Probability, Populations, Phylogenetics, and Hominin Speciation

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 mitochondrial DNA (mtDNA) sequences from the fossils of a number of Neandertals and the Denisovans in an attempt to understand the evolution of Middle Pleistocene human ancestors. These articles introduce a number of problems in the interpretation of speciation in hominins. One concerns the degradation of the ancient DNA and its interpretation as authentic genetic information. Another problem concerns the ideas of "species" versus "population" and the use of these ideas in building evolutionary diagrams to indicate ancestry and extinction. A third issue concerns the theory of haplotypes in the mtDNA. Given the severe constraints on mutations in the mtDNA genome to maintain functionality and the purifying processes to reduce such mutations in the ovaries, putative geographic and historical variations seem contradictory. Local diversity and variations in supposed "macrohaplotypes" are explained as back migrations or back mutations, which dilutes the robust nature of the theory. A central issue involves what human variation means, how much population variation there has been in the past, and whether this variation distinguishes hominid speciation or is simply a process of anagenesis. This brings up the question of how much can be interpreted from the analysis of DNA. 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.