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1. A Genomic Perspective on Species Delimitation

   https://doi.org/10.1146/annurev-ecolsys-102723-055311  

   Singhal, Sonal; Leaché, Adam D; Fujita, Matthew K; Cadena, Carlos Daniel; Zapata, Felipe (November 2025, Annual Review of Ecology, Evolution, and Systematics)

   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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2. Incorporating the speciation process into species delimitation

   https://doi.org/doi.org/10.1371/journal.pcbi.1008924  

   Sukumaran, Jeet (May 2021, PLoS computational biology)

   Barraclough, Timothy G. (Ed.)

   The “multispecies” coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself. 

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3. SODA: multi-locus species delimitation using quartet frequencies

   https://doi.org/10.1093/bioinformatics/btaa1010  

   Rabiee, Maryam; Mirarab, Siavash (December 2020, Bioinformatics)

   Ponty, Yann (Ed.)

   Abstract Motivation Species delimitation, the process of deciding how to group a set of organisms into units called species, is one of the most challenging problems in computational evolutionary biology. While many methods exist for species delimitation, most based on the coalescent theory, few are scalable to very large datasets, and methods that scale tend to be not accurate. Species delimitation is closely related to species tree inference from discordant gene trees, a problem that has enjoyed rapid advances in recent years. Results In this article, we build on the accuracy and scalability of recent quartet-based methods for species tree estimation and propose a new method called SODA for species delimitation. SODA relies heavily on a recently developed method for testing zero branch length in species trees. In extensive simulations, we show that SODA can easily scale to very large datasets while maintaining high accuracy. Availability and implementation The code and data presented here are available on https://github.com/maryamrabiee/SODA. Supplementary information Supplementary data are available at Bioinformatics online. 

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4. Species Delimitation of Eastern Pinesnake Complex (Pituophis melanoleucus)

   https://doi.org/10.18061/bssb.v2i1.9423  

   Khakurel, Basanta; Nikolakis, Zachary L; Crother, Brian I; Wright, April (July 2023, Bulletin of the Society of Systematic Biologists)

   Carstens, Bryan (Ed.)

   The eastern Pinesnake (Pituophis melanoleucus) is found throughout eastern United States. Taxonomy in this group has been controversial with several conflicting species designations. Three subspecies of the eastern Pinesnake have prevailed in the literature to their geographic locations and scale coloration: the northern Pinesnake (P. m. melanoleucus), the Florida Pinesnake (P. m. mugitus), and the Black Pinesnake (P. m. lodingi). Within the region, there are several major barriers to dispersal, particularly major river drainage systems and human modification of the longleaf pine habitat. Consistently, a lack of phylogenetic resolution has plagued these taxa in prior studies. The goal of this study was to examine the taxonomic validity of the eastern Pinesnake complex using single nucleotide polymorphisms (SNPs) isolated from ultra-conserved elements (UCEs) in phylogenetic and population genetic approaches. Molecular species delimitation approaches indicated that the population of eastern Pinesnake exhibits population structure across its range that may rise to the level of being new species. 

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5. A Review of Taxonomic Concepts and Species Delimitation in Cycadales

   https://doi.org/10.1007/s12229-023-09293-x  

   Martínez-Domínguez, Lilí; Nicolalde-Morejón, Fernando; Vergara-Silva, Francisco; Stevenson, Dennis Wm. (November 2023, The Botanical Review)

   Abstract Taxonomic data is essential to advance the discovery and description of biodiversity, as well as the study of evolutionary processes. Emerging large-scale datasets and new methods of analysis have provided different approaches to describe biodiversity. Here, we present a review of the taxonomic history in Cycadales including an analysis of historical taxonomic concepts and approaches used for species delimitation. We examine the trends in the publication of new species following taxonomic works in books, journals and horticultural catalogues, monographic projects and floras where species treatments were published. In addition, we review the studies concerning species delimitations using the literature available in scientific journals appearing in the database ISI Web of Knowledge. The approaches used were discussed throughout all research focused on empirical and theoretical considerations in each study. We review the current state of the studies on causal processes that have given rise to the currently recognized diversity. The trend shows that taxonomic work on discovery and description of species has been intensive in the last 40 years culminating in 38.8% of binomials published. As a result, we consider the relevance of the monographs and floras for identification of species for other biological disciplines and the content of these contributions is compared and discussed. A total of six criteria (diagnosability, phenetic, phylogenetic, genotypic cluster, niche specialization and coalescent) were detected from the following three approaches to species delimitation within Cycadales: traditional, integrative taxonomy, and monophyletic. In all cases, the results from these species delimitations not only provided a taxonomic treatment or proposed a new species, but also supposedly clarified the other species involved as a result of the new taxonomic concept of the new species described. Most investigations of species delimitation used the traditional approach or a phenetic criteria. Finally, we discuss evolutionary studies on causal processes involved in cycad diversity. This is considered in the context of species delimitation as hypothesis testing for a successful evaluation of variation in both genetic and morphological understanding. 

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