A single IGF1 allele is a major determinant of small size in dogs

The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs.     

Ecological speciation in South Atlantic island finches

Examples of sympatric speciation in nature are rare and hotly debated. We describe the parallel speciation of finches on two small islands in the Tristan da Cunha archipelago in the South Atlantic Ocean. Nesospiza buntings are a classic example of a simple adaptive radiation, with two species on each island: an abundant small-billed dietary generalist and a scarce large-billed specialist. Their morphological diversity closely matches the available spectrum of seed sizes, and genetic evidence suggests that they evolved independently on each island. Speciation is complete on the smaller island, where there is a single habitat with strongly bimodal seed size abundance, but is incomplete on the larger island, where a greater diversity of habitats has resulted in three lineages. Our study suggests that the buntings have undergone parallel ecological speciation.     

The abundance of a threatened arboreal marsupial in relation to anthropogenic disturbances at local and landscape scales in Mediterranean-type forests in south-western Australia

This study investigated associations between the relative abundance of the threatened ngwayir (western ringtail possum, Pseudocheirus occidentalis) and anthropogenic disturbances at local and landscape scales within the publicly-managed jarrah (Eucalyptus marginata) forests of south-western Australia. Logging, fire, fox (Vulpes vulpes) control and forest fragmentation were investigated in relation to the relative abundance of ngwayir at 90 sites within an area of 285,000 ha east of Manjimup; the location of the last remaining substantial population of ngwayir in jarrah forest. Overall, ngwayir abundance was greatest in areas with limited anthropogenic disturbance. At the local-scale, ngwayir abundance was negatively associated with greater fire intensity. At the landscape-scale, it was positively associated with fox control and negatively associated with forest fragmentation and distance from non-remnant vegetation (i.e., agriculture and tree plantations). Abundance was also greatest in predominantly unlogged landscapes and in forests that had been regrowing for an average of 40 years since the landscape was most recently logged, in other words, where logging was historically least intense. Interactions between fox control efforts and forest fragmentation were also important. This study emphasises the importance of conducting research at appropriate spatial scales and to account for the synergistic effects of the causes of decline. An adaptive management approach to the mitigation of the agents of decline is recommended.Indirect evidence indicates that high value habitat for ngwayir has in all likelihood been selectively cleared for agriculture, owing to its fertile and productive nature. Habitat loss is, therefore, also likely to be a major cause of the modern decline of the species. While many jarrah forest areas that support remaining high abundances of the ngwayir have been incorporated into reserves, conservation of ngwayir habitat and populations outside reserves also will be essential for the recovery and long-term viability of the species.     

Degradation of selected polycyclic aromatic hydrocarbons in coastal sediments: Importance of microbes and polychaete worms

Rates of degradation of polycyclic aromatic hydrocarbons (PAH) were examined after addition of crude oil enriched with anthracene, fluoranthene, benz(a)anthracene, and benzo(a)pyrene to coastal sediments in a laboratory (20°) flowing seawater system. Three types of sediment (fine sand, medium sand, and marsh sediment) with and without the benthic polychaete worm, Capitella capitata, were used. After extraction from the sediment, PAH concentrations were measured by liquid chromatography with fluorescent detection. Microbial degradation was studied by incubating sediments with radioactive PAH and measuring subsequent production of ¹⁴C0₂. Concentrations of the four PAH decreased significantly with time in fine and medium sized sands. PAH levels also decreased in marsh sediment but trends were not significant (P < 0.05). C. capitata stimulated PAH degradation. Microbial degradation was more rapid in upper surfaces than in lower layers of the sediments.     

Incorporating LASSO effects into a mixed model for quantitative trait loci detection

The identification of quantitative trait loci (QTL) can be viewed as a subset selection problem. In a simulation study the least absolute selection and shrinkage operator (LASSO) is shown to be a useful and powerful tool for QTL identification. LASSO effects are embedded into a mixed model allowing simultaneous modeling of genetic and experimental effects. This provides the flexibility to model the experiment in conjunction with the power of LASSO QTL identification. Estimation is performed using an approximation to the restricted likelihood and modified Gaussian elimination. The extended mixed model is used to analyze a cattle gene mapping dataset.