Genetic differences between species - humans and chimpanzees

We do not know exactly what needs to be different in DNA for a new species to form. What is always true however, despite popular claims, is that the difference in the genomes of different species is large. Once two groups of animals can no longer breed, their DNA starts to diverge strongly. However, in the early stages of speciation, quite a lot of crossbreeding may occur if the different lines are not completely kept apart.

Statements such as “chimpanzee DNA is 98.8% the same as human DNA” are rather misleading and depend on the precise definition of similarity. In fact, as we shall see, chimpanzee DNA is overall only about 70% the same as human DNA.

Errors in DNA copying

Differences in DNA occur because of copying errors - in just the way that a video or sound file will deteriorate if copied multiple times. Each time a cell divides, three billion nucleotides have to be copied exactly. Our genetic code is exposed to a variety of insults which can damage the DNA prior to or during division and replication.The body is loaded with an arsenal of editing mechanisms to prevent copying error when cells duplicate or when sperm and eggs are formed - but they do not always work. 

If the editing mechanisms get it wrong, for example, they will cut out bad DNA and replace it with something different. In the case of larger insults - if an entire chromosome breaks due to ionizing radiation, efforts to piece it back together can lead to chromosomal rearrangements. Once an error gets past the editors, it will be recognised as "normal" and promulgated. If it is in a cell that can form gametes, the errors may be passed along to offspring. 

Direct substitutions and SNPs: 
DNA is coded with four amino acid bases held in a sugar-phosphate backbone. A potentially serious kind of error is when there is direct substitution of one of the bases by another - which is known as a SNP and causes two different sequences or alleles of a gene. SNPs are rare and occur usually only once at a particular site in the lifetime of a species - but they build up across the whole genome. Most of these SNPs do nothing, but some may lead the gene in which they occur to code a different protein, changing some part of the body or its function.

Insertions, deletions, duplications and STRs
Due to strand slippage during copying, one or more nucleotides may be inserted or deleted at a particular site. 

Insertions and deletions happen with larger pieces of code. A second copy of a short or long sequence or a gene can be inserted during the copying process, or copies can be removed. A Single Tandem Repeat (STR) is a zone in junk DNA with multiple repeats; these mutate relatively frequently to give new numbers of repeat counts and so are used in genetic genealogy

Reversals, splits and combinations.
Whole long strings or segments can end up reversed in order. Chromosomes can split or fuse together at their endpoints. 

Chimpanzee DNA

The International Chimpanzee Genome Sequencing Consortium has performed detailed work on sequencing the full chimpanzee genome and comparing the genomes of chimps and humans. The genomes, while having a lot of material with near identical sequencing, are structurally different – chimps and other great apes actually have 24 pairs of chromosomes, one more than us, since in humans two ape chromosomes have fused.  There are also large segment inversions on nine chromosomes. 

The 98.8% of DNA that is found to be similar refers only to the active DNA and the 1.2% difference refers to about 35 million SNP changes. 

Single-nucleotide substitutions occur at a mean rate of 1.23% between copies of the human and chimpanzee genome… An observed difference at a site nearly always represents a single event, not multiple independent changes over time. Most of the differences reflect random genetic drift … Hidden among the differences is a minority of functionally important changes that underlie the phenotypic differences between the two species”. 

So therefore the percentage refers only to those functional parts of the human and chimp DNA that can be lined up with each other, and only to substitutions. At this stage we don’t really know which of the 35 million SNP changes actually do anything important.

As well as the SNPs, about twice as much material is altered through insertions and deletions. The duplication of particular genes may be responsible for many of the functional differences between the two species.

From a study of one chromosome: “By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level.” [1]

So in fact the changes are sufficient to make many of the generated proteins different.

The creation scientist Tomkins [2] does a fair job of trying to match together the two genomes by taking optimal sequence slices and comparing them. The best comparison he can get is that overall, including junk DNA, only 43% of the chimpanzee Y chromosome is similar to human, and about 70% of other chromosomes. The former (along with the different number of chromosomes) probably explains why the two species can not breed.

While the functional area of the two genomes is quite similar, showing at standard mutation rates that chimps and humans parted company about six or seven million years ago, it still generates many functional changes. The junk part of the DNA has been shuffled all over the place during that period. It is not known what role if any it plays.

Interesting findings

Attempts by a Russian scientist to form human-chimpanzee hybrids in the 1930s  were unsuccessful. The different numbers of chromosomes probably prevent hybridisation.

The human X-chromosome is about 2 million years younger (more similar to chimp) than the rest of the genome, suggesting that back breeding was possible during the early years of differentiation of the two lines.

Some of the genes that show the greatest differences are the ones that have been subject to selection pressure. For example, several genes determining skin colour show considerable change in humans.

A sequencing of the gorilla genome once again has cast doubt on "linear" models of evolutionary descent and implies considerable admixture during the early stages of species formation. Fifteen per cent  of the human genome was found to be more like that of the gorilla than the chimpanzee. In addition, 30% of the gorilla genome "is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression". [3]

---

[1] Fujiyama et al (2004). DNA sequence and comparative analysis of chimpanzee chromosome 22.  Nature 429, 382-388.

[2] Tompkins, J P (2013). Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70%. http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome
[3] Aylwyn Scally, et al. (2012). "Insights into hominid evolution from the gorilla genome sequence". Nature 483 (7388): 169–175.