Biogeography in the air: fungal diversity over land and oceans

Biogenic aerosols are relevant for the Earth system, climate, and public health on local, regional, and global scales. Up to now, however, little is known about the diversity and biogeography of airborne microorganisms. We present the first DNA-based analysis of airborne fungi on global scales, showing pronounced geographic patterns and boundaries. In particular we find that the ratio of species richness between Basidiomycota and Ascomycota is much higher in continental air than in marine air. This may be an important difference between the 'blue ocean' and 'green ocean' regimes in the formation of clouds and precipitation, for which fungal spores can act as nuclei. Our findings also suggest that air flow patterns and the global atmospheric circulation are important for the understanding of global changes in biodiversity.

Cyanobacterial diversity in the phyllosphere of a mangrove forest

The cyanobacterial community colonizing phyllosphere in a well-preserved Brazilian mangrove ecosystem was assessed using cultivation-independent molecular approaches. Leaves of trees that occupy this environment (Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa) were collected along a transect beginning at the margin of the bay and extending upland. The results demonstrated that the phyllosphere of R.similar to mangle and L.similar to racemosa harbor similar assemblages of cyanobacteria at each point along the transect. A.similar to schaueriana, found only in the coastal portions of the transect, was colonized by assemblages with lower richness than the other trees. However, the results indicated that spatial location was a stronger driver of cyanobacterial community composition than plant species. Distinct cyanobacterial communities were observed at each location along the coast-to-upland transect. Clone library analysis allowed identification of 19 genera of cyanobacteria and demonstrated the presence of several uncultivated taxa. A predominance of sequences affiliated with the orders Nostocales and Oscillatoriales was observed, with a remarkable number of sequences similar to genera Symphyonemopsis/Brasilonema (order Nostocales). The results demonstrated that phyllosphere cyanobacteria in this mangrove forest ecosystem are influenced by environmental conditions as the primary driver at the ecosystem scale, with tree species exerting some effect on community structure at the local scale.

A revision of species diversity in the Neotropical genus Oreobates (Anura: Strabomantidae), with the description of three new species from the Amazonian slopes of the Andes

We revisit species diversity within Oreobates (Anura: Strabomantidae) by combining molecular phylogenetic analyses of the 16S rRNA amphibian barcode fragment with the study of the external morphology of living and preserved specimens. Molecular and morphological evidence support the existence of 23 species within Oreobates, and three additional candidate species (Oreobates sp. [Ca JF809995], Oreobates sp. [Ca EU368903], Oreobates cruralis [Ca EU192295]). We describe and name three new species from the Andean humid montane forests of Departamento Cusco, southern Peru: O. amarakaeri New Species from Rio Nusinuscato and Rio Mabe, at elevations ranging from 670 to 1000 m in the Andean foothills; O. machiguenga, new species, from Rio Kimbiri (1350 m), a small tributary of the Apurimac River, in the western versant of Cordillera Vilcabamba; and O. gemcare, new species, from the Kosnipata Valley at elevations ranging from 2400 to 2800 m. The three new species are readily distinguished from all other Oreobates by at least one qualitative morphological character. Three species are transferred to Oreobates from three genera of Strabomantidae: Hypodactylus lundbergi, Pristimantis crepitans, and Phrynopus ayacucho (for which the advertisement call, coloration in life, and male characteristics are described for first time). Oreobates simmonsi is transferred to the genus Lynchius. Hylodes verrucosus is considered a junior synonym of Hylodes philippi. In addition, H. philippi is removed from the synonymy of O. quixensis and considered a nomem dubium within Hypodactylus. The inclusion of Phrynopus ayacucho in Oreobates extends the ecological range of the genus to the cold Andean puna. Oreobates is thus distributed from the Amazonian lowlands in southern Colombia to northern Argentina, reaching the Brazilian Atlantic dry forests in eastern Brazil, across an altitudinal range from ca. 100 to 3850 m.

Global pharmacogenomics: Impact of population diversity on the distribution of polymorphisms in the CYP2C cluster among Brazilians

The impact of biogeographical ancestry, self-reported 'race/color' and geographical origin on the frequency distribution of 10 CYP2C functional polymorphisms (CYP2C8*2, *3, *4, CYP2C9*2, *3, *5, *11, CYP2C19*2, *3 and *17) and their haplotypes was assessed in a representative cohort of the Brazilian population (n = 1034). TaqMan assays were used for allele discrimination at each CYP2C locus investigated. Individual proportions of European, African and Amerindian biogeographical ancestry were estimated using a panel of insertion-deletion polymorphisms. Multinomial log-linear models were applied to infer the statistical association between the CYP2C alleles and haplotypes (response variables), and biogeographical ancestry, self-reported Color and geographical origin (explanatory variables). The results showed that CYP2C19*3, CYP2C9*5 and CYP2C9*11 were rare alleles (<1%), the frequency of other variants ranged from 3.4% (CYP2C8*4) to 17.3% (CYP2C19*17). Two distinct haplotype blocks were identified: block 1 consists of three single nucleotide polymorphisms (SNPs) (CYP2C19*17, CYP2C19*2 and CYP2C9*2) and block 2 of six SNPs (CYP2C9*11, CYP2C9*3, CYP2C9*5, CYP2C8*2, CYP2C8*4 and CYP2C8*3). Diplotype analysis generated 41 haplotypes, of which eight had frequencies greater than 1% and together accounted for 96.4% of the overall genetic diversity. The distribution of CYP2C8 and CYP2C9 (but not CYP2C19) alleles, and of CYP2C haplotypes was significantly associated with self-reported Color and with the individual proportions of European and African genetic ancestry, irrespective of Color self-identification. The individual odds of having alleles CYP2C8*2, CYP2C8*3, CYP2C9*2 and CYP2C9*3, and haplotypes including these alleles, varied continuously as the proportion of European ancestry increased. Collectively, these data strongly suggest that the intrinsic heterogeneity of the Brazilian population must be acknowledged in the design and interpretation of pharmacogenomic studies of the CYP2C cluster in order to avoid spurious conclusions based on improper matching of study cohorts. This conclusion extends to other polymorphic pharmacogenes among Brazilians, and most likely to other admixed populations of the Americas. The Pharmacogenomics Journal (2012) 12, 267-276; doi: 10.1038/tpj.2010.89; published online 21 December 2010

Phylogeographic Structure and Karyotypic Diversity of the Brazilian Shrew Mouse (Blarinomys breviceps, Sigmodontinae) in the Atlantic Forest

Blarinomys breviceps possesses cryptic and burrowing habits with poorly documented genetics and life history traits. Due to its rarity, only a few specimens and DNA sequences have been deposited in collections worldwide. Here, we present the most comprehensive cytogenetic and molecular characterization of this rare genus. Phylogenetic analyses based on partial cytochrome b sequences were performed, attempting to establish the relationships among individuals with distinct karyotypes along the geographic distribution of the genus in the Atlantic Forest. Classical and molecular cytogenetics, using banding patterns and FISH of telomeric and whole chromosome X-specific painting probes (obtained from the Akodontini Akodon cursor) were used to characterize and compare the chromosomal complements. Molecular phylogenetic analyses recovered 2 main geographically structured clades, northeastern and southeastern with pair-wise sequence divergences among specimens varying between 4.9 and 8.4%. Eight distinct karyomorphs are described: (A) 2n = 52 (50A, XX), (B) 2n = 52 (48A, XY+2Bs), (C) 2n = 45 (42A, XY+1B), (D) 2n = 43 (37A, XX+4Bs), (E) 2n = 37 (34A, XY+1B), (F) 2n = 34 (32A, XX), (G) 2n = 31 (27A, XX+2Bs), (H) 2n = 28 (26A, XY), all with the same number of autosomal arms (FNA = 50). Variation of 0-4 supernumerary chromosomes (Bs) presenting heterogeneity in morphology and distribution of interstitial telomeric sequences (ITSs) is reported. ITSs are also found in some metacentric autosomes. The phylogeographic separation between 2 major lineages with high levels of genetic divergence, and the wide karyotypic diversity indicate that B. breviceps is a diverse group that warrants taxonomic re-evaluation. Copyright (C) 2012 S. Karger AG, Basel

Bird species diversity in the Atlantic Forest of Brazil is not explained by the Mid-domain Effect

The Atlantic Forest is an excellent case study for the elevational diversity of birds, and some inventories along elevational gradients have been carried out in Brazil. Since none of these studies explain the patterns of species richness with elevation, we herein review all Brazilian studies on bird elevational diversity, and test a geometric constraint null model that predicts a unimodal species-altitude curve, the Mid-domain Effect (MDE). We searched for bird inventories in the literature and also analysed our own survey data using limited-radius point counts along an 800 m elevational gradient in the state of São Paulo, Brazil. We found 10 investigations of elevational diversity of Atlantic Forest birds and identified five different elevational patterns: monotonic decreasing diversity, constant at low elevations, constant at low elevations but increasing towards the middle, and two undescribed patterns for Atlantic Forest birds, trough-shaped and increasing diversity. The average MDE fit was low (r² = 0.31) and none of the MDE predictions were robust across all gradients. Those studies with good MDE model fits had obvious sampling bias. Although it has been proposed that the MDE may be positively associated with the elevational diversity of birds, it does not fit the Brazilian Atlantic Forest bird elevational diversity.