Recent research in microalgal ecology, physiology, systematics, and genomics has revealed a vast, unexpected diversity. The estimation of microalgal biodiversity has been hindered by cultivating microalgae for commercial products. Molecular iden­tification serves as a prominent tool to distinguish inter — and intra-specific morpho­logically similar species (Olmos et al., 2000) and mixed populations (Olsen et al., 1986). The developments of modern biotechnological tools, such as polymerase chain reaction (PCR)- and rDNA-based technologies facilitate in detecting small numbers of microalgae in complex natural populations and are widely applied to ascertain the systematic position of species. Sequence analysis has been used to clarify the taxonomic affinities of a wide range of taxa (McInnery et al., 1995;

FIGURE 2.1 (See color insert.) Morphological diversity of microalgae: (a) Mastogloia paradoxa Grun., (b) Rhabdonema adriatium Ktz., (c) Synedra gruvei Grun.

Baker et al., 1999) and as a powerful tool for assessing the genetic diversity of environmental samples (Van Waasberngen et al., 2000; Baker et al., 2001). Apart from detecting genetic diversity, molecular tools may also help in detecting the spatial repartition of an organism, both in marine and freshwater microalgae. PCR — based methods are more commonly utilized due to their rapid results. They have been successfully used to detect the genetic make-up of various natural samples.

FIGURE 2.4 (See color insert.) Morphological diversity of microalgae: (a) Ceratium hirun — dinella (Muller) Dujardin, (b) Ceratium longipeps (Bailey) Grun., (c) Ceratium trichoceros (Ehrenberg) Kofoid, (d) Gymnodinium sanguineum Hirasaka.

However, a problem with several commonly used primers is that they are con­structed theoretically and from an incomplete database of 18S rRNA sequences from cultured organisms. Therefore, experiential testing is pivotal to confirm PCR primer specificity prior to their use in environmental samples. Thus far, a large number of primer sequences have been produced for amplification and sequencing of ssu-rRNA genes. Some of them have been designed as taxa specific, whereas others, designed to amplify all prokaryotic ssu-rRNA genes, are referred to as uni­versal primers. Because the database of 18S rRNA gene sequences has grown, new
taxonomic groups have been revealed. Formal analyses of species borders have been made possible due to modern advances in techniques for sequence-based spe­cies delimitation (Wiens, 2007; Zhang et al., 2008). A variety of methods for detect­ing species are based on analytical character variation limits from DNA sequence data. Hence, these methods are rooted in phylogenetic species insight, aggregating a population that lacks separate variations into a single species, and distinguish­ing other species by distinct nucleotide differences (Wiens and Penkrot, 2002; Monaghan et al., 2005). Among these methods, statistical parsimony (Templeton et al., 1992) segregates a group of sequences if genotypes are connected by long branches that are affected by homoplasy. In recent times, the maximum likeli­hood approaches aim to connect between statistics and sequence data by analyz­ing the dynamics of lineage branching in phylogenetic trees for determining the species boundaries. This t echnique attempts to determine the point of transition from species-level (speciation) to population-level (coalescent) evolutionary pro­cesses (Pons et al., 2006; Fontaneto et al., 2007). The similar morphological or polymorphic traits of many algal groups that can be achieved by sequence-based identification are, in fact, valuable discoveries in this field (Harvey and Goff, 2006; Lilly et al., 2007; Vanormelingen et al., 2007). The taxonomy of the most common microalgal species is sorted using available distributional information that is reli­able. The distribution records, along with physiological information, will allow for designing ecological models incorporating the special effects of climatic param­eters, which in turn would be very useful to predict transfer in distribution due to climatic changes. At present, such models are nonexistent for microalgae. As a general conclusion, the biogeography of algae is a poorly explored area, but holds great potential for exciting research and is definitely worthy of much greater inter­est than received thus far.