Species Delimitation

by

L. Lacey Knowles

• LAST REVIEWED: 12 January 2022
• LAST MODIFIED: 12 January 2022
• DOI: 10.1093/obo/9780199941728-0140

Introduction

Species delimitation is the process of determining whether a group of sampled individuals belong to the same species or to different species. The criteria used to delimit species differ across taxonomic groups, and the methods for delimiting species have changed over time, with a dramatic rise in the popularity of genomic approaches recently. Because inferred species boundaries have ramifications that extend beyond systematics, affecting all fields that rely upon species as a foundational unit, controversy has unsurprisingly surrounded not only the practices used to delimit species boundaries, but also the idea of what species are, which varies across taxa (e.g., the use of subspecies varies across the tree of life). This lack of consensus has no doubt contributed to the appeal of genetic-based delimitation. Specifically, genomic data can be collected from any taxon. Moreover, it can be analyzed in a common statistical framework (as popularized by the multispecies coalescent as a model for species delimitation). With the ease of collecting genetic data, the power of genomics, and the purported standardization for diagnosing species limits, genetic-based species delimitation is displacing traditional time-honored (albeit time-consuming) taxonomic practices of species diagnosis. It has also become an invaluable tool for discovering species in understudied groups, and genetic-based approaches are the foundation of international endeavors to generate a catalogue of DNA barcodes to illuminate biodiversity for all of life on the planet. Yet, genomic applications, and especially the sole reliance upon genetic data for inferring species boundaries, are not without their own set of challenges.

Overview, Textbooks and Journals

There are no textbooks on species delimitation per se. However, as a foundational unit in biology, chapters on both species and their formation can be found in any evolutionary biology texts, such as those that target undergraduate biology majors, as well as a recently published book on species (Barraclough 2019). Recent textbooks address the delimitation of species under different species concepts, describe the different processes involved in the formation of species (i.e., speciation), and include background on the process of gene lineage coalescence—a key concept applied in genetic-based delimitation of species, although these textbooks do not explicitly discuss gene lineage coalescence in the context of species delimitation (e.g., Bergstrom and Dugatkin 2016, Futuyma and Kirkpatrick 2017). These treatments provide a general overview, including the power of genomics, but do not address the reliability of inferences. It is not uncommon for discussions of species to center on their definition under a variety of different species concepts (Noor 1998), as opposed to their delimitation, with species delimitation classically viewed as a question for specialized taxonomists whose years of training provide a particular skillset to recognize and determine the traits that differentiated species. However, in the genomic era, and with the rise in popularity of models for delimiting species, the relevant background for teaching species delimitation now has more in common with texts describing population genetic and phylogenetic inference, topics that also have entire chapters dedicated to them in general evolutionary biology textbooks. Moreover, with recognition of commonalities across species concepts, as captured by the general lineage concept (de Queiroz 2007), species concepts now play less of a central role in discussions of species delimitation, although they arguably are implicit in the interpretation of genetic-based delimitation models (Sukumaran and Knowles 2017). Shifts in the practices for delimiting species have also spurred shifts in where such studies might be published. Classic treatments of species descriptions based on careful consideration of phenotypic differences (i.e., differences in morphological traits, behavior, and ecology) are published as monographs and journals dedicated to specific taxa. However, now it is not uncommon for the primary literature on species delimitation to be published in more general journals (see General Journals with Published Works on Species Delimitation), especially when the work addresses a common set of core challenges or general approaches for increasing the accuracy of inferred species boundaries using genomics. This broadening of publishing venues also reflects the expanded set of topics spanned by genetic-based species delimitation, including direct overlap with studies of speciation. Likewise, with the sophistication of approaches and the vast amounts of genomic data for delimiting species, computational and theoretical biologists now play an increasingly important role in advancing the field.

• Barraclough, T. G. 2019. The evolutionary biology of species. New York: Oxford Univ. Press.

  DOI: 10.1093/oso/9780198749745.001.0001

  This book provides a thorough overview of species as a fundamental unit of biology, their recognition, and the dynamics associated with their formation and history. In particular, chapter 2 discusses the nature of species, including the various complications with their definition (pp. 10–15). Chapter 3 summarizes both phenotypic and genetic evidence for species (pp. 20–25), and chapter 4 explains why there are species (pp. 25–30). 288 pp.

• Bergstrom, C. T., and L. A. Dugatkin. 2016. Evolution. New York: W. W. Norton.

  Chapter 8.2 (“Coalescent Theory and the Genealogy of Genes,” p. 272) summarizes why gene lineages coalesce and describes the dynamics of the coalescent process and how this process relates to observed patterns of genetic variation and divergence. Chapter 14.1 (“The Species Problem,” p. 490) discusses what a species is, summarizing different species concepts and how species are recognized under the different concepts, as well as how new species are formed (i.e., speciation).

• de Queiroz, K. 2007. Species concepts and species delimitation. Systematic Biology 56:879–886.

  DOI: 10.1080/10635150701701083

  A classic must-read on the controversies surrounding species delimitation. By emphasizing the distinction between the conceptualization of species versus methodologies to detect species, the paper highlights clear commonalities shared among species concepts. Specifically, a common theme, a unified species concept, shifts the emphasis away from debates about the definition of species as a category, toward a conversation on differences in detecting diverging lineages based on the different properties such lineages exhibit.

• Futuyma, D. J., and M. Kirkpatrick. 2017. Evolution. 4th ed. Sunderland, MA: Sinauer Associates.

  A general evolutionary text used in undergraduate college courses that provides background on a number of different areas of study relevant to species delimitation, including species concepts, genetic models (including those based on coalescent theory), and evolutionary relationships. 602 pp.

• Noor, M. A. F. 1998. Is the biological species concept showing its age? Trends in Ecology & Evolution 17:153–154.

  DOI: 10.1016/S0169-5347(02)02452-7

  A succinct summary of a debate surrounding the utility of different species concepts with a targeted focus on the most popular species concept—the biological species concept—and recent challenges that have been leveraged at it using genetic data.

• Sukumaran, J., and L. L. Knowles. 2017. Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences of the United States of America 114:1607–1612.

  DOI: 10.1073/pnas.1607921114

  This study is the first to draw attention to the implicit species concepts associated with genetic-based delimitation overlooked by many researchers when applying the popular multispecies coalescent models for delimiting species. That is, it implicitly equates all detectable genetic structure with species boundaries, thereby implying that species do not exhibit any geographic structuring of genetic variation. This species concept is not appropriate for many, if any, species in nature.