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The Human Nature Review 2002 Volume 2: 317-321 ( 19 August )
URL of this document http://human-nature.com/nibbs/02/caldararo.html
Ancient DNA and Human origins:
The role of gene sequence variation in the species concept
Niccolo Caldararo, Department of Anthropology, San Francisco State University, 1600 Holloway Ave., San Francisco, Ca. 94132, USA.
The analysis of variations in DNA sequences has become a standard method of determining the classification of plant and animals today. Sequence variation is not being considered within the context of natural selection due to Neutral Theory. The argument over DNA substitutions and speciation is one which rekindles the great debate between selectionists and mutationists . Most disturbing is the assault on the concept of species in which some phylogeneticists seem near to be arguing that every gene variation is a speciation event replacing Mayr's biological species concept. In this paper fundamental problems with the interpretation of DNA variations specific to PCR is presented in the context of recent developments in the question of human origins and the species concept.
Fundamental changes in our understanding of the human genome, gene function and the concept of the gene have taken place in the past few years (1). Recent publication of ancient DNA sequences from the Australian site of Mungo (2) has caused a controversy among researchers in the field and enlightens us on new issues in phylogenetics. This new controversy centers on technical aspects of preservation of aDNA and on consideration of the legitimacy of sequences produced by different laboratories. However, this is just a fragment of a larger argument raging in the biological sciences over how to balance sequence data and evolutionary studies as well as the taxonomic utility of DNA variations. Since the use of PCR has become an increasingly important tool in determining species, it is important to focus on the significance of base pair variation in individuals. This becomes increasingly complex when we consider paleospecies. I would like to use the recent Mungo debate as an example.
DNA substitutions and the Species Concept
In their response to Constance Holden's article, "Oldest human DNA reveals Aussie oddity", (Science, News of the Week, 12 Jan., 2001:230), Cooper, Rambaut, Macaulay, et al., provide some assertions to question the authenticity of the Mungo sequences ("Human Origins and Ancient Human DNA", Science, v. 292, 1 June 2001:1655-6). Among these assertions, Cooper, et al., note that Ancient DNA is easily contaminated and PCR of such samples carry "a considerable burden of proof" when novel sequences are reported in "surprising examples of preservation". They characterize the Mungo samples (2) as falling into this category specifically because they come from a hot and dry environment. They assert that DNA is not expected to survive outside cold environments for this length of time (up to 60,000 BP). As I have shown in several publications (3), the survival of ancient tissue is dependant on several factors which vary despite the general local climate due to specific microenvironments. The fact that significant finds of ancient tissue and DNA have been found in arid environments (Egypt and Peru) indicates that stability and lack of moisture are important factors. The fact that few animal remains are found outside of special environments is due primarily to scavenging rather than general preservation conditions. Ideal conditions for preservation are the result of a unique confluence of local microenvironmental conditions which must remain stable (lack of cycling) for long periods of time. This is true of fossilization as well.
Cooper, et al. 2001, claim that certain criterion must be followed in the discovery of ancient tissue for authentic DNA analysis to be considered. Cooper, et al. 1997 (4) widely criticized the published ancient DNA literature for a perceived lack of rigorous methodology. However, some of these authors have cited claims of necessary conditions (e.g., D/L ratios) for authentic DNA to be retrieved in the past only to change these requirements due to what they consider to be unknown but unique and undefined, special conditions of their finds (4,5). Cooper et al., 2001 require independent replication of results as the hallmark of authenticity. I noted with Gabow (6) the fact that even the Krings, et al. (1997) report of Neandertal DNA (7) was done without actual independent verification of the reported sequence. Also, this sample was found to be outside of the expected limits of preserved DNA (5). Cooper, et al. 2001 complain that the Mungo samples have been handled over the years complicating DNA analysis, but this is true of the samples used in the Krings, et al. report from Feldhofer (6). They also note the high proportion of cytosine-thymidine transitions in the Mungo samples arguing these are due to deamination, but the Krings, et al. report also shows a high proportion of C-T transitions (6). In fact, much of the distribution of the substitutions in the reported Neandertal sequence can be explained by miscoding lesions as noted by Hansen, et al. (8). Finally, the phylogenetic model used by Cooper, et al. (4) in discounting the Mungo relationship, relies on outdated neutral models of DNA substitutions. These models are now in question due to new considerations concerning the concepts fundamental to DNA operation, arising from the results of the Human Genome Project, discussed, for example, by Strohman (9), and can no longer be considered valid in the manner they have been applied. Guthrie and I discussed other problems with neutral theory in detail in our 1998 paper in Homo (10). Relethford (11) has summarized the major issues in using DNA sequence variation as a phylogenetic tool in human evolutionary studies. He has noted that population size is an important element in determining population diversity which is usually assumed to derive from the antiquity of a population. However, researchers have noted that species diversity has a latitudinal gradient, with the greatest diversity nearest the equator (12). It has also been demonstrated that linguistic diversity is also greatest at the equator and grades from there towards the poles (13, 14, 15, 16,17). Cashdan (18) has also shown that ethnic diversity has the same gradient. It therefore would seem reasonable to assume that such diversity has some selective advantage rather than an artifact of random mutations which accumulate over time . “lineages” and hierarchies have been constructed from these mutations to produce phylogenetic “networks” (19) which sometimes contradict phylogenetic decisions made on the basis of morphology from living and fossil specimens (11, 20). Analysis of DNA sequence variation of autosomal DNA, mtDNA and Ychromosome DNA have resulted in contradictory phylogenetic histories of the genus Homo (21, 22, 23).
A new article by Gemmel and Sin (24) reports on studies of mtDNA mutations and Y chromosome evolution. The authors argue that unlike the current theory that low levels of nucleotide variation of the Y chromosome reflects historic reductions in the human male population, a very recent common ancestry, or frequent selective sweeps acting on genes borne on the Y chromosome, their findings propose an alternative theory in which human Y Chromosome evolution is driven by mutations in the maternally inherited mitochondrial genome, which impair male fertility and ultimately lead to a reduction in the effective population size and consequently the variability of the Y chromosome.
Wayne, et al. (25) has demonstrated how significant DNA divergence in breeding populations exist in canids sufficient in other groups to have resulted in species designations (8%). While in other cases, in wolves and the domestic dog, there is little genetic variation in mtDNA and yet we recognize species distinctions (26) and considerable morphologic variation. Dogs are, as Wayne puts it, grey wolves. One major assumption of neutral theory as applied to phylogenetic analysis is that introns or "non-coding" sequences are junk DNA and base substitutions in these sequences are not subject to selective pressure. We have detailed the problems with this assumption elsewhere (10). It is sufficient to say here that recent research has shown (27) that non-coding regions often have functional roles, e.g., intronic recombination (28), RNA polymerase II promoters, retrotransposons as epigenetic mediators (29), snoRNAs (30) and therefore would be subject to selective constraints. The survival of paternal mtDNA has been demonstrated possible, though slight (31), yet the dogma of mtDNA analysis (e.g., 32) dismisses its possibility as that of mtDNA recombination which has been reported (33). Programs for developing phylogenetic relationships should include these biological facts as variables in their projections. We should keep in mind that our knowledge is constantly expanding, and that we should never say never.
While Gabow and I (6) raised concerns that establishing species designations based on base pair variations alone seemed to create a new species concept, undermining the synthesis of modern biology between the mutationists and the selectionists in the 1930s, and affecting the whole taxonomic edifice. A more cautious approach is prudent.
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© Niccolo Caldararo.
Caldararo, N. (2002). Ancient DNA and Human origins: The role of gene sequence variation in the species concept. Human Nature Review. 2: 317-321.