Species Delimitation: New Approaches for Discovering Diversity

Abstract

Systematics can be considered to have two major goals: (1) to discover and describe species and (2) to determine the phylogenetic relationships of these species. But even a quick perusal of titles in Systematic Biology throughout most of its 15-year history will confirm an obvious fact: most articles focus on reconstructing phylogenies and on using these phylogenies to address evolutionary or biogeographic questions, with few papers on the methodology underlying this first major goal of systematics research (Fig. 1). The number of papers published in Systematic Biology that deal (at least in part) with the topic of species delimitation (closed circles), relative to the total number of papers published in the journal (open circles), from 1992 to 2006. Both major articles and Points of View were considered, but not book reviews, editorial comments, or brief symposium introduction essays. Given that there were so few papers that could potentially be considered as dealing with the theory or practice of species delimitation, I was generous about assigning papers to this category. Nevertheless, species delimitation, the process by which species boundaries are determined and new species are discovered, may finally be emerging as a major topic in modern systematics (e.g., Sites and Marshall, 2003). New methods for species delimitation are being developed (e.g., Puorto et al., 2001; Templeton, 2001; Wiens and Penkrot, 2002; Morando et al., 2003; Pons et al., 2006) and compared (e.g., Marshall et al., 2006; Pons et al., 2006). Ambitious proposals have been made, with the goal of accelerating the rate at which new species are discovered and described, including DNA barcoding (e.g., Hebert et al., 2003, 2004), DNA taxonomy (Tautz et al., 2003), and Web-based taxonomy (e.g., Godfray, 2002; Scoble, 2004; Knapp et al., 2007). Controversies are raging in the literature over these proposals (especially over DNA barcoding: Will et al., 2005; Brower, 2006; Hickerson et al., 2006; Meier et al., 2006) and other aspects of species delimitation and over the consequences of new approaches in species delimitation for other fields, such as ecology and conservation (Agapow et al., 2004; Isaac et al., 2004; Padial and de la Riva, 2006). This new emphasis on species delimitation has arisen (at least in part) because of growing concern over threats to biodiversity and the desire to describe as many species as possible as quickly and accurately as possible before they disappear. However, an increased interest in species delimitation is barely reflected in the pages of Systematic Biology, if at all (Fig. 1). This disconnect was my major motivation for organizing a symposium for the Society of Systematic Biologists on this topic. At the evolution meetings in Stony Brook last year (2006), we held the first symposium in the history of the Society of Systematic Biologists dedicated to the topic of species delimitation. After a brief introduction, there were 11 speakers. Six of these led to the papers you see now; presenting but not publishing were Keith Crandall, Paul Hebert, Marshal Hedin, Loren Rieseberg, and Jack Sullivan. Of course, the field of species delimitation is too large and diverse to be adequately covered by 6 or even 11 papers. Nevertheless, the present papers provide an overview of some of the important ideas and a diversity of cutting-edge research in this area. We begin with a paper by Kevin de Queiroz on species concepts. Species delimitation obviously depends on having some idea of what species are, and it is easy to imagine a symposium on species delimitation degenerating into endless disagreements about species concepts. Not so. In fact, there has been real progress made in thinking about species concepts, which now makes some general agreement seem possible. Part of this progress comes from recognizing a distinction between what species are and the evidence used to recognize them (e.g., Frost and Kluge 1995; Mayden 1997; de Queiroz 1998). Here, de Queiroz (2007) discusses the underlying unity of species concepts and the implications this has for species delimitation. As evidence of some of this progress, there seems to be general agreement among almost all participants that species are lineages (e.g., de Queiroz, 2007; Knowles and Carstens, 2007; Shaffer and Thomson, 2007; Raxworthy et al., 2007; Rissler and Apodaca, 2007, this paper). This lets us focus on the challenge of how we go about delimiting those lineages. The paper by Knowles and Carstens (2007) addresses how molecular data (i.e., gene trees from DNA sequence data) can be used in species delimitation. I suspect that this will be the single topic of greatest interest to most readers of Systematic Biology. They propose a new method that uses coalescent simulations to test hypotheses about species limits. Their method is particularly valuable in that it can incorporate data from multiple loci and does not require that species have diverged to the point of being