Although these features may not be apparent to the naked eye, many groups of plants are distinguished by biochemical, physiological, or other features. For example, betalains (nitrogenous pigments) are found only in all but two families of the Caryophyllales. Judd et al. (1999, pp. 84-9) describe these and other examples of secondary plant compounds that characterize different groups of plants. Photosynthetic pathways also vary in ways that may be taxonomically significant, as in the Crassulaceae and Poaceae (not an exhaustive list!). These biochemical and physiological differences are often correlated with equally significant morphological and (or) anatomical variation (Judd et al. 1999, p. 73; cf. the characteristic vascular bundle anatomy of C4 grasses), which is why we recognize these features as being taxonomically relevant.
Probably the single most important development in systematics in the past 20 years has been the acquisition of DNA sequence data from many sources (chloroplast, mitochondrial, nuclear) and from increasing numbers of plant (and animal) taxa. These data have made it possible to infer increasingly plausible and robust phylogenies that have confirmed, in many cases, the inferences drawn earlier from patterns of morphological, biochemical, physiological, and other variation. Just as importantly, these results have also indicated where these other sources of data have been imperfectly understood or interpreted. Click HERE for examples of the trees that have been produced in recent years as a result of studies of vascular plant phylogeny.
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