Biomedical subjects

Ralph Haygood

Publications and source records attributed to Ralph Haygood.

5 recordsLinked to original sources

PubMed2006

The genome of the sea urchin Strongylocentrotus purpuratus.

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Animals↗

PubMed2006

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Mutation rate and the cost of complexity.

Two recent theoretical studies of adaptation suggest that more complex organisms tend to adapt more slowly. Specifically, in Fisher's "geometric" model of a finite population where multiple traits are under optimizing selection, the average progress ensuing from a single mutation decreases as the number of traits increases--the "cost of complexity." Here, I draw on molecular and histological data to assess the extent to which on a large phylogenetic scale, this predicted decrease in the rate of adaptation per mutation is mitigated by an increase in the number of mutations per generation as complexity increases. As an index of complexity for multicellular organisms, I use the number of visibly distinct types of cell in the body. Mutation rate is the product of mutational target size and population mutation rate per unit target. Despite much scatter, genome size appears to be positively correlated with complexity (as indexed by cell-type number), which along with other considerations suggests that mutational target size tends to increase with complexity. In contrast, effective population mutation rate per unit target appears to be negatively correlated with complexity. The net result is that mutation rate probably does tend to increase with complexity, although probably not fast enough to eliminate the cost of complexity.

Animals↗

PubMed2004

Sexual conflict and protein polymorphism.

Sexual conflict, where male and female reproductive interests differ, is probably widespread and often mediated by male or sperm proteins and female or egg proteins that bind to each other during mating or fertilization. One potential consequence is maintenance of polymorphism in these proteins, which might result in reproductive isolation between sympatric subpopulations. I investigate the conditions for polymorphism maintenance in a series of mathematical models of sexual conflict over mating or fertilization frequency. The models represent a male or sperm ligand and a female or egg receptor, and they differ in whether expression of either protein is haploid or diploid. For diploid expression, the conditions imply that patterns of dominance, which involve neither overdominance nor underdominance, can determine whether polymorphism is maintained. For example, suppose ligand expression is diploid, and consider ligand alleles L1 and L2 in interactions with a given receptor genotype; if L1/L1 males are fitter than L2/L2 males in these interactions, then polymorphism is more likely to be maintained when L1/L2 males more closely resemble L1/L1 males in these interactions. Such fitter-allele dominance might be typical of a ligand or its receptor due to their biochemistry, in which case polymorphism might be typical of the pair.

Animals↗

PubMed2003

Consequences of recurrent gene flow from crops to wild relatives.

Concern about gene flow from crops to wild relatives has become widespread with the increasing cultivation of transgenic crops. Possible consequences of such gene flow include genetic assimilation, wherein crop genes replace wild ones, and demographic swamping, wherein hybrids are less fertile than their wild parents, and wild populations shrink. Using mathematical models of a wild population recurrently receiving pollen from a genetically fixed crop, we find that the conditions for genetic assimilation are not stringent, and progress towards replacement can be fast, even for disfavoured crop genes. Demographic swamping and genetic drift relax the conditions for genetic assimilation and speed progress towards replacement. Genetic assimilation can involve thresholds and hysteresis, such that a small increase in immigration can lead to fixation of a disfavoured crop gene that had been maintained at a moderate frequency, even if the increase in immigration is cancelled before the gene fixes. Demographic swamping can give rise to 'migrational meltdown', such that a small increase in immigration can lead to not only fixation of a disfavoured crop gene but also drastic shrinkage of the wild population. These findings suggest that the spread of crop genes in wild populations should be monitored more closely.

Crops, Agricultural↗

PubMed2002

Coexistence in MacArthur-style consumer-resource models.

The nature of and conditions for permanent coexistence of consumers and resources are characterized in a family of models that generalize MacArthur's consumer-resource model. The generalization is of the resource dynamics, which need not be of Lotka-Volterra form but are subject only to certain restrictions loose enough to admit many resource dynamics of biological interest. For any such model, (1) if there is an interior equilibrium, then it is globally attracting, else some boundary equilibrium is globally attracting-thus permanent coexistence is coexistence at a globally attracting equilibrium; (2) there is an interior equilibrium if and only if for any species, the equilibrium approached in the absence of that species and the presence of the others is invasible by that species--thus permanent coexistence is equivalent to mutual invasibility; (3) for resources without direct interactions, the conditions for permanent coexistence of the consumers admit an instructive formulation in terms of regression statistics. The significance and limitations of the models and results are discussed.

Animals↗