Wow, that's quite a spurious claim, Easyrider.
Evidence
Human Chromosome 2:
Human chromosome 2 is the result of the fusion of two ancestral chromosomes in our lineage. This is evidenced by
telomere sequence in it's center and two
centromeres within the chromosome, one being deactivated. Human chromosome 2 is highly similar in sequence to two chromosomes which remain seperate in the chimpanzee lineage suggesting that we share a common ancestor with chimpanzees and that the fusion event occured after the divergance of our respective linages.
General reading/viewing:
[1] [2] [3]
Journal reading:
[1]Human chromosome 2 was formed by the head-to-head fusion of two ancestral chromosomes that remained separate in other primates.
[2]The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions.
[3]We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.
Similarities in chromosome banding patterns and hybridization homologies between ape and human chromosomes suggest that human chromosome 2 arose out of the fusion of two ancestral ape chromosomes (1-3).
[4]Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes.
Endogenous Retroviruses:
Endogenous retroviruses are the
genomes of viruses permanently inserted into a population's
gene pool due to being inherited through the
germ line. When incorporated into a random location along the genome, or
locus, the endogenous retrovirus remains and can even be 'copy pasted' to other areas of the genome. When two or more endogenous retroviruses of the same locus between humans and chimps are found, the only reliable explanation to avoid the miniscule chance of them having integrated independantly is inheritance from a common ancestor.
General reading:
[1]
Journal reading:
[1]The human endogenous retrovirus type II (HERVII) family of HERV genomes has been found by Southern blot analysis to be characteristic of humans, apes, and Old World monkeys. New World monkeys and prosimians lack HERVII proviral genomes. Cellular DNAs of humans, common chimpanzees, gorillas, and orangutans, but not lesser ape lar gibbons, appear to contain the HERVII-related HLM-2 proviral genome integrated at the same site (HLM-2 maps to human chromosome 1). This suggests that the ancestral HERVII retrovirus(es) entered the genomes of Old World anthropoids by infection after the divergence of New World monkeys (platyrrhines) but before the evolutionary radiation of large hominoids.
[2]The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers.
The genomes of vertebrate species contain dozens to thousands of ERV sequences (2), some of which were acquired in evolutionarily recent times, whereas others derive from "ancient" times, as indicated by their identical site of integration in more than one species (1, 3, 4).
Cross-hybridization and PCR studies consistently reveal that most HERV families are also found in other primates, including apes and Old World monkeys (OWMs) (12-19). Many HERVs, including the ones used in this study, are the result of integration events that took place between 5 and 50 million years ago, as indicated by the distribution of specific proviruses at the same integration sites (or "loci") among related species.
[3]Like other transposable elements, HERVs are thought to have played an important role in the evolution of mammalian genomes, and the human genome sequence has already been of use in phylogenetic studies of HERVs. By analyzing HERV integration sites, the evolution of these elements has been tracked through the primate lineage. Measurement of the divergence of LTR sequences has also been used as a 'molecular clock' to estimate the age of HERVs (given that the LTRs are identical at the time of integration) [5]. Class I and class III HERVs are the oldest groups and are present throughout the primate lineage, while class II includes HERVs that have been active most recently. Many class II loci are restricted to chimpanzees and humans and a few proviruses of the HERV-K(HLM-2) subgroup are human-specific [6], indicating that these viruses have been active within the last 5 million years.
[4]We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans.
Nine families of chimpanzee endogenous retroviruses have been transpositionally active since chimpanzees and humans diverged from a common ancestor. Seven of these transpositionally active families have orthologs in humans, one of which has also been transpositionally active in humans since the human-chimpanzee divergence about six million years ago.
[5] Most of the 68 HERV-K14I and 23 HERV-K14CI proviruses are severely mutated, frequently displaying uniform deletions of retroviral genes and long terminal repeats (LTRs). Both HERV families entered the germ line 39 million years ago, as evidenced by homologous sequences in hominoids and Old World primates and calculation of evolutionary ages based on a molecular clock.
The 'Alu' Sequence:
An Alu sequence is a small segment of DNA of around 300
base pairs in length and is repeated millions of times throughout our genome taking up roughly 10% of it's total sequence. Similarly to endogenous retroviruses, the Alu sequence is a
transposon (more specifically a
retrotransposon) and can 'copy paste' itself, which explains its sheer abundance and distribution around our genome. When two or more Alu sequences of the same locus between humans and chimps are found, the only reliable explanation to avoid the miniscule chance of them having integrated independantly is inheritance from a common ancestor.
General reading:
[1]
Journal reading:
[1]The [alpha globin pseudogenes] genes of both human and chimpanzee are flanked by the same Alu family member. The structure and position of this repeat have not been altered since the divergence of human and chimpanzee, and it is at least as well conserved as its immediate flanking sequence. Comparing human and chimpanzee, the 300 bp Alu repeat has accumulated only two base substitutions and one length mutation; the adjacent 300 bp flanking region has accumulated five base substitutions and twelve length mutations.
[2]Here we compare the sequences of seven pairs of chimpanzee and human Alu repeats. In each case, with the exception of minor sequence differences, the identical Alu repeat is located at identical sites in the human and chimpanzee genomes. The Alu repeats diverge at the rate expected for nonselected sequences. Sequence conversion has not replaced any of these 14 Alu family members since the divergence between chimpanzee and human.
[3]Phylogenetic analysis of Alu Ye5 elements and elements from several other subfamilies reveals high levels of support for monophyly of Hominidae, tribe Hominini and subtribe Hominina. Here we present the strongest evidence reported to date for a sister relationship between humans and chimpanzees while clearly distinguishing the chimpanzee and human lineages.
At eight Alu Ye5 loci and two previously identified Alu Yi and Yd loci (18, 45), amplification of filled sites was obtained in human, bonobo, and common chimpanzee.
The utility of SINE insertions, and mobile elements in general, for phylogenetic analysis continues to be bolstered by studies such as this one. Here, we present the first application of SINEs to fully elucidate the phylogeny of the hominid lineage and present the strongest evidence to date for phylogenetic relationships among the hominid lineages. Of the 133 Alu insertion loci, 95 were unambiguously informative for determining the relative divergence of each of the major lineages.
[4]The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes.
For the Ye subfamilies, 120 of the 153 elements identified in the draft human genomic sequence were amplified by PCR. Examination of the orthologous regions of the various species genomes displayed a series of different PCR patterns indicative of the time of retroposition of each of the elements into the primate genomes. Results from a series of these experiments showed a gradient of Ye Alu repeats beginning with some elements that are recent in origin and unique to the human genome (e.g. Ye5AH110) and ending with elements that are found within all ape genomes (e.g. Ye5AH148). The distribution of all the Ye elements in various primate genomes is summarized in Additional File 2. [See the word document file]
[5]Repetitive elements, particularly SINEs (short interspersed elements) and LINEs (long interspersed elements), provide excellent markers for phylogenetic analysis: their mode of evolution is predominantly homoplasy-free, since they do not typically insert in the same locus of two unrelated lineages, and unidirectional, since they are not precisely excised from a locus with the flanking sequences preserved (Shedlock and Okada 2000 ). Indeed, the use of SINEs and LINEs to elucidate phylogeny has a rich history. SINEs and LINEs have been used to show that hippopotamuses are the closest living relative of whales (Shimamura et al. 1997 ; Nikaido et al. 1999 ), to determine phylogenetic relationships among cichlid fish (Takahashi et al. 2001a ,b ; Terai et al. 2003 ), and to elucidate the phylogeny of eight Primate species, providing the strongest evidence yet that chimps are the closest living relative of humans (Salem et al. 2003 ). In each one of these studies, the presence or absence of a repetitive element at a specific locus in a given species was determined experimentally by PCR analysis, using flanking sequences as primers.
Pseudogenes:
Pseudogenes are defunct genes being either a copy of the original or the original itself. Copies of a gene can arise due to duplication of a genetic segment thus duplicating any genes contained on it where as pseudogenes arising from the original copy arise due to the loss of function of the gene in question. For example, the human olfactory (smell) system is coded for by many genes, 40% of which having become redundant pseudogenes in our linage and prior to. As for endogenous retroviruses and the Alu sequence, when two or more of the same pseudogene sequences of the same locus between humans and chimps are found, the only reliable explanation to avoid the miniscule chance of them having come about independantly is inheritance from a common ancestor. Also, the same pseudogenes present as defunct copies of functional genes,
with the same mistakes in thier code, in both humans and chimps allude to common ancestry.
General reading:
[1] [2] (the molecular biology section)
Journal reading:
[1]The olfactory receptor (OR) subgenome harbors the largest known gene family in mammals, disposed in clusters on numerous chromosomes. We have carried out a comparative evolutionary analysis of the best characterized genomic OR gene cluster, on human chromosome 17p13. Fifteen orthologs from chimpanzee (localized to chromosome 19p15), as well as key OR counterparts from other primates, have been identified and sequenced.
We also demonstrate that the functional mammalian OR repertoire has undergone a rapid decline in the past 10 million years: while for the common ancestor of all great apes an intact OR cluster is inferred, in present-day humans and great apes the cluster includes nearly 40% pseudogenes.
[2]We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates.
Pseudogenes are usually considered the evolutionary endpoint of genomic material whose ultimate fate is to be removed from a genome. Nevertheless, millions of years of evolution has left the human genome with thousands of pseudogenes (Torrents et al. 2003 ; Zhang et al. 2003 ). Within the ENCODE project, the MSA group has identified and sequenced the orthologous regions of the individual ENCODE target regions in 20–28 vertebrate (mostly mammalian) species (see Methods for the list). Several algorithms such as TBA (Threaded Blockset Aligner) (Blanchette et al. 2004 ) have also been applied to construct multispecies sequence alignments across the entire ENCODE regions (The ENCODE Project Consortium 2007 ; Margulies et al. 2007 ). With these data, it is possible to survey the preservation of sequences corresponding to the human pseudogenes in other species to get a glimpse of the evolutionary process leading to the human lineage.
These results demonstrate that most ( 80%) human processed pseudogenes arise from sequences specific to the primate lineage and are in good agreement with previous data estimated with molecular clocks using pseudogenes and SINE (short interspersed elements) repeats (Ohshima et al. 2003 ).
[3]We have determined the sequence of 2400 base pairs upstream from the human pseudo alpha globin (psi alpha) gene, and for comparison, 1100 base pairs of DNA within and upstream from the chimpanzee psi alpha gene. The region upstream from the promoter of the psi alpha gene shows no significant homology to the intergenic regions of the adult alpha 2 and alpha 1 globin genes. The chimpanzee gene has a coding defect in common with the human psi alpha gene, showing that the product of this gene, if any, was inactivated before the divergence of human and chimpanzee. However the chimpanzee gene contains a normal ATG initiation codon in contrast to the human gene which has GTG as the initiation codon. The psi alpha genes of both human and chimpanzee are flanked by the same Alu family member. The structure and position of this repeat have not been altered since the divergence of human and chimpanzee, and it is at least as well conserved as its immediate flanking sequence. Comparing human and chimpanzee, the 300 bp Alu repeat has accumulated only two base substitutions and one length mutation; the adjacent 300 bp flanking region has accumulated five base substitutions and twelve length mutations.
Aside from thier use as direct phylogenetic markers, pseudogenes such as L-gulono-gamma-lactone oxidase, the gene which is supposed to code for the
enzyme which synthesises vitamin c, are predicted by evolutionary theory, i.e. if we share common ancestry with organisms which have a functioning copy of the vitamin c enzyme and we do not have the enzyme, it's imperative, by evolutionary standards, that we find a pseudogene of the enzyme in it's place. Perhaps not surprisingly, evolutionary theory also predicts to find the same pseudogene in other primates as they all lack the ability to synthesise thier own vitamin c as well.
[4]Man is among the exceptional higher animals that are unable to synthesize L-ascorbic acid because of their deficiency in L-gulono-gamma-lactone oxidase, the enzyme catalyzing the terminal step in L-ascorbic acid biosynthesis. In the present study, we isolated a segment of the nonfunctional L-gulono-gamma-lactone oxidase gene from a human genomic library, and mapped it on chromosome 8p21.1 by spot blot hybridization using flow-sorted human chromosomes and fluorescence in situ hybridization. Sequencing analysis indicated that the isolated segment represented a 3'-part of the gene, where the regions corresponding to exons VII, IX, X, and XII of the rat L-gulono-gamma-lactone oxidase gene remain with probable deletion of the regions corresponding to exons VIII and XI. In the identified exon regions were found various anomalous nucleotide changes, such as deletion and insertion of nucleotide(s) and nonconformance to the GT/AG rule at intron/exon boundaries. When the conceptual amino acid sequences deduced from the four exon sequences were compared with the corresponding rat sequences, there were a large number of nonconservative substitutions and also two stop codons. These findings indicate that the human nonfunctional L-gulono-gamma-lactone oxidase gene has accumulated a large number of mutations without selective pressure since it ceased to function during evolution.
[5]Humans and other primates have no functional gene for L-gulono-gamma-lactone oxidase that catalyzes the last step of L-ascorbic acid biosynthesis. The 164-nucleotide sequence of exon X of the gene was compared among human, chimpanzee, orangutan, and macaque, and it was found that nucleotide substitutions had occurred at random throughout the sequence with a single nucleotide deletion, indicating that the primate L-gulono-gamma-lactone oxidase genes are a typical example of pseudogene.
As another example of common pseudogenes, notice those of the RT6 gene - a gene coding for a cell membrane protein - in both humans and chimpanzees. Interestingly, notice the exact same
nonsense stop codon within the gene sequence for all human and chimpanzee genes tested. And as the final example for the time being, notice the beta-globin pseudogene - a gene once coding for a hemoglobin protein - in both humans, chimps and gorillas. Interestingly, notice the exact same mistakes throughout each; a single substitution in the initiator codon, a single substitution in codon 15 which makes the same stop codon and the same single frame shifting deletion in codon 20.
[6]We have now cloned and sequenced the homologues of the RT6 genes from humans of distinct ethnic backgrounds and of the chimpanzee. Surprisingly, in each case, three premature in-frame stop codons preclude expression of the single copy RT6 gene as a cell surface protein. Otherwise, the RT6 genes of human and chimpanzee exhibit high structural conservation to their rodent counterparts. RNA expression analyses indicate that the RT6 gene is not transcriptionally active in human T cells or any other human tissue analyzed so far. To our knowledge, RT6 represents the first mammalian membrane protein identified that has been lost universally in the human and chimpanzee species due to gene inactivation.
[7]The beta-globin gene cluster of human, gorilla and chimpanzee contain the same number and organization of beta-type globin genes: 5'-epsilon (embryonic)-G gamma and A gamma (fetal)-psi beta (inactive)-delta and beta (adult)-3'. We have isolated the psi beta-globin gene regions from the three species and determined their nucleotide sequences. These three pseudogenes each share the same substitutions in the initiator codon (ATG----GTA), a substitution in codon 15 which generates a termination signal TGG----TGA, nucleotide deletion in codon 20 and the resulting frame shift which yields many termination signals in exons 2 and 3. The basic structure of these psi beta-globin genes, however, remains consistent with that found for functional beta-globin genes: their coding regions are split by two introns, IVS 1 (which splits codon 30, 121 base-pairs in length) and IVS 2 (which splits codon 104, 840 to 844 base-pairs in length). These introns retain the normal splice junctions found in other eukaryotic split genes. The three hominoid psi beta-globin genes show a high degree of sequence correspondence, with the number of differences found among them being only about one-third of that predicted for DNA sites evolving at the neutral rate (i.e. for sites evolving in the absence of purifying selection). Thus, there appears to be a deceleration in the rate of evolution of the psi beta-globin locus in higher primates.
The redundancy of the genetic code:
The genetic code is redundant. This essentially means that different sequences of
nucleotides can code for the same protein product. This is due to the fact that there are often multiple
codons encoding the release of one
amino acid into a
polypeptide chain during the cellular process of
translation.
Here is a picture of the universal genetic code –
Each three letter sequence, or codon (shown as the RNA version in this case) shows it’s amino acid product. To show an example for the redundancy of the genetic code, take the amino acid
Leucine (Leu) as an example. From the universal genetic code, we can see that no less than four codons code for it. This means that the DNA sequences (codons) that code for the amino acid Leucine are GAA, GAG, GAT and GAC (the biologists here will understand why). As a result of this redundancy, it’s not unreasonable to expect that if humans and chimps had arisen independently, that they should have no reason to have any identical genes barring any uncanny and low chance coincidence. Also, any identical genes we do find should go some way to bolstering the inferential evidence for our common ancestry.
General reading:
[1]
Journal reading:
[1]Interestingly, there are several genes that showed the identical nucleotide sequence between different species (see Table 3). For example, both amino acid and nucleotide (coding part) sequences of beta-2 microglobulin were identical among human, chimp, and gorilla genomes, while the interleukin-2 precursor gene sequences from human and gibbon were identical. (Data for other three species were not available.)
[2]Among the 231 genes associated to a canonical ORF, 179 show a coding sequence of identical length in human and chimpanzee and exhibit similar intron–exon boundaries. For those 179 genes, the average nucleotide and amino acid identity in the coding region is 99.29% and 99.18%, respectively. Of these, 39 genes show an identical amino acid sequence between human and chimpanzee, including seven in which the nucleotide sequence of the coding region is also identical (Supplementary Table 3).
[3]Here we have sequenced Tau [gene] exons 1-13, including flanking intronic regions, and the region in intron 9 that contains Saitohin in chimpanzees, gorillas, and gibbons. Partial sequences were obtained for cynomolgus macaque and green monkey. Chimpanzee brain tau was 100% identical to human tau. Identities were 99.5% for gorilla tau and 99.0% for gibbon tau. Chimpanzee DNA was polymorphic for a repeat in intron 9, which was present in human and gorilla tau, and for the nucleotide at position +29 of the intron that follows exon 10.
Downsides:
The main downfall of this line of evidence is the fact that there exists a
codon bias whereby certain codons are favoured over others. However, one wonders why the codon biases between Pan Troglodytes (common chimpanzee) and Homo Sapiens are so similar:
http://www.kazusa.or.jp/codon/cgi-bin/s ... es+[gbpri]
http://www.kazusa.or.jp/codon/cgi-bin/s ... ns+[gbpri]
These are evidences as, according to the theory of evolution, many of them must be true in order for us and chimps to share common ancestry. There were hypotheses of what we must find, if evolution were true, these hypotheses were tested upon investigation of DNA, and, unsurprisigly to anyone who knows how strong evolutionary theory is, they all came up trumps, thus making all of the DNA in question evidence.
