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Developing ancestry informative marker panel for Nigeria-Cameroonian chimpanzees

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Abstract

Chimpanzees (Pan troglodytes), with a dwindling population size, are distributed across sub-Saharan Africa. They are classified into two biogeographical clusters comprising of four subspecies: a western African cluster that includes P. t. verus and P. t. ellioti and a central/eastern African cluster that includes P. t. troglodytes and P. t. schweinfurthii. While the genetic distinctness of Nigeria-Cameroonian chimpanzees (P. t. ellioti) from western chimpanzees has been known for a while, the fine structures within P. t. ellioti population has remained under-studied. In this study, we developed the first ever ancestry informative marker (AIMs) panel that can detect the fine population structure within Nigeria-Cameroonian chimpanzees with high resolution. We compared four commonly used AIMs-determining strategies, namely Infocalc algorithm, Wright’s FST, smart principal component analysis (SmartPCA) and ADMIXTURE to first identify the best approach and then developed an AIMs panel of 435 SNPs employing the consensus of the four approaches (n = 129), with additional supplements from the best two approaches (Infocalc and ADMIXTURE). To the best of our knowledge, we have developed the first-ever AIMs panel for chimpanzees, which can greatly aid in their planned reintroduction to the natural habitat, maintaining their genetic integrity through planned captive breeding, and in tracking illegal trading across the globe.

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Authors and Affiliations

  1. Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India

    S. Anjana & Sai Pradivya Sammeta

  2. Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575 018, India

    Ranajit Das

Authors
  1. S. Anjana
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  2. Sai Pradivya Sammeta
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  3. Ranajit Das
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Corresponding author

Correspondence to Ranajit Das.

Additional information

Corresponding editor: H. A. Ranganath

Conceptualization and methodology, R. Das. Software, R. Das and S. Anjana. Formal analysis, S. Anjana and S. Pradivya. Investigation, S. Anjana and S. Pradivya. Resources, R. Das. Data curation, S. Anjana and R. Das. Writing – original draft preparation, S. Anjana and S. Pradivya. Writing – review and editing, R. Das. Visualization, R. Das and S. Anjana. Supervision, R. Das. Project administration, R. Das. Funding acquisition, R. Das.

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Anjana, S., Sammeta, S.P. & Das, R. Developing ancestry informative marker panel for Nigeria-Cameroonian chimpanzees. J Genet 99, 39 (2020). https://doi.org/10.1007/s12041-020-01192-z

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  • DOI: https://doi.org/10.1007/s12041-020-01192-z

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