Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

Background

Recent research has indicated a positive association between rates of molecular evolution and diversification in a number of taxa. However debate continues concerning the universality and cause of this relationship. Here, we present the first systematic investigation of this relationship within the mammals. We use phylogenetically independent sister-pair comparisons to test for a relationship between substitution rates and clade size at a number of taxonomic levels. Total, non-synonymous and synonymous substitution rates were estimated from mitochondrial and nuclear DNA sequences.

Results

We found no evidence for an association between clade size and substitution rates in mammals, for either the nuclear or the mitochondrial sequences. We found significant associations between body size and substitution rates, as previously reported.

Conclusions

Our results present a contrast to previous research, which has reported significant positive associations between substitution rates and diversification for birds, angiosperms and reptiles. There are three possible reasons for the differences between the observed results in mammals versus other clades. First, there may be no link between substitution rates and diversification in mammals. Second, this link may exist, but may be much weaker in mammals than in other clades. Third, the link between substitution rates and diversification may exist in mammals, but may be confounded by other variables.     

Parentage and host preference in the common cuckoo Cuculus canorus

Microsatellite DNA markers were used to investigate parentage relationships in a population of common cuckoo Cuculus canorus . Thirty adults and 55 nestlings were genotyped at six loci from blood samples collected over a four-year period. To test whether each cuckoo female specialises in parasitising one single host species (Host Preference Hypothesis), the maternal relationships were used to record each female's host choice. The results supported the Host Preference Hypothesis since no female (N=3) was recorded to have parasitised more than one of four congeneric host species breeding in the area. In contrast, the males (N=4) did not show such specialisation since two of them sired offspring reared by different host species.     

Scrotal circumference of Australian beef bulls

Normal range for scrotal circumference in Australian beef bulls was established using more than 300,000 measurements of breed, management group, age, liveweight, and scrotal circumference. The data used were derived from Australian bull breeders and two large research projects in northern Australia. Most bulls were within 250 to 750 kg liveweight and 300 to 750 days of age. The differences between breeds and variances within breeds were higher when scrotal circumference was predicted from age rather than liveweight, because of variance in growth rates. The average standard deviation for predicted scrotal circumference from liveweight and age was 25 and 30 mm, respectively. Scrotal circumference by liveweight relationships have a similar pattern across all breeds, except in Waygu, with a 50 to 70 mm range in average scrotal circumference at liveweights between 250 and 750 kg. Temperate breed bulls tended to have higher scrotal circumference at the same liveweight than tropically adapted breeds. Five groupings of common beef breeds in Australian were identified, within which there were similar predictions of scrotal circumference from liveweight. It was concluded that liveweight and breed are required to identify whether scrotal circumference is within normal range for Australian beef bulls that experience a wide range of nutritional conditions.     

Phylogeography of a widespread North American migratory songbird (Setophaga ruticilla)

Genetic analyses for many widespread North American species have revealed significant east-west differentiation, indicating that many survived through the Pleistocene in 2 glacial refugia-1 in the eastern and 1 in the western part of the continent. It remains unclear, however, whether other areas may have served as important glacial refugia. Moreover, many such species exhibit widespread genetic similarity within eastern and western regions because of recent expansion from small refugial populations, making it difficult to evaluate current-day levels of gene flow. In this study, we used mitochondrial DNA (mtDNA) control region sequence and amplified fragment length polymorphism markers to survey genetic variation in a widespread migratory bird, the American redstart (Setophaga ruticilla). mtDNA analyses revealed a pattern that contrasts with that found for most other widespread species studied to date: most redstart populations across North America appear to have spread out from a single glacial refugium, possibly located in the southeastern United States, whereas populations in far-eastern Canada may have survived in a second glacial refugium located on the now-submerged Atlantic coastal shelf off the coast of Newfoundland. A pattern of isolation by distance in mtDNA suggested some constraints on current-day gene flow among extant redstart populations. This study thus reveals a recent evolutionary history for this species that differs from that of most other widespread North American passerines and provides evidence for limited gene flow in a species with potentially large dispersal distances.     

Effect of inhA and katG on isoniazid resistance and virulence of Mycobacterium bovis

Isoniazid (INH) resistance of the Mycobacterium tuberculosis Complex (MtbC) is associated with both loss of catalase activity and mutation of the inhA gene. However, the relative contributions of these changes to resistance and to the loss of virulence for guinea-pigs is unknown. In this study, a virulent strain of Mycobacterium bovis, a member of the MtbC., was exposed to increasing concentrations of INH. Two INH-resistant strains were produced which had lost catalase activity. Strain WAg405, which had a higher resistance to INH, also had a mutation in the inhA gene. This demonstrated that loss of catalase activity and mutation of inhA had a cumulative effect on INH resistance. When a functional katG gene was integrated into the genome of WAg405 the INH resistance was greatly reduced. This indicated that most of the resistance had been caused by loss of catalase activity. While the parent INH-sensitive strain was virulent for guinea-pigs, the INH-resistant strains were significantly less virulent. Integration of a functional katG gene into the most resistant strain restored full virulence. This clearly established that katG is a virulence factor for M. bovis and that mutation of the inhA gene has no effect on virulence.     

Manipulation of immune responses to Mycobacterium bovis by vaccination with IL-2- and IL-18-secreting recombinant bacillus Calmette Guerin

Bacillus Calmette Guerin (BCG) has been reported to show variable efficacy as a vaccine against tuberculosis. We demonstrated that the secretion of biologically active IL-2 (rBCG/IL-2),but not IL-18 (rBCG/IL-18), by BCG improves its ability to induce and maintain a strong type 1 immune response in BALB/c mice. rBCG/IL-2 induced significantly higher Ag-specific proliferative responses, high IFN-gamma production and serum titres of IgG2a 16 weeks after vaccination. This immune profile was correlated to an increased rate of clearance of non-pathogenic mycobacteria (live BCG delivered intranasally). Surprisingly, however,this strong type 1 immune profile induced no greater protective immunity against aerosol challenge with virulent Mycobacterium bovis than that induced by normal BCG (nBCG). By comparison,vaccination with rBCG/IL-18 was found to induce significantly less IFN-gamma production in splenic lymphocytes than nBCG.This impaired induction of IFN-gamma was correlated to a significantly lower protective efficacy against M. bovis challenge, as compared to nBCG. The data suggest that manipulation of the immune response to tuberculosis and tuberculosis vaccines will require a more complete understanding of the factors that are important in generating a protective immune response.     

世居及移居高原青少年最大有氧能力的特征

本文报道海拔３４１７ｍ和４２８０ｍ地区世居藏族和移居汉族青少年运动状态下心肺功能的对比研究。结果显示：３４１７ｍ和４２８０ｍ世居藏族的最大氧耗量、无氧阈值及最大心输出量都明显大于汉族,血氧饱和度（Ｓａｏ２）随运动负荷的增加而降低。海拔３４１７ｍ藏、汉族的△Ｓａｏ２分别为７．４６％和１０．０３％,４２８０ｍ处为８．５７％和１３．７５％,最大心率随海拔升高而下降。研究提示,藏族青少年有较高的最大有氧能力,反映了他们对低氧环境的适应优势。