palaeo

BEAST2 tip-date operators for fossil sites and stratigraphic sequences. This BEAST 2 package provides MCMC proposals for fossil sites, in particular it allows sampling of tip dates while keeping fossils from the same site at the same age. It also allows correct ordering of fossil sites within a sequence, while still allowing them to have overlapping age uncertainty ranges.

This package is associated with the following publication: King, B. and Rücklin, M. (2020). Tip dating with fossil sites and stratigraphic sequences. PeerJ 8:e9368.

A tutorial for this package can be found here.

Installing package manually

Ensure dependencies (beast2, BeastLabs and SA) are installed, at least beast2.v2.6.0 and SA.v2.0.2. Download the zip file from releases. Copy this zip file to the BEAST addon directory in your computer and unzip it. To find out where the addon directory is, open beauti, File - manage packages, click on the question mark in the bottom right corner. You may also need to clear the beast class path. This is possible in the file menu of beauti.

Building package from source

Ensure Apache Ant is installed. To build this package from source, download the source code and unzip the folder. In terminal, navigate to the archive and type "ant" This will create a "dist" folder inside the archive, within which is a zip file containing the package. Then install this folder manually as above. You may need to build the dependencies (beast2, BeastLabs and SA) from source first.

Archive Contents

• README.md : this file
• build.xml : Ant build script
• /examples : Example beast2 xml files
• /src : source files. See below for details.
• version.xml : BEAST package version file.
• /R_xml_tools : An R function for producing xml blocks with operators from tables of fossil site occurences. Includes example templates
• /tutorial : A tutorial for how to use this package.
• /results : Analysis scripts and results for the manuscript describing the package.

The Java packages in the palaeo BEAST2 package are:

beast.evolution.operators

• 'FossilSiteDateRandomWalker' - An operator that takes a list of taxa from a single site or layer, and a range of ages. All taxa in the taxon list will be assigned the same age with each move. Can take sampled ancestor or offset trees
• 'RelativeFossilSiteDateRandomWalker' - An extension of FossilSiteDateRandomWalker that allows fossil sites to be ordered relative to each other, while having overlapping possible age ranges. This is useful where dates are only known for the top and bottom of a stratigraphic sequence, and fossils are known from multiple layers within this sequence. the 'taxonbelow' input is a taxon from an older layer, while the 'taxonabove' input is from a younger layer. This operator should always be used in reciprocal pairs i.e. a younger and an older fossil site with reciprocal 'taxonbelow' and 'taxonabove' inputs. Middle layers, when there is more than two, can have both inputs

beast.evolution.tree

• 'FossilSiteSamplingDate' - Sampling dates, an input class for the operators. Same as SamplingDate but without the requirement of a taxon input

beast.math.distributions

• 'RelativeAgePrior' - An alternative method for ordering the ages of taxa. Takes a 'younger' and 'older' input. Use of RelativeFossilSiteDateRandomWalker is probably advised instead, as it runs faster and is more flexible