The genetic history of Portugal over the past 5,000 years.

Background: Recent ancient DNA studies uncovering large-scale demographic events in Iberia have presented very limited data for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we present the most comprehensive collection of Portuguese ancient genome-wide data, from 67 individuals spanning 5000 years of human history, from the Neolithic to the nineteenth century.

Results: We identify early admixture between local hunter-gatherers and Anatolian-related farmers in Neolithic Portugal, with a northeastern-southwestern gradient of increasing Magdalenian-associated ancestry persistence in Iberia.

Genetic transitions in the Neolithic and Bronze Age at Mas d'en Boixos (Catalonia, Spain).

Mas d'en Boixos is a key prehistoric site in Northeastern Iberia spanning from the Early Neolithic to the Late Iron Age. We analyzed genome-wide data from eight individuals and ten mitogenomes, dated to the Middle Neolithic and Early Bronze Age, alongside three previously published Iron Age individuals. Two Middle Neolithic individuals buried together were first-degree maternal relatives and carried Western Hunter-Gatherer, Anatolian, and residual Magdalenian-associated ancestries.

Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context.

Ongoing advances in population genomic methodologies have recently enabled the study of millions of loci across hundreds of genomes at a relatively low cost, by leveraging a combination of low-coverage shotgun sequencing and innovative genotype imputation methods. This approach has the potential to provide abundant genotype information at low costs comparable to another widely used cost-effective genotyping approach-that is, SNP panels-while avoiding potential issues related to loci being ascertained in distantly related populations. Nonetheless, the wide adoption of imputation methods in humans and other species is currently constrained by the lack of publicly available reference panels that capture diversity representative of the target genomes-though the recent development of 'joint' imputation approaches, which allow genetic information from the target population to be used in genotype calling, may potentially mitigate this shortcoming.

Optimized in-solution enrichment of over a million ancient human SNPs.

Background: In-solution hybridization enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmark the commercial "Twist Ancient DNA" reagent from Twist Biosciences using sequencing libraries from ancient human samples of diverse demographic origin with low to high endogenous DNA content (0.1-44%).

Shrouded in history: Unveiling the ways of life of an early Muslim population in Santarém, Portugal (8th- 10th century AD).

In around 716 AD, the city of Santarém, Portugal, was conquered by the Berber and Arab armies that swept the Iberian Peninsula and went on to rule the region until the 12th century. Archaeological excavations in 2007/08 discovered an Islamic necropolis (Avenida 5 de Outubro #2-8) that appears to contain the remains of an early Muslim population in Santarém (8th- 10th century). In this study, skeletal material from 58 adult individuals was analysed for stable carbon (δ13Ccol; δ13Cap), nitrogen (δ15N) and sulphur (δ34S) isotope ratios in bones, and stable oxygen (δ18O), carbon (δ13Cen) and radiogenic strontium (87Sr/86Sr) isotopes in tooth enamel.

Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA.

Aneuploidies, and in particular, trisomies represent the most common genetic aberrations observed in human genetics today. To explore the presence of trisomies in historic and prehistoric populations we screen nearly 10,000 ancient human individuals for the presence of three copies of any of the target autosomes. We find clear genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome), and all cases are present in infant or perinatal burials.

Economic and financial model to the mass-rearing of Macrolophus pygmaeus (Rambur) (Heteroptera: Miridae), a biological control agent against the tomato moth Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) in protected culture.

Background: Tuta absoluta (Meyrick) is a major pest of tomato produced in glasshouses and open field, causing severe damages to crops, reducing the quality of tomato fruits. The current maintenance of the pest populations below the economic threshold is not achieved by natural and classical control, thus requiring the continuous application of biological control agents (BCAs), under an augmentative or inoculative approach. The present study aims to develop an economic and financial model to evaluate the commercial viability of a continuous mass production of Macrolophus pygmaeus (Rambur), a BCA commonly used against the tomato moth, Tuta absoluta, in protected culture.

Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects.

Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants.

Admixture has obscured signals of historical hard sweeps in humans.

The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species.

The immunogenetic impact of European colonization in the Americas.

The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence.

Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact.

The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul-i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level-by 50,000 years ago.

Regional Features of Long-Term Exposure to PM Air Quality over Asia under SSP Scenarios Based on CMIP6 Models.

This study investigates changes in fine particulate matter (PM) concentration and air-quality index (AQI) in Asia using nine different Coupled Model Inter-Comparison Project 6 (CMIP6) climate model ensembles from historical and future scenarios under shared socioeconomic pathways (SSPs). The results indicated that the estimated present-day PM concentrations were comparable to satellite-derived data. Overall, the PM concentrations of the analyzed regions exceeded the WHO air-quality guidelines, particularly in East Asia and South Asia.

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America.

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites.

The inflated significance of neutral genetic diversity in conservation genetics.

The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species.

Adverse reactions and adherence to capecitabine: A prospective study in patients with gastrointestinal cancer.

Introduction: Capecitabine is an oral anticancer drug which can cause some adverse reactions and the great challenge for its use is to ensure the medication adherence. The aim of this study was to analyze adverse reactions and adherence to capecitabine in patients with gastrointestinal cancer.

Methods: A prospective study was performed in a tertiary teaching hospital in Brazil.

Ancient DNA Studies in Pre-Columbian Mesoamerica.

Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period.

Genetic susceptibility to severe childhood asthma and rhinovirus-C maintained by balancing selection in humans for 150 000 years.

Selective pressures imposed by pathogens have varied among human populations throughout their evolution, leading to marked inter-population differences at some genes mediating susceptibility to infectious and immune-related diseases. Here, we investigated the evolutionary history of a common polymorphism resulting in a Y529 versus C529 change in the cadherin related family member 3 (CDHR3) receptor which underlies variable susceptibility to rhinovirus-C infection and is associated with severe childhood asthma. The protective variant is the derived allele and is found at high frequency worldwide (69-95%).

Using hominin introgression to trace modern human dispersals.

The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known.

Signatures of Long-Term Balancing Selection in Human Genomes.

Balancing selection maintains advantageous diversity in populations through various mechanisms. Although extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here, we describe the Non-central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test.

Arthroscopic treatment of synovial osteochondromatosis of the elbow. Case report and literature review.

Synovial osteochondromatosis is a benign proliferative disorder with metaplasia of the synovial membrane that affects the fibroblasts of the synovial joints, tendons and bursae. In literature, there are few descriptions of synovial osteochondromatosis of the elbow. The objective of this article was to report a case of synovial osteochondromatosis of the elbow in a patient aged 32, basketball athlete, in which surgical treatment was chosen because of the pain and functional limitation and stage of disease with multiple loose bodies.

Sternoclavicular dislocation: case report and surgical technique.

Sternoclavicular dislocations account for less than 5% of all dislocations of the scapular belt. Most cases of anterior dislocation of the sternoclavicular joint do not present symptoms. However, some patients may develop chronic anterior instability and remain symptomatic, and surgical treatment is indicated in these cases.

Portuguese crypto-Jews: the genetic heritage of a complex history.

The first documents mentioning Jewish people in Iberia are from the Visigothic period. It was also in this period that the first documented anti-Judaic persecution took place. Other episodes of persecution would happen again and again during the long troubled history of the Jewish people in Iberia and culminated with the Decrees of Expulsion and the establishment of the Inquisition: some Jews converted to Catholicism while others resisted and were forcedly baptized, becoming the first Iberian Crypto-Jews.