An extended admixture pulse model reveals the limitations to human-Neandertal introgression dating

Neandertal DNA makes up 2–3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted

Composición de los agregados no dispersables de sedimentos pampeanos

Dispersion by conventional treatrnents for grain-size analysis do not work efficiently when used in Pampean sediments modified either by pedogenesis or groundwater circulation. Although aggregation decreases when free Fe oxides are removed, most of the sedirnent remains aggregated by a Si-Al rich cement which forms sand size nodules made up of smaller size particles. Total dispersion of samples is obtained with a 0,5 M NaOH dispersing agent on a hot plate. This produces the remo val of amorphous and poorly crystallized aluminosilicate cements. However, trus procedure is not generally used due lo lhe high alkali-sample ratio required. The origin of silica cement found in nodules is probably related to Si02 leaching during pedogenesis.Los sedimentos pampeanos que presentan rasgos paleopedológicos o reestructuración por acción ácuea son difíciles de dispersar con los tratamientos convencionales previos al análisis granulométrico. Con la remoción de los óxidos de hierro libre disminuye la agregación; no obstante, gran parte del material persiste aglutinado por un cemento rico en sílice y alúmina constituyendo verdaderos durinódulos; los mismos son de tamaño arena y engloban partículas de menor tamaño. Para obtener la dispersión total de las muestras es necesario aplicar un tratamiento con NaOH 0,5 M en caliente, con el cual se eliminan los cementantes amorfos o pobremente cristalinos de composición aluminosilicática; sin embargo, este método no es aplicable en forma rutinaria por la alta relación álcali! muestra requerida. La formación de estos durinódulos (agregados) se relacionaría con la lixiviación de sílice durante los procesos pedológicos sufridos por los materiales

Genetic insights into the social organization of Neanderthals

Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans1–8, but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave9,10 and 2 from Okladnikov Cave11—making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father–daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals’ genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone

Lymphangioma of the cervical esophagus associated with an inlet patch

Background: Lymphangiomas of the esophagus are extremely rare benign tumors of lymphatic origin. Localization in the proximal esophagus in association with an inlet patch and treatment by minimally invasive esophagectomy have not been reported. Case report: A 74-year-old woman with a 12-year history of multiple endoscopic dilatations was referred because of progressive dysphagia and aspiration. A 1.5-cm stricture of the cervical esophagus with a residual diameter of 5 mm was confirmed at endoscopy. Biopsies were negative for dysplasia/neoplasia. Results: Laparoscopic transhiatal esophagectomy with cervical esophagogastric anastomosis was successfully performed. Pathological examination of the surgical specimen demonstrated the presence of a lymphangioma. Interestingly, heterotopic gastric mucosa was present in the epithelium overlying the lymphangioma. Conclusions: Dysphagia was successfully relieved with a minimally invasive esophagectomy and lymphangioma of the cervical esophagus was found to be the cause of obstruction and aspiration in this patient, who was a non-responder to endoscopic dilatation. The inlet patch was an incidental finding unrelated to symptoms