Trends in Ecology & Evolution
OpinionCoalescent-based species delimitation in an integrative taxonomy
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Coalescent theory takes its place in species delimitation
Systematics is a vital discipline in biology that focuses on investigating the origins and causes of biological diversity. The species category is a fundamental unit in biology, and developing robust and highly replicable measures for identifying distinct evolutionary lineages is a central goal of species delimitation (see Glossary). Morphological data and approaches have necessarily dominated species delimitation for centuries, and the emergence of molecular and genomic data sets, together
Coalescent theory provides an opportunity to calculate the probability of speciation
The central aim of coalescent-based approaches is to identify independently evolving lineages, each representing a species. Until recently, species delimitation using molecular data relied on reciprocal monophyly or diagnostic states (e.g., fixed differences) as important criteria for identifying species [3]. Although a single locus can support these criteria, this is often not the case across multiple loci. Alternatively, coalescent-based species delimitation methods use probabilistic
Coalescent-based species delimitation as a component of integrative taxonomy
Coalescent-based species delimitation alone cannot fully illuminate all features of the lineage diversification process, which is a major goal of integrative taxonomy. In many instances, researchers first suspect that they have discovered new species by identifying divergences among individuals or groups using morphological or single-locus barcode data. In an integrative framework, further evidence is collected and analyzed to determine whether patterns of divergence are seen in different data
Species concepts have different criteria for delimiting species
A species is a hypothesis based on data that supports its evolutionary independence from other lineages. Coalescent-based species delimitation identifies independent evolutionary lineages and, as such, satisfies the criteria of several species concepts under the umbrella of the General Lineage Concept, such as the Evolutionary Species Concept (which equates to the BSC assuming no gene flow between species [38]). Subsequent to identification, systematists must name new species according to
Limitations of coalescent-based species delimitation: feasibility, assumptions, selection, and sampling
From a practical standpoint, coalescent-based species delimitation can be difficult for some researchers for whom collection of multilocus data is impractical. First, the method cannot be used for fossil taxa or taxa that lack suitable genetic resources. Second, collecting multilocus data can still be prohibitively expensive for some researchers, thereby preventing their adoption of coalescent methods. Unfortunately, this can be the case in regions that urgently need these methods, including
Concluding remarks
There have been tremendous advances in analytical methods to study speciation, species delimitation, and species relationships, many of which are founded on coalescent theory. Along with the ability to collect large multilocus data sets, researchers can implement coalescent models to identify the evolutionary processes that contribute to speciation. It is perhaps this framework that has fueled a sharpened focus of speciation studies that aim to understand the processes of lineage divergence [51]
Acknowledgement
The authors would like to thank the editor and two anonymous reviewers for their insightful comments that have improved the quality of this manuscript.
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