![]() ![]() Thus, all life seemed related, but in what way? What are the patterns of the relationships? Evolutionary patterns within animals, plants, and a few other kinds of organisms could be inferred from morphological and developmental properties, but the major kingdoms could not be related to one another. Because of the complexity of life processes and the consequent improbability of their independent evolution in different organisms, the universality of biochemistry indicated that all life had common ancestry. Discoveries in the first half of the 20th century established that all life, microbes and large organisms, had similar biochemistry. Indeed, the microbial world was barely acknowledged by most biologists of that time, brushed aside as “monera,” perhaps nonliving.Įarly biologists speculated as to whether life had a common or multiple origins, but there was no way of determining the truth. However, where the microbial world fit into the rest of life could not be known. A derivative of one of Ernst Haeckel's 1866 trees ( 23) is seen in textbooks today as the five-kingdoms model for large-scale evolution. Some of the ideas of the early evolutionists are still with us. That, of course, was not an evolutionary model, but treelike portrayals of biological relationships-specific evolutionary models-were proposed by the mid-19th century ( 58). ![]() The classical “great chain of being” was an imagined, treelike hierarchy of existence reaching from minerals through simple life to humans and the gods. The notion of some sort of connectedness between all of life is ancient. I conclude that we have in place the outlines of a universal ToL, but the details of the patterns of deep evolution in all the phylogenetic domains remain obscure. Therefore, I show how the recent explosion of environmental sequences has heavily influenced the patterns seen in the trees. Progress toward assembly of a universal phylogenetic ToL also relies on how comprehensive is our knowledge of the extent and the richness of life's diversity. Consequently, I discuss the building of phylogenetic trees and emphasize the intrinsic limitations of any results. A molecular perspective on life's diversity and evolution is only now unfolding, and there is much controversy and paradox, only some of which I can address here.Īll molecular phylogenetic trees have systematic limitations that cloud our view of the deeper branches in the tree of life (ToL). My view is from the molecular standpoint, mainly from the perspective of rRNA phylogeny. The intent of this article is to assess critically our current understanding of life's phylogenetic diversity on a large scale. Sequence variation can also serve as the basis for inference of the patterns of evolution from precellular life until now. Gene sequence variation between different organisms provides a metric for biological diversification. Obstacles to accurate inference of deep phylogenetic relationships are both systematic, in molecular phylogenetic calculations, and practical, due to a paucity of sequence representation for many groups of organisms. Although the three-domain structure of the ToL is established, the deep phylogenetic structure of each of the domains remains murky and sometimes controversial. Environmental rRNA sequences, which now far outnumber those from cultivars, expand our knowledge of the extent of microbial diversity and contribute increasingly heavily to the emerging ToL. The sequence-based perspective on microbial identification additionally opened the way to the identification of environmental microbes without the requirement for culture, particularly through analysis of rRNA gene sequences. Three decades of molecular phylogenetic studies with various molecular markers have provided the outlines of a universal tree of life (ToL), the three-domain pattern of archaea, bacteria, and eucarya. Phylogenetic comparison of gene sequences is a natural way to identify microorganisms and can also be used to infer the course of evolution. Summary: The intent of this article is to provide a critical assessment of our current understanding of life's phylogenetic diversity. ![]()
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