Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, Caviidae) in Colombia

The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05), genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations

Contribución de los datos genómicos en la definición de la composición racial de bovinos doble propósito

Animal heterosis is key in obtaining more productive animals and better adapted to the tropics. However, inadequate genetic management leads to the obtaining of mosaics of breeds that includes the loss of the productive potential of the herd. The objective of this study was to define the breed composition of dual-purpose crossbred cattle in the piedmont plains, department of Meta-Colombia. A total of 126 crossbred (CRO) individuals from six herds were evaluated by a phenotypic (APP) and a genotypic (GBA) approach. For GBA, the control breeds associated with Bos taurus taurus and Bos taurus indicus were included, for this they were genotyped with a GeneSeek GGP-LD chip of 26K of SNP and analyzed by principal component analysis (PCA) and Bayesian probabilistic assignment of ADMIXTURE. The breed groups generated by APP varied with respect to GBA. Molecular analysis detected seven (k=7) genetic groups in the breed composition of the study animals. The three breeds with the highest participation in the breed composition of crossbred individuals were: Holstein, Gyr, Brahman with 23.4, 21.4, and 21 % respectively, while the remaining, Blanco Orejinegro, Brown Swiss, Normande and Jersey did not exceed 13 %. Unlike APP, the GBA approach effectively allowed the identification of the breed composition of crossbred cattle and provided key information for the development of mating programs that seek to improve productive indicators, and in turn tend to the adaptation of animals, an essential requirement for dual-purpose bovine systems.La heterosis animal es clave en la obtención de animales más productivos y mejor adaptados al trópico. Sin embargo, el inadecuado manejo genético conlleva a la obtención de mosaicos de razas que incluye la pérdida del potencial productivo del hato. El objetivo de este estudio fue definir la composición racial de bovinos mestizos doble propósito en el piedemonte Llanero departamento del Meta-Colombia. Un total de 126 individuos mestizos (MEZ) de seis hatos fueron evaluados por una aproximación fenotípica (APF) y una genotípica (ARG). Para ARG se incluyeron las razas control asociadas a Bos taurus taurus y Bos taurus indicus, para ello se genotiparon con un chip de GeneSeek GGP-LD de 26K de SNP y se analizaron mediante análisis de componentes principales (PCA) y asignación probabilística bayesiana de ADMIXTURE. Las agrupaciones raciales generadas por APF variaron respecto de ARG. El análisis molecular detectó siete (k= 7) grupos genéticos en la composición racial de los animales de estudio. Las tres razas con mayor participación en la composición racial de los individuos mestizos fueron: Holstein, Gyr, Brahman con 23.4, 21.4, y 21 % respectivamente, mientras que las restantes Blanco Orejinegro, Pardo Suizo, Normando y Jersey no superaron el 13 %.  A diferencia de APF, la aproximación ARG permitió de forma efectiva la identificación de la composición racial de bovinos mestizos y suministró información clave en miras de desarrollo de programas de apareamiento que buscan mejorar indicadores productivos, y a su vez propendan por la adaptación de los animales requisito indispensable para los sistemas bovino doble propósito

EL TLC CON ESTADOS UNIDOS: EFECTOS Y RETOS PARA LA CADENA LÁCTEA DE NARIÑO

En este artículo se presenta una descripción general de la Cadena Láctea en Colombia y en la cuenca lechera del departamento de Nariño e igualmente se mencionan las posibles consecuencias que se derivarán, para este importante sector de la economía regional, cuando entren en vigencia los puntos acordados en el Tratado de Libre Comercio con los Estados Unidos. Como elementos imprescindibles para el análisis se incluyen los indicadores que determinan, en buena medida, la competitividad del renglón lácteo de Colombia y Nariño, los contingentes asignados a cada país, las condiciones acordadas para el libre comercio de productos lácteos, las potencialidades de los productos colombianos, los problemas y dificultades que actualmente limitan la productividad en Nariño y los retos que tendrán que afrontar todos los eslabones de la cadena láctea por efecto del TLC

Comparación del ramoneo entre la cabra salvaje mallorquina (Capra aegagrus Erxleben, 1777) y la cabra doméstica asilvestrada (Capra hircus L. 1758) en Mallorca

El objetivo de este estudio fue comparar el nivel de ramoneo de la cabra salvaje Mallorquina y la cabra doméstica asilvestrada en la sierra Tramuntana de Mallorca durante los periodos de primavera, verano e invierno. Los resultados muestran que las especies más ramoneadas, en orden decreciente, fueron: Olea europea, Ampelodesmos mauritanica, Cistus albidus, Chamaerops humilis, Phillyrea angustifolia, Cistus monspeliensis y Pistacia lentiscus. En las zonas pastoreadas por cabras asilvestradas Olea europaea aparece más ramoneada que en las zonas pastoreadas por cabras salvajes. Lo contrario ocurre con Cistus albidus que es más ramoneada en las zonas pastoreadas por cabras salvajes. La diferencia del ramoneo entre periodos varía en función de cada especie, así por ejemplo, el ramoneo disminuye en invierno en Chamaerops humilis, mientras que el consumo de Cistus albidus aumenta. Se concluye que la intensidad de ramoneo realizada por cada tipo de cabra depende de factores de variación como el periodo del año y la zona de pastoreo

Genome data from a sixteenth century pig illuminate modern breed relationships

Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds

Diversidad genética y estructura poblacional en ovinos de pelo de la Región Caribe colombiana

The sheep populations of the Colombian Caribbean Region are characterized by having a high phenotypic heterogeneity mainly due to the use of Creole animals in crossbreeding with exotic breeds. The aim of this study was to estimate the genetic diversity and the population structure of sheep in this region. In total, 459 sheep from 26 farms in 19 municipalities were selected. The DNA samples were genotyped with the ovine low-density chip (15K). Analyses of molecular variance, genetic diversity and population structure were performed. At the phenotypic level, 65.8% of the sampled animals were assigned to the Criollo population, while 15.7% showed signs of introgression with other commercial breeds (mestizos). The populations presented a high degree of genetic diversity within individuals (90.6%) and low levels of genetic variation between populations (FST = 0.075). This low differentiation, together with the low levels of genetic variation between populations, could be attributed to a lack of selection pressure and the existence of gene flow (crossbreeding) between populations.Las poblaciones ovinas de la Región Caribe colombiana se caracterizan por tener una alta heterogeneidad fenotípica debido principalmente al uso de animales criollos en cruzamiento con razas exóticas. El presente estudio tuvo como objetivo estimar la diver-sidad genética y la estructura poblacional de ovinos de esta región. Se seleccionaron 459 animales ovinos de 26 granjas de 19 municipios. Las muestras de ADN fueron genotipadas con el chip ovino de baja densidad (15K). Se realizaron análisis de varianza molecular, diversidad genética y estructura poblacional. A nivel fenotípico, se asignó el 65.8% de los animales muestreados a la población Criollo mientras que 15.7% presentaron señales de introgresión con otras razas comerciales (mestizos). Las poblaciones presentaron un alto grado de diversidad genética dentro de los individuos (90.6%) y bajos niveles de variación genética entre poblaciones (FST = 0.075). Esta baja diferenciación, junto con los bajos niveles de variación genética entre poblaciones podría atribuirse a una falta de presión de selección y a la existencia de un flujo genético (mestizaje) entre las poblaciones

Amygdala inputs to prefrontal cortex guide behavior amid conflicting cues of reward and punishment

Orchestrating appropriate behavioral responses in the face of competing signals that predict either rewards or threats in the environment is crucial for survival. The basolateral nucleus of the amygdala (BLA) and prelimbic (PL) medial prefrontal cortex have been implicated in reward-seeking and fear-related responses, but how information flows between these reciprocally connected structures to coordinate behavior is unknown. We recorded neuronal activity from the BLA and PL while rats performed a task wherein competing shock- and sucrose-predictive cues were simultaneously presented. The correlated firing primarily displayed a BLA→PL directionality during the shock-associated cue. Furthermore, BLA neurons optogenetically identified as projecting to PL more accurately predicted behavioral responses during competition than unidentified BLA neurons. Finally photostimulation of the BLA→PL projection increased freezing, whereas both chemogenetic and optogenetic inhibition reduced freezing. Therefore, the BLA→PL circuit is critical in governing the selection of behavioral responses in the face of competing signals.National Institutes of Health (U.S.) (Award 1R25-MH092912-01)National Institute of Mental Health (U.S.) (Grant R01- MH102441-01)National Institutes of Health (U.S.) (Award DP2- DK-102256-01

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Ancestry and diversity of American village pigs

Los avances en las tecnologías de genotipado masivo están revolucionando la comprensión de los genomas de animales domésticos, incluyendo su historia y cómo los eventos demográficos y selectivos han dado forma a la variación de los genomas de los individuos. En este trabajo analizamos por primera vez una amplia muestra de poblaciones de cerdos criollos de América y se estimó su relación genética con las poblaciones de cerdos en todo el mundo. Adicionalmente, se analizó el genoma de un cerdo que vivió en el siglo XVI a fin de proporcionar nuevas evidencias sobre eventos históricos y genéticos importantes como la domesticación y cruzamientos. Estos estudios mostraron una alta diferenciación entre las poblaciones de cerdos de Europa y Asia, siendo especialmente pronunciada para la región no pseudoautosómica del cromosoma X. A pesar del origen ibérico de los primeros cerdos introducidos en América, se observó una reducción sustancial de éste origen genético en el casi todas las poblaciones Americanas de cerdos estudiadas. El origen genético observado en las actuales poblaciones de cerdos en América se debió primero al los cerdos Ibéricos en el siglo XV y la reciente introgresión de las razas porcinas comerciales. Además se detectó origen genético proveniente de Asia, probablemente por causa de la introgresión de las razas comerciales que llevan haplotipos asiáticos, aunque no se puede descartar el cruzamiento con razas Chinas. Debido a la gran diversidad de condiciones del medio ambiente en América, se compararon las frecuencias alélicas observadas entre las poblaciones para estimar huellas de selección en el genoma, detectándose algunos genes relacionados con el sistema cardiovascular y la conformación de las extremidades. El ADN antiguo proporciona una valiosa información a cerca de los acontecimientos históricos que han modelado el genoma de los individuos modernos. En el capítulo 5 se analizó una parte del genoma de un cerdo que vivió en el siglo XVI en el noreste de España, junto a tres nuevos genomas de individuos modernos, un cerdo Ibérico, un jabalí de España y un cerdo criollo de Guatemala. Los genomas fueron obtenidos por métodos de secuenciación masiva. Los datos arqueológicos y genómicos sugirieron que el cerdo antiguo era domestico y estrechamente relacionado con los cerdos Ibéricos actuales y el jabalí Europeo, y con señales genéticas de cruzamiento entre ellos. Sorprendentemente, la comparación del cerdo antiguo y el cerdo Ibérico moderno con el genoma del cerdo criollo de Guatemala, mostró que ellos son igualmente cercanos a los cerdos criollos de América, y podría apoyar la hipótesis de la reducción de origen ibérico en cerdos Americanos causado por la introgresión de otras razas. Por último, entre los genes altamente diferenciadas se encontraron aquellos que participan en el color de la capa y el aumento del rendimiento reproductivo, ambas funciones asociadas con el primeros procesos de domesticación. Una de las estrategias de análisis para describir las relaciones de la población de cerdos utilizados en esta tesis, y ampliamente utilizado en estudios similares, es el análisis de componentes principales (PCA). Sin embargo, las proyecciones de PCA son sensibles a tamaño de muestra desbalanceado. En el capítulo 6 se evaluó una corrección en el PCA que tenga en cuenta el tamaño de la muestra de las poblaciones evaluadas ó su FST para corregir el sesgo en las proyecciones de los individuos. Las simulaciones sugieren que el método propuesto mejora las proyecciones de los individuos en dos dimensiones y en algunos caso, recupera los patrones de relaciones de la población, incluso cuando el tamaño de muestra es tan bajo como n = 1. El método ponderado de PCA puede recuperar una estructura más realista de los datos que la inferida con el PCA tradicional en poblaciones genéticamente diferenciadas.Advances in high throughput genetic technologies are revolutionizing the understanding of domestic animal genomes, including their history and how demography and selective processes have shaped the variation of individuals’ genomes. Here we studied for the first time a large survey of village pig populations from America and estimate their relatedness with worldwide pig populations. In complement, we also analysed an ancient pig genome of 16th century to provide new evidence on important historical and genetic events like domestication and admixture. These studies showed the high differentiation between European and Asian pig populations, being particularly pronounced for the non-pseudoautosomal region of chromosome X. Despite the Iberian origin of pigs firstly introduced to America, a substantial reduction of this ancestry was observed in almost all American village pig populations. The actual ancestry observed in America is likely the result of admixing Iberian pigs in 15th century and recent introgression of commercial pig breeds. Additionally, some Asian ancestry also was observed probably due to introgression of commercial breeds carrying Asian haplotype, although direct admixture with Chinese breeds cannot be ruled out. Because the large diversity of environmental condition in the American continent, we compared the allele frequencies observed between populations to estimate signatures of selection in the genome, detecting some genes related with cardiovascular system and limbs conformation. Ancient DNA provides valuable information about the historical events that have modelled the genome of modern individuals. In chapter 5 we performed the analysis of the partial genome of a pig that lived in 16th century at North eastern Spain together three new modern genomes from Iberian pig, Spanish wild boar and a Guatemalan Creole pig obtained by whole genome shotgun sequencing. Archaeological and genomic data suggested that ancient pig was domestic, closely related to extant Iberian pigs and to European wild boar with some genetic signals of admixture with wild boar. Surprisingly, the comparison of ancient pig and modern Iberian pig to American sample from Guatemala, showed that they are equally close to American Creole pigs, and could support the hypothesis of reduction of Iberian origin in American village pigs driven by introgression of other breeds. Finally, among the highly differentiated genes we found those involved in coat colour and an increase the reproductive performance, both known functions associated with early domestication process. One of the analytical strategies to describe the population relationships of pigs used in this thesis, and widely used in similar studies is the principal component analysis (PCA). Nonetheless, PCA projections are sensitive to unequal sample size. In Chapter 6 we evaluated a correction in PCA that consider either sample size of evaluated populations or their FST estimates to correct bias in individual projections. Simulations suggest that the proposed method improves the two-dimensional projections of PCA data and, in some cases, entirely recovers population relationships patterns, even when sample size is as low as n=1. The weighted PCA can recover a more realistic structure than inferred with traditional PCA in well-structured populations