Total body fat mass (TBFM) and total body lean mass (TBLM) are the major components of the human body. Although these highly correlated phenotypic traits are frequently used to characterize obesity, the specific shared genetic factors that influence both traits remain largely unknown. Our study was aimed at identifying common quantitative trait loci (QTLs) contributing to both TBFM and TBLM. We performed a whole genome-linkage scan study in a large sample of 3255 subjects from 420 Caucasian pedigrees. Bivariate linkage analysis was carried out in both the entire sample and gender-specific subsamples. Several potentially important genomic regions that may harbour QTLs important for TBFM and TBLM were identified. For example, 20p12-11 achieved a LOD score of 2·04 in the entire sample and, in the male subsample, two genomic regions, 20p12 (LOD=2·08) and 3p26-25 (LOD=1·92), showed suggestive linkage. In addition, two-point linkage analyses for chromosome X showed suggestive linkages on Xp22 in the entire sample (LOD=2·14) and significant linkage on Xp22 in the female subsample (LOD=3·05). Complete pleiotropy was suggested for 20p12 and 3p26-25 in males. Our results suggest that QTLs on chromosomes 20p12, 3p26-25 and Xp22 may jointly influence TBFM and TBLM. Further fine mapping and gene identification studies for these pleiotropic effects are needed.

To increase our understanding of the relationships of trunk fat mass (FMtrunk) and four anthropometric indices in Chinese males, 1090 males aged 20–40 years were randomly recruited from the city of Changsha, China. Waist circumference (WC) and hip circumference (HC) were measured using standardized equipment, and three other anthropometric indices of BMI, waist:hip ratio (WHR) and conicity index (CoI) were calculated using weight, height, HC and WC. FMtrunk (in kg) was measured using a Hologic QDR 4500 W dual-energy X-ray absorptiometry scanner. There was an increasing trend of FMtrunk, %FMtrunk (percentage of FMtrunk) and BMI, WC, WHR, CoI in successively older age groups (e.g. the mean FMtrunk values were 4·63 (sd 2·58), 5·39 (sd 2·74), 5·93 (sd 2·82), 6·57 (sd 2·94) in four 5-year age groups, respectively). FMtrunk and %FMtrunk were significantly correlated with four anthropometric indices with the Pearson's correlation coefficients ranging from 0·25 to 0·86. Principal component analysis was performed to form three principal components that interpreted over 99·5% of the total variation of four related anthropometric indices in all age groups, with over 65% of the total variation accounted by principal component 1. Multiple regression analyses showed that three principal components explained a greater variance (R2 70·0–80·1%) in FMtrunk than did BMI or WC alone (R2 57·8–74·1%). The present results suggest that there is an increasing trend of FMtrunk and four anthropometric indices in successively older age groups; that age has important effects on the relationships of FMtrunk and studied anthropometric indices; and that the accuracy of predicting FMtrunk using four anthropometric indices is higher than using BMI or WC alone.

Unbiased or upper limit estimates of the rate (U) of genomic mutations to mildly deleterious alleles are crucial in genetic and conservation studies and in human health care. However, only a few estimates of the lower bounds of U are available. We present a fairly robust estimation that yields an upper limit of U and a nearly unbiased estimate of the per generation fitness decline due to new deleterious mutations. We applied the approach to three species of the freshwater microcrustacean Daphnia and revealed that the upper limit of U for egg survivorship is 0·73 (SD=0·30) in 14 D. pulicaria populations. For the first four clutches, per generation decline in fecundity due to deleterious mutations ranged from 2·2% to 7·8% in 20 D. pulex populations and from 1·1% to 5·1% in 8 D. obtusa populations. These results indicate the mutation pressure is high in natural Daphnia populations. The approach investigated here provides a potential way to quickly and conveniently characterize U and per generation effects of deleterious genomic mutations on fitness or its important components such as fecundity.

Cabot's tragopan Tragopan caboti, a pheasant that inhabits subtropical montane forests in south-east China, is categorized as Vulnerable on the IUCN Red List. Nesting in trees, it routinely makes use of natural platforms and the old nests of other species, both of which may sometimes be in short supply. This study was designed to test how much use would be made of artificial nest platforms, and to identify factors influencing their occupation. Basketry platforms made of bamboo were erected in parts of Wuyanling National Nature Reserve, Zhejiang Province, China. The tragopans used 16 platforms (8%) in 2002 and 12 (5%) in the following year. A census of the population in spring suggested that a high proportion of the females (41% in 2002, 36% in 2003) in the study area made use of the platforms. There were significant preferences for platforms in mixed conifer/broadleaf forest, as opposed to pure stands, as well as for sites on the upper part of hill slopes. Principal component scores were used to represent variation in 11 variables measured at each platform site. Binary logistic regressions employing these scores as predictors for each year separately did not reveal a consistent model for distinguishing used from unused platforms, although short distances to the forest edge were associated with use in both years. These nest platforms are cheap and easy to erect, and may have the potential to halt or reverse a perceived downward population trend for this species across the whole of its fragmented range. Further trials are therefore advocated.

The distribution of genetic diversity between Oryza sativa L. ssp. indica and O. sativa L. ssp. japonica covering different ecological zones in Yunnan was studied, and specific markers of indica/japonica subspecies, paddy/upland rice and different ecological zones were screened, using 36 microsatellite primers and 113 accessions in the Yunnan landrace rice core collection. The genetic diversity of japonica was higher than that of indica, and the ecological zone with the highest and smallest genetic diversity lay in south-east and north-east Yunnan, respectively. This distribution was consistent at morphological and isozyme levels with studies on the entire Yunnan rice resources and core collection. In addition, the results showed that, among 416 markers, there were six indica/japonica-specific markers, 15 specific markers for paddy/upland rice and three specific markers in different ecological zones. The main conclusions are that the landrace rice core collection in Yunnan genetically represents the entire landrace rice resources in Yunnan, the centre of genetic diversity at DNA level lies in south-east Yunnan, and the DNA differentiation between indica and japonica is small. Furthermore, microsatellite markers were useful for studying the genetic diversity, classification and ecotype of germplasm resources and their core collection.

We investigate how sampling of parents or children based on their extreme phenotypic values selected from clinical databases would affect the power of identification of quantitative trait loci (QTL) by a transmission disequilibrium test (TDT). We consider three selective sampling schemes based on the selection of phenotypic values of parents or children in nuclear families: (1) two children, one of extreme value, the other random; (2) two children extremely discordant; (3) one parent of extreme value. Other family members not specified will be recruited randomly with regard to phenotypic values. Our study shows that the second sampling scheme can always enhance the power for QTL identification, sometimes dramatically so. The increase in the statistical power of the TDT is particularly dramatic when h2 at the QTL under test is small or intermediate (e.g. 0·05 or 0·10). For the other two sampling schemes, under dominant effects at the QTL, the power is always increased relative to random sampling; however, under recessive or additive genetic effects, the power gain is generally minor or even decreased a little sometimes. Allele frequencies at the QTL and the selection stringency are important for determining the effect of selective sampling on the power of QTL identification. Our study is useful as a practical guideline on how to perform the TDT efficiently in practice by taking advantage of the extensive databases accumulated that are enriched with people of extreme phenotypic values.

The transmission disequilibrium test (TDT) customarily uses affected children and their parents (often case–parent trios, TDTD). Control–parent trios are necessary to guard against spurious significant results due to segregation distortion but are not generally utilized in the identification of disease susceptibility loci (DSL). Controls are often easy to recruit and the TDT can easily be extended to include control–parent trios into the analyses with unrelated case–parent trios. We present an extension of the TDT (TDTDC) that incorporates unrelated cases and controls and their parents into a single analysis. We develop a simple and accurate analytical method for computing the statistical power of various TDT (e.g. the TDTD, TDTDC, TDTDC and TDTC that employ control–parent trios only) under any genetic model. We investigated the power of these TDT, and particularly compared the relative power of the TDTD and TDTDC. We found that the TDTDC is almost always more powerful than the TDTC and TDTD. The relative power of the TDTDC and TDTD depends largely upon a number of parameters identified in the study. This study provides a basis for efficient use of control–parent trios in DSL identification.

Characterizing deleterious genomic mutations is important. Most of the few current estimates come from the mutation–accumulation (M-A) approach, which has been extremely time- and labour-consuming. There is a resurgent interest in implementing this approach. However, its estimation properties under different experimental designs are poorly understood. By simulations we investigate these issues in detail. We found that many of the previous M-A experiments could have been more efficiently implemented with much less time and expense while still achieving the same estimation accuracy. If more than 100 lines are employed in M-A and if each line is replicated at least 10 times during each assay, an experiment of 10 M-A generations with two assays (at the beginning and at the end of M-A) may achieve at least the same estimation quality as a typical M-A experiment. The number of replicates per M-A line necessary for each assay largely depends on the magnitude of environmental variance. While 10 replicates are reasonable for assaying most fitness traits, many more are needed for viability, which has an exceptionally large environmental variance. The investigation is mainly carried out using Bateman–Mukai's method of moments for estimation. Estimation using Keightley's maximum likelihood is also investigated and discussed. These results should not only be useful for planning efficient M-A experiments, but also may help empiricists in deciding to adopt the M-A approach with manageable labour, time and resources.

Due to the tremendous cost of the traditional mutation-accumulation approach (the Bateman–Mukai technique), data are rare for deleterious mutation parameters such as genomic mutation rate, selection and dominance coefficients. Two alternative approaches have been developed (the Morton–Charlesworth and Deng–Lynch techniques). Except for the Deng–Lynch method, the statistical properties (bias and sampling variance) of these techniques are poorly understood; therefore we investigated them using computer simulation. With constant fitness effects of mutations, the Bateman–Mukai (assuming additive effects) and Deng–Lynch (assuming multiplicative effects) techniques are unbiased; the Morton–Charlesworth technique (assuming multiplicative effects) is very biased if fitness is used in the regression to estimate h, but slightly biased if the logarithm of fitness is used. With variable fitness effects, all techniques are biased. The Deng–Lynch technique is statistically better than the others except when fitness is used to estimate the average degree of dominance in selfing populations with the Morton–Charlesworth technique. If fitness effects are multiplicative but additivity is assumed, the Bateman–Mukai technique is biased under constant fitness effects, and less biased under variable fitness effects relative to when fitness effects are additive (as assumed by the technique). Our study not only quantifies the degree of bias under the biologically plausible situations investigated, thus forming a basis for correct inference of the true parameters by using these techniques, but also provides insights into the relative efficiencies of these techniques when the same number of genotypes are handled experimentally.