Heuristic optimization for global species clustering of DNA sequence data from multiple loci

Abstract

Summary1. Hierarchical clustering of molecular data is commonly used for estimation of species diversity in all forms of life. Parameters appropriate for species-level clustering are usually derived from reference data and applied for the delineation of sequences of unknown species membership, although it is not clear how this should be carried out in a multilocus scenario. 2. We introduce a novel means of concurrent clustering parameter optimization and delineation for multilocus data. A simulated annealing heuristic search is performed, whereby clustering thresholds are independently varied for each locus, but optimized according to the recovery of expected taxonomic species globally over loci. For each iteration of the search, one or more loci are randomly selected and a different threshold is separately proposed to cluster each, then the loci are linked to form global species units. Where the set of thresholds group the reference (species labelled) data with high taxonomic congruence, they are adopted for clustering of the subject (nonlabelled) sequences into global molecular operational taxonomic units (global MOTU). Four mined test data sets composed of both reference and subject sequences are combined with a newly sequenced three gene Apoidea data set, and subject to the proposed method. 3. Even optimizing four loci and thousands of sequences, the approach rapidly convergences on a set of parameters with maximal optimality score, although the method masks a high degree of incongruence, and does not always converge on a single set of thresholds. For example, of the 476 Apoidea sequences, 70 global MOTU were inferred over the heuristic search, although the number of single gene MOTU were much lower for the 28S RNA locus, and a range of equally optimal clustering thresholds were observed for the CytB gene. 4. We demonstrate the approach as a scalable species delineation solution for heterogeneous data sets composed of incompletely and inconsistently labelled data from public DNA data bases, for newly sequenced multilocus data, or both. The delineation over a heuristic search of clustering parameters facilitates the estimation of species diversity in multilocus data, giving species estimates that take into account uncertainty regarding choice of clustering thresholds.

Cryptic diversity, diversification and vicariance in two species complexes ofTomocerus(Collembola,Tomoceridae) fromChina

“…; Chesters et al . ). However, GMYC has been shown to perform favourably when compared with other single‐locus approaches particularly distance‐based methods (Fujisawa & Barraclough ; Zhang et al .…”

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

“…A multi-locus identification approach has not only been promoted as a standard barcoding method for difficult groups, such as plants ( 10 , 11 ), but also improved barcoding efficiencies in insects ( 12 ) and fungi ( 13 ), where a single-locus approach has been predominantly applied. A multi-locus system has been argued to deliver better taxonomic resolution in general ( 14 – 17 ). In addition to improving taxonomic delineation, a multi-locus approach can also alleviate false negatives caused by random missing of a given target gene caused by insufficient sequencing or DNA degradation.…”

“…Therefore, the acquisition of reference sequences for non-standard-barcode genes will greatly facilitate the expansion of the current single-gene barcoding approach by taking advantage of additional informative markers. Recent studies ( 15 , 17 ) have also discussed mechanisms in utilizing multiple markers in biodiversity analysis.…”

The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA

“…In summary, reliable molecular markers of stored-product psocids are urgently needed to accurately identify species, particularly when morphological approaches cannot be used, for example, for the identification of nymphs, males, super species, and specific geographical strains 28 . Multiple molecular markers would ultimately lead to a more accurate molecular diagnostic approach with a wide range of applications in practice 35 36 , including species identification, quarantine confirmation, international trade regulation, and pest control, i.e., assisting in the determination of the origins of infestations 25 .…”