Phylodynamic analysis of an emergent Mycobacterium bovis outbreak in an area with no previously known wildlife infections

1. Understanding how an emergent pathogen successfully establishes itself and persists in a previously unaffected population is a crucial problem in disease ecology, with important implications for disease management. In multi-host pathogen systems this problem is particularly difficult, as the importance of each host species to transmission is often poorly characterised, and the disease epidemiology is complex. Opportunities to observe and analyse such emergent scenarios are few. 2. Here, we exploit a unique dataset combining densely-collected data on the epidemiological and evolutionary characteristics of an outbreak of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) in a population of cattle and badgers in an area considered low-risk for bTB, with no previous record of either persistent infection in cattle, or of any infection in wildlife. We analyse the outbreak dynamics using a combination of mathematical modelling, Bayesian evolutionary analyses, and machine learning. 3. Comparison to M. bovis whole-genome sequences from Northern Ireland confirmed this to be a single introduction of the pathogen from the latter region, with evolutionary analysis supporting an introduction directly into the local cattle population six years prior to its first discovery in badgers. 4. Once introduced, the evidence supports M. bovis epidemiological dynamics passing through two phases, the first dominated by cattle-to-cattle transmission before becoming established in the local badger population. 5. Synthesis and applications. The raw data object of this analysis were used to support decisions regarding the control of a M. bovis emergent outbreak, of considerable concern because of the geographical distance from previously known high-risk areas. Our further analyses, estimating the time of introduction (and therefore the likely magnitude of any hidden outbreak) and the rates of cross-species transmission, provided valuable confirmation that the extent and focus of the imposed controls were appropriate. Not only these findings strengthen the call for genomic surveillance, but they also pave the path for future outbreaks control, providing insights for more rapid and decisive evidence-based decision-making. As the methods we used and developed are agnostic to the disease itself, they are also valuable for other slowly transmitting pathogens

Influence of handaxe size and shape on cutting efficiency: a large-scale experiment and morphometric analysis

Handaxes represent one of the most temporally enduring and geographically widespread of Palaeolithic artifacts and thus comprised a key technological strategy of many hominin populations. Archaeologically observable variation in the size (i.e., mass) and shape properties of handaxes has been frequently noted. It is logical to ask whether some of this variability may have had functional implications. Here, we report the results of a large-scale (n = 500 handaxes) experiment designed to examine the influence of variation in handaxe size and shape on cutting efficiency rates during a laboratory task. We used a comprehensive dataset of morphometric (size-adjusted) shape variables and statistical methods (including multivariate methods) to address this issue. Our first set of analyses focused on handaxe mass/size variability. This analysis demonstrated that, at a broad-scale level of variation, handaxe mass may have been free to vary independently of functional (cutting) efficiency. Our analysis also, however, identified that there will be a task-specific threshold in terms of functional effectiveness at the lower end of handaxe mass variation. This implies that hominins may have targeted design forms to meet minimal (task-specific) thresholds, and may also have managed handaxe reduction and discard in respect to such factors. Our second set of analyses focused on handaxe shape variability. This analysis also indicated that considerable variation in handaxe shape may occur independently of any strong effect on cutting efficiency. We discuss how these results have several implications for considerations of handaxe variation in the archaeological record. At a general level, our results demonstrate that variability within and between handaxe assemblages in terms of their size and shape properties will not necessarily have had immediate or strong impact on their effectiveness when used for cutting, and that such variability may have been related to factors other than functional issues