The evolution of genetic architecture. I. Diversification of genetic backgrounds by genetic drift

The genetic architecture of a phenotype plays a critical role in determining phenotypic evolution through its effects on patterns of genetic variation. Genetic architecture is often considered to be constant in evolutionary quantitative genetic models. However, genetic architecture may be variable and itself evolve when there are dominance and epistatic interactions among alleles at the same and different loci, respectively. The evolution of genetic architecture by genetic drift is examined here by testing the breeding value of four standard inbred mouse strains mated across a set of 26 related recombinant quasi-inbred (RqI) lines generated from the intercross of the Large (LG/J) and Small (SM/J) inbred mouse strains. Phenotypes of interest include age-specific body weights, growth, and adult body composition. If the genetic architecture of these traits has differentiated by genetic drift during the production of the RqI strains, we should observe interactions between tester strain and RqI strain. The breeding values of the tester strains will change relative to one another depending on which RqI strain they are crossed to. The study included an average of 15.1 offspring per cross, over a total of 100 different crosses. Multivariate and univariate analyses of variance indicate that there is strongly significant interaction for all traits. Interaction is more pronounced in males than in females and accounted for an average of about 40% of the explained variation in males and 30% in females. These results indicate that the genetic architecture of these traits has differentiated by genetic drift in the RqI strains since their isolation from a common founder population. Further analysis indicates that this differentiation results in changes in the order of tester strain effects so that common patterns of selection in these differentiated populations could result in the fixation of different alleles.     

Population-based genetic screening.

A preventive genetic programme aimed to control beta-thalassemia in the Sardinian population is based on a combination of increased awareness of the population, carrier screening, genetic counselling and prenatal diagnosis. As a result, the registry of thalassemia major demonstrated a profound decline in the incidence of this disease from 1 per 250 to 1 per 1200 live births, with 90% of cases effectively prevented.     

The load of genetic and partially genetic diseases in man. III. Mental retardation

This paper summarizes estimates of detriment associated with different etiologic categories of mental retardation (MR) in Hungary. The basic data derive from an earlier study carried out in Budapest on 1276 school-age mentally retarded children (with some etiologic reclassification based on recent studies). Detriment associated with these different categories of MR is expressed in terms of years of lost and impaired life. About 30 per 10(3) school-age children in Hungary are mentally retarded (mild + severe MR), one-tenth of whom have severe MR (IQ less than or equal to 50); 50% of the latter are institutionalized. The breakdown on the basis of etiology is as follows: gene mutations and chromosomal abnormalities, about 4 per 10(3); 'familial' (multifactorial) causes, 12 per 10(3); adverse pre-, peri- and post-natal causes, 11 per 10(3); and 'causes as yet unknown', the remainder. The estimates of mean number of years of lost life range from 42 to 68 (depending on the etiologic category), with an overall mean of 58. The total number of years of lost life is about 36,000 per 10(4) live births of which over 70% is due to pre-, peri- and post-natal causes, 18% due to 'familial' causes and the remainder due to Mendelian and chromosomal diseases. The total number of years of impaired life is about 7300 per 10(4) livebirths, 50% of which is due to 'familial' causes. While admittedly approximate, these estimates suggest that detriment associated with MR-related causes is not inconsiderable. Additionally, they provide some indication of causes of MR which are minimizable.     

Reconstructing pathways in large genetic networks from genetic perturbations.

I present an algorithm that determines the longest path between every gene pair in an arbitrarily large genetic network from large scale gene perturbation data. The algorithm's computational complexity is O(nk(2)), where n is the number of genes in the network and k is the average number of genes affected by a genetic perturbation. The algorithm is able to distinguish a large fraction of direct regulatory interactions from indirect interactions, even if the accuracy of its input data is substantially compromised.     

The genetic structure of finland.

The Finnish gene pool derives primarily from a relatively homogeneous Finno-Ugric population established during the Iron Age (100 B.C.-800 A.D.) in the southwest and southeast of Finland. Gene flow from Sweden to the southwest coastal areas, dating from prehistoric times, as well as the patterns of settlement and migration throughout Finland during the past 1000 years, appear to have been the major biosocial factors underlying the genetic structure of the contemporary population. Analysis of genetic variation and covariation at nine polymorphic loci in a large random sample of rural Finns, partitioned into either 8 countries or 27 geographic districts, showed that all of the essential features of the genetic structure suggested by the archaeological and historical data could be distinguished. Procedures for obtaining inference on the genetic structure of such a population are reviewed, including coefficients of similarity and (genetic) distance among subpopulations, the relation between linear or planar geographic structure and genetic covariation, and the methods for describing allelic differentiation. Bias resulting from the inappropriate assumption of a simple phylogenetic model can be substantial, expecially for the analysis of isolation by distance; procedures for avoiding misleading inference on the genetic structure are demonstrated.     

Evolution of the genetic code.

Comparative path lengths in amino acid biosynthesis and other molecular indicators of the timing of codon assignment were examined to reconstruct the main stages of code evolution. The codon tree obtained was rooted in the 4 N-fixing amino acids (Asp, Glu, Asn, Gln) and 16 triplets of the NAN set. This small, locally phased (commaless) code evidently arose from ambiguous translation on a poly(A) collector strand, in a surface reaction network. Copolymerisation of these amino acids yields polyanionic peptide chains, which could anchor uncharged amide residues to a positively charged mineral surface. From RNA virus structure and replication in vitro, the first genes seemed to be RNA segments spliced into tRNA. Expansion of the code reduced the risk of mutation to an unreadable codon. This step was conditional on initiation at the 5'-codon of a translated sequence. Incorporation of increasingly hydrophobic amino acids accompanied expansion. As codons of the NUN set were assigned most slowly, they received the most nonpolar amino acids. The origin of ferredoxin and Gln synthetase was traced to mid-expansion phase. Surface metabolism ceased by the end of code expansion, as cells bounded by a proteo-phospholipid membrane, with a protoATPase, had emerged. Incorporation of positively charged and aromatic amino acids followed. They entered the post-expansion code by codon capture. Synthesis of efficient enzymes with acid-base catalysis was then possible. Both types of aminoacyl-tRNA synthetases were attributed to this stage. tRNA sequence diversity and error rates in RNA replication indicate the code evolved within 20 million yr in the preIsuan era. These findings on the genetic code provide empirical evidence, from a contemporaneous source, that a surface reaction network, centred on C-fixing autocatalytic cycles, rapidly led to cellular life on Earth.     

Ethical aspects of genetic testing.

No research study or significant medical treatment can be done involving patients without their informed consent. In workplaces and environmental settings, individuals are often exposed to mutagenic or carcinogenic substances, usually without their knowledge, and not with their informed consent. Such exposures can lead to evermore easily documentable genetic changes. As genetic testing becomes more widespread, there are significant ethical implications regarding employment, insurance coverage, and confidentiality regarding medical information. With an increased ability to detect genetic changes, or 'unfavorable' genetic polymorphisms, this information should not be used to deny employment or increase insurance rates. Rather, such information should be used to increasingly provide appropriately safe workplaces, and place workers in less hazardous settings.     

Prospective study of genetic counselling.

A prospective study was carried out on 200 consecutive subjects seen for counselling (consultands) for serious genetic disorders. Educational and social background of consultands and their knowledge and understanding of their particular problem were assessed before counselling, and their response was determined immediately afterwards and three months and two years later by an independent observer not concerned in the genetic counselling. The husband''s educational background was particularly important in influencing a couple''s comprehension of counselling. X-linked recessive and chromosomal disorders presented the most difficulties in comprehension. The counsellors'' assessment of comprehension was a good guide to the consultands'' comprehension as assessed at subsequent follow-up. The proportion deterred from having children increased with time and over a third had been sterilised within two years of counselling. It is suggested that follow-up after counselling should be routine, especially when the counsellor suspects that comprehension has not been good, in X-linked recessive and chromosomal disorders, and when the risks of having an affected child are considered to be high.     

The evolution of genetic diversity.

The existence within natural populations of large amounts of genetic variation in molecules and morphology presents an evolutionary problem. The 'neutralist' solution to this problem, that the variation is usually unimportant to the organism displaying it, has now lost much of its strength. Interpretations that assume widespread heterozygous advantage also face serious difficulties. A resolution is possible in terms of frequency-dependent selection by predators, parasites and competitors. The evidence for pervasive frequency-dependent selection is now very strong. It appears to follow naturally from the behaviour of predators, from the evolutionary lability of parasites, from the ecology of competition and, at the molecular level, from the phenomena of enzyme kinetics. Such selection can explain the maintenance not only of conventional polymorphism but also of continuous variation in both molecular and morphological characters. It can account for the occurrence of diversity within groups of haploid and self-fertilizing organisms, and for the evolution of differences between individuals in their systems of genetic control.