Interactions between anthropogenic litter and birds: A global review with a 'black-list' of species.

The interaction of anthropogenic litter (by incorporation litter in nests, ingestion, and entanglement) with birds was systematically reviewed using Google Scholar database. A 'black-list' of 258 species was compiled. Among them 206 (79.8%) were seabirds. Four seabird orders (Gaviiformes, Phaetontiformes, Procellariformes, Sphenisciformes) showed the highest percentage of interacting species. At family level, >70% of species of Gaviidae, Diomedeidae, Sulidae, Stercoraridae and Alcidae were involved in interactions with litter. We observed (i) a significant correlation between Scholar recurrences and species citations about anthropogenic litter only when considering seabirds; (ii) a low number of references before 1981 with a bimodal pattern showing a first peak in 1986-90 and a progressively increasing trend in the 2000s. Regarding the type of interaction, there was a significantly higher percentage of species involved in ingestion when compared to the percentage involved in entanglement. We suggest the use of consolidated standardized litter nomenclature and characterization and the adoption of a logical causal chain helping researchers in defining suitable frameworks.

Analytical Biases Associated with GC-Content in Molecular Evolution.

Molecular evolution is being revolutionized by high-throughput sequencing allowing an increased amount of genome-wide data available for multiple species. While base composition summarized by GC-content is one of the first metrics measured in genomes, its genomic distribution is a frequently neglected feature in downstream analyses based on DNA sequence comparisons. Here, we show how base composition heterogeneity among loci and taxa can bias common molecular evolution analyses such as phylogenetic tree reconstruction, detection of natural selection and estimation of codon usage. We then discuss the biological, technical and methodological causes of these GC-associated biases and suggest approaches to overcome them.

Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology.

Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics.

Ethnozoology in Brazil: analysis of the methodological risks in published studies / Etnozoologia no Brasil: análise de riscos metodológicos nos trabalhos publicados

Abstract There has been a growth in the field of Ethnozoology throughout the years, especially in Brazil, where a considerable number of scientific articles pertaining to this subject has been published in recent decades. With this increase in publications comes the opportunity to assess the quality of these publications, as there are no known studies assessing the methodological risks in this area. Based on this observation, our objectives were to compile the papers published on the subject of ethnozoology and to answer the following questions: 1) Do the Brazilian ethnozoological studies use sound sampling methods?; 2) Is the sampling quality influenced by characteristics of the studies/publications? The studies found in databases and using web search engines were compiled to answer these questions. The studies were assessed based on their nature, sampling methods, use of hypotheses and tests, journal’s impact factor, and animal group studied. The majority of the studies analyzed exhibited problems associated with the samples, as 144 (66.98%) studies were classified as having a high risk of bias. With regard to the characteristics analyzed, we determined that a quantitative nature and the use of tests are essential components of good sampling. Most studies classified as moderate and low risk either did not provide these data or provided data that were not clear; therefore, these studies were classified as being of a quali-quantitative nature. Studies performed with vertebrate groups were of high risk. Most of the papers analyzed here focused on fish, insects, and/or mollusks, thus highlighting the difficulties associated with conducting interviews regarding tetrapod vertebrates. Such difficulties are largely related to the extremely strict Brazilian laws, justified by the decline and extinction of some species, related to the use of wild tetrapod vertebrates.

Resumo Ao longo dos anos a Etnozoologia vem crescendo, principalmente no Brasil, no qual se observa um expressivo número de publicações científicas nas últimas décadas. Com isto abriu-se a oportunidade para avaliar a qualidade das publicações, já que não existem pesquisas que avaliem os riscos metodológicos na área. Partindo desta premissa objetivamos compilar os artigos publicados na área e responder as seguintes questões: os trabalhos etnozoológicos brasileiros possuem boa qualidade amostral? A qualidade amostral é influenciada por características dos estudos/publicações? Para responder tais perguntas foi realizado levantamento das publicações em bases de dados e sites de busca. As características avaliadas foram relacionadas à natureza, amostragem, uso de hipóteses e testes, fator de impacto do periódico e grupo animal pesquisado. A maior parte dos artigos analisados apresentaram problemas amostrais, 144 (66,98%) foram classificados como sendo de alto risco de viés. Quanto às características analisadas percebemos que a natureza quantitativa e a utilização de testes, são essenciais para uma boa amostragem. A maioria das publicações classificada com moderado e baixo risco não apresentava ou não deixava claro esses dados, sendo classificadas como de natureza quali-quantitativa. Percebemos também que artigos desenvolvidos com grupos vertebrados apresentaram alto risco, levando a crer que as restrições da legislação brasileira limitam as informações mais precisas a respeito do tema.

Ethnozoology in Brazil: analysis of the methodological risks in published studies

Abstract There has been a growth in the field of Ethnozoology throughout the years, especially in Brazil, where a considerable number of scientific articles pertaining to this subject has been published in recent decades. With this increase in publications comes the opportunity to assess the quality of these publications, as there are no known studies assessing the methodological risks in this area. Based on this observation, our objectives were to compile the papers published on the subject of ethnozoology and to answer the following questions: 1) Do the Brazilian ethnozoological studies use sound sampling methods?; 2) Is the sampling quality influenced by characteristics of the studies/publications? The studies found in databases and using web search engines were compiled to answer these questions. The studies were assessed based on their nature, sampling methods, use of hypotheses and tests, journals impact factor, and animal group studied. The majority of the studies analyzed exhibited problems associated with the samples, as 144 (66.98%) studies were classified as having a high risk of bias. With regard to the characteristics analyzed, we determined that a quantitative nature and the use of tests are essential components of good sampling. Most studies classified as moderate and low risk either did not provide these data or provided data that were not clear; therefore, these studies were classified as being of a quali-quantitative nature. Studies performed with vertebrate groups were of high risk. Most of the papers analyzed here focused on fish, insects, and/or mollusks, thus highlighting the difficulties associated with conducting interviews regarding tetrapod vertebrates. Such difficulties are largely related to the extremely strict Brazilian laws, justified by the decline and extinction of some species, related to the use of wild tetrapod vertebrates.

Resumo Ao longo dos anos a Etnozoologia vem crescendo, principalmente no Brasil, no qual se observa um expressivo número de publicações científicas nas últimas décadas. Com isto abriu-se a oportunidade para avaliar a qualidade das publicações, já que não existem pesquisas que avaliem os riscos metodológicos na área. Partindo desta premissa objetivamos compilar os artigos publicados na área e responder as seguintes questões: os trabalhos etnozoológicos brasileiros possuem boa qualidade amostral? A qualidade amostral é influenciada por características dos estudos/publicações? Para responder tais perguntas foi realizado levantamento das publicações em bases de dados e sites de busca. As características avaliadas foram relacionadas à natureza, amostragem, uso de hipóteses e testes, fator de impacto do periódico e grupo animal pesquisado. A maior parte dos artigos analisados apresentaram problemas amostrais, 144 (66,98%) foram classificados como sendo de alto risco de viés. Quanto às características analisadas percebemos que a natureza quantitativa e a utilização de testes, são essenciais para uma boa amostragem. A maioria das publicações classificada com moderado e baixo risco não apresentava ou não deixava claro esses dados, sendo classificadas como de natureza quali-quantitativa. Percebemos também que artigos desenvolvidos com grupos vertebrados apresentaram alto risco, levando a crer que as restrições da legislação brasileira limitam as informações mais precisas a respeito do tema.

Prevalence of Sexual Abuse in Childhood: Some Critical Methodological Reflections.

This article attempts to analyze the prevalence rates of sexual abuse in childhood reported in comparative empirical studies, giving an overview of a selection of representative studies reporting high rates of abuse and comparing it to an overview of studies reporting lower rates. Extremely discrepant rates of childhood sexual abuse are reported in a number of empirical studies conducted in this field over the past 26 years, particularly those looking beyond prevalence to study the links between this type of trauma and future motherhood. To shed light on the disparities in the reported prevalence rates, the article reviews the principal methodological biases that have contaminated the findings. The authors then offer several suggestions for improvement that might be implemented in future studies.

Bacterial taxa-area and distance-decay relationships in marine environments.

The taxa-area relationship (TAR) and the distance-decay relationship (DDR) both describe spatial turnover of taxa and are central patterns of biodiversity. Here, we compared TAR and DDR of bacterial communities across different marine realms and ecosystems at the global scale. To obtain reliable global estimates for both relationships, we quantified the poorly assessed effects of sequencing depth, rare taxa removal and number of sampling sites. Slope coefficients of bacterial TARs were within the range of those of plants and animals, whereas slope coefficients of bacterial DDR were much lower. Slope coefficients were mostly affected by removing rare taxa and by the number of sampling sites considered in the calculations. TAR and DDR slope coefficients were overestimated at sequencing depth <4000 sequences per sample. Noticeably, bacterial TAR and DDR patterns did not correlate with each other both within and across ecosystem types, suggesting that (i) TAR cannot be directly derived from DDR and (ii) TAR and DDR may be influenced by different ecological factors. Nevertheless, we found marine bacterial TAR and DDR to be steeper in ecosystems associated with high environmental heterogeneity or spatial isolation, namely marine sediments and coastal environments compared with pelagic ecosystems. Hence, our study provides information on macroecological patterns of marine bacteria, as well as methodological and conceptual insights, at a time when biodiversity surveys increasingly make use of high-throughput sequencing technologies.