Lecture 2: Describing Microbial Diversity: the ... - MCD Biology

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Thus, organisms in same “genus” (a collection of “species”) would have similar properties in a fundamental
sense; the representatives of a “species” are expected to share most properties with other representatives of
that species, perhaps with specialized gimmicks (“subspecies”, serovars, etc.).
1. A relatedness group at any level is a “clade”, a natural (phylogenetic) grouping. Representatives of a
clade are more closely related to one another than to any “outgroup” (non-clade) organism. “Phylotype” would
refer to the collection of organisms that make-up the clade, the phylogenetic type.
2. The question of what is a microbial “species” has recently become really complex with the revelation of
the concept of “pangenome” (text, p. 651-2). More later on this important topic, one issue in the description of
“microbial diversity”.
B. A natural taxonomy of macrobes has long been possible:
Large organisms have many easily distinguished features, e.g. morphology, body-plans and developmental
processes, that can be used to describe hierarchies of relatedness.
C. Microbes usually have few distinguishing properties that relate them, so a hierarchical taxonomy mainly was
not possible until molecular comparisons (not only sequence) came along.
2. Recent advances in molecular phylogeny have changed the picture a lot: we now have a relatively non-
subjective, semi-quantitative way to view “biodiversity”, in the context of phylogenetic “maps” - evolutionary trees.