No abstract

BackgroundEpigenetic mechanisms provide an interface between environmental factors and the genome and are known to play a role in complex diseases such as obesity. These mechanisms, including DNA methylation, influence the regulation of development, differentiation and the establishment of cellular identity. Here we employ two approaches to identify differential methylation between two white adipose tissue depots in obese individuals before and after gastric bypass and significant weight loss. We analyse genome-wide DNA methylation data using (a) traditional paired t tests to identify significantly differentially methylated loci (Bonferroni-adjusted P ≤ 1 × 10−7) and (b) novel combinatorial algorithms to identify loci that differentiate between tissue types.ResultsSignificant differential methylation was observed for 3239 and 7722 CpG sites, including 784 and 1129 extended regions, between adipose tissue types before and after significant weight loss, respectively. The vast majority of these extended differentially methylated regions (702) were consistent across both time points and enriched for genes with a role in transcriptional regulation and/or development (e.g. homeobox genes). Other differentially methylated loci were only observed at one time point and thus potentially highlight genes important to adipose tissue dysfunction observed in obesity. Strong correlations (r > 0.75, P ≤ 0.001) were observed between changes in DNA methylation (subcutaneous adipose vs omentum) and changes in clinical trait, in particular for CpG sites within PITX2 and fasting glucose and four CpG sites within ISL2 and HDL. A single CpG site (cg00838040, ATP2C2) gave strong tissue separation, with validation in independent subcutaneous (n = 681) and omental (n = 33) adipose samples.ConclusionsThis is the first study to report a genome-wide DNA methylome comparison of subcutaneous abdominal and omental adipose before and after weight loss. The combinatorial approach we utilised is a powerful tool for the identification of methylation loci that strongly differentiate between these tissues. This study provides a solid basis for future research focused on the development of adipose tissue and its potential dysfunction in obesity, as well as the role DNA methylation plays in these processes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-017-0344-4) contains supplementary material, which is available to authorized users.

Seagrasses are in decline globally due to sustained pressure from coastal development, water quality declines and the ongoing threat from climate change. The result of this decline has been a change in coastal productivity, a reduction in critical fisheries habitat and increased erosion. Attempts to slow this decline have included legislative protection of habitat and direct restoration efforts. Monitoring the success of these approaches requires tracking changes in the abundance of seagrasses, but such monitoring is frequently conducted at either too coarse a spatial scale, or too infrequently to adequately detect changes within individual meadows. Here, we used high resolution aerial imagery to quantify the change in meadows dominated by Posidonia australis over five years at 14 sites in five estuaries in south-eastern Australia. Australia has some of the world's most diverse and extensive seagrass meadows, but the widely distributed P. australis has a slow growth rate, recovers poorly after disturbance, and suffers runaway attrition if the conditions for recovery are not met. In 2010, after declines of 12–57% between the 1940s and 1980s, P. australis was listed as a threatened ecological community in New South Wales. We quantified changes in area at fine spatial scales and, where loss was observed, describe the general patterns of temporal decline within each meadow. Our results demonstrate that seagrass meadows dominated by P. australis underwent declines of ~ 2–40% total area at 11 out of 14 study sites between 2009 and 2014. In the iconic Sydney Harbour, our analyses suggest that P. australis meadows are declining at an average rate greater than 10% yr-1, exceeding the global rate of seagrass decline. Highlighting these alarming declines across the study region should serve as means to prioritise management action and review the effectiveness of legislative listing as a method to limit impacts at an ecosystem level.

Network analysis provides a unified framework for investigating different types of species interactions at the community level. Network analysis is typically based on null models that test for specific patterns in network topology. Here we use a novel predictive approach to investigate the topology of a mistletoe-host network. It has been hypothesised that Australian mistletoes mimic the phenotype of their preferred hosts to avoid herbivory. We developed a deterministic model based on phenotypic similarity to predict the topology of a quantitative network between Lauranthaceaous mistletoes and their hosts. We quantified mistletoe-host interactions in a semi-arid woodland central Australia, along with the size, shape and colour of leaves produced by both players in the interaction. Traditional null model analyses showed support for negative co-occurrence patterns, web specialisation and strong links between species pairs. However, our deterministic model showed that the observed network topology could not be predicted by phenotypic similarity, suggesting that Australian mistletoes do not mimic their hosts.

Questions: Are liana–host interactions structured at the community level? Do liana–host interactions differ between species, growth form guilds or habitats? Location: Otari‐Wilton's Bush, on the southern tip of North Island, New Zealand. The forest contains 75 ha of mature and regenerating conifer–broadleaf forest. Methods: Nine liana species were quantified among 217 trees to test for negative co‐occurrence patterns. We also conducted additional analyses within and among compartments embedded in the community‐level matrix. Liana and host abundance distributions were assessed across two contrasting habitats. Results: Community‐level analyses revealed negative co‐occurrence patterns. Positive, neutral and negative co‐occurrence patterns were found among compartments within the community‐level matrix. Host species compartments were consistent with randomized expectations, while positive co‐occurrence patterns were found within the host species matrix. Negative co‐occurrence patterns were found inconsistently among lianas that share the same region of host space, and those that do not. Conclusions: Overall, results indicate the liana community is structured non‐randomly. Liana–host interactions appear to follow an opportunistic growth strategy and interactions are due mostly to habitat partitioning.

No abstract

1. Shifts in flowering phenology have been studied in detail in the northern hemisphere and are a key plant response to climate change. However, there are relatively fewer data on species' phenological shifts in the southern hemisphere.2. We combined historic field data, data from herbarium specimens dating back to 1842 and modern field data for 37 Australian species to determine whether species were flowering earlier in the year than they had in the past. We also combined our results with data compiled in the southern and northern hemispheres, respectively, to determine whether southern hemisphere species are showing fewer advances in flowering phenology through time.3. Across our study species, we found that 12 species had undergone significant shifts in flowering time, with four species advancing their flowering and eight species delaying their flowering. The remaining 25 species showed no significant shifts in their flowering phenology. These findings are important because delays or lack of shifts in flowering phenology can lead to mismatches in trophic interactions between plants and pollinators or seed dispersers, which can have substantial impacts on ecosystem functioning and primary productivity. Combining our field results with data compiled from the literature showed that only 58.5% of southern hemisphere species were advancing their flowering time, compared with 81.6% of species that were advancing their flowering time in the northern hemisphere. Our study provides further evidence that it is not adequate for ecologists to assume that southern hemisphere ecosystems will respond to future climate change in the same way as ecosystems north of the Equator.

Detecting the effects of water regime on wetland plant communities: Which plant indicator groups perform best?.Aquatic Botany http://dx.doi.org/10. 1016/j.aquabot.2015.02.002 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.