stranded breaks and repeat the cycle. the fusion of two sister chromatids can cause inverted duplication and when these events are repeated throughout the cycle, the inverted region will be repeated leading to an increase in copy number. the last mechanism that can lead to copy number variations is polymerase slippage, which is also known as template switching. during normal dna replication, the polymerase on the lagging strand is required to unclamp and re-clamp the replication region continuously. when small scale repeats in the dna sequence exist already, the polymerase can be 'confused' when it re-clamps to continue replication and instead of clamping to the correct base pairs, it may shift a few base pairs and replicate a portion of the repeated region again. note that although this has been experimentally observed and is a widely accepted mechanism, the molecular interactions that led to this error remains unknown. in addition, because this type of mechanism requires the polymerase to jump around the dna strand and it is unlikely that the polymerase can re-clamp at another locus some kilobases apart, therefore this is more applicable to short repeats such as dinucleotide or trinucleotide repeats. alpha-amylase gene timeline of the change in hominin diet throughout late paleolithic, mesolithic, and neolithic periods. as seen, root vegetables rich in starch are consumed around 20,000 years ago when the amy1 diploid gene number was estimate to increase. amylase is an enzyme in saliva that is responsible for the breakdown of starch into monosaccharides, and one type of amylase is encoded by the alpha-amylase gene (amy1). the amy1 locus, as well as the amylase enzyme, is one of the most extensively studied and sequenced gene in the human genome. its homologs are also found in other primates and therefore it is likely that the primate amy1 gene is ancestral to the human amy1 gene and was adapted early in primate evolution. amy1 is one of the most well studied genes which has wide range of variable numbers of copies throughout different human populations. the amy1 gene is also one of the few genes that had been studied that displayed convincing evidence which correlates its protein function to its copy number. copy number is known to alter transcription as well as translation levels of a particular gene, however research has shown that the relationship between protein levels and copy number is variable. in the amy1 genes of european americans it is found that the concentration of salivary amylase is closely correlated to the copy number of the amy1 gene. as a result, it was hypothesized that the copy number of the amy1 gene is closely correlated with its protein function, which is to digest starch. the amy1 gene copy number has been found to be correlated to different levels of starch in diets of different populations. eight populations from different continents were categorized into high starch diets and low starch diets and their amy1 gene copy number was visualized using high resolution fish and qpcr. it was found that the high starch diet populations which consists of the japanese, hadza, and european american populations had a significantly higher (two times higher) average amy1 copy number than the low starch diet populations including biaka, mbuti, datog, yakut populations. it was hypothesized that the levels of starch in one’s regular diet, the substrate for amy1, can directly affect the copy number of the amy1 gene. since it was concluded that the copy number of amy1 is directly correlated with salivary amylase, the more starch present in the population’s daily diet, the more evolutionarily favorable it is to have multiple copies of the amy1 gene. the amy1 gene was the first gene to provide strong evidence for evolution on a molecular genetics level. moreover, using comparative genomic hybridization, copy number variations of the entire genomes of the japanese population was compared to that of the yakut population. it was found that the copy number variation of the amy1 gene was significantly different from the copy number variation in other genes or regions of the genome, suggesting that the amy1 gene was under a strong selective pressure that had little or no influence on the other copy number variations. finally, the variability of length of 783 microsatellites between the two populations were compared to copy number variability of the amy1 gene. it was found that the amy1 gene copy number range was larger than that of over 97% of the microsatellites examined. this implies that natural selection played a considerable role in shaping the average number of amy1 genes in these two populations. however, as only six populations were studied, it is important to consider the possibility that there may be other factors in their diet or culture that influenced the amy1 copy number other than starch. simplified phylogenetic tree of the great ape lineage and the number of diploid amy1 gene that each species has. amy1 gene number shown to increase after split with the chimpanzee lineage. although it is unclear when the amy1 gene copy number began to increase, it is known and confirmed that the amy1 gene existed in early primates. chimpanzees, the closest evolutionary relatives to humans, were found to have two diploid copies of the amy1 gene that is identical in length to the human amy1 gene, which is significantly less than that of humans. on the other hand, bonobos, also a close relative of modern humans, was found to have more than two diploid copies of the amy1 gene. nonetheless, the bonobo amy1 genes were sequenced and analyzed, and it was found that the coding sequences of the amy1 genes were disrupting, which may lead to the production of dysfunctional salivary amylase. it can be inferred from the results that the increase in bonobo amy1 copy number is likely not correlated to the amount of starch in their diet. it was further hypothesized that the increase in copy number began recently during early hominin evolution as none of the great apes had more than two copies of the amy1 gene that produced functional protein. in addition, it was speculated that the increase in the amy1 copy number began around 20,000 years ago when humans shifted from a hunter-gatherer lifestyle to agricultural societies, which was also when humans relied heavily on root vegetables high in starch. this hypothesis, although logical, lacks experimental evidence due to the difficulties in gathering information on the shift of human diets, especially on root vegetables that are high in starch as they cannot be directly observed or tested. recent breakthroughs in dna sequencing has allowed researchers to sequence older dna such as that of neanderthals to a certain degree of accuracy. perhaps sequencing neanderthal dna can provide a time marker as to when the amy1 gene copy number increased and offer insight into human diet and gene evolution. currently it is unknown which mechanism gave rise to the initial duplication of the amylase gene, and it can imply that the insertion of the retroviral sequences was due to non-homologous end joining, which caused the duplication of the amy1 gene. however, there is currently no evidence to support this theory and therefore this hypothesis remains conjecture. the recent origin of the multi-copy amy1 gene implies that depending on the environment, the amy1 gene copy number can increase and decrease very rapidly relative to genes that do not interact as directly with the environment. the amy1 gene is an excellent example of how gene dosage affects the survival of an organism in a given environment. the multiple copies of the amy1 gene gives those who rely more heavily on high starch diets an evolutionary advantage, therefore the high gene copy number persists in the population. brain cells among the neurons in the human brain, somatically derived copy number variations are frequent. copy number variations show wide variability (9 to 100% of brain neurons in different studies). most alterations are between 2 and 10 mb in size with deletions far outnumbering amplifications. copy number variations appear to be higher in brain cells than in other cell types. a likely source of copy number variation is incorrect repair of dna damage. genomic duplication and triplication of the gene appear to be a rare cause of parkinson's disease, although more common than point mutations. copy number variants in rcl1 gene are associated with a range of neuropsychiatric phenotypes in children. gene families, and natural selection possible mechanism of how multiple copies of a gene can lead to a protein family over years with natural selection. here, gene x is the gene of interest that is duplicated and gene x1 and gene x2 are genes that acquired mutations and became functionally different to gene x. recently, there had been discussion connecting copy number variations to gene families. gene families are defined as a set of related genes that serve similar functions but have minor temporal or spatial differences and these genes likely derived from one ancestral gene. the main reason copy number variations are connected to gene families is that there is a possibility that genes in a family may have derived from one ancestral gene which got duplicated into different copies. mutations accumulate through time in the genes and with natural selection acting on the genes, some mutations lead to environmental advantages allowing those genes to be inherited and eventually clear gene families are separated out. an example of a gene family that may have been created due to copy number variations is the globin gene family. the globin gene family is an elaborate network of genes consisting of alpha and beta globin genes including genes that are expressed in both embryos and adults as well as pseudogenes. these globin genes in the globin family are all well conserved and only differ by a small portion of the gene, indicating that they were derived from a common ancestral gene, perhaps due to duplication of the initial globin gene. research has shown that copy number variations are significantly more common in genes that encode proteins that directly interact with the environment than proteins that are involved in basic cellular activities. it was suggested that the gene dosage effect accompanying copy number variation may lead to detrimental effects if essential cellular functions are disrupted, therefore proteins involved in cellular pathways are subjected to strong purifying selection. in addition, proteins function together and interact with proteins of other pathways, therefore it is important to view the effects of natural selection on bio-molecular pathways rather than on individual proteins. with that being said, it was found that proteins in the periphery of the pathway are enriched in copy number variations whereas proteins in the center of the pathways are depleted in copy number variations. it was explained that proteins in the periphery of the pathway interact with fewer proteins and so a change in protein dosage affected by a change in copy number may have a smaller effect on the overall outcome of the cellular pathway. in the past few years, researchers seem to have shifted their focus from detecting, locating, and sequencing copy number variations to in depth analyses of the role of these copy number variations in the human genome and in nature in general. evidence is needed to further validate the relationship between copy number variations and gene families as well as the role that natural selection plays in shaping these relationships and changes. furthermore, researchers are also aiming to elucidate the molecular mechanisms involved in copy number variations as it may reveal essential information regarding structural variations in general. taking a step back, the area of structural variation in the human genome seems to be a rapidly growing research topic. not only can these research data provide additional evidence for evolution and natural selection, it can also be used to develop treatments for a wide range of genetic diseases.