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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #321730
Title: Topological Signatures for Population Admixture

Author
item PARIDA, LAXMI - Computational Biology Center, Ibm, Tj Watson Research
item UTRO, FILIPPO - Computational Biology Center, Ibm, Tj Watson Research
item YOROKOGLU, DENIZ - Computational Biology Center, Ibm, Tj Watson Research
item CARRIERI, A - Computational Biology Center, Ibm, Tj Watson Research
item Kuhn, David
item BASU, SAUGATA - Purdue University

Submitted to: Research Computational Molecular Biology (RECOMB)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/15/2015
Publication Date: 4/16/2015
Citation: Parida, L., Utro, F., Yorokoglu, D., Carrieri, A.P., Kuhn, D.N., Basu, S. 2015. Topological Signatures for Population Admixture. In: Przytycka, T. (eds). Research in Computational Molecular Biology RECOMB 2015. Lecture notes in computer science. Vol 9029, springer, Cham.
DOI: https://doi.org/10.1007/978-3-319-16706-0_27

Interpretive Summary: The Subtropical Horticulture Research Station in Miami, Florida houses living collections of tropical and subtropical fruit trees, such as avocado. These germplasm collections are resources for plant breeders, scientists studying fruit trees and nurseries hoping to expand their holdings to whom we distribute living plant material through our online request system (Germplasm Resource Information Network, http://www.ars-grin.gov/). It is not only important to understand the genetic diversity in our germplasm collection, but also the pedigree relationships among the accessions. Relatedness of populations is an interesting problem and has been studied extensively in the population genetics community. In the context of plant breeding and germplasm collections, this understanding is very important in gauging the diversity in the genetic pool and using it effectively in breeding programs. The algorithm presented in the paper is a significant advance in understanding relatedness

Technical Abstract: Topological Signatures for Population AdmixtureDeniz Yorukoglu1, Filippo Utro1, David Kuhn2, Saugata Basu3 and Laxmi Parida1* Abstract Background: As populations with multi-linear transmission (i.e., mixing of genetic material from two parents, say) evolve over generations, the genetic transmission lines constitute complicated networks. In contrast, uni-linear transmission leads to topologically simpler structures (trees). The genetic exchange in multi-linear transmission is further inuenced by migration,incubation, mixing and so on. The question we address in the paper is whether it is possible to tease apart subtle admixtures from the usual interrelationships of related populations. Methods: We present a combinatorial approach based on persistence in topology to detect admixture in populations. Results and Conclusions: We show, based on controlled simulations, that topological characteristics have the potential for detecting subtle admixture in related populations. We then apply the technique successfully to a set of avocado germplasm data indicating that the approach has the potential for novel characterizations of relatedness in populations. We believe that this approach also has the potential for not only detecting but also discriminating ancient from recent admixture. Keywords: topology; persistence; TDA; admixture; population genomics;avocado; germplasm