Phylogenetics

“ 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. ”

“ 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) ”

“ The moment of high type that passes ontogenetically the stages of phylogenetic evolution does it in a general, and, so to say, sketchy form, each stage of ontogenesis in reality fundamentally differing from that of the parallel stage in phylogenesis. Just as the human embryo in the course of its growth and passing the stages that reflect phylogenesis is not necessarily once a worm, then a fish, then a bird, but only approaches these types in a most general form, so also is it in the case of the moment in the different stages of its growth ”

“ 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. ”

“ If we take a genus having a score of species, recent and extinct, and destroy four-fifths of them, no one doubts that the remainder will stand much more distinct from each other. If the extreme forms in the genus happen to have been thus destroyed, the genus itself will stand more distinct from other allied genera. What geological research has not revealed, is the former existence of infinitely numerous gradations, as fine as existing varieties, connecting together nearly all existing and extinct species. ”

“ 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. ”

“ 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. ”

“ 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. ”

“ By the theory of natural selection all living species have been connected with the parent-species of each genus, by differences not greater than we see between the varieties of the same species at the present day; and these parent-species, now generally extinct, have in their turn been similarly connected with more ancient species; and so on backwards, always converging to the common ancestor of each great class. So that the number of intermediate and transitional links, between all living and extinct species, must have been inconceivably great. ”

“ 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] ”

“ We must act in this way in constructing the phylogeny of man. We must try to piece together a fairly complete picture of the series of our ancestors from the various phylogenetic fragments that we find in the different groups of the animal kingdom. We shall see that we are really in a position to form an approximate picture of the evolution of man and the mammals by a proper comparison of the embryology of very different animals—a picture that we could never have framed from the ontogeny of the mammals alone. ”

“ 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. ”

“ Finally, then, we see that all the leading facts in the affinities and classification of organic beings can be explained on the theory of the natural system being simply a genealogical one. The similarity of the principles in classifying domestic varieties and true species, both those living and extinct, is at once {213} explained; the rules followed and difficulties met with being the same. The existence of genera, families, orders, &c., and their mutual relations, naturally ensues from extinction going on at all periods amongst the diverging descendants of a common stock. ”

“ 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. ”

“ 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? ”

“ 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." ”

“ It must not be forgotten that, on our theory, all the species of the same genus are the descendants of some one species; so that, if six genera, each having eight species, be found in one geological formation, and in a succeeding formation there be six other allied or representative genera, each with the same number of species, then we may conclude that generally only one species of each of the older genera has left modified descendants, which constitute the new genera containing the several species ”

“ 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. ”

“ 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. ”

“ These causes, taken conjointly, will to a large extent explain why — though we do find many links — we do not find interminable varieties, connecting together all extinct and existing forms by the finest graduated steps. It should also be constantly borne in mind that any linking variety between two forms, which might be found, would be ranked, unless the whole chain could be perfectly restored, as a new and distinct species; for it is not pretended that we have any sure criterion by which species and varieties can be discriminated. ”

“ Hence modifications of structure, viewed by systematists as of high value, may be wholly due to the laws of variation and correlation, without being, as far as we can judge, of the slightest service to the species.
We may often falsely attribute to correlated variation structures which are common to whole groups of species, and which in truth are simply due to inheritance; for an ancient progenitor may have acquired through natural selection some one modification in structure, and, after thousands of generations, some other and independent modification ”

“ From the foregoing considerations it cannot be doubted that the geological record, viewed as a whole, is extremely imperfect; but if we confine our attention to any one formation, it becomes more difficult to understand, why we do not therein find closely graduated varieties between the allied species which lived at its commencement and at its close. Some cases are on record of the same species presenting distinct varieties in the upper and lower parts of the same formation, but, as they are rare, they may be here passed over. ”

“ 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 ”

“ But I do think that a very serious difficulty is raised when to this fact we add another—namely, that on every biological region we encounter species related to other species in genera, and usually also genera related to other genera in families. For if each of all the constituent species of a genus, and even of a family, were separately created, we must hence conclude that in depositing them there was an unaccountable design manifested to make areas of distribution correspond to the natural affinities of their inhabitants. ”

“ Some writers have objected to any extinct species, or group of species, being considered as intermediate between any two living species, or groups of species. If by this term it is meant that an extinct form is directly intermediate in all its characters between two living forms or groups, the objection is probably valid. But in a natural classification many fossil species certainly stand between living species, and some extinct genera between living genera, even between genera belonging to distinct families. ”

“ Ontogenetic development is lost sight of in the march of phylogenetic development. The individual is merged in the species, the species in the genus, the order, the class, and all are finally swallowed up in the tout ensemble of organized existence. ”

“ The system of binomial nomenclature has led to the development of the science of taxonomy, the systematic classification and naming of plants and animals according to their relationships.
THE UNITS OF CLASSIFICATION
The world of organic life has been divided into the plant and animal kingdoms. These kingdoms have been further divided into larger divisions called phyla (from the Greek word phylon, a race) . Each phylum is composed of organisms with certain characteristics in common. For example, all animals with a spinal cord (or notochord) are assigned to the phylum Chordata. ”