Multilocus, DNA-based phylogenetic analyses reveal three new species lineages in the Phellinus gabonensis-P. caribaeo-quercicola species complex, including P. amazonicus sp. nov.

Species complexes in the poroid Hymenochaetaceae are well documented in the temperate areas. Potential species complexes are less known in tropical areas, however. In the last ten years, four phylogenetically and morphologically closely related species of Phellinus (Hymenochaetaceae) were described from various tropical/subtropical areas viz. P. caribaeo-quercicola, P. gabonensis, P. ellipsoideus, and P. castanopsidis They are characterized by cushion-shaped basidiomata, ventricose, commonly hamate hymenial setae, and broadly ellipsoid, thick-walled, pale yellowish basidiospores. Pursuing the studies of this complex, a phylogenetic approach based on DNA sequence data from the nuc rDNA regions ITS1-5.8S-ITS2 (ITS) and partial 28S (including the domains D1, D2, D3) and on part of the translation elongation factor 1-α (tef1, region between exons 4 and 8) revealed three new lineages or phylogenetic species. Two of these phylogenetic species are composed of exclusively on Neotropical specimens. One of them, described below as Phellinus amazonicus sp. nov., is represented by multiple collections originating from Neotropical, lowland, dense, moist forest at the western edge of the Amazon Basin in Ecuador, the Guiana Shield in French Guiana and (more likely) Trinidad. The second Neotropical phylogenetic species is represented in our phylogenetic analyses by a single collection from northeastern Argentina. It is also potentially known from two herbarium specimens originating from southern Brazil, for which no sequence data is available. It is left for now as Phellinus sp. 1, waiting to gather more specimens and DNA sequences data. The third new phylogenetic species is known by a single collection (pure culture) of uncertain origin. It is thought to represent Phellinus setulosus, a Southeast Asian taxa. From an evolutionary perspective, tree species occurring in the Neotropics (P. amazonicus, P. caribaeo-quercicola, and Phellinus sp. 1) have a closely related genetic background and form a well supported Neotropical lineage.

Hymenochaetaceae from the Guineo-Congolian rainforest: three new species of Phylloporia based on morphological, DNA sequences and ecological data.

Four species are added to Phylloporia. Three species, originating from the western edge of the Guineo-Congolian rainforest in Gabon (central Africa), are described as new. Phylloporia afrospathulata sp. nov. forms seasonal, stipitate, solitary basidiomata emerging from soil, more likely connected to buried roots, and has broadly ellipsoid basidiospores. Phylloporia inonotoides sp. nov. forms seasonal sessile, soft basidiomata, solitary at the base of small-stemmed trees including Crotonogyne manniana (Euphorbiaceae) and Garcinia cf. smeathmannii (Clusiaceae). It has a homogeneous context, large pores (2-3 mm), and oblong-ellipsoid to suballantoid basidiospores. Phylloporia fulva sp. nov. forms sessile, conchate, mostly pendant, gregarious basidiomata emerging from the trunk of an unidentified small-stemmed tree and has small, subglobose basidiospores. This species is compared to Polyporus pullus and Phylloporia pulla comb. nov. and proposed based on the study of the type specimen. Phylogenetic inferences using partial nuc 28S DNA sequence data (region including the D1/D2/D3 domains) and the most exhaustive dataset available to date resolved these new morphospecies as three distinct terminal lineages. No sequence data of P. pulla currently is available. The 28S-based phylogenic inferences poorly resolved the interspecific relationships within the Phylloporia clade.

Fomes weberianus, 50 years of taxonomic confusion: lectotypification and taxonomic notes.

Fomes weberianus Bres. & Henn. ex Sacc. is currently the basionym of two very distinct polypores (Basidiomycota), Ganoderma weberianum (Polyporales) and Phylloporia weberiana (Hymenochaetales). This fact has led to almost fifty years of taxonomic confusion. Fomes weberianus was first lectotypified by Steyaert, who accepted the species as G. weberianum. However, studies of Weber's original material in B, duplicate material in S, the protologue, and early interpretations of the name have shown that Steyaert's choice conflicts with the protologue and early interpretations, and that his interpretation as a species of Ganoderma is erroneous. A new lectotype was designated and the species was re-described under the correct interpretation Phylloporia weberiana.

Fomitiporia castilloi sp. nov. and multiple clades around F. apiahyna and F. texana in Meso- and South America evidenced by multiloci phylogenetic inferences.

Fomitiporia castilloi sp. nov. from the lowland rainforest in French Guyana is described, illustrated and its phylogenetic affinities are discussed. This species is characterized by pileate basidiomata, a plicate margin, abundant, variably shaped hymenial setae and basidiospores averaging ≅ 6 × 5 µm. In phylogenetic inferences based on a DNA sequence dataset of four loci (5' end of the LSU, ITS-5.8S, partial tef1 and rpb2), F. castilloi occupies an isolated position, basal to a clade that is composed exclusively of Neotropical species with resupinate basidiomata. The phylogenetic inferences also provide evidence of an unreported complexity within the Neotropical taxa, with multiple clades closely related to F. apiahyna and F. texana, representing additional potential species.

Genetic characterization of a group of commercial African timber species: From genomics to barcoding.

In the last decades, illegal logging has posed a serious threat for the integrity of forest ecosystems and for biodiversity conservation in tropical Africa. Although international treaties and regulatory plans have been implemented to reduce illegal logging, much of the total timber volume is harvested and traded illegally from tropical African forest regions. As a result, the development and the application of analytical tools to enhance the traceability and the identification of wood and related products is critical to enforce international regulations. Among available techniques, DNA barcoding is a promising approach for the molecular identification of plant species. However, although it has been used successfully for the discrimination of animal species, no set of genetic markers is available for the universal identification of plant species. In this work, we firstly characterized the genetic diversity of 17 highly-valuable African timber species from five genera (Afzelia, Guibourtia, Leplea, Milicia, Tieghemella) across their distribution ranges in West and Central Africa using the genome skimming approach in order to reconstruct their chloroplast genomes and nuclear ribosomal DNA. Next, we identified single-nucleotide polymorphisms (SNPs) for the discrimination of closely-related species. In this way, we successfully developed and tested novel species-specific genetic barcodes for species identification.

Fomitiporia cupressicola sp. nov., a parasite on Cupressus arizonica, and additional unnamed clades in the southern USA and northern Mexico, determined by multilocus phylogenetic analyses.

Fomitiporia cupressicola sp. nov., found in living Cupressus arizonica, is described on the basis of several collections originating from a high altitude forest in the northern Sierra Madre Occidental, Mexico. The species forms a monophyletic clade, basal to a larger lineage comprising species originating mainly from temperate to Mediterranean areas of the northern hemisphere. The phylogenetic approach in Fomitiporia also revealed multiple unnamed clades within the F. robusta complex in the southern USA and northern Mexico, representing potential species. The status of the F. robusta complex in North America is discussed briefly.

Diversity of Fusarium associated banana wilt in northern Viet Nam.

Fusarium is one of the most important fungal genera of plant pathogens that affect the cultivation of a wide range of crops. Agricultural losses caused by Fusariumoxysporumf.sp.cubense (Foc) directly affect the income, subsistence, and nourishment of thousands of farmers worldwide. For Viet Nam, predictions on the impact of Foc for the future are dramatic, with an estimated loss in the banana production area of 8% within the next five years and up to 71% within the next 25 years. In the current study, we applied a combined morphological-molecular approach to assess the taxonomic identity and phylogenetic position of the different Foc isolates collected in northern Viet Nam. In addition, we aimed to estimate the proportion of the different Fusarium races infecting bananas in northern Viet Nam. The morphology of the isolates was investigated by growing the collected Fusarium isolates on four distinct nutritious media (PDA, SNA, CLA, and OMA). Molecular phylogenetic relationships were inferred by sequencing partial rpb1, rpb2, and tef1a genes and adding the obtained sequences into a phylogenetic framework. Molecular characterization shows that c. 74% of the Fusarium isolates obtained from infected banana pseudostem tissue belong to F.tardichlamydosporum. Compared to F.tardichlamydosporum, F.odoratissimum accounts for c.10% of the Fusarium wilt in northern Viet Nam, demonstrating that Foc TR4 is not yet a dominant strain in the region. Fusariumcugenangense - considered to cause Race 2 infections among bananas - is only found in c. 10% of the tissue material that was obtained from infected Vietnamese bananas. Additionally, one of the isolates cultured from diseased bananas was phylogenetically not positioned within the F.oxysporum species complex (FOSC), but in contrast, fell within the Fusariumfujikuroi species complex (FFSC). As a result, a possible new pathogen for bananas may have been found. Besides being present on several ABB 'Tay banana', F.tardichlamydosporum was also derived from infected tissue of a wild Musalutea, showing the importance of wild bananas as a possible sink for Foc.

An Unexpectedly High Number of New Sutorius (Boletaceae) Species From Northern and Northeastern Thailand.

Sutorius is a poroid genus in Boletaceae that typically has chocolate brown to reddish brown or purplish brown basidiomata with a finely scaly stipe and produces a reddish brown spore deposit. During the survey on diversity of boletes in Northern and Northeastern Thailand, several Sutorius collections were obtained. Combined evidence from morphology and phylogenetic analyses of a combined three-gene data set (atp6, tef1 and rpb2) of the Sutorius collections along with selected Boletaceae in the Pulveroboletus group indicated that Thai collections represent seven new Sutorius species. The analyses also indicated that Tylopilus maculatoides belongs in Sutorius. Therefore, the transfer of T. maculatoides to Sutorius is proposed. Full descriptions and illustrations of the seven new species and S. maculatoides are presented in this study. With the seven new species and the new combination, eight of the eleven described Sutorius species are known to occur in Northern and Northeastern Thailand, whereas only one species is known from each of two continents, the Americas and Australia.

Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species.

Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation.

Fomitiporia in sub-Saharan Africa: morphology and multigene phylogenetic analysis support three new species from the Guineo-Congolian rainforest.

Fomitiporia nobilissima sp. nov., F. gabonensis sp. nov. and F. ivindoensis sp. nov., three species from the rainforest of the Guineo-Congolian phytogeographic region in Gabon, are described and illustrated. These species share a pileate basidiome, small basidiospores and an absence of setae. The critical morphological features that differentiate them are the pileus habit or shape, pore surface color, pore diameter and possibly ecology. Each new species forms distinct but closely related clades in phylogenetic analysis of DNA sequences from nuclear ribosomal LSU, ITS and translation elongation factor 1-α. Other species in sub-Saharan Africa are discussed briefly. A key to six species of Fomitiporia from sub-Saharan Africa is provided. The new combination Fomitiporia apiahyna is proposed.

Perenniporiella chaquenia sp. nov. and further notes on Perenniporiella and its relationships with Perenniporia (poriales, basidiomycota).

Perenniporiella chaquenia sp. nov. is described from Argentina. New records of P. pendula and P. micropora are discussed. A key to Perenniporiella species is presented. Preliminary phylogenetic relationships of Perenniporiella are inferred from parsimony and Bayesian analysis of a combined set of DNA sequence data (nuclear ribosomal partial LSU and ITS). It demonstrated that Perenniporiella forms a well resolved monophyletic clade distantly related to Perenniporia s.s. It also clearly showed that within Perenniporia as usually conceived other morphologically homogeneous group of taxa, such as the P. ochroleuca or P. vicina alliances, form well resolved clades, which could be recognized as distinct genera. The differentiation of the hyphal system and the basidiospores morphology are outlined as critical features for the definition of genera in the Perenniporia complex.

Two new Erythrophylloporus species (Boletaceae) from Thailand, with two new combinations of American species.

Erythrophylloporus is a lamellate genus in the family Boletaceae that has been recently described from China based on E.cinnabarinus, the only known species. Typical characters of Erythrophylloporus are reddish-orange to yellowish-red basidiomata, including lamellae, bright yellow basal mycelium and smooth, broadly ellipsoid, ellipsoid to nearly ovoid basidiospores. During our survey on diversity of Boletaceae in Thailand, several yellowish-orange to reddish- or brownish-orange lamellate boletes were collected. Based on both morphological evidence and molecular analyses of a four-gene dataset (atp6, tef1, rpb2 and cox3), they were recognised as belonging in Erythrophylloporus and different from the already known species. Two new species, E.paucicarpus and E.suthepensis are therefore introduced from Thailand with detailed descriptions and illustrations. Moreover, two previously described Phylloporus species, P.aurantiacus and P.fagicola, were also revised and recombined in Erythrophylloporus. A key to all known Erythrophylloporus species is provided.

Two new species of Amanitasect.Phalloideae from Africa, one of which is devoid of amatoxins and phallotoxins.

Two new species of Amanitasect.Phalloideae are described from tropical Africa (incl. Madagascar) based on both morphological and molecular (DNA sequence) data. Amanitabweyeyensis sp. nov. was collected, associated with Eucalyptus, in Rwanda, Burundi and Tanzania. It is consumed by local people and chemical analyses showed the absence of amatoxins and phallotoxins in the basidiomata. Surprisingly, molecular analysis performed on the same specimens nevertheless demonstrated the presence of the gene sequence encoding for the phallotoxin phallacidin (PHA gene, member of the MSDIN family). The second species, Amanitaharkoneniana sp. nov. was collected in Tanzania and Madagascar. It is also characterised by a complete PHA gene sequence and is suspected to be deadly poisonous. Both species clustered together in a well-supported terminal clade in multilocus phylogenetic inferences (including nuclear ribosomal partial LSU and ITS-5.8S, partial tef1-α, rpb2 and ß-tubulin genes), considered either individually or concatenated. This, along with the occurrence of other species in sub-Saharan Africa and their phylogenetic relationships, are briefly discussed. Macro- and microscopic descriptions, as well as pictures and line drawings, are presented for both species. An identification key to the African and Madagascan species of Amanitasect.Phalloideae is provided. The differences between the two new species and the closest Phalloideae species are discussed.