Disentangling signatures of selection before and after European colonization in latin Americans

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas

Análisis de la opinión de estudiantes sobre conductas de riesgo de jóvenes en Puerto Rico

The main purpose of the study was to analyze the opinion that students of the University of Puerto Rico, Río Piedras Campus (UPRRP) have about some risk behaviors in teenagers of both genders between the ages of 13-18. We administered an online survey, which was taken by 1,836 students enrolled during the first semester of the 2017-18 academic year. We used mixed methods: descriptive statistics analysis and content analysis. The findings reveal that the opinion of students is that youth is a stage of confusion and turbulence; that some risk behaviors have increased during the past five years and that it tends to be associated to male youth. These results suggest that university students tend to reproduce the dominant social imaginary in terms of risk behavior in youth. Further investigations should take into consideration the consequences of youth stigmatization, since this is a heterogeneous and diverse group.El objetivo de nuestro estudio fue analizar la opinión que tienen los/as estudiantes de la Universidad de Puerto Rico, Recinto de Río Piedras (UPRRP), sobre algunas conductas de riesgo en jóvenes de ambos géneros, de 13-18 años.  Administramos un cuestionario en línea que fue contestado por 1,836 estudiantes matriculados/as durante el primer semestre del año académico 2017-18. Utilizamos un método mixto: análisis estadístico descriptivo y análisis de contenido. Los hallazgos revelan que la opinión de la mayoría de los/as estudiantes universitarios/as es que la juventud es una etapa de confusión y turbulencia; que algunas conductas de riesgo han aumentado durante los pasados cinco años y que se asocian más con los jóvenes que con las jóvenes. Estos hallazgos sugieren que los/as estudiantes tienden a reproducir los imaginarios sociales dominantes sobre la conducta de riesgo en jóvenes entre las edades de 13-18 años. Futuros trabajos deben considerar las consecuencias de la estigmatización hacia los/as jóvenes, ya que este es un grupo heterogéneo y variado

Disentangling Signatures of Selection Before and After European Colonization in Latin Americans

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

OBJECTIVES: Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. MATERIALS AND METHODS: Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. RESULTS: Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. DISCUSSION: Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains

Genomic insights into the early peopling of the Caribbean

The Caribbean was one of the last regions of the Americas to be settled by humans, but how, when, and from where they reached the islands remains unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200-400 cal. BP and find evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detect genetic differences between the early settlers and the newcomers from South America with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas