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Molecular clock

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	Molecular clock - Wikipedia, the free encyclopedia
		The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in genetics, which researchers use to date when two species diverged.
		The notion of a "molecular clock" was first attributed to Emile Zuckerkandl and Linus Pauling who, in 1962, noticed that the quantity of amino acid differences in hemoglobin between lineages roughly matched the known evolutionary rate of divergence based upon fossil evidence.
		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.
	en.wikipedia.org /wiki/Molecular_clock (424 words)

	BEAST: Bayesian Evolutionary Analysis Sampling Trees
		Molecular clock hypothesis - The molecular clock is a hypothesis that mutation rates and substitution rates do not vary among lineages in a tree.
		An extension of the molecular clock concept to sequences from different times implies that the distance of a particular sequence from the root of the tree should be proportional to the amount of time that has accumulated from the root to the sampling time of that sequence.
		The molecular clock hypothesis is a fundamental assumption of all models in BEAST.
	evolve.zoo.ox.ac.uk /beast/glossary.html (822 words)

	Molecular Clock [MT Dorak]
		M.Tevfik Dorak, B.A. Hons), M.D., Ph.D. The controversial hypothesis of molecular clock (MC) is a consequence of the neutral theory of evolution.
		Molecular differences between species are used to infer phylogenetic relationships.
		Molecular evolution from living fossils provides an example that constant rate of molecular evolution occurs independent of morphological evolution.
	dorakmt.tripod.com /evolution/clock.html (819 words)

	Lecture 27 - Molecular clocks and estimating divergence
		"Molecular clock hypothesis" - rate of molecular change constant enough (within bounds of particular genes and taxa) to be useful in predicting times of divergence.
		Early protein clock hypo based on hypothesis that many amino acid and nuke substitutions have little or no functional consequence; most are of this kind and not the kind strongly constrained by natural selection.
		The molecular clock hypothesis: biochemical evolution, genetic differentiation and systematics.
	www.biology.usu.edu /courses/biol6750/Lecture_27.htm (1664 words)

	Untitled Document (Site not responding. Last check: 2007-10-24)
		By contrast, if the molecular clock hypothesis is rejected, then there is heterogeneity of process and one goal is to discover the correlates of heterogeneity.
		Second, molecular clocks provide the basis to place the origination of genes or species in the context of historical events.
		Models assuming a molecular clock necessarily imply a common ancestor of all sampled lineages; therefore, it is necessary to root the tree (in other words, to add a common ancestor of all taxa).
	stripe.colorado.edu /~am/TestingClocks.html (846 words)

	MOLECULAR EVOLUTION
		MOLECULAR EVOLUTION: Phylogenetic analysis and evolutionary processes (Information on molecular evolution relevant to this section is in Freeman and Herron (2001) Chapter 18; information on mutation that is relevant to this section is in Freeman and Herron Chapter 4.
		Explain what is meant by the molecular clock, how it is calibrated, and how it is used in phylogenetic reconstruction.
		You would like to use the molecular clock to estimate the times of speciation of the clam species, and you have a date of speciation for two species from the fossil record.
	www.utm.edu /departments/cens/biology/rirwin/391/391ManChXII.htm (1670 words)

	Histone deletion mutants challenge the molecular clock hypothesis: ARN Book Review
		Early in the development of the molecular clock hypothesis, it was discovered that not all proteins "ticked" at the same rate.
		When compared across a range of species, the fibrinopeptides, for instance, were much "faster clocks" (i.e., having a higher rate of amino acid substitution) than the very conservative, "slowly ticking" histones.
		These differences, writes Michael Behe (Chemistry, Lehigh University), required a modification to the clock hypothesis: the postulate of functional constraints.
	www.arn.org /docs/reviews/rev009.htm (490 words)

	Kitzmiller v. Dover: Day 11, AM: Michael Behe (continued)
		And they have a section on the molecular clock hypothesis and on cytochrome C in which they discuss these issues.
		They discuss the molecular clock, the standard molecular clock model, the naive molecular clock model, and then they discuss complications with it.
		That means that, for the molecular clock idea to be correct, there must be not one molecular clock, but thousands.
	www.talkorigins.org /faqs/dover/day11am2.html (9595 words)

	Virus Evolution Workgroup: 1999 Workshop Abstract
		The finding of a molecular clock may therefore serve as an indication of neutrality dominating the evolution of the gene in question, and a calibrated clock may be used to date important evolutionary events such as speciation or epidemiological events.
		Alternatively, the rejection of the hypothesis may aid in the formulation and testing of hypotheses which seek to establish the biological basis of rate variation such as taxonomical differences in generation times, DNA repair rates, variation in gene function and selective pressures (Sorhannus 1999).
		This allows for the likelihood ratio testing of the molecular clock hypothesis even when sequences are temporally dispersed and provides simultaneous maximum likelihood estimation of the absolute rate of evolution and the times of evolutionary events.
	www.noble.org /VirusEvolution/abstracts/PrintLayout_1_78879_78879.html (811 words)

	Molecular Population Genetics and Evolution (Site not responding. Last check: 2007-10-24)
		This controlfile is used to estimate the likelihood in an unrooted tree with no molecular clock, fill out the ‘?’ and save the controlfile.
		It is twice the difference in the log likelihood values, they have to be evaluated in a chi-square distribution with a number of degrees of freedom equal to the difference in number of parameters in the two nested models.
		Clock: Specifies whether or not the model shall assume a molecular clock.
	www.daimi.au.dk /~mheide/MPGE/2003computer4.htm (2280 words)

	The Molecular Clock Problem
		The hypothesis of the molecular evolutionary clock asserts that informational macromolecules (i.e., proteins and nucleic acids) evolve at rates that are constant through time and for different lineages.
		The clock hypothesis has been extremely powerful for determining evolutionary events of the remote past for which the fossil and other evidence is lacking or insufficient.
		If we assume a molecular clock and use the Drosophila rate for estimating the divergence of remote organisms, GPDH yields estimates of 2,500 My for the divergence between the animal phyla (occurred 650 My) and 3,990 My for the divergence of the kingdoms (occurred 1,100 My).
	www.cs.unc.edu /~plaisted/ce/clock.html (592 words)

	Early empirical observations
		When the sequences were compared, investigators began to notice that the number of amino acid differences between different pairs of mammals seemed to be roughly proportional to the time since they had diverged from one another, as inferred from the fossil record.
		7] used the molecular clock hypothesis to propose that humans and apes diverged approximately 5 million years ago.
		While that proposal may not seem particularly controversial now, it generated enormous controversy at the time, because at the time many paleoanthropologists interpreted the evidence to indicate humans diverged from apes as much as 30 million years ago.
	darwin.eeb.uconn.edu /eeb348/lecture-notes/molevol-neutral/node2.html (265 words)

	Mauricio Oliveira Carneiro (Site not responding. Last check: 2007-10-24)
		The molecular clock hypothesis in molecular evolutionary studies has been controversial since it was first proposed (Zuckerkandl and Pauling, 1965).
		A variety of methods have been developed to test the molecular clock and these have been applied to many studies, including the molecular evolution of viruses.
		The many studies and discussions about the existence of a molecular clock suitable to the different genes of the HIV-1 have been based on very small data sets what could likely create biased results.
	www.procc.fiocruz.br /~carneiro/publications.html (200 words)

	Robinson, Noah E. (2003-12-15) Investigations of peptide and protein deamidation. ...
		This reaction--which occurs spontaneously and non-enzymatically in many proteins under physiological conditions--has been hypothesized to be a general molecular clock, which could be used as a timer for protein turnover, development, or aging, and for the controlled conversion of one protein into another.
		Since this hypothesis was first proposed, amide molecular clocks have been demonstrated in several biological systems.
		The fact that this property is present within the thousands of proteins of currently known three-dimensional structure markedly strengthens the molecular clock hypothesis.
	etd.caltech.edu /etd/available/etd-09212004-154502 (851 words)

	AWC Projects:Jennifer Hay
		The “molecular clock” hypothesis is based on the observation that the rate of change in a given region of DNA appears constant over time and organism.
		To test the molecular clock hypothesis, we are using the same methods of analysis in tuatara, kiwi, fish and humans.
		Tuatara provide an extreme test of the molecular clock, because of their unique phylogenetic position, low metabolic rate and long generation time.
	awcmee.massey.ac.nz /project_JHay.htm (240 words)

	Changes in the Recombinational Environment Affect Divergence in the yellow Gene of Drosophila -- Munte et al. 18 (6): ...
		On the molecular mechanism of gypsy-induced mutations at the yellow locus of Drosophila melanogaster.
		Molecular evolution of the Amy multigenes in the subgenus Sophophora of Drosophila.
		Molecular phylogeny of the subgenus Sophophora derived from large subunit of ribosomal RNA sequences.
	mbe.oxfordjournals.org /cgi/content/full/18/6/1045 (6168 words)

	A Compound Poisson Process for Relaxing the Molecular Clock -- Huelsenbeck et al. 154 (4): 1879 -- Genetics
		Despite the observation that the molecular clock hypothesis
		The branch lengths of the tree conform to a molecular clock.
		The null hypothesis is that the molecular clock
	www.genetics.org /cgi/content/full/154/4/1879 (5887 words)

	Introduction to evolution
		The molecular clock hypothesis states that most mutations that become fixed are neutral, since beneficial mutations are rare and natural selection quickly rids populations of harmful mutations.
		If the molecular clock hypothesis is true, to put a time scale on a phylogeny we need to know the rate at which a particular stretch of DNA (for example, a
		hypothesis is supported and we are justified in using it to find dates on our phylogeny.
	www.utm.edu /departments/cens/biology/rirwin/391/391MolEvolPhylog.htm (2818 words)

	EMBOSS: fdnamlk (Site not responding. Last check: 2007-10-24)
		This program implements the maximum likelihood method for DNA sequences under the constraint that the trees estimated must be consistent with a molecular clock.
		The molecular clock is the assumption that the tips of the tree are all equidistant, in branch length, from its root.
		Thus the assessment of 95% of the likelihood, in tabulating the ancestral states, refers to 95% of the likelihood that is accounted for by that particular combination of rates.
	emboss.sourceforge.net /embassy/phylipnew/fdnamlk.html (2851 words)

	Selecting Models of Nucleotide Substitution: An Application to Human Immunodeficiency Virus 1 (HIV-1) -- Posada and ...
		Molecular clock of viral evolution, and the neutral theory.
		Limitations of a molecular clock applied to the considerations of the origin of HIV-1.
		Molecular epidemiology of HIV transmission in a dental practice.
	mbe.oxfordjournals.org /cgi/content/full/18/6/897 (4079 words)

	PHYLIP Heuristic search programs
		The use of the two programs together permits a likelihood ratio test of the molecular clock hypothesis to be made.
		Estimates phylogenies from distance matrix data under the "ultrametric" model which is the same as the additive tree model except that an evolutionary clock is assumed.
		This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with distances from DNA hybridization measurements, and with genetic distances computed from gene frequencies.
	evolution.genetics.washington.edu /phylip/progs.algs.heur.html (783 words)

	[No title]
		Title: Estimating the Deviation from a Molecular Clock Authors: L. Nakhleh, U. Roshan, L. Vawter, and T. Warnow Abstract: We address the problem of estimating the degree to which the evolutionary history of a set of molecular sequences violates a strong molecular clock hypothesis.
		We then explore the performance of standard techniques in systematics for estimating the deviation of a dataset from a molecular clock.
		This suggests that current approximations of the degree to which data sets deviate from a molecular clock may significantly underestimate these deviations.
	www.cs.utexas.edu /users/usman/research/phylogenetics/stretch_abs (197 words)

	Recent Problems in Evolution - 1990
		Molecular clock does not tick for eukaryotic histone
		Evolutionists have proposed a hypothesis called the molecular clock hypothesis, which states that the rate of
		Recent studies have shown this hypothesis to be irreconcilable with the large spatial separation between the aminoacylation site and the
	www.godandscience.org /evolution/evol1990.html (482 words)

	ANNOTATIONS 17(1)
		This has been interpreted as evidence against the hypothesis that mutations occur at a generally constant rate through evolutionary time (the molecular clock hypothesis).
		The author of this paper prefers the molecular clock hypothesis over evidence from the fossil record, and concludes that molecular differences indicate that mammal orders arose at different times, but the fossil record is too incomplete to indicate the order in which they arose.
		Archie, J. Phylogenies of plant families: a demonstration of phylogenetic randomness in DNA sequence data derived from proteins.
	www.grisda.org /origins/17027.htm (1452 words)

	Molecular Population Genetics and Evolution (Site not responding. Last check: 2007-10-24)
		Yoder A D, Yang Z. Estimation of primate speciation dates using local molecular clocks.
		open the codeml.ctl file and study it, you should be able to set a value of 0 for no clock and 1 for a global clock.
		Now modify the clock option in the codeml.ctl file to 0 (no clock) and give another outfile name (f.ex.
	www.daimi.au.dk /~mheide/ME04/computer2004no4.htm (1053 words)

	Arial Ancestors? CHEM-647 Case Study Problem 2 pg 2 - Fall 2000
		However, it was not until the 1950's when it became possible to determine the amino acid sequences of proteins that the actual differences could be characterized.
		Hemoglobins from various species were among the first proteins to be studied and thus, along with cytochrome c, it became an archetype of protein sequence comparisons for evolutionary studies and the source of the Molecular Clock Hypothesis (12a).
		L., and Goodman, M. (1992) Rejection of the "flying primate" hypothesis by phylogenetic evidence from the epsilon-globin gene.
	www.udel.edu /chem/white/C647/CSP2BatsPg2.html (563 words)

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