A performance study of the impact of recombination on species tree analysis.

Zhiwei Wang,Kevin J Liu

doi:10.1186/s12864-016-3104-5

Abstract

BackgroundThe most widely used state-of-the-art methods for reconstructing species phylogenies from genomic sequence data assume that sampled loci are identically and independently distributed. In principle, free recombination between loci and a lack of intra-locus recombination are necessary to satisfy this assumption. Few studies have quantified the practical impact of recombination on species tree inference methods, and even fewer have used genomic sequence data for this purpose. One prominent exception is the 2012 study of Lanier and Knowles. A main finding from the study was that species tree inference methods are relatively robust to intra-locus recombination, assuming free recombination between loci. The latter assumption means that the open question regarding the impact of recombination on species tree analysis is not fully resolved.ResultsThe goal of this study is to further investigate this open question. Using simulations based upon the multi-species coalescent-with-recombination model as well as empirical datasets, we compared common pipeline-based techniques for inferring species phylogenies. The simulation conditions included a range of dataset sizes and several choices for recombination rate which was either uniform across loci or incorporated recombination hotspots. We found that pipelines which explicitly utilize inferred recombination breakpoints to delineate recombination-free intervals result in greater accuracy compared to widely used alternatives that preprocess sequences based upon linkage disequilibrium decay. Furthermore, the use of a relatively simple approach for recombination breakpoint inference does not degrade the accuracy of downstream species tree inference compared to more accurate alternatives.ConclusionsOur findings clarify the impact of recombination upon current phylogenomic pipelines for species tree inference. Pipeline-based approaches which utilize inferred recombination breakpoints to densely sample loci across genomic sequences can tolerate intra-locus recombination and violations of the assumption of free recombination between loci.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3104-5) contains supplementary material, which is available to authorized users.

Highlights

The most widely used state-of-the-art methods for reconstructing species phylogenies from genomic sequence data assume that sampled loci are identically and independently distributed
We revisit the larger question captured by the title of the Lanier and Knowles study: “is recombination a problem for species tree analysis”? We focus in particular on the major open question regarding widely used phylogenomic inference pipelines and their use of various techniques to satisfy the assumption of free recombination between loci
Simulation study We began by comparing the topological accuracy of the linkage disequilibrium (LD)-based and breakpoint-based methods on model conditions which incorporated a range of recombination rates and dataset sizes

Summary

Introduction

The most widely used state-of-the-art methods for reconstructing species phylogenies from genomic sequence data assume that sampled loci are identically and independently distributed. Few studies have quantified the practical impact of recombination on species tree inference methods, and even fewer have used genomic sequence data for this purpose. A main finding from the study was that species tree inference methods are relatively robust to intra-locus recombination, assuming free recombination between loci. The latter assumption means that the open question regarding the impact of recombination on species tree analysis is not fully resolved. One of the main conclusions was that violations of the assumption of zero intra-locus recombination was of secondary concern in terms of species tree inference accuracy, assuming free recombination between loci. A gene tree is the phylogeny of a single locus.)

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