About 100 years ago, it was found out that we humans shared common ancestry with the African apes. In the book “On the Origins of Species” by Charles Darwin, human evolution was discussed extensively about this prediction. Today’s advancements in research made many milestones in confirming this prediction in various branches of science and redefined many branches evolution. One of the strongest branches, perhaps it could be viewed as the trunk of the tree for biologists and geneticists, is the one that has refined comparison of similarities and differences between the chimpanzees and the Homo sapiens (humans). This correlation that the chimpanzees being our closest relatives, is the first step, and a very significant piece of information that we humans learn fundamentally.
Thus, the chimpanzees are specially adapted to teach humans about the similarities and the differences that they may exhibit with the humans. Astounding similarities such as the usage of tools and group aggression have been shown by Goodall’s pioneering as some of the common behavioral similarities’ humans have with the chimpanzees.  This genomic comparison also helps us find answers as to why only humans have the human specific features that are very visibly common, such as the habitual bipedality, complex language system, and wonderfully complex and enlarged brain. Some of the specific similarities and differences can also be accounted for the prevalence and asperity of distinct human diseases, which could possibly be cracked by gene sequence comparisons.
Many questions arise in the field of genomics and bioinformatics, but one of such hard questions is the quintessential question- what really makes us human when compared to the other species that coexist with us? While adaptive changes could be a possible answer, it comprises only a slight minority of the complete genetic variation amongst two species. Comparisons in genomes remarkably defines the quest for the significant differences between any two species.
It wasn’t until less than approximately ten years ago that the genome of the chimpanzee was got into light, but recently, much to the interest of the scientific community, the sequence analysis papers became available. One such very informational paper that is going to be discussed in this essay is “The Chimpanzee Sequencing and Analysis Consortium 2005,” along with many other companion articles. In this article, the genome that was published was from a single captive-born male of the subspecies Pan troglodytes verus from West Africa.
Essential question(s)- How was this comparison made? What is the basis to the quantification of the research?
The data of the sequence was obtained by the means of a whole-genome shotgun approach (WGS). This data was then assembled using the programs the Parallel Contig Assembly Program (PCAP) and the ARACHNE (ARACHNE is a tool for assembling genome sequence from whole-genome shotgun readings, almost always in the forward-reverse pairs that are obtained by sequencing the clone ends).  Since the ARACHNE had greater continuity as seen in Table 1, it was mostly used for the purposes of analysis in the article. The article mentioned that the draft genome assembly was generated from approximately 3.6-fold sequence redundancy of the autosomes, and approximately 1.8-fold redundancy of both the sex chromosomes, which covers approximately 94 percent of the chimpanzee genome with greater than 98 percent of the sequence in the high-quality bases. The length of a total 50 percent of the sequence that is contained in contigs is greater than 15.6 kb, and the length of the super contigs is greater than 8.6 Mb.
The nucleotide-level accuracy is also kept track of in this article and the accuracy was high in various measures. Approximately 98% of the chimpanzee genome sequence has the quality scores of at least 40 (Q40), with a corresponding error rate of ≤ 10-4. The draft sequence of the chimpanzee genome done in this paper assists in the progress of studies of genetic distinctiveness among the chimpanzee species. The authors have identified a total of about 1.66 million high-quality single nucleotide polymorphisms (SNPs) within the primary donor. After the estimating, studying and comparing the Heterozygosity rates of various African chimpanzees from various regions of Africa, the diversity in West African chimpanzees’ diversity is similar to that seen for human populations. 
Essential question(s) – How has this alignment of mere alphabets in the nucleotides and proteins of the genomes lead to many innovations, and discoveries? Examples of specific genes or groups of genes revealed by the sequence and discuss them in terms of their biochemical implication.
The article clearly studied the mutational events that might have shaped the human and chimpanzee genomes from the time of their last common ancestry. Small insertions, deletions, changes at the level of single nucleotides, repeats and chromosomal rearrangements were also explored. The genome-wide nucleotide divergence between human and chimpanzee is about 1.23 percent, which confirms the recent results from various studies that were already established. After correcting the estimated coalescence times in the populations of human and the chimpanzee, the authors estimated that the polymorphism is accounted for 14-22 percent of the observed divergence rate- hence, the fixed divergence came out to be approximately 1.06 percent or less.
The divergence rates in the nucleotides are variant throughout the genome.  According to Figure 1a , we can see that the average divergence in 1-Mb segments vacillates with a standard deviation of 0.25 percent (and coefficient variation of 0.20), which is significantly greater than the 0.02 percent that was expected assuming the uniform divergence rate. Such regional variations in the divergence resonates local variation in either the mutation rate or evolutionary forces such as genetic drift. Genetic drift could cause substantial dissimilarities in divergence time throughout the loci as we compare the related species closely. However, one thing that we certainly can learn from this finding is that due to the historical recombination, the characteristic scale of such fluctuations is on the order of tens of kb’s that is significantly small to account for the variation which was observed for the 1-Mb regions above. The large- scale variation in the divergence rate human and chimpanzee fundamentally reflects a regional variation in the mutation rate.
The divergence studies of the human and chimpanzee genomes also helped in finding explanations for the genetic basis or the specific biology of humans and the chimpanzees. When the claim is made that the apes and the humans share common ancestry, it is only rightful, if anything but genome sequence alignments, comparisons in divergences and similarities help us in knowing how we humans have evolved to the current form. There were ample amounts of neutral mutations, but only a very tiny subdivision of the gene variations is most possibly responsible for the major phenotypic changes in the physiology, behavioral, morphology and complexity between chimpanzees and humans.
Some novel examples of such genetic changes include apoptosis, inflammatory responses, parasite resistance, and the role of sialic acid biology related proteins. Humans seem to lack the protein function of apoptosis that occurs in response to the troubled calcium homeostasis. While, the chimpanzee gene encrypts an unblemished open reading frame and SGH box, indicating the loss in functionality occurred in the lineage of humans, leading to the specific pathology in humans of Alzheimer’s disease that involves demented calcium homeostasis and amyloid- induced neurotoxicity.
Amazingly, the chimpanzee genome can also tell us a tremendous amount of information on the human population genetics, a field that is extensively becoming dear kith and kin to human medical genetics.  Chimpanzee sequences allow us to recognize the human alleles that impersonate two states- the derived and ancestral, while also allowing us to estimate the rates of local mutations that in turn are pragmatic in serving as an essential criterion when searching for the natural selection signs. The initial analysis of patterns in gene expressions and the promoter regions also suggest the close mirroring of the overall patterns of the evolution to that of protein-coding regions.
Currently, in the public database, there approximately 7.2 million SNPs mapped to the human genome and this could be assigned to the alleles as derived or ancestral in 80 percent of the situations bestowing to which allele agrees with the genome sequence of the chimpanzees.  There was no assignment for the remaining cases as the orthologous chimpanzee base was different from both the alleles of humans or there is a chance of 18.8 percent that it just could not be identified surely with the draft sequence that is currently available of the chimpanzee. The ancestral alleles in general, tend to have a high frequency when compared to the derived alleles as it is shown in Figure S9. However, approximately 9.1 percent of derived alleles have the frequency of greater than or equal to 80 percent.
Human genetic variations hold tremendous amounts of information about the events of selection, which have in turn shaped our entire species! A strong positive selection causes the creation of a unique signature of a sweep that is very selective- hence, an allele that is rare quickly rises to fixation, while also carries the haplotype, which generally occurs in a high frequency. This effect is also called the hitchhiking effect. There should be a significant distinctive signature in the surrounding regions, which is a sign of significant reduction in the overall diversity. This is also an indication of an excess of the alleles that are derived with high frequency in the population because of the hitchhiking of the derived alleles on the haplotype that is selected. This pattern could possibly be detectable until 250,000 post the ending of the selective sweep. 
Essential question(s)- What does the similarities and differences in the genomes mean to us?
The chimpanzee genome sequencing is the most awaited turning point, which provided many opportunities to explore the primate evolution along with contributions to the genetic aspects of human diseases and physiology. The difference between the two genomes is about 4 percent, which is comprised of 35 million single nucleotide differences and approximately 90 Mb of deletions and insertions.
While the similarities and differences help us find answers to many disease conditions, there is also the responsibility of practicing the gene sequencing ethically. The genome sequence might have been acquired without any injury to the chimpanzees, but as the authors mentioned in their article it is sadly very true that the availability of genome sequence will suddenly hike the obdurate pressure and needs to use chimpanzees in many experiments. The ultimate goal of comparisons of genomes – besides advancing humans in a healthy state of manner in to the future – is to increase our awareness of their endangerment and enhance our responsibilities towards these species that have very less differences with us.
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