Biomedical subjects

Louise J Johnson

Publications and source records attributed to Louise J Johnson.

5 recordsLinked to original sources

PubMed2006

The evolution of mobile DNAs: when will transposons create phylogenies that look as if there is a master gene?

Some families of mammalian interspersed repetitive DNA, such as the Alu SINE sequence, appear to have evolved by the serial replacement of one active sequence with another, consistent with there being a single source of transposition: the "master gene." Alternative models, in which multiple source sequences are simultaneously active, have been called "transposon models." Transposon models differ in the proportion of elements that are active and in whether inactivation occurs at the moment of transposition or later. Here we examine the predictions of various types of transposon model regarding the patterns of sequence variation expected at an equilibrium between transposition, inactivation, and deletion. Under the master gene model, all bifurcations in the true tree of elements occur in a single lineage. We show that this property will also hold approximately for transposon models in which most elements are inactive and where at least some of the inactivation events occur after transposition. Such tree shapes are therefore not conclusive evidence for a single source of transposition.

Alu Elements↗

PubMed2005

A test of the master gene hypothesis for interspersed repetitive DNA sequences.

Many families of interspersed repetitive DNA elements, including human Alu and LINE (Long Interspersed Element) elements, have been proposed to have accumulated through repeated copying from a single source locus: the "master gene." The extent to which a master gene model is applicable has implications for the origin, evolution, and function of such sequences. One repetitive element family for which a convincing case for a master gene has been made is the rodent ID (identifier) elements. Here we devise a new test of the master gene model and use it to show that mouse ID element sequences are not compatible with a strict master gene model. We suggest that a single master gene is rarely, if ever, likely to be responsible for the accumulation of any repeat family.

Alu Elements↗

PubMed2005

The evolution of intratetrad mating rates.

Intratetrad mating, the fusion of gametes formed in a single meiosis, has unusual consequences for genetic diversity, especially in genome regions linked to mating type loci. Here we investigate the fate of modifier alleles that alter the rate of intratetrad mating, under models of heterozygote advantage and of genetic load resulting from recurrent mutation. In both cases, intratetrad mating is favored if the recombination rate between the selected locus and mating type is less than the frequency of lethal recessive alleles at that locus in the population. Positive feedback often accelerates the invasion of modifiers to the intratetrad mating rate. Recombination rate and intratetrad mating rate exert indirect selection on one another, resulting in a cascading decline in outcrossing, even in the absence of any cost of sex. However, under recurrent mutation, alleles for obligate intratetrad mating invade only very slowly, perhaps explaining why outcrossing can persist at low frequencies in a largely intratetrad mating population.

Biological Evolution↗

PubMed2004

Population genetics of the wild yeast Saccharomyces paradoxus.

Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population structure, and linkage disequilibrium. Synonymous site diversity is approximately 0.3%. Extensive incompatibilities between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species.

Base Sequence↗

PubMedDate not supplied

Evolution of spatial expression pattern.

How can complex patterns of gene expression evolve? Understanding the near-precise repeatability of morphology created by animal development, through the interactions between morphogens and networks of transcription factors, is one of the most difficult outstanding problems in developmental biology. Spatial patterns are created in part by interactions between transcription factors and their DNA targets. Here we simulate the evolution of such interactions to compare the success and the evolvability of simple and complex gene networks in reaching a desired spatial pattern of expression along an embryo. We find that adding more genes to a network makes only a slight difference to evolvability. Expression patterns can evolve within a few hundred mutational events, and some simulations show partial redundancy. However, there is wide variation between simulations, with both simple and complex networks being liable to reach evolutionary "dead ends" that can only be escaped by means of an advantageous combination of individually deleterious mutations.

Biological Evolution↗