Abstract
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
Highlights
During the last 15 years, following the success of the DNA-barcoding projects and the increase in sequencing capacities, many methods of species delimitation based on DNA sequences have been developed
We describe a new method of species delimitation, still based on pairwise genetic distances, but which implementation provides a score for each defined partition and overcomes the challenge of a priori defining P
We first report the number of species predicted in the partition with the best asapscore (ASAP 1st): we found that in 4/10 of the datasets, the partition with the best asap-score is very close to the reference one and that 8/10 is close
Summary
During the last 15 years, following the success of the DNA-barcoding projects and the increase in sequencing capacities, many methods of species delimitation based on DNA sequences have been developed. 2014) and BFD (Leaché, Fujita, Minin, & Bouckaert, 2014), reviewed (with other methods) in several articles (Camargo & Sites, 2013; Carstens, Pelletier, Reid, & Satler, 2013; Fujita, Leaché, Burbrink, McGuire, & Moritz, 2012; Leavitt, Moreau, & Lumbsch, 2015; Rannala, 2015). They were designed for multilocus data and are computationally (extremely) demanding. They have been mainly applied to datasets with limited number of sequences and species, and to well-studied groups, for which competing partitions of species have been proposed in the literature; they generally correspond to species complexes, typically in the grey zone (De Queiroz, 2005)
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