Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.

P Kapli,K Kobert,A Stamatakis,S Lutteropp,P Pavlidis,T Flouri,J Zhang,Alfonso Valencia

doi:10.1093/bioinformatics/btx025

Abstract

MotivationIn recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced “Poisson Tree Processes” (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences.ResultsWe introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size.Availability and ImplementationmPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

Species are fundamental units of life and form the most common basis of comparison in evolutionary studies
The novel multi-rate PTP (mPTP) method delimited a total of 1190 species which is the closest to the total number of taxonomic species (1041)
We presented mPTP, a novel approach for single-locus delimitation that consistently provides faster and more accurate species estimates than Poisson Tree Processes” (PTP) and other popular delimitation methods

Summary

Introduction

Species are fundamental units of life and form the most common basis of comparison in evolutionary studies. In line with the species concept of De Queiroz (2007) and the integrative taxonomy approach (Dayrat, 2005), a reliable identification of a new species involves data from multiple sources (e.g., ecology, morphology, evolutionary history) Such an approach is necessary for meticulous comparative evolutionary studies but is tremendously difficult to apply, if at all possible, in large biodiversity studies (e.g., vast barcoding, environmental, microbial samples). In such studies, researchers use alternative units of comparison that are easier to delimit [Molecular Operational Taxonomic Units (Blaxter et al, 2005), Recognizable Taxonomic Units (Oliver and Beattie, 1993)] rather than going through the cumbersome task of delimiting and describing full species. They are practical for biodiversity and b-diversity estimates (Valentini et al, 2009)

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Discussion

Conclusion