Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas.

Understanding the processes that generate and maintain biodiversity at and below the species level is a central goal of evolutionary biology. Here we explore the spatial and temporal drivers of diversification of the treefrog subgroup Dendropsophus rubicundulus, a subgroup of the D. microcephalus species group, over periods of pronounced geological and climatic changes in the Neotropical savannas that they inhabit. This subgroup currently comprises 11 recognized species distributed across the Brazilian and Bolivian savannas, but the taxonomy has been in a state of flux, necessitating reexamination. Using newly generated single nucleotide polymorphism (SNP) data from restriction-site associated DNA sequencing (RADseq) and mitochondrial 16S sequence data for ∼150 specimens, we inferred phylogenetic relationships, tested species limits using a model-based approach, and estimated divergence times to gain insights into the geographic and climatic events that affected the diversification of this subgroup. Our results recognized at least nine species: D. anataliasiasi, D. araguaya, D. cerradensis, D. elianeae, D. jimi, D. rubicundulus, D. tritaeniatus, D. rozenmani, and D. sanborni. Although we did not collect SNP data for the latter two species, they are likely distinct based on mitochondrial data. In addition, we found genetic structure within the widespread species D. rubicundulus, which comprises three allopatric lineages connected by gene flow upon secondary contact. We also found evidence of population structure and perhaps undescribed diversity in D. elianeae, which warrants further study. The D. rubicundulus subgroup is estimated to have originated in the Late Miocene (∼5.45 million years ago), with diversification continuing through the Pliocene and Early Pleistocene, followed by the most recent divergence of D. rubicundulus lineages in the Middle Pleistocene. The epeirogenic uplift followed by erosion and denudation of the central Brazilian plateau throughout the Pliocene and Pleistocene, in combination with the increasing frequency and amplitude of climatic fluctuations during the Pleistocene, was important for generating and structuring diversity at or below the species level in the D. rubicundulus subgroup.

Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity.

Troglomorphism-any morphological adaptation enabling life to the constant darkness of caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and olfactory organs-has long intrigued biologists. However, inferring the proximate and ultimate mechanisms driving the evolution of troglomorphism (stygomorphism) in freshwater fish requires a sound understanding of the evolutionary relationships between surface and stygomorphic lineages. We use Restriction Site Associated DNA Sequencing (RADseq) to better understand the evolution of the Sinocyclocheilus fishes of China. With a remarkable array of derived stygomorphic traits, they comprise the largest cavefish diversification in the world, emerging as a multi-species model system to study evolutionary novelty. We sequenced a total of 120 individuals throughout the Sinocyclocheilus distribution. The data comprised a total of 646,497 bp per individual, including 4378 loci and 67,983 SNPs shared across a minimum of 114 individuals at a given locus. Phylogenetic analyses using either the concatenated RAD loci (RAxML) or the SNPs under a coalescent model (SVDquartets, SNAPP) showed a high degree of congruence with similar topologies and high node support (>95 for most nodes in the phylogeny). The major clades recovered conform to a pattern previously established using Sanger-based mt-DNA sequences, with a few notable exceptions. We now recognize six major clades in this group, elevating the blind cavefish S. tianlinensis and the micro-eyed S. microphthalmus as two new distinct clades due to their deep divergence from other clades. PCA plots of the SNP data also support the recognition of six major clusters of species congruent with the identified clades in ordination space. A Bayes factor delimitation (BFD) analysis showed support for 21 species, recognizing 19 previously described species and two putative new cryptic ones. Two species whose identities were previously disputed, S. furcodorsalis and S. tianeensis, are supported here as distinct species. In addition, our multi-species calibrated tree in SNAPP suggests that the genus Sinocyclocheilus originated around 10.16 Mya, with most speciation events occurring in the last 2 Mya, likely favored by the uplift of the Qinghai-Tibetan Plateau and cave occupation induced by climate-driven aridification during this period. These results provide a firm basis for future comparative studies on the evolution of Sinocyclocheilus and its adaptations to cave life.

Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna.

Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post-Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability," highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.

Oral bacteriome of HIV-1-infected children from Rio de Janeiro, Brazil: Next-generation DNA sequencing analysis.

BACKGROUND AND AIM: This study compared the oral bacteriome between HIV-1-infected and non-HIV-1-infected Brazilian children/teenagers. METHODS: Whole saliva, biofilm from the dorsal surface of the tongue and biofilm from supragingival and subgingival sites were collected from 27 HIV-1-infected and 30 non-HIV-1-infected individuals. Bacterial genomic DNA was extracted and 16S rRNA genes were sequenced using next-generation sequencing technology (Ion Torrent). RESULTS: In the supragingival biofilm, the phylum Firmicutes and genus Streptococcus sp. were more frequent in HIV-1-infected (95% and 78%, respectively) than in non-HIV-1-infected individuals (40% and 24%, respectively). In the subgingival biofilm of HIV-infected participants, the relative abundance of the Veillonella sp. and Prevotella sp. genera were higher than in non-HIV-1-infected participants. On the tongue, the genera with greater relative abundance in HIV-1-infected individuals were Neisseria sp. (21%). In saliva, the difference of the genus Prevotella sp. between non-HIV-1-infected and HIV-1-infected individuals was 15% and 7%, respectively. The Chao index revealed an increase in the richness of both sub- and supragingival biofilms in the HIV-1-infected samples compared with non-HIV-1-infected samples. CONCLUSION: HIV-1-infected children/teenagers have a higher frequency of the phyla Firmicutes and genus Streptococcus, and their oral microbiome shows more complexity than that of non-HIV-1-infected children/teenagers.

Sex-related differences in aging rate are associated with sex chromosome system in amphibians.

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture-recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the "unguarded X/Z effect") or repeat-rich Y/W chromosome (the "toxic Y/W effect") could accelerate aging in the heterogametic sex in some vertebrate clades.

Digest: Dispersal reduction drives rapid diversification in alpine grasshoppers.

Dispersal-associated traits -such as flight ability- influence how species move across the landscape, and can dramatically impact their distributions and patterns of genetic structure. Ortego et al. examine genomic data from two recently diverged alpine grasshopper lineages with distinct wing sizes to assess the demographic impacts of flight loss. The authors showed that flight loss may lead to asymmetric introgression during speciation, and can significantly increase rates of intraspecific diversification.

Bisphophonate alterations of the jaw bones in individuals with multiple myeloma.

OBJECTIVES: To verify quantitative differences of the mandibular cortical and trabecular bone between patients with multiple myeloma (MM) under bisphosphonate (BP) therapy and a control group never exposed to BP. METHODS: Clinical and demographic characteristics were collected through medical records and interviews. Mandibular cortical thickness (MCT) and fractal dimension (FD) were measured on cone beam computed tomography (CBCT) images, on the molar region, in both groups. Additionally, FD was measured on periapical digital intraoral radiography and results were compared to CBCT measurements. RESULTS: There were 33 patients with MM under BP therapy and 28 controls, with no significant differences in gender and age between groups. Pamidronate was used by all MM patients, either associated or not to other types of BP. The median MCT was higher in MM group exposed to BP (5.20 mm) than in controls (3.50 mm, p < 0.001). There were no significant differences in the median FD between patients in the MM group and controls, on CBCT (0.95 vs 0.90, p = 0.814) and periapical digital intraoral radiography (0.98 vs 0.96, p = 0.963), respectively, even when more than one type of BP was used. CONCLUSIONS: The MCT represents an useful tool in the detection of bone dimensional changes caused by BP, in patients with MM. Additional studies are necessary to improve the knowledge on the quantitative evaluation of trabecular jaw bone, in individuals with MM, under BP therapy.

Análise preliminar do tratamento de Diabetes mellitus com Polissacarídeo de Tremella fuciformis / Preliminary analysis of the treatment of Diabetes mellitus with Tremella fuciformis polysaccharide

Introdução: O Diabetes mellitus é uma desordem metabólica que ocorre no mundo inteiro, caracterizada por hiperglicemia associada a problemas com secreção ou ação da insulina ou, ainda por alterações no metabolismo intermediário de carboidratos, proteína e lipídeos. O cogumelo Tremella fuciformis (Basideomycota) foi isolado no Brasil e levado para a China onde tem sido produzido e utilizado como alimento por apresentar diversas atividades biológicas como anti-inflamatório, anti-mutagênico, reduz hipertensão, reduz diabetes entre outras propriedades relacionadas com imunidade. A Embrapa de Brasília tornou isolar o cogumelo e enviou a universidade para os testes preliminares. Objetivo: O presente trabalho teve como objetivo induzir a diabetes em ratos e realizar tratamento com polissacarídeo (PS) extraído do cogumelo gelatinoso Tremella fuciformis, desenvolvido em frascos no laboratório. Método: Ratos, no total de 28 animais foram divididos em 4 grupos sendo: 1-Normal) grupo recebendo dieta normal e água; 2-Sacarose) grupo recebendo ração normal e uma solução de sacarose 20% por 65 dias; 3-Sacarose + PS) grupo recebendo ração normal + solução de sacarose (65dias) e por gavagem PS na concentração de 1mmol (nos últimos 20 dias sendo uma vez/semana) ; 4-idem ao grupo 3, entretanto PS com concentração de 2mmol. No período, os ratos (uma vez/semana) foram pesados e submetidos a teste de glicose (fita Accu Check) e, depois sacrificados com dose letal de analgésico e coleta do sangue para testes de glicose, colesterol, triglicérides, creatinina e HDL. Resultados: Os resultados parciais demonstraram que os animais submetidos à dieta com sacarose aumentaram o peso e glicemia. Já os animais submetidos a tratamento com o PS permaneceram com o peso praticamente constante e, redução da glicemia. A creatinina tem sido um parâmetro para diagnosticar problemas renais, mas os animais em todos os tratamentos, não apresentaram diferença estatística. Para colesterol os animais submetidos ao tratamento com o PS apresentaram valores abaixo dos encontrados no grupo com sacarose, entretanto, com triglicérides e HDL apresentaram diminuição, mas houve, aumento em relação aos animais do grupo normal, indicando controle nos lipídeos. Por conclusão os resultados preliminares demonstraram que o PS extraído do cogumelo Tremella fuciformis apresenta grande potencial como produto natural contra diabetes.