Aporte al conocimiento de la conectividad del manglar de Las Lisas-La Barrona, Guatemala

El  presente  estudio  es  una  primera  aproximación  al  conocimiento  de  la  conectividad  del  ecosistema  manglar de Las Lisas-La Barrona, departamentos  de Santa Rosa y Jutiapa. La conectividad  es la característica  del paisaje  que  facilita  la  dispersión  de  las  especies  a  través  del  hábitat,  la  pérdida  de  esta  conectividad,  podría  poner  en peligro  la  sobrevivencia  de  las  poblaciones  de  aves.  El  objetivo  de  este  estudio  fue  determinar  la  conectividad  del manglar  a  través  de  análisis  basados  en  las  teorías  de  grafos  y  circuitos.  Se  incluyó  en  el  análisis  la  conectividad  en sus componentes  estructural  y funcional.  El  componente  estructural  se determinó  mediante  el  Análisis del  Patrón Espacial  Morfológico  (MSPA  por  sus siglas  en  inglés).  El  componente  funcional  fue  evaluado  con  el  Diferencial del  êndice  Integral  de  Conectividad  (dIIC),  evaluando  el  aporte  de  cada  parche  a  la  conectividad  del  manglar. Se encontró que la conectividad  del área está determinada  por parches nœcleo con alto aporte a la conectividad como  los  parches  de  vegetación  de  mangle  de  La  Barrona  y  El  Jiote,  parche  puente  o  corredor  como  el  canal  de Chiquimulilla  y  un  cuello  de  botella  en  el  segmento  Las  Lisas-El  ahumado,  los  cuales  son  elementos  estratégicos a considerar en la planificación e intervenciones futuras en el área

Searching for specific binding sites of the secretory glycoproteins of the subcommissural organ

The molecular organization of Reissner's fiber (RF), the structure of its proteins, and the permanent turnover of these proteins are all facts supporting the possibility that RF may perform multiple functions. There is evidence that CSF-soluble RF-glycoproteins may occur under physiological conditions. The present investigation was designed to investigate the probable existence within the CNS of specific binding sites for RF-glycoproteins. Three experimental protocols were used: (1) immunocytochemistry of the CNS of bovine fetuses using anti-idiotypic antibodies, raised against monoclonal antibodies developed against bovine RF-glycoproteins; (2) in vivo binding of the RF glycoproteins, perfusing into the rat CSF 125I-labeled RF-glycoproteins, or grafting SCO into a lateral ventricle of the rat; (3) in vitro binding of unlabeled RF-glycoproteins to rat and bovine choroid plexuses maintained in culture. One of the anti-idiotypic antibody generated by a Mab raised against RF-glycoproteins binds to choroidal cells. Furthermore, binding of RF-glycoproteins to the rat choroid plexus was obtained when: (1) the choroid plexus was cultured in the presence of unlabeled RF-glycoproteins; (2) the concentration of soluble RF-glycoproteins in the CSF was increased by isografting SCOs into a lateral ventricle; (3) radiolabeled glycoproteins were perfused into the ventricular CSF. This evidence suggests that the apical plasma membrane of the ependymal cells of the choroid plexus has specific binding sites for RF-glycoproteins, of unknown functional significance. The radiolabeled RF-glycoproteins perfused into the rat CSF also bound to the paraventricular thalamic nucleus, the floor of the Sylvian aqueduct and of the rostral half of the fourth ventricle, and title meninges of the brain and spinal cord. The labeling of the paraventricular thalamic nucleus points to a functional relationship between this nucleus and the SCO. The possibility that; the SCO may be a component of the circadian timing system is discussed. Microsc. Res. Tech. 52:541-551, 2001. (C) 2001 Wiley-Liss, Inc

Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum)

The South American arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum) are emblematic species widely distributed in the Amazon and surrounding basins. Arowana species are under strong anthropogenic pressure as they are extensively exploited for ornamental and food purposes. Until now, limited genetic and cytogenetic information has been available, with only a few studies reporting to their genetic diversity and population structure. In the present study, cytogenetic and DArTseq-derived single nucleotide polymorphism (SNP) data were used to investigate the genetic diversity of the two Osteoglossum species, the silver arowana O. bicirrhosum, and the black arowana O. ferreirai. Both species differ in their 2n (with 2n = 54 and 56 for O. ferreirai and O. bicirrhosum, respectively) and in the composition and distribution of their repetitive DNA content, consistent with their taxonomic status as different species. Our genetic dataset was coupled with contemporary and paleogeographic niche modeling, to develop concurrent demographic models that were tested against each other with a deep learning approach in O. bicirrhosum. Our genetic results reveal that O. bicirrhosum colonized the Tocantins-Araguaia basin from the Amazon basin about one million years ago. In addition, we highlighted a higher genetic diversity of O. bicirrhosum in the Amazon populations in comparison to those from the Tocantins-Araguaia basin. © 2019 by the authors. Licensee MDPI, Basel, Switzerland

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone

Estudo de estrutura genética da espécie de Cactácea colunar Pilosocereus machrisii utilizando DNA microssatélite

Pilosocereus machrisii is a columnar cacti with natural fragmented distribution; restrict to campos rupestres vegetation patches or rocky outcrops on the Cerrado domain; in Central and eastern Brazil. These features makes P. machrisii an appropriate biological model for population genetic studies aiming to gather information on population structure; since small and isolated populations are often vulnerable to genetic drift and high levels of inbreeding. Genetic diversity and population structure were assessed for ten microsatellite loci in 12 P. machrisii populations; covering the majority of the species distribution. Genetic diversity levels were relatively similar on sampled populations; except for Brotas-SP samples; that showed lower levels than those observed for other locations. Significant Hardy Weinberg Equilibrium departures were detected in eight different populations; for one or two loci. High levels of genetic differentiation and private alleles with elevated frequencies were detected; with total FST value of 0.357. The genetic structure of P. machrisii was analyzed with STRUCTURE and SAMOVA softwares; and populations were grouped in four main clusters; with secondary structure on two of these clusters. Significative levels of correlation between genetic and geographic distances were observed for the whole dataset; however; when the genetic groups were analyzed separately; no correlation was verified. Furthermore; the genetic relationship between the populations was observed with a principal coordinate analysis (PCA) and an UPGMA dendrogram. The genetic structure observed in P. machrisii suggests that historical factors caused populations fragmentation; with subsequent geographic isolation and high genetic differentiation between them.Universidade Federal de Minas GeraisPilosocereus machrisii é um cacto colunar com distribuição naturalmente fragmentada no centro e leste do Brasil; restrito aos enclaves de vegetação de campos rupestres ou de afloramentos rochosos no domínio Cerrado. Essas características tornam a espécie um modelo biológico apropriado para a realização de estudos de estrutura populacional; uma vez que suas populações pequenas e isoladas podem estar altamente vulneráveis a efeitos de deriva genética e endogamia. Foram estimados os níveis de diversidade genética e estruturação populacional a partir de dez locos marcadores microssatélite em doze populações de ocorrência natural de P. machrisii; cobrindo a maior parte de sua distribuição. Os níveis de diversidade genética dentro das populações apresentaram resultados relativamente similares nas localidades amostradas; exceto pelas amostras do município de Brotas-SP; com índices menores que os observados em outras populações. Desvios significativos em relação às proporções do Equilíbrio de Hardy-Weinberg foram detectados para um ou dois locos em oito populações diferentes. Alelos privados em alta frequência foram detectados; assim como altos níveis de diferenciação genética; com um valor de FST total de 0;357. A estrutura genética das populações; verificada a partir da análise com os programas STRUCTURE e SAMOVA apresentou uma estruturação mais provável em quatro grupos principais e níveis secundários de estruturação dentro desses grupos. Níveis significativos de correlação entre as distâncias genéticas e geográficas entre pares de populações foram detectados para o conjunto total de dados; no entanto não houve correlação quando os agrupamentos genéticos foram analisados separadamente. Além disso; foi possível verificar as relações genéticas entre as diferentes populações a partir de uma análise de coordenadas principais (PCA) e de um dendrograma construído a partir do método UPGMA. A estrutura genética observada em P. machrisii aponta para um importante efeito de eventos históricos que causaram a fragmentação das populações; com posterior isolamento geográfico e aquisição de elevada diferenciação genética

Fortification of low-fat yogurt with melloco flour (Ullucus tuberosus): Physicochemical and rheological effects

Yogurt is a fermented milk product containing Lactic Acid Bacteria (BAL) (Lactobacillus bulgaricus and Streptococcus thermophilus). Although the application of additives is not mandatory, the use of gums or dairy extenders have been studied to establish the effect on the product. Among the additives most used in yogurt, production is focalized on natural or artificial sweeteners, stabilizing agents, flavors and colorants. Nowadays, consumers are looking for products that seem less artificial and more natural. In this sense, melloco, an Andean crop that, thanks to its mucilaginous content, could become an excellent additive that provides stability and viscosity. This study aimed to evaluate the effect of melloco flour (Ullucus tuberorus) yellow variety (INIAP-Quillu) on low-fat yogurt's quality properties. In this study, semi-skimmed milk (2% fat) was supplemented with 0.9% (w / v) of melloco flour, fermented and stored at 4°C for 20 days. Sensory attributes such as color, texture, taste, smell and overall acceptability were evaluated; the proximal analysis was performed using official methods of the Association of Official Analytical Chemists (AOAC). The physical and rheological properties and microbiological analysis were evaluated during 20 days of refrigerated storage. The use of melloco flour to enrich the reduced-fat yogurt improved acid production during fermentation. The average pH of the samples decreased from 4.8 to 4.18 after 20 days of storage. The color parameters did not differ significantly in all samples and remained constant during storage. The viscosity showed a rheological behavior of the pseudoplastic fluid. This study evidenced that the acid production in the yogurt enriched with melloco flour was higher during fermentation than the control sample, the typical end-point of pH (4.5) was reached by enriched yogurt in 5.5 hours compared to 7 hours for control. Sensory attributes also allowed establishing that the sample with 0.9% of flour presents the best overall acceptability. In general, the results suggest that melloco flour can be considered as good gelling and nutritional agent for the production of yogurt

Data from: Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species

Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches which presently harbor these populations operate as refugia during the current interglacial. However, owing to limitations of the standard phylogeographic approaches used in these studies, this hypothesis was not explicitly tested. Here we use Approximate Bayesian Computation to refine the previous inferences and test the role of different events in the diversification of two species within P. aurisetus group. We used molecular data from chloroplast DNA and simple sequence repeats loci of P. machrisii and P. aurisetus, the two species with broadest distribution in the complex, in order to test if the diversification in each species was driven mostly by vicariance or by long-dispersal events. We found that both species were affected primarily by vicariance, with a refuge model as the most likely scenario for P. aurisetus and a soft vicariance scenario most probable for P. machrisii. These results emphasize the importance of distributional fragmentation in these species, and add support to the hypothesis of long-term isolation in interglacial refugia previously proposed for the P. aurisetus species complex diversification

Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America

Supportive data related to the article “Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America” (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny. Keywords: Species tree, Next generation sequencing, Molecular markers, Phylogeography, Non-model specie

runPPC_Pmac

Retrieve parameter values from the parameter estimates of the selected in the P. machrisii dataset and use them to simulate new data to perform PPC analysis