A comparative description of mitochondrial DNA differentiation in selected avian and other vertebrate genera

Levels of mitochondrial DNA (mtDNA) sequence divergence between species within each of several avian (Anas, Aythya, Dendroica, Melospiza, and Zonotrichia) and nonavian (Lepomis and Hyla) vertebrate genera were compared. An analysis of digestion profiles generated by 13-18 restriction endonucleases indicates little overlap in magnitude of mtDNA divergence for the avian versus nonavian taxa examined. In 55 interspecific comparisons among the avian congeners, the fraction of identical fragment lengths (F) ranged from 0.26 to 0.96 (F = 0.46), and, given certain assumptions, these translate into estimates of nucleotide sequence divergence (p) ranging from 0.007 to 0.088; in 46 comparisons among the fish and amphibian congeners, F values ranged from 0.00 to 0.36 (F = 0.09), yielding estimates of P greater than 0.070. The small mtDNA distances among avian congeners are associated with protein-electrophoretic distances (D values) less than approximately 0.2, while the mtDNA distances among assayed fish and amphibian congeners are associated with D values usually greater than 0.4. Since the conservative pattern of protein differentiation previously reported for many avian versus nonavian taxa now appears to be paralleled by a conservative pattern of mtDNA divergence, it seems increasingly likely that many avian species have shared more recent common ancestors than have their nonavian taxonomic counterparts. However, estimates of avian divergence times derived from mtDNA- and protein-calibrated clocks cannot readily be reconciled with some published dates based on limited fossil remains. If the earlier paleontological interpretations are valid, then protein and mtDNA evolution must be somewhat decelerated in birds. The empirical and conceptual issues raised by these findings are highly analogous to those in the long-standing debate about rates of molecular evolution and times of separation of ancestral hominids from African apes.      

MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms

The genome‐wide association studies (GWASs) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of the model and nonmodel organisms. For this research question, the GWAS replication testing different parameters and models to validate the results'' reproducibility is common. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software packages, two designed for polyploid data (GWASpoly and SHEsis) and two designed for diploid data (GAPIT and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in a graphical interface; it manages different genotype formats, including VCF. Moreover, it allows control for population structure, relatedness, and several quality control checks on genotype data. Besides, MultiGWAS can test for additive and dominant gene action models, and, through a proprietary scoring function, select the best model to report its associations. Finally, it generates several reports that facilitate identifying false associations from both the significant and the best‐ranked association Single Nucleotide Polymorphisms (SNPs) among the four software packages. We tested MultiGWAS with public tetraploid potato data for tuber shape and several simulated data under both additive and dominant models. These tests demonstrated that MultiGWAS is better at detecting reliable associations than using each of the four software packages individually. Moreover, the parallel analysis of polyploid and diploid software that only offers MultiGWAS demonstrates its utility in understanding the best genetic model behind the SNP association in tetraploid organisms. Therefore, MultiGWAS probed to be an excellent alternative for wrapping GWAS replication in diploid and tetraploid organisms in a single analysis environment.     

Urban exploiters have broader dietary niches than urban avoiders

Urbanization is currently one of the most pervasive threats to biodiversity worldwide, yet traits permitting birds to exploit urban environments are not fully understood. I used bird traits related to diet (dietary item and foraging stratum), accounting for latitude, body size, development mode and phylogeny, to compare diet breadths of urban exploiters and urban avoiders, using a global dataset (463 bird species). Urban exploiters (urban species) were larger, consumed more vertebrates and carrion, and fed more frequently on the ground or aerially, and also had broader diets than urban avoiders (non-urban species). In contrast, urban species had narrower foraging strata ranges than non-urban species. These results not only support the hypothesis that urban species share dietary traits allowing them to cope with urban environments but also highlight the importance of considering multiple dietary traits to properly quantify species niches when assessing a species’ response to environmental change.     

Generalist Species Have a Central Role In a Highly Diverse Plant–Frugivore Network

Analysis of plant–frugivore interactions provides a quantitative framework for integrating community structure and ecosystem function in terms of how the roles and attributes of individual species contribute to network structure and resilience. In this study, we used centrality metrics to rank and detect the most important species in a mutualistic network of fruit‐eating birds and plants in a cloud forest in the Colombian Andes. We identified a central core of ten bird and seven plant species in a network of 135 species that perform dual roles as local hubs and connectors. The birds were mostly large forest frugivores, such as cracids, cotingas, and toucans, which consume fruits of all sizes. The plants were species of intermediate successional stages with small‐ to medium‐sized seeds that persist in mature forest or forest borders (e.g., Miconia, Cecropia, Ficus). We found the resilience of our network depends on super‐generalist species, because their elimination makes the network more prone to disassemble than random extinctions, potentially disrupting seed‐dispersal processes. At our study site, extirpation of large frugivores has already been documented, and if this continues, the network might collapse despite its high diversity. Our results suggest that generalist species play critical roles in ecosystem function and should be incorporated into conservation and monitoring programs.     

Unravelling the mechanisms for plant survival on gypsum soils: an analysis of the chemical composition of gypsum plants from Turkey

Depending on their specificity to gypsum, plants can be classified as gypsophiles (gypsum exclusive) and gypsovags (non‐exclusive). The former may further be segregated into wide and narrow gypsophiles, depending on the breadth of their distribution area. Narrow gypsum endemics have a putative similar chemical composition to plants non‐exclusive to gypsum (i.e. gypsovags), which may indicate their similar ecological strategy as stress‐tolerant plant refugees on gypsum. However, this hypothesis awaits testing in different regions of the world. We compared the chemical composition of four narrow gypsum endemics, one widely distributed gypsophile and six gypsovags from Turkey. Further, we explored the plasticity in chemical composition of Turkish gypsovags growing on high‐ and low‐gypsum content soils. Differences were explored with multivariate analyses (RDA) and mixed models (REML). Narrow gypsum endemics segregated from gypsovags in their chemical composition according to RDAs (mainly due to higher K and ash content in the former). Nevertheless, differences were small and disappeared when different nutrients were analysed individually. All the gypsovags studied accumulated more S and ash when growing on high‐gypsum than on low‐gypsum soils. Similar to narrow gypsum endemics from other regions of the world, most local gypsum endemics from Turkey show a similar chemical composition to gypsovags. This may indicate a shared ecological strategy as stress‐tolerant plants not specifically adapted to gypsum. Nevertheless, the narrow gypsum endemic Gypsophila parva showed a chemical composition typical of gypsum specialists, indicating that various strategies are feasible within narrowly distributed gypsophiles.     

Scedosporium apiospermum external otitis.

We report a case of Scedosporium apiospermum external otitis. The patient was topically treated with miconazole cream and achieved a clinical and mycological cure. The etiology, diagnosis and treatment of external fungal otitis are discussed.     

Dermatophytes isolated in Hospital Universitario 12 de Octubre (Madrid, Spain).

Over a 10 year period (January 1988 - December 1997), 3,241 dermatophyte strains were isolated from 18,465 specimens from patients in whom dermatophytosis was suspected clinically. This represents a 17.5% rate of isolation. Trichophyton rubrum (38.44%), Microsporum canis (28.75%), Epidermophyton floccosum (14.5%) and Trichophyton mentagrophytes (13.5%) were the dominant species, and Trichophyton tonsurans (2.09%) has emerged, whilst in the previous decade it had virtually disappeared. Our study is basically based on an out-patient selected population, and tinea corporis (30.79%), followed by tinea cruris (16.69%) and tinea unguium (16.69%) were the most prevalent clinical forms.     

Validation of the Diagnostic Interview for Genetic Studies (DIGS) in Colombia

An interview tool, Diagnostic Interview for Genetic Studies (DIGS 3.0), was translated into Spanish for application in studies of psychiatric disorders in Colombia. Two Spanish translations of the original English version of DIGS were prepared and back-translated into English. A review committee verified the linguistic and cultural equivalence of the translations. The evaluator and test-retest reliability were assessed calculating Cohen's kappa for samples of 65 and 91 patients respectively. DIGS proved valid in both appearance and content. The confidence interval (C.I.) was excellent for schizophrenia (kappa = 0.81, C.I. 95% = 0.68-0.93), bipolar disorder (kappa = 0.87, C.I. 95% = 0.75-0.99), major depressive disorder (kappa = 0.86, C.I. 95% = 0.70-1.00), and for a normal diagnosis (kappa = 0.65, C.I. 95% = 0.41-0.89); it was good for other psychiatric diagnosis (kappa = 0.65, C.I. 95% = 0.41-0.89) and poor for schizoaffective disorder (kappa = 0.37, C.I. 95% = -0.02-0.76). Test-retest reliability was excellent for all diagnoses (kappa > 0.8), except for "other psychiatric diagnoses" (kappa = 0.64, C.I. 95% = 0.31-0.96). The Spanish translation of the DIGS was comprehensible, with face and content validity, and good test-retest and evaluator reliability. This translation will be a useful tool for genetic studies of psychiatric disorders in Latin America, particularly where schizophrenia and affective disorders are involved.     

Cryptococcus neoformans arthritis in a renal transplant recipient

We present a Cryptococcus neoformans knee joint infection in a diabetic renal transplant patient treated with steroids, cyclosporin, and mycofenolate mofetil. We discuss reported cases of cryptococcal arthritis.     

Early diagnosis of invasive aspergillosis in neutropenic patients with bi-weekly serial screening of circulating galactomannan by Platelia Aspergillus

The diagnosis of invasive aspergillosis in neutropenic individuals is difficult and lengthy since non-invasive diagnostic tests lack sensitivity and specificity. The diagnosis of invasive aspergillosis in 154 prolonged neutropenic patients was prospectively bi-weekly validated by screening circulating galactomannan. The global sensitivity was 73% and specificity was 96%. The positive and negative predictive values were 73% and 98% respectively. False positive reactions occurred at a rate of 2%. Antigenemia was detected before clinical suspicion of invasive aspergillosis (median, 6 days before) in 30% of patients and anticipated the onset of radiologic signs 9 days in 60% of patients. CONCLUSION: the prospective screening of galactomannan is a sensitive and non-invasive tool for early diagnosis of invasive aspergillosis in high-risk adult hematology patients.