DOI: 10.5061/dryad.3cb25
title: Data from: A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets

description: Multilocus sequence data provide far greater power to resolve species
 limits than the single locus data typically used for broad surveys of
 clades. However, current statistical methods based on a multispecies
 coalescent framework are computationally demanding, because of the number
 of possible delimitations that must be compared and time-consuming
 likelihood calculations. New methods are therefore needed to open up the
 power of multilocus approaches to larger systematic surveys. Here, we
 present a rapid and scalable method that introduces 2 new innovations.
 First, the method reduces the complexity of likelihood calculations by
 decomposing the tree into rooted triplets. The distribution of topologies
 for a triplet across multiple loci has a uniform trinomial distribution
 when the 3 individuals belong to the same species, but a skewed
 distribution if they belong to separate species with a form that is
 specified by the multispecies coalescent. A Bayesian model comparison
 framework was developed and the best delimitation found by comparing the
 product of posterior probabilities of all triplets. The second innovation
 is a new dynamic programming algorithm for finding the optimum
 delimitation from all those compatible with a guide tree by successively
 analyzing subtrees defined by each node. This algorithm removes the need
 for heuristic searches used by current methods, and guarantees that the
 best solution is found and potentially could be used in other systematic
 applications. We assessed the performance of the method with simulated,
 published, and newly generated data. Analyses of simulated data
 demonstrate that the combined method has favorable statistical properties
 and scalability with increasing sample sizes. Analyses of empirical data
 from both eukaryotes and prokaryotes demonstrate its potential for
 delimiting species in real cases.
description: Supplementary
 figuresSupplementary figures
 for Fujisawa et al. 2016SupplementaryFigures.pdfSupplementary text S1Online appendix for Fujisawa et al. 2016. Supplementary text S1.SupplementaryTextS1_rev160202.docxAlignments of BacillusSequence alignments of seven house keeping genes of Bacillus isolates in Nexus format.bacillus.alignments.zipBeast MCC trees of BacillusBeast MCC trees of seven house keeping genes of Bacillus isolatesbacillus.7hk.MCC.treClonalframe consensus tree of BacillusClonalframe consensus tree build with seven house keeping genes of Bacillus isolatesbacillus.clonalframe.consensus.treThree speices simulationsSimulated gene trees for three species simulations. Twenty five loci are interleaved as line1-locus1, line2-locus2, ... line26-locus1, ...sim3sp_25loci.zipTen species simulation (Simulation A&B)Simulated gene trees for ten species simulations. Forty loci are interleaved.sim10sp.40loci.zipTen species simulation (simulation C)Gene trees reconstructed from simulated sequences. Forty loci are interleaved.sim10sp.40loci.simulationC.ziptr2-delimitation bitbucket repositoryA link to the bitbucket repository of tr2-delimitation. The revision number 133 is the version of tr2 used for the simulation and empirical studies in Fujisawa et al. 2016.