Genotype by environment interactions for Pinus radiata in New South Wales, Australia

Historical data from 26 progeny trials in the NSW breeding program was analyzed to determine the extent and practical importance of genotype by environment (G×E) interactions for a range of traits. Significant G×E interaction was present for diameter (DBH) with 75% of the 35 estimated between-site genetic correlations falling below the threshold value of 0.6 where regionalization should be considered. Estimated genetic correlations for stem straightness, branch quality, and outerwood density were much higher, indicating these traits are not as affected by G×E. Levels of G×E for DBH are sufficient to have serious impacts on the expression of genetic gain in deployed material. For DBH, altitude differences between sites appear to be the key factor driving the G×E with a difference of greater than 280 m in altitude leading to a breakdown in correlations. Two groups of sites were identified as having limited G×E within each group: one for sites above 900 m elevation plus a lower-altitude group. Sites included in the higher-altitude group were located across the entire north–south geographic range of NSW. Equations for prediction of site mean DBH indicate that altitude, prior land use, and underlying geology are key driving variables. A more complex model was developed for predicting the between-site genetic correlations for DBH with the model accounting for approximately 50% of the observed variation.     

Targeted control of widespread exotic species for biodiversity conservation: The Red Fox (Vulpes vulpes) in New South Wales, Australia

Summary   Widespread exotic species provide one of the greatest challenges to biodiversity conservation because they often have devastating impacts on native biota but are near impossible to eradicate. The Red Fox ( Vulpes vulpes ) is established across most of mainland Australia, where it has been linked to severe declines and extinctions of a broad suite of native fauna. A targeted approach to reducing the impacts of Foxes on biodiversity was instigated in New South Wales in 2001 under the New South Wales Fox Threat Abatement Plan. It is based on three simple steps. First, explicit priorities for Fox control are established by identifying which native species are at greatest risk from Fox predation and at which sites Fox control for these species is most critical. Second, high-frequency broad-area Fox-control programmes are established across all land tenures at these priority sites. Third, monitoring programmes are established to measure the response of targeted native fauna and Foxes to Fox control. Monitoring helps refine the priorities for control and the methods used over time. This approach provides a model for the strategic control of widespread exotic pests which threaten biodiversity.     

Multilocus sequence analysis (MLSA) of ‘Rickettsiella costelytrae' and ‘Rickettsiella pyronotae’, intracellular bacterial entomopathogens from New Zealand

Aims

Larvae of scarab beetles live in the soil and are frequently hosts for microbial pathogens. In New Zealand, larvae of the grass grub, Costelytrae zealandica (Coleoptera: Scarabaeidae), and manuka beetles, Pyronota spp. (Coleoptera: Scarabaeidae), have been collected from field populations showing loss of vigour and a whitened appearance. Diagnosis indicated an intracellular infection of fat body tissues by Rickettsiella‐like micro‐organisms. Rickettsiella bacteria are under evaluation as a possible new source of insect bio‐control agents for important agricultural pests as, e.g. scarabaeid and elaterid larvae. The present study aimed at the unequivocal molecular taxonomic identification and comparison of the bacteria associated with Costelytra and Pyronota.

Methods and Results

Electron microscopy and phylogenetic reconstruction using a multilocus sequence analysis approach based on the 16S ribosomal RNA gene together with four protein‐encoding markers (ftsY, gidA, rpsA, and sucB) demonstrated that both bacteria from New Zealand are phylogenetically closely related, but not identical, and belong to the taxonomic genus Rickettsiella.

Conclusions

The bacteria under study should be referred to as pathotypes ‘Rickettsiella costelytrae’ and ‘Rickettsiella pyronotae’, respectively. Moreover, on the basis of the currently accepted systematic organization of the genus Rickettsiella, both pathotypes should be considered synonyms of the nomenclatural type species, Rickettsiella popilliae.

Significance and Impact of the Study

The study demonstrates that Rickettsiella bacteria are geographically widespread pathogens of scarabaeid larvae. Implications of the phylogenetic findings presented for the stability of host adaptation by Rickettsiella bacteria are critically discussed.     

Identifying spatial components of ecological and evolutionary processes for regional conservation planning in the Cape Floristic Region, South Africa

Abstract. Conservation seeks ultimately to protect and maintain biodiversity indefinitely. Most biodiversity features targeted in past conservation planning have been largely aspects of ecological and biogeographical pattern rather than process. However, the persistence of biodiversity can only be ensured through consideration of the ecological and evolutionary processes that underpin biodiversity, as well as its present spatial pattern. This paper identifies spatial surrogates of ecological and evolutionary processes for regional conservation planning in one of the world's biodiversity hotspots, the Cape Floristic Region. We identified six types of spatial components (namely edaphic interfaces, upland–lowland interfaces, sand movement corridors, riverine corridors, upland–lowland gradients and macroclimatic gradients) as surrogates for key processes such as ecological and geographical diversification, and species migration. Spatial components were identified in a GIS using published data and expert knowledge. Options for achieving targets for process components have been seriously compromised by habitat transformation. Between 30 and 75% of the original extent of the spatial components currently remain functional. Options for achieving upland–lowland and macroclimatic gradients are very limited in the lowlands where most of the habitat has been transformed by agriculture. We recommend that future studies place their research on ecological and evolutionary processes in a spatially explicit framework. Areas maintaining adaptive diversification (e.g. environmental gradients, ecotones) or containing historically isolated populations should be identified and protected. The spatial dimensions of eco-logical processes such as drought and fire refugia also need to be determined and such insights incorporated in conservation planning. Finally, connectivity within these areas should be ensured to maintain species migration and gene flow.     

Changes in prostate cancer incidence,mortality and survival in relation to prostate specific antigen testing in New South Wales,Australia

BackgroundTo examine changes in prostate cancer incidence and mortality rates, and 5-year relative survival, in relation to changes in the rate of prostate specific antigen (PSA) screening tests and the use of radical prostatectomy (RP) in the Australian population.MethodsProstate cancer stage-specific incidence rates, 5-year relative survival and mortality rates were estimated using New South Wales Cancer Registry data. PSA screening test rates and RP/Incidence ratios were estimated from Medicare Benefits Schedule claims data. We used multiple imputation to impute stage for cases with “unknown” stage at diagnosis. Annual percentage changes (APC) in rates were estimated using Joinpoint regression.ResultsTrends in the age-standardized incidence rates for localized disease largely mirrored the trends in PSA screening test rates, with a substantial ‘spike’ in the rates occurring in 1994, followed by a second ‘spike’ in 2008, and then a significant decrease from 2008 to 2015 (APC −6.7, 95% CI −8.2, −5.1). Increasing trends in incidence rates were observed for regional stage from the early 2000s, while decreasing or stable trends were observed for distant stage since 1993. The overall RP/Incidence ratio increased from 1998 to 2003 (APC 9.6, 95% CI 3.8, 15.6), then remained relatively stable to 2015. The overall 5-year relative survival for prostate cancer increased from 58.4% (95% CI: 55.0–61.7%) in 1981–1985 to 91.3% (95% CI: 90.5–92.1%) in 2011–2015. Prostate cancer mortality rates decreased from 1990 onwards (1990–2006: APC −1.7, 95% CI −2.1, −1.2; 2006–2017: APC −3.8, 95% CI −4.4, −3.1).ConclusionsOverall, there was a decrease in the incidence rate of localized prostate cancer after 2008, an increase in survival over time and a decrease in the mortality rate since the 1990s. This seems to indicate that the more conservative use of PSA screening tests in clinical practice since 2008 has not had a negative impact on population-wide prostate cancer outcomes.     

Models for predicting enteric methane emissions from dairy cows in North America,Europe, and Australia and New Zealand

There are several models in the literature for predicting enteric methane (CH₄) emissions. These models were often developed on region or country‐specific data and may not be able to predict the emissions successfully in every region. The majority of extant models require dry matter intake (DMI) of individual animals, which is not routinely measured. The objectives of this study were to (i) evaluate performance of extant models in predicting enteric CH₄ emissions from dairy cows in North America (NA), Europe (EU), and Australia and New Zealand (AUNZ) and (ii) explore the performance using estimated DMI. Forty extant models were challenged on 55, 105, and 52 enteric CH₄ measurements (g per lactating cow per day) from NA, EU, and AUNZ, respectively. The models were ranked using root mean square prediction error as a percentage of the average observed value (RMSPE) and concordance correlation coefficient (CCC). A modified model of Nielsen et al. (Acta Agriculturae Scand Section A, 63 , 2013 and 126) using DMI, and dietary digestible neutral detergent fiber and fatty acid contents as predictor variables, were ranked highest in NA (RMSPE = 13.1% and CCC = 0.78). The gross energy intake‐based model of Yan et al. (Livestock Production Science, 64 , 2000 and 253) and the updated IPCC Tier 2 model were ranked highest in EU (RMSPE = 11.0% and CCC = 0.66) and AUNZ (RMSPE = 15.6% and CCC = 0.75), respectively. DMI of cows in NA and EU was estimated satisfactorily with body weight and fat‐corrected milk yield data (RMSPE < 12.0% and CCC > 0.60). Using estimated DMI, the Nielsen et al. (2013) (RMSPE = 12.7 and CCC = 0.79) and Yan et al. (2000) (RMSPE = 13.7 and CCC = 0.50) models still predicted emissions in respective regions well. Enteric CH₄ emissions from dairy cows can be predicted successfully (i.e., RMSPE < 15%), if DMI can be estimated with reasonable accuracy (i.e., RMSPE < 10%).     

Species richness–environment relationships within coastal sclerophyll and mesophyll vegetation in Ku‐ring‐gai Chase National Park,New South Wales,Australia

Abstract Patterns in species richness from a wide range of plant communities in Ku‐ring‐gai Chase National Park, New South Wales, Australia, were examined in relation to a number of environmental variables, including soil physical and chemical characteristics. Total species richness and richness of three growth‐form types (trees, shrubs and ground cover) were determined in duplicate 500‐m² quadrats from 50 sites on two geological substrata: Hawkesbury Sandstone and Narrabeen shales and sandstones. Generalized linear models (GLM) were used to determine the amount of variation in species richness that could be significantly explained by the measured environmental variables. Seventy‐three per cent of the variation in total species richness was explained by a combination of soil physical and chemical variables and site attributes. The environmental variables explained 24% of the variation in tree species richness, 67% of the variation in shrub species richness and 62% of the variation in ground cover species richness. These results generally support the hypothesis of an environmental influence on patterns in total species richness and richness of shrubs and ground cover species. However, tree species richness was not adequately predicted by any of the measured environmental variables; the present environment exerts little influence on the richness of this growth‐form type. Historical factors, such as fire or climatic/environmental conditions at time of germination or seedling establishment, may be important in determining patterns in tree species richness at the local scale.     

Plant/pathogen interactions observed during host range testing of the rust fungus Uromyces pencanus,a classical biological control agent for Chilean needle grass (Nassella neesiana) in Australia and New Zealand

Nassella neesiana (Chilean needle grass) is a South American grass species that is a serious weed in Australia and New Zealand. The rust fungus Uromyces pencanus is a promising biocontrol agent that could be used to control the weed in both countries. Extensive host range testing has been conducted to explore the specificity of the rust. In this paper we discuss the different degrees of invasion by the rust of the tissues of target and non-target species; the plant defences elicited by such invasion at the cellular level; and their relevance to the biological control of Chilean needle grass.     

Colorectal cancer and country of birth in New South Wales,Australia: All-of-population data for prioritising health service delivery and research

IntroductionCancer care and outcomes differ across cultural groups in Australia. Quantifying these differences facilitates prioritisation and targeting of services and research. All-of-population data are needed by health agencies to understand and fulfil their cancer-control responsibilities. Compiling these data can be challenging while maintaining privacy. We have used data linkage to gain population-wide colorectal cancer data on stage (degree of spread), treatment, and survival in New South Wales (NSW), Australia, by country of birth (COB), and consider service implications.MethodsWe studied colon and rectal cancers diagnosed in 2003–2016 and recorded on the NSW Cancer Registry (n = 41,575), plus linked hospital data and data from Australian Medical and Pharmaceutical Benefits payments, other treatment data and death records. Outcomes for 12 COB categories were analysed using multiple logistic and proportional hazards regression, with Australia as the reference category.ResultsCompared with Australian born, the adjusted odds ratio for distant spread of colon cancer was higher for people born in Lebanon and the United Kingdom. Treatment was less common for people born in China (surgery), Germany (systemic), Italy (surgery), New Zealand (any treatment) and Vietnam (all treatments), while treatment for rectal cancer was more common for people born in Italy (surgery), United Kingdom (radiotherapy, systemic therapy), and Vietnam (surgery), and less frequent for people born in China (radiotherapy). Adjusted 5-year survival was higher for people born in China, Italy, Vietnam, Greece (colon), Lebanon (colon) and other non-English speaking countries. More advanced stage was negatively related to having surgery and survival.ConclusionsThis study illustrates how linked data can enable comparisons of multiple outcomes for colorectal cancer by country of birth across an entire population. Results disclose “big picture” variations in population characteristics, stage, treatment and survival. This will enable better targeting and prioritisation of services and inform research priorities to address disparities.     

In Situ Fe and S isotope analyses in pyrite from the 3.2 Ga Mendon Formation (Barberton Greenstone Belt,South Africa): Evidence for early microbial iron reduction

On the basis of phylogenetic studies and laboratory cultures, it has been proposed that the ability of microbes to metabolize iron has emerged prior to the Archaea/Bacteria split. However, no unambiguous geochemical data supporting this claim have been put forward in rocks older than 2.7–2.5 giga years (Gyr). In the present work, we report in situ Fe and S isotope composition of pyrite from 3.28‐ to 3.26‐Gyr‐old cherts from the upper Mendon Formation, South Africa. We identified three populations of microscopic pyrites showing a wide range of Fe isotope compositions, which cluster around two δ⁵⁶Fe values of ?1.8‰ and +1‰. These three pyrite groups can also be distinguished based on the pyrite crystallinity and the S isotope mass‐independent signatures. One pyrite group displays poorly crystallized pyrite minerals with positive Δ³³S values > +3‰, while the other groups display more variable and closer to 0‰ Δ³³S values with recrystallized pyrite rims. It is worth to note that all the pyrite groups display positive Δ³³S values in the pyrite core and similar trace element compositions. We therefore suggest that two of the pyrite groups have experienced late fluid circulations that have led to partial recrystallization and dilution of S isotope mass‐independent signature but not modification of the Fe isotope record. Considering the mineralogy and geochemistry of the pyrites and associated organic material, we conclude that this iron isotope systematic derives from microbial respiration of iron oxides during early diagenesis. Our data extend the geological record of dissimilatory iron reduction (DIR) back more than 560 million years (Myr) and confirm that micro‐organisms closely related to the last common ancestor had the ability to reduce Fe(III).