Portugaliae Acta Biologica - 1949
A Cytophysiological Theory of the Gene, Gene Mutation
and Position Effect

J. A. Serra

Secção de Zoologia-Anthropologia, Faculdade de Ciências. Universidade, Coimbra

6. GENE AND CHROMONEMA EVOLUTION

Many questions on gene nature and gene physiology are not fully comprehensible without some points on gene evolution being also discussed, if only very briefly. Unhappily there are few facts on this subject and the matter is rather speculative; obviously, this state of affairs cannot be easily remedied in view of the difficulties involved. Therefore, it is to be expected that in the present chapter the balance between thoughts and facts is rather dislocated in favour of the former.

INTRA- AND INTER-GROUP GENETIC DIFFERENCES

*No responsibility as to the nature of these mutations is taken here; the designation refers only to the amplitude of the phenotypic effect produced by the mutation.
By their very nature, the methods of Genetics, of crossing and analysing the separation of characters in the offspring, are not proper for a comparison of gene differences between a reptile and a bird, or between a moss and an alga. The genetic differences between widely separated groups may only be presumed as an extrapolation from what is known of the differences between groups more akin and from a consideration of the similarities and diversities of the phenotypes. A further hint on this question is given by the existence of two interesting classes of mutations which contrast with one another: the so called systemic mutations*, and the parallel series of mutations.

Systemic mutations, which produce characters corresponding to a difference of at least supra-specific level, are known in the better studied species. For instance, homoeotic mutations converting legs into wings or vice-versa and the total disappearance of wings in Insects, chalicanthemia and complete tepal loss in Phanerogams and in general rudimentation and substitution cases, are of this class. A striking case is that of the mutation which in mosses causes that the plant is not able to pass from the protonema stage and therefore brings a Bryophita to a stage found in algae. However, these mutations do not produce by themselves the passage from a group to another, as the groups differ not in one but in a lot of characters which must work harmoniously in order that the new form might be able to fill in a vacant ecological niche. It is possible that in certain cases "hopeful monsters" (as said by Goldschmidt 1938, 1940) with possibilities of evolution, giving birth to a new order, or class, etc., may appear, but such extreme orms will have a reasonable chance of surviving only if the ambient is rapidly changing. This may have been the case in other geological eras but seems not to hold true in our relatively quiet contemporary interglaciary time. In the actually prevalent conditions only gradual changes seem to be capable of furnishing the material of further evolution. The systemic mutations usually produce inviable or poorly viable abnormalities, while evolution requires an integratd whole being, with adaptational characters able to fit in an ecological niche.

The case of the parallel series of mutations is more easily analysable. It has been found that similar mutations may appear in a whole group, of order or even class rank; for instance, pigmentation mutations in Rodents are almost identical in the whole order and strikingly similar phenotypes are met with in Carnivora, Ruminants and even in Man. Other examples of parallel mutation series are exposed in Haldane (1927) and Green (1938). Only in suitable cases, when crossing is yet possible, may an homology in the genes which bring about similar phenotypes be practically demonstrated, and this rarely is possible. However, it seems a sound inference to admit that in general a similarity in mutation phenotype corresponds to an homology in the nature of the genes involved. According to this interpretation, the genes which belong to parallel series have resisted evolution, passing from a species to another and continue to exist in a whole group.

Another class of genes passing almost inaltered from a species to another during evolution is that which controls basic properties of a whole group, particularly characters which define the group, for instance the existence of milk glands and hairs in Mammals, of feathers and wings in Birds, of a sporogenous capsule in Briophytae, etc. These basic properties must be controled by a complex system of genes working together in integrated phenogenetic chains. A rupture in these chains may be brought about by a mutation in a gene of the complex and then an inviable form or sometimes perhaps a "hopeful monster" may appear, but more generally mutation in the genes of the system is of a quantitative gradual order which modifies, but does not suppress, the basic properties.

Therefore, the two kinds of genetic characters which resist evolution from species to species concern either basic properties common to a whole group, which can not be dispensed of without a lethal effect; or the other extreme, properties such as pigmentation, markings and other peculiarities of an accessory nature, which constitute a common source of intraspecific variation. The majority of the interspecific differences concern properties of a marked quantitative or metrical nature, especially differences of size in certain parts in relation to others, or pattern differences. Size differences come into effect by changes either in absolute or relative growth or both, and as a rule depend upon the work of polymerous factors scattered over numerous loci of the chromosomes. Differences in pattern are generally also polygenic and brought about by changes in several staps of one or more morphogenetic reaction chains. That is, the majority of the differences between species are of a polygenic quantitative nature.

On the other hand, many differences which within a species distinguish the varieties are also of a quantitative character, with a polygenic basis. According to the neodarwinian point of view, interspecific differences are of the same kind but at an higher level than intraspecific ones and the common observation of systematists, field ecologists and palaeontologists gives support to such an assumption. Only the passage from a group to another, for instance from Reptiles to Birds or Mammals, or the appearance of the roots of a whole group such as the Chordates or the Arthropoda seem to have necessitated of another process of rapid evolution, or of the same kind of process working at a very much higher rate (saltations). Although recognising the importance of a possible macroevolution type of changes, as these are unanalysable by the existing genetic means, we will not consider further this problem here and will concentrate upon a discussion of the differences found at a specific and infraspecific level.

GENETIC CONTROL OF MUTATION RATE AND AMPLITUDE

Leaving aside the possible saltations which give birth to new types of class or higher rank, the chief genetic changes, both for intraspecific variation and interspecific evolution, concern chiefly the quantitative and viability alterations, these latter resulting from changes in physiological functions. Size and growth, as well as physiological functions, are as a rule governed by a series of polymeric factors, according to a safety principle which ordinarly preserves the most vital functions and characters from being strongly altered in one step. Generally, mutations affecting the factors of polygenic characters cause effects of a small amplitude, because the rest of the factors form a kind of "buffer" which slows down any change.

It is perfectly comprehensible that the chief properties of the organisms, strongly subject to natural selection, will work according to this safety principle of a buffering effect with many alternatives. In a stabilized genotype of a species well adapted to a relatively stable ambient it would be expected that mutations with a strong effect upon important characters should be extremely rare. Such a species would have reached a good adaptability at the cost of a lowering of its possibilities of further evolution. Generally, in our interglaciary, quaternary, time a kind of compromise between a state of fixity and adaptation on one side, and evolutive possibilities on the other, is characteristic of many species, with the balance rather towards the adaptability. The most stable species must have acquired a certain control, not only of the number, as also of the amplitude of effects of mutations, while the species in full evolution would show an inverse picture—a greater rate of mutation and a relatively loose control of the amplitude of mutation effects.

The control of mutation thus has a twofold aspect, quantitative and qualitative. While a qualitative control clearly is attained chiefly by the establishment of a buffer system of polygenic factors, the quantitative control seems at first sight to have other basis but in the end it turns out to be of the same kind. This subject of the quantitative control of mutations will be discussed again in chapters 7 and 8; here we refer only to the chief facts on it. The most important conclusion about the causes which affect the mutation rate is that the chief factor concerned is the breakage of the chromonemata; all causes which increase breakage frequency also increase mutation rate and there is reason to admit that the reverse is also true, a decrease in the breakability of the chromosomes being accompanied by a lower mutation rate. The chief factors controlling mutation rate very probably are those which influence the breakability of the chromonemata through modifications both in breakage and in reunion frequency, the latter being perhaps more easily changed than the former. In the last analysis, those agents influencing breakage and reunion act at the cell physiological level and therefore fall into the category of polygenic charcters, controlled by polymeric factors.

Of course, the conclusion that both the quantitative and qualitative aspects of mutation are generally controlled by polygenic systems of factors of the buffer type does not exclude that in some cases, even in the genetically stabilized species, some mutations of an extraordinary amplitude are capable of upsetting the balance, so as to result a strongly modified phenotype. Examples of these mutations with great amplitude are the morphogenetic factors with outstanding effects and many of those which act in the early part of ontogeny. A case of a factor with a marked action on the quantitative aspect of mutation is the stickiness gene in maize (Beadle 1932). Such mutations which in a jump upset the mutation process do exist, but the respective genes or chromonema structures will tend to be eliminated by natural selection if the mutations affect essential processes. The end result is that in most vital processes and characters the great majority of mutations will be of the small amplitude type or "minute mutants", which furnish the essential materials for ordinary intra-genus or even intra-order or -class evolution, while in the details of pattern and in morphological and biochemical characters, such as markings and pigmentation, mutation of the great amplitude type or "ordinary mutations" will also be tolerated.

GENETIC NATURE OF SMALL AMPLITUDE MUTATIONS

These conclusions on the role of small amplitude mutations are important for an understanding of the nature of the usual changes in the genetic make-up of the organisms. The evidence on this point is rather indirect, obtained from a study of chromosome numeric and structural changes and from the pheonmenon of hybrid vigour. Numerical changes of the chromosomes, of the polyploid and heteroploid types, generally bring about viability differences and phenotypic changes of a quantitative order and will be dealt with below. Chromosome structural changes not visibly associated with position effects may have an effect on the viability, as is demonstrated by selection studies of the distribution of chromosomic types under different ambiental conditions. Inversions are common in natural populations of Drosophila species, "an almost bewilering amount of variation in the gene arrangement" (Dobzhansky, 1941, p. 120) being encountered in D. pseudoobscura of different geographic origins. These inversions could be brought about by chance variations, or be adaptative. Newer observations of Dobzhansky, Wright, and Dubinin and Tiniakov (1943-1948) have demonstrated that different inversions have a selective value; for instance in D. pseudoobscura two inversions responded to selection in population cages (Dobzhansky 1948) and in D. funebris it was shown that hybernation, city or country environments and other selective conditions cause different frequencies of inversions (Dubinin and Tiniakov 1947). These observations leave no doubt that inversions have in themselves a selective value, which in the case of Drosophila manifests already in the larva.

The phenomenon of hybrid vigour points out to the same conclusion, that many viability and vigour differences are connected with chromosome rearrangements. In effect, it is known that hybrid vigor in maize may be obtained by crossing two "degenerate" individuals which were separated from a common source only a few generations ago (Jones 1945) and similar results were observed in barley (Müntzing 1945, Gustafsson 1946). An explanation of these cases by an accumulation of deleterious recessive mutations is highly improbable or simply impossible, and the only valid interpretation is that several chromosome rearrangements with a lower viability in the homozygote at once mutually cover one anothers and produce an heterozygote of higher vigour. In concordance with this interpretation, Dobzhansky (1947) found in Dros. pseudoobscura that inversion heterozygotes had a slightly increased frequency in population cages. Though exceptionally the inverse result may also be obtained (Dubinin and Tiniakov 1947), generally it is the heterozygote condition that presents a greater selective value. Cases in which the homozygote has a greater selective value may perhaps be explained by gene mutations with an higher selective value than the inversion.

It must be taken as a sound generalization that—at least potentially, for certain ambiental conditions—chromosome rearrangements have a differential viability value, that is can influence physiological and metrical properties of the organism. A part of thie small amplitude mutations is constituted, therefore, by position effects with a modifyer action and probably in part belonging to the pure type.

Other small amplitude mutations must correspond to intragenic changes, that is to gene mutations. In effect, according to the known data several "isoalleles" with quanta above D, which in heterozygous condition produce the maximum phenotype, show unchanged salivary chromosomes. It is not possible as yet to evaluate the part of the minute mutants which is constituted by gene mutations in comparison with that corresponding to rearrangements, but in view of the frequency of inversions in natural populations of Drosophila and the many cases of multiple alleles also due to rearrangement effects, it must be presumed that the two causes may perhaps give an almost equivalent amount of mutations. These are themes for further research on the composition of population karyotypes.

THE ORIGIN OF NEW GENIC MATERIALS

From what has been said above it follows that a part, perhaps about one half, of the minute mutations are rearrangement effects. The class of ordinary mutations includes also a considerable proportion, though probably much less, of rearrangement effects. Rearrangement effects alone make perhaps one third of all intraspecific variation and furnish an indispensible condition for interspecific evolution must yet be more important. In effect, during progressive evolution, that is evolution towards increased organization or complexity, new systems of genes must come into action and if the principle of unitary genic action is to be maintained, new genes must be created for the new functions. That is, the quantity of hereditary units must be increased at the measure that species evolutionate to higher organisation levels. This is valid both for intra-group and inter-group evolution.

Considering, for the sake of simplicity, only the evolution within a certain chass, or order, or even family, as a rule an increase in the quantity of genes from the primitive to the more complex species must have taken place. Two exceptions, however, are possible to this rule: specialization and parasitism, which have played a great role in evolution, and especially the first. Specialization may signify a genetic simplification by the disappearance of several functions not necessary for adaptation to a certain niche. Straight specialization is an evolutive dead alley, very similar to that of parasitism; the extreme of adaptation and the loss of genetic variation concur to hindering the evolution of strongly specialized forms.

Parasitism is a kind of specialization in which the vital functions are reduced chiefly to the digestive and reproductive systems. Genetic regression may reach an extraordinary level of simplification, especially in the case of endoparasites of small size. Several virus, if not all, must have been derived by simplification from more highly organized parasites. In view of the importance usually attributed to the viruses in discussions on the nature of the gene, this point would merit of being discussed more lengthy but, for considerations of space, this is not possible here.

Excepting parasitism and specialiation, evolution must have depended upon an increase in the number of genes, followed by a diversification of them in new phenogenic functions. An increase in the number of genes may take place only either by subdivision of the preexisting genes or by increasing the length of the chromonemata. The first way has a limit, since in general a subdivision of the gene results in mimic position effect, usually of the inactivation type. It is chiefly through the second process, increase of chromonema length, and therefore of the number of genes, that genetic complexity must realize.

An increase in chromonema length may be brought about by increasing the number of chromosomes and by duplications within the chromosomes. Both processes actually have taken place in species evolution, the first being encountered chiefly in plants, the second in animals. Probably the difference between animals and plants in this respect derives from the animals possessing an higher degree of integration in their organization, as is demonstrated by their possessing a nervous system and several peculiar chemical coordinators or endocrines; the genetic changes must in them be more gradual, while in plants a sudden great quantitative change may be more easily tolerated. A simple increase in chromosome number, especially if of the euploid type, ordinarily brings about a change to a greater cell size, though this is not always the case and may be regulated again by a decreasing in the rate of mitoses, especially in animals (for instance in the case of Amphibians). For evolution, chromosome numeric changes are important especially because they make possible a further diversification of the genes by mutation and position effects. We are of the opinion that this is the chief role of polyploidy in evolution and not the mere increase in cell size which, as time goes on, tends again to be brought down to an equilibrium value, characteristic of the species. Of course, the great role of allopolyploidy in the appearance of new species, especially in plants, can not be denied, but for our main theme this is of a small relevance because allopolyploidy and hibridization in themselves are merely a way to new gene combinations and at most only allow that new position effects appear by translocation between chromosomes of the two species.

In animals it seems that, at least in intra-genus evolution, a great role is played by small duplications, of the relocation and repeat types, especially of this latter, which may appear by unequal crossing-over. To judge from the aspect of the salivary chromosomes, in Drosophila melanogaster repeats very frequent (Bridges 1935, 1936, 1938) and the published salivary maps of other species, though not so detailed, suffice to show a chromosome structure where the repeats seem so frequent as in D. melanogaster. After Bridges, several workers have referred also to the importance of repeats in the structure of the chromosomes, especially Metz (1937) and Lewis (1946). It seems that we may safely assume that small repeats, by the relatively mild unbalance they produce, are one of the chief factors in chromosome evolution, especially in animals. Following the establishment of a duplication, two processes come into action: appearance of position effects of the mimic and pure types, and diversification by gene mutation. A pure position effect is especially important in progressive evolution if the gene was not yet "saturated", that is if the quantum number D was not yet previously obtained by the work of the structures forming a unit. Then a more efficient gene results and a kind of orthogenesis, if the process is repeated, may be the important phenotypic result. After passing an optimum, the reverse may happen and a regressive change, with lowering of the viability, may result. Such a case is probably that of Bar, which seems to be a repeat over a repeat already present in the 16A section of the +X chromosome; it seems that in this case the optimum has already been passed and the quantum being over Q a decrease in viability was brought about. If, however, a mutation or a small chromosome change causes reversion to full viability and normal phenotype, the duplication may become established and a diversification of the new piece by gene mutation or any position effect brings about new possibilities of evolution.

If this theory is admitted, if follows that, at least in animals, usually in the process of gene increase and diversification gradual changes are the rule, a conclusion which accords well with the palaentological data and the findings of experimental neodarwinism. Another important corollary of the theory is that in many instances it will be possible to find relatively extense pieces of the chromonema having similar functions, that is having similar genes; or put in another manner, the genes in certain pieces of the chromonema must show imprecise limits, due to the fact that several genes may act similarly, their action being not markedly diversified. It is to be expected that this similarity of action in relatively long chromosome pieces will have a limit, which is reached when a further duplication brings about a pure position effect of the Bar type, with a lowering of the viability. In practice, it has been found difficult to trace the limits of certain genes.

Another interesting corollary of the hypothesis is that the genes are not widely different in the whole genotype. Though controlling many different processes, they maintain essentially the same composition throughout, only the details of the produced haptogenes vary. It follows that, scattered throughout the genotype, many genes will do about the same functions, according to a safety mechanism which works when a mutation or a rearrangement bring about inactivation of an important gene. The loci of important genes of the lethal type must be found scattered all over the chromosomic set, and this is what actually happens. The loci of visible mutations of the "ordinary type", not so important for basic life processes, may be more restrict and less frequent.

GENE INACTIVATION: ORIGIN OF HETEROCHROMATIN

It would be advantageous for a stabilized species if a sudden great increase in gene number could be counteracted by a total or almost total inactivation of the genes concerned. This inactivation in mass, which is different from the gradual inactivation by mutation and mimic position effect, is effected through heterochromatization of the unbalanced segment or the chromosome. The property of carrying on this mass inactivation must be controlled by genes present either in the chromosome, or the piece in question, or more probably elsewhere in the genotype. Species possessing these genes of heterochromatization have an advantage over those deprived of them in what concerns stabilisation, and perhaps a small disadvantage in what respects evolutionary possibilities; therefore, heterochromatization genes must be selected in stabilized species where chromosome numerical changes, especially of the aneuploid type, are frequent, that is chiefly in plants. Heterochromatic supranumerary chromosomes have been discovered in several plant species, for instance maize, rye, Narcissus, Sorghum, etc. (Darlington, Thomas, Fernandes, Östergren and others, refs, Serra, 1949). The genetic nature of the control of heterochromatization in Narcissus seems to be simple, due to one or only a few genes (Fernandes 1943 and unpublished). In species where heterochromatic supranumerary chromosomes are frequent it seems more probable that the genetic control of heterochromatization is polygenic, according to the safety principle.

In animals there are also examples of supranumerary heterochromatic chromosomes (refs. White 1945); a more important role, however, is played by heterochromatization in the determination of sex. All transitions are found, from a pair of similarly looking and completely homologous chromosomes only different in one or a few sex genes, to the condition found in Drosophila, of a XY pair in which the homology is reduced to a minimum, or the more extreme case of certain Orthoptera, in which the Y has altogether disappeared as an independent chromosome. Heterochromatization appears as a mechanism by which a group of factors, among which are those concerned with sex determination, contained in the X or the Y, or both, remain without alleles in the other member of the pair. In this manner a stable sex determination mechanism is assured, not so easily liable to sex reversal by crossing-over and gene mutation.

The maintenance of an Y chromosome, though almost completely heterochromatic, may be advantageous in allowing a better distribution of the X in meiosis and because the Y may carry genes important for fertility. It is very interesting that in the case of a XO determination mechanism (and perhaps in some cases of XY differentiation in haplonts) the X may itself become heterochromatic when not paired, while the same chromosome in paired condition is euchromatic. This condition is found in Orthoptera with XO males, where the X is heterochromatic in the male and the pair XX is euchromatic in the female. As the X is handed down from the father to his daughters, it follows that generation after generation a same X (barring the cross-over, of course) is alternatively heterochromatic and euchromatic. This is a typical case of conditioned heterochromatization which must be controlled by the sex genes, probably realized through the balance heterochromosomes/autosomes, the female ones in the X, and the heterochromatization of the sole X of the male should improve the mechanism of sex determination if the female-determining genes of the X were so strong that even in one dose the balance in the male was not much towards maleness. Heterochromatization would in such a case improve the sex determination mechanism.

These are cases of heterochromatiation controlled by genes but which concern relatively great extensions of, or even a whole, chromosome. There are also other cases in which the heterochromatization is limited to a small region, for instance to the extremes of the chromosomes, or adjoining the centromere, or in connection with the nucleolar zone. The reason for these preferential localizations is to be sought for in the advantages they confer either to the variability or to the stability of the genetic constitution of the species. Since heterochromatin is devoid of, or poor in, genes of the oligogenic or "ordinary mendelian" type, mutation in its genes does not bring a perceptible genetic alteration, that is, within heterochromatic segments any losses or gains, deletions or duplications, as well as other rearrangements, are of no appreciable effect. At most, the genes of small effect, of the polygenic type, which may yet be able to work under heterochromatized conditions, may become more or less altered, but owing to the buffering exerted by other genes the only result is the modification of the general background of some physiological functions, one of which probably is the synthesis of nucleoproteins. The presence of heterochromatin in the so called telomeres of the chromosomes, as also adjoining primary constrictions and nucleolar zones (constituting in these latter the improperly called "nucleolar organizer") may bring about stabilization of these important chromosome "organites".

On the other hand, once established in an evolutive group a preferential location of heterochromatin, it is to be expected that the amount of heterochromatin will tend to increase by position effect, until an optimum is reached which depends upon the chromosome length relative to the length of the heterochromatic segments: a greater length of these latter would be deleterious as an overcharge of chromonema only capable of a residual genetic action. The presence and the amount of heterochromatin is, therefore, controlled by the balance of the genotype, a mean charge being as a rule an index of stabilization, while an excessive charge is a sure sign of recent changes in the amount of genetic material, which probably was increased too much for the species. The reverse, absence or almost absence of heterochromatin, is to be found in less stabilized genotypes or in cases where extensive chromonema changes, for instance polyploidy and heteroploidy, are well tolerated without great phenotype alterations; this is to be expected particularly in hermaphrodites with a long evolutionary history of polyploidy, especially in hermaphrodite polyploid plant species derived from other polyploid species. Little heterochromatin must be found, therefore, in two cases without sex separation: forms with a recent evolution, and species with an ancient evolutionary history derived from polyploid sources. The extent and localization of heterochromatin must be causally related with the evolutionary history of the species or form, and is an interesting property from which certain deductions may be drawn.

Besides this origin of heterochromatin by a genetic control upon a sudden increase of the chromonema length, a gradual appearance of a heterochromatic region by repeated mutation or repeated position effect followed of heterochromatization is also possible, and we have referred to it above (chapter 5). It must be expected, however, that this mode of origin will give only small intercalary pieces of heterochromatin. The localization of greater heterochromatic pieces is preferentially in differential chromosome sections. A formal distinction between primary and secondary heterochromatization may be established, the former being due to genic control, the second to position effect. Secondary heterochromatin is found adjoining the centromere, at the nucleolar zones, the telomeres and in loci of position effect. In many cases, however, the distinction between primary and secondary heterochromatization is difficult.

After it has been established in a chromosome, heterochromatin engenders a different "ambient", in the first place for the neighboring loci and in the second for the whole chromosomic set. We have already referred (see chapter 4.) to the effects of the euchromatin-heterochromatin balance and to heterochromatin position effects, so that it is not necessary to deal again with this topic here. Heterochromatin is one of the means by which an integration of the whole genotype is obtained, and by its intermediary, ambient actions may perhaps reflect in subsequent generations. This is an interesting field to explore. A certain, not too excessive, possibility of heterochromatization confers a greater plasticity to the changes in the genotype of the species by furnishing a mechanism of mass and individual inactivation of sudden gene increases, and by conferring a greater stability to chromosome organization.