EVOLUTION: NEMATODE WORMS

Nematode worms are typically long, round, unsegmented, gradually tapered at both ends.

"Nematodes have many species with relatively little difference in body form.  Many are parasitic and it is thought that most species of vertebrates may have one or more parasitic nematode species unique to them.  Nematodes parasitize many other groups of animals and plants.  Many live in the intestines of animals.  One free-living nematode species lives in organic rich soil but can also live as a parasite in humans. Rotting organic matter in soil is not so different from the intestinal contents of some animals.  Both are rich in bacteria that the nematodes can feed upon.  Adapting to the rich soil made them somewhat "pre-adapted" to life as an intestinal parasite. This adaptation included an ability to live in environments with oxygen so limited many other animals could not survive." (from my unpublished 2010 manscript)

The similarity of structure of different species disappears when the mouth end, and often the anal end, are examined microscopically.  Three jaws are present in some.  The pharanyx may have a muscular bulb that probably helps ingestion of food without losing pressure, the body contents act as a hydrostatic skeleton.  The cuticular covering of the body is molted or shed typically several times in early development.  During the process of development portions of the chromosomal material can be ejected from the chromosomes; this is perhaps a result of selection for the small size of ancestors living among the sand grains of soils. In one species the ejection of chromatin occurs in all cells except the stem cell until the 32 cell stage.  Body cells of many achelminths other than nematodes also seem to have the loss of ability to regenerate that is thought to be a result of the reduced chromosomal material in body cell nuclei (or nuclei when tissues are syncytial).  Near constant number of nuclei or cells of the species are present in the tissues of many aschelminths.

I was reviewing some of Libbie Hyman's work on Aschelminthes (not accepted as a valid cluster by many zoologists), but unfortunately she did not have the benefit of knowing about gnathostomulids (first described in 1956) which were later.  Gnathostomulids seem to be descendents of the simple early flatworms that are not flat, but are adapted to living in sediments that are often anoxic.  Reidel, 1969, suggests the gnathostomulids can be placed in either the Platyhelminthes or the Aschelminthes.  The gastrotrichs may be the connecting link to rotifers.  Nematodes may have been the termination of a line orginating early in the cluster of achelminth groups; but they have a complete lack of cilia, a fact that makes them unlikely to have given rise to any other groups since arthropods also lack cilia but are so clearly derived from annelids that do have cilia.  Thus the lack of cilia in nematodes and arthropods is an analagous, not homologous, trait.

The reason I referred to Hyman was to find out about the adhesive glands or pedal glands, commonly paired on most ashelminths' posteriors, but absent in the gnathostomulids.  The glands are very small and difficult to see, especially in nematodes.  I did not see them in some nematodes I had watched in water on a microscope slide at low magnification, but those nematodes were clearly adhering by their tail as the writhed around.  One researcher (Chitwood) divided nematodes into two groups depending on whether they had phasmids at their posterior.  The mouth area and anal areas of nematodes show great variation in microcopic details not conducive to casual observation.

Such fine details can be a great help in identifying species and often show revealing variation suitable for showing evolutionary relationships.  The October 20, 2017, issue of Science has a research report detailing such a fact with feather-like hairs on water-strider feet.  In the case of water-striders, the details are limited to very close relatives.  In arthropods, similar microscopic comparisons can be made of structures limited to closely related species of the same genus and sometimes of different orders.

When the very small and the very large features match, relationship seems more likely.  To determine evolutionary relationships, neither can be ignored.  Over-dependence on one may lead to error and demonstrate why the novice or student may see things the specialist or teacher does not see, a relationship affecting creativity as noted by Tinbergen.

Among the larger features distinctive for nematodes, that show them as a terminal group in an evolutionary sense, are the muscle cells of the body of the intestinal parasite, Ascaris.  All are longitudinal and each passes a muscle cell process to the nerve enervating the muscle.  Other lines of evidence that the Ecdysozoa are an invalid group are indicated by some of the references appended.

Ascaris can grow to a foot long during it time in the intestine.  It has a simple life cycle with transmission of eggs, typically ingested with fecal contaminated food, hatching in the intestine and larve going through tissue and blood to the lungs where they break out and get coughed up, swallowed, and then comlete their life in the intestine.  Another nematode parasite of humans is thought to be the fiery serpent mentioned by Moses.  It has a big name, Dracunculus medinensis, and is known as the guinea worm.  The adult female can be as much as a meter long and live in the subcutaneous tissue under the skin.  The larvae are discharged through a hole in the skin and, if ingested by an aquatic microcrustacean named Cyclops, complete their larval development and, if Cyclops is ingested by a human, eventually reach their location under the skin.

The great variations in size, number of host species needed to complete life cycles, and adaption to a single or limited number of final hosts of most vertebrates, as well as many invertebrates, seems to indicate an ancient origin for nematodes.

Joseph G. Engemann    Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan   October 30, 2017

REFERENCES (comments added)

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. Unfortunately, textbooks have picked up their grouping of nematodes with arthropods and some other molting animals in a group they named Ecdysozoa; based on 18s ribosomal DNA sequences, it is inadequate to support such a group.  They even say “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.”   -page 491 has discussion of unequal rates found in other nematode studies (documented and ignored) and their search for and choice of slowly evolving representatives [almost guaranteed to put an outgroup in where it doesn’t belong]

Fraser, Hunter B., Aaron E. Hirsh, Lars M. Steinmetz, Curt Sharfe, and Marcus W. Feldman.  2002.  Evolutionary rate in the protein interaction network.  Science, 296:750-752.  (26 Apr 2002)  “We show that the connectivity of well-conserved proteins in the network is negatively correlated with their rate of evolution.”  “interacting proteins evolve at similar rates.” - used “putatively orthologous sequences between Saccharomyces cerevisiae and the nematode Caenorhabditis elegans.” 

Halanych, Kenneth M.  1996.  Testing hypotheses of chaetognath origins: long branches revealed by 18S ribosomal DNA.  Syst. Biol., 45(223-246.   Well-done study but long branches and small sample size make result of relationships beyond the nematode-chaetognath affinity somewhat dubious.

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.  “we propose the node-based name (16)[K. de Queiroz and J. Gauthier, Syst. Zool. 39, 307 (1990)] Lophotrochozoa, which is defined as the last common ancestor of the three traditional lophorate taxa, the mollusks, and the annelids, and all of the descendants of that common ancestor.”  Note 10 includes the following statement “Regions that could not be readily aligned were excluded from the analyses.”  Their proposal is ridiculous when all data are considered.

Halanych, Kenneth M., and Yale Passamaneck.  2001.  A brief review of metazoan phylogeny and future prospects in Hox-research.  Amer. Zool., 41:629-639.  maintain Hox gene research supports the earlier ridiculous proposals of ecdysozoans and lophotrochozoans.  Has numerous references.

Hobert, Oliver, and Gary Ruvkun.  1998.  A common theme for LIM homeobox gene function across phylogeny?  Biol. Bull., 195:377-380.  neurogenesis regulatory genes and transcription factors are very similar in vertebrates, insects, and nematodes

Hobmayer, Bert, Fabian Rentzsch, Kerstin Kuhn, Christoph M. Happel, Christoph Cramer von Laue, Petra Snyder, Ute Rothbackerm, & Thomas W. Holstein.  2000.  WNT signaling molecules act in axis formation in the diploblastic metazoan Hydra.  Nature, 407:186-189.  the WNT signaling pathway had been found in nematodes, insects and vertebrates.

Kappen, Claudia.  2000.  Analysis of a complete homeobox gene repertoire: implications for the evolution of diversity.  Proc. Natl. Acad. Sci. USA, 97:4481-4486.  used the nematode, C. elegans

Sarnat, Harvey B.  1984.  Muscle histochemistry of the planarian Dugesia tigrina (Turbellaria: Tricladida): implications in the evolution of muscle.  Trans. Am. Microsc. Soc., 103(3):284-294.  Says striated muscle is in every metazoan phylum except Porifera and adult Platyhelminthes. (oblique striations in nematodes – Rosenbuth 1965, 67  Wright 62) 

Van Auken, Kimberly, Daniel C. Weaver, Lois G. Edgar, and William B. Wood.  2000.  Caenorhabditis elegans embryonic axial patterning requires two recently discovered posterior-group Hox genes.  Proc. Natl. Acad. Sci. USA, 97:4499-4503.  “essential embryonic patterning in C. elegans requires only Hox genes of the anterior and posterior paralog groups, raising interesting questions about evolution of the medial-group genes.” Three Hox genes in the nematode

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

MUSCLES AND EVOLUTION

MUSCLES

Muscles are almost the definition of the animal kingdom.  The larger the animal the larger its proportion of muscle.  It is a consequence of the strength of a muscle being proportional to its cross-sectional area which increases in amount with the square of lineal dimensions.  The strength needed to move its mass increases with the cube of the lineal dimensions.  Thus muscles scale up in size with increasing animal size faster than do most animal organs.

Two types of muscle are found in vertebrates and most other advanced groups of animals.  Striated muscle, often referred to as skeletal muscle in vertebrates, is usually the most abundant.  Intestines and blood vessels are the major locations of smooth muscle.  The sliding filaments of actin and myosin are aligned in the fibrils of the muscle fiber so striations are evident, keeping their orientation as they contract or relax and lengthen as the biochemical reactions powering the movement is regulated by control by voluntary nerves.  Smooth muscle is the other type of muscle and is controlled mostly by nerve fibers of the autonomic nervous system.  Smooth muscle is the muscle type responsible for contraction of veins and intestines.  Like skeletal muscle it works only by contracting.

A special type of striated muscle, not associated with the skeleton, is found in the heart and called cardiac muscle.  Cardiac muscle fibers branch and fuse forming a network.  The network probably is needed to prevent blood from separating fibers and pushing through the wall of the heart.  The fibers of cardiac muscle are partitioned at intervals by intercalated disks.  Intercalated disks are also found in some protostome hearts thus providing some evidence supporting the annelid ancestry of advanced protostomes and deuterostomes.

MUSCLE ATTACHMENTS

Bone
Skeletal muscles, which do their work by contracting as do all muscles, have an origin on a bone at one end and an insertion at the other end on an adjacent bone that is moved when the muscle contracts.  To move the bone back to its original position and opposing muscle must contract on the other side of the bones and joint.

Soft tissue
So how do we stick out our tongue.  We do it by contracting other muscles within the tongue oriented in directions other than the length of the tongue in which muscles are relaxing.  If they relax more on one side the tongue will curve more to the other side.

Hydrostatic or hydraulic skeletons
The earthworm provides a good example of this type of skeleton.  Under the cuticle and epidermis, the outer layer of muscle is circular muscle.  The soft tissue and fluid in the coelom is forced by contractions of the circular muscle into lengthening the worm as it gets thinner in the segments containing the contracting muscle.  Interior to the circular muscles are longitudinal muscles that lengthen.  If all the segments lengthen, the worm gets long and thin, the total worm volume remains the same.  Conversely, when the longitudinal muscles contract the worm shortens and gets much thinker, but total volume remains the same.

The leech also is dependent on the muscular system using the transmission of fluid and flexible soft tissue moved by the opposing contractions of outer circular and inner longitudinal muscles.  But the body is flattened by transverse muscles connected to dorsal and ventral surface tissues.  Thus movement involves less lengthening and shortening but more up and down bending to either swim by undulations of the body or move along surfaces my bringing the posterior sucker up close to the attached anterior sucker which is then released as the body straightens its bend to attach it further forward.

The photo above is a cross-section of a portion of a leech showing the thin layer of circular muscles under the cells of the epidermis.  Bundles of longitudinal muscles underlie the circular muscles.  A few transverse muscles are shown as dark tracts, some with lighter connections passing between longitudinal muscle bundles to tissue associated with the circular muscles.  The coelom is mostly filled with soft organs.

Hydras do much the same, but the interior of the hydra is fluid filled and the body has the circular muscle fibrils of the gastrodermal cells inside the longitudinal fibrils of the epidermal cell where the fibrils are in more of a network.  The fibrils of both layers of the layers are in close association with the thin layer of connective tissue separating the two cell layers.

Resolving the evolutionary switch from outer longitudinal to outer circular muscle

It is evident that the cnidarian medusa to planarian flatworm suggested in earlier posts and illustrated in [ http://evolutioninsights.blogspot.com/2015/03/evolution-quiet-pre-cambrian-genes.html ] provides a plausible mechanism for the transition.

I gained some insight into the functioning of hydra's hydrostatic skeleton when I had students study the feeding reaction of hydra.  When a weak solution of glutathione is introduced into the water near a hungry hydra it will start moving its tentacles toward its mouth in the same manner it would do if a small crustacean had been captured by a tentacle.  I was amazed to see that the mouth was wide open.  I was thinking it was impossible for it to maintain its posture if the fluid in the gastrovascular cavity was not prevented from exiting the open mouth.  Examination of hydra sections, in particular the tentacles, showed the gastrodermal cells were very large, almost balloon like, and the cavities in the tentacles were almost non-existent.

It made sense that each gastrodermal cell had a single circular muscle fibril so that contraction would be most directly applied to the cell and not slip between cells.  And the thick gasterodermis near the mouth allowed longitudinal fibers of the epidermis to open the mouth more efficiently.

Although the bloated gastrodermal cells may be a more important part of hydra's hydrostatic skeleton, large anthozoan anemones do utililize the fluid filling the gastrovascular cavity to a much greater extent.  Many have one or two siphonoglyphs which are ciliated grooves of the gastrodermis extending from near the mouth to near the basal disk.  Siphonoglyphs enable the anemone to remain inflated and/or reinflate itself after major contractions reducing size for self-protection.

Nematode muscles and evolution

The muscular system of large nematodes such as Ascaris is unique in that the muscles of the body wall are all longitudinal muscles.  The fibrils are enclosed in cells that are long tapering tubes with the nuclei containing part projecting into the pseudocoel.  From the bulbous part containing the nucleus, a slender tubular extension runs to one of two major nerves extending the length of the worm in dorsal or ventral positions; the synaptic connection to the nerve is made at the nerve by the muscle cell rather than at the muscle as in most organisms.  The muscular pharynx is a characteristic of nematodes important in maintaining fluid volume of the worm enabling its hydrostatic skeleton to function.  The cuticle is strong enough to keep the fluid retained for its function as a skeleton.  As a result, when the muscles of dorsal and ventral halves of the worm alternate contractions, the nematode bends or undulates up and down.

The peculiarity of the muscular system of nematodes and their lack of motile cilia are reason enough to reject the Ecdysozoa as a legitimate phylogenetic group.  The molecular basis for its formation is unsustainable if the evidence presented in [ http://evolutioninsights.blogspot.com/2013/05/science-screw-up-no-1.html  ]  is known.

Joseph G. Engemann     Kalamazoo, Michigan     January 28, 2016

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

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

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.