Abstract
Founder analysis is a sophisticated application of phylogeographic analysis. It comprises the estimation of timing and impact of migrations in current populations by taking advantage of the non-recombining property of certain marker systems (in the first instance, mitochondrial DNA) and therefore the possibility of building realistic phylogenetic trees. Given two populations, a source and a sink, and an assumed direction of migration between them, we can identify founder haplotypes, date the founder clusters deriving from them, and also estimate the proportions of lineages in each migration event. Despite being a methodology dating back nearly two decades and having been featured in numerous research articles, its use has mostly been restricted to a handful of research groups due to the cumbersome and time-consuming calculations it entails, a hindrance which stems not only from the often prohibitively large volume of data being dealt with but also the intricacies involved in the detection of founders. We have developed a Python-based tool with a user-friendly interface in response to these issues, providing a fast, automatized approach to the founder analysis pipeline and additional useful features within this context, expediting this step efficiently and allowing more hypotheses to be tested in a reliable and easily reproducible manner.
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Acknowledgements
D.V., P.S. and M.B.R. acknowledge FCT support through project PTDC/EPH-ARQ/4164/2014 partially funded by FEDER funds (COMPETE 2020 project 016899). PS is supported by FCT, European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme and acknowledges CBMA strategic programme UID/BIA/04050/2019 funded by national funds through the FCT I.P. M.B.R. received support from a Leverhulme Trust Doctoral Scholarship programme.
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Vieira, D., Almeida, M., Richards, M.B., Soares, P. (2020). An Efficient and User-Friendly Implementation of the Founder Analysis Methodology. In: Fdez-Riverola, F., Rocha, M., Mohamad, M., Zaki, N., Castellanos-Garzón, J. (eds) Practical Applications of Computational Biology and Bioinformatics, 13th International Conference. PACBB 2019. Advances in Intelligent Systems and Computing, vol 1005 . Springer, Cham. https://doi.org/10.1007/978-3-030-23873-5_15
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DOI: https://doi.org/10.1007/978-3-030-23873-5_15
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