Genomic variation in recently collected maize landraces from Mexico

AbstractThe present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE=0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE=0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law

Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes.

Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico's Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations

Producción de hojarasca y retorno potencial de nutrientes en tres sitios del Estado de Nuevo León, México = Litterfall and potential nutrient return in three sites of the state of Nuevo León, México

RESUMEN Los objetivos de este estudio fueron estimar y cuantificar la dinámica mensual (enero a diciembre 2009) de la deposición de la hojarasca y macro (Ca, K, Mg, N y P) y microminerales (Cu, Fe, Mn, y Zn) de las hojas de la hojarasca en los municipios Los Ramones, China y Linares, del estado de Nuevo León, México. La vegetación está caracterizada como matorral espinoso tamaulipeco. La deposición anual total de hojarasca fue de 321.5 (Los Ramones), 431.6 (China) y 462.9 (Linares) g/m2/año. Las hojas representaron el mayor componente (154.4 a 304.5 g/m2/año) del total de hojarasca depositada. La deposición de ramas varió de 48.25 a 75.16 g/m2/año y la de estructuras reproductivas de 58.4 a 98.9 g/m2/año. La de otros componentes (material vegetal no identifi cado, cuerpos y heces de insecto) varió de 19.9 a 29.2 g/m2/año. La deposición anual de Caen los tres sitios fl uctuó de 3.4 a 8.1; K de 1.4 a 3.2; Mg de 0.76 a 1.6; N de 3.0 a 5.5 y P de 0.05 a 0.11 g/m2/año. El Cu fl uctuó de 0.84 a 2.8; Fe de 14.7 a 21.7; Mn de 5.5 a 11.8 y Zn de 3.3 a 5.2 mg/m2/año. En invierno se depositó la mayor cantidad de minerales. Además, en Linares se depositó la mayor cantidad de minerales y en Los Ramones la menor. Hubo diferencias espaciales y temporales en cantidad de hojarasca colectada y retorno de minerales, mas no así en la calidad foliar entre los sitios de estudio. ABSTRACT The aims of the study were to estimate and quantify the monthly dynamics (January to December 2009) of litterfall deposition and macro (Ca, K, Mg, N y P) and microminerals (Cu, Fe, Mn, y Zn) of litterfall leaves in the counties Los Ramones, China y Linares, of Nuevo León State, México. The plant community is named as Tamaulipan Thornscrub Annual deposition was 321.5 (Los Ramones), 431.6 (China) and 462.9 (Linares) g/m2/year. Leaves represented the highest component (154.4 to 304.5 g/m2/year) of total litterfall production. Branches varied from 48.25 to 75.16 g/m2/year. Reproductive structures from 58.4 to 98.9 g/m2/year and other components (unidentifi ed material, bodies and insect feces) ranked from 19.9 to 29.2 g/m2/year. Annual deposition of Ca in the three sites varied from 3.4 to 8.1; K from 1.4 to 3.2; Mg from 0.76 to 1.6; N from 3.0 to 5.5 and P from 0.05 to 0.11 g/m2/year. Cu ranked from 0.84 to 2.8; Fe from 14.7 to 21.7; Mn from 5.5 to 11.8 and Zn from 3.3 to 5.2 mg/m2/year. In winter mineral deposition was higher. Moreover, the highest mineral deposition occurred in Linares and Los Ramones was the lowest. There were spatiotemporal variations in quantity of literfall collected and return of minerals, but not so in leaf quality between study sites

Propuesta de diseño de una estrategia de formación mediada por las TIC para fomentar la lectura en los estudiantes de grado sexto del Colegio Celestin Freinet de Chía.

Este proyecto de investigación está enfocado en el diseño de una estrategia de formación a partir de la mediación de las TIC, para fortalecer el interés de los alumnos del colegio Celestin Freinet de Chía por la lectura. La realización de este proyecto tiene como fin lograr un impacto hacia la formación y el apoyo en los procesos pedagógicos en las aulas, aprovechando las nuevas tecnologías que permiten ejecutar un cambio favorable en la educación. Para alcanzar resultados significativos se apoya este trabajo en el modelo de investigación IAP (Investigación Acción Participativa), el cual maneja unas fases acordes a los objetivos que se plantearon para promover nuestra estrategia de mediación con las TIC en el aula de clase. Las fases del modelo IAP son: la planificación, la actuación, la observación y la reflexión, los cuales se van a describir a continuación

Litterfall production and nutrient deposition through leaf fallen in three tamaulipan thornscrub communities, north-eastern Mexico

Litterfall and the contents of macro- and micro-nutrients derived from its decomposition contribute greatly to the growth and productivity of forest ecosystem. The present study was undertaken to know the variability during two years in the deposition of litterfall and deposition of nutrients through leaf fallen litterfall in three sites of the state of Nuevo Leon (Los Ramones, China and Linares), north-eastern Mexico, which encompasses the Tamaulipan thornscrub plant community. The quantities of litterfall production and its constituents varied between 2009 and 2010, being the year 2010 where higher litterfall and nutrients occured. Mean litterfall production during the two years showed the following trend: Los Ramones (364.8), China (522.7) and Linares (583.1 g m-2 year-1). For leaf constituent, mean deposition ranged from 200.9 (Los Ramones) to 409.8 g m-2 year-1 (Linares), twigs from 62.4 (Los Ramones) to 89.3 (Linares), reproductive structures from 62.5 (Linares) to 80.3 (Los Ramones) and the miscellaneous component, constituted by unidentified plant material, body and insect feces, ranged from 21.1 (Linares) to 32.7 g m-2 year-1 (China). During the two years, mean annual deposition of Ca+K+Mg+P+N for Los Ramones, China and Linares was 10.1, 21.5 and 24.8 g m-2 year-1, respectively. Regardless of the research site, the order of macro and micro-nutrients deposition was as follows: Ca>N>K>Mg>P and Fe>Mn>Zn>Cu, respectively. There were spatial and temporal variations in litterfall deposition in terms of quantity, quality and potential nutrient returns. It is documented that the variability of litterfall and contents of nutrients derived from litterfall is influenced by the physioco-chemical characteristics of soils, diversity in vegetation and climatic conditions prevailing in different sites and year

Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD

9 pages, 2 figures, 4 additional files.[Background] It is well known that the pattern of linkage disequilibrium varies between human populations, with remarkable geographical stratification. Indirect association studies routinely exploit linkage disequilibrium around genes, particularly in isolated populations where it is assumed to be higher. Here, we explore both the amount and the decay of linkage disequilibrium with physical distance along 211 gene regions, most of them related to complex diseases, across 39 HGDP-CEPH population samples, focusing particularly on the populations defined as isolates. Within each gene region and population we use r2 between all possible single nucleotide polymorphism (SNP) pairs as a measure of linkage disequilibrium and focus on the proportion of SNP pairs with r2 greater than 0.8.[Results] Although the average r2 was found to be significantly different both between and within continental regions, a much higher proportion of r2 variance could be attributed to differences between continental regions (2.8% vs. 0.5%, respectively). Similarly, while the proportion of SNP pairs with r2 > 0.8 was significantly different across continents for all distance classes, it was generally much more homogenous within continents, except in the case of Africa and the Americas. The only isolated populations with consistently higher LD in all distance classes with respect to their continent are the Kalash (Central South Asia) and the Surui (America). Moreover, isolated populations showed only slightly higher proportions of SNP pairs with r2 > 0.8 per gene region than non-isolated populations in the same continent. Thus, the number of SNPs in isolated populations that need to be genotyped may be only slightly less than in non-isolates.[Conclusion] The "isolated population" label by itself does not guarantee a greater genotyping efficiency in association studies, and properties other than increased linkage disequilibrium may make these populations interesting in genetic epidemiology.This research was supported by "Fundación Genoma España" (proyectos piloto CEGEN 2004–2005), Dirección General de Investigación, Ministerio de Educación y Ciencia of Spain (grants BFU2005-00243, BFU2006-01235, BFU2006-15413-CO2-01, SEJ2006-13537) and Direcció General de Recerca, Generalitat de Catalunya (2005SGR00608). SNP genotyping services were provided by the Spanish "Centro Nacional de Genotipado"Peer reviewe

SISTEMA DE MEDIÇÃO DA QUALIDADE DA EDUCAÇÃO FÍSICA NO CHILE E SUA INFLUÊNCIA NA REALIDADE ESCOLAR

El actual SIMCE-EF (Sistema de Medición de la Calidad de la Educación Física), evalúa componentes de la condición física, que poco tienen que ver con los objetivos de la disciplina. El objetivo es determinar la influencia percibida por los docentes a sus prácticas educativas y en el entorno escolar, atribuida a la aplicación de la prueba SIMCE-EF. Se encuestan y entrevistan a 17 profesores de EF, pertenecientes al 100%  de los establecimientos de la Comuna de  Viña del Mar, Chile, que se les aplicó el SIMCE-EF en los años, 2010, 2011 y 2012. Según los docentes, la prueba no tiene impacto en el ámbito escolar, lo que podría mantener los resultados en las aplicaciones futuras, mientras se evalúe solo la  condición física y en un formato piloto. The current SIMCE-EF (Measurement System Quality Physical Education), which measures certain fitness components, has little to do with the learning goals of the discipline. The objective of this study is to determine how the SIMCE-EF exam's influence is perceived by teachers in relation to their own teaching performance and the school environment. Seventeen P.E teachers participated in surveys and were interviewed, which is a hundred percent of the public system personnel in the area working in Viña del Mar, where the exams were given in 2010, 2011, and 2012. According to the teachers, this exam has no impact on the school environment and such results can remain in the future as long  as SIME-EF only measures overall physical fitness in a pilot format. O atual SIMCE-EF (Sistema de Medição da Qualidade da Educação Física) avalia os componentes da condição física que pouco tem a ver com os objetivos da disciplina de educação física. O objetivo deste trabalho é determinar a influência percebida pelos professores para as suas práticas educativas e do ambiente escolar, atribuídos à implementação do teste SIMCE-EF. Foram  entrevistados 17 professores de Educação Física, pertencentes a 100% do município de Viña del Mar (Chile) que se lhes aplicou o SIMCE-EF, nos anos de 2010, 2011 e 2012. Segundo os docentes, os resultados encontrados indicam que SIMCE-EF, não apresentam impacto no âmbito escolar. Este resultado poderia assegurar resultados em aplicações futuras, sempre que se avalie somente a condicao fisica em formato de estudo piloto.

Producción de hojarasca y retorno potencial de nutrientes en tres sitios del estado de Nuevo León, México

Los objetivos de este estudio fueron estimar y cuantificar la dinámica mensual (enero a diciembre 2009) de la deposición de la hojarasca y macro (Ca, K, Mg, N y P) y micro-minerales (Cu, Fe, Mn, y Zn) de las hojas de la hojarasca en los municipios Los Ramones, China y Linares, del estado de Nuevo León, México. La vegetación está caracterizada como matorral espinoso tamaulipeco. La deposición anual total de hojarasca fue de 321.5 (Los Ramones), 431.6 (China) y 462.9 (Linares) g/m2/año. Las hojas representaron el mayor componente (154.4 a 304.5 g/m2/año) del total de hojarasca depositada. La deposición de ramas varió de 48.25 a 75.16 g/m2/año y la de estructuras reproductivas de 58.4 a 98.9 g/m2/año. La de otros componentes (material vegetal no identifi cado, cuerpos y heces de insecto) varió de 19.9 a 29.2 g/m2/año. La deposición anual de Ca en los tres sitios fluctuó de 3.4 a 8.1; K de 1.4 a 3.2; Mg de 0.76 a 1.6; N de 3.0 a 5.5 y P de 0.05 a 0.11 g/m2/año. El Cu fluctuó de 0.84 a 2.8; Fe de 14.7 a 21.7; Mn de 5.5 a 11.8 y Zn de 3.3 a 5.2 mg/m2/año. En invierno se depositó la mayor cantidad de minerales. Además, en Linares se depositó la mayor cantidad de minerales y en Los Ramones la menor. Hubo diferencias espaciales y temporales en cantidad de hojarasca colectada y retorno de minerales, mas no así en la calidad foliar entre los sitios de estudio

Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.Facultad de Ciencias Naturales y MuseoInstituto Multidisciplinario de Biología Celula

Diversidad genética y relaciones filogenéticas del ganado criollo colombiano

Studies of genetic characterisation of Colombian criollo cattle (gcc) has shown the value of these breeds in tropical production systems; consequently attention is noticeably growing to develop conservation and multiplication programs. A genetic analysis study was conducted including the seven criollo cattle breeds: Blanco Orejinegro (BON), Romosinuano (R), Costeño Con Cuernos (CCC), Sanmartinero (SM), Chino Santandereano (Ch), Hartón del Valle (H) and Casanareño (C), using Cebu as external control breed, with the purpose to evaluate genetic diversity and philogenetic relations. Seven microsatellite (STR) were used to detect length variations amplified by the PCR and sized by means of ɣ32 P, runned in PAGE or tagged with a fluorescent dye and electrophoresis. Data were analysed using Genepop, GDA and Phylip programs. Mean number of alleles by loci were 8.9 and mean heterozygocity was o.52. The phylogenetic tree developed using Phylip program, the Nei's distance and the neighbour-joining aglorithm grouped in two the gcc. Group one included: Bon, SM, R,CCC and H, and the second group included Ch, Ca, C. Results of the phylogenetic relations of gcc showed that these breeds have adequate genetic diversity for breeding Programs; however we suggest to carry out studies including higher number of genetic markers.  Copyright (c) 2001 Corpoica Ciencia y Tecnología Agropecuaria La caracterización genética del ganado criollo colombiano (gcc) ha demostrado el valor de estas razas en los sistemas productivos tropicales, lo que ha despertado el interés para desarrollar programas de conservación y multiplicación. Se adelantó un estudio de análisis genético con las siete razas de ganado criollo colombiano, (rgcc): Blanco Orejinegro (BON), Romosinuano (R), Costeño Con Cuernos (CCC), Sanmartinero (SM), Chino Santandereano (Ch), Hartón del Valle (H) y Casanareño (Ca), utilizando el Cebú (C) como control, con el objeto de evaluar su diversidad genética y relaciones filogenéticas. Se usaron 7 microsatélites (STR) para establecer las distancias genéticas amplificadas mediante PCR. El tamaño de los loci se definió mediante marcaje con ɣ32 P seguido de un pase en geles de poliacrilamida (PAGE) o marcados con fluorescencia y electroforesis capilar. Los datos se analizaron usando los programas Genepop, GDA y Phylip. El número promedio de alelos por locus fue de 8,9 y Ia heterocigosidad promedia observada fue de o,52. El árbol filogenético construido con el programa Phylip, empleando la distancia de Nei y el algoritmo de Neighbour-joining, agrupó en dos las gcc. En el grupo uno las razas: BON, SM, R, CCC y H; y en el grupo dos las razas: Ch, Ca y C. Los resultados de evaluación filogenética de las gcc indicaron que existe diversidad genética adecuada en estas razas para programas de mejoramiento genético; sin embargo, se recomienda continuar el estudio con un mayor número de marcadores genéticos.