Tuesday, November 25, 2014



Here are a few copied and pasted annotated references, from a file of references on the computer I currently use, that may help show the validity of my 6th post – Science Screw-up No. 1 – posted May 31, 2013.  I shudder when I think how many others were lost in various ways from the overwhelming amount of literature on the topics that interested me enough to make index cards, entries on earlier computers, and stacks of journals and clippings still unpacked from moves.  Some were cited in the post noted above, but lacked the annotations and/or quotes from the articles.

Because structure and functions of organisms are the direct targets of natural selection they can be a better clue to branching pattern of the tree of life until the generation time of organisms is properly incorporated in the process of tree construction.  Many of my posts rely on this concept for interpreting relationships as well as the views of natural history oriented biologists.


Ayala, Francisco J.  1997.  Vagaries of the molecular clock.  Proc. Natl. Acad. Sci. USA, 94:7776-7783.  Found as much as a ten-fold difference between divergence times estimated by two different Drosophila genes (GPDH and SOD, or, glycerol-3-phosphate dehydrogenase and super oxide dismutase).  Generation times were identical in this study so did not affect the rate variation determined.

Bleiweiss, Robert.  1998.  Slow rate of molecular evolution in high-elevation hummingbirds.  Proc. Natl. Acad. Sci. USA, 95:612-616.  “A slower rate of single-copy DNA change at higher elevations suggests that the dynamics of molecular evolution cannot be separated from the environmental context.” The effect remained “significant even after taking into account a significant negative association between body mass and molecular rate.”

Britten, Roy J.  1986.  Rates of DNA sequence evolution differ between taxonomic groups.  Science, 231:1393-1398.  “Examination of available measurements shows that rates of DNA change of different phylogenetic groups differ by a factor of 5.  The slowest rates are observed for some higher primates and..”
Buckley, Thomas R., Chris Simon, and Geoffrey K. Chambers.  2001.  Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support.  Syst. Biol., 50(1):67-86.  variation in variability across data sets changes estimates, under different model assumptions, of nodal support and branch length   

Campbell, J. H.  1987.  The New Gene and Its Evolution.  Pp. 283-309 in Campbell, K. S. W., and M. F. Day (Eds.).  Rates of Evolution.  Allen and Unwin, London.  314 pp.  Rates of evolution pp 303- “To the extent that biological mechanisms participate in evolutionary change they allow its rate to be programmed internally as an attribute of the species.”

 Clegg, Michael T., Michael P. Cummings, and Mary L. Durbin.  1997.  The evolution of plant nuclear genes.  Proc. Natl. Acad. Sci. USA, 94:7791-7798.  “Analyses of synonymous nucleotide substitution rates for Adh genes in monocots reject a linear relationship with clock time.”  New genes that encode the enzymes ribulose-1,5-biphosphate carboxylase and alcohol dehydrogenases occurred at ten times the rate of new genes for alcohol dehydrogenases.    

Denver, Dee R., Krystalynne Morris, Michael Lynch, Larissa L. Vassilieva, W. Kelley Thomas.  2000.  High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegansScience, 289:2342-2344.  generation time of 4 days, used 74 lines of single worms, analyzed base pairs for mutations; 9.7 x 10 to the minus 8 per site per generation or 8.9 per site per million years.  “ . . . revealed a mutation rate that is two orders of magnitude higher than previous indirect estimates,”

Field, Katharine G., Gary J. Olsen, David J. Lane, Stephen J. Giovannoni, Michael T. Ghiselin, Elizabeth C. Raff, Norman R. Pace, and Rudolf A. Raff.  1988.  Molecular phylogeny of the animal kingdom.  Science, 239:748-753.  “Coelomates are thus monophyletic, and they radiated rapidly into four groups: chordates, echinoderms, arthropods, and eucoelomate protostomes.”  “The use of cellular RNA for these studies guarantees that sequences will represent commonly transcribed RNA genes, not minor or inactive genes.  The method provides sequences in the most conservative portions of the 18S rRNA molecule, which are the most useful for broad phylogenetic comparisons.” see following sentence page 748 also [“For distantly related organisms, it is not possible to establish homology between nucleotides in the rapidly evolving portions of the molecule; thus, even if the entire 18s rRNA sequence is known, only some parts of it can be used for phylogenetic inference.”].  Study was based on 18S ribosomal RNA sequences. Pogonophoran used was a thermal-vent species, annelids were a polychaete and an earthworm, chordates were a tunicate, amphioxus, a frog, and a human.

Fitch, Walter M., Robin M. Bush, Catherine A. Bender, and Nancy J. Cox.  1997.  Long term trends in the evolution of H(3) HA1 human influenza type A.  Proc. Natl. Acad. Sci. USA, 94:7712-7718.  Variation of replacement substitution rate of codons as much 7.2 times greater in a hypervariable one.  Rate lowest in trunk codons, intermediate in twigs, and greatest in tip branches.  [thought added 2/6/03 – might be an expression of selection against deleterious substitutions eliminated more effectively due to time as one goes to older twigs and trunk. (jge) I had just been thinking of that while trying to improve on method of calibrating molecular clocks with generation time corrections for both calibration species (if not from lines studied) and generation time difference of branch species (A correction of up to 199.999% of uncorrected bifurcation value is needed if generation time of shortest lived species was used; whereas estimate could need reduction of up to 99.999% if based on longest lived species); therefore two separate generations time corrections must be considered if calibration species is a third species; no correction for generation time is needed if all three have same generation time.]

Gillooly, James F., Andrew P. Allen, Geoffrey B. West, and James H. Brown.  2005.  The rate of DNA evolution: effects of body size and temperature on the molecular clock.  Proc. Natl. Acad. Sci. USA, 102:140-145.  support a single molecular clock, “but that it “ticks” at a constant substitution rate per unit of mass-specific metabolic energy rather than per unit of time.”

Keightley, Peter D., and Adam Eyre-Walker.  2000.  Deleterious mutations and the evolution of sex.  Science, 290:331-333.  [13 Oct 2000]  Deleterious mutations were eliminated more rapidly in short generation time species.  The study did not support (MD) “mutational deterministic” hypothesis for obligate sexuality.

Kimura, Motoo, and Tomoko Ohta.  1971. On the rate of molecular evolution.  J. Molec. Evolution, 1:1-17. citing various sources for a rate of about one centipauling for histones to four paulings for Fibrinopeptide A.  (1 pauling = “rate of substitution of 10 [to minus 9] per amino acid site per year.)

Kuman, Sudhir, and S. Blair Hedges.  1998.  A molecular timescale for vertebrate evolution.  Nature, 392:917-920.  [30 Apr 1998]  In estimates of divergence times using different genes, a standard error of about 10% was found using ten genes, but the standard error was only 5% if 50 genes were used and 3% with use of 100 genes.  Their study used 658 genes distributed among 207 species of vertebrates (mostly mammals).  [note added 11/25, 2014 -  this shows the ability of statistical analysis to give a more precise wrong answer, if a uniform rate premise is wrong – a point of my May 31, 2013 post; see Maley and Marshall, 1998 below also]

Laird, Charles D., Betty L. McConaughy, and Brian J. McCarthy.  1969.  Rate of fixation of nucleotide substitutions in evolution.  Nature, 224:149-154. a ten-fold higher rate of nucleotide sequence variation for rodents compared to artiodactyls is found when time estimates are in years  “This difference diminishes if generations, rather than years, represent the appropriate interval of evolutionary divergence.”

Maley, Laura E., and Charles R. Marshall.  1998.  The coming of age of molecular systematics.  Science, 279:505-506.  “Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought.” . . .  “In extreme cases the inferred relationships between groups may change when different representative species are used.” . . “as the amount of data analyzed increases, so does the apparent statistical support for an incorrect phylogenetic tree.”

Mishmar, Dan, Eduardo Ruiz-Pesini, Pawel Golik, Vincent Macaulay, Andrew G. Clark, Seyed Hosseini, Martin Brandon, Kirk Easley, Estella Chen, Michael D. Brown, Rem I. Sukernik, Antonel Olckers, and Douglas C. Wallace.  2003.  Natural selection shaped regional mtDNA variation in humans.  Proc. Nat. Acad. Sci. USA, 100(1):171-176.  p. 171-“multiple amino acid changes found in ATP6, cytochrome b, and cytochrome oxidase I appeared to be functionally significant.  From these analyses we conclude that selection may have played a role in shaping human regional mtDNA variation and that one of the selective influences was climate.”  P. 176 –“If selection has played an important role in the human mtDNA lineages, then the rate of mtDNA molecular clock may not have been constant throughout human history.  If this is the case, then conjectures about the timing of human migrations may need to be reassessed.” 

Miyamoto, Michael M., Jerry L. Slightom, and Morris Goodman.  1987.  Phylogenetic relations of humans and African apes from DNA sequences in the ψη-globin region.  Science, 238:369-373.  “. . the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans.” 

Mooers, Arne Ø., and Edward C. Holmes.  2000.  The evolution of base composition and phylogenetic inference.  Trends in Ecology and Evolution (TREE), 15(9):365-369. “. . , in the early 1990s, phylogeneticists discovered that the variation in GC content among organisms could wreak havoc on attempts to reconstruct evolutionary history.  This was because the tree-building techniques then in use often grouped together unrelated species with similar GC content.” 

Nichols, Richard.  2001.  Gene trees and species trees are not the same.  Trends in Ecology and Evolution (TREE), 16(7):358-364.  different genes may evolve at different points in time in the same lineage giving different times of separation if only one is considered to calculate divergence time

Shaw, Kerry L.  2002.  Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets.  Proc. Natl. Acad. Sci. USA, 99:16122-16127.  “The discrepancy between mtDNA and nDNA phylogenies reveals that speciation histories based on mtDNA alone can be extensively misleading.”

Simmonds, P., and D. B. Smith.  1999.  Structural constraints on RNA virus evolution.  Journal of Virology, 73(7):5787-5794.  Evidence of rate of mutations variation with nucleotide location in relation to secondary structure of GB virus C.  In this case, molecular clock assumptions are incorrect.  

Joseph Engemann    Kalamazoo, Michigan   November 25, 2014

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