Molecular Systematics and the Diatom Species

Diatoms are unicellular heterokont algae known most notably for their elaborately ornamented cell walls of opaline silica. The scanning electron microscope (SEM) revolutionized diatom systematics, revealing taxonomically important ultrastructural features that were otherwise hidden from the light microscope. The SEM quickly became an important tool for taxon delimitation, and SEM data are now foundational to nearly all levels of the diatom classification system (Round et al. 1990). The introduction of multivariate statistical methods to diatom studies represented a similar advance, revealing complex sets of continuous morphometric characters to taxonomists for the first time. Although less commonly employed than the SEM, morphometric analysis has facilitated the discovery of numerous previously undescribed taxa (e.g., Mann et al. 2004; Theriot and Stoermer 1984). Most recently, the application of molecular biological techniques to systematic studies of diatoms has revealed still more variation, and these methods now play an important role in the discovery and delimitation of diatom species. Each of these tools enhanced our ability to detect and extract subtle differences, and in each case the diatom species category became effectively smaller and more exclusive. This is evident in the increasingly common discovery of "cryptic" species—morphologically similar but genetically distinct species that, at some point, shared the same specific epithet. In some cases, DNA sequence data have indeed provided compelling evidence for the existence of cryptic species, in which the rates of morphological and molecular evolution have apparently been decoupled. In other cases, DNA sequence data retrained the eye to reveal subtle morphological differences, so there was corroborating evidence from morphology and molecules to differentiate multiple species from what previously had been considered one. These species are sometimes referred to as "semi-" or "pseudo-cryptic," but the term "previously undetected" seems to apply equally well. The power of the molecular systematic approach to species research, though fully established (Avise 2000), is just being realized for diatoms. This article focuses on the burgeoning use of molecular data to discover and delimit diatom species. The reader is referred to Mann (1999) for valuable historical context and a more thorough account of the traditional approaches to diatom taxonomy. This review instead will focus on studies that use phylogenetic analysis of DNA sequences to identify and delimit species of diatoms. The approach has a proven history of success, particularly in animal systems. A simple glance at the animal literature on species-level molecular systematics, and the closely related field of phylogeography, demonstrates the great potential of this approach to transform species research in diatoms. The molecular systematic approach is not without its challenges, however, as is clear from the general literature (e.g., Funk and Omland 2003) and the handful of diatom studies undertaken so far. This review will draw from those examples to highlight both the promises and problems of the molecular systematic approach to species delimitation. First, the extent to which common diatom species concepts influence or constrain species delimitation, and the advantages of adopting a lineage-based species concept, will be discussed. Second, different genetic markers can provide conflicting evidence about species boundaries, highlighting the importance of marker choice, particularly for single-locus studies. Several advantageous properties of mitochondrial DNA (mtDNA) for species-level studies are reviewed, which together recommend mtDNA as a better "first pass" molecular marker over the traditional nuclear ribosomal DNA (rDNA). Finally, the importance of species monophyly is discussed. To date, most species-level molecular systematic studies of diatoms have focused on the detection of cryptic species, which are, with rare exceptions (Slapeta et al. 2006), very likely to be recently diverged and therefore unlikely to exhibit reciprocal monophyly in their gene trees. This underscores the need to develop and evaluate numerous low-copy nuclear markers for systematics research in diatoms.