# Dating changes

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The molecular clock is figurative term for a technique that uses the of to in when two or more. The biomolecular data used for such calculations are usually for or sequences for. The benchmarks for determining the mutation rate are often fossil or archaeological dates. The molecular clock was first tested in 1962 on the hemoglobin protein variants of various animals, and is commonly used in to estimate times of or. It is sometimes called a gene clock or an evolutionary clock. They generalized this observation to assert that the rate of change of any specified was approximately constant over time and over different lineages based on the molecular clock hypothesis MCH. If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds. Since fish diverges from the main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish. Similarly, all vertebrate cytochrome c should be equally different from the yeast protein. Similarly, the difference between the cytochrome c of a bacterium and yeast, wheat, moth, tuna, pigeon, and horse ranges from 64% to 69%. Together with the work of Emile Zuckerkandl and Linus Pauling, the genetic equidistance result directly led to the formal postulation of the molecular clock hypothesis in the early 1960s. The observation of a clock-like rate of molecular change was originally purely. Later, the work of developed the , which predicted a molecular clock. Let there be N individuals, and to keep this calculation simple, let the individuals be i. Let the rate of neutral i. If most changes seen during are neutral, then in a population will accumulate at a clock-rate that is equal to the rate of neutral in an individual. The molecular clock alone can only say that one time period is twice as long as another: it cannot assign concrete dates. For viral phylogenetics and studies—two areas of evolutionary biology where it is possible to sample sequences over an evolutionary timescale—the dates of the intermediate samples can be used to more precisely calibrate the molecular clock. However, most phylogenies require that the molecular clock be against independent evidence about dates, such as the record. There are two general methods for calibrating the molecular clock using fossil data: node calibration and tip calibration. Node calibration Sometimes referred to as node dating, node calibration is a method for calibration that is done by placing fossil constraints at nodes. A node calibration fossil is the oldest discovered representative of that , which is used to constrain its minimum age. Due to the fragmentary nature of the fossil record, the true most recent common ancestor of a clade will likely never be found. In order to account for this in node calibration analyses, a maximum clade age must be estimated. Determining the maximum clade age is challenging because it relies on —the absence of older fossils in that clade. There are a number of methods for deriving the maximum clade age using birth-death models, fossil distribution analyses, or controls. Alternatively, instead of a maximum and a minimum, a of the divergence time can be established and used to calibrate the clock. There are several prior probability distributions including , , , , , etc. The placement of calibration nodes on the tree informs the placement of the unconstrained nodes, giving divergence date estimates across the phylogeny. Historical methods of clock calibration could only make use of a single fossil constraint non-parametric rate smoothing , while modern analyses and allow for the use of multiple fossils to calibrate the molecular clock. Simulation studies have shown that increasing the number of fossil constraints increases the accuracy of divergence time estimation. Tip calibration Sometimes referred to as tip dating, tip calibration is a method of molecular clock calibration in which fossils are treated as and placed on the tips of the tree. This is achieved by creating a matrix that includes a dataset for the along with a dataset for both the extinct and the extant taxa. Unlike node calibration, this method reconstructs the tree topology and places the fossils simultaneously. Molecular and morphological models work together simultaneously, allowing morphology to inform the placement of fossils. Tip calibration makes use of all relevant fossil taxa during clock calibration, rather than relying on only the oldest fossil of each clade. This method does not rely on the interpretation of negative evidence to infer maximum clade ages. Total evidence dating This approach to tip calibration goes a step further by simultaneously estimating fossil placement, topology, and the evolutionary timescale. In this method, the age of a fossil can inform its phylogenetic position in addition to morphology. By allowing all aspects of tree reconstruction to occur simultaneously, the risk of biased results is decreased. This approach has been improved upon by pairing it with different models. One current method of molecular clock calibration is total evidence dating paired with the fossilized birth-death FBD model and a model of morphological evolution. This allows fossils to be placed on a branch above an extant organism, rather than being confined to the tips. Methods Bayesian methods can provide more appropriate estimates of divergence times, especially if large datasets—such as those yielded by —are employed. Sometimes only a single divergence date can be estimated from fossils, with all other dates inferred from that. Other sets of species have abundant fossils available, allowing the MCH of constant divergence rates to be tested. DNA sequences experiencing low levels of showed divergence rates of 0. In the same study, genomic regions experiencing very high negative or purifying selection encoding rRNA were considerably slower 1% per 50 Myr. In addition to such variation in rate with genomic position, since the early 1990s variation among taxa has proven fertile ground for research too, even over comparatively short periods of evolutionary time for example. Effects of are also likely to confound molecular clock analyses. Researchers such as Francisco Ayala have more fundamentally challenged the molecular clock hypothesis. Woody bamboos tribes and have long generation times and lower mutation rates, as expressed by short branches in the , than the fast-evolving herbaceous bamboos. Molecular clock users have developed workaround solutions using a number of statistical approaches including techniques and later. In particular, models that take into account rate variation across lineages have been proposed in order to obtain better estimates of divergence times. These models are called relaxed molecular clocks because they represent an intermediate position between the 'strict' molecular clock hypothesis and Joseph Felsenstein's many-rates model and are made possible through techniques that explore a weighted range of tree topologies and simultaneously estimate parameters of the chosen substitution model. It must be remembered that divergence dates inferred using a molecular clock are based on statistical and not on direct. The molecular clock runs into particular challenges at very short and very long timescales. At long timescales, the problem is. When enough time has passed, many sites have undergone more than one change, but it is impossible to detect more than one. This means that the observed number of changes is no longer with time, but instead flattens out. Even at intermediate genetic distances, with phylogenetic data still sufficient to estimate topology, signal for the overall scale of the tree can be weak under complex likelihood models, leading to highly uncertain molecular clock estimates. At very short time scales, many differences between samples do not represent of different sequences in the different populations. Instead, they represent alternative that were both present as part of a polymorphism in the common ancestor. The inclusion of differences that have not yet become leads to a potentially dramatic inflation of the apparent rate of the molecular clock at very short timescales. The molecular clock technique is an important tool in , the use of information to determine the correct of organisms or to study variation in selective forces. Knowledge of approximately constant rate of molecular evolution in particular sets of lineages also facilitates establishing the dates of events, including those not documented by , such as the divergence of living and the formation of the. In these cases—especially over long stretches of time—the limitations of MCH above must be considered; such estimates may be off by 50% or more. Academic Press, New York. Molecular Biology and Evolution. Molecular Biology and Evolution. Molecular Phylogenetics and Evolution. Systematic Biology 1 : 1—17. Proceedings of the Royal Society B: Biological Sciences. Journal of Molecular Evolution. Molecular Biology and Evolution. Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia Hemiptera: Cicadidae: Cicadettini. Journal of the History of Biology. Evolving Genes and Proteins. Academic Press, New York.
