The evolution of hominins, members of the zoological tribe Hominini, has been a much-studied topic, and the construction of phylogenetic trees has been the key method in molecular evolutionary studies. How scientists determine the phylogenetic trees are governed by the assumptions they place on the construction of similarities and differences in morphological traits, the differences in the number of base pairs in the genomes, and the number of similar gene clusters that code for traits (haplotypes) or are error sequences (SNPs). Among the several methods employed for the construction of a phylogenetic tree, mathematical methods (utilized for sorting data, including fabrication of algorithms) are the most significant ones; also, the nature of population structuring plays an important role in the evolutionary process. In this paper, I will not only describe the drawbacks of current assumptions in hominin evolution during the Middle Pleistocene era (based on fossil evidence) but also the aspects of brain evolution and the self-domestication of our species. The evolution of the brain is usually associated with an increase in neurons and other types of cells associated with signal processing (connectivity) and memory. Assessing actual neuron counts in fossils is challenging; moreover, new research has shown decreased neuron numbers in the neocortex and demonstrated large counts in the cerebellum, leading to a decreased focus on brain size. The idea of increased brain size in the Pleistocene era without a substantial increase in the evidence of cognitive activity in complex behavior residues might be explained by increased myelination to provide additional insulation in Ice Age conditions and faster transition of signals due to increased competition for reduced food supplies. Other cold-adaptation features can also be noted. Such a model can provide a new approach to assess the apparent brain size reduction in the Upper Paleolithic period.

A number of recent articles have appeared on the hominin Denisova fossil remains. Many of them focus on attempts to produce DNA sequences from the extracted samples. Often these project mtDNA sequences from the fossil remains of a number of Neandertal fossils and the Denisovans in an attempt to understand the evolution of Mid Pleistocene human ancestors. There are two problems with these papers, one concerns the degradation of the ancient DNA and its interpretation as authentic genetic information and the other concerns the idea of "species" versus that of "population" and the use of these ideas in the building of evolutionary diagrams to indicate ancestry and extinction. Since I have dealt with the issue of degradation elsewhere [1]. I will limit this paper to ideas of species and population. A central issue is what does human variation mean, how much population variation has there been in the past and how does this variation distinguish hominid speciation or simply a process of anagenesis. Some businesses today claim to be able to use DNA analysis to discover past ethnic identities and a new niche in restaurants is producing DNA menus. Perhaps some caution is in order.