Biomedical subjects

Xin-Sheng Hu

Publications and source records attributed to Xin-Sheng Hu.

6 recordsLinked to original sources

PubMed2005

Background selection and population differentiation.

A general analytical formula is derived, which predicts the effects of background selection on population differentiation at a neutral locus as a result of its linkage with selected loci of deleterious mutations. The theory is based on the assumptions of random mating, multiplicative fitness, and weak selection in hermaphrodite plants in the island model of population structure. The analytical results show that Fst at the neutral locus increases as a result of the effects of background selection, regardless of the dependence or independence among linked background selective loci. The increment in Fst is closely related to the magnitude of linkage disequilibria between the neutral locus and selected loci, and can be estimated by the ratio of Fst with background selection to Fst without background selection minus one. The steady-state linkage disequilibrium between a neutral locus and a selected locus in subpopulations, primarily attained by gene flow, decreases with the recombination rate, and can be enhanced when there are dependence among linked selected loci. Monte Carlo computer simulations with two- and three-locus models show that the analytical formulae perform well under general conditions. Application of the present theory may aid in analyzing the genome-wide mapping of the effect of background selection in terms of Fst.

Computer Simulation↗

PubMed2005

Tension versus ecological zones in a two-locus system.

Previous theories show that tension and ecological zones are indistinguishable in terms of gene frequency clines. Here I analytically show that these two types of zones can be distinguished in terms of genetic statistics other than gene frequency. A two-locus cline model is examined with the assumptions of random mating, weak selection, no drift, no mutation, and multiplicative viabilities. The genetic statistics for distinguishing the two types of zones are the deviations of one- or two-locus genotypic frequencies from Hardy-Weinberg equilibrium (HWE) or from random association of gametes (RAG), and the deviations of additive and dominance variances from the values at HWE. These deviations have a discontinuous distribution in space and different extents of interruptions in the ecological zone with a sharp boundary, but exhibit a continuous distribution in the tension zone. Linkage disequilibrium enhances the difference between the deviations from HWE and from RAG for any two-locus genotypic frequency.

Ecosystem↗

PubMed2005

Genetic structure and migration from mainland to island populations in Abies procera Rehd.

Noble fir (Abies procera Rehd) is a narrowly distributed conifer with a typical mainland-island structure of natural distribution. Here, we examined the genetic structure of populations native to the Pacific coast from Oregon to Washington (5 island and 16 mainland populations) with 14 polymorphic allozyme loci. A general method for estimating the number of unidirectional migrants from the mainland to island populations is presented in terms of the relation of average heterozygosity between the mainland and island populations. The results indicated that there were substantial island-mainland population differentiations (Fst = 0.107+/-0.029~0.154+/-0.039) but small differentiation within the mainland/submainland populations (0.037+/-0.008 approximately 0.054+/-0.010). Significant isolation by distance existed among the island-mainland populations and among the populations in Washington submainland. Four islands investigated received different numbers of migrants from the mainland/submainland. The southern island populations received a smaller number of migrants from the mainland but had greater genetic diversity, implying that there could be introgression with A. magnifica and (or) they represented possible glacial refuges and had expanded northwards after the last glaciations. The island populations close to the Pacific coast were more likely mainland-dependent.

Abies↗

PubMed2004

Joining genetic linkage maps using a joint likelihood function.

We present an efficient method to join genetic maps derived from different crosses, which is especially appropriate for dominant markers. In contrast to the "JoinMap" algorithm, which estimates information about recombination in a given cross from the LOD values and then combines estimates among crosses assuming a binomial sampling distribution, we construct a joint likelihood function that combines information across all crosses, to obtain a joint estimate of recombination. Simulations indicated that the difference between these two approaches is small when codominant markers are used, but that the joint likelihood approach shows substantially improved estimates when dominant or a mixture of dominant and codominant markers are used. This is because the joint likelihood implicitly finds the optimal weights among different classes of data, while the former method does not accurately predict the information from crosses involving dominant markers. Application of our method is illustrated by the construction of a linkage map for Linanthus using both backcrosses and the F2 of a cross between Linanthus jepsonii and L. bicolor, assayed with amplified fragment length polymorphisms (AFLP).

Chromosome Mapping↗

PubMed2003

On migration load of seeds and pollen grains in a local population.

We have extended Wright's model of migration load to hermaphrodite plants showing variation at a single locus with two alleles. The model incorporates independent migration of seeds and pollen grains, the selection at both the haploid gametophyte and the diploid sporophyte stages, and a mixed mating system. The analytical relations between migration load and migration rate of seeds and pollen grains are explicitly formulated. The results show that under certain conditions, seed flow can have a more effect on migration load than pollen flow. Pollen selection at the gametophyte stage cannot substantially affect the migration load at the sporophyte stage. Selection at the diploid sporophyte stage is critical in determining the migration load of pollen grains. The relative migration loads of pollen versus seeds can be approximately estimated in predominantly outcrossing populations by the ratio of pollen flow to twice the seed flow, when the selection coefficient (s(T)) is greater than, or approximately equal to, the migration rate (m).

Models, Genetic↗

PubMed2002

Seed and pollen flow and cline discordance among genes with different modes of inheritance.

The relationships between seed and pollen flow and cline discordance/concordance between cytoplasmic and nuclear genes, with the incorporation of the effects of natural selection, are formulated for one locus with two alleles, under assumptions of random mating, no drift and no mutation. Results show that under certain conditions, the relative roles of seed and pollen flow in shaping cline discordance/ concordance are very similar to their roles in influencing population differentiation for selectively neutral markers with different modes of inheritance. Where the disequilibria between cytoplasmic and nuclear genes are of the order similar to selection coefficient, cline discordance/concordance can be predicted from the relative values of the ratio of pollen to seed flow and the ratio of selection coefficients. Where the disequilibria attained by seed and pollen flow are significant, the integrated cytonuclear data are recommended for cline analysis. In both cases, the relative rates of selection coefficients between cytoplasmic and nuclear genes can be roughly estimated according to their characteristic length.

Alleles↗