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Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.
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This content will become publicly available on November 5, 2026
A Genomic Perspective on Species Delimitation
Genomic species delimitation is transforming how we understand and define species by enabling a process-oriented and efficient approach to identifying species boundaries. This review outlines the two key steps in genomic species delimitation: (a) discovering species-level units and (b) assessing their validity. Validity can be evaluated by a diversity of approaches, including applying the multispecies coalescent to delineate the population–species boundary and using estimated gene flow as a proxy for reproductive isolation. We illustrate the utility of these methods across the tree of life through a comprehensive review of published articles and case studies on birds, siphonophores, and bacteria. Despite the many benefits of genomic species delimitation, challenges remain. In particular, genomic divergence does not always accurately reflect ecological divergence and reproductive barriers, and genome heterogeneity can complicate the overall understanding of genetic divergence. We discuss these challenges and potential solutions.
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- Award ID(s):
- 2023723
- PAR ID:
- 10652237
- Publisher / Repository:
- AREES
- Date Published:
- Journal Name:
- Annual Review of Ecology, Evolution, and Systematics
- Volume:
- 56
- Issue:
- 1
- ISSN:
- 1543-592X
- Page Range / eLocation ID:
- 467 to 489
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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