Hierarchical clustering in baraminology revisited: nested versus netted hierarchies

Do phylogenetic patterns in the unconstrained regions of the genome prove evolution? What evidence is there for molecular evolution? What about homoplasies? This article explores various arguments against nested hierarchical patterns and shows how they can be used to support the baraminology model. First, genetic data is only available for less than 1% of all organisms that ever lived on earth. Conspicuously missing are ancient DNA for 99% of all species, that have gone extinct. This would be the very meat of evolutionary theory, but it is missing. Genetic homologies are necessary for evolutionary theory, but they do not decisively prove evolution. Correlation does not necessarily mean causation. Different gene families can be viewed as functionally designed elements. Homoplasies include genes that misplace either species or whole entire organismal groups on the evolutionary tree. Such genes include the prestin gene, which plays a role in echolocation in microbats, whales, and dolphins. This gene places whales and dolphins nested in between two groups of bats. A better interpretation of the data would mean splitting these three groups into separate holobaramins of independent origin. Homoplasies are also quite common in genomics. Functional elements in endogenous retroviruses and pseudogenes provide further evidence against the junk DNA hypothesis, questioning the validity of the designation of certain parts of the genome as unconstrained regions. Lastly, alternative genetic codes are large-scale discontinuities that disrupt evolutionary relationships.