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IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count

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Abstract

We propose an extension of the distance matrix methods NJst and ASTRID to infer species trees from incongruent gene trees having Incomplete Lineage Sorting. Both approaches consider the average internode distance (ID) between individual taxa pairs as the distance measure. The measure ID does not use the root of a tree, and thus may not always infer the relative position of a taxon with respect to the root. We define a novel distance measure excess gene leaf count (XL) between individual couplets. The XL measure is computed using the root of a tree. It is proved to be additive, and is shown to infer the relative order of divergence among individual couplets better. We propose a novel method IDXL which uses both the XL and ID measures for species tree construction. IDXL is shown to perform better than NJst and other distance matrix approaches for most of the biological and simulated datasets. Having the same computational complexity as NJst, IDXL can be applied for species tree inference on large-scale biological datasets.

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Notes

  1. Statistical consistency means that as the number of error-free gene trees approaches infinity, the method recovers the correct species tree with high probability.

  2. details of this dataset is discussed in “Experimental Results” section.

  3. Here K denotes \(10^3,\) and M denotes \(10^6.\)

  4. Values inside the third bracket and separated by ‘/,’ denote multiple model conditions.

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Acknowledgements

The first author acknowledges Tata Consultancy Services (TCS) for providing the research scholarship. We acknowledge the anonymous reviewers for their insightful comments and suggestions towards improvement of this work.

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  1. Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India

    Sourya Bhattacharyya & Jayanta Mukherjee

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  1. Sourya Bhattacharyya
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Correspondence to Sourya Bhattacharyya.

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Bhattacharyya, S., Mukherjee, J. IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count. J Mol Evol 85, 57–78 (2017). https://doi.org/10.1007/s00239-017-9807-7

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