An Efficient and User-Friendly Implementation of the Founder Analysis Methodology

Daniel Vieira, Mafalda Almeida, Martin B. Richards, Pedro Soares

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

LanguageEnglish
Title of host publicationPractical Applications of Computational Biology and Bioinformatics
Subtitle of host publication13th International Conference, PACBB 2019
EditorsMohd Saberi Mohamad, Nazar Zaki, José A. Castellanos-Garzón, Florentino Fdez-Riverola, Miguel Rocha
PublisherSpringer Verlag
Pages121-128
Number of pages8
ISBN (Print)9783030238728
DOIs
Publication statusPublished - 22 Jun 2019
Event13th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2019 - Ávila, Spain
Duration: 26 Jun 201928 Jun 2019

Publication series

NameAdvances in Intelligent Systems and Computing
Volume1005
ISSN (Print)2194-5357

Conference

Conference13th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2019
CountrySpain
CityÁvila
Period26/06/1928/06/19

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User interfaces
DNA
Pipelines

Cite this

Vieira, D., Almeida, M., Richards, M. B., & Soares, P. (2019). An Efficient and User-Friendly Implementation of the Founder Analysis Methodology. In M. S. Mohamad, N. Zaki, J. A. Castellanos-Garzón, F. Fdez-Riverola, & M. Rocha (Eds.), Practical Applications of Computational Biology and Bioinformatics: 13th International Conference, PACBB 2019 (pp. 121-128). (Advances in Intelligent Systems and Computing; Vol. 1005). Springer Verlag. https://doi.org/10.1007/978-3-030-23873-5_15
Vieira, Daniel ; Almeida, Mafalda ; Richards, Martin B. ; Soares, Pedro. / An Efficient and User-Friendly Implementation of the Founder Analysis Methodology. Practical Applications of Computational Biology and Bioinformatics: 13th International Conference, PACBB 2019. editor / Mohd Saberi Mohamad ; Nazar Zaki ; José A. Castellanos-Garzón ; Florentino Fdez-Riverola ; Miguel Rocha. Springer Verlag, 2019. pp. 121-128 (Advances in Intelligent Systems and Computing).
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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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Vieira, D, Almeida, M, Richards, MB & Soares, P 2019, An Efficient and User-Friendly Implementation of the Founder Analysis Methodology. in MS Mohamad, N Zaki, JA Castellanos-Garzón, F Fdez-Riverola & M Rocha (eds), Practical Applications of Computational Biology and Bioinformatics: 13th International Conference, PACBB 2019. Advances in Intelligent Systems and Computing, vol. 1005, Springer Verlag, pp. 121-128, 13th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2019, Ávila, Spain, 26/06/19. https://doi.org/10.1007/978-3-030-23873-5_15

An Efficient and User-Friendly Implementation of the Founder Analysis Methodology. / Vieira, Daniel; Almeida, Mafalda; Richards, Martin B.; Soares, Pedro.

Practical Applications of Computational Biology and Bioinformatics: 13th International Conference, PACBB 2019. ed. / Mohd Saberi Mohamad; Nazar Zaki; José A. Castellanos-Garzón; Florentino Fdez-Riverola; Miguel Rocha. Springer Verlag, 2019. p. 121-128 (Advances in Intelligent Systems and Computing; Vol. 1005).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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AU - Almeida, Mafalda

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Y1 - 2019/6/22

N2 - 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.

AB - 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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BT - Practical Applications of Computational Biology and Bioinformatics

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A2 - Zaki, Nazar

A2 - Castellanos-Garzón, José A.

A2 - Fdez-Riverola, Florentino

A2 - Rocha, Miguel

PB - Springer Verlag

ER -

Vieira D, Almeida M, Richards MB, Soares P. An Efficient and User-Friendly Implementation of the Founder Analysis Methodology. In Mohamad MS, Zaki N, Castellanos-Garzón JA, Fdez-Riverola F, Rocha M, editors, Practical Applications of Computational Biology and Bioinformatics: 13th International Conference, PACBB 2019. Springer Verlag. 2019. p. 121-128. (Advances in Intelligent Systems and Computing). https://doi.org/10.1007/978-3-030-23873-5_15