Local Scale Comparisons of Biodiversity as a Test for Global Protected Area Ecological Performance: A Meta-Analysis

Terrestrial protected areas (PAs) are cornerstones of global biodiversity conservation. Their efficacy in terms of maintaining biodiversity is, however, much debated. Studies to date have been unable to provide a general answer as to PA conservation efficacy because of their typically restricted geographic and/or taxonomic focus, or qualitative approaches focusing on proxies for biodiversity, such as deforestation. Given the rarity of historical data to enable comparisons of biodiversity before/after PA establishment, many smaller scale studies over the past 30 years have directly compared biodiversity inside PAs to that of surrounding areas, which provides one measure of PA ecological performance. Here we use a meta-analysis of such studies (N = 86) to test if PAs contain higher biodiversity values than surrounding areas, and so assess their contribution to determining PA efficacy. We find that PAs generally have higher abundances of individual species, higher assemblage abundances, and higher species richness values compared with alternative land uses. Local scale studies in combination thus show that PAs retain more biodiversity than alternative land use areas. Nonetheless, much variation is present in the effect sizes, which underscores the context-specificity of PA efficacy.     

Contingent absences account for range limits but not the local abundance structure of an invasive springtail

Understanding spatial variation in abundance is essential for forecasts of responses to environmental change impacts on diversity and the consequent conservation actions. However, few studies have sought to distinguish the causal basis of abundance structure and range limits. Here we do so for an invasive springtail species, Pogonognathellus flavescens, in a cold temperate island setting. Local microclimate variables and physiological tolerances of this habitat generalist suggest that it should be widely distributed across a range of habitats below 200 m elevation on the island. By contrast, island‐wide and local abundance surveys show that it is restricted to indigenous Poa cookii tussock grassland habitats in the southeast. Preference for this habitat is correlated with the presence of vertebrates and a threshold response to soil Ca and pH, with preference for low values of both. Habitat specificity may be the consequence of a founder effect because the species is characterized by only a single mitochondrial COI haplotype. Nonetheless, P. flavescens is absent from many other areas of suitable P. cookii habitat around the island. The most plausible explanation appears to be dispersal limitation (i.e. a contingent absence). Despite high locomotion speeds measured in the laboratory at optimum and mean annual soil temperatures (0.97 and 0.42 cm s^?1 at 26°C and 6.5°C, respectively), dispersal in the field indicated that >100 yr would be required to reach all available habitat in the absence of jump dispersal, for which few vectors exist. Thus, current range limits are set by dispersal limitation (i.e. contingent absences) whilst abundance structure is a function of variation in soil substrate quality. Edaphic variables both in this species and other soil invertebrates may be more significant than climatic factors in determining abundance and occurrence, indicating that they should be routinely included in species distribution models. Low genetic diversity and high habitat preference suggest that in the absence of introduction of additional individuals, the species will not spread rapidly at the island. However, over time, the widening distribution of its preferred habitat, P. cookii, as a consequence of a major management intervention (the eradication of feral cats), may enable it to colonize all suitable areas.     

Updated list of Collembola species currently recorded from South Africa

Understanding the abundance and richness of species is one of the most fundamental steps in effecting their conservation. Despite global recognition of the significance of the below-ground component of diversity for ecosystem functioning, the soil remains a poorly studied terrestrial ecosystem. In South Africa, knowledge is increasing for a variety of soil faunal groups, but many still remain poorly understood. We have started to address this gap in the knowledge of South African soil biodiversity by focusing on the Collembola in an integrated project that encompasses systematics, barcoding and ecological assessments. Here we provide an updated list of the Collembola species from South Africa. A total of 124 species from 61 genera and 17 families has been recorded, of which 75 are considered endemic, 24 widespread, and 25 introduced. This total number of species excludes the 36 species we consider to be dubious. From the published data, Collembola species richness is high compared to other African countries, but low compared to European countries. This is largely a consequence of poor sampling in the African region, as our discovery of many new species in South Africa demonstrates. Our analyses also show that much ongoing work will be required before a reasonably comprehensive and spatially explicit picture of South Africa’s springtail fauna can be provided, which may well exceed 1000 species. Such work will be necessary to help South Africa meet its commitments to biodiversity conservation, especially in the context of the 2020 Aichi targets of the Convention on Biological Diversity.     

Association of 25-Hydroxyvitamin D status and genetic variation in the vitamin D metabolic pathway with FEV1 in the Framingham Heart Study

Background

Vitamin D is associated with lung function in cross-sectional studies, and vitamin D inadequacy is hypothesized to play a role in the pathogenesis of chronic obstructive pulmonary disease. Further data are needed to clarify the relation between vitamin D status, genetic variation in vitamin D metabolic genes, and cross-sectional and longitudinal changes in lung function in healthy adults.

Methods

We estimated the association between serum 25-hydroxyvitamin D [25(OH)D] and cross-sectional forced expiratory volume in the first second (FEV₁) in Framingham Heart Study (FHS) Offspring and Third Generation participants and the association between serum 25(OH)D and longitudinal change in FEV₁ in Third Generation participants using linear mixed-effects models. Using a gene-based approach, we investigated the association between 241 SNPs in 6 select vitamin D metabolic genes in relation to longitudinal change in FEV₁ in Offspring participants and pursued replication of these findings in a meta-analyzed set of 4 independent cohorts.

Results

We found a positive cross-sectional association between 25(OH)D and FEV₁ in FHS Offspring and Third Generation participants (P = 0.004). There was little or no association between 25(OH)D and longitudinal change in FEV₁ in Third Generation participants (P = 0.97). In Offspring participants, the CYP2R1 gene, hypothesized to influence usual serum 25(OH)D status, was associated with longitudinal change in FEV₁ (gene-based P < 0.05). The most significantly associated SNP from CYP2R1 had a consistent direction of association with FEV₁ in the meta-analyzed set of replication cohorts, but the association did not reach statistical significance thresholds (P = 0.09).

Conclusions

Serum 25(OH)D status was associated with cross-sectional FEV₁, but not longitudinal change in FEV₁. The inconsistent associations may be driven by differences in the groups studied. CYP2R1 demonstrated a gene-based association with longitudinal change in FEV₁ and is a promising candidate gene for further studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0238-y) contains supplementary material, which is available to authorized users.     

Reconsidering connectivity in the sub‐Antarctic

Extreme and remote environments provide useful settings to test ideas about the ecological and evolutionary drivers of biological diversity. In the sub‐Antarctic, isolation by geographic, geological and glaciological processes has long been thought to underpin patterns in the region's terrestrial and marine diversity. Molecular studies using increasingly high‐resolution data are, however, challenging this perspective, demonstrating that many taxa disperse among distant sub‐Antarctic landmasses. Here, we reconsider connectivity in the sub‐Antarctic region, identifying which taxa are relatively isolated, which are well connected, and the scales across which this connectivity occurs in both terrestrial and marine systems. Although many organisms show evidence of occasional long‐distance, trans‐oceanic dispersal, these events are often insufficient to maintain gene flow across the region. Species that do show evidence of connectivity across large distances include both active dispersers and more sedentary species. Overall, connectivity patterns in the sub‐Antarctic at intra‐ and inter‐island scales are highly complex, influenced by life‐history traits and local dynamics such as relative dispersal capacity and propagule pressure, natal philopatry, feeding associations, the extent of human exploitation, past climate cycles, contemporary climate, and physical barriers to movement. An increasing use of molecular data – particularly genomic data sets that can reveal fine‐scale patterns – and more effective international collaboration and communication that facilitates integration of data from across the sub‐Antarctic, are providing fresh insights into the processes driving patterns of diversity in the region. These insights offer a platform for assessing the ways in which changing dispersal mechanisms, such as through increasing human activity and changes to wind and ocean circulation, may alter sub‐Antarctic biodiversity patterns in the future.     

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer

DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.     

Physiological tolerances account for range limits and abundance structure in an invasive slug

Despite the importance of understanding the mechanisms underlying range limits and abundance structure, few studies have sought to do so. Here we use a terrestrial slug species, Deroceras panormitanum, that has invaded a remote, largely predator-free, Southern Ocean island as a model system to do so. Across Marion Island, slug density does not conform to an abundant centre distribution. Rather, abundance structure is characterized by patches and gaps. These are associated with this desiccation-sensitive species'' preference for biotic and drainage line habitats that share few characteristics except for their high humidity below the vegetation surface. The coastal range margin has a threshold form, rapidly rising from zero to high density. Slugs do not occur where soil-exchangeable Na values are higher than 3000 mg kg⁻¹, and in laboratory experiments, survival is high below this value but negligible above it. Upper elevation range margins are a function of the inability of this species to survive temperatures below an absolute limit of −6.4°C, which is regularly exceeded at 200 m altitude, above which slug density declines to zero. However, the linear decline in density from the coastal peak is probably also a function of a decline in performance or time available for activity. This is probably associated with an altitudinal decline in mean annual soil temperature. These findings support previous predictions made regarding the form of density change when substrate or climatic factors set range limits.