Systematics within Gyps vultures: a clade at risk

Background  

Populations of the Oriental White-backed Vulture (Gyps bengalensis) have declined by over 95% within the past decade. This decline is largely due to incidental consumption of the non-steroidal anti-inflammatory veterinary pharmaceutical diclofenac, commonly used to treat domestic livestock. The conservation status of other Gyps vultures in southern Asia is also of immediate concern, given the lack of knowledge regarding status of their populations and the continuing existence of taxonomic uncertainties. In this study, we assess phylogenetic relationships for all recognized species and the majority of subspecies within the genus Gyps. The continuing veterinary use of diclofenac is an unknown but potential risk to related species with similar feeding habits to Gyps bengalensis. Therefore, an accurate assessment of the phylogenetic relationships among Gyps vultures should aid in their conservation by clarifying taxonomic uncertainties, and enabling inference of their respective relatedness to susceptible G. bengalensis.     

Influence of Nutrient Availability on the Interaction Between Spotted Knapweed and Bluebunch Wheatgrass

Centaurea maculosa (Lam.) (spotted knapweed) reduces wildlife and livestock habitat biodiversity and increases erosion. Nutrient availability to plants may be used to accelerate succession away from spotted knapweed. Early‐successional plant communities often have high nutrient availability, whereas late‐successional communities are often found on lower nutrient soils. We hypothesized that removal of nutrients would change the competitive advantage from spotted knapweed to Pseudoroegneria spicatum (bluebunch wheatgrass) (late seral). In two addition series matrices, background densities of Secale cereale (annual rye) and Elymus elimoides (bottlebrush squirreltail) (3,000 seeds/m²) were used to remove nutrients from the soil. In another set of addition series matrices, nitrogen (33 kg/ha) or phosphorus (33 kg/ha) were added to the soil. Nutrient analysis of soil and vegetation indicated that annual rye and bottlebrush squirreltail reduced nutrient availability in soils. In another matrix, neither a background density nor nutrients were added. Data were fit into Watkinson's curvilinear model to determine the competitive relationship between bluebunch wheatgrass and spotted knapweed. This allowed comparison of the equivalence ratios (C) generated from each addition series. The C parameters are the per‐plant equivalent of bluebunch wheatgrass or spotted knapweed and can be interpreted as the ratio of intra‐to‐interspecific competition. The C parameters are also the equivalence ratio of the number of spotted knapweed it takes to have equivalent effect on bluebunch wheatgrass or the number of bluebunch wheatgrass having the equivalent effect on spotted knapweed. Without nutrient manipulation, spotted knapweed was more competitive than bluebunch wheatgrass. The C for bluebunch wheatgrass was 0.17, indicating that 0.17 knapweed plants were competitively equivalent to one wheatgrass. Annual rye changed the competitive balance in favor of bluebunch wheatgrass (C = 9.9). Addition of nitrogen, phosphorus, or the mid‐seral species did not change the competitive relationship between the two species. This preliminary study suggests that succession from spotted knapweed to late‐seral bluebunch wheatgrass community may be accelerated by altering resource availability.     

Plant litter effects on soil nutrient availability and vegetation dynamics: changes that occur when annual grasses invade shrub-steppe communities

Changes in the quantity and quality of plant litter occur in many ecosystems as they are invaded by exotic species, which impact soil nutrient cycling and plant community composition. Such changes in sagebrush-steppe communities are occurring with invasion of annual grasses (AG) into a perennial grass (PG) dominated system. We conducted a 5-year litter manipulation study located in the northern Great Basin, USA. Springtime litter was partially or completely removed in three communities with differing levels of invasion (invaded, mixed, and native) to determine how litter removal and litter biomass affected plant-available soil N and plant community composition. Litter biomass (prior to the removal treatment) was negatively correlated with plant-available N in the invaded community, but was positively correlated in the native community. Plant-available N had greater intra- and inter-annual fluctuations in the invaded compared to the mixed or native communities, but was not generally affected by removal treatments. Litter removal had negative effects on AG cover during a warm/dry year and negative effects on PG cover during a cool/wet year in the mixed community. Overall, the effectiveness of springtime litter manipulations on plant-available N were limited and weather dependent, and only removal treatments >75 % had effects on the plant community. Our study demonstrates how communities invaded by AGs have significantly increased temporal variability in nutrient cycling, which may decrease ecosystem stability. Further, we found that the ecological impacts from litter manipulation on sagebrush communities were dependent on the extent of AG invasion, the timing of removal, and seasonal precipitation.     

Isocitrate dehydrogenase 1 R132C mutation occurs exclusively in microsatellite stable colorectal cancers with the CpG island methylator phenotype

The CpG Island Methylator Phenotype (CIMP) is fundamental to an important subset of colorectal cancer; however, its cause is unknown. CIMP is associated with microsatellite instability but is also found in BRAF mutant microsatellite stable cancers that are associated with poor prognosis. The isocitrate dehydrogenase 1 (IDH1) gene causes CIMP in glioma due to an activating mutation that produces the 2-hydroxyglutarate oncometabolite. We therefore examined IDH1 alteration as a potential cause of CIMP in colorectal cancer. The IDH1 mutational hotspot was screened in 86 CIMP-positive and 80 CIMP-negative cancers. The entire coding sequence was examined in 81 CIMP-positive colorectal cancers. Forty-seven cancers varying by CIMP-status and IDH1 mutation status were examined using Illumina 450K DNA methylation microarrays. The R132C IDH1 mutation was detected in 4/166 cancers. All IDH1 mutations were in CIMP cancers that were BRAF mutant and microsatellite stable (4/45, 8.9%). Unsupervised hierarchical cluster analysis identified an IDH1 mutation-like methylation signature in approximately half of the CIMP-positive cancers. IDH1 mutation appears to cause CIMP in a small proportion of BRAF mutant, microsatellite stable colorectal cancers. This study provides a precedent that a single gene mutation may cause CIMP in colorectal cancer, and that this will be associated with a specific epigenetic signature and clinicopathological features.     

Linking nitrogen partitioning and species abundance to invasion resistance in the Great Basin

Resource partitioning has been suggested as an important mechanism of invasion resistance. The relative importance of resource partitioning for invasion resistance, however, may depend on how species abundance is distributed in the plant community. This study had two objectives. First, we quantified the degree to which one resource, nitrogen (N), is partitioned by time, depth and chemical form among coexisting species from different functional groups by injecting ¹⁵N into soils around the study species three times during the growing season, at two soil depths and as two chemical forms. A watering treatment also was applied to evaluate the impact of soil water content on N partitioning. Second, we examined the degree to which native functional groups contributed to invasion resistance by seeding a non-native annual grass into plots where bunchgrasses, perennial forbs or annual forbs had been removed. Bunchgrasses and forbs differed in timing, depth and chemical form of N capture, and these patterns of N partitioning were not affected by soil water content. However, when we incorporated abundance (biomass) with these relative measures of N capture to determine N sequestration by the community there was no evidence suggesting that functional groups partitioned different soil N pools. Instead, dominant bunchgrasses acquired the most N from all soil N pools. Consistent with these findings we also found that bunchgrasses were the only functional group that inhibited annual grass establishment. At natural levels of species abundance, N partitioning may facilitate coexistence but may not necessarily contribute to N sequestration and invasion resistance by the plant community. This suggests that a general mechanism of invasion resistance may not be expected across systems. Instead, the key mechanism of invasion resistance within a system may depend on trait variation among coexisting species and on how species abundance is distributed in the system.     

Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals

alpha 1-Proteinase inhibitor (alpha 1-PI), a member of the serine proteinase inhibitor superfamily, has a primary role in controlling neutrophil elastase activity within the mammalian circulation. Several studies have indicated that the reactive center region of alpha 1-PI, the amino acid sequence of which is critical to recognition of and binding to target proteinases, is highly divergent within and among species. This appears to be a consequence of accelerated rates of evolution that may have been driven by positive Darwinian selection. In order to examine this and other features of alpha 1-PI evolution in more detail, we have isolated and sequenced cDNAs representing alpha 1- PI mRNAs of the mouse species Mus saxicola and Mus minutoides and have compared these with a number of other mammalian alpha 1-PI mRNAs. Relative to other mammalian mRNAs, the extent of nonsynonymous substitution is generally high throughout the alpha 1-PI mRNA molecule, indicating greater overall rates of amino acid substitution. Within and among mouse species, the 5'-half of the mRNA, but not the 3'-half, has been homogenized by concerted evolution. Finally, the reactive center is under diversifying or positive Darwinian selection in murid rodents (rats, mice) and guinea pigs yet is under purifying selection in primates and artiodactyls. The significance of these findings to alpha 1-PI function and the possible selective forces driving evolution of serpins in general are discussed.      

Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae

Arginine decarboxylase (ADC) is an important enzyme in the production of putrescine and polyamines in plants. It is encoded by a single or low-copy nuclear gene that lacks introns in sequences studied to date. The rate of Adc amino acid sequence evolution is similar to that of ndhF for the angiosperm family studied. Highly conserved regions provide several target sites for PCR priming and sequencing and aid in nucleotide and amino acid sequence alignment across a range of taxonomic levels, while a variable region provides an increased number of potentially informative characters relative to ndhF for the taxa surveyed. The utility of the Adc gene in plant molecular systematic studies is demonstrated by analysis of its partial nucleotide sequences obtained from 13 representatives of Brassicaceae and 3 outgroup taxa, 2 from the mustard oil clade (order Capparales) and 1 from the related order Malvales. Two copies of the Adc gene, Adc1 and Adc2, are found in all members of the Brassicaceae studied to data except the basal genus Aethionema. The resulting Adc gene tree provides robust phylogenetic data regarding relationships within the complex mustard family, as well as independent support for proposed tribal realignments based on other molecular data sets such as those from chloroplast DNA.