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Posted: June 26, 2009 07:16 pm  | |||
      IRC Nickname: Owennnn Group: Emeritus Posts: 1447 Member No.: 37 Joined: December 30, 2007 Total Events Attended: 55    | “Evidence for and Applications of the Molecular Clock” Abstract Since the first discovery of fossils, mankind has pondered the species that dwelt on the Earth before humans, and after Darwin’s publication of “On the Origin of Species” in 1859 scientists have investigated and theorised as to the evolution and divergence that lead up to the organisms that live on the Earth today. Until fairly recently, the only timescale of evolution, and methods of deducing evolutionary pathways has come from the fossil record, however, new techniques in molecular genetics has provided a new insight into the time and rates of evolution. By the comparison of genetic macromolecules (Proteins, DNA, and RNA) of 2 or more different living species, or samples from extinct species, it can be possible to determine how long ago they shared a common ancestor; when they diverged from each other. The term ‘Molecular Clock’ refers to the hypothesis that nucleotide base substitutions (Evolution/Divergence) accumulate at a constant rate. (Wilson et al., 1987). The term ‘Absolute rates of evolution’ implies that the evolution of a gene occurs at an identical or similar rate across species, and taxa. This review intends to discuss studies which have attempted to support or dispute the Molecular Clock Hypothesis (MCH). As well as highlight studies which have been undertaken where the MCH has been applied to provide an insight and timescale into evolutionary history. Main Body Evidence supporting the Molecular Clock Hypothesis The molecular clock does not compare divergence between 2 species and their Last Common Ancestor (LCA), more it compares the difference in divergence to each species. For example, if comparing all extant organisms with their LCA (The first ever organism), the differences in divergence will be very slight. Since it has been an equal amount of time since the divergence between humans, chimpanzee, horse, mice, carp, Tetrahymena and their LCA, the extent of divergence of a gene (assuming a steady rate of evolution) will be roughly equal.  Table 1. Table 1 shows the percentage homology of mitochondrial cytochrome c between the organisms up and along each side of the table. What is notable about the data in Table 1, is that when comparing the percentage homology of cytochrome c, the difference between all the organisms and their LCA (Tetrahymena) the values are very similar (44.0 to 48.5 percent homology). As time since divergence decreases, percentage homology increases. This suggests that percentage homology is an inverse function of time since divergence, supporting the MCH.  Figure 1 better illustrates the connection between increased time since divergence and increase substitution in a gene. While comparing one protein sequence between species can support the MCH, it may not help determine the LCA of 2 organisms; as such it is best to use multiple genes to get the best comparison between 2 species. Some support for the MCH came from Vawter et al., (1980) where the divergence of Eastern Pacific and Western Atlantic/Caribbean fish species was studied. The Eastern Pacific and the Caribbean were once connected until the rise of the Isthmus of Panama, this isolated the 2 waters and caused speciation in fish populations caught either side. The rise of the Isthmus has been estimated to between 2 and 5 million years ago (Woodring, 1966). By comparing allele frequencies between Eastern Pacific and Caribbean populations of fish, Vawter et al., calculated Nei’s Genetic Distance value D, which is an estimate of the average number of codon differences per locus. Nei (1972) suggested that D values are correlated with time. In order to calibrate their molecular clock they used an internal and external source. Their internal source was the assumption that the mean interocean D value for conspecifics and germinate pairs would be equivalent to 3.5 million years of divergence. They chose 3.5 million years, as the mid point of the estimate of the rise of the Panama Isthmus. Their external calibration for the clock was a genetic distance-divergence time correlation obtained for other vertebrates, by Sarich (1977). Sarich observed a correlation between Albumin Immunological Distance estimates (A.I.D.) and Nei’s aforementioned D value; 1 D value = 35 A.I.D units. Carlson et al., (1978) found that the best calibration of A.I.D to divergence time resulted in 1 A.I.D = 0.54 million years; thus 1 D value = 18.9 million years since divergence. To support the MCH, Vawter et al.’s results needed to show a D value of roughly 0.2, since 1 D value = 18.9 million years, 0.2 D value = 3.78 million years. Their results showed a mean D value of 0.214 with a range of 0.131 to 0.361. Using the ratio of 1 D value: 18.9 million years, they calculated a divergence time between 2.1 and 5.9 million years ago, this is during the accepted time span for the rise of the Isthmus of Panama, suggesting that the Isthmus did isolate the fish populations in the Eastern Pacific and Caribbean. Since both Vawter’s external and internal calibrations matched, this suggested that rate of protein divergence conforms to a time function and strongly supports the MCH. Chen et al., (2009) studied the rates of nuclear and mitochondrial DNA substitution in 48 species of coral, particularly Acropora spp. Using nuclear Calmodulin (CaM) and mitochondrial intergenic space (IGS). They found that coral mitochondrial genomes evolve between 2 to 5 times slower than the coral nuclear genome. Coincidentally this is a similar divergence rate ratio to the one found in plants. (Wolfe et al., 1987) Evidence disputing the Molecular Clock Hypothesis A study by Nabholz et al., (2009), into the variations of mutation rate of mtDNA in birds disputed the MCH by showing that mtDNA substitution rates were highly variable, among birds and mammals. They studied the substitution rates of mitochondrial cytochrome b in 1571 bird species ( ~15% of total living bird species), as well as comparing them to 1696 mammal species from an earlier study (Nabholz et al., 2008). Their results showed that bird species had highly variable cytb substitution rates, passerines having the highest, with the fastest species substitution rates being 30 times higher than the slowest species. When the data was compared to the 1696 mammal species it was shown that mammals’ cytb substitution rates were significantly higher than the majority of bird species. However, when comparing birds and mammals with similar body mass, it was shown that mtDNA substitution rates were much higher in birds. Much of the evidence from studies seems to point towards a gene specific molecular clock, and an increased propensity for some genes to conform to a more uniform rate of evolution than others. Applications of the Molecular Clock Being able to determinate, or estimate rates and times of divergence can be a useful tool in a large number of scientific disciplines, including palaeontology, phylogenetics, cladistics, and many others. This section of the review will discuss a number of studies in different areas of biology which apply the Molecular Clock Hypothesis to their studies to provide a deeper insight into the results found. The Molecular Clock in Ecology Hibbet et al., (2009), were studying symbiotic funghi and their plant hosts to determine the evolution of the Ectomycorrhizal (ECM) symbiotic habit, in particular, in that of Agaricomycetes, a polyphyletic group of funghi containing a large number of ECM forming species. Working from nodes in the Agaricomycetes phylogenetic tree that subtend to species with the ECM habit, they used Bayesian Molecular Clock analyses to determine whether ECM forming species evolved before or after their hosts. If evolution occurred after, they ask whether it is plausible that their ancestors may have been involved in ancient ECM habits, with ancient or extant hosts.  Fig 2 (Hibbet et al., 2009), shows that the hosts of the Agaricomycetes funghi evolved after the Agaricomycetes themselves and other ECM forming funghi, meaning they were not involved in an ECM forming relationship and the ECM habit evolved after the divergence of the hosts. The Molecular Clock in Species Discrimination Smith et al., (2009) used Molecular Clock analyses, using mtDNA markers, to identify genetic and morphologic divergence among South Pacific Seaperches and estimate a time of divergence using cytb and the mitochondrial control region Smith et al. identified 4 distinct clades of seaperch as well as 2 outlying species in their own clades. Assuming a molecular clock it was estimated that these species diverged 0.7-2.6mya.  Figure 3 shows a phylogenetic tree based on cytochrome b divergence. The clades discovered (bracketed on the right) are: NZ–TV inshore, coastal waters around New Zealand, Norfolk Ridge, Lord Howe Rise and includes the inshore morph from Tasmania and Victoria; TV offshore, Tasmania and Victoria; FS–LR, Foundation Seamounts and Louisville Ridge; CR–KR–NR, Chatham Rise–Kermadec Ridge–Norfolk Ridge. The Molecular Clock in Phylogeography In phylogeography, the study of genetic dispersal and colonization, Garb et al. (2009) studied “Diversity despite dispersal”, in particular, the contradictory tendencies of crab spiders to i) show dramatic ecological diversity within the Hawaiian islands, and ii) show widespread distribution of some species across the archipelago. Using both nuclear DNA and mtDNA sampled from six islands Garb et al. generated phylogenetic hypotheses for the Mecaphesa (crab spider) species and populations. Using molecular clock analyses they estimated arrival times on different islands. Their results showed a large number of clades, some isolated to certain islands in the archipelago, some dispersed across a number of islands, and this suggested that dispersal occurred at a higher rate than mutation. Using their molecular clock analyses, the majority of estimated divergence, and arrival times on newly formed islands fell either from <1mya to between 4-5mya, based on assumptions of immediate colonization of newly formed islands. Conclusion The Molecular Clock Hypothesis is still a much disputed subject in the scientific community, and while it can be agreed that there is no overriding Clock governing the rate of evolution of every gene on the planet, the hypothesis cannot be easily dismissed due to a large amount of studies (Vawter et al., Chen et al.) displaying almost uniform rates of gene substitution across species and taxa which can not be put down to coincidence. Further research will obviously be required, in particular comparing gene substitution rates between different orders or families, as well as multi gene substitution rates in single species or families with a well documented genetic history. -------------------- | ||
Posted: June 26, 2009 10:11 pm | |||
 IRC Nickname: Dnovelta Group: Emeritus Posts: 2750 Member No.: 130 Joined: January 20, 2008 Total Events Attended: 137 | I agree wholeheartedly. Actually didn´t read through it. Read the first bit and knew it was all way over my head. Looks interesting and is something I´ll probably have to study myself since I´ll be doing into medicine. Seems interesting though. --------------------   | ||
Posted: June 27, 2009 04:21 am | |||
| IRC Nickname: Stokenut Group: Guest Posts: 2062 Member No.: 805 Joined: June 10, 2008 Total Events Attended: 112 | Noone reads long posts. My essay would be...
A* for creativity. -------------------- Over 6 years of history and friendship, deleted over a difference in an opinion. --- Challenge any creationist to a debate. They'll run away and aggressively accuse you of "attacking" them and their "beliefs". I'm sorry, please, keep teaching our kids that they'll burn in hell if they don't believe. Mutilate their genitals against their will while you're at it. Keep influencing politics and holding back vital scientific research. I'll just keep my mouth shut to "respect" your "beliefs". | ||
MY ESSAY