Code sharing in ecology and evolution increases citation rates but remains uncommon.

Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here, we conduct a literature review estimating temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influence of code sharing on citation rate. We find that code is rarely published (only 6% of papers), with little improvement over time. We also found there may be incentives to publish code: Publications that share code have tended to be low-impact initially, but accumulate citations faster, compensating for this deficit. Studies that additionally meet other Open Science criteria, open-access publication, or data sharing, have still higher citation rates, with publications meeting all three criteria (code sharing, data sharing, and open access publication) tending to have the most citations and highest rate of citation accumulation.

Ecuadorian Provinces with High Morbidity and Mortality Rates Due to Asthma among the Working-Age Population: An Ecological Study to Promote Respiratory Health.

Asthma is a significant public health concern. This study identified the provinces with the highest morbidity and mortality rates due to asthma among the working-age population (15-69 years) in the Republic of Ecuador. The secondary objective was to explain the possible differences attributable to occupational exposure. This nationwide ecological study was conducted in 24 provinces between 2016 and 2019. Government databases were used as sources of information. Age-standardized rates were calculated for codes J45 and J46. The hospitalization morbidity rate for asthma decreased from 6.51 to 5.76 cases per 100,000 working-age population, and the mortality rate has consistently been low and stable from 0.14 to 0.15 deaths per 100,000 working-age population. Geographic differences between the provinces were evident. The risk of hospitalization and death due to asthma was higher in the Pacific coast (Manabí with 7.26 and 0.38, Esmeraldas with 6.24 and 0.43, Los Ríos with 4.16 and 0.40, El Oro with 7.98 and 0.21, Guayas with 4.42 and 0.17 and the Andean region (Azuay with 6.33 and 0.45, Cotopaxi (5.84 and 0.48)). The high rates observed in provinces with greater agricultural and industrial development could be national heterogeneity's main determinants and act as occupational risk factors. The contribution of occupational hazards in each province should be examined in depth through ad hoc studies. The findings presented here provide valuable information that should prompt further detailed studies, which will assist in designing public policies aimed at promoting and safeguarding the respiratory health of the population, particularly that of workers. We believe that this study will inspire the creation of regional networks for the research and surveillance of occupational health.

Nutritional status and its relationship with COVID-19 prognosis in hemodialysis patients.

Introduction: Introduction: among the groups more affected by the COVID-19 pandemic were patients undergoing chronic hemodialysis (HD) treatment due to their comorbidities, advanced age, impaired innate and adaptive immune function, and increased nutritional risk due to their underlying inflammatory state. All of these factors contribute to a higher risk of severe complications and worse outcomes compared to the general population when infected with SARS-CoV-2. Objective: the objective of this study was to describe the nutritional characteristics of and their potential association with the prognosis of COVID-19 in patients undergoing chronic HD treatment. Method: a descriptive, retrospective, observational design. All cases of COVID-19 in patients undergoing chronic treatment at the Hemodialysis Unit of Hospital de Manises, Valencia, Spain, from the start of the pandemic to before vaccination were included. Results: for that, 189 patients were studied, who received chronic HD treatment in the hospital unit, 22 patients were diagnosed with COVID-19 (12 %) in that period. The mean age was 71 years, 10 were women, the Charlson index was 6.59 points, diabetes mellitus 10, vintage HD 51.6 months, 2 patients had previously received a currently non-functioning kidney transplant, 16 had arteriovenous fistula as vascular access, and 6 had central vascular access. The mean dialysis session time was 220.14 minutes and the initial value of the single dose of the Kt/V pool was 1.7. 16 patients had body composition measurement, a strong association (p < 0.05) was identified between mortality and BMI, as well as mortality and FTI. Furthermore, the differences between deceased and surviving groups in the serum levels of various variables related to nutritional status were analyzed, finding significant differences with p < 0.05 in the value of triglycerides and ferritin. Conclusions: higher body mass index and higher body fat content, along with lower baseline levels of triglycerides and ferritin, were significantly associated with higher COVID-19 mortality in patients on chronic hemodialysis. These findings suggest that the initial nutritional status of these patients can significantly influence the prognosis of SARS-CoV-2 infection.

Introducción: Introducción: entre los grupos más afectados por la pandemia de COVID-19 se encuentran los pacientes en tratamiento crónico de hemodiálisis (HD) por sus comorbilidades, edad avanzada, deterioro de la función inmune innata y adaptativa, y mayor riesgo nutricional por su estado inflamatorio de base. Todos estos factores contribuyen a un mayor riesgo de complicaciones graves y peores resultados en comparación con la población general cuando se infectan con SARS-CoV-2. Objetivo: el objetivo de este estudio es describir las características nutricionales y su potencial asociación con el pronóstico de COVID-19 en pacientes en tratamiento crónico de HD. Método: diseño observacional retrospectivo y descriptivo. Se incluyeron todos los casos de COVID-19 en pacientes en tratamiento crónico en la Unidad de Hemodiálisis del Hospital de Manises, Valencia, desde el inicio de la pandemia hasta antes de la vacunación. Resultados: de 189 pacientes que recibieron tratamiento de HD crónica en la unidad hospitalaria, 22 pacientes fueron diagnosticados con COVID-19 (12 %) en ese período. La edad media fue de 71 años, 10 eran mujeres, índice de Charlson de 6,59 puntos, diabetes mellitus 10, tiempo en diálisis 51,6 meses, 2 pacientes habían recibido previamente un trasplante renal actualmente no funcionante, 16 tenían fístula arteriovenosa como acceso vascular, y 6 tenían acceso vascular central. El tiempo medio de la sesión de diálisis fue de 220,14 minutos y el valor inicial de la dosis única del pool de Kt/V fue de 1,7. Tenían medición de la composición corporal 16 pacientes, se identificó una fuerte asociación (p < 0,05) entre mortalidad e IMC, así como mortalidad y FTI. Además las diferencias entre los grupos de fallecidos y sobrevivientes en los niveles séricos de diversas variables relacionadas con el estado nutricional fueron analizados, encontrando diferencias significativas con p < 0,05 en el valor de triglicéridos y ferritina. Conclusiones: un índice de masa corporal más alto y un mayor contenido de grasa corporal, junto con niveles basales más bajos de triglicéridos y ferritina, se asocian significativamente a una mayor mortalidad por COVID-19 entre los pacientes en hemodiálisis crónica. Estos hallazgos sugieren que el estado nutricional inicial de estos pacientes puede influir significativamente en el pronóstico de la infección por SARS-CoV-2.

Treemendous: an R package for integrating taxonomic information across backbones.

Standardizing and translating species names from different databases is key to the successful integration of data sources in biodiversity research. There are numerous taxonomic name-resolution applications that implement increasingly powerful name-cleaning and matching approaches, allowing the user to resolve species relative to multiple backbones simultaneously. Yet there remains no principled approach for combining information across these underlying taxonomic backbones, complicating efforts to combine and merge species lists with inconsistent and conflicting taxonomic information. Here, we present Treemendous, an open-source software package for the R programming environment that integrates taxonomic relationships across four publicly available backbones to improve the name resolution of tree species. By mapping relationships across the backbones, this package can be used to resolve datasets with conflicting and inconsistent taxonomic origins, while ensuring the resulting species are accepted and consistent with a single reference backbone. The user can chain together different functionalities ranging from simple matching to a single backbone, to graph-based iterative matching using synonym-accepted relations across all backbones in the database. In addition, the package allows users to 'translate' one tree species list into another, streamlining the assimilation of new data into preexisting datasets or models. The package provides a flexible workflow depending on the use case, and can either be used as a stand-alone name-resolution package or in conjunction with existing packages as a final step in the name-resolution pipeline. The Treemendous package is fast and easy to use, allowing users to quickly merge different data sources by standardizing their species names according to the regularly updated database. By combining taxonomic information across multiple backbones, the package increases matching rates and minimizes data loss, allowing for more efficient translation of tree species datasets to aid research into forest biodiversity and tree ecology.

Female researchers are under-represented in the Colombian science infrastructure.

Worldwide women have increased their participation in STEM, but we are still far from reaching gender parity. Although progress can be seen at the bachelor's and master's level, career advancement of women in research still faces substantial challenges leading to a 'leaky pipeline' phenomenon (i.e., the continuous decrease of women's participation at advanced career stages). Latin America exhibits encouraging rates of women participation in research, but the panorama varies across countries and stages in the academic ladder. This study focuses on women's participation in research in natural sciences in Colombia and investigates career progression, leadership roles, and funding rates by analyzing data on scholarships, grants, rankings, and academic positions. Overall, we found persistent gender imbalances throughout the research ecosystem that were significant using classical statistical analyses. First, although women constitute >50% graduates from bachelors in natural sciences, <40% of researchers in this field are female. Second, women win <30% of research grants, and in turn, their scientific productivity is 2X lower than that of men. Third, because of the less research funding and output women have, their promotion to senior positions in academic and research rankings is slower. In consequence, only ~25% of senior researchers and full professors are women. Fourth, the proportion of women leading research groups and mentoring young scientist in Colombia is <30%. Our study deepens our understanding of gender gaps in STEM research in Colombia, and provides information to design initiatives that effectively target gender disparities by focusing on key areas of intervention, and then gradually building up, rather than tackling structural inequities all at once.

Pangenome Reconstruction of Mycobacterium tuberculosis as a Guide to Reveal Genomic Features Associated with Strain Clinical Phenotype.

Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by Mycobacterium tuberculosis can occur in the lungs, causing pulmonary tuberculosis (PTB), or in any other organ of the body, resulting in extrapulmonary tuberculosis (EPTB). There is no consensus on the genetic determinants of this pathogen that may contribute to EPTB. In this study, we constructed the M. tuberculosis pangenome and used it as a tool to seek genomic signatures associated with the clinical presentation of TB based on its accessory genome differences. The analysis carried out in the present study includes the raw reads of 490 M. tuberculosis genomes (PTB n = 245, EPTB n = 245) retrieved from public databases that were assembled, as well as ten genomes from Mexican strains (PTB n = 5, EPTB n = 5) that were sequenced and assembled. All genomes were annotated and then used to construct the pangenome with Roary and Panaroo. The pangenome obtained using Roary consisted of 2231 core genes and 3729 accessory genes. On the other hand, the pangenome resulting from Panaroo consisted of 2130 core genes and 5598 accessory genes. Associations between the distribution of accessory genes and the PTB/EPTB phenotypes were examined using the Scoary and Pyseer tools. Both tools found a significant association between the hspR, plcD, Rv2550c, pe_pgrs5, pe_pgrs25, and pe_pgrs57 genes and the PTB genotype. In contrast, the deletion of the aceA, esxR, plcA, and ppe50 genes was significantly associated with the EPTB phenotype. Rv1759c and Rv3740 were found to be associated with the PTB phenotype according to Scoary; however, these associations were not observed when using Pyseer. The robustness of the constructed pangenome and the gene-phenotype associations is supported by several factors, including the analysis of a large number of genomes, the inclusion of the same number of PTB/EPTB genomes, and the reproducibility of results thanks to the different bioinformatic tools used. Such characteristics surpass most of previous M. tuberculosis pangenomes. Thus, it can be inferred that the deletion of these genes can lead to changes in the processes involved in stress response and fatty acid metabolism, conferring phenotypic advantages associated with pulmonary or extrapulmonary presentation of TB. This study represents the first attempt to use the pangenome to seek gene-phenotype associations in M. tuberculosis.

A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest.

Monitoring biodiversity change is key to effective conservation policy. While it is difficult to establish in situ biodiversity monitoring programs at broad geographical scales, remote sensing advances allow for near-real time Earth observations that may help with this goal. We combine periodical and freely available remote sensing information describing temperature and precipitation with curated biological information from several groups of animals and plants in the Brazilian Atlantic rainforest to design an indirect remote sensing framework that monitors potential loss and gain of biodiversity in near-real time. Using data from biological collections and information from repeated field inventories, we demonstrate that this framework has the potential to accurately predict trends of biodiversity change for both taxonomic and phylogenetic diversity. The framework identifies areas of potential diversity loss more accurately than areas of species gain, and performs best when applied to broadly distributed groups of animals and plants.

Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium.

Salmonella enterica constitutes a global public health concern as one of the main etiological agents of human gastroenteritis. The Typhimurium serotype is frequently isolated from human, animal, food, and environmental samples, with its sequence type 19 (ST19) being the most widely distributed around the world as well as the founder genotype. The replacement of the ST19 genotype with the ST213 genotype that has multiple antibiotic resistance (MAR) in human and food samples was first observed in Mexico. The number of available genomes of ST213 strains in public databases indicates its fast worldwide dispersion, but its public health relevance is unknown. A comparative genomic analysis conducted as part of this research identified the presence of 44 genes, 34 plasmids, and five point mutations associated with antibiotic resistance, distributed across 220 genomes of ST213 strains, indicating the MAR phenotype. In general, the grouping pattern in correspondence to the presence/absence of genes/plasmids that confer antibiotic resistance cluster the genomes according to the geographical origin where the strain was isolated. Genetic determinants of antibiotic resistance group the genomes of North America (Canada, Mexico, USA) strains, and suggest a dispersion route to reach the United Kingdom and, from there, the rest of Europe, then Asia and Oceania. The results obtained here highlight the worldwide public health relevance of the ST213 genotype, which contains a great diversity of genetic elements associated with MAR.

Whole-genome comparative analysis at the lineage/sublineage level discloses relationships between Mycobacterium tuberculosis genotype and clinical phenotype.

BACKGROUND: Human tuberculosis (TB) caused by members of the Mycobacterium tuberculosis complex (MTBC) is the main cause of death among infectious diseases worldwide. Pulmonary TB (PTB) is the most common clinical phenotype of the disease, but some patients develop an extrapulmonary (EPTB) phenotype in which any organ or tissue can be affected. MTBC species include nine phylogenetic lineages, with some appearing globally and others being geographically restricted. EPTB can or not have pulmonary involvement, challenging its diagnosis when lungs are not implicated, thus causing an inadequate treatment. Finding evidence of a specific M. tuberculosis genetic background associated with EPTB is epidemiologically relevant due to the virulent and multidrug-resistant strains isolated from such cases. Until now, the studies conducted to establish associations between M. tuberculosis lineages and PTB/EPTB phenotypes have shown inconsistent results, which are attributed to the strain predominance from specific M. tuberculosis lineages/sublineages in the samples analyzed and the use of low-resolution phylogenetic tools that have impaired sublineage discrimination abilities. The present work elucidates the relationships between the MTBC strain lineages/sublineages and the clinical phenotypes of the disease as well as the antibiotic resistance of the strains. METHODS: To avoid biases, we retrieved the raw genomic reads (RGRs) of all (n = 245) the M. tuberculosis strains worldwide causing EPTB available in databases and an equally representative sample of the RGRs (n = 245) of PTB strains. A multiple alignment was constructed, and a robust maximum likelihood phylogeny based on single-nucleotide polymorphisms was generated, allowing effective strain lineage/sublineage assignment. RESULTS: A significant Odds Ratio (OR range: 1.8-8.1) association was found between EPTB and the 1.1.1, 1.2.1, 4.1.2.1 and ancestral Beijing sublineages. Additionally, a significant association between PTB with 4.3.1, 4.3.3, and 4.5 and Asian African 2 and Europe/Russia B0/W148 modern Beijing sublineages was found. We also observed a significant association of Lineage 3 strains with multidrug resistance (OR 3.8; 95% CI [1.1-13.6]), as well as between modern Beijing sublineages and antibiotic resistance (OR 4.3; 3.8-8.6). In this work, it was found that intralineage diversity can drive differences in the immune response that triggers the PTB/EPTB phenotype.

Hospitalized population diagnosed with Covid-19 in public health centers in the southeastern region of Greater Buenos Aires / [Población hospitalizada con diagnóstico de Covid-19 en los centros de salud públicos de la región sudeste del Gran Buenos Aires]

Introduction: The present work describes the clinical characteristics and interventions to minimize morbidity and mortality in hospitalized patients diagnosed with COVID-19. Methods: It is a prospective cohort investigation of patients who received a response from the Health Centers in the southeast region (RS) of the metropolitan area (AMBA) from April 8 to September 30, 2020. A Situation Room was used epidemiological with two monitoring and follow-up boards, one for bed management and the other for patient management. Results: During the analyzed period, 2,588 patients with confirmed COVID-19 diagnosis were admitted, 1,943 with suspected COVID-19 pathology, and 1,464 subjects with other pathologies. 55% of the patients were men and the mean age was 51 years. There were 82.8% patients with pre-existing diseases, hypertension and diabetes were the most frequent. 14% were hospitalized in the Intensive Care Unit. The mortality of the cohort was 15.05%, mortality was higher for men, with a mean age of 60 years, 92.65% had some pre-existing disease. Conclusion: Our cohort is younger than other published works. Older people, men, and people with comorbidities are at increased risk for COVID-19-related mortality. The public health system was able to respond to the demand without collapsing the hospital institutions.

Introducción: En el presente trabajo se describen las características clínicas y las intervenciones para minimizar la morbimortalidad en pacientes hospitalizados con diagnóstico de COVID-19. Métodos: Es una investigación de cohorte prospectiva de pacientes que recibieron respuesta de los Centros de Salud en la región sudeste (RS) del área metropolitana (AMBA) desde el 8 de abril hasta el 30 de septiembre de 2020. Se utilizó una Sala de Situación epidemiológica con dos tableros de monitoreo y seguimiento, uno de gestión de camas y otro de gestión de pacientes. Resultados: Durante el periodo analizado se internaron2.588pacientes con diagnóstico COVID-19 confirmados, 1.943 con sospecha de patología COVID-19, y 1.464sujetos con otras patologías. El 55% de los pacientes eran hombres y la edad media fue de 51 años. Hubo 82,8% pacientes con enfermedades preexistentes, hipertensión y diabetes fueron las más frecuentes. El 14% fue hospitalizado en la Unidad de Terapia Intensiva. La mortalidad de la cohorte fue del 15,05%, la mortalidad fue mayor para los hombres, con una edad media de 60 años, el 92,65% tenía alguna enfermedad preexistente. Conclusión: Nuestra cohorte es más joven que otros trabajos publicados. Las personas mayores, los hombres y las personas con comorbilidades tienen mayor riesgo de mortalidad relacionada con COVID-19. El sistema de salud público pudo responder a la demanda sin llegar a colapsar las instituciones hospitalarias.

Potential vascular α1-adrenoceptor blocking properties of metformin in rat aorta and tail artery.

Metformin is a widely used drug for the treatment of type 2 Diabetes Mellitus. Several studies have also suggested that metformin decreases blood pressure; although an interaction with α-adrenoceptors has been proposed, this mechanism needs to be further investigated. Since α1-adrenoceptors play a significant role to regulate vascular tone, this study has analysed the potential ability of metformin to block α1-adrenoceptors in rat aorta and tail artery. For this purpose, the contractile responses induced by noradrenaline, methoxamine, and phenylephrine were determined in the absence or presence of metformin in rat aorta and tail artery rings. In both arteries, noradrenaline, methoxamine, and phenylephrine produced concentration-dependent contractile responses. Interestingly, the contractile responses to noradrenaline, methoxamine, and phenylephrine were significantly and differentially blocked by metformin (1, 3.1 and/or 10 mM) but not by vehicle. These results suggest that metformin is capable to block α1-adrenoceptors and may explain, at least in part, the anti-hypertensive effect observed in several clinical trials.

Links between prey assemblages and poison frog toxins: A landscape ecology approach to assess how biotic interactions affect species phenotypes.

Ecological studies of species pairs showed that biotic interactions promote phenotypic change and eco-evolutionary feedbacks. However, it is unclear how phenotypes respond to synergistic interactions with multiple taxa. We investigate whether interactions with multiple prey species explain spatially structured variation in the skin toxins of the neotropical poison frog Oophaga pumilio. Specifically, we assess how dissimilarity (i.e., beta diversity) of alkaloid-bearing arthropod prey assemblages (68 ant species) and evolutionary divergence between frog populations (from a neutral genetic marker) contribute to frog poison dissimilarity (toxin profiles composed of 230 different lipophilic alkaloids sampled from 934 frogs at 46 sites). We find that models that incorporate spatial turnover in the composition of ant assemblages explain part of the frog alkaloid variation, and we infer unique alkaloid combinations across the range of O. pumilio. Moreover, we find that alkaloid variation increases weakly with the evolutionary divergence between frog populations. Our results pose two hypotheses: First, the distribution of only a few prey species may explain most of the geographic variation in poison frog alkaloids; second, different codistributed prey species may be redundant alkaloid sources. The analytical framework proposed here can be extended to other multitrophic systems, coevolutionary mosaics, microbial assemblages, and ecosystem services.

Salud feminista: soberanía de los cuerpos, poder y organización / Feminist health: sovereignty of bodies, power and organization

Este libro se ofrece como una notable ampliación de los tópicos, de los problemas y de las existencias afectadas tanto por los procesos de salud-enfermedad como por las concepciones y los imaginarios relativos al cuerpo, en un sentido polisémico, que se distancia por completo de los determinantes biológicos. El conjunto de los textos reta a las tentaciones normativas del contrapunto normal vs. patológico, tan entrañable a las formas canónicas de la medicina. El propio título del libro es una toma de posición que constituye un desafío, porque resitúa en llave sociocultural a la dimensión de la salud, y de manera singular se propone un alzamiento contra lo prescriptivo alegando la soberanía sanitaria... Libro que ofrece a su vez un conjunto de reflexiones que el campo de la salud debe absorber para incidir con conductas que promuevan la autonomía y la dignidad. Resulta consternadora la rémora de las viejas concepciones acerca de los procesos de salud-enfermedad, la ceguera cognitiva respecto de la generización inexorable de tales fenómenos y, muy especialmente, la recusa de percepción contextual para hacer inteligible el lenguaje del cuerpo que enuncia sus significados contrariando a los presupuestos naturales. A menudo he sostenido una advertencia, y me parece más que adecuado dar la bienvenida a este libro volviendo a ella: para quienes creen a pie juntillas que hay una lectura trasparente de los fenómenos de la naturaleza, es bueno que sepan que la naturaleza no sabe que se llama naturaleza. Su lenguaje es el que hemos inventado, una arbitraria operación mediadora con la que damos por sentado principios y leyes. Conviene abdicar de su prepotencia, y hacer de la salud un estatuto libertario, tal como emerge como acicate de las páginas de este texto (Dora Barrancos)

Sequencing and Annotation of the Genome of Mycobacterium tuberculosis MYC004, a Strain Causing Meningitis in Mexico.

Mycobacterium tuberculosis strain MYC004 was isolated from a Mexican patient with tuberculous meningitis, the most aggressive form of tuberculosis. The draft genome sequence is the first of a meningeal strain of M. tuberculosis reported from Latin America and consists of 4,411,530 bp, including 4,251 protein-encoding genes.

Diversity patterns, Leishmania DNA detection, and bloodmeal identification of Phlebotominae sand flies in villages in northern Colombia.

Leishmaniases are neglected tropical diseases exhibiting complex transmission cycles due to the number of parasite species circulating, sand fly species acting as vectors and infected mammals, including humans, which are defined in the New World as accidental hosts. However, current transmission scenarios are changing, and the disease is no longer exclusively related to forested areas but urban transmission foci occur, involving some species of domestic animals as suspected reservoirs. The aim of this study was to determine the transmission cycles in urban environments by evaluating sand fly diversity, detection of Leishmania DNA, and bloodmeal sources through intra and peridomestic collections. The study was carried out in Colombia, in 13 municipalities of Cordoba department, implementing a methodology that could be further used for the evaluation of vector-borne diseases in villages or towns. Our sampling design included 24 houses randomly selected in each of 15 villages distributed in 13 municipalities, which were sampled in two seasons in 2015 and 2016. Sand flies were collected using CDC light traps placed in intra and peridomestic habitats. In addition to the morphological identification, molecular identification through DNA barcodes was also performed. A total of 19,743 sand flies were collected and 13,848 of them (10,268 females and 3,580 males) were used in molecular procedures. Circulation of two known parasite species-Leishmania infantum and Leishmania panamensis was confirmed. Blood source analyses showed that sand flies fed on humans, particularly in the case of the known L. infantum vector, P. evansi; further analyses are advised to evaluate the reservoirs involved in parasite transmission. Our sampling design allowed us to evaluate potential transmission cycles on a department scale, by defining suspected vector species, parasite species present in different municipalities and feeding habits.

Entomological characterization of malaria in northern Colombia through vector and parasite species identification, and analyses of spatial distribution and infection rates.

BACKGROUND: Malaria remains a worldwide public health concern and, in Colombia, despite the efforts to stop malaria transmission, the incidence of cases has increased over the last few years. In this context, it is necessary to evaluate vector diversity, infection rates, and spatial distribution, to better understand disease transmission dynamics. This information may contribute to the planning and development of vector control strategies. RESULTS: A total of 778 Anopheles mosquitoes were collected in fifteen localities of Córdoba from August 2015 to October 2016. Six species were identified and overall, Anopheles albimanus was the most widespread and abundant species (83%). Other species of the Nyssorhynchus subgenus were collected, including Anopheles triannulatus (13%), Anopheles nuneztovari (1%), Anopheles argyritarsis (< 1%) and two species belonging to the Anopheles subgenus: Anopheles pseudopunctipennis (3%) and Anopheles neomaculipalpus (< 1%). Four species were found naturally infected with two Plasmodium species: Anopheles nuneztovari was detected naturally infected with Plasmodium falciparum and Anopheles pseudopunctipennis with Plasmodium vivax, whereas An. albimanus and An. triannulatus were found infected with both parasite species and confirmed by nested PCR. CONCLUSIONS: In general, the obtained results were contrasting with previous studies in terms of the most abundant and widespread collected species, and regarding infection rates, which were higher than those previously reported. A positive relationship between mosquito local abundance at the locality level and human infection at the municipality level was found. Mosquito local abundance and the number of houses with mosquitoes in each village are factors explaining malaria human cases in these villages. The obtained results suggest that other factors related to the apparent variation in malaria eco-epidemiology in northern Colombia, must be identified, to provide health authorities with better decision tools aiming to design control and prevention strategies.

Cryptic diversity revealed by DNA barcoding in Colombian illegally traded bird species.

Colombia is the country with the largest number of bird species worldwide, yet its avifauna is seriously threatened by habitat degradation and poaching. We built a DNA barcode library of nearly half of the bird species listed in the CITES appendices for Colombia, thereby constructing a species identification reference that will help in global efforts for controlling illegal species trade. We obtained the COI barcode sequence of 151 species based on 281 samples, representing 46% of CITES bird species registered for Colombia. The species analysed belong to nine families, where Trochilidae and Psittacidae are the most abundant ones. We sequenced for the first time the DNA barcode of 47 species, mainly hummingbirds endemic of the Northern Andes region. We found a correct match between morphological and genetic identification for 86-92% of the species analysed, depending on the cluster analysis performed (BIN, ABGD and TaxonDNA). Additionally, we identified eleven cases of high intraspecific divergence based on K2P genetic distances (up to 14.61%) that could reflect cryptic diversity. In these cases, the specimens were collected in geographically distant sites such as different mountain systems, opposite flanks of the mountain or different elevations. Likewise, we found two cases of possible hybridization and incomplete lineage sorting. This survey constitutes the first attempt to build the DNA barcode library of endangered bird species in Colombia establishing as a reference for management programs of illegal species trade, and providing major insights of phylogeographic structure that can guide future taxonomic research.

Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait-based phylogeographic approach.

Hypotheses to explain phylogeographic structure traditionally invoke geographic features, but often fail to provide a general explanation for spatial patterns of genetic variation. Organisms' intrinsic characteristics might play more important roles than landscape features in determining phylogeographic structure. We developed a novel comparative approach to explore the role of ecological and life-history variables in determining spatial genetic variation and tested it on frog communities in Panama. We quantified spatial genetic variation within 31 anuran species based on mitochondrial DNA sequences, for which hierarchical approximate Bayesian computation analyses rejected simultaneous divergence over a common landscape. Regressing ecological variables, on genetic divergence allowed us to test the importance of individual variables revealing that body size, current landscape resistance, geographic range, biogeographic origin and reproductive mode were significant predictors of spatial genetic variation. Our results support the idea that phylogeographic structure represents the outcome of an interaction between organisms and their environment, and suggest a conceptual integration we refer to as trait-based phylogeography.

DNA Barcoding Survey of Anurans across the Eastern Cordillera of Colombia and the Impact of the Andes on Cryptic Diversity.

Colombia hosts the second highest amphibian species diversity on Earth, yet its fauna remains poorly studied, especially using molecular genetic techniques. We present the results of the first wide-scale DNA barcoding survey of anurans of Colombia, focusing on a transect across the Eastern Cordillera. We surveyed 10 sites between the Magdalena Valley to the west and the eastern foothills of the Eastern Cordillera, sequencing portions of the mitochondrial 16S ribosomal RNA and cytochrome oxidase subunit 1 (CO1) genes for 235 individuals from 52 nominal species. We applied two barcode algorithms, Automatic Barcode Gap Discovery and Refined Single Linkage Analysis, to estimate the number of clusters or "unconfirmed candidate species" supported by DNA barcode data. Our survey included ~7% of the anuran species known from Colombia. While barcoding algorithms differed slightly in the number of clusters identified, between three and ten nominal species may be obscuring candidate species (in some cases, more than one cryptic species per nominal species). Our data suggest that the high elevations of the Eastern Cordillera and the low elevations of the Chicamocha canyon acted as geographic barriers in at least seven nominal species, promoting strong genetic divergences between populations associated with the Eastern Cordillera.