NATURE & SCIENCE MISS THE MARK
I was thinking about my previous post and it seemed to me the obvious answer to determining animal phylogeny stared me in the face. The data I had cited from Francis S. Collin's book, The Language of God, seemed to provide proof of the point I have been trying to make in many evolutioninsights.blogspot.com posts. On page 127 his Table 5.1 compares the liklihood of finding comparable DNA sequences of humans in other organisms. It makes the comparison, first of protein coding genes from humans with six other species, then randomly selected DNA from between genes of those species.
Human compared Protein coding Random DNA
with DNA between genes
Chimp 100% 98%
Dog 99% 52%
Mouse 99% 40%
Chicken 75% 4%
Fruit fly 60% -0%
Roundworm 35% -0%
Your first thought might be that the protein coding genes make more sense to use for determining relationships. That is probably the rationale the two flawed studies proposing Ecdysozoa (in Nature, 1997) and Lophotrochozoa (in Science, 1995) used in selecting 18S ribosomal DNA. But there would be stringent selection to keep that DNA from changing, with a proportionality to its functional importance.
The random DNA from non-coding regions would lack selection and thus could change proportional to the number of generations between the two being compared. Thus if liklihood percentages are apportioned inversely to generation time in constructing the branch lengths from common ancestors, an ancestral tree could be determined better than by any other available method. Of course, pairwise comparisons would need to be made for each other possible combination of species considered.
Looking at the data in the table, because mice have shorter generation time they would accumulate more changes since our common ancestry and may thus actually be closer in common ancestry to us than the dog, even though there has been greater change in their between genes DNA. The big jump between the chicken and the mammals is due to the much greater antiquity of the separate lines from early ancestral reptiles. With very low liklihood of DNA relationship the accuracy of relationship determination is greatly reduced and fossils and anatomical analysis may be more useful.
I would send this as letters to the editors of Nature & Science, but I doubt they would be any more likely to publish them than my previous submissions many years ago. Too bad, it might have prevented the Ecdysozoa error which put the roundworm and fruit fly in relatively close relationship. The same method used for the Lophotrochozoa is consequently almost equally erroneous.
Science and Nature are two excellent science journals. I am puzzled by the fact that the error has not been corrected. Perhaps others read it much as I have in the past when reading things I am not very familiar with, assuming the research finding are accurate. I did so despite the fact that long ago I realized not everything in print, or on internet, must be correct.
Joseph G. Engemann Emeritus Professor of Biological Science, Western Michigan University, Kalamazoo, MI March 7, 2015
Showing posts with label generation time error. Show all posts
Showing posts with label generation time error. Show all posts
Friday, March 6, 2015
Saturday, January 24, 2015
UNRECOGNIZED PRINCIPLES OF EVOLUTION
HELP NEEDED - TELL YOUR FRIENDS - SEND A LINK
Any biologist doing evolution type studies of phylogeny
should understand the concepts of the following posts which are not currently
appreciated, especially by those doing molecular phylogeny studies.
June 9, 2014, Variable rates of evolution
June 22, Evolution in the deep sea
May 31, 2013 or June 1, 2013 Science screw-up no. 1 - Why molecular
phylogeny experts have gone astray with the introduction of Ecdysozoa and
Lophotrochozoa has been archived as below
January 23, 2015 -
Salvaging data for evolution studies, it should be read in conjunction
with the blog post listed above, may be a view principally of interest to
biologists studying evolution.
IF YOU KNOW
A BIOLOGIST THAT RESEARCHES IN EVOLUTIONARY STUDIES PLEASE EMAIL HIM A LINK TO
THIS POST
My demise is not expected, but at my age I would hate to leave a world lacking a link to ideas needed for the advance of animal evolution studies.
Joseph G. Engemann Kalamazoo, Michigan January 24, 2015
Monday, June 16, 2014
MAJOR PHYLOGENY ERROR EXPLAINED
THE IMPACT OF DIFFERENT RATE ON ESTIMATES OF ORIGIN
Current phylogenetic trees that include Ecdysozoa and, to a lesser extent, Lophotrochozoa are grossly incorrect. Because DNA neucleotide sequences are subject to selection and have had different rates in different groups the direct calculation of rates from comparative differences produces flawed evoutionary trees.
This can be shown graphically by comparing two branches of a phylogeny using the different assumptions involved. The determination of when and how fast the differences in longevity develop is subject to error also, but, in the case of the descendants of pogonophorans, may rapidly move to shorter life cycles as soon as the transition from abyssal to shallow depths occurs. Thus very few new species may make the connection of ancient pogonophorans to those that became the earliest shallow water deuterostomes.
The first figure illustrates two types of error made in calculating phylogenies, generation time error and calibration error.
Generation time error is the one that produces incorrect branching in a phylogeny. The figures illustrate generation time error for two species assuming that half the change occurs in each line as in the 5 and 5 of the right figure of each pair. When 90% of the change occurs in the right branch, the estimated time from origin at the ancestral node is nearly doubled. With pogonophorans having generation times several thousands of years longer than modern non-abyssal species, the node where deuterostome phyla branched off is clearly during Pre-Cambrian times as is also suggested by the Paleozoic emergence of chordates.
Calibration error is one that can cause overestimates or underestimates in the time of divergence in two lines from the ancestral node. The two right figures keep the generation time error intact, if it is in error. The calibration error occurs when the time per nucleotide change is based on a calibration species whose rate of change is different from the species to which the rate is applied. Selection of a calibration species or a rate of change is not likely to be a major problem when closely related species are studied.
If you think about the result of the generation time error introduced by the central position of pogonophorans in the protostome, deuterostome radiation, it is not surprising that their relatively unchanged DNA shows affinity with widely diverse phyla.
A similar problem is probably operating in the nematodes being a significant group in the erroneous group, Ecdysozoa. The small size of nematodes is probably a selective reason nematodes have a single gene per gene family and thus a more rigid selection producing relatively unchanged genotypes over a long. time. Thus the "long-branch attraction" is not recognized as the error compounded in the Ecdysozoa concept.
The last figure illustrates one possible view of the development of two species having different longevity from a common ancestor. It is perhaps worthless as an illustration because the common ancestor of related species, one with a one year life cycle, the other with a two year life cycle, could very well have resulted from all the change in one line, or both from greater change from some extreme value. Rates of change are also unlikely to be so uniform.
Until I stumbled across what seemed to be an unlikely ancestral role of the pogonophorans I would have been been very likely joining my peers in welcoming the Ecdysozoa and Lophotrochozoa. I hope I have included enough information in the blogs on this site to help my peers make the same transition I have made.
Joseph G. Engemann June 16, 2014
Current phylogenetic trees that include Ecdysozoa and, to a lesser extent, Lophotrochozoa are grossly incorrect. Because DNA neucleotide sequences are subject to selection and have had different rates in different groups the direct calculation of rates from comparative differences produces flawed evoutionary trees.
This can be shown graphically by comparing two branches of a phylogeny using the different assumptions involved. The determination of when and how fast the differences in longevity develop is subject to error also, but, in the case of the descendants of pogonophorans, may rapidly move to shorter life cycles as soon as the transition from abyssal to shallow depths occurs. Thus very few new species may make the connection of ancient pogonophorans to those that became the earliest shallow water deuterostomes.
The first figure illustrates two types of error made in calculating phylogenies, generation time error and calibration error.
Generation time error is the one that produces incorrect branching in a phylogeny. The figures illustrate generation time error for two species assuming that half the change occurs in each line as in the 5 and 5 of the right figure of each pair. When 90% of the change occurs in the right branch, the estimated time from origin at the ancestral node is nearly doubled. With pogonophorans having generation times several thousands of years longer than modern non-abyssal species, the node where deuterostome phyla branched off is clearly during Pre-Cambrian times as is also suggested by the Paleozoic emergence of chordates.
Calibration error is one that can cause overestimates or underestimates in the time of divergence in two lines from the ancestral node. The two right figures keep the generation time error intact, if it is in error. The calibration error occurs when the time per nucleotide change is based on a calibration species whose rate of change is different from the species to which the rate is applied. Selection of a calibration species or a rate of change is not likely to be a major problem when closely related species are studied.
If you think about the result of the generation time error introduced by the central position of pogonophorans in the protostome, deuterostome radiation, it is not surprising that their relatively unchanged DNA shows affinity with widely diverse phyla.
A similar problem is probably operating in the nematodes being a significant group in the erroneous group, Ecdysozoa. The small size of nematodes is probably a selective reason nematodes have a single gene per gene family and thus a more rigid selection producing relatively unchanged genotypes over a long. time. Thus the "long-branch attraction" is not recognized as the error compounded in the Ecdysozoa concept.
The last figure illustrates one possible view of the development of two species having different longevity from a common ancestor. It is perhaps worthless as an illustration because the common ancestor of related species, one with a one year life cycle, the other with a two year life cycle, could very well have resulted from all the change in one line, or both from greater change from some extreme value. Rates of change are also unlikely to be so uniform.
Until I stumbled across what seemed to be an unlikely ancestral role of the pogonophorans I would have been been very likely joining my peers in welcoming the Ecdysozoa and Lophotrochozoa. I hope I have included enough information in the blogs on this site to help my peers make the same transition I have made.
Joseph G. Engemann June 16, 2014
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