30 research outputs found
Testing the existence of an unadmixed ancestor from a specific population t generations ago
Datos y cĂłdigos en: https://figshare.com/articles/dataset/Testing_the_existence_of_an_unadmixed_ancestor_from_a_specific_population_t_The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how
many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples
Indigenous ancestry and admixture in the uruguayan population
The Amerindian group known as the CharrĂșas inhabited Uruguay at the timing of European colonial contact. Even though they were extinguished as an ethnic group as a result of a genocide, CharrĂșan heritage is part of the Uruguayan identity both culturally and genetically. While mitochondrial DNA studies have shown evidence of Amerindian ancestry in living Uruguayans, here we undertake whole-genome sequencing of 10 Uruguayan individuals with self-declared Charruan heritage. We detect chromosomal segments of Amerindian ancestry supporting the presence of indigenous genetic ancestry in living descendants. Specific haplotypes were found to be enriched in âCharrĂșasâ and rare in the rest of the Amerindian groups studied. Some of these we interpret as the result of positive selection, as we identified selection signatures and they were located mostly within genes related to the infectivity of specific viruses. Historical records describe contacts of the CharrĂșas with other Amerindians, such as GuaranĂ, and patterns of genomic similarity observed here concur with genomic similarity between these groups. Less expected, we found a high genomic similarity of the CharrĂșas to Diaguita from Argentinian and Chile, which could be explained by geographically proximity. Finally, by fitting admixture models of Amerindian and European ancestry for the Uruguayan population, we were able to estimate the timing of the first pulse of admixture between European and Uruguayan indigenous peoples in approximately 1658 and the second migration pulse in 1683. Both dates roughly concurring with the Franciscan missions in 1662 and the foundation of the city of Colonia in 1680 by the Spanish.ANII: FSDA_1_2017_1_14364
Phylogeography of native mitogenomes from Uruguay
Recientemente, diversos estudios sobre la poblaciĂłn uruguaya han demostrado que estĂĄ conformada por desiguales aportes de europeos, africanos y pueblos originarios, entre otros. El aporte indĂgena es mayor cuando se analiza la contribuciĂłn por lĂnea materna, aunque su origen Ă©tnico/geogrĂĄfico no es claro, ni tampoco cuĂĄndo ni cĂłmo llegaron los distintos grupos. Para aportar al conocimiento del poblamiento prehistĂłrico e histĂłrico del territorio y sus relaciones con otras poblaciones se analizan, por secuenciaciĂłn masiva, 32 genomas mitocondriales completos (mitogenomas) de habitantes actuales del paĂs, identificados previamente por sus regiones hipervariables como correspondientes a los cuatro haplogrupos principales de origen americano. Se determinaron siete nuevos subhaplogrupos (A2be, A2bf, B2an, C1d1h, C1b30, C1b31 y D1x), otro se redenominĂł (C1d1d - actual C1d1g) y se plantea la revisiĂłn de los criterios de asignaciĂłn de B2b6 y D1g5. Se estimĂł la antigĂŒedad de los subhaplogrupos nuevos, que varĂa entre 4554 y 11985 años, con la excepciĂłn de C1d1g, cuya edad fue estimada en 20736 años. Algunas secuencias pudieron ser vinculadas a distintos grupos Ă©tnicos o a diversas regiones geo-grĂĄficas, como Amazonia, Chaco, Pampa, o Andes. Se discuten las nuevas asignaciones de subhaplogrupos y las de algunos previamente definidos, asĂ como su distribuciĂłn geo-grĂĄfica y antigĂŒedad, con relaciĂłn al panorama general de AmĂ©rica del Sur.Recently, several studies on the Uruguayan population have shown that it is formed by unequal contributions from Europeans, Africans, Native Americans, and others. The native component is larger when maternal contribution is analyzed, but its ethnic/geographic origin remains unclear, as it is also unclear how and when these groups arrived. To contribute to the knowledge about prehistoric and historic peopling of the territory and its relations with other populations, 32 complete mitochondrial genomes (mitogenomes) were obtained by next generation sequencing. They belong to present inhabitants of the country, whose hypervariable regions were previously analyzed and whose identified haplogroups belonged to one of the four main haplogroups of Native American origin. Seven new subhaplogroups (A2be, A2bf, B2an, C1d1h, C1b30, C1b31 and D1x) were determined, another was redenominated (C1d1d - present C1d1g), and the criteria to assign B2b6 and D1g5 were reviewed. The age of the new subhaplo-groups was estimated between 4.554 and 11.985 years, while the age of C1d1g was estimated in 20.736 years. Some sequences could be related to different ethnic groups, or to several geographic regions such as Amazonia, Chaco, Pampa or Andes. The new subhaplogroup assignations, together with their geographic distribution and chronology, are discussed in relation to the general panorama of South America.AsociaciĂłn de AntropologĂa BiolĂłgica Argentin
Recurrent dissemination of SARS-CoV-2 through the UruguayanâBrazilian border
Uruguay is one of the few countries in the Americas that successfully contained the coronavirus disease 19 (COVID-19) epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to investigate the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in Uruguayan localities bordering Brazil as well as to measure the viral flux across this âŒ1,100 km uninterrupted dry frontier. Using complete SARS-CoV-2 genomes from the UruguayanâBrazilian bordering region and phylogeographic analyses, we inferred the virus dissemination frequency between Brazil and Uruguay and characterized local outbreak dynamics during the first months (MayâJuly) of the pandemic. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 Brazilian lineages B.1.1.28 and B.1.1.33 into Uruguayan localities at the bordering region. The most probable sources of viral strains introduced to Uruguay were the Southeast Brazilian region and the state of Rio Grande do Sul. Some of the viral strains introduced in Uruguayan border localities between early May and mid-July were able to locally spread and originated the first outbreaks detected outside the metropolitan region. The viral lineages responsible for Uruguayan urban outbreaks were defined by a set of between four and 11 mutations (synonymous and non-synonymous) with respect to the ancestral B.1.1.28 and B.1.1.33 viruses that arose in Brazil, supporting the notion of a rapid genetic differentiation between SARS-CoV-2 subpopulations spreading in South America. Although Uruguayan borders have remained essentially closed to non-Uruguayan citizens, the inevitable flow of people across the dry border with Brazil allowed the repeated entry of the virus into Uruguay and the subsequent emergence of local outbreaks in Uruguayan border localities. Implementation of coordinated bi-national surveillance systems is crucial to achieve an efficient control of the SARS-CoV-2 spread across this kind of highly permeable borderland regions around the world
Emergence and spread of a B.1.1.28-derived P.6 lineage with Q675H and Q677H spike mutations in Uruguay
Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020âFebruary 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. P.6 probably arose around November 2020, in Montevideo, Uruguayâs capital department, and rapidly spread to other departments, with evidence of further local transmission clusters; it also spread sporadically to the USA and Spain. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest
Real-Time genomic surveillance for SARS-CoV-2 variants of concern, Uruguay
We developed a genomic surveillance program for realtime monitoring of severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARSCoV-
2 VOCs, the surveillance workflow, and multiple independent introductions and community transmission of
the SARS-CoV-2 P.1 VOC in Uruguay
Mecanismos de diferenciación y auto-renovación de células madre mesenquimales a adipocitos
Supervisores: Dr. Bruno Dallagiovanna, Dr. Hugo Nay
Data on thermal conductance for 127 rodent species
Data on minimal thermal conductance for 127 rodent species, together with data on body mass, basal metabolic rate, and several geographic, climatic and ecological variables
Data from: Thermal conductance and basal metabolic rate are part of a coordinated system for heat transfer regulation
Thermal conductance measures the ease with which heat leaves or enters an organism's body. Although the analysis of this physiological variable in relation to climatic and ecological factors can be traced to studies by Scholander and colleagues, only small advances have occurred ever since. Here, we analyse the relationship between minimal thermal conductance estimated during summer (Cmin) and several ecological, climatic and geographical factors for 127 rodent species, in order to identify the exogenous factors that have potentially affected the evolution of thermal conductance. In addition, we evaluate whether there is compensation between Cmin and basal metabolic rate (BMR)âin such a way that a scale-invariant ratio between both variables is equal to oneâas could be expected from the ScholanderâIrving model of heat transfer. Our major findings are (i) annual mean temperature is the best single predictor of mass-independent Cmin. (ii) After controlling for the effect of body mass, there is a strong positive correlation between log10 (Cmin) and log10 (BMR). Further, the slope of this correlation is close to one, indicating an almost perfect compensation between both physiological variables. (iii) Structural equation modelling indicated that Cmin values are adjusted to BMR values and not the other way around. Thus, our results strongly suggest that BMR and thermal conductance integrate a coordinated system for heat regulation in endothermic animals and that summer conductance values are adjusted (in an evolutionary sense) to track changes in BMRs
Unveiling Polysomal Long Non-Coding RNA Expression on the First Day of Adipogenesis and Osteogenesis in Human Adipose-Derived Stem Cells
Understanding the intricate molecular mechanisms governing the fate of human adipose-derived stem cells (hASCs) is essential for elucidating the delicate balance between adipogenic and osteogenic differentiation in both healthy and pathological conditions. Long non-coding RNAs (lncRNAs) have emerged as key regulators involved in lineage commitment and differentiation of stem cells, operating at various levels of gene regulation, including transcriptional, post-transcriptional, and post-translational processes. To gain deeper insights into the role of lncRNAsâ in hASCsâ differentiation, we conducted a comprehensive analysis of the lncRNA transcriptome (RNA-seq) and translatome (polysomal-RNA-seq) during a 24 h period of adipogenesis and osteogenesis. Our findings revealed distinct expression patterns between the transcriptome and translatome during both differentiation processes, highlighting 90 lncRNAs that are exclusively regulated in the polysomal fraction. These findings underscore the significance of investigating lncRNAs associated with ribosomes, considering their unique expression patterns and potential mechanisms of action, such as translational regulation and potential coding capacity for microproteins. Additionally, we identified specific lncRNA gene expression programs associated with adipogenesis and osteogenesis during the early stages of cell differentiation. By shedding light on the expression and potential functions of these polysome-associated lncRNAs, we aim to deepen our understanding of their involvement in the regulation of adipogenic and osteogenic differentiation, ultimately paving the way for novel therapeutic strategies and insights into regenerative medicine