Ancient DNA, a Neolithic legging from the Swiss Alps and the early history of goat

Ancient DNA from a Neolithic legging (1st half of the 3rd millennium BC) found at Lenk, Schnidejoch (2750 m a.sl.) in the Swiss Alps has demonstrated, that modern distribution of genetic variation does not reflect past spatio-temporal signatures. The legging was made from the skin of a domestic goat (Capra hircus), belonging to the caprine haplogroup B1, which is marginal in Europe today, but represents a third highly diverse goat haplogroup entering Europe already in the Neolithic. Population expansion of lineage B therefore happened more than 4500 years ago, but their members were at some point almost completely replaced by goats of today's common A and C haplogroups.

gems: An R Package for Simulating from Disease Progression Models

Mathematical models of disease progression predict disease outcomes and are useful epidemiological tools for planners and evaluators of health interventions. The R package gems is a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome. Disease progression is represented by a series of events (e.g., diagnosis, treatment and death), displayed in a directed acyclic graph. The vertices correspond to disease states and the directed edges represent events. The package gems allows simulations based on a generalized multistate model that can be described by a directed acyclic graph with continuous transition-specific hazard functions. The user can specify an arbitrary hazard function and its parameters. The model includes parameter uncertainty, does not need to be a Markov model, and may take the history of previous events into account. Applications are not limited to the medical field and extend to other areas where multistate simulation is of interest. We provide a technical explanation of the multistate models used by gems, explain the functions of gems and their arguments, and show a sample application.

Ancient History as a Means of Transforming Colonial India in the Late-Eighteenth and Early-Nineteenth Centuries

This article focuses on the studies and discourses of mostly British scholars of the early colonial period belonging to two schools of thought. It shows how the studies of both schools – European orientalism and utilitarianism – were intricately connected to the political development of the emerging British paramountcy over the South Asian sub-continent, as both were looking for means of establishing and/or strengthening colonial rule. Nevertheless, the debate was not just a continuation of discussions in Europe. Whereas the ideas of the European Enlightenment had some influence, the transformation of the Mughal Empire and especially the idea of a decline of Muslim rule offered ample opportunities for understanding the early history of India either as some sort of “Golden Age,” as the orientalists and their indigenous supporters did, or as something static and degenerate, as the utilitarians did, and from which the population of sub-continent had to be saved by colonial rule and colonial values. Fearing the spread of the ideas of the French Revolution, the first group of British scholars sought to persuade the native elites of South Asia to take the lessons of their past for the future development of their homeland. Just as the classicists back in Europe, these scholars were convinced that large-scale explanations of the past could also teach political and moral lessons for the present although it was important to deal with the distant past in an empirical manner. The utilitarians on the other hand believed that India had to be saved from its own depravity through the English language and Western values, which amounted to nothing less than the modern transformation of the true Classical Age.

Comparison against 186 canid whole genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor.

Canine transmissible venereal tumor (CTVT) is a parasitic cancer clone that has propagated for thousands of years via sexual transfer of malignant cells. Little is understood about the mechanisms that converted an ancient tumor into the world's oldest known continuously propagating somatic cell lineage. We created the largest existing catalog of canine genome-wide variation and compared it against two CTVT genome sequences, thereby separating alleles derived from the founder's genome from somatic drivers of clonal transmissibility. We show that CTVT has undergone continuous adaptation to its transmissible allograft niche, with overlapping mutations at every step of immunosurveillance, particularly self-antigen presentation and apoptosis. We also identified chronologically early somatic mutations in oncogenesis- and immune-related genes that may represent key initiators of clonal transmissibility. Thus, we provide the first insights into the specific genomic aberrations that underlie CTVT's dogged perseverance in canids around the world.