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The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in molecular evolution to relate the divergence time of two species diverged to the number of molecular differences measured between the species' DNA sequences or proteins. Foundations of modern biology There are five unifying principles eVolution is the third Album by eLDee, it was due to be released in 2008 An adaptation is a characteristic of an Organism that has been favored by Natural selection and In Population genetics, genetic drift is the accumulation of random events that change the makeup of a gene pool slightly but often compound over time In Population genetics, gene flow (also known as gene migration) is the transfer of Alleles of Genes from one Population to another In biology mutations are changes to the Nucleotide sequence of the Genetic material of an organism Natural selection is the process by which favorable Heritable traits become more common in successive Generations of a Population of Speciation is the Evolutionary process by which new biological Species arise The wide range of evidence of common descent of living things strongly indicates the occurrence of Evolution and provides a wealth of information on the natural processes Although evidence of early Life is scarce and often difficult to interpret it appears that life appeared on Earth relatively soon (on the Geologic time scale) after Evolutionary thought, the idea that species change over time has roots in antiquity in the ideas of the Greeks, Romans, Chinese and Muslims theory of transmutation had early origins in the speculations and hypotheses of Erasmus Darwin, and Jean-Baptiste Lamarck. Objections to evolution have been raised ever since various evolutionary ideas came to prominence around the start of the nineteenth century Cladistics is the hierarchical classification of Species based on evolutionary ancestry Ecological genetics is the study of Genetics in the context of the interactions among organisms and between the organisms and their environment Evolutionary developmental biology ( evolution of development or informally evo-devo) is a field of Biology that compares the developmental processes Human evolution, or anthropogenesis, is the part of biological Evolution concerning the emergence of Homo sapiens as a distinct Species Molecular evolution is the process of evolution at the scale of DNA, RNA, and Proteins Molecular evolution emerged as a scientific field in the 1960s as Population genetics is the study of the Allele frequency distribution and change under the influence of the four evolutionary forces Natural selection, Genetic Molecular evolution is the process of evolution at the scale of DNA, RNA, and Proteins Molecular evolution emerged as a scientific field in the 1960s as In Biology, a species is one of the basic units of Biological classification and a Taxonomic rank. Speciation is the Evolutionary process by which new biological Species arise A DNA sequence or genetic sequence is a succession of letters representing the Primary structure of a real or hypothetical DNA Molecule It is sometimes called a gene clock or evolutionary clock.

Contents 1 Early discovery 2 Calibration 3 Uses 4 See also 5 References 6 Further reading 7 External links

Early discovery

The notion of the existence of a so-called "molecular clock" was first attributed to Emile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between lineages scales roughly with divergence times, as estimated from fossil evidence^[1]. Emile Zuckerkandl (born July 4, 1922) is an Austrian-American biologist considered one of the founders of the field of Molecular evolution. Linus Carl Pauling (February 28 1901 – August 19 1994 was an American Scientist, Peace activist, Author and educator. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Hemoglobin ( also spelled haemoglobin and abbreviated Hb or Hgb) is the Iron -containing Oxygen -transport Metalloprotein They generalized this observation to assert that the rate of evolutionary change of any specified protein was approximately constant over time and over different lineages. eVolution is the third Album by eLDee, it was due to be released in 2008 Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl

Later Allan Wilson and Vincent Sarich built upon this work and the work of Motoo Kimura observed and formalized that rare spontaneous errors in DNA replication cause the mutations that drive molecular evolution, and that the accumulation of evolutionarily "neutral" differences between two sequences could be used to measure time, if the error rate of DNA replication could be calibrated. Allan Charles Wilson ( 18 October 1934 – 21 July 1991) was a pioneer in the use of molecular approaches to understand Vincent M Sarich (born 1934) is an American Anthropology professor Motoo Kimura (木村資生 Kimura Motoo) ( November 13, 1924 - November 13, 1994) was a Japanese biologist best known for introducing DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules In biology mutations are changes to the Nucleotide sequence of the Genetic material of an organism Molecular evolution is the process of evolution at the scale of DNA, RNA, and Proteins Molecular evolution emerged as a scientific field in the 1960s as ^[2][3] One method of calibrating the error rate was to use as references pairs of groups of living species whose date of speciation was already known from the fossil record.

Calibration

Originally, the possibility was explored that all of the variables influencing DNA replication error-rate might cancel somewhat and show some level of constancy when averaged over time, across species and over parts of the genome. In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby Because the enzymes that replicate DNA only vary slightly between species, the assumption might have seemed reasonable a priori to Pauling or Zuckerkandl as in vitro biochemists. "A priori" redirects here For other uses see A priori. In vitro ( Latin: within the glass refers to the technique of performing a given experiment in a controlled environment outside of a living Organism This pioneering effort to integrate the fields of evolutionary and molecular biology can be said to have set aside the variation in rate of DNA repair and natural selection in time, space, and across taxa until molecular evidence accumulated enough to make those variations suitable topics of study in their own light. Natural selection is the process by which favorable Heritable traits become more common in successive Generations of a Population of While the MCH cannot be blindly assumed to be true, individual molecular clocks can be tested for accuracy and utilized in many cases. In general terms, they need to be calibrated against material evidence such as fossils before firm conclusions can be based on them (see also Lovette^[4]). Calibration is the process of establishing the relationship between a measuring device and the units of measure Measures in regions of low selection (silent substitutions) showed rates of 0. 7-0. 8% per Myr in bacteria, mammals, invertebrates, and plants ^[5]. This article is about the unit of time For the Magic the Gathering creatures see Creatures of Magic The Gathering. In the same study, genomic regions of very high 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^[6] , even over comparatively short periods of evolutionary time (for example mockingbirds^[7] ). A taxon (plural taxa) or taxonomic unit, is a name designating an organism or a group of Organisms In Biological nomenclature according to Mockingbirds are a group of New World Passerine Birds from the Mimidae family. Tube-nosed seabirds have molecular clocks that on average run at half speed of many other birds^[8] , possibly due to long generation times, and many turtles have a molecular clock running at one-eighth the speed it does in small mammals or even slower^[9]. Procellariiformes is an order of Seabirds that comprises four families: the Albatrosses procellariids, Storm-petrels and Diving Generation (from the Greek γενεά) also known as procreation, is the act of producing Offspring. Effects of small population size are also likely to confound molecular clock analyses; cheetahs for example, having gone through at least 2 population bottlenecks, could not be adequately studied based on a molecular clock model alone. Populations with small population size behave differently to larger populations The cheetah ( Acinonyx jubatus) is an atypical member of the cat family ( Felidae) that is unique in its speed while lacking climbing abilities Researchers like Ayala and the anthropologist Jeffrey H. Schwartz in 2006 have more fundamentally challenged the molecular clock hypothesis. Jeffrey Hugh Schwartz, PhD (b March 6 1948 is an American physical anthropologist and Professor of biological Anthropology at the University ^[10][11] According to Ayala's 1999 study, 5 factors combine to limit applications molecular clock models:

• Changing generation times (A mutation generally becomes fixed only from one generation to another. The shorter this timespan is, the more mutations can become fixed)
• Population size (Apart from effects of small population size, genetic diversity will "bottom out" as populations become larger as the fitness advantage of any one mutation becomes smaller)
• Species-specific differences (due to differing metabolism, ecology, evolutionary history,. . . )
• Evolving functions of the encoded protein (can be ameliorated by utilizing non-coding DNA sequences or emphasizing silent mutations)
• Changes in the intensity of natural selection

Molecular clock users have developed workaround solutions using a number of statistical approaches including maximum likelihood techniques and later Bayesian modeling. In Genetics, non-coding DNA describes DNA which does not contain instructions for making Proteins (or other cell products such as Noncoding Silent mutations are DNA Mutations that do not result in a change to the Amino acid sequence of a Protein. Maximum likelihood estimation ( MLE) is a popular statistical method used for fitting a mathematical model to some data Bayesian inference is Statistical inference in which evidence or observations are used to update or to newly infer the Probability that a hypothesis may be true In particular, models that take into account rate variation across lineages have been proposed in order to obtain better estimates of divergence times (and other parameters that may be estimated from substitution rates, such as effective population size. ) These models are called relaxed molecular clocks^[12] because they represent an intermediate position between the 'strict' molecular clock hypothesis and Felsenstein's many-rates model and are made possible through MCMC techniques that explore a weighted range of tree topologies and simultaneously estimate parameters of the chosen substitution model. It must be remembered that these are still based on statistical inference and not on direct evidence and that therefore, strictly speaking even a relaxed molecular clock can only support but never prove a scientific hypothesis. Inference is the act or process of deriving a Conclusion based solely on what one already knows Evidence in its broadest sense includes anything that is used to determine or demonstrate the Truth of an assertion Scientific method refers to bodies of Techniques for investigating phenomena This problem is approached by using the fossil record, which quite often is good and well-documented enough to provide hard evidence, to calibrate the molecular clock accordingly. FOSSIL is a standard protocol for allowing serial communication for Telecommunications programs under the DOS Operating system. Alternatively, for viral phylogenetics and ancient DNA studies, two areas of evolutionary biology where it is possible to sample sequences over an evolutionary timescale, the dates of the sequence themselves can be used to calibrate the molecular clock. Adna redirects here For the unincorporated community in Washington see Adna Washington.

Uses

The molecular clock technique is an important tool in molecular systematics, the use of molecular genetics information to determine the correct scientific classification of organisms or to study variation in selective forces. Molecular genetics is the field of Biology which studies the structure and function of Genes at a molecular level

Knowledge of approximately-constant rate of molecular evolution in particular sets of lineages also facilitates establishing the dates of phylogenetic events, including those not documented by fossils, such as the divergence of living taxa and the formation of the phylogenetic tree. FOSSIL is a standard protocol for allowing serial communication for Telecommunications programs under the DOS Operating system. A taxon (plural taxa) or taxonomic unit, is a name designating an organism or a group of Organisms In Biological nomenclature according to A phylogenetic tree, also called an evolutionary tree, is a tree showing the Evolutionary relationships among various biological Species or other But 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.

See also

• Molecular evolution
• Mitochondrial Eve
• Neutral theory of molecular evolution
• Y-chromosomal Adam

References

Further reading

• Morgan, G. J. (1998). "Emile Zuckerkandl, Linus Pauling, and the Molecular Evolutionary Clock, 1959-1965". Journal of the History of Biology 31 (2): 155-178. doi:10.1023/A:1004394418084. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  
• Zuckerkandl, E. and Pauling, L.B. (1965). Emile Zuckerkandl (born July 4, 1922) is an Austrian-American biologist considered one of the founders of the field of Molecular evolution. Linus Carl Pauling (February 28 1901 – August 19 1994 was an American Scientist, Peace activist, Author and educator. "Evolutionary divergence and convergence in proteins", in Bryson, V. and Vogel, H. J. (editors): Evolving Genes and Proteins. Academic Press, New York, 97–166.  
• Vincent Sarich and Frank Miele (2004). Vincent M Sarich (born 1934) is an American Anthropology professor Frank Miele is an American journalist and senior editor at Skeptic best known for his controversial advocacy of Hereditarian hypotheses Race: the Reality of Human Difference. Westview Press, Boulder.  

External links

• Allan Wilson and the molecular clock
• Molecular clock explanation of the molecular equidistance phenomenon

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