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What is used as a molecular clock to measure human evolution?

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Technique to deduce the time in prehistory when two or more than life forms diverged

The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when 2 or more than life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for Deoxyribonucleic acid, RNA, or amino acrid sequences for proteins. The benchmarks for determining the mutation rate are oftentimes 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 molecular evolution to approximate times of speciation or radiation. It is sometimes chosen a cistron clock or an evolutionary clock.

Early discovery and genetic equidistance [edit]

The notion of the being of a so-called "molecular clock" was first attributed to Émile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin betwixt different lineages changes roughly linearly with time, every bit estimated from fossil evidence.[1] They generalized this ascertainment to assert that the rate of evolutionary change of any specified poly peptide was approximately constant over fourth dimension and over unlike lineages (known as the molecular clock hypothesis).

The genetic equidistance phenomenon was beginning noted in 1963 by Emanuel Margoliash, who wrote: "Information technology appears that the number of residue differences betwixt cytochrome c of any ii species is mostly conditioned by the time elapsed since the lines of evolution leading to these 2 species originally diverged. If this is correct, the cytochrome c of all mammals should exist every bit dissimilar 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 dissimilar from the cytochrome c of fish. Similarly, all vertebrate cytochrome c should exist as different from the yeast protein."[ii] For example, the departure between the cytochrome c of a carp and a frog, turtle, chicken, rabbit, and horse is a very abiding 13% to 14%. Similarly, the difference betwixt the cytochrome c of a bacterium and yeast, wheat, moth, tuna, pigeon, and horse ranges from 64% to 69%. Together with the piece of work of Emile Zuckerkandl and Linus Pauling, the genetic equidistance effect direct led to the formal postulation of the molecular clock hypothesis in the early 1960s.[iii]

Similarly, Vincent Sarich and Allan Wilson in 1967 demonstrated that molecular differences amidst modern Primates in albumin proteins showed that approximately constant rates of change had occurred in all the lineages they assessed.[4] The basic logic of their analysis involved recognizing that if one species lineage had evolved more than quickly than a sister species lineage since their common ancestor, then the molecular differences betwixt an outgroup (more distantly related) species and the faster-evolving species should be larger (since more molecular changes would have accumulated on that lineage) than the molecular differences betwixt the outgroup species and the slower-evolving species. This method is known every bit the relative rate test. Sarich and Wilson's newspaper reported, for instance, that human (Homo sapiens) and chimpanzee (Pan troglodytes) albumin immunological cross-reactions suggested they were well-nigh as different from Ceboidea (New World Monkey) species (within experimental error). This meant that they had both accumulated approximately equal changes in albumin since their shared common ancestor. This blueprint was too found for all the primate comparisons they tested. When calibrated with the few well-documented fossil branch points (such as no Primate fossils of modern aspect constitute before the Thousand-T boundary), this led Sarich and Wilson to fence that the man-chimp divergence probably occurred simply ~four–6 one thousand thousand years ago.[five]

Relationship with neutral theory [edit]

The observation of a clock-like rate of molecular change was originally purely phenomenological. Later, the work of Motoo Kimura[vi] adult the neutral theory of molecular evolution, which predicted a molecular clock. Permit in that location exist Due north individuals, and to continue this adding simple, let the individuals be haploid (i.e. accept ane re-create of each factor). Let the rate of neutral mutations (i.due east. mutations with no upshot on fitness) in a new private be ÎĽ {\displaystyle \mu } . The probability that this new mutation will become fixed in the population is so 1/N, since each copy of the factor is as skillful as any other. Every generation, each individual tin can accept new mutations, so at that place are ÎĽ {\displaystyle \mu } N new neutral mutations in the population as a whole. That means that each generation, ÎĽ {\displaystyle \mu } new neutral mutations will become stock-still. If most changes seen during molecular evolution are neutral, then fixations in a population volition accumulate at a clock-rate that is equal to the rate of neutral mutations in an private.

Scale [edit]

The molecular clock lonely tin can simply say that one time period is twice as long as another: it cannot assign concrete dates. For viral phylogenetics and aboriginal DNA 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 calibrated confronting independent evidence about dates, such every bit the fossil record.[7] There are ii full general methods for calibrating the molecular clock using fossil information: node calibration and tip calibration.[viii]

Node calibration [edit]

Sometimes referred to as node dating, node scale is a method for phylogeny calibration that is washed by placing fossil constraints at nodes. A node calibration fossil is the oldest discovered representative of that clade, which is used to constrain its minimum age. Due to the bitty nature of the fossil tape, the true most recent common ancestor of a clade will probable never exist found.[8] In guild to account for this in node calibration analyses, a maximum clade historic period must be estimated. Determining the maximum clade historic period is challenging because information technology relies on negative show—the absence of older fossils in that clade. At that place are a number of methods for deriving the maximum clade age using birth-death models, fossil stratigraphic distribution analyses, or taphonomic controls.[9] Alternatively, instead of a maximum and a minimum, a prior probability of the divergence time can be established and used to calibrate the clock. In that location are several prior probability distributions including normal, lognormal, exponential, gamma, compatible, etc.) that can be used to express the probability of the true historic period of divergence relative to the age of the fossil;[10] however, there are very few methods for estimating the shape and parameters of the probability distribution empirically.[11] The placement of calibration nodes on the tree informs the placement of the unconstrained nodes, giving divergence engagement estimates across the phylogeny. Historical methods of clock calibration could only make use of a single fossil constraint (non-parametric rate smoothing),[12] while mod analyses (BEAST[10] and r8s[13]) allow for the utilize of multiple fossils to calibrate the molecular clock. Simulation studies have shown that increasing the number of fossil constraints increases the accurateness of divergence fourth dimension estimation.[14]

Tip calibration [edit]

Sometimes referred to as tip dating, tip calibration is a method of molecular clock scale in which fossils are treated as taxa and placed on the tips of the tree. This is achieved by creating a matrix that includes a molecular dataset for the extant taxa along with a morphological dataset for both the extinct and the extant taxa.[9] Unlike node calibration, this method reconstructs the tree topology and places the fossils simultaneously. Molecular and morphological models work together simultaneously, assuasive morphology to inform the placement of fossils.[viii] Tip calibration makes use of all relevant fossil taxa during clock calibration, rather than relying on simply the oldest fossil of each clade. This method does not rely on the interpretation of negative show to infer maximum clade ages.[9]

Expansion calibration [edit]

Demographic changes in populations tin can exist detected as fluctuations in historical coalescent constructive population size from a sample of extant genetic variation in the population using coalescent theory.[xv] [sixteen] [17] Ancient population expansions that are well documented and dated in the geological record can be used to calibrate a charge per unit of molecular evolution in a manner similar to node scale. However, instead of calibrating from the known historic period of a node, expansion calibration uses a two-epoch model of abiding population size followed by population growth, with the time of transition between epochs existence the parameter of interest for calibration.[xviii] [19] Expansion calibration works at shorter, intraspecific timescales in comparison to node scale, because expansions tin can but be detected later the most recent common ancestor of the species in question. Expansion dating has been used to bear witness that molecular clock rates can be inflated at brusque timescales[xviii] (< ane MY) due to incomplete fixation of alleles, as discussed below[20] [21]

Full testify dating [edit]

This approach to tip scale goes a step farther by simultaneously estimating fossil placement, topology, and the evolutionary timescale. In this method, the historic period of a fossil tin inform its phylogenetic position in addition to morphology. By allowing all aspects of tree reconstruction to occur simultaneously, the adventure of biased results is decreased.[eight] This arroyo has been improved upon by pairing it with unlike models. One electric current method of molecular clock calibration is total evidence dating paired with the fossilized nascence-death (FBD) model and a model of morphological evolution.[22] The FBD model is novel in that it allows for "sampled ancestors," which are fossil taxa that are the directly antecedent of a living taxon or lineage. This allows fossils to be placed on a co-operative to a higher place an extant organism, rather than being confined to the tips.[23]

Methods [edit]

Bayesian methods tin can provide more appropriate estimates of difference times, particularly if large datasets—such as those yielded past phylogenomics—are employed.[24]

Not-constant rate of molecular clock [edit]

Sometimes simply a single divergence engagement can exist estimated from fossils, with all other dates inferred from that. Other sets of species accept abundant fossils available, allowing the hypothesis of constant divergence rates to be tested. DNA sequences experiencing depression levels of negative choice showed deviation rates of 0.7–0.viii% per Myr in bacteria, mammals, invertebrates, and plants.[25] In the same study, genomic regions experiencing very high negative or purifying pick (encoding rRNA) were considerably slower (1% per fifty Myr).

In addition to such variation in rate with genomic position, since the early 1990s variation amidst taxa has proven fertile ground for inquiry too,[26] even over comparatively short periods of evolutionary time (for example mockingbirds[27]). Tube-nosed seabirds take molecular clocks that on average run at half speed of many other birds,[28] 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 fifty-fifty slower.[29] Effects of small population size are also likely to confound molecular clock analyses. Researchers such every bit Francisco J. Ayala have more fundamentally challenged the molecular clock hypothesis.[thirty] [31] [32] According to Ayala's 1999 study, v factors combine to limit the awarding of molecular clock models:

  • Irresolute generation times (If the rate of new mutations depends at least partly on the number of generations rather than the number of years)
  • Population size (Genetic migrate is stronger in pocket-sized populations, and then more mutations are effectively neutral)
  • Species-specific differences (due to differing metabolism, ecology, evolutionary history, ...)
  • Change in function of the protein studied (tin can be avoided in closely related species by utilizing non-coding Dna sequences or emphasizing silent mutations)
  • Changes in the intensity of natural selection.

Phylogram showing three groups, one of which has strikingly longer branches than the two others

Molecular clock users have developed workaround solutions using a number of statistical approaches including maximum likelihood techniques and later Bayesian modeling. In particular, models that have into account rate variation across lineages have been proposed in order to obtain better estimates of difference times. These models are called relaxed molecular clocks [33] considering they represent an intermediate position betwixt the 'strict' molecular clock hypothesis and Joseph Felsenstein's many-rates model[34] and are made possible through MCMC techniques that explore a weighted range of tree topologies and simultaneously guess parameters of the called substitution model. It must be remembered that difference dates inferred using a molecular clock are based on statistical inference and not on direct evidence.

The molecular clock runs into particular challenges at very short and very long timescales. At long timescales, the problem is saturation. When enough fourth dimension has passed, many sites have undergone more i alter, but it is impossible to detect more than than one. This means that the observed number of changes is no longer linear with time, just instead flattens out. Even at intermediate genetic distances, with phylogenetic data still sufficient to guess topology, bespeak for the overall scale of the tree can exist weak under complex likelihood models, leading to highly uncertain molecular clock estimates.[35]

At very brusk time scales, many differences between samples do not correspond fixation of different sequences in the unlike populations. Instead, they represent culling alleles that were both present as part of a polymorphism in the mutual ancestor. The inclusion of differences that take non however get fixed leads to a potentially dramatic inflation of the apparent rate of the molecular clock at very brusque timescales.[21] [36]

Uses [edit]

The molecular clock technique is an important tool in molecular systematics, the apply of molecular genetics information to determine the right scientific classification of organisms or to study variation in selective forces. Knowledge of approximately constant rate of molecular evolution in particular sets of lineages also facilitates interpretation of the dates of phylogenetic events, including those not documented by fossils, such equally the divergences between living taxa. In these cases—peculiarly over long stretches of time—the limitations of the molecular clock hypothesis (to a higher place) must exist considered; such estimates may be off by 50% or more.

Meet besides [edit]

  • Charles Darwin
  • Cistron orders
  • Homo mitochondrial molecular clock
  • Mitochondrial Eve and Y-chromosomal Adam
  • Models of Dna development
  • Molecular evolution
  • Neutral theory of molecular evolution

References [edit]

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  18. ^ a b Crandall ED, Sbrocco EJ, Deboer TS, Barber PH, Carpenter KE (February 2012). "Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Final Glacial Maximum". Molecular Biology and Evolution. 29 (2): 707–719. doi:ten.1093/molbev/msr227. PMID 21926069.
  19. ^ Hoareau TB (May 2016). "Tardily Glacial Demographic Expansion Motivates a Clock Overhaul for Population Genetics". Systematic Biology. 65 (three): 449–464. doi:10.1093/sysbio/syv120. PMID 26683588.
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  22. ^ Heath TA, Huelsenbeck JP, Stadler T (July 2014). "The fossilized birth-death process for coherent scale of divergence-time estimates". Proceedings of the National Academy of Sciences of the United states of america of America. 111 (29): E2957–E2966. arXiv:1310.2968. Bibcode:2014PNAS..111E2957H. doi:10.1073/pnas.1319091111. PMC4115571. PMID 25009181.
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  30. ^ Ayala FJ (Jan 1999). "Molecular clock mirages". BioEssays. 21 (1): 71–75. doi:x.1002/(SICI)1521-1878(199901)21:1<71::AID-BIES9>3.0.CO;two-B. PMID 10070256. Archived from the original on sixteen Dec 2012.
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    • "No Missing Link? Evolutionary Changes Occur Of a sudden, Professor Says". ScienceDaily (Press release). 12 Feb 2007.
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  33. ^ Drummond AJ, Ho SY, Phillips MJ, Rambaut A (May 2006). "Relaxed phylogenetics and dating with confidence". PLoS Biology. four (5): e88. doi:10.1371/journal.pbio.0040088. PMC1395354. PMID 16683862.
  34. ^ Felsenstein J (2001). "Taking variation of evolutionary rates between sites into account in inferring phylogenies". Journal of Molecular Evolution. 53 (iv–v): 447–455. Bibcode:2001JMolE..53..447F. doi:ten.1007/s002390010234. PMID 11675604. S2CID 9791493.
  35. ^ Marshall, D. C., et al. 2016. Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiations from Australasia (Hemiptera: Cicadidae: Cicadettini). Systematic Biology 65(1):xvi–34.
  36. ^ Peterson GI, Masel J (November 2009). "Quantitative prediction of molecular clock and ka/ks at short timescales". Molecular Biology and Development. 26 (11): 2595–2603. doi:10.1093/molbev/msp175. PMC2912466. PMID 19661199.

Further reading [edit]

  • Ho, Southward.Y.Due west., ed. (2020). The Molecular Evolutionary Clock: Theory and Practise. Springer, Cham. doi:10.1007/978-3-030-60181-2. ISBN978-three-030-60180-5. S2CID 231672167.
  • Kumar South (August 2005). "Molecular clocks: four decades of evolution". Nature Reviews. Genetics. 6 (viii): 654–662. doi:10.1038/nrg1659. PMID 16136655. S2CID 14261833.
  • Morgan GJ (1998). "Emile Zuckerkandl, Linus Pauling, and the molecular evolutionary clock, 1959-1965". Periodical of the History of Biology. 31 (2): 155–178. doi:10.1023/A:1004394418084. PMID 11620303. S2CID 5660841.
  • Zuckerkandl Due east, Pauling LB (1965). "Evolutionary divergence and convergence in proteins". In Bryson V, Vogel HJ (eds.). Evolving Genes and Proteins. Academic Press, New York. pp. 97–166.

External links [edit]

  • Allan Wilson and the molecular clock
  • Molecular clock caption of the molecular equidistance phenomenon
  • Appointment-a-Clade service for the molecular tree of life

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Source: https://en.wikipedia.org/wiki/Molecular_clock#:~:text=The%20molecular%20clock%20is%20a,amino%20acid%20sequences%20for%20proteins.

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