mtDNAcombine: tools to combine sequences from multiple studies

Abstract

10Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. 11For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a 12 result, there is a large volume of mtDNA data available in these repositories for a wide range of 13 species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most 14 non-model organisms' classical markers such as mtDNA remain widely used. By compiling existing 15 data from multiple original studies, it is possible to build powerful new datasets capable of exploring 16 many questions in ecology, evolution and conservation biology. One key question that these data 17 can help inform is what happened in a species' demographic past. However, compiling data in this 18 manner is not trivial, there are many complexities associated with data extraction, data quality and 19 data handling. Here we present the mtDNAcombine package, a collection of tools developed to 20 manage some of the major decisions associated with handling multi-study sequence data with a 21 particular focus on preparing mtDNA data for Bayesian Skyline Plot demographic reconstructions. 22