Molecular Clock Hypothesis in Explaining the Divergence of Species - Essay Example

? Discuss How the Molecular Clock Hypothesis (Gene Clock, Evolutionary Clock, or Molecular Clock) Can Be Used to Explain the Divergence of Species Name: Institution: Discuss How the Molecular Clock Hypothesis (Gene Clock, Evolutionary Clock, or Molecular Clock) Can Be Used to Explain the Divergence of Species In the last forty years, the molecular clock hypothesis was deemed an invaluable tool for the creation of evolutionary timescales. The molecular clock hypothesis also serves as a null model, which is usable in testing both the rates of mutation and evolution in various species. Molecular clocks continue to influence significantly the development of molecular evolution theories. Following the noted progress in technologies that focus on DNA sequencing, the use of molecular clocks has also experienced a marked increase, allowing for profound effects on the appreciation of the temporal diversification of genomes and species. This paper will discuss the manner in which the molecular clock hypothesis can be utilised to explain the divergence evident in species. The molecular clock hypothesis focuses on the idea that molecular evolution typically takes place at a roughly uniform rate over the course of time. The molecular clock bases its processes on the contention that to date the materialization of different species, it is assumed that the degree of molecular evolution is primarily homogeneous among duplicable proteins as well as species. The molecular clock, which focuses on the molecular clock hypothesis, refers to a system used in molecular evolution, which utilises fossil constraints, and the extent of molecular change achieved to foresee the time in geologic history when taxa diverged or two independent species diverged. In essence, the molecular clock approximates when key events such as radiation and speciation took place. The molecular information used to make these calculations primarily include nucleotide sequences for amino acid and DNA sequences in proteins (Ayala 1996, p. 11731). The molecular clock is also from time to time referred to as the evolutionary clock or gene clock. Rather than calculating hours, minutes and seconds, the molecular clock computes the extent of mutations and changes that build up within the genetic order of various species over time. This means that evolutionary biologists can take advantage of this data to conclude the method through which species evolve, and to construe the time when two species diverged, particularly with regard to the evolutionary timeline. The molecular clock is comparable to a normal wristwatch so as to appreciate how the molecular clock works in providing information on the divergence of species. Notably, while a wristwatch measures time from ticks, which are essentially regular changes in time (seconds), a molecular clock, on the other hand, measures time using random changes such as DNA mutations. The originators of the molecular clock, biologist Emile Zucherkandl and chemist Linus Pauling posit that the concept of the molecular clock centres on the notion that although genetic mutations take place rather randomly, they typically occur at a moderately constant rate. As a consequence, the number of differences noted between any two gene sequences continues to increase with time. This led to the conception that the degree of mutations within a certain DNA stretch can be used effectively to measure the time of species divergence (Britten 1986, p. 1394). However, similar to other clocks, the molecular clock also needs to be calibrated. Therefore, setting a molecular clock starts with known information such as the fossil record for a certain species. Subsequently, when the rate of mutation is ascertained, calculating the species’ divergence time becomes rather straightforward. For instance, if the rate of mutation in a certain species is five every millennium and 25 mutations exist in the species’ DNA, then it becomes quite clear that the species’ sequences diverged five million years ago. A prominent element of molecular clocks lies in the fact that different genes typically evolve at distinctive rates, and this provides flexibility in terms of dating events throughout the course of the history of life. On the whole, the evolution of significant genes takes place more slowly than the evolution of genes with less critical roles in the species’ body. When using the molecular clock, speedily altering genes can be utilised to date recent evolutionary events while slowly evolving genes can effectively map ancient divergences. In essence, the molecular clock is vital for the acquisition of evolutionary data, particularly in the event that there is little or no fossil record available. For instance, fungi, which are squishy and soft, do not create fossils effectively. However, researchers can take the degree of alternation in the genes of plants or vertebrates, which have appropriate fossil records, and apply the information to the unknown group of species. Evidently, the molecular clock is also effective in placing a series of evolutionary events in a chronological sequence. This is attainable through the comparison of sequences from diverse species in order to ascertain when the species last shared common ancestry. This, in effect, also draws the species’ family tree. It is usually rather difficult to come across common ancestors between species through the use of fossils, regardless of the organism. However, although the molecular clock is somewhat controversial, it effectively enhances understanding of genome sequences. Admittedly, the molecular clock hypothesis appreciates the similarities in protein evolutionary rates between morphologically dissimilar species including those with significantly different traits of life history. The molecular clock makes use of the relative rate approach, which does not require the investigator to know the exact timing of divergence among species. The relative rate approach is primarily effective for the comparison of evolutionary rates among in-group species relative to out-groups species. The molecular clock hypothesis essentially centres on the neutral theory; comparative examinations of cytochrome c and haemoglobin protein sequences shows that the degree of amino acid substitution in the aforementioned proteins is nearly similar amongst most mammalian lineages (Li & Graur 1991, p. 67). The functioning of the molecular clock indicates that the rate of these substitutions is approximately proportional to time when considered against fossil record. Molecular data acquired from different species is applicable in the construction of phylogenetic relations among the species, thereby facilitating knowledge regarding where fossil records are either inadequate or nonexistent. In addition, the molecular clock can be used to examine serum albumin proteins, noting that these proteins also alter at regular rates. As a consequence, molecular clock can use albumins from different species as evolutionary clocks to determine the time of species divergence and reconstruct phylogenies (Radinsky 1978. p. 1182). Notably, through the molecular clock, the albumin immunological distance is relatively correlated with the time of divergence as deduced from paleontological information. On the basis of the molecular clock theory, each protein or gene in an organism can effectively function as a distinctive molecular clock. This centres on the fact that each protein has a unique rate of evolution, which is dependent on how vital the protein’s function is within the organism’s body. A lowly functional molecular constraint produces a faster evolution, particularly with regard to mutant substitution than molecules typically subjected to stronger constraints (Nei & Koehn 1983, p. 561). For instance, histones typically bind DNA within chromosomes and normalise DNA activity. Therefore, the structure of a histone is precisely defined since its capacity to bind DNA is mostly dependent on its shape and structure. The 103 amino acids present in this protein are one and the same for almost all animals and plants. While it has been approximately one billion years since animals and plants separated, of the 103 amino acids found in the protein, there is only a single dissimilarity between a cow and a pea (Zihlman 2001, p. 96). This emanates from the massive quantity of functional constraints found in this molecule as a consequence of its vital function. On the other hand, fibrinopeptides can carry out their function in blood clotting with nearly any change in amino acid. The protein’s 20 amino acids are dissimilar by approximately 86% between a human being and a horse (Zihlman 2001, p. 165). Fibrinopeptides typically present extremely fast rates of change because they experience minimal functional constraints. As a consequence of differing constraints as well as ensuing differing mutation rates, diverse molecules can time occurrences in differing evolutionary time frames. For instance, fibrinopeptides clock changes in the last five million years while histones clock events that occur once in a billion years. Therefore, when conducting a study using the molecular clock, it is pertinent to choose a molecule, which is suitable to the time frame of significance. Notably, due to the arbitrariness of the molecular substitution in nucleotides, it is quite evident that the molecular clock is a stochastic clock. Researchers (Fitch 1977, p. 944) have established that inconsistency with regard to the time gap between nucleotide substitutions is nearly twice that of an accurately stochastic process. As a consequence, in order to attain the same precision level, one needs to count twofold the number of nucleotide substitutions as radioactive disintegrations. According to Fitch (1977, p. 451), if a person averages over an appropriate quantity of nucleotide substitutions, in differing proteins and species, one can anticipate reasonable evolutionary divergence rates. Consequently, it is clear that the molecular clock is indeed a clock, albeit an abnormally erratic one. Two tests effectively determine the effectiveness of the molecular clock; firstly, the quantity of nucleotide dissimilarities is either ascertained through inference from difference in amino acids or directly. In this test, the nucleotide difference acts as a measure of the genetic distance existent among species. This figure is subsequently plotted against the divergence time that is predicted from the species’ fossil records. A linear relationship typically suggests a constant divergence rate per annum (Futuyuma 1986, p. 754). This relationship can act as a calibration to approximate the time of divergence, particularly when fossil record is absent or inadequate. For this form of test, which is typically utilised in molecular studies, viable fossil records are vital to help calibrate the clock. However, there are numerous problems with fossil records. Consequently, some scientists posit that paleontological information is usually inadequate to offer accurate approximations of times of divergence by which they can calibrate the clock (Kumar & Hedges 1998, p. 918). Therefore, in the molecular clock, calibration is an immensely significant issue, which needs intense consideration. However, since much of the present debate concerning the molecular clock hypothesis entails conflict regarding paleontological information, specifically dates of divergence among species, researchers Sarich and Wilson (1973, p. 1149) developed a test, which does not need knowledge regarding the times of divergence. This means that no information from the fossil record is needed. This test is referred to the previously mentioned relative rate test which is the second method of testing the constant rate of species divergence. In the molecular clock, while the relative rate test does away with the requirement of paleontological information, it only allows for a person to investigate the molecular clock hypothesis for two lineages in relation to a third lineage. Furthermore, it disallows one to investigate the variation among lineages, or, for instance, to become aware of deceleration or acceleration rates within the lineage. However, other exceptionally sophisticated phylogenetic tests facilitate the molecular clock hypothesis to be examined through the use of a number of sequences simultaneously. Some of the most common phylogenetic tests in the molecular clock test include the Branch length test, Log-likelihood ratio test and Two-cluster test. None of these tests is suitable for all situations since each test encompasses distinctive advantages and disadvantages. In conclusion, while the validity of the molecular clock hypothesis continues to be debated from many fronts, the hypothesis has been widely utilised in the approximation of times of divergence as well as the reconstruction of phylogenetic trees. Futuyama (1986, p. 184) posits that most of the phylogenetic trees generated from molecular data typically tally with those developed from morphological data. A viable example is the tree created on the basis of amino acid sequences of protein cytochrome c. Notably, the protein resembled the conventional phylogeny in a vast majority of details. According to Goodman (1981, p. 146), the basic procedure for using the molecular clock hypothesis for establishing rates of evolution entails noting the distribution of mutations found on the branches of genealogical trees formed from amino acid sequence data. While conducting this examination, one needs to evaluate divergence times from fossil record and selecting an ancestral node to set the clock accurately for the assortment of dates to be calculated from it. Secondly, the use of the molecular clock involves noting duration to the present. This is equivalent to the number of nucleotide substitutions to date, presented as an average of the lineages that descend from it. Other nodes are dated through extrapolation from the ratio of each individual node span over the span of ancestral nodes. A variety of methods are in existence to facilitate the reconstruction of molecular phylogenetic. However, no single method is suitable for all possible solutions. References Ayala, FJ 1996, ‘Molecular clock or erratic evolution? A tale of two genes’, Proceedings of the National Academy of Sciences, vol. 93, pp. 11729-11734. Britten, RJ 1986, ‘Rates of DNA sequence evolution differ between taxonomic groups’, Science, vol. 231, pp. 1393-1398. Fitch, WM 1977, ‘The phylogenetic interpretation of macromolecular sequence information: simple methods’, in MK Hecht, PC Goody & BM Hecht (eds), Major patterns in vertebrate evolution, pp. 169-204, Plenum Press, New York. Futuyama, DJ 1986, Evolutionary biology, Sinauer Associates Incorporation, Sunderland. Goodman, M 1981, ‘Decoding the pattern of protein evolution’, Progress in Biophysics & Molecular Biology, vol. 38, pp. 105-64. Kumar, S & Hedges, SB 1998, ‘A molecular timescale for vertebrate evolution’, Nature, vol. 392, pp. 917-920. Li, WH & and Graur, D 1991, Fundamentals of molecular evolution, Sinauer Associates Incorporation, Sunderland. Nei, M & Koehn, RK 1983, Evolution of genes and proteins, Sinauer Associates Incorporation, Sunderland. Radinsky, L 1978, ‘Do albumin clocks run on time?’ Science, vol. 200, pp. 1182-3. Sarich, VM & Wilson, AC 1973, ‘Generation time and genomic evolution in primates’, Science, vol. 179, pp. 1144-47. Zihlman, AL 2001, The human evolution colouring book, Colouring Concepts Incorporation, Harper Collins, New York. Read More