THE TREE OF LIFE
The tree of life, as currently accepted by main-stream science, has an unaccounted for error. It is no secret to you if you have read all my posts, but the molecular phylogeny of major phyla has major errors for lack of understanding long-branch attraction. Or as I have shown from numerous citations elsewhere, abundant evidence that direct measurement of DNA differences of species is almost certain to produce an erroneous tree-of-life for phyla if it is calculated from those differences.
LONG BRANCH ATTRACTION
Molecular phylogenies are sometimes plagued with the pogonophorans or some other group appearing in some central position in a phylogeny when the researcher is quite certain it should not be there. They may note that it doesn't seem to belong there, or, I suspect, sometimes they leave it out because they think it is a long-branch attraction appropriate to ignore. Maybe they just remember not to use the group for an out-group [a group inserted that is reasonably presumed to be outside the cluster being investigated]. The correct solution is to figure out why it happened - something they cannot do without introducing a major variable of molecular clocks all ignore. I have discussed elsewhere how the nematodes may also have a slower rate of change in their genome and thus produce an example of long branch attraction.
THE POGONOPHORA
The Pogonophora are specialized descendants of polychaete annelids of which the ancient ones are ancestral to all vertebrates via hemichordates and cephalochordates as indicated in Our Evolutionary Lineage (Post 79). [ http://evolutioninsights.blogspot.com/2014/12/our-evolutionary-lineage.html ]
That post also lists approximate times of origins of groups in that lineage. From that we can see that the pogonophorans evolved about a billion years ago. Some are little changed to this day, if they stayed in the abyss, from perhaps 600 million years ago when the hemichordate line branched off from some of the pogonophorans moving into shallower waters. From hemichordates the cephalochordates branched off, perhaps 500 million years ago.
THE CAMBRIAN
About 500 million years ago the Cambrian began. Most major phyla had representatives in the Cambrian. Trilobites were arthropods whose fossils are only found in rocks through the Cambrian to the end of the Palaeozoic. Arthropods are obvious annelids descendants that have an origin from polychaetes, as do pogonophorans. Mollusks had a comparable origin from polychaetes.
The stability of conditions in the Cambrian enabled pogonophorans ancestors to migrate to shallower seas and survive following the end of major asteroid bombardment episodes. As they established themselves in shallow seas, the reduced pressure enabled physiological processes involving diffusion to speed up to a 1,000 times greater speed. A better food supply also contributed to the process. The recovery of gut development by the hemichordate descendants accompanied other developments as the worms moved out of their tubes and took on a more active life getting particulate food, mostly by filtration instead of the diffusion on which the pogonophorans had become dependent.
Parallel lines from the polychaete-pogonophora line gave rise to echinoderms and probably some of the lophophorate phyla that also made their appearance in the Cambrian.
CALCULATING THE LONG BRANCH ATTRACTION
We can ignore the fact that pogonophoran tube analysis (in earlier blogs) indicates the individuals can live from 10,000 to a million or more years. Just taking the pressure differential effect on physiology indicates evolutionary selection is likely to be 1,000 times more rapid in shallow seas than in abyssal ones.
The ancestor that remained and reproduced in the abyss over the past billion years would be expected to have one million nucleotide substitutions in their DNA while a descendant that had been near the surface has 500 million nucleotide substitutions in the past half-billion years. Another descendant branching off at the same time would also have 500 million nucleotide substitutions in the past half-billion years.
Others branching from the new lines, say one from each line 400 million years ago, each would have 400 million nucleotide substitutions in each of their lines as differences.
THE SURPRISE
Now, the four groups would all have more in common with the pogonophoran that now has half a million changes from the point of common ancestry with the other four groups that each has 500 million changes.
The branching of the new groups would be correctly interpreted from the differences as *800.0 million changes from their nearest relative and *1,000.0 million from each of their more distant pair of relatives, but only *500.5 million changes from the pogonophoran. The pogonophoran now looks closest to all by the long branch attraction, an artifact of different rates of evolution whether by physiological speed or long generation time, or by both as I think it is.
The closer the groups studied, in a phylogenetic study of relationships, the more likely it is that pogonophorans will not show up as a close relative within a group. Thus species, genus, and families in an order are unlikely to appear related to pogonophorans unless the study is of pogonophorans.
If you look at the estimated times of origins you can see that terrestrial vertebrate classes had their origins over three hundred million years ago. but most modern orders were likely beginning almost two hundred million years ago. Nearly the same thing could be said about the insects. Whereas echinoderms are a more ancient group with classes going back to the Cambrian; they even have several extinct classes.
Until the molecular phylogeneticists calculate a major tree of life taking the above into consideration they will continue to be wrong about their view of relationships of phyla. They have a lot to contribute if they stop making that error.
*The numbers used in the examples above are not precise and are only used for a simplified example of the principles involved and are calculated by summing the changes of both ancestral lines from their point of branching.
Joseph G. Engemann Kalamazoo, Michigan February 2, 2015
Showing posts with label phylogeny. Show all posts
Showing posts with label phylogeny. Show all posts
Monday, February 2, 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
Friday, October 17, 2014
MOLECULAR BIOLOGY AND EVOLUTION
Molecular clues to evolutionary relationships
Before molecular phylogeny, with varied
nucleic acid studies became an important part contributing to our understanding
of the tree of life, there were many precursor applications guiding our attempt to classify plants and animals.
Molecular evidence guiding our view of
evolution, was compatible from the earliest days, with our classification schemes
based on the assumption that each species was discrete from others and
separately created. Today, we know that
the origin of species from prior species was a gradual process dependent on the
accumulation of numerous changes preceding the advent of reproductive isolation
of new species from their ancestral species.
The separation of new from old is typically enhanced by other isolating
mechanisms of location, time, and changed aspects of biology.
Chlorophyll, or its green color, was an
early clue separating plants and animals that must have been known before
written records developed. As molecular
biology developed, we found that there are different variants of chlorophyll
and photosynthetic pathways. Green algae
and blue-green algae are easily distinguished from one another by the color
of their chlorophylls; they also have many other significant differences not
involving color or chlorophyll. There
are efficiency differences, between the C-3 or C-4 pathway, and vascular plants
abilities to convert solar energy into glucose which can be stored as sugars
and starches.
Cellulose, a polymer of
glucose, is a structural material of plant cell walls that is lacking in
animals.
Insect and other arthropod exoskeletons
contain chitin. Chitin is limited to
animals known as protostomes, and is not found in the other main branch of
animals leading to vertebrates. It is a
polymer that can be broken down into n-acetyl glucosamine by the digestive
processes of a few animals.
Surprisingly, cellulose and chitin digesting enzymes are uncommon in
most higher animals, so those using them as a food source usually need the aid
of microorganisms.
Hidden Origins of Similar Compounds?
Most biochemical molecules we often think of belonging to recent groups may have had origins much earlier than current evidence shows. The presumption is that two different groups having a unique compound must either represent descent from a common ancestor or they must be a case of convergent evolution. But compounds active in minute amounts, such as hormones, may have been present in common ancestors in such low levels they have not been detected.
One possible bit of evidence might be the presence of ecdysone, a hormone important in controlling molting of insects, has also been found in bracken ferns. If it were present at extremely low levels, in ancestral species reaching back to a common ancestor among one-celled organisms and had little use, it might not be detected until it was produced in sufficient amounts as part of a new process to benefit insect molting. The near ancestors of bracken ferns that developed increased levels of ecdysone sufficient to disrupt fern-eating insect adults and/or larvae would eventually survive better and replace those being killed by insect activity.
The long periods involved in evolution of different forms of similar compounds is likely to allow the demise of intermediate stages of the evolution once a perfected solution is reached. Until the activity of a substance is useful in larger amounts there is a selective advantage of not making larger or detectable quantities. So a substance produced in the cell and doing an activity within the cell by inducing gene action within the cell is not needed in the high levels the amounts hormones transported by the blood require. My attempt to discover "protozoan hormones" as noted in an earlier post was based on this line of reasoning.
The Genetic Code Evolution and Phylogeny
The example of cytochrome c, a compound required by all higher animals and one of the first successes of molecular phylogeny relating diverse phyla, should be revisited. The use of the polymerase chain reaction (PCR) for studying nucleotide sequences might be applicable to the regions of DNA coding the cytochrome. The data could then be used for groups where adequate amounts for comparing cystochromes were not available at the time of the original study*.
*Fitch, Walter M., and Emanuel Margoliash. 1967. Construction of phylogenetic trees. Science, 155:279-284. [
Joseph G. Engemann Emeritus Professor of Biology WMU, Kalamazoo October 17, 2014
Sunday, June 23, 2013
EVOLUTION
ORIGIN OF DEUTEROSTOMES
Abandoned views
Once natural selection was
accepted as the way evolution of species produced the variety of life on earth,
it became a goal to determine the ancestral line of intermediate forms leading
to the major groups of animals. A series
of successive creations suggested by the drastic changes in the geologic fossil
record had earlier been suggested but abandoned. Likewise the concept of inheritance of
acquired characteristics was seldom considered after an understanding of
genetic inheritance developed.
Features of some value
Radial symmetry versus
bilateral symmetry was given some emphasis for a while. The grades of body complexity were, and still
are, given considerable significance.
Grades went from cellular level, to tissue level, to organ system
level. The most primitive of those with
organ systems had only a mouth opening, whereas the more advanced had both
mouth and anus. Blood vascular systems
represented a greater advance. Skeletal
systems, segmentation, and metamerism complicated the picture as different
branches of the ancestral tree diverged.
Invertebrates and vertebrates
were treated as two vastly different groups in some ways and may have been a
major factor in the annelid theory of chordate origin never getting full
acceptance. The recognition of
embryological differences of protostomes and deuterostomes made the presumption
of the deuterostome line separating from the protostome line at about the time
of the early flatworms a generally accepted view; the speed and ancestry
involved in the shift will be shown to differ from the recent views as well as
indicating the error of recently accepted proposals.
Time for return of the
annelid theory
The annelid theory of origin
was a result of the comparison of annelid worms and vertebrates when one was
inverted. When one is inverted and then
compared, the arrangement of nervous system and blood vessels and directions of
flow are similar. But the embryological
differences seemed insurmountable.
Biochemistry and genetics, as well as greater understanding of
embryology and biology made it evident that embryonic and larval features were
not a sure guide to determining ancestral paths. But, as Stephen J. Gould noted in his book (2002. The
Structure of Evolutionary Theory. The
Belknap Press of Harvard University Press, Cambridge, Massachusetts. 1433 pp.), the annelid theory was not revived when the developmental grounds for
its dismissal were eliminated. The developmental
grounds do not need to be completely discounted; they can still be helpful if used with some
flexibility.
The inversion the annelid
theory encompasses still troubles the investigators below who imply other
explanations are needed for the inversion.
Arendt, D., and K. Nübler-Jung. 1994.
Inversion of dorsoventral axis? Nature, 371:26.
De Robertis, E. M. , and Yoshiki Sasai. 1996.
A common plan for dorsoventral patterning in Bilateria. Nature,
380:37-40.
Their efforts are
commendable, but unnecessary if the annelid theory is reinstated. Numerous other reasons to reinstate the
annelid theory of chordate origin exist.
Others have not yet shared in
my 1983 awakening to the validity of the annelid theory. By that time it was evident that the
Pogonophora were near relatives of polychaete annelids. But a conflicting paper revived the notion
that they were deuterostomes based on embryology. The article, quote, and notes from my
reference file are as follows:
Gans,
Carl, and R. Glenn Northcutt. 1983. Neural crest and the origin of vertebrates: a
new head. Science, 220:268-274. (15
April 1983) Includes Pogonophora in the
deuterostomes. “Both the neural crest and the epidermal placodes for
special sense organs and other neural structures. These structures may be homologous to
portions of the epidermal nerve plexus of protochordates. The transition to vertebrates apparently was
associated with a shift from a passive to an active mode of predation, so that
many of the features occurring only in vertebrates became concentrated in the
head.” This is the article that
triggered my (1983 eureka event) awareness of the pogonophorans as the
protostome-deuterostome link after initial disgust of their inclusion in the
deuterostomes.
Other factors lend support to the need for reinstatement of the annelid theory with the addition of the Pogonophora as a formerly missing link. A hint of the overwhelming evidence will be provided in blogs on embryology, inversion, anatomical, and other evidence.
Joseph G. Engemann June 23, 2013
Thursday, June 6, 2013
PHYLOGENY AND MEDICAL RESEARCH
EVOLUTION, PHYLOGENY,
AND MEDICAL RESEARCH
Evolution refers to the gradual changes giving
rise to new forms over many generations.
Phylogeny is the description of the relationships of species
sharing a common ancestor. The less
ancient the common ancestor, the more alike its descendants are expected to be.
Errors in research studies of evolution and
phylogeny can waste your money and your health when inaccuracies creep in as
described in my previous post (Science Screw-up #1). The direct cost of the research is minor and
somewhat compensated for by educational opportunities provided graduate
students.
How
accurate studies of evolution and phylogeny can help you
Basic
biomedical research can use organisms other than humans and other
primates. Even bacteria, especially E. coli (Escherichia coli), have revealed basic information about gene
functioning and basic biochemistry common to all animals. Simple animals can provide some additional
information of value, especially when they are in the ancestral line leading to
us.
A phylogenetic
“tree” representing the ancestral branching pattern along which the existing
animals evolved can be helpful if it is accurate. If system and organ features of animals are
compared and two are found to be alike, all others on the tree that branch
after the common origin of the two are better prospects for research into that
common function. Even better are the ones
that are not on side branches. The
ultimate sample to study may be your own cells if the genetics of a disease has
been determined.
The
preceding approach, using a close phylogenetic relationship, may be more
fruitful in solving more finely targeted problems. Some instances of remarkable progress have
been made using organisms more distantly related that have other valuable
features. Two examples are provided by
the fruit fly and the squid.
The fruit
fly
The fruit
fly (Drosophila melanogaster) was especially
useful in early studies of chromosomal inheritance. Their short life cycle, completed in a few
weeks, and their small size and ability to go through the cycle in a small
bottle, growing on some inexpensive nutrient, enabled students to repeat findings
about heredity. The salivary glands of
the larvae have giant chromosomes due to multiple strands of DNA. That is more of a curiosity, but a more
distantly related insect had chromosomes that showed puffing due to
developmental hormones in specific locations that led to further studies about
how genes are controlled.
The squid
Squids have
relatively enormous nerve fibers extending from two major nerve cell clusters
to enervate mantle muscles forming their tubular body. The largest fibers go the greatest distance,
but transmit the nerve impulse faster.
The graded speeds make the impulse reach all parts of the tube
simultaneously so the contraction is most powerful for expelling water used for
their “jet propulsion”.
The fibers
(axons) are so large they were the first nerve fibers for which the molecular
events (depolarization waves consisting of ion release and transport back
across the axon membrane) of a nerve impulse were discovered. The fundamentals of the process seem to be
much the same for us and other animals.
The power
of phylogeny
An accurate
view of phylogeny gives us the power to multiply the value of biomedical
research to speed the treatment of disease.
Dollars are spent more wisely if the phylogeny upon which research is
designed is accurate. Phylogeny should
not be the major determinant if other considerations are known to be
important. For example, mice may be
better a better choice than monkeys because of small size, short life cycles,
and mice are not on the endangered species list.
Joseph G. Engemann June 6, 2013
Friday, May 31, 2013
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.
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