The Tree of Life is the result of the interplay of changes in information and speciation. Almost 100 years after publication of Darwin's Origin, the inception of Phylogenetic Systematics has resulted in a revolution in data inference. I briefly trace the development of this revolution and show examples of how data are interpreted relative to phylogenetic trees. I then provide brief discussions of how to read tree diagrams and the need to access the quality of phylogenetic inference.
Keywords Phylogenetic systematics . Phylogenetic trees . CladisticsAs a first principle, we adopt the Darwinian idea that all life is related. Life is diverse, being composed of many species, not one. So while there may have been only one line of descent initially, there are now many lines of descent, many "families" reproducing through time. This means that evolution is not simply "change through time," although it certainly is that; it means, minimally, that speciation is also occurring such that lines of descent are divided by various processes into two or more lines of descent which can then follow their own, independent, evolutionary pathways. I say minimally because speciation mechanisms are diverse, sometimes two lineages found a third through other mechanisms, or one lineage spins off a new lineage through other processes. So we can conceive of the Tree of Life in nature as a diverging hierarchy of lineages composed of one or more populations with a few too many individual organisms, with most of the divergence being caused by the establishment of new lineages through speciation. Thus there are two general processes at work in evolutionary descent. One is change in information; ultimately change in the genetic code and how genes interact during development. When played out over time, this general process is termed "anagenesis" and the mechanisms include natural selection, sexual selection, and genetic drift operating on single evolving lineages. The other general process is speciation, the origin of new species. Although speciation can take many forms (various modes of speciation), these forms involve the establishment of two or more lineages where only a single lineage existed before: an ancestral species gives rise to daughter species through lineage splitting. This lineage splitting has been called "cladogenesis" and this is the origin of the term "cladist."Over the past 40 or so years, a revolution has occurred in the way that many biologists look at data. The revolution is fairly simple but profound. Data are interpreted relative to trees of descent which are the inferred genealogical relationships of entities linked by history. From this perspective, the data are dynamic; information changes through time, and these changes can be studied by following lines of genealogical descent. Trees can depict our hypotheses of the histories of individual organisms, populations, genes, proteins, morphological characters, developmental patterns, species, groups of species, and even areas of the Earth. In short, trees can con...