Pine cones that remain closed and retain seeds until fire causes the cones to open (cone serotiny) represent a key adaptive trait in a variety of pine species. In lodgepole pine, there is substantial geographical variation in serotiny across the Rocky Mountain region. This variation in serotiny has evolved as a result of geographically divergent selection, with consequences that extend to fores...

The vast majority of genome-wide association study (GWAS) risk loci fall in non-coding regions of the genome. One possible hypothesis is that these GWAS risk loci alter the individual's disease risk through their effect on gene expression in different tissues. In order to understand the mechanisms driving a GWAS risk locus, it is helpful to determine which gene is affected in specific tissue ty...

The species divergence times and demographic histories of Drosophila melanogaster and its three sibling species, D. mauritiana, D. simulans, and D. yakuba, were investigated using a maximum likelihood (ML) method. Thirty-nine orthologous loci for these four species were retrieved from DDBJ/EMBL/GenBank database. Both autosomal and X-linked loci were used in this study. A significant degree of r...

A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the rang...

Human gene mapping would be greatly facilitated if marker loci with sufficient heterozygosity were generally available. As a source of such markers, we have used cosmids from a human genomic library. We have developed a rapid method for screening random cosmids to identify those that are homologous to genomic regions especially rich in restriction fragment length polymorphisms. This method allo...

A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the muta...

The calculation of exact likelihoods from pedigree data is limited to datasets containing either a small number of meioses, or a small number of linked genetic loci. In particular, the computation of likelihoods from data collected at multiple loci on large, extended pedigrees is infeasable. We perform multipoint linkage analysis on such datasets by estimating ratios of these otherwise intracta...

We propose a method (fastBAT) that performs a fast set-based association analysis for human complex traits using summary-level data from genome-wide association studies (GWAS) and linkage disequilibrium (LD) data from a reference sample with individual-level genotypes. We demonstrate using simulations and analyses of real datasets that fastBAT is more accurate and orders of magnitude faster tha...

Electrophoretic expression of 20 enzymes coded by a minimum of 30 gene loci is reported for sea lamprey. ADA, ADH. AGP, AAT, CPK, G6PDH, GAPDH, LDH. MDH, PEP, 6PCD, PGI, PGK, PGM, PK, PMI, and SDH yielded gel resolution satisfactory for use in future population studies. Six loci, AGP, !LZDH-1, PGI-I, PGI-2, PGi%f-l, and PlMI were polymorphic. Enzyme expresion did not vary between life stages (a...

The spectral loci of both unique blue and unique yellow were measured over a 16-month period. Using the method of constant stimuli, two neutrally adapted observers made forced-choice green or red responses to monochromatic test flashes. Results showed a consistent difference between observers (about 5 nm), considerable within-subject variability (standard deviation 3 nm), and significant long-t...