This paper provides a general method for constructing generalized p-value via the fiducial inference.Furthermore,the power properties of the generalized test are discussed.As illustrations, the two-parameter exponential distribution and unbalanced two-fold nested design are researched.It is shown that the resulting generalized p-values are of good frequency property.
Xin-min LI~(1+) Xing-zhong XU~2 Guo-ying LI~3 1 Institute of Applied Mathematics,Shandong University of Technology,Zibo 255049,China
In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as ＂evolutionary transients＂, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.
Positive correlation between recombination rate and nucleotide diversity has been observed in a wide variety of eukaryotes on megabase scale. On the basis of genome-wide chicken genetic variation map generated by comparing three domestic breeds with wild ancestor and the positions of markers on the genetic linkage map, we found that SNPs rates were similar for all chromosomes while the recombina-tion rates increased in micro chromosomes. In other words no correlation exists in chromosome size. Nevertheless, when we scanned the genome by calculating the values of each characteristic within non-overlapping windows, instead of single value for each chromosomes, the nucleotide diversity was found to be significantly correlated with the recombination rate (r=0.27, P<0.0005). Furthermore, the significant association not only existed between these two features, but also existed between all 6 pairwise combinations of nucleotide diversity, recombination rate, GC content and average gene length. This co-variation is very meaningful for the studies of sequence evolution.
FANG LinYE JiaLI NingZHANG YongLI SongGangGANE Ka-Shu WONGWANG Jun
To understand the genetic basis that underlies the phenotypic divergence between human and non- human primates, we screened a total of 7176 protein-coding genes expressed in the human brain and compared them with the chimpanzee orthologs to identify genes that show evidence of rapid evolution in the human lineage. Our results showed that the nonsynonymous/synonymous substitution (Ka/Ks) ratio for genes expressed in the brain of human and chimpanzee is 0.3854, suggesting that the brain-expressed genes are under functional constraint. The X-linked human brain-expressed genes evolved more rapidly than autosomal ones. We further dissected the molecular evolutionary patterns of 34 candidate genes by sequencing representative primate species to identify lineage-specific adaptive evolution. Fifteen out of the 34 candidate genes showed evidence of positive Darwinian selection in human and/or chimpanzee lineages. These genes are predicted to play diverse functional roles in em- bryonic development, spermatogenesis and male fertility, signal transduction, sensory nociception, and neural function. This study together with others demonstrated the usefulness and power of phy- logenetic comparison of multiple closely related species in detecting lineage-specific adaptive evolu- tion, and the identification of the positively selected brain-expressed genes may add new knowledge to the understanding of molecular mechanism of human origin.
QI XueBinYANG SuZHENG HongKunWANG YinQiuLIAO ChengHongLIU YingCHEN XiaoHuaSHI HongYU xiaoJingAlice A. LINLuca L. CAVALLI-SFORZAWANG JunSU Bing
Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) platform.The protocol involves two-stage library construction.The specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of 33-fold.Comparison of our results with whole genome shot-gun resequencing results showed that the exome SNP calls gave only 0.97% false positive and 6.27% false negative variants.Our protocol is also well suited for use with whole genome amplified DNA.The results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach.
