied, five were identified based on phenotypical and molecular approaches (four Russula spp., and Amanita loosei). The studied mushrooms proved to be a rich source of carbohydrates, proteins, and ashes, also presenting low amounts of fat. Chemical analyses further revealed mannitol as the main free sugar in all samples, and organic acids, namely, oxalic, quinic, malic, citric, and fumaric acids in low amounts. Additionally, the α-tocopherol isoform and monounsaturated fatty acids were predominant. Regarding phenolic acids, protocatechuic, p-hydroxybenzoic, p-coumaric, and cinnamic acids were detected in all mushroom hydroethanolic extracts, being responsible for their antioxidant, antibacterial, and antifungal activities. Our investigation contributes to the identification and knowledge of WEMs as important complementary food sources in Angola, some of which were reported for the first time, promoting their utilization as a basis of nutritional and functional ingredients, as being able to be part of a balanced diet and to be used in new bio-based formulations.
In this new series of Fungal Biodiversity Profiles, the authors provide descriptions for ten new taxa: Ilytheomyces uncinatus W. Rossi & M. Leonardi, sp. nov. (Ascomycota, Laboulbeniales) and several Basidiomycota: in family Entolomataceae for Entoloma aurantioalpinum Armada, Vila, Bellanger, Noordel., Krisai & Dima, sp. nov. and E. nigroflavescens Armada, Bellanger, Noordel. & Dima, sp. nov., both from France; in family Inocybaceae for Inocybe hebes Eyssart. & Buyck, sp. nov., I. media Eyssart. & Buyck, sp. nov. and I. leucophaea Eyssart. & Buyck, sp. nov., all three gathered from miombo woodland in Zambia (Africa); in family Russulaceae, Russula ferruginea subsp. ferruginea Corrales & Vera, sp. nov. and subsp. panamanensis Corrales & Manz, subsp. nov. from Central America; in Laetiporaceae Jlich for the Indian Phaeolus sharmae Hembrom, A. Parihar, K. Das & A. Ghosh, sp. nov.; in family Vuilleminiaceae Maire for Vuilleminia tropica Hembrom, A. Ghosh, A. Parihar & K. Das, sp. nov., equally from India. All new species of Basidiomycota are supported by newly provided sequence data or already published phylogenetic analyses of sequence data.
Panamanian montane forests harbor a high diversity of fungi, particularly of ectomycorrhizal (ECM) fungi; however their taxonomy and diversity patterns remain for the most part unexplored. We present state of the art fungal taxonomy and diversity patterns at Fortuna Forest Reserve based on morphological and molecular identification of more than 1,000 fruiting body collections of macromycetes made over a period of 5 years. We compare these new results with previously published work based on environmental sampling of Oreomunnea mexicana root tips. We compiled a preliminary list of species and report new records of 22 genera and 33 species for Panama. Based on fruiting body collection data, we compare the species composition of ECM fungal communities associated with Oreomunnea stands across sites differing in soil fertility and amount of rainfall. We also examine the effect of a long-term nitrogen addition treatment on the fruiting body production of ECM fungi. Finally, we discuss the biogeographic importance of Panama collections,
which fill in the knowledge gap of ECM fungal records between Costa Rica and Colombia. Given that the Isthmus of Panama was an important migration route of ECM tree and fungal species from northern temperate areas to South America, the ECM fungal communities of Panama might show a high degree of isolation and therefore a high level of endemism. We expect that the forests at Fortuna will continue to yield new ECM macromycete data as we continue to study the collected specimens
and describe new species.
This study reports on the discovery of a new subgenus, Russula subg. Glutinosae, having an Eastern North American-East Asian distribution. A multigene phylogeny places this new subgenus sister with strong support to a well-supported clade composed of subgenera Compactae and Archaeae. It holds only two very rare, northern hemisphere species, the North American R. glutinosa and the Asian R. glutinosoides sp. nov., thereby adding support to a northern hemisphere origin of the genus. Russula fattoensis is here shown to be a synonym of R. glutinosa. Detailed morphological descriptions and illustrations of holotype collections are provided and potential affinities and similarities with other subgenera are discussed. The new subgenus is a perfect illustration of the fact that nBLAST of nrITS does not always provide the appropriate sampling for phylogenetic analyses.
In a continued effort to catalog the numerous phylogenetically detected and predicted species of Cora in the Americas, we focus here on the diversity of the genus in Mexico and the phylogenetic relationships of the taxa present in this area. Based on previous results and new collections, 12 taxa are recognized in Mexico, including eight new species and one new subspecies. The 12 taxa form 11 unrelated lineages within the genus, indicating multiple independent colonization from Central and South America. While the new subspecies is nested within a species known from the northern Andes in South America, the other species are all putative endemics for Mexico, resulting in endemism of 92% at species level and 100% at taxon level. Considering the rather narrow area of origin of the sequenced specimens in southeastern Mexico and the previously documented range of Cora including the northwestern part of the country, plus the underlying topography, we predict that the 12 species and subspecies now known represent only about 20% of the total richness of Cora in the country, and that many more endemic lineages are to be found in the western and northwestern parts (Sierra Madre Occidental). The new taxa from Mexico formally introduced in this study are Cora benitoana sp. nov., with a strongly projecting, cyphelloid hymenophore; C. buapana sp. nov., with elongate, finger-like and partly branched appendages on the lower medullary hyphae; C . dewisanti subsp. mexicana subsp. nov., with a marginally protruding hymenophore; C. guzmaniana sp. nov., with a partly setose lobe surface; C. ixtlanensis sp. nov., a phenotypically cryptic species similar but unrelated to C. terrestris ; C. lawreyana sp. nov., with globose hyphal appendages; C. marusae sp. nov., a phenotypically cryptic species similar but unrelated to C. comaltepeca ; C. totonacorum sp. nov., a phenotypically cryptic species similar but phylogenetically distant to C. davidia ; and C. zapotecorum sp. nov., with a very thinly pilose lobe surface.
The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa. The authors assemble and analyse previously generated mycobiome data linked to geographical locations across the world. They describe the distribution of fungal taxa and show that climate is an important driver of fungal biogeography and that fungal diversity appears to be concentrated at high latitudes.
Since 2007, the quality of Russula descriptions has improved and the use of molecular support for species delimitation and the number of published new species has increased. However, the description style is not consistent and has regional or author-specific patterns. Most recent publications still favour descriptions of spores compared to hymenium and pileipellis elements, and usually only the spore size is provided with statistical support. This study proposes standards for descriptions of the microscopic structure of Russula species (Russulaceae, Agaricomycetes). We present the description template, the template measurements table, the specific terminology and the essential chemical reagents. The proposed standards were tested by mycologists from 11 countries who met at the Russula Microscopy Workshop in Slovakia. Descriptions of 26 species from 9 countries and four continents were prepared, among them R. amarissima, R. castanopsidis, R. seperina and R. subtilis are re-described and 15 species are introduced as new: R. abietiphila, R. amerorecondita, R. aurantioflava, R. echidna, R. flavobrunnescens, R. fluvialis, R. fortunae, R. garyensis, R. gemmata, R. laevis, R. madrensis, R. olivaceohimalayensis, R. purpureogracilis, R. sancti-pauli and R. wielangtae. Seven descriptions for candidate new species are provided without a formal name assignment. Pairwise comparison of species described in this study with available similar descriptions of related species suggests that microscopic characters from all parts of the basidiomata can be equally important for species recognition and they deserve the same treatment including number of measurements and statistics. The majority of recent studies does not recognise differences between the pileus margin and centre, but more than one-third of the species described in this study show distinct differences between the pileus areas, emphasizing the importance to specify the origin of pileipellis observations. This study proved that there is frequently insufficient difference in the ITS barcode between closely related species and that it is necessary to use more genetic markers combined with ecological and geographical data.
The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.
We utilize fossil data and restriction‐site associated DNA sequencing ( RAD ‐seq) for 632 individuals representing nearly 250 Quercus species to infer a time‐calibrated phylogeny of the world's oaks. We use a reversible‐jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among‐clade sampling biases. We then map the > 20 000 RAD ‐seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.
Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.
The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
The Russula globispora lineage is a morphologically and phylogenetically well-defined group of ectomycorrhizal fungi occurring in various climatic areas. In this study we performed a multi-locus phylogenetic study based on collections from boreal, alpine and arctic habitats of Europe and Western North America, subalpine collections from the southeast Himalayas and collections from subtropical coniferous forests of Pakistan. European and North American collections are nearly identical and probably represent a single species named R. dryadicola distributed from the Alps to the Rocky Mountains. Collections from the southeast Himalayas belong to two distinct species: R. abbottabadensis sp. nov. from subtropical monodominant forests of Pinus roxburghii and R. tengii sp. nov. from subalpine mixed forests of Abies and Betula. The results suggest that speciation in this group is driven by a climate disjunction and adaptation rather than a host switch and geographical distance.
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.
p>Se describen los Patrones de Distribución Espacial de las formaciones de encinos en el estado de Tamaulipas, México, a partir de los factores bioclimáticos y litológicos. Para lo anterior se utilizó el Método de Regímenes Ecodinámicos a través de un análisis espacial en un Sistema de Información Geográfico (SIG) con verificación en campo. Se analizaron los patrones de distribución de las formaciones vegetales de encinos: bosque mixto, bosque de encino, chaparral y bosque húmedo montano. Se presentan mapas de distribución de cada formacion vegetal en función del su bioclima y litología. Los modelos generados arrojan cinco tipos principales de regímenes para las formaciones de encinos (Critropófilo, Euritermo-tropófilo, Euritermo-mesófilo Mesófilo-subhúmedo y Tropófilo). Los resultados anteriores permiten hacer un diagnóstico ecológico a fin de poder establecer propuestas de conservación de las áreas con una mayor diversidad de Quercus en la región.</p
In this paper, the authors present modern microscopical studies for 28 type specimens of Russula species described by C.H. Peck, thereby completing the revision of all 44 Russula taxa described by this author and for which type specimens were available. Our results suggest that with eventual exception of R. granulata var. lepiotoides (a likely synonym of the type variety) and R. magnifica (a likely synonym of R. polyphylla), all other Russulas described by Peck correspond to well-defined North American taxa. Having been described more than one century ago, Peck’s names represent the majority of the earliest described North American Russula species and our type revisions are therefore important both for nomenclatural aspects, as well as typification and identification purposes. All studied taxa are illustrated in detail and accompanied by notes including a short recapitulation of previous type revisions, as well as our own re-evalutation of their systematic position as a result of this study.
Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis. The ITS DNA sequences of ECM root tips from 14 studies were included in the meta-analysis. In total, 1065 species of ECM fungi have been documented worldwide; however, 812 species have been only found at one site. Oak forests in Europe contain 416 species, Mexico 307, USA 285, and China 151. Species with wider distributions are Sebacinaceae sp. SH197130, Amanita subjunquillea, Cenococcum geophilum, Cortinarius decipiens, Russula hortensis, R. risigallina, R. subrubescens, Sebacinaceae sp. SH214607, Tomentella ferruginea, and T. lapida. The meta-analysis revealed (1) that Mexico is not only a hotspot for oak species but also for their ECM mycobionts. (2) There is a particularly high diversity of ECM Pezizales in oak seasonal forests from western USA to southwestern Mexico. (3) The oak forests in southwestern Mexico have the largest number of potential endemic species. (4) Globally, there is a high turnover of ECM fungal species associated with oaks, which indicates high levels of alpha and beta diversity in these communities.
Russula is one of the most speciose genera of mushroom-forming fungi, but phylogenetic relationships among species and subgeneric groupings are poorly understood. Our multi-locus phylogenetic reconstruction places R. firmula, R. rubra, R. rutila and R. veternosa in a well-supported Rubrinae clade, belonging to the Integrae clade of the Crown clade of the genus Russula. Traditional morphology-based classifications placed these four species in two different subsections based on the presence or absence of incrustations on pileocystidia. The Integrae clade also contains R. integra and related species that are traditionally placed in other groups based on their mild taste. Ancestral state reconstruction suggests that the common ancestor of the Crown clade and the Integrae clade probably did not have any incrustations in the pileipellis, had a mild taste, yellow spore print and were associated with angiosperms. All four species of the Rubrinae clade are defined by a darker yellow or ochre spore print, acrid taste and incrustations on pileocystidia. This last character contradicts the former splitting of the group because incrustations were apparently overlooked in R. firmula and R. veternosa. Incrustation type is now highlighted as being important for the delimitation of species and groups within the Crown clade. Pink or red staining of the incrustations in sulphovanillin is present in all species of the Rubrinae clade and a majority of the analysed species of the Integrae clade. The delimitation of the Rubrinae clade and its species circumscriptions are summarised here in a new diagnostic key.
The tropical montane cloud forests are recognized as one of the most biodiverse ecosystems. In spite of this, they are among the most threatened ecosystems in the world. This study integrates three ecological approaches generally studied separately: climate change scenery, ecological niche and population dynamics of Oreomunnea mexicana (an endangered and relict species), to understand how environmental change affects the population structure in the cloud forest that will allow its conservation. Potential distribution under future climatic scenarios of the species at national and regional levels was generated from the Maxent algorithm. Also, the current abundance, distribution and the ecological niche of the species were analyzed at the regional level. Changes in potential distribution under two climatic models suggest a habitat reduction from 36% to 55% nationally, and 2% to 9% at a regional level, for 2050 and 2070, respectively. The current distribution of the species is fragmented and consists of subpopulations that have spatial structures of aggregated populations and a size structure in reversed "J" form. The ecological niche of the species is highly specialized and sensitive to environmental changes. O. mexicana is a flagship species of biological and cultural importance to the region's inhabitants and could be fundamental to the conservation of tropical montane cloud forests.
Interest in the study of macrofungi has increased in Colombia during the past 50 years. Mountain forests have been the sites better explored, from the mycological point of view, providing the largest number of genera and species. So far, the country's literature reports 605 macrofungi species belonging to the Agaricales, Boletales, Cantharellales, and Russulales orders (Basidiomycota). This new list, which is a continuation of work carried out by Franco Molano and Uribe-Calle in the year 2000, includes 175 species, distributed into 73 genera: 151 belonging to Agaricales, 14 to Boletales, 9 to Russulales, and only one to Cantharellales. 31 species constitute new records for the country.
p>La eutrofización es un proceso natural en los ecosistemas acuáticos, se produce por el enriquecimiento del cuerpo de agua con nutrientes. Durante los últimos años el ser humano ha acelerado estos procesos de eutrofización modificando tanto la calidad de las aguas como la estructura de las comunidades biológicas, debido al aumento en la carga orgánica e inorgánica de los cuerpos de agua. La eutrofización reduce los usos potenciales de los recursos hídricos ya que induce a la mortalidad de especies animales, a la descomposición del agua y al crecimiento de microorganismos. Además, en muchas ocasiones los microorganismos se convierten en un riesgo para la salud humana, como es el caso de los agentes patógenos transmitidos por el agua, que constituyen un problema mundial.
Para establecer la calidad microbiológica del agua, se evaluaron once puntos del Parque Natural Chicaque en época de lluvias (noviembre del 2010) y época seca (agosto del 2011). Se emplearon los indicadores coliformes totales, Escherichia coli y Enterococcus, la técnica utilizada fue la filtración por membrana, y la identificación de algunos microorganismos aislados se realizó con pruebas bioquímicas rápidas BD BBL Crystal. El aislamiento de coliformes totales, Escherichia coli y Enterococcus en el agua del Parque, indica la contaminación fecal de las aguas. La presencia de estos grupos de bacterias está relacionada con el impacto de las actividades del hombre y animales sobre los cuerpos de agua y el manejo de las aguas residuales.</p
Montane cloud forests in the Neotropics harbor a great wealth of biological diversity and a large number of endemic species. Here, we present (i) a comprehensive data mining exercise of fungi from Neotropical montane cloud forests (NMCF), (ii) an extensive review of the current knowledge of fungal richness, distribution and composition, and (iii) a preliminary analysis of fungal endemicity in Mexican montane cloud forests. Based on a survey of literature and other sources, we assembled a database of 6349 records representing 2962 fungal species in NMCF. The computed individual-based species rarefaction curve remained non-asymptotic, and the extrapolation curve estimated an expected increment of 42% in the number of species by doubling the sampling effort. Fungal species richness was highest in NMCF from Mesoamerica, particularly from Mexico and Costa Rica. Fungi from Mesoamerica, Caribbean and South America are significantly different at diverse taxonomic levels, and there is a little overlap in the fungal species recorded from these regions. The analyses of endemicity of the Mexican dataset performed with parsimony and Bayesian methods were highly complementary. They showed the following areas of endemicity supported by the congruent distribution of fungal species: (i) two main regions in the Trans-Mexican Volcanic Belt (TMVB); (ii) a region in the southern part of Veracruz; and (iii) a region located in the eastern part of TMVB with affinities with Sierra Madre Oriental and the Chiapan-Guatemala Highlands. This last area was supported by five species of Glomeromycota and is consistent with an area of endemicity previously found in vascular plants. In this study, we provide a perspective on gaps in knowledge regarding the diversity and distribution of fungi in NMCF, and provide a full dataset of fungal records with geographical, bibliographic and taxonomic information.
Background
Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be discovered and characterized. One important factor hindering progress is the difficulty in correctly identifying fungi. Morphological and molecular characteristics have been applied in such tasks. Later, DNA barcoding has emerged as a new method for the rapid and reliable identification of species. The nrITS region is considered the universal barcode of Fungi, and the ITS1 and ITS2 sub-regions have been applied as metabarcoding markers. In this study, we performed a large-scale analysis of all the available Basidiomycota sequences from GenBank. We carried out a rigorous trimming of the initial dataset based in methodological principals of DNA Barcoding. Two different approaches (PCI and barcode gap) were used to determine the performance of the complete ITS region and sub-regions.
Results
For most of the Basidiomycota genera, the three genomic markers performed similarly, i.e., when one was considered a good marker for the identification of a genus, the others were also; the same results were observed when the performance was insufficient. However, based on barcode gap analyses, we identified genomic markers that had a superior identification performance than the others and genomic markers that were not indicated for the identification of some genera. Notably, neither the complete ITS nor the sub-regions were useful in identifying 11 of the 113 Basidiomycota genera. The complex phylogenetic relationships and the presence of cryptic species in some genera are possible explanations of this limitation and are discussed.
Conclusions
Knowledge regarding the efficiency and limitations of the barcode markers that are currently used for the identification of organisms is crucial because it benefits research in many areas. Our study provides information that may guide researchers in choosing the most suitable genomic markers for identifying Basidiomycota species.
Electronic supplementary material
The online version of this article (doi:10.1186/s12866-017-0958-x) contains supplementary material, which is available to authorized users.
Most conservation efforts in seasonally dry tropical forests have overlooked less obvious targets for conservation, such as mycorrhizal fungi, that are critical to plant growth and ecosystem structure. We documented the diversity of ectomycorrhizal (EMF) and arbuscular mycorrhizal (AMF) fungal communities in Quercus oleoides (Fagaceae) in Guanacaste province, Costa Rica. Soil cores and sporocarps were collected from regenerating Q. oleoides plots differing in stand age (early vs late regeneration) during the wet season. Sequencing of the nuclear ribosomal ITS region in EMF root tips and sporocarps identified 37 taxa in the Basidiomycota; EMF Ascomycota were uncommon. The EMF community was dominated by one species (Thelephora sp. 1; 70% of soil cores), more than half of all EMF species were found only once in an individual soil core, and there were few conspecific taxa. Most EMF taxa were also restricted to either Early or Late plots. Levels of EMF species richness and diversity, and AMF root colonization were similar between plots. Our results highlight the need for comprehensive spatiotemporal samplings of EMF communities in Q. oleoides to identify and prioritize rare EMF for conservation, and document their genetic and functional diversity.
Florestas em solos arenosos são consideradas como hospedeiras de muitos fungos ectomicorrízicos (EM), como demonstrado pelas numerosas coletas feitas por Rolf Singer na região do Rio Negro, Amazonas, no final dos anos 70. Apesar do reconhecimento da importância dos fungos ectomicorrízicos em florestas em solos arenosos, não houve nenhum estudo sistemático da diversidade e da composição taxonômica nas florestas em solos arenosos ou mesmo mais amplamente nas terras baixas da Floresta Amazônica. Para ter uma visão global da diversidade e da distribuição de fungos EM em florestas em solos arenosos, foram coletados basidiomas desses fungos em 10 parcelas de florestas em solos arenosos no Brasil e na Guiana Francesa entre 2012 e 2014. Além disso, uma busca foi feita por espécimes depositados em herbários brasileiros que tinham a informação de serem coletas feitas em solo arenoso. Nas 10 parcelas amostradas foram coletados 221 espécimes e 62 morfoespécies, o que confirma que todas as florestas em solos arenosos hospedam fungos EM. Recuperamos 1006 espécimes registrados em 18 herbários brasileiros, dos quais 137 espécimes e 52 espécies são registros de florestas em solos arenosos principalmente no estado do Amazonas, Brasil. Russulaceae e Amanitaceae foram frequentes em todos os habitats e Cortinarius foi o táxon mais frequente em solo arenoso. Os resultados apresentados enfatizam a alta diversidade e heterogeneidade das comunidades de EM em florestas em solos arenosos, assim como a ampla distribuição de fungos em todo o Brasil, não exclusivamente em florestas em solos arenosos.
Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyper-diverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the 'generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms. This article is protected by copyright. All rights reserved.
Five new species from Cortinarius sect. Cortinarius are formally described, four from the Americas (Corti-narius palatinus Harrower, sp. nov., Cortinarius atrotomentosus Harrower, sp. nov., Cortinarius altissimus Harrower & T.W. Henkel, sp. nov., Cortinarius neotropicus Harrower, sp. nov.) and one from Australasia (Cortinarius carneipallidus Harrower & E. Horak, sp. nov.) based on molecular, morphological, and ecological circumscription. Additional collections of the Australasian species Cortinarius hallowellensis Wood and Cortinarius kioloensis Wood reveal wider host associations and geographic ranges than previously recorded. Morphological descriptions, photomicrographs and a dichotomous key to all species in Corti-narius sect. Cortinarius are provided. This work raises the number of species in sect. Cortinarius to twelve.
Quercus forests reach their southern limit of distribution in Colombia, where they are represented by Quercus humboldtii. In the inner slopes of the Western and Eastern cordilleras of Colombia, oak forests are located in areas with annual rainfall between 1260 and 1960 mm. Oak forests can also be found in the eastern slope of the Central cordillera (annual rainfall 2300 mm). Oak forests from massifs of the Caribbean were characterized and grouped in the alliance Billio roseae-Quercion humbodtii. Tovomito werddelianae-Quercetum humboldtii is found in well preserved areas between 750 and 950 m on the wet foothills of the Western cordillera (annual rainfall up to 3000 mm). Wettinio praemorsae-Quercetum humboldtii is found
between 1600 and 1800 m.s.l.m.) in the south of the Perija´ mountains (annual rain fall 1600–1800 mm). We did not find a direct relationship between the amount of rainfall and species richness in both the higher strata and the total number of species. Oak forests are distributed from warm climates with temperatures over 248C and 700 m of altitude with precipitation close to 2800 mm/year, to cold climates with temperatures under 108C in altitudes over 3000 m and with annual rainfall between 700 and 3000 mm.
Significance
The formation of the Isthmus of Panama, which linked North and South America, is key to understanding the biodiversity, oceanography, atmosphere, and climate in the region. Despite its importance across multiple disciplines, the timing of formation and emergence of the Isthmus and the biological patterns it created have been controversial. Here, we analyze molecular and fossil data, including terrestrial and marine organisms, to show that biotic migrations across the Isthmus of Panama began several million years earlier than commonly assumed. An earlier evolution of the Isthmus has broad implications for the mechanisms driving global climate (e.g., Pleistocene glaciations, thermohaline circulation) as well as the rich biodiversity of the Americas.
Detailed descriptions are given for Russula cartaginis and R. quercophila associated with endemic Quercus in Costa Rica. Both species are compared with the closely resembling and very rare R. eccentrica from southeastern North America and R. imitatrix from northeastern North America. Microscopic features for all four species are here illustrated in more detail for the first time.
Premise of research. The most important diversity hot spot of genus Quercus (Fagaceae) in America is situated in southern Mexico. From this area down to the Colombian Andes, oak species diversity decreases considerably, but the pattern of species distribution and turnover has not been analyzed. This study aimed at determining geographical patterns of species turnover, species distribution, and endemism for Neotropical Quercus species.
Methodology. Occurrence records for 58 oak species belonging to the Quercus and Lobatae sections were obtained. Patterns of species turnover were determined by comparing species composition among latitudinal/longitudinal units. Areas of endemism were determined using weighted networks. The potential distribution of oak species was determined using ecological niche models. Finally, a principal component analysis was used to identify changes in the oak species’ ecological niche across areas.
Pivotal results. The species composition analysis indicated that the Tehuantepec Isthmus, the Nicaraguan Depression, and the Panamanian Isthmus represent species turnover points. Nine areas of endemism were recovered, distributed through mountainous ranges from Mexico to Costa Rica. Most of these areas were delimited by the species turnover points detected. Ecological niche modeling indicated that the turnover points represent areas with low climatic suitability for most oak species and represent discontinuities in the distribution of Quercus. Niche comparisons suggest niche differentiation among species distributed in different areas of endemism or on opposite sides of turnover points.
Conclusions. The results indicate that the Tehuantepec Isthmus, the Nicaraguan Depression, and the Panamanian Isthmus have acted as important barriers to the dispersal of oak species, influencing species diversity, biogeographic patterns, and niche divergence.
The fungus/plant root association known as a mycorrhizal symbiosis appears to have evolved in the Devonian. Of the two general morphological types of mycorrhizae among plant families, arbuscular mycorrhizae appear earlier in the fossil record and are more widespread than are ectomycorrhizae. The latter type of symbiosis most likely evolved with the vascular plant progenitors of modern Pinaceae in the Jurassic, but also developed with the ancestors of a dozen or so extant Angiosperm families. The significance of the ectomycorrhizal relationship is evident in that the symbionts profit by acquiring resources from their partners that would otherwise be unavailable. In natural environments where ectomycorrhizal communities exist, the symbiosis may be restricted or not depending on the particular plants and fungi Involved. The presence of an obligate specificity of a particular fungus with a particular plant has a profound consequence on biogeographic distribution.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
A checklist of the species of Colombian macrofungi cited in the literature is presented. A total of 114 published articles were reviewed. These reported 1219 species of macrofungi belonging to 34 orders and 110 families of Ascomycota and Basidiomycota. Lichens were not included.
The increasing aridity during the Last Glacial Maximum (LGM) has been proposed as a major factor affecting Neotropical species. The character and intensity of this change, however, remains the subject of ongoing debate. This review proposes an approach to test contrasting paleoecological hypotheses by way of their expected demographic and genetic effects on Neotropical cloud forest species. We reviewed 48 paleoecological records encompassing the LGM in the Neotropics. The records show contrasting evidence regarding the changes in precipitation during this period. Some regions remained fairly moist and others had a significantly reduced precipitation. Many paleoecological records within the same region show apparently conflicting evidence on precipitation and forest stability. From these data, we propose and outline two demographic/genetic scenarios for cloud forests species based on opposite precipitation regimes: the dry refugia and the moist forests hypotheses. We searched for studies dealing with the population genetic structure of cloud forest and other montane taxa and compared their results with the proposed models. To date, the few available molecular studies show insufficient genetic evidence on the predominance of glacial aridity in the Neotropics. In order to disentangle the climatic history of the Neotropics, the present study calls for a general multi-disciplinary approach to conduct future phylogeographic studies. Given the contradictory paleoecological information, population genetic data on Neotropical cloud forest species should be used to explicitly test the genetic consequences of competing paleoecological models.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including
options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained
alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples
to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to
clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Concerted evolution of the ribosomal DNA array has been studied in numerous eukaryotic taxa, yet is still poorly understood. rDNA genes are repeated dozens to hundreds of times in the eukaryotic genome (Eickbush and Eickbush 2007) and it is believed that these arrays are homogenized through concerted evolution (Zimmer et al., 1980, Dover, 1993) preventing the accumulation of intragenomic, and intraspecific, variation. However, numerous studies have reported rampant intragenomic and intraspecific variation in the rDNA array (Ganley and Kobayashi, 2011, Naidoo et al., 2013, Hughes and Petersen, 2001, Lindner and Banik, 2011, Li et al., 2013; Lindner, Carlsen, et al. 2013; Hughes, Tulloss, et al. 2018), contradicting our current understanding of concerted evolution. The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi (Schoch et al. 2012), and rely on concerted evolution to homogenize the rDNA array leading to a “barcode gap” (Puillandre et al. 2012). Here we show that in Boletus edulis Bull., ITS intragenomic variation persists at low allele frequencies throughout the rDNA array, this variation does not correlate with genomic relatedness between populations, and rDNA genes may not evolve in a strictly concerted fashion despite the presence of unequal recombination and gene conversion. Under normal assumptions, heterozygous positions found in ITS sequences represent hybridization between populations, yet through allelic mapping of the rDNA array we found numerous heterozygous alleles to be stochastically introgressed throughout, presenting a dishonest signal of gene flow. Moreover, despite the signal of gene flow in ITS, our organisms were highly inbred, indicating a disconnect between true gene flow and barcoding signals. In addition, we show that while the mechanisms of concerted evolution are ongoing in pseudo-heterozygous individuals, they are not fully homogenizing the ITS array. Concerted evolution of the rDNA array may insufficiently homogenize the ITS gene, allowing for misleading signals of gene flow to persist, vastly complicating the use of the ITS locus for DNA barcoding in Fungi.
Numerous lineages of mushroom-forming fungi have been subject to bursts of diversification throughout their evolutionary history, events that can impact our ability to infer well-resolved phylogenies. However, groups that have undergone quick genetic change may have the highest adaptive potential. As the second largest genus of mushroom-forming fungi, Russula provides an excellent model for studying hyper-diversification and processes in evolution that drives it. This study focuses on the morphologically defined group – Russula subsection Roseinae. Species hypotheses based on morphological differentiation and multi-locus phylogenetic analyses are tested in the Roseinae using different applications of the multi-species coalescent model. Based on this combined approach, we recognize fourteen species in Roseinae including the Albida and wholly novel Magnarosea clades. Reconstruction of biogeographic and host association history suggest that parapatric speciation in refugia during glacial cycles of the Pleistocene drove diversification within the Roseinae, which is found to have a Laurasian distribution with an evolutionary origin in the Appalachian Mountains of eastern North America. Finally, we detect jump dispersal at a continental scale that has driven diversification since the most recent glacial cycles.
Using specimens collected from subtropical pine-fagaceous mixed forests and phylogenetic analysis of DNA sequence data of ITS, 28S rDNA, rpb2 and tef1, we describe two new species, R. maguanensis and R. substriata, in R. subg. Heterophyllidia, subsect. Substriatinae subsect. nov. Russula maguanensis and R. substriata are similar to Indian R. shingbaensis in the tuberculate-striate pileus and spores with isolated warts but have more vividly coloured pileus and associate with pines and/or fagaceous trees rather than with Abies. In our multi-gene phylogeny, the new subsection and a representative of tropical African R. subsect. Aureotactinae compose one of the four major clades of R. subg. Heterophyllidia, the three remaining ones corresponding to R. sect. Heterophyllae, R. sect. Ingratae and R. subsect. Cyanoxanthinae. The overall characters of this new section combine those of some other sections in the same subgenus: mostly tuberculate-striate but more vivid pileus, spores with isolated warts, orthochromatic pileipellis with abundant erect aggregate mucronate pileocystidia in the suprapellis but absent in the subpellis and numerous cystidioid hyphae at the bottom of subpellis and trama beneath it. It differs from its sister clade R. subsect. Aureotactinae in lacking the intense yellowing of surface and context of their fruiting bodies and having pileal cystidioid elements clearly separated by the loose tissue of subpellis from the pileocystidia at the pileus surface. In order to compare our two new species with recently described Asian species and investigate their geographical distributions, we produced an ITS genealogy including also environmental sequences. This ITS genealogy suggests that R. subsect. Substriatinae includes at least seven potential species, shows an amphi-pacific distribution and its members associate with at least four families of host trees.
The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world, and their ubiquity as ectomycorrhizal symbionts in both temperate and tropical forested biomes. Although much research has been focused on this group, a comprehensive or cohesive synthesis by which to understand the functional diversity of the group has yet to develop. Interest in ectomycorrhizal fungi, of which Russulaceae is a key lineage, is prodigious due to the important roles they play as plant root mutualists in ecosystem functioning, global carbon sequestration, and a potential role in technology development toward environmental sustainability. As one of the most species-diverse ectomycorrhizal lineages, the Russulaceae has recently been the focus of a dense sampling and genome sequencing initiative with the Joint Genome Institute aimed at untangling their functional roles and testing whether functional niche specialization exists for independent lineages of ectomycorrhizal fungi. Here we present a review of important studies on this group to contextualize what we know about its members' evolutionary history and ecosystem functions, as well as to generate hypotheses establishing the Russulaceae as a valuable experimental system.
Two rather different elements combine to explain the origin of this volume: one scientific and one personal. The broader of the two is the scientific basis-the time for such a volume had arrived. Geology had made remarkable progress toward an understanding of the phys ical history of the Caribbean Basin for the last 100 million years or so. On the biological side, many new discoveries had elucidated the distributional history of terrestrial orga nisms in and between the two Americas. Geological and biological data had been combined to yield the timing of important events with unprecedented resolution. Clearly, when each of two broad disciplines is making notable advances and when each provides new insights for the other, the rewards of cross-disciplinary contacts increase exponentially. The present volume represents an attempt to bring together a group of geologists, paleontologists and biologists capable of exploiting this opportunity through presentation of an interdisciplinary synthesis of evidence and hypothesis concerning interamerican connections during the Cretaceous and Cenozoic. Advances in plate tectonics form the basis for a modern synthesis and, in the broadest terms, dictate the framework within which the past and present distributions of organisms must be interpreted. Any scientific dis cipline must seek tests of its conclusions from data outside of its own confines.
Detailed illustrated descriptions are given for Russula panamae sp.nov, Russula aucarum, R. puiggarii and R. venezueliana, all of which are reported for the first time from Panamá. For Russula venezueliana and R. aucarum, it is also the first record since their original description. Taxonomy, systematic position, and related species are discussed for each species. Russula ochrostraminea is probably a synonym of R. venezueliana and section Delicoarchaeae is considered a possible synonym of subsection Lactarioideae or of section Metachromaticae.
Species ofRussulasubsect.Xerampelinaeare notoriously difficult to identify and name and have not been subject to molecular study. A group of species, referred to here as theR. clavipescomplex, growing in association withSalix,BetulaandPopulusas well as coniferous tree species from temperate to arctic and alpine habitats, were examined. Analyses of the nuc rDNA internal transcribed spacer (ITS) region and a numerical analysis of morphological characters were used. TheR. clavipescomplex is a monophyletic group withinRussulasubsect.Xerampelinae, according to molecular results. The complex includes three species:R. nuoljaeis a phylogenetically and morphologically well-supported species while the other two,R. clavipesandR. pascua, are similar based on ITS data and morphology but separate based on their ecology.Russula pseudoölivascensis conspecific withR. clavipes Several combinations of characters traditionally used in the taxonomy ofR.subsect.Xerampelinaeare inappropriate for species delimitation in this group and the adequacy of the ITS for species identification in this group is discussed. Detailed microscopic observations on the type collection ofR. nuoljaeare presented and illustrated, along with a key to the European members ofR.subsect.Xerampelinae.
Neotropical montane forests are often dominated by ectomycorrhizal (EM) tree species, yet the diversity of their EM fungal communities remains poorly explored. In lower montane forests in western Panama, the EM tree species Oreomunnea mexicana (Juglandaceae) forms locally dense populations in forest otherwise characterized by trees that form arbuscular mycorrhizal (AM) associations. The objective of this study was to compare the composition of EM fungal communities associated with Oreomunnea adults, saplings, and seedlings across sites differing in soil fertility and the amount and seasonality of rainfall. Analysis of fungal nrITS DNA (nuclear ribosomal internal transcribed spacers) revealed 115 EM fungi taxa from 234 EM root tips collected from adults, saplings, and seedlings in four sites. EM fungal communities were equally species-rich and diverse across Oreomunnea developmental stages and sites, regardless of soil conditions or rainfall patterns. However, ordination analysis revealed high compositional turnover between low and high fertility/rainfall sites located ca. 6 km apart. The EM fungal community was dominated by Russula (ca. 36 taxa). Cortinarius, represented by 14 species and previously reported to extract nitrogen from organic sources under low nitrogen availability, was found only in low fertility/high rainfall sites. Phylogenetic diversity analyses of Russula revealed greater evolutionary distance among taxa found on sites with contrasting fertility and rainfall than was expected by chance, suggesting that environmental differences among sites may be important in structuring EM fungal communities. More research is needed to evaluate whether EM fungal taxa associated with Oreomunnea form mycorrhizal networks that might account for local dominance of this tree species in otherwise diverse forest communities.
Microscopical characters of type specimens for five species in Russula subgenus Heterophyllidia: R. albiduliformis Murrill, R. flocculosa Burl., R. maculosa Murrill, R. heterosporoides Murrill and R. subgraminicolor Murrill are described in detail. Taxonomy, systematic placement and nomenclatural aspects are discussed. Both R. heterosporoides Murrill and R. subgraminicolor Murrill are likely good species of subsection Virescentinae, whereas the other three species are more difficult to place with precision, but show affinities with both Virescentinae and Heterophyllinae.
The isolation of South America from Central America and Africa during the Tertiary Period left a strong imprint on the flora of the Neotropics. South American Eocene through Miocene fossil assemblages, both pollen and macrofossils, document a rich tropical flora on the continental margins, and represent some of the only data on pre-landbridge lowland taxa in South America. Lowland Miocene floras from Amazonia are remarkably similar in their high diversity to Amazonian floras today based on lists of dominant families. Recent geophysical data on the uplift of the northern Andes show a strong correlation between uplift and the development and diversification of montane forests in Colombia and Venezuela. The emergence of a continuous landbridge at 3 Ma between Central and South America is well documented and is demonstrated by the arrival of temperate elements in South American highlands and concurrent appearance of South American taxa in Central America. There is no evidence for displacement of lowland tropical plants in South America by northern immigrants, which appears to stand in contrast to the published record for mammals. The mix of taxa in extant Mexican tropical floras derived from tropical South America, tropical Central America, and from remnants of northern tropical Eocene floras is strong evidence for the impact that the landbridge through the Panamanian isthmus had on the neotropical flora. The early appearance of low-elevation savannas is inferred from an increase in grass pollen in the middle Pliocene of Panama; however, widespread savannas are not indicated by pollen data from the Central American region. Rather, beginning in the latest Miocene Epoch and continuing up to the Quaternary, a mix of tropical rainforest and mixed tropical woodlands is suggested for the lowlands, based on pollen evidence. Accumulating data on temperature changes during the late Tertiary and Quaternary Periods points to low-latitude temperature fluctuations of up to 6 degrees C. Proposals of accompanying widespread rainfall fluctuations are more equivocal. Rainfall probably varied regionally, resulting in a mosaic of habitats controlled by river migration, sea level fluctuations. local dryness, and local uplift. Zones postulated as refugia provide testable hypotheses using neoecological and paleoecological data. The paleoecological data to test three hypotheses are still limited taxonomically and spatially. It is important to stress that the effect of the isolation of South American neotropical floras has not been erased in the 3 million years since their connection with Central America. New data front middle and late Miocene floras in South America will be critical in determining the degree to which the composition of South American floras has been influenced by immigration of plants from the better-known Central American area to the north.
Based on recently collected specimens, four new records of the Russulaceae are presented for Panama: Russula aff. densissima, R. luteotacta, R. mexicana and Lactarius aff. lilacinus. R. aff. densissima is reported for the first time for the Americas. The Panamanian specimens of R. luteotacta, R. mexicana and L. aff. lilacinus are the most southern records for the Americas. All species are described and illustrated. A discussion of their known distribution, delimitation from morphologically similar species, and their taxonomy is added, where applicable.
Fog interception and rainfall were measured at 14 stations across the Central Cordillera in western Panamá. Fog interception and rainfall were measured monthly during 1988–1989 with artificial fog catchers and rain gauges, respectively. Fog interception was highest on ridges and increased with increasing altitude. Fog interception contributed between 2.4 and 60.6% of the total water input, depending on altitude and exposure to the prevailing winds. Absolute amounts of annual fog interception ranged from 142 to 2295 mm. Although low clouds were more frequent in montane forests, clouds close to the ground also occurred in the lowlands. During the study period, there was a gradient of increasing total rainfall from the Caribbean (3355 mm) to the Pacific side (5759 mm) of the Central Cordillera. Nevertheless, rainfall was more seasonal on the leeward side of the mountain range. Seasonal variation in fog intereption was different from rainfall patterns and no correlation was found between monthly (or annual) rainfall and fog interception. The results of this study showed the importance of montane forests for the preservation of water sources, particularly along ridges of the Fortuna drainage basin that provides more than 50% of the electricity of the Republic of Panamá.
We have designed two taxon-selective primers for the internal transcribed spacer (ITS) region in the nuclear ribosomal repeat unit. These primers, ITS1-F and ITS4-B, were intended to be specific to fungi and basidiomycetes, respectively. We have tested the specificity of these primers against 13 species of ascomycetes, 14 of basidiomycetes, and 15 of plants. Our results showed that ITS4-B, when paired with either a ‘universal’ primer ITS1 or the fungal-specific primer ITS1-F, efficiently amplified DNA from all basidiomycetes and discriminated against ascomycete DNAs. The results with plants were not as clearcut. The ITS1-F/ITS4-B primer pair produced a small amount of PCR product for certain plant species, but the quantity was in most cases less than that produced by the ‘universal’ ITS primers. However, under conditions where both plant and fungal DNAs were present, the fungal DNA was amplified to the apparent exclusion of plant DNA. ITS1-F/ITS4-B preferential amplification was shown to be particularly useful for detection and analysis of the basidiomycete component in ectomycorrhizae and in rust-infected tissues. These primers can be used to study the structure of ectomycorrhizal communities or the distribution of rusts on alternate hosts.
The “Great American Biotic Interchange” (GABI) is regarded as a defining event in the biogeography of the Americas. It is hypothesized to have occurred when the Isthmus of Panama closed ca three million years ago (Ma), ending the isolation of South America and permitting the mixing of its biota with that of North America. This view of the GABI is based largely upon the animal fossil record, but recent molecular biogeographic studies of plants that show repeated instances of long-distance dispersal over major oceanic barriers suggest that perhaps the land bridge provided by the isthmus may have been less necessary for plant migration. Here we show that plants have significantly earlier divergence time estimates than animals for historical migration events across the Isthmus of Panama region. This difference in timing indicates that plants had a greater propensity for dispersal over the isthmus before its closure compared with animals. The GABI was therefore asynchronous for plants and animals, which has fundamental implications for the historical assembly of tropical biomes in the most species-rich forests on the planet.