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• Depending on methodology and philosophy, there are between 50,000 and 10 million different algal species
• Algal taxonomy and systematics is under constant discussion and change, even more after introduction of molecular techniques
• The history of algal classification went from morphology to ultrastructure to genomic analyes; sometimes genetic and morphological classifications contradict
• Sometimes morphology can mislead when one species exhibits several „growth forms“, dependent on envrionmental conditions:

• Classical definition: If two individuals can produce viable offspring, they belong to one species. 
• Problems: Sexual reproduction is not observed in some algal groups and occurs rarely in others; culture material may not be available or environmental conditions to induce sexual reproduction are unknown
• Hybrids: intergenetic as well as fertile hybrids from morphologically distinct species occur in algae, particularily in kelp
• Morphological species concept: one species can exhibit different growth forms, physiological attributes may differ among morphologically identical isolates
• Phylogenetic species concept: address the genetic similarity among specimens; also provide evolutionary information. Ideally, a species should be monophyletic, i.e. have one common ancestor. Some species, however, appear paraphyletic (groups of analyzed strains do not include all of the descendants of a commong ancestor)

• Morphologically deduced phylogeny can be misleading due to parallel or convergent evolution (e.g. squid and human eyes)
• Molecular sequeces can also undergo parallel and convergent evolution; it is not possible to conclude that molecular phylogenies represent the „ultimate truth“
• Sole reliance upon molecular data excludes important data
• Modern approaches check molecular phylogeny against morpholo-gical phylogenies, or two molecular phylogenies based on different genetic information (SSU rRNA vs plastid DNA) for congruence
• Addressed sequences: Ribosomal RNA, protein-coding genes, internal spacer regions (ITS, nuclear-encoded ribosomal RNA), DNA fingerprinting (randomly amplified polymorphic DNA, restriction fragment-length polymorphism), microsatellite DNA, presence and location of introns

• The tree: Statistical analyses (computer-based) produce dichotomous trees and group similar species in close clusters; the length of the branches indicates the genetic similarity (kinship) between branches
• Bootstrep values indicate how solid a certain branch is supported by the data; value should be >50, max 100

• Revisit species concept: molecular phylogenetic studies showed that zooxanthellae in corals are more genetically diverse than thought; evidence that prochlorophytes (Prochlorococcus), the smallest phytoplankton (0.4 µm), are not a coherent cluster but strains are often closer related to coccoid cyanobacteria than to other prochlorophyte strains
• Evolutionary utility: assess monophyletic or polyphyletic origin of algal groups or algal characteristics
  
• Ecologically utility: diversity of plankton communities; prove of N₂-fixation by the filamentous cyanobacterium Trichodesmium because its nifH gene is different from those of bacteria; which organisms are capable of which physiological processes (presence/ absence of the necessary gene)