THE TREE OF LIFE

REVISED TREE OF LIFE

The revised tree of life described in the previous post lacked any illustration to aide understanding.  The transfer of files to a new computer, operating system and associated software (Windows Vista to Windows 10) has delayed production of something suitable.  I was eventually able to find Paint embedded in 10.  But my attempt to modify the diagram below with color to clarify the protostome and deuterostome groupings left an illustration dangling somewhere in a jpg file that I have not been able to migrate to this blog.

 The protostomes began with platyhelminthes, the flatworms ancestral to other protostomes, and eventually deuterostomes via annelids.  The anthropocentric view showing primates upper right as the ultimate chordates is only for illustration of our lineage.  Every living group could have an illustration showing their group at the peak.  Some hint of this is shown with wasps and flies being groups of insects at the upper left.  And at the far left the cephalopods are perhaps the ultimate mollusks.

The boldface names in the above diagram represent groups in the direct ancestral line to primates.  All animals with a eucoelomate body cavity are included in the annelids and those above them in he diagram.  Phylum names are in all capital letters.  Polychaetes are probably the ancestral annelids for other annelids (oligochaetes and their descendants the leeches), mollusks, and arthropods, as well as the pogonophorans.  Echinoderms and lophophorates were probably each derived from ancestors intermediate between polychaetes and hemichordates; echinoderms perhaps being farther along the line to chordates in their origin.

The various other groups are not all fairly treated in showing how advanced they are in an evolutionary sense.  Their position is generally more an estimate of the antiquity of their origin.

OLDER VERSIONS OF THE TREE OF LIFE

A.  Prior to the erroneous Lophotrochozoa and Ecdysozoa proposals the "Tree of Life" would have looked much like the version presented above with the following evident.
 1. a separate origin of the deutrostomes from much earlier connecting the Hemichordates via unknown intermediates to the platyhelminthes.
2. a consequence is the assumption of a separate origin of coelom and blood vascular system of deuterostomes and advanced protostomes.
3. inexplicable cellular, histological, and moleular similarities in advanced protostomes and deuterostomes.

B.  The Lophotrochoza error may some value as an assessment of lophophorate invertebrates but is not much use as showing relationships to vertebrates and some other phyla.

C.  The Ecdysozoa error is made worthless by trying to make nematodes an important part of the evolutionary history of other some other phyla.  Nematodes, as partially indicated in the diagram above, are probably part of an aschelminth group derived from turbellarian flatworms miniaturized by selection for adaptation for life in the interstices of marine, then freshwater and terrestrial sediments.  The extreme specialization of nematodes did not provide a good base for selection of new groups.  The superficial resemblance of their outer covering with the exoskeleton of arthropods is misleading.  Surprisingly or fortunately, they did not make reptiles part of the group for shedding their skin.  The post of May 31, 2013 should make it evident why the molecular data they used as a basis for Ecdysozoa is worthless.

D.  Other versions of the "tree of life" based on symmetry and other features such as segmentation are not in vogue today, although the data used for them may have application in limited portions of "the tree of life".  The antiquity of brachiopods and bryozoans as well as considerable differences in the lophophores would seem to argue for separate origins, perhaps from somewhere along the polychaete to pogonophora line.

E.  The ancient annelid theory (over 100 years old) can be tweaked by insertion of the pogonophora to explain several things as shown elsewhere in the blog and indicated by the above diagram.
1. How the pogonophora turned an annelid arrangement of systems in to the chordate pattern.
2. How the anterior nervous system could fuse into a brain without an esophagus penetrating it.
3. How the drastic embryological changes of spiral to radial cleavage were simply made.
4. How molecular homologies of chordates and advanced protostomes came about.


Joseph G. Engemann   Emeritus Professor of Biological Science, Western Michigan University, Kalamazoo, Michigan     May 16, 2016

Disclaimer: All errors, mistakes, and omissions are my own and not the responsibility of Michigan State University, The University of Tasmania, nor Western Michigan University, nor the U. S. Fulbright Agency; although their assistance was valuable enabling me to make them.  jge

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

http://evolutioninsights.blogspot.com/2014/06/variable-rates-of-evolution.html

June 22, Evolution in the deep sea

http://evolutioninsights.blogspot.com/2013/06/evolution-in-deep-sea.html

http://evolutioninsights.blogspot.com/2013/06/evolution-protostome-deuterstome-link.html

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

http://evolutioninsights.blogspot.com/2013_05_01_archive.html

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.

http://evolutioninsights.blogspot.com/2015/01/salvaging-data-for-evolution-studies.html

IF YOU KNOW A BIOLOGIST THAT RESEARCHES IN EVOLUTIONARY STUDIES PLEASE EMAIL HIM A LINK TO THIS POST

http://evolutioninsights.blogspot.com/2015/01/unrecognized -principles-of-evolution.html

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

SALVAGING DATA FOR EVOLUTION STUDIES

MOLECULAR DATA

It occurred to me within the past day that I have ignored one of the things I learned in my youth - how to get some use out of discarded materials in the city dump!

Such experiences were something few children in modern cities get.  So many of the products we use are not designed to be repaired, just throw the whole thing away and get a new one, or at best, get a module to replace a portion.

So my criticism of the Ecdysozoa and Lophotrochozoa studies [post of May 31, 2013] overlooked the fact that, if the errors introduced by linking most ancient ancestors were taken in to consideration, and some such ancestors were omitted in a new analysis, the remaining data might lead us closer to the reality of the ancestral paths.  Even so, the inadequate sample sizes and the limited portion of the genomes examined are unlikely to be very useful.

I don't think it is worth trying because the sample sizes were already inadequate and might still be if clusters could be reanalyzed omitting the nematodes in the Ecdysozoa study.  Nematodes need omission not only because they may have extreme retention of genomic identity giving them "long-branch attraction" to diverse distantly related groups, but they also are a separate lineage that is not basal to any other major modern group.

The Lophotrochozoa represent newer evolutionary events.  Because uncertainty due to variable length of lineages from common ancestry of early coelomate animals, and the "long-branch attraction" problem affecting some of the members descended from annelids via the Pogonophora, the relationship of various "lophophorate" clusters can not be determined with simple corrections.

EMBRYOLOGICAL DATA

As discussed in my posts regarding isopod egg comparisons it is clear that the old idea of the "biogenetic law" where animals were thought to repeat some steps of their evolutionary development in their individual embryonic development is not valid.  But I hope I made it clear that the concept is still a useful model that may suggest investigation for support from other evidence.

The isopod eggs, and ecological factors involved in deep-sea selection, helped me see how the Pogonophora explain the close relationship of ancestry of deuterostomes to advanced protostomes.  Judging from the number of views of my blogs on the topics, I think people studying such things are unlikely to know about them and thus will be unable to apply the concepts.

ANATOMICAL DATA

Amazing data can be found in studies of anatomy.  But it is increasingly unlikely to be helpful, not because it can't be, but because modern researchers are swamped with so much useful information they will never get far into older studies and approaches.  Anatomy and its changes not only reflect evolutionary history but are intimately connected with the genomes of animals.

The environment imprints it natural selection role on structure, development, and the responsible genes.  But the complex interaction is so nebulous I pity the researchers of today who are certainly more technically advanced than I have ever been.  The day is not long enough, nor their life long enough, to have much chance of putting it all together.  Still, I anticipate the continuation of the string of remarkable advances science can make in many areas.  I hope they can still get the benefits study of the humanities can make in their lives.

Joseph G. Engemann    Kalamazoo, Michigan    January 23, 2015

SCIENCE SCREW-UP NO. 1

The Lophotrochozoa Ecdysozoa mistake

A big mistake in the tree of life – ignoring generation time

How it started

What should be one of the crowning jewels of achievement in molecular biology has been plagued by an unwarranted suggestion in an otherwise outstanding seminal paper (Zuckerkandl and Pauling, 1965) detailing the theory of molecular clocks.  They clearly laid out the factors determining genetic changes over time.  One of the factors was generation time of organisms.  They opined that it was impossible to determine the past generation times involved in the evolution of species, but that variation in generation time factors speeding and slowing rates would average out so generation time could be ignored.  The big mistake had its basis in this presumption.

Why it should have stopped

Within a few years, Kimura and Ohta (1971) noted that the pauling (a rate of substitution of ten to the minus nine per amino acid site per year) varied from one centipauling for histones to four paulings for fibrinopeptide A.  Of course the mutation rate for the nucleotides of DNA would be somewhat higher than 400-fold because of the redundancies in the DNA coding for amino acids. 

Laird, McConaughy, and McCarthy (1969) already had reported a ten-fold higher rate of nucleotide sequence variation for rodents compared to artiodactyls when time estimates were in years and said “This difference diminishes if generations, rather than years, represent the appropriate interval of evolutionary divergence.”  Britten (1986) noted that “Examination of available measurements shows that rates of DNA change of different phylogenetic groups differ by a factor of 5.”

Miyamoto, Sllghtom, and Goodman (1987) reported “. . the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans.”  Field et al. (1988) noted that “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.”

What should have stopped

Publication and acceptance by scientists in general of the Lophotrochozoa and Ecdysozoa; papers describing the Lophotrochozoa in 1995 (Halanych et al.), the Ecdysozoa in 1997 (Aguinaldo et al.), should have been rejected by peer review.  Both studies were based on 18S ribosomal DNA sequences.  Both run counter to results of classical phylogeny studies preceding molecular phylogenies; then the establishment accepts the contrary results of these two small samples although the authors noted several things that should have raised questions. 

For the 1995 Lophotrochozoa study, note 10 includes the following statement “Regions that could not be readily aligned were excluded from the analyses.”  And the 1997 Ecdysozoa paper says “It was unexpected to find nematodes contained within the Ecdysozoa because in previous molecular studies they diverged deep in the protostome tree, even before the deuterostome-protostome bifurcation.”  It seems that both reports were state of the art for molecular phylogeny studies of smaller evolutionary units having less variation in basic life cycles and molecular features.  So the problem is one of scale; errors are compounded when generation time is ignored.  The fact that small scale projections are not greatly affected must have made the authors and their peers think the new broad-scale studies were correct.  Big mistake.

It has been said that hindsight is 20/20

Sanderson (1996) would have shown them their sample size was too small.  Other alerts are now available from Maley and Marshall (1998), Martin and Palumbi (1993), Wägele (1999), and many others.  But with no correction for generation time in their algorithms, it was GIGO.  Computers can generate trees regardless of the quality of the input.  Unfortunately, the flawed results have been accepted and perpetuated in textbooks and additional research.

Disclaimer for conflict of interest

I admit to a certain amount of pique with both Nature and Science for having rejected manuscripts I submitted years ago that might have had a role in providing a better solution to the evolutionary tree of life.   I understand the need to reject over 90% of submissions means life is not necessarily fair for those seeking publication.  I made a 1988 presentation to the Michigan Academy entitled “A life cycle adjustment is needed for molecular clocks”.  In 2004 I presented “Ecdysozoa, Lophotrochozoa, and Other Molecular Phylogeny, Peer-Review Failures. “  The abstract was in the Michigan Academician, 36(1):118-119. I intended to submit the full paper to Science, but found their new submission rules beyond my digital capabilities.  More about the answers I have for evolutionary questions will be presented in future postings.   I might have accepted the Lophotrochozoa and Ecdysozoa proposal if I did not already have knowledge of a tree of life that better fits the facts; the pogonophorans provide critical information supporting the tree.

Joseph G. Engemann, Emeritus Professor of Biological Science, Western Michigan University,  Kalamazoo, MI   May 31, 2013

References cited

Aguinaldo, Anna Marie A., James M. Turbeville, Lawrence S. Linford, Maria C. Rivera, James R. Garey, Rudolf A. Raff, and James A. Lake.  1997.  Evidence for a clade of nematodes, arthropods and other moulting animals.  Nature, 387:489-493.

Britten, Roy J.  1986.  Rates of DNA sequence evolution differ between taxonomic groups.  Science, 231:1393-1398.  

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.

Halanych, Kenneth M., John D. Bacheller, Anna Marie A. Aguinaldo, Stephanie M. Liva, David M. Hillis, and James A. Lake.  1995.  Evidence from 18S ribosomal DNA that the lophophorates are protostome animals.  Science, 267:1641-1643. 

Kimura, Motoo, and Tomoko Ohta.  1971. On the rate of molecular evolution.  J. Molec. Evolution, 1:1-17.

Laird, Charles D., Betty L. McConaughy, and Brian J. McCarthy.  1969.  Rate of fixation of nucleotide substitutions in evolution.  Nature, 224:149-154.

Maley, Laura E., and Charles R. Marshall.  1998.  The coming of age of molecular systematics.  Science, 279:505-506. 

Martin, Andrew P., and Stephen R. Palumbi.  1993.  Body size, metabolic rate, generation time, and the molecular clock.  Proc. Natl. Acad. Sci. USA, 90:4087-4091.

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.

Sanderson, Michael J.  1996.  How many taxa must be sampled to identify the root node of a large clade?  Syst. Biol., 45:168-173. 

Wägele, Johann-Wolfgang.  1999.  Major sources of errors in phylogenetic systematics.  Zool. Anz., 283:329-337. 

Zuckerkandl, Emile, and Linus Pauling.  1965.  Evolutionary divergence and convergence in proteins.  Pp. 97-166.  In: V. Bryson and H. J. Vogel (eds.).  Evolving Genes and Proteins.  Academic Press, N. Y.