Phylogenesis

“ The similarity, in some important respects, of ontogenesis to phylogenesis was inevitable, provided that animals were to be of different grades of complexity, since the development of the individual must necessarily be from a more simple to a more complex condition. On any hypothesis, the parallelism between embryological facts and the history of animals in geological time affords many interesting and important coincidences. ”

“ The moment in phylogenesis is independent and is fully developed, while the corresponding stage in ontogenesis is but a stage in the growth of another and higher moment, and as such is certainly different in nature from the phylogenetic moment. ”

“ The introduction of the phylogenetic factor has very much increased the difficulty of determining homologies; for the data necessary for tracing phylogeny can only be obtained by the study of a series of allied, presumably ancestral, forms. One of the chief difficulties met with in this line of research, which is one of the more striking developments of modern morphology, is that of distinguishing between organs which are “reduced,” and those which are really “primitive.” The object of the phylogenetic study of any organ is to trace it back to its primitive form. ”

“ But any transformistic theory, which locates the very principle of phylogeny in the organism itself, and to which therefore even organic forms would be not accidental but essential, might be forced to regard the descent of organisms as a true evolution. The singularities in phylogenetic history would thus become links in one whole: history proper would become more than history. But I only say that phylogeny might be evolution, and in fact I cannot admit more than this a priori, even on the basis of an internal transformistic principle, as has been assumed. ”

“ Saying that polarizing phylogeny is 'incredibly difficult' is an exaggeration, but not one that in any way contradicts my assertion that positioning the root and establishing the properties of the most ancient cells is the most difficult phylogenetic problem. ”

“ Provided one understands the important conceptual difference between taxa on the one hand and grades and clades on the other [ [66] , and the radical nature of quantum evolution that is the typical cause of the huge gulfs separating such higher taxa as kingdoms and phyla [ [127] , one can easily see why some kingdoms (Bacteria, Protozoa) must be paraphyletic and others (Animalia, Fungi, Plantae, Chromista) are holophyletic. In cladistic phylogeny one can reasonably speak of eukaryotes being nested within bacteria (lower case, referring to a grade) ”

“ Both laws were of paramount importance, as direct evidence of Darwin’s theory of descent, which, it will be remembered, was at the time regarded merely as an hypothesis. Nevertheless, the tracing of phylogeny, or direct lines of descent, suddenly began to attract far more interest than the naming and description of species.
The Law of Recapitulation. Acceleration. Retardation.—This law, that in the stages of growth of individual development (ontogeny) , an animal repeats the stages of its ancestral evolution (phylogeny) was, as we have stated, anticipated by d’Orbigny. ”

“ If heredity and variation are defined according to the true nature of organisms, they are only apparent opposites. Since idioplasm alone is transmitted from one ontogeny to the next following, the phylogenetic development consists solely in the continual progress of the idioplasm and the whole genealogical tree from the primordial drop of plasma up to the organism of the present day (plant or animal) is, strictly speaking, nothing else than an individual consisting of idioplasm, which at each ontogeny forms a new individual body, corresponding to its advance. ”

“ From a further consideration of the foregoing principles it will be seen that all existing species are held to be descended by true generation from pre-existing species, and that, consequently, all the relationships we observe between species are explained by community of origin. The most natural system of classification is, therefore, that which best reveals the scheme of descent, or, as it is termed, the phylogeny, of the group of organisms classified. ”

“ From this assumption we are apt to go on to the drawing of new conclusions or the framing of new theories as to the ancestral history, the clas­si­fi­ca­tory position, the natural affinities of the several organisms: in fact, to apply our embryological knowledge mainly, and at times exclusively, to the study of phylogeny. When we find, as we are not long of finding, that our phylogenetic hypotheses, as drawn from embryology, become complex and unwieldy, we are nevertheless reluctant to admit that the whole method, with its fundamental postulates, is at fault. ”

“ Along with the above named phylogenetic processes, which take place by the automatic increase of the idioplasm, external influences are always active. These lend to the organism at times a local stamp corresponding to its environment, and follow the law of adaptation.
21. ALTERNATION OF GENERATIONS IN RELATION TO PHYLOGENY.
Since the simplest plants are cells and the more complex ones are formed from cells, a whole phylogenetic line may be regarded as a series of cell generations following one after another. In the lowest forms all cell generations are like each other ”

“ Much support is given also by palæontology, for the order in which the fossil remains of the various classes of vertebrates succeed each other in the course of organic evolution reveals to us, to some extent, the gradual growth of their psychic power as well as their phyletic connection. We must admit that we are here, as we are in every branch of phylogenetic research, driven to the construction of a number of hypotheses in order to fill up the considerable lacunæ of empirical phylogeny. ”

“ We may confidently put the total number of these at more than a million species. The number of animals whose organisation has been studied up to the present in comparative anatomy is proportionately very small. Here, again, future research will yield incalculable treasures. But, for the present, in view of this patent incompleteness of our chief sources of evidence, we must naturally be careful not to lay too much stress in human phylogeny on the particular animals we have studied, or regard all the various stages of development with equal confidence as stem-forms. ”

“ It is a basic fallacy to regard bacteria or eukaryotes as being simply the product of their genes and genomes. Genes can do nothing outside this structural framework. It is not clear even in theory how lateral gene transfer could cause a structural innovation like the origin of thylakoids or the addition or loss of an outer membrane. To use the word phylogeny to apply just to gene sequence trees is, as you candidly admit, a too narrow interpretation. One must consider structures and morphogenesis as well as genes in phylogeny. ”

“ This is only one example out of many which go to show that, in attempting to reconstruct the genealogy, or phylogeny, as it is called, of the animal kingdom, we must constantly admit the possibility of "convergent evolution." ”

“ The second chief source of evidence, ontogeny, is not less incomplete. It is the most important source of all for special phylogeny; but it has great defects, and often fails us. We must, above all, clearly distinguish between palingenetic and cenogenetic phenomena. We must never forget that the laws of curtailed and disturbed heredity often make the original course of development almost unrecognisable. The recapitulation of phylogeny by ontogeny is only fairly complete in a few cases, and is never wholly complete. ”

“ In order to understand the relation of Ontogeny to Phylogeny, it must be carefully borne in mind that the simple and lowly organized creatures on the globe at the first appearance of life were performing the two great functions that all living creatures perform, viz.: those of nutrition and reproduction. These functions imply that organisms were reacting to environment, and, therefore, undergoing modifications and adaptations; and at the same time the organisms were giving origin to offspring—they were reproducing their kind through heredity. ”

“ It is also noteworthy that internal branches in the phylogenetic tree based on the 13-protein data set (Fig. 2) presented higher bootstrap support than the ones in the phylogenetic tree based on the allnuc data set (Fig. 3) . This result is in agreement with the preferential use of amino acids to reconstruct deep phylogenies because they (1) have a larger character-state space compare to nucleotides, (2) show a slower rate of evolution compare to silent substitutions, and (3) are less influenced by compositional bias [46] ”

“ If the extinct species of plants and animals of the later geological periods were the progenitors of the living species, and gave origin to them by variation and natural selection, where are all the intermediate forms, fossil and living, through which the lost types must have passed during their conversion into the living ones? And why do we not find almost everywhere passages between the nearest allied species and genera, instead of such strong lines of demarcation, and often wide intervening gaps? ”

“ In other words, sights, sounds, and odors are symbols which awaken phylogenetic association. If a species has become adapted to make a specific response to a certain object, then that response will occur automatically in an individual of that species when he hears, sees, or smells that object. Suppose, for example, that the shadow of a hawk were to fall simultaneously on the eyes of a bird, a rabbit, a cow, and a boy. That shadow would at once activate the rabbit and the bird to an endeavor to escape, each in a specific manner according to its phylogenetic adaptation ”

“ The inferences which ontogeny, guided by a few scattered paleontological characters, permits us to draw with regard to phylogeny, will never possess more than a very restricted degree of probability. It will ever be open to the individual understanding to take whatever way it chooses amid the confusion of innumerable and complex possibilities, and, excepting a few indisputable points, which, however, were understood long ago, to conceive a great many different modes of development of the organic world as it exists now. ”

“ The parameter d returns a measure of phylogenetic signal — no phylogenetic signal when d = 0, existent and significant phylogenetic signal when d is significantly greater than zero [24] , [62] . These three models form a continuum between assuming a star phylogeny with no hierarchical structure (OLS) , a phylogeny that was specified by the user (PGLS) and a phylogeny that can exhibit intermediate values between the star and the specified hierarchical phylogeny (RegOU) . ”

“ We recommend increasing the lineages sampled and the number of diverse taxa within lineages. We are optimistic that as data become available from a greater diversity of taxa, eukaryotic phylogeny will become increasingly more resolved.
Multiple character sets.
We further anticipate that support for clades will increase as additional character sets are incorporated. Phylogenies based on single characters, whether genes, morphology, or ultrastructure, are subject to biases in the data and are not reliable by themselves. Hence, multiple character sets should be used to corroborate results. ”

“ As it is plain that the strictest construction of the proper scope and limits of scientific thought does not make any such demands as this, we may feel at liberty to speculate upon phylogeny with such a basis as is furnished by the comparative study of the systematic relationship of living animals, but we are not able to go very far in this direction, for nearly all living animals fall into a few great well defined groups, and generalized types are the exception. Our conclusions must, therefore, be very vague and general, and we turn to the paleontological record for more exact data ”

“ If vital units ever originate de novo at all, it is only conceivable in the case of the very simplest biophors, as we shall see later when we come to speak of 'Spontaneous Generation.' Specific biophors and the determinants composed of them have behind them a phylogeny, a history, which conditions that they shall arise only from their like.
Thus we see that germ-cells can only arise where all the determinants of the relevant species arranged as ids are already present. ”

“ If two or three, or even more linking forms were discovered, they would simply be ranked by many naturalists as so many new species, more especially if found in different geological sub-stages, let their differences be ever so slight. Numerous existing doubtful forms could be named which are probably varieties; but who will pretend that in future ages so many fossil links will be discovered, that naturalists will be able to decide whether or not these doubtful forms ought to be called varieties? Only a small portion of the world has been geologically explored. ”

“ According to Nägeli, the stages of phylogeny are based upon true qualitative differences in the idioplasm: the germ-plasm of a worm is qualitatively different from that of Amphioxus, a frog, or a mammal. But if such phyletic stages occur crowded together in the ontogeny of a single species, they are said to be based upon different ‘conditions of tension and movement’ of one and the same idioplasm! ”

“ A detailed examination of the facts would not be intelligible to anybody who is not a practical biologist; but I am fully warranted in asserting that every organism in the course of its life-history (technically called ontogeny) is a recapitulation of the history of the race—technically known as phylogeny. ”