Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics

Only relatively recently have researchers turned to molecular methods for nematode phylogeny reconstruction. Thus, we lack the extensive literature on evolutionary patterns and phylogenetic usefulness of different DNA regions for nematodes that exists for other taxa. Here, we examine the usefulness of mtDNA for nematode phylogeny reconstruction and provide data that can be used for a priori character weighting or for parameter specification in models of sequence evolution. We estimated the substitution pattern for the mitochondrial ND4 gene from intraspecific comparisons in four species of parasitic nematodes from the family Trichostrongylidae (38-50 sequences per species). The resulting pattern suggests a strong mutational bias toward A and T, and a lower transition/transversion ratio than is typically observed in other taxa. We also present information on the relative rates of substitution at first, second, and third codon positions and on relative rates of saturation of different types of substitutions in comparisons ranging from intraspecific to interordinal. Silent sites saturate extremely quickly, presumably owing to the substitution bias and, perhaps, to an accelerated mutation rate. Results emphasize the importance of using only the most closely related sequences in order to infer patterns of substitution accurately for nematodes or for other taxa having strongly composition-biased DNA. ND4 also shows high amino acid polymorphism at both the intra- and interspecific levels, and in higher level comparisons, there is evidence of saturation at variable amino acid sites. In general, we recommend using mtDNA coding genes only for phylogenetics of relatively closely related nematode species and, even then, using only nonsynonymous substitutions and the more conserved mitochondrial genes (e.g., cytochrome oxidases). On the other hand, the high substitution rate in genes such as ND4 should make them excellent for population genetics studies, identifying cryptic species, and resolving relationships among closely related congeners when other markers show insufficient variation.      

Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences

Nucleotide sequences from two nuclear loci, alcohol dehydrogenase and internal transcribed spacer-1 of the nuclear ribosomal DNA repeats, and two mitochondrial genes, cytochrome oxidase I and cytochrome oxidase II, were determined from nine species in the Drosophila saltans species group. The partition homogeneity test and partitioned Bremer support were used to measure incongruence between phylogenetic hypotheses generated from individual partitions. Individual loci were generally congruent with each other and consistent with the previously proposed morphological hypothesis, although they differed in level of resolution. Since extreme conflict between partitions did not exist, the data were combined and analyzed simultaneously. The total evidence method gave a more resolved and highly supported phylogeny, as indicated by bootstrap proportions and decay indices, than did any of the individual analyses. The cordata and elliptica subgroups, considered to have diverged early in the history of the D. saltans group, were sister taxa to the remainder of the saltans group. The sturtevanti subgroup, represented by D. milleri and D. sturtevanti, occupies an intermediate position in this phylogeny. The saltans and parasaltans subgroups are sister clades and occupy the most recently derived portion of the phylogeny. As with previous morphological studies, phylogenetic relationships within the saltans subgroup were not satisfactorily resolved by the molecular data.      

Phylogenetic analysis supports horizontal transfer of P transposable elements

Nucleotide sequence comparisons were used to investigate the evolution of P transposable elements and the possibility that horizontal transfer has played a role in their occurrence in natural populations of Drosophila and other Diptera. The phylogeny of P elements was examined using published sequences from eight dipteran taxa and a new, partial sequence from Scaptomyza elmoi. The results from a number of different analyses are highly consistent and reveal a P-element phylogeny that contradicts the phylogeny of the species. At least three instances of horizontal transfer are necessary to explain this incongruence, but other explanations cannot be ruled out at this time.      

Weight loss in postmenopausal obesity: no adverse alterations in body composition and protein metabolism

We sought to determine if decrements in the mass of fat-free body mass (FFM) and other lean tissue compartments, and related changes in protein metabolism, are appropriate for weight loss in obese older women. Subjects were 14 healthy weight-stable obese (BMI > or =30 kg/m(2)) postmenopausal women >55 yr who participated in a 16-wk, 1, 200 kcal/day nutritionally complete diet. Measures at baseline and 16 wk included FFM and appendicular lean soft tissue (LST) by dual-energy X-ray absorptiometry; body cell mass (BCM) by (40)K whole body counting; total body water (TBW) by tritium dilution; skeletal muscle (SM) by whole body MRI; and fasting whole body protein metabolism through L-[1-(13)C]leucine kinetics. Mean weight loss (+/-SD) was 9.6+/-3.0 kg (P<0.0001) or 10.7% of initial body weight. FFM decreased by 2.1+/-2.6 kg (P = 0.006), or 19.5% of weight loss, and did not differ from that reported (2.3+/-0.7 kg). Relative losses of SM, LST, TBW, and BCM were consistent with reductions in body weight and FFM. Changes in [(13)C]leucine flux, oxidation, and synthesis rates were not significant. Follow-up of 11 subjects at 23.7 +/-5.7 mo showed body weight and fat mass to be below baseline values; FFM was nonsignificantly reduced. Weight loss was accompanied by body composition and protein kinetic changes that appear appropriate for the magnitude of body mass change, thus failing to support the concern that diet-induced weight loss in obese postmenopausal women produces disproportionate LST losses.     

The DNA Barcode Linker

DNA barcoding is based on the use of short DNA sequences to provide taxonomic tags for rapid, efficient identification of biological specimens. Currently, reference databases are being compiled. In the future, it will be important to facilitate access to these databases, especially for nonspecialist users. The method described here provides a rapid, web-based, user-friendly link between the DNA sequence from an unidentified biological specimen and various types of biological information, including the species name. Specifically, we use a customized, Google-type search algorithm to quickly match an unknown DNA sequence to a list of verified DNA barcodes in the reference database. In addition to retrieving the species name, our web tool also provides automatic links to a range of other information about that species. As the DNA barcode database becomes more populated, it will become increasingly important for the broader user community to be able to exploit it for the rapid identification of unknown specimens and to easily obtain relevant biological information about these species. The application presented here meets that need.     

Body mass index and all-cause mortality in a large Chinese cohort

Background

Obesity is known to be associated with an increased risk of death, but current definitions of obesity are based on data from white populations. We examined the association between body mass index (BMI) and the risk of death in a large population of adult Chinese people.

Methods

We examined the association between body mass index (BMI) and all-cause mortality prospectively among 58 738 men and 65 718 women aged 20 years and older enrolled in 1998–1999 from four national health screening centres in Taiwan. We used Cox proportional hazards regression analyses to estimate the relative risks of all-cause mortality for different BMI categories during a maximum follow-up of 10 years.

Results

A total of 3947 participants died during the follow-up period. The lowest risk of death was observed among men and women who had a BMI of 24.0–25.9 (mean 24.9). After adjustment for age, smoking status, alcohol intake, betel-nut chewing, level of physical activity, income level and education level, we observed a U-shaped association between BMI and all-cause mortality. Similar U-shaped associations were observed when we analyzed data by age (20–64 or ≥ 65 years), smoking (never, < 10 pack-years or ≥ 10 pack-years) and presence of a pre-existing chronic disease, and after we excluded deaths that occurred in the first three years of follow-up.

Interpretation

BMI and all-cause mortality had a U-shaped association among adult Chinese people in our study. The lowest risk of death was among adults who had a BMI of 24.0–25.9 (mean 24.9). Our findings do not support the use of a lower cutoff value for overweight and obesity in the adult Chinese population.The prevalence of obesity has dramatically increased in past decades in both developed and developing countries. The World Health Organization (WHO) reported that 1.6 billion adults are overweight and at least 400 million are obese.¹ The WHO further predicted that by the year 2015, about 2.3 billion adults will be overweight and more than 700 million will be obese.¹ In Taiwan, according to a national survey performed between 1993–1996 and 2005–2008, the prevalence of overweight and obesity (defined as body mass index [BMI] ≥ 24 kg/m²) had increased dramatically, from 33.4% to 50.8% among men and from 31.7% to 36.9% among women.²Overweight and obesity have been recognized as important and independent risk factors for many chronic diseases such as diabetes mellitus, hypertension, stroke, cardiovascular diseases and malignant diseases.^3–7 Substantial epidemiologic evidence shows that obesity is associated with an increased risk of cardiovascular-related and all-cause mortality.^8,9 Therefore, obesity has become a major public health problem around the world.Current definitions of obesity and overweight in adults are based on data from white populations. The WHO has proposed another definition for Asian people, but most of the data it used were from cross-sectional studies.¹⁰ One study showed that, for a given BMI, Asian people had higher body fat than white people.¹¹ Furthermore, the association between BMI and all-cause mortality has been reported to be J-shaped or U-shaped. Most of the studies involved white people, with only a few involving Asian populations. Gu and colleagues reported a U-shaped association between BMI and all-cause mortality among Chinese people.¹² However, they included only middle-aged adults over 40 years old and not all adults over 20 years.We designed a large prospective cohort study to assess the association between BMI and all-cause mortality in a nationwide representative sample of Chinese adults over 20 years old in Taiwan. We also intended to find the optimal BMI cutoff values for overweight and obesity among Chinese adults.