Species Delimitation Methods in Molecular Taxonomy

Molecular taxonomy leverages DNA sequence data to delineate species as independently evolving lineages, moving beyond purely morphological criteria. Distance-based methods group sequences into operational taxonomic units (OTUs) using fixed similarity thresholds, offering rapid proxies for species richness but risking over‐ or under‐splitting when arbitrary cut-offs misalign with true divergence. Coalescent-informed approaches infer species boundaries by fitting models of lineage branching to phylogenetic trees: the Generalized Mixed Yule-Coalescent (GMYC) model detects the transition from between-species (Yule) to within-species (coalescent) branching rates, while Poisson Tree Processes (PTP) and its multi-rate extensions estimate species limits directly from substitution rates on non-ultrametric trees. Assembly algorithms such as Automatic Barcode Gap Discovery (ABGD) and ASAP partition sequence datasets by identifying empirical gaps in genetic distances. Integrative workflows combine single-locus delimitations with multilocus data, cytological or morphological evidence, and biogeographical patterns to resolve cryptic or polyploid complexes. High-throughput and environmental DNA surveys now apply these methods at unprecedented scales, informing biodiversity inventories, conservation priorities and the management of disease-vector species. Persistent challenges include calibrating barcoding gaps across taxa, accommodating heterogeneity in population structure, and reconciling outputs from diverse algorithms. Best practice emphasises transparent threshold choice, rigorous phylogenetic reconstruction and the complementary application of coalescent and distance-based methods to underpin robust species hypotheses.

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Species Delimitation Methods in Molecular Taxonomy publication trend

The graph below shows the total number of articles in species delimitation methods in molecular taxonomy across all publications each year (not limited to Nature Index journals).

Technical terms

DNA barcoding: Use of a standard gene region (often mitochondrial COI) to assign specimens to species or OTUs based on sequence similarity.

Operational Taxonomic Unit (OTU): A proxy for a species defined by clustering sequences above a similarity threshold.

Barcoding gap: A distinct difference between maximum intraspecific and minimum interspecific genetic distances used to delimit species.

Generalized Mixed Yule-Coalescent (GMYC): A coalescent-based method that partitions ultrametric gene trees into between- and within-species branching regimes.

Poisson Tree Processes (PTP): A phylogeny-aware delimitation approach inferring species limits from branch length distributions on non-ultrametric trees.

ASAP (Assemble Species by Automatic Partitioning): A clustering algorithm that identifies barcode gaps in pairwise distance matrices to propose species partitions.

References

1. DNA barcoding as a valuable tool for delimiting mollusk species of the genus Biomphalaria Preston, 1910 (Gastropoda: Planorbidae). Frontiers in Cellular and Infection Microbiology (2023).
2. Limitations of 18S rDNA Sequence in Species-Level Classification of Dictyostelids. Microorganisms (2025).
3. Species Delimitation in a Polyploid Group of Iberian Jasione (Campanulaceae) Unveils Coherence between Cryptic Speciation and Biogeographical Regionalization. Plants (2023).
4. Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets. Systematic Biology (2013).
5. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics (2017).
6. Effects of phylogenetic reconstruction method on the robustness of species delimitation using single‐locus data. Methods in Ecology and Evolution (2014).