The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important r...

In this study, we present a detailed family-level phylogenetic hypothesis for the largest avian order (Aves: Passeriformes) and an unmatched multi-calibrated, relaxed clock inference for the diversification of crown passerines. Extended taxon sampling allowed the recovery of many challenging clades and elucidated their position in the tree. Acanthisittia appear to have diverged from all other passerines at the early Paleogene, which is considerably later than previously suggested. Thus, Passeriformes may be younger and represent an even more intense adaptive radiation compared to the remaining avian orders. Based on our divergence time estimates, a novel hypothesis for the diversification of modern Suboscines is proposed. According to this hypothesis, the first split between New and Old World lineages would be related to the severing of the Africa-South America biotic connection during the mid-late Eocene, implying an African origin for modern Eurylaimides. The monophyletic status of groups not recovered by any subsequent study since their circumscription, viz. Sylvioidea including Paridae, Remizidae, Hyliotidae, and Stenostiridae; and Muscicapoidea including the waxwing assemblage (Bombycilloidea) were notable topological findings. We also propose possible ecological interactions that may have shaped the distinct Oscine distribution patterns in the New World. The insectivorous endemic Oscines of the Americas, Vireonidae (Corvoidea), Mimidae, and Troglodytidae (Muscicapoidea), probably interfered with autochthonous Suboscines through direct competition. Thus, the Early Miocene arrival of these lineages before any other Oscines may have occupied the few available niches left by Tyrannides, constraining the diversification of insectivorous Oscines that arrived in the Americas later. The predominantly frugivorous-nectarivorous members of Passeroidea, which account for most of the diversity of New World-endemic Oscines, may not have been subjected to competition with Tyrannides. In fact, the vast availability of frugivory niches combined with weak competition with the autochthonous passerine fauna may have been crucial for passeroids to thrive in the New World.

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SummaryRecent ornithological surveys of humid forest remnants in the Serra da Ouricana near Boa Nova, southern Bahia, Brazil, revealed the existence of an as yet unnoticed montane Atlantic forest avifauna. Among the 220 species recorded, 27 represent range extensions of several hundred kilometres, several others were preceded only by single or a few old, disputed records from Bahia, and at least two are undescribed taxa. A portion of this avifauna has been recorded in other mountainous areas of interior Bahia (Chapada Diamantina, plateau of Maracas), where a complex vegetation mosaic that includes patches of humid forest is found.In addition to the two undescribed passerines, nine other threatened and thirteen near-threatened species have been recorded in the study area. Considered together with the adjoining and also highly endangered "mata-de-cipo", forest habitats in the Boa Nova area are probably the most neglected habitats in Brazil concerning bird conservation.Levantamentos ornitologicos recentemente feitos em remanescentes florestais umidos na Serra da Ouricana perto de Boa Nova, sul da Bahia, Brasil, revelaram a existencia nessa regiao de uma avifauna monticola da mata Atlantica. Entre as 220 especies registradas, estao 27 que tiveram sua area de distribuicao estendida por centenas de quilometros, muitas outras conhecidas da Bahia apenas atraves de registros antigos e contestados, alem de ao menos duas aves nao descritas. Parte dessa avifauna foi tambem registrada em outras areas montanhosas do interior da Bahia (Chapada Diamantina, Chapadao Maracas), onde se encontra um complexo mosaico de vegetacao que inclui manchas de floresta umida. Alem dos dois passaros nao descritos, outras nove especies ameacadas e treze quase-ameacadas foram registradas na area de estudo. Considerando-se em conjunto essa area com a vizinha "mata-de-cipo", tambem muito ameacada, pode-se dizer que os ambientes florestais na regiao de Boa Nova sao os habitats mais negligenciados em relacao a conservacao de aves no Brasil.

Sakesphorus luctuosus (Glossy Antshrike) is endemic to Brazil, harboring two subspecies. The nominal subspecies is widespread in the Amazon region, and S. l. araguayae is endemic to the Rio Araguaia valley. In this paper we investigated the hypothesis that S. l. araguayae represents the end of a cline. We examined 588 specimens housed in Brazilian, North American and European museums and based our conclusions on plumage coloration and morphometric characters. We found no significant differences in morphometric characters between subspecies, except for culmen length, which was slightly shorter in S. l. araguayae, but with wide overlap in measurements. The main proposed diagnostic character between subspecies (length of the white tips to tail feathers) showed clinal variation, with northern birds showing more white on the tail, and southern birds showing less white on the tail, irrespective of hydrographic basin. The other diagnostic character proposed (width of the white edges to the outer webs of the scapular feathers) showed high individual variation and no taxonomic consistency. We conclude that S. l. araguayae is a junior synonym of the nominal taxon. On the other hand, S. hagmanni, known only from the holotype and long thought to be a junior synonym of the nominal taxon, proved to be a unique specimen that should be considered as species inquirenda until further investigations determine its status.

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The Eurylaimides is one of the few passerine groups with a pantropical distribution. In this study, we generated a multi-calibrated tree with 83% of eurylaimid species diversity based on 30 molecular loci. Particular attention was given to the monotypic Sapayoidae to reconstruct the biogeography of this radiation. We conducted several topological tests including nonoverlapping subsampling of the concatenated alignment and coalescent species tree reconstruction. These tests firmly placed the South American Sapayoidae as the sister group to all other Eurylaimides families (split at ∼28 Ma), with increasing branch support as highly variable sites were removed. This topology is consistent with the breakup of the insular connection between Africa and South America (Atlantogea) that took place between the middle Eocene and the early Oligocene. We recovered Africa as the cradle of the core Eurylaimides, and this result is supported by all African lineages corresponding to the oldest splits within each family in this group. Our timescale suggests that desertification and the uplift of the Tibetan Plateau caused a parallel divergence between African and Asian lineages in all major clades in the core Eurylaimides at 22-9 Ma. We also propose that the ground-foraging behavior in the Pittidae ancestor allowed the pitta lineage to thrive and coexist with the older arboreal lineages of the core Eurylaimides. In contrast, the diversification of pittas in Australia was likely hindered by direct competition with the endemic ground-foraging oscines that had been well established in that continent since the Eocene.

Formicivora grantsaui sp. nov. (Sincorá Antwren) is described from a series of specimens from the valley of the Rio Cumbuca (12 o 58’29”S, 41 o 21’29”W, elevation 860 m), 3.5 km northeast of Mucugê, Bahia, Brazil, and adjacent areas. It is more closely related to F. acutirostris, F. grisea, and F. rufa than to other species of the genus, differing from them by a combination of plumage and vocal characters. The new species is known only from the campo rupestre vegetation of the Serra do Sincorá between 850 m and 1100 m in the Chapada Diamantina, which is part of the Espinhaço Range, a distinctive area of endemism for birds and other groups of organisms in South America. In places it occurs sympatrically with F. rufa, but the two occupy different habitats.