Syrett P.,Landcare Research |
Forrester G.J.,Landcare Research |
Harman H.M.,MAF |
Meurk C.D.,Landcare Research |
And 2 more authors.
BioControl | Year: 2012
To test the theory that successful biocontrol of invasive hawkweeds (Pilosella and Hieracium spp.) would increase bare ground and accelerate erosion, small areas of hawkweed were suppressed with herbicide in a nine-year study. An increase in bare ground resulting from the treatments was maintained throughout. No new invasive species were recorded, and apart from a temporary increase in a perennial grass, no existing exotic species moved into the gaps created. Indigenous plants did not respond either, although at one site where mat plants were prevalent, treatments slowed their decline. As recovery of existing vegetation was minimal, it is likely that invasion of hawkweed is a consequence of degradation rather than the reverse, and if biocontrol is successful, degraded grasslands may suffer further damage, especially in areas that are grazed. The effect may be ameliorated since biocontrol agents are predicted to perform less well under conditions of low fertility and low moisture. Our results emphasize the importance of pre-release ecological studies to clarify the role of invasive plants proposed for biocontrol. © 2011 International Organization for Biological Control (IOBC). Source
Lienhard P.,CIRAD - Agricultural Research for Development |
Panyasiri K.,NAFRI |
Sayphoummie S.,MAF |
Leudphanane B.,MAF |
And 3 more authors.
International Journal of Agricultural Sustainability | Year: 2013
In north-eastern Laos, the savannah grasslands of the Plain of Jars cover vast areas of potentially cultivable land. However, soil acidity, low inherent fertility, and the absence of alternatives to tillage represent significant constraints to the development of sustainable smallholder agriculture. Our objective was to evaluate the potential for conservation agriculture (CA) to enhance soil productivity and farming system profitability. A three-year rotation of rice/maize/soybean was tested under three fertilization levels and four agricultural systems: one conventional tillage-based (CT) system and three CA systems based on no-tillage with cover crops. After four cropping seasons, our results show that, compared with CT, CA systems led to similar-to-higher grain production, similar-to-higher profits, higher opportunity of livestock system intensification, and higher labour productivity regardless of fertilization levels. While CA represents a relevant alternative to current practices, our results suggest that its contribution to the emergence of a sustainable smallholder agriculture is conditioned by broader institutional transformations, including the enrolment of local manufacturers and traders for deploying no-till implements and seed market channels for cover crops, long-term public support to maintain active research and technical mentoring to farmers, and possibly the integration of ecosystem services in agricultural policy. © 2013 Copyright Taylor and Francis Group, LLC. Source
Deleterious variants are expected to have lower allele frequencies than neutral ones, due to negative selection. This theoretical property has been demonstrated previously in human population sequencing data12, 13 and here (Fig. 1d, e). This allows inference of the degree of selection against specific functional classes of variation. However, mutational recurrence as described earlier indicates that allele frequencies observed in ExAC-scale samples are also skewed by mutation rate, with more mutable sites less likely to be singletons (Fig. 2c and Extended Data Fig. 1d). Mutation rate is in turn non-uniformly distributed across functional classes. For example, variants that result in the loss of a stop codon can never occur at CpG dinucleotides (Extended Data Fig. 1e). We corrected for mutation rates (Supplementary Information section 3.2) by creating a mutability-adjusted proportion singleton (MAPS) metric. This metric reflects (as expected), strong selection against predicted PTVs, as well as missense variants predicted by conservation-based methods to be deleterious (Fig. 2e). The deep ascertainment of rare variation in ExAC also allows us to infer the extent of selection against variant categories on a per-gene basis by examining the proportion of variation that is missing compared to expectations under random mutation. Conceptually similar approaches have been applied to smaller exome data sets11, 14, but have been underpowered, particularly when analysing the depletion of PTVs. We compared the observed number of rare (minor allele frequency (MAF) <0.1%) variants per gene to an expected number derived from a selection neutral, sequence-context based mutational model11. The model performs well in predicting the number of synonymous variants, which should be under minimal selection, per gene (r = 0.98; Extended Data Fig. 3b). We quantified deviation from expectation with a Z score11, which for synonymous variants is centred at zero, but is significantly shifted towards higher values (greater constraint) for both missense and PTV (Wilcoxon P < 10−50 for both; Fig. 3a). The genes on the X chromosome are significantly more constrained than those on the autosomes for missense (P < 10−7) and loss-of-function mutations (P < 10−50), in line with previous work15. The high correlation between the observed and expected number of synonymous variants on the X chromosome (r = 0.97 versus 0.98 for autosomes) indicates that this difference in constraint is not due to a calibration issue. To reduce confounding by coding sequence length for PTVs, we developed an expectation-maximization algorithm (Supplementary Information section 4.4) using the observed and expected PTV counts within each gene to separate genes into three categories: null (observed ≈ expected), recessive (observed ≤ 50% of expected), and haploinsufficient (observed <10% of expected). This metric—the probability of being loss-of-function (LoF) intolerant (pLI)—separates genes of sufficient length into LoF intolerant (pLI ≥ 0.9, n = 3,230) or LoF tolerant (pLI ≤ 0.1, n = 10,374) categories. pLI is less correlated with coding sequence length (r = 0.17 as compared to 0.57 for the PTV Z score), outperforms the PTV Z score as an intolerance metric (Supplementary Table 15), and reveals the expected contrast between gene lists (Fig. 3b). pLI is positively correlated with the number of physical interaction partners of a gene product (P < 10−41). The most constrained pathways (highest median pLI for the genes in the pathway) are core biological processes (spliceosome, ribosome, and proteasome components; Kolmogorov–Smirnov test P < 10−6 for all), whereas olfactory receptors are among the least constrained pathways (Kolmogorov–Smirnov test P < 10−16), as demonstrated in Fig. 3b, and this is consistent with previous work5, 16, 17, 18, 19. Crucially, we note that LoF-intolerant genes include virtually all known severe haploinsufficient human disease genes (Fig. 3b), but that 72% of LoF-intolerant genes have not yet been assigned a human disease phenotype despite clear evidence for extreme selective constraint (Supplementary Table 13). We note that this extreme constraint does not necessarily reflect a lethal disease or status as a disease gene (for example, BRCA1 has a pLI of 0), but probably points to genes in which heterozygous loss of function confers some non-trivial survival or reproductive disadvantage. The most highly constrained missense (top 25% missense Z scores) and PTV (pLI ≥ 0.9) genes show higher expression levels and broader tissue expression than the least constrained genes20 (Fig. 3c). These most highly constrained genes are also depleted for expression quantitative trait loci (eQTLs) (P < 10−9 for missense and PTV; Fig. 3d), yet are enriched within genome-wide significant trait-associated loci (χ2 test, P < 10−14, Fig. 3e). Genes intolerant of PTV variation would be expected to be dosage-sensitive, as in such genes natural selection does not tolerate a 50% deficit in expression due to the loss of single allele. It is thus unsurprising that these genes are also depleted of common genetic variants that have a large enough effect on expression to be detected as eQTLs with current limited sample sizes. However, smaller changes in the expression of these genes, through weaker eQTLs or functional variants, are more likely to contribute to medically relevant phenotypes. Finally, we investigated how these constraint metrics would stratify mutational classes according to their frequency spectrum, corrected for mutability as in the previous section (Fig. 3f). The effect was most dramatic when considering nonsense variants in the LoF-intolerant set of genes. For missense variants, the missense Z score offers information orthogonal to Polyphen2 and CADD classifications, which are measures predicting the likely deleteriousness of variants, indicating that gene-level measures of constraint offer additional information to variant-level metrics in assessing potential pathogenicity.