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Abstract We present multiwavelength observations of the Swift shortγ-ray burst GRB 231117A, localized to an underlying galaxy at redshiftz= 0.257 at a small projected offset (∼2 kpc). We uncover long-lived X-ray Chandra X-ray Observatory and radio/millimeter (VLA, MeerKAT, and ALMA) afterglow emission, detected to ∼37 days and ∼20 days (rest frame), respectively. We measure a wide jet (∼10 $\stackrel{\text{°}}{.}$4) and relatively high circumburst density (∼0.07 cm⁻³) compared to the short GRB population. Our data cannot be easily fit with a standard forward shock model, but they are generally well fit with the incorporation of a refreshed forward shock and a reverse shock at <1 day. We incorporate GRB 231117A into a larger sample of 132 X-ray detected events, 71 of which were radio-observed (17 cm-band detections), for a systematic study of the distributions of redshifts, jet and afterglow properties, galactocentric offsets, and local environments of events with and without detected radio afterglows. Compared to the entire short GRB population, the majority of radio-detected GRBs are at relatively low redshifts (z < 0.6) and have high circumburst densities (>10⁻²cm⁻³), consistent with their smaller (<8 kpc) projected galactocentric offsets. We additionally find that 70% of short GRBs with opening angle measurements were radio-detected, indicating the importance of radio afterglows in jet measurements, especially in the cases of wide (>10°) jets where observational evidence of collimation may only be detectable at radio wavelengths. Owing to improved observing strategies and the emergence of sensitive radio facilities, the number of radio-detected short GRBs has quadrupled in the past decade. 

Abstract MotivationGene deletion is traditionally thought of as a nonadaptive process that removes functional redundancy from genomes, such that it generally receives less attention than duplication in evolutionary turnover studies. Yet, mounting evidence suggests that deletion may promote adaptation via the “less-is-more” evolutionary hypothesis, as it often targets genes harboring unique sequences, expression profiles, and molecular functions. Hence, predicting the relative prevalence of redundant and unique functions among genes targeted by deletion, as well as the parameters underlying their evolution, can shed light on the role of gene deletion in adaptation. ResultsHere, we present CLOUDe, a suite of machine learning methods for predicting evolutionary targets of gene deletion events from expression data. Specifically, CLOUDe models expression evolution as an Ornstein–Uhlenbeck process, and uses multi-layer neural network, extreme gradient boosting, random forest, and support vector machine architectures to predict whether deleted genes are “redundant” or “unique”, as well as several parameters underlying their evolution. We show that CLOUDe boasts high power and accuracy in differentiating between classes, and high accuracy and precision in estimating evolutionary parameters, with optimal performance achieved by its neural network architecture. Application of CLOUDe to empirical data from Drosophila suggests that deletion primarily targets genes with unique functions, with further analysis showing these functions to be enriched for protein deubiquitination. Thus, CLOUDe represents a key advance in learning about the role of gene deletion in functional evolution and adaptation. Availability and implementationCLOUDe is freely available on GitHub (https://github.com/anddssan/CLOUDe). 

An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level. 

Abstract The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former Indigenous ethnic diversity into the narrative of a singular people that all but died out. Here, we present the first whole genome sequences of the Indigenous people of the region before the arrival of Europeans, from an archaeological site in eastern Uruguay that dates from 2,000 years before present. We find a surprising connection to ancient individuals from Panama and eastern Brazil, but not to modern Amazonians. This result may be indicative of a migration route into South America that may have occurred along the Atlantic coast. We also find a distinct ancestry previously undetected in South America. Though this work begins to piece together some of the demographic nuance of the region, the sequencing of ancient individuals from across Uruguay is needed to better understand the ancient prehistory and genetic diversity that existed before European contact, thereby helping to rebuild the history of the Indigenous population of what is now Uruguay. 

Abstract ObjectivesSince 2010, genome‐wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present‐day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019. Materials and MethodsThe genomic data from ancient Americas was merged with a worldwide reference panel of 278 present‐day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE,D‐statistics, PCA, t‐SNE, and UMAP. ResultsWe find largely similar population structures in ancient and present‐day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present‐day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample. DiscussionOverall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level. 

e-Print: arXiv:1902.03808 [hep-lat]