Phylogenetic trees are crucial to many aspects of taxonomic and comparative biology. Many researchers have adopted Bayesian methods to estimate their phylogenetic trees. In this family of methods, a model of morphological evolution is assumed to have generated the data observed by the researcher. These models make a variety of assumptions about the evolution of morphological characters, and these assumptions are translated into mathematics as parameters. The incorporation of prior distributions further allows researchers to quantify their prior beliefs about the value any one parameter can take. How to translate biological knowledge into mathematical language is difficult, and can be confusing to many biologists.This review aims to help systematics researchers understand the biological meaning of common models and assumptions. Using examples from the insect fossil record, I will demonstrate empirically what assumptions mean in concrete terms, and discuss how researchers can use and understand Bayesian methods for phylogenetic estimation.

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

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Fault scarps and uplifted terraces in young alluvium are frequent occurrences along the trace of the northerly dipping Himalayan frontal thrust (HFT). Generally, it was expected that the 25 April 2015 M 7.8 Gorkha earthquake of Nepal would produce fresh scarps along the fault trace. Contrary to expectation, Interferometric Synthetic Aperture Radar and aftershock studies soon indicated the rupture of the HFT was confined to the subsurface, terminating on the order of 50 km north of the trace of the HFT. We undertook a field survey along the trace of the HFT and along faults and lineaments within the Kathmandu Valley eight days after the earthquake. Our field survey confirmed the lack of surface rupture along the HFT and the mapped faults and lineaments in Kathmandu Valley. The only significant ground deformation we observed was limited to an similar to 1-km-long northeast-trending fracture set in the district of Kausaltar within Kathmandu. This feature is interpreted not to be the result of tectonic displacement, but rather a localized extension along a ridge. Our survey also shows the ubiquitous presence of fallen chimneys of brick kilns along the HFT and within the Kathmandu Valley. Measurements of a small subset of fallen chimneys across the region suggest a degree of systematic fall direction of the chimneys when subdivided geographically. Online Material: Color versions of Figures 3 and 4; additional photographs of the Kausaltar fracture.