Chimpanzee Genome Project

The Chimpanzee Genome Project is an effort to determine the DNA sequence of the Chimpanzee genome. It is expected that by comparing the genomes of humans and other apes, it will be possible to better understand what makes humans distinct from other species from a genetic perspective.

Human and chimpanzee chromosomes are very similar. The primary difference is that humans have one fewer pair of chromosomes than do other great apes. Humans have 23 pairs of chromosomes and other great apes have 24 pairs of chromosomes. In the human evolutionary lineage, two ancestral ape chromosomes fused at their telomeres, producing human chromosome 2.[3] There are nine other major chromosomal differences between chimpanzees and humans: chromosome segment inversions on human chromosomes 1, 4, 5, 9,12, 15, 16, 17, and 18. After the completion of the Human genome project, a common chimpanzee genome project was initiated. In December 2003, a preliminary analysis of 7600 genes shared between the two genomes confirmed that certain genes such as theforkhead-box P2 transcription factor, which is involved in speech development, are different in the human lineage. Several genes involved in hearing were also found to have changed during human evolution, suggesting selection involving human language-related behavior. Differences between individual humans and common chimpanzees are estimated to be about 10 times the typical difference between pairs of humans.[4]

About 600 genes have been identified that may have been undergoing strong positive selection in the human and chimp lineages; many of these genes are involved in immune system defense against microbial disease (example: granulysin is protective against Mycobacterium tuberculosis [8]) or are targeted receptors of pathogenic microorganisms (example: Glycophorin C and Plasmodium falciparum). By comparing human and chimp genes to the genes of other mammals, it has been found that genes coding fortranscription factors, such as forkhead-box P2 (FOXP2), have often evolved faster in the human relative to chimp; relatively small changes in these genes may account for the morphological differences between humans and chimps. A set of 348 transcription factor genes code for proteins with an average of about 50 percent more amino acid changes in the human lineage than in the chimp lineage.

Six human chromosomal regions were found that may have been under particularly strong and coordinated selection during the past 250,000 years. These regions contain at least one marker allele that seems unique to the human lineage while the entire chromosomal region shows lower than normal genetic variation. This pattern suggests that one or a few strongly selected genes in the chromosome region may have been preventing the random accumulation of neutral changes in other nearby genes. One such region on chromosome 7 contains the FOXP2 gene (mentioned above) and this region also includes the Cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is important for ion transport in tissues such as the salt-secreting epithelium of sweat glands. Human mutations in the CFTR gene might be selected for as a way to survivecholera.[9]

Another such region on chromosome 4 may contain elements regulating the expression of a nearby protocadherin gene that may be important for brain development and function. Although changes in expression of genes that are expressed in the brain tend to be less than for other organs (such as liver) on average, gene expression changes in the brain have been more dramatic in the human lineage than in the chimp lineage.[10] This is consistent with the dramatic divergence of the unique pattern of human brain development seen in the human lineage compared to the ancestral great ape pattern. The protocadherin-beta gene cluster on chromosome 5 also shows evidence of possible positive selection.[11]

Results from the human and chimp genome analyses should help in understanding some human diseases. Humans appear to have lost a functional caspase-12 gene, which in other primates codes for an enzyme that may protect against Alzheimer’s disease.

The results of the chimpanzee genome project suggest that when ancestral chromosomes 2A and 2B fused to produce human chromosome 2, no genes were lost from the fused ends of 2A and 2B. At the site of fusion, there are approximately 150,000 base pairs of sequence not found in chimpanzee chromosomes 2A and 2B. Additional linked copies of the PGML/FOXD/CBWD genes exist elsewhere in the human genome, particularly near the p end of chromosome 9. This suggests that a copy of these genes may have been added to the end of the ancestral 2A or 2B prior to the fusion event. It remains to be determined if these inserted genes confer a selective advantage.

  • PGML. The phosphoglucomutase-like gene of human chromosome 2. This gene is incomplete and may not produce a functional transcript.[12]
  • FOXD. The forkhead box D4-like gene is an example of an intronless gene. The function of this gene is not known, but it may code for a transcription control protein.
  • CBWD. Cobalamin synthetase is a bacterial enzyme that makes vitamin B12. In the distant past, a common ancestor to mice and apes incorporated a copy of a cobalamin synthetase gene (see: Horizontal gene transfer). Humans are unusual in that they have several copies of cobalamin synthetase-like genes, including the one on chromosome 2. It remains to be determined what the function of these human cobalamin synthetase-like genes is. If these genes are involved in vitamin B12 metabolism, this could be relevant to human evolution. A major change in human development is greater post-natal brain growth than is observed in other apes. Vitamin B12is important for brain development, and vitamin B12 deficiency during brain development results in severe neurological defects in human children.
  • CXYorf1-like protein. Several transcripts of unknown function corresponding to this region have been isolated. This region is also present in the closely related chromosome 9p terminal region that contains copies of the PGML/FOXD/CBWD genes.
  • Many ribosomal protein L23a pseudogenes are scattered through the human genome.

The origin of language in the human species has been the topic of scholarly discussions for several centuries. In spite of this, there is no consensus on the ultimate origin or age of human language. One problem makes the topic difficult to study: the lack of direct evidence. Consequently, scholars wishing to study the origins of language must draw inferences from other kinds of evidence such as the fossil record, archaeological evidence, contemporary language diversity, studies of language acquisition, and comparisons between human language and systems of communication existing among other animals (particularly other primates). Many argue that the origins of language probably relate closely to the origins of modern human behavior, but there is little agreement about the implications and directionality of this connection.

This shortage of empirical evidence has led many scholars to regard the entire topic as unsuitable for serious study. In 1866, the Linguistic Society of Paris banned any existing or future debates on the subject, a prohibition which remained influential across much of the western world until late in the twentieth century.[1] Today, there are numerous hypotheses about how, why, when, and where language might have emerged.[2] Despite this, there is scarcely more agreement today than a hundred years ago, when Charles Darwin‘s theory of evolution by natural selection provoked a rash of armchair speculations on the topic.[3] Since the early 1990s, however, a number of linguists, archaeologists,psychologists, anthropologists, and others have attempted to address with new methods what some consider “the hardest problem in science.”[4]

Noam Chomsky, a prominent proponent of discontinuity theory, argues that a single chance mutation occurred in one individual in the order of 100,000 years ago, instantaneously installing the language faculty (a component of the mind-brain) in “perfect” or “near-perfect” form.[6] According to this view, emergence of language resembled the formation of a crystal; with digital infinity as the seed crystal in a super-saturated primate brain, on the verge of blossoming into the human mind, by physical law, once evolution added a single small but crucial keystone.[7][8] It follows from this theory that language appeared rather suddenly within the history of human evolution.

A majority of linguistic scholars as of 2015 hold continuity-based theories, but they vary in how they envision language development. Among those who see language as mostly innate, some — notably Steven Pinker[9] — avoid speculating about specific precursors in nonhuman primates, stressing simply that the language faculty must have evolved in the usual gradual way.[10] Others in this intellectual camp — notably Ib Ulbæk[5] — hold that language evolved not from primate communication but from primate cognition, which is significantly more complex.

Those who see language as a socially learned tool of communication, such as Michael Tomasello, see it developing from the cognitively controlled aspects of primate communication, these being mostly gestural as opposed to vocal.[11][12] Where vocal precursors are concerned, many continuity theorists envisage language evolving from early human capacities for song.[13][14][15][16]

Transcending the continuity-versus-discontinuity divide, some scholars view the emergence of language as the consequence of some kind of social transformation[17] that, by generating unprecedented levels of public trust, liberated a genetic potential for linguistic creativity that had previously lain dormant.[18][19][20] “Ritual/speech coevolution theory” exemplifies this approach.[21][22] Scholars in this intellectual camp point to the fact that even chimpanzees and bonobos have latent symbolic capacities that they rarely – if ever – use in the wild.[23] Objecting to the sudden mutation idea, these authors argue that even if a chance mutation were to install a language organ in an evolving bipedal primate, it would be adaptively useless under all known primate social conditions. A very specific social structure — one capable of upholding unusually high levels of public accountability and trust — must have evolved before or concurrently with language to make reliance on “cheap signals” (words) an evolutionarily stable strategy.

Because the emergence of language lies so far back in human prehistory, the relevant developments have left no direct historical traces; neither can comparable processes be observed today. Despite this, the emergence of new sign languages in modern times — Nicaraguan Sign Language, for example — may potentially offer insights into the developmental stages and creative processes necessarily involved.[24] Another approach inspects early human fossils, looking for traces of physical adaptation to language use.[25][26] In some cases, when the DNA of extinct humans can be recovered, the presence or absence of supposedly language-relevant genes — FOXP2, for example — may prove informative.[27] Another approach, this time archaeological, involves invoking symbolic behavior (such as repeated ritual activity) that may leave an archaeological trace — such as mining and modifying ochre pigments for body-painting — while developing theoretical arguments to justify inferences from symbolism in general to language in particular.[28][29][30]

The time range for the evolution of language and/or its anatomical prerequisites extends, at least in principle, from the phylogenetic divergence of Homo (2.3 to 2.4 million years ago) from Pan (5 to 6 million years ago) to the emergence of full behavioral modernity some 150,000 – 50,000 years ago. Few dispute that Australopithecus probably lacked vocal communication significantly more sophisticated than that of great apes in general,[31] but scholarly opinions vary as to the developments since the appearance of Homosome 2.5 million years ago. Some scholars assume the development of primitive language-like systems (proto-language) as early as Homo habilis, while others place the development of symbolic communication only with Homo erectus (1.8 million years ago) or with Homo heidelbergensis (0.6 million years ago) and the development of language proper with Homo sapiens, currently estimated at less than 200,000 years ago.

Using statistical methods to estimate the time required to achieve the current spread and diversity in modern languages, Johanna Nichols — a linguist at the University of California, Berkeley — argued in 1998 that vocal languages must have begun diversifying in our species at least 100,000 years ago.[32] A further study by Q. D. Atkinson[14]suggests that successive population bottlenecks occurred as our African ancestors migrated to other areas, leading to a decrease in genetic and phenotypic diversity. Atkinson argues that these bottlenecks also affected culture and language, suggesting that the further away a particular language is from Africa, the fewer phonemes it contains. By way of evidence, Atkinson claims that today’s African languages tend to have relatively large numbers of phonemes, whereas languages from areas in Oceania (the last place to which humans migrated), have relatively few. Relying heavily on Atkinson’s work, a subsequent study has explored the rate at which phonemes develop naturally, comparing this rate to some of Africa’s oldest languages. The results suggest that language first evolved around 350,000-150,000 years ago, which is around the time when modern Homo sapiensevolved.[33] Estimates of this kind are not universally accepted but genetic, archaeological, palaeontological and much other evidence has led to a near-consensus that language probably emerged somewhere in sub-Saharan Africa during the Middle Stone Age, roughly contemporaneous with the speciation of Homo sapiens.[34]

Evolutionary linguistics is the scientific study of the psychosocial development and cultural evolution of individual languages as well as the origins and development of human language itself.[1] The main challenge in this research is the lack of empirical data: spoken language leaves practically no traces. This led to an abandonment of the field for more than a century. Since the late 1980s, the field has been revived in the wake of progress made in the related fields of psycholinguistics, neurolinguistics, evolutionary anthropology, evolutionary psychology, universal grammar, and cognitive science.

Evolutionary linguistics as a field is rapidly emerging as a result of developments in neighboring disciplines. To what extent language’s features are determined by genes, a hotly debated dichotomy in linguistics, has had new light shed upon it by the discovery of the FOXP2 gene.[7][8] An English family with a severe, heritable language dysfunction was found to have a defective copy of this gene.[9][10] Mutations of the corresponding gene in mice (FOXP2 is fairly well conserved; modern humans share the same allele as Neanderthals)[11][12] cause reductions in size and vocalization rate. If both copies are damaged, the Purkinje layer (a part of the cerebellum that contains better-connected neurons than any other) develops abnormally, runting is more common, and pups die within weeks due to inadequate lung development.[13] Additionally, higher presence of FOXP2 in songbirds is correlated to song changes, with downregulation causing incomplete and inaccurate song imitation in zebra finches. In general, evidence suggests that the protein is vital to neuroplasticity. There is little support, however, for the idea that FOXP2 is ‘the grammar gene’ or that it had much to do with the relatively recent emergence of syntactical speech.[14]

Another controversial dichotomy is the question of whether human language is solely human or on a continuum with (admittedly far removed) animal communication systems. Studies in ethology have forced researchers to reassess many claims of uniquely human abilities for language and speech. For instance, Tecumseh Fitch has argued that the descended larynx is not unique to humans. Similarly, once held uniquely human traits such as formant perception, combinatorial phonology and compositional semantics are now thought to be shared with at least some nonhuman animal species. Conversely, Derek Bickerton and others argue that the advent of abstract words provided a mental basis for analyzing higher-order relations, and that any communication system that remotely resembles human language utterly relies on cognitive architecture that co-evolved alongside language.

Forkhead box protein P2 (FOXP2) is a protein that, in humans, is encoded by the FOXP2 gene, also known as CAGH44,SPCH1 or TNRC10, and is required for proper development of speech and language.[1] Initially identified as the genetic factor of speech disorder in KE family, its gene is the first gene discovered associated with speech and language.[2] The gene is located on chromosome 7 (7q31, at the SPCH1 locus), and is expressed in fetal and adult brain, heart, lung and gut.[3][4] FOXP2 orthologs[5] have also been identified in other mammals for which complete genome data are available. The FOXP2 protein contains a forkhead-box DNA-binding domain, making it a member of the FOX group of transcription factors, involved in regulation of gene expression. In addition to this characteristic forkhead-box domain, the protein contains a polyglutamine tract, a zinc finger and a leucine zipper. The gene is more active in females than in males, to which could be attributed better language learning in females.[6]

In humans, mutations of FOXP2 cause a severe speech and language disorder.[1][7] Versions of FOXP2 exist in similar forms in distantly related vertebrates; functional studies of the gene in mice[8] and in songbirds[9] indicate that it is important for modulating plasticity of neural circuits.[10] Outside the brain FOXP2 has also been implicated in development of other tissues such as the lung and gut.[11]

FOXP2 is popularly dubbed the “language gene”, but this is only partly correct since there are other genes involved in language development.[12] It directly regulates a number of other genes, including CNTNAP2, CTBP1, and SRPX2.[13][14]

Two amino acid substitutions distinguish the human FOXP2 protein from that found in chimpanzees,[15] but only one of these two changes is unique to humans.[11] Evidence from genetically manipulated mice[16] and human neuronal cell models[17] suggests that these changes affect the neural functions of FOXP2.

FOXP2 is required for proper brain and lung development. Knockout mice with only one functional copy of the FOXP2 gene have significantly reduced vocalizations as pups.[28] Knockout mice with no functional copies of FOXP2 are runted, display abnormalities in brain regions such as the Purkinje layer, and die an average of 21 days after birth from inadequate lung development.[11]

FOXP2 is expressed in many areas of the brain[15] including the basal ganglia and inferior frontal cortex where it is and is essential for brain maturation and speech and language development.[13]

A knockout mouse model has been used to examine FOXP2’s role in brain development and how mutations in the two copies of FOXP2affect vocalization. Mutations in one copy result in reduced speech while abnormalities in both copies cause major brain and lung developmental issues.[11]

The expression of FOXP2 is subject to post-transcriptional regulation, particularly micro RNA, which binds to multiple miRNA binding-sites in the neocortex, causing the repression of FOXP2 3’UTR.[29]

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