The Chasm between the Human and Chimpanzee Genomes: a Review of the Evolutionary Literature

Data has been extracted from secular literature that is contrary to the common claim that very few genetic differences exist between chimpanzees and humans. We found that significant reported differences exist in genomic similarity and gene regulation between chimpanzees and humans. The DNA sequence differences and genetic mechanisms reported in the literature support the conclusion that significant and unbridgeable genetic differences exist between humans and chimpanzees that defy evolutionary claims of a common ancestor. INTRODUCTION A common claim is that the chimpanzee (Pan troglodytes) and human (Homo sapiens) genomes are about 98 to 99% similar. The roots of this paradigm are based on DNA reassociation kinetics technology popular in the 1970’s in the early days of the molecular biology revolution. Reassociation kinetics uses heat and/or chemistry to separate double-stranded DNA into single strands. When the DNA is allowed to reassociate in a controlled manner, it can be fractionated by various protocols. Three types of DNA can be recovered; high-copy (highly repetitive—gene poor), low-copy (moderately repetitive—low levels of genes), and single-copy (gene-rich). Comparative studies collect the single-copy fraction of DNA from two species that are mixed together, then disassociated and allowed to reassociate so that human and chimp DNA can recombine. The level of complementary base matching between strands can be measured indirectly by a variety of methods. These early estimates of similarity used only the single-copy fractions of human and chimp genomes while the majority of DNA in the genome was omitted. The first 99% similarity claim was made in 1975 by Allen Wilson and Mary-Claire King using reassociation kinetics of single-copy DNA (Cohen, 2007). Other similar studies came up with an average divergence in single-copy DNA that measured about 1.5%, producing the widely quoted 98.5% DNA sequence similarity (Hoyer, et al., 1972, Sibley and Ahlquist 1984; Sibley, et al., Proceedings of the Seventh International Conference on Creationism. Pittsburgh, PA: Creation Science Fellowship 1990). Although the vast majority of the human and chimp genomes were actually excluded in these studies, the estimated high similarities in the relatively small portions represented by single copy fractions surprised researchers. The eventual consensus was that the dramatic differences between human and chimp anatomy and behavior were based on the assumption that small genetic differences produced enormous physical difference (Gibbons, 1998). These initial reports fueled the early claims by popular evolutionists such as Richard Dawkins, who stated that chimps and humans “share more than 99 percent” of their genes” (Dawkins, 1986, p. 263). This statement was mooted with the publication of the initial drafts of the human and chimp genomes, announced in 2001 and 2005, respectively. GENOMICS RESEARCH CHALLENGES THE MYTH A major problem with this type of selective analysis is that nearly all of the entire genome is now believed to be functional, as stated in the recent ENCODE project consortium reports (2012). The non-coding regions have been shown to provide many critical control features and nucleotide templates (Dunham, et al., 2012; Wells, 2011; Bergman, 2001). Biochemical functions have been determined for at least 80% of the human genome and most of the rest is also predicted to be functional (Dunham, et al., 2012) to at least some degree. This research is significant for chimp-human comparisons because often only protein-coding sequences were compared under the widely accepted, but now debunked assumption that 95 percent of the genome is junk. One of the first human-chimp DNA sequence papers that appeared at the beginning of the chimpanzee genome project used DNA segments from the chimp genome that were known to be similar to human (Britten, 2002). The total length of the DNA sequence for all five chimp segments was 846,016 bases. However, only 92% of this could be aligned to human DNA, thus the final statistics reported on only 779,132. The filtered data showed a DNA similarity of 95%. However, an accurate figure that includes the entire amount of DNA sequence being compared gives a final similarity of 87%. For a more thorough review of secular studies in this area, see Tomkins and Bergman (2012). Most DNA sequence similarity studies between human and chimp use multiple levels of data pre-selection and the researchers only report the “best of the best” data. In many cases, this has involved only the protein coding gene sequences of pre-selected highly similar DNA present in both species – virtually guaranteeing high levels of similarity. One of the most widely cited efforts purporting to show high levels of human-chimp DNA similarity was the initial 5X rough draft of the chimpanzee genome assembly report in 2005 by the Chimpanzee Sequencing and Analysis Consortium. The researchers only reported the DNA similarity of the highly similar cherry-picked regions of the genomes and carefully avoided the issue of overall genome similarity. Perhaps the best synopsis of the data came from geneticist Richard Buggs, who published a short news article in 2008 wherein he utilized the chimpanzee genome data to derive an accurate overall DNA similarity between humans and chimps: To compare the two genomes, the first thing we must do is to line up the parts of each genome that are similar. When we do this alignment, we discover that only 2400 million of the human genome’s 3164.7 million ‘letters’ align with the chimpanzee genome – that is, 76% of the human genome. Looking closely at the chimpanzee-like 76% of the human genome, we find that to make an exact alignment, we often have to introduce artificial gaps in either the human or the chimp genome. These gaps give another 3% difference. So now we have a 73% similarity between the two genomes. In the neatly aligned sequences we now find another form of difference, where a single ‘letter’ is different between the human and chimp genomes. These provide another 1.23% difference between the two genomes. Thus, the percentage difference is now at around 72%. We also find places where two pieces of human genome align with only one piece of chimp genome, or two pieces of chimp genome align with one piece of human genome. This “copy number variation” causes another 2.7% difference between the two species. Therefore the total similarity of the genomes could be below 70%. This figure does not include differences in the organization of the two genomes. At present we cannot fully assess the difference in structure of the two genomes, because the human genome was used as a template (or “scaffold”) when the chimpanzee draft genome was assembled. GENOME STRUCTURAL DIFFERENCES Several key reports have called the primate evolutionary paradigm dogma into question. Ebersberger, et al. (2007) used a large pool of human, chimp, orangutan, rhesus and gorilla genomic sequences in constructing phylogenies–multiple DNA alignments analyzed in an evolutionary tree format. As typical with these types of studies, the DNA sequence data was preselected for similarity, trimmed and filtered to achieve optimal alignments and maximum evolutionary outcome. Despite extensive data filtering designed to produce the most favorable evolutionary alignment and trees, the results did not show a clear path of human common ancestry with any of the various apes. What emerged was a mosaic of unique human and primate DNA sequences. The authors concluded that “For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee” (Ebersberger, et al., 2007). They also state: ...in two-thirds of the cases a genealogy results in which humans and chimpanzees are not each other’s closest genetic relatives. The corresponding genealogies are incongruent with the species tree. In accordance with the experimental evidences, this implies that there is no such thing as a unique evolutionary history of the human genome. Rather, it resembles a patchwork of individual regions following their own genealogy... (emphasis added) and ~40% of the alignments provide no clear support for a single branching pattern. The authors rationalized the lack of support for a consistent and clear evolutionary tree among humans and other primates by claiming the “inclusion of alignments with no clear phylogenetic signal”. This is a highly significant statement, given the fact that they used extremely high levels of data filtering and selection to favor an evolutionary outcome. Structural differences resulting in DNA tree discrepancies between human, chimp, and other ape genomes have been reported in numerous papers (Tayler, et al., 2009; Cheng, 2005; Newman, 2005; Marques-Bonet, et al., 2009; Hobolth, 2007; Hughes, 2010). The results are always the same – stretches of DNA sequences show no consistent multiple alignment pattern (DNA fragment comparisons) leading to DNA-based genealogies that are different from the predicted Darwinian evolutionary trees (Chen, 2001; Yang, 2002; Wall, 2003; Patterson, 2006; Hobolth, 2007). These extreme evolutionary anomalies are typically obfuscated by obscure technical verbiage and data smoothing techniques. Consequently, these important results never become common public knowledge. The many human and ape genome sections that show no pattern of common ancestry comprise a phenomenon called ‘Incomplete Lineage Sorting’ (ILS) and is a major problem for evolutionists in human-chimpanzee DNA similarity research. Before the advent of the molecular biology revolution, depending on the trait, various anatomical trait comparisons also produced very different evolutionary trees. Ebersberger, et al. (2002) say that as “both amount of data and number of studies increased” the problem emerges that “Regardless of the type of phylogenetically informative data chosen for analysis, the evolutionary history of humans is reconstructed differently with different sets of data.” Related to the ILS phenomena, Cheng, et al. (2005) were one of the first groups that researched the structural variation between human and chimp genomes. These researchers compared the numbers of repeated regions of the human and chimp genomes that showed evidence of shared and lineage specific duplication. Repeated sequence blocks compared were pre-selected to be highly identical (>94%) and the level of duplication (repetition) for these blocks was evaluated between genomes. For the autosomes (the non-sex chromosomes), only 66% of the total number of duplicated blocks were found in both humans and chimp, 33% were duplicated in human and not in chimp, and a number of these characterized duplications contained genes. Of 177 gene sequences in these repeats, 88 were duplicated in human and not chimpanzee while 94 were duplicated in chimpanzee and not human. Since gene copy number is a major regulator of gene expression, this was a significant finding. They also found that DNA sequences with a similarity higher than 97% were five times more likely to be “incorrectly” assembled in the chimp genome as a result of using the human genome assembly as the framework when building the chimpanzee genome. GENE REGULATION DIFFERENCES The Darwinian interpretation of the accumulating human-chimp molecular data is reflected in Oldham, et al., (2006), that the: ...high extent of sequence homology between human and chimpanzee proteins supports the longstanding hypothesis that many phenotypic differences between the species reflect differences in the regulation of gene expression, in addition to differences in amino acid sequences. We would expect small regulation differences between humans and chimps in housekeeping genes that perform similar biochemical functions in not only primates, but in mammals in general. Evolutionists have therefore focused on the major features that make humans and apes different, such as regulation differences between genes expressed in the brain. One study of brain gene regulation identified 169 genes that were differentially expressed in human, chimp and macaque cerebral cortexes, and 90% were up-regulated at significantly higher levels in humans compared to chimps. In contrast, the liver house-keeping genes showed more similar levels of expression (Cáceres, 2003). The authors concluded “the human brain displays a distinctive pattern of gene expression relative to non-human primates, with higher expression levels for many genes belonging to a wide variety of functional classes.” A similar study by Uddin, et al. (2004) confirmed these differences, stating that “in the ancestry of both humans and chimpanzees, but to a greater extent in humans, are the up-regulated expression profiles of aerobic energy metabolism genes and neuronal functionrelated genes, suggesting that increased neuronal activity required increased supplies of energy” (see also Fu, et al., 2011). Khaitovich, et al. (2005) examined gene expression differences in brain, heart, liver, kidney, and testis between human and chimp. They found significant differences in expression levels for kidney, liver and testis but brain expression and Y-chromosome genes differences were highly significant. These results were later supported by a study that showed dramatic differences between the humans and chimp Y-chromosomes structure, particularly for testis-expressed genes (Hughes, et al., 2010). A study of the promoter regulatory sequences of certain human, chimp and macaque genes identified 575 human gene promoters that were very different from those in chimps (Haygood, et al., 2007). Most of the promoter chimp-human differences control nerve cell development, but some were involved in metabolism. Increased metabolism coincides with enhanced levels of brain activity. Like protein coding regions of genes (exons), promoter regions often involve a relatively small number of nucleotides but small DNA differences in these regions can have an enormous effect. As “comparisons of gene expression between human and non-human primate brains have identified hundreds of differentially expressed genes, yet translating these lists into key functional distinctions between species has proved difficult” (Oldham, et al., 2006). Gene comparisons between different animals requires the study of a large number of gene products to understand both the magnitude and qualitative differences. Complicating matters in these types of analyses is the fact that a majority of genes in the genome produce multiple transcript variants (Barash, 2010).