The spatial scaling of beta diversity

Beta diversity is an important concept used to describe turnover in species composition across a wide range of spatial and temporal scales, and it underpins much of conservation theory and practice. Although substantial progress has been made in the mathematical and terminological treatment of different measures of beta diversity, there has been little conceptual synthesis of potential scale dependence of beta diversity with increasing spatial grain and geographic extent of sampling. Here, we evaluate different conceptual approaches to the spatial scaling of beta diversity, interpreted from ‘fixed’ and ‘varying’ perspectives of spatial grain and extent. We argue that a ‘sliding window’ perspective, in which spatial grain and extent covary, is an informative way to conceptualize community differentiation across scales. This concept more realistically reflects the varying empirical approaches that researchers adopt in field sampling and the varying scales of landscape perception by different organisms. Scale dependence in beta diversity has broad implications for emerging fields in ecology and biogeography, such as the integration of fine‐resolution ecogenomic data with large‐scale macroecological studies, as well as for guiding appropriate management responses to threats to biodiversity operating at different spatial scales.     

Underwater acoustic behavior of bearded seals (Erignathus barbatus) in the northeastern Chukchi Sea, 2007–2010

Bearded seal (Erignathus barbatus) calls were recorded using autonomous passive acoustic recorders deployed in the northeastern Chukchi Sea between October 2007 and October 2010. Continuous acoustic data were acquired during summer (August to mid‐October), and overwinter data (mid‐October through July) were acquired on a duty cycle of 40/48 min every 4 h. We investigated the spatio‐temporal distribution and acoustic behavior of vocalizing bearded seals in this multiyear data set. Peaks in calling occurred in spring, coinciding with the mating period, and calls stopped abruptly in late June/early July. Fewer calls were detected in summer, and the vocal presence of seals increased with the formation of pack ice in winter. Vocal activity was higher at night than during the day, with a peak around 0400 (AKST). Monthly patterns in proportional use of each call type and call duration were examined for the first time. The proportion and duration of AL1(T) and AL2(T) call types increased during the mating period, suggesting that males advertise their breeding condition by producing those specific longer trills. The observed seasonal and diel trends were consistent between years. These results improve our understanding of occurrence and acoustic behavior of bearded seals across the northeastern Chukchi Sea.     

Restoration potential of threatened ecosystem engineers increases with aridity: broad scale effects on soil nutrients and function

Species extinctions alter ecosystem services, and the magnitude of this impact is likely to change across environmental gradients. In Australia, soil‐disturbing mammals that are now considered ecologically extinct are thought to be important ecosystem engineers. Previous studies have demonstrated microsite‐level impacts of reintroduced soil‐disturbing mammals on soil functions, but effects are yet to be tested across larger scales. Further, it is unclear how impacts vary across environmental gradients and if the restoration potential of reintroductions changes with climate. We examined the effects of soil‐disturbing mammal reintroductions across a large rainfall gradient in Australia to test the hypothesis that ecosystem engineering effects on soil function depend on climate. We compared soil labile carbon, available nitrogen and the activity of four enzymes associated with nutrient cycling in three microsite types with and without soil‐disturbing mammals in five sites along a large rainfall gradient (166–870 mm). Soil enzyme activity was greatest in the presence of soil‐disturbing mammals and increased with rainfall, but soil available carbon and nitrogen varied across the gradient and among microsites. Microsite effects were often stronger than any effects of soil‐disturbing mammals, with soil beneath vegetated patches (shrubs and trees) having greater enzyme activity, carbon and nitrogen than bare soils. However, soil‐disturbing mammals homogenised nutrient distributions across microsites. The impacts of soil‐disturbing mammals on soil function previously detected at micro‐scales was detected at a landscape‐scale. However, the overall effects of soil‐disturbing mammals on soil functions varied with productivity (rainfall). The context of soil‐disturbing mammal reintroductions is thus likely to be critical in determining their effectiveness in restoring soil function.     

Ixodid ticks feeding on humans in South Africa: with notes on preferred hosts,geographic distribution,seasonal occurrence and transmission of pathogens

This paper records the identities of 558 ixodid ticks feeding on 194 humans in South Africa. These ticks belonged to 20 species in six genera and those most frequently encountered were Amblyomma hebraeum, Haemaphysalis leachi, Hyalomma marginatum rufipes, Hyalomma truncatum, Rhipicephalus appendiculatus, Rhipicephalus gertrudae and Rhipicephalus simus. With the exception of the larvae of R. appendiculatus, the incidents of these ticks feeding on humans correlated well with their seasonal occurrences on preferred hosts. Ticks were also collected at monthly intervals, for 14 consecutive months, from the clothing of a game-guard providing protection for field-workers engaged in the collection, by means of flannel strips, of free-living ticks from the vegetation of four localities in the southern region of the Kruger National Park. In addition, with the exception of 3 months when the particular worker was absent, ticks that fed on one of the field-workers were collected over the same 14-month period. A total of 54,429 free-living ticks belonging to 14 species and six genera were collected from the vegetation at the four localities during this time and 3751 ticks belonging to 11 species and six genera from the clothing of the game-guard. The larvae of A. hebraeum and Boophilus decoloratus were the most numerous of the immature ticks, and H. leachi and R. simus of the adults on both the vegetation and the guard’s clothing. Ticks fed on the field-worker on six occasions and 14 were collected, all of which were A. hebraeum larvae. This revised version was published online in July 2006 with corrections to the Cover Date.     

Stabilization of the retinal vascular network by reciprocal feedback between blood vessels and astrocytes

Development of the retinal vasculature is controlled by a hierarchy of interactions among retinal neurons, astrocytes and blood vessels. Retinal neurons release platelet-derived growth factor (PDGFA) to stimulate proliferation of astrocytes, which in turn stimulate blood vessel growth by secreting vascular endothelial cell growth factor (VEGF). Presumably, there must be counteractive mechanisms for limiting astrocyte proliferation and VEGF production to prevent runaway angiogenesis. Here, we present evidence that the developing vessels provide feedback signals that trigger astrocyte differentiation--marked by cessation of cell division, upregulation of glial fibrillary acidic protein (GFAP) and downregulation of VEGF. We prevented retinal vessel development by raising newborn mice in a high-oxygen atmosphere, which leads, paradoxically, to retinal hypoxia (confirmed by using the oxygen-sensing reagent EF5). The forced absence of vessels caused prolonged astrocyte proliferation and inhibited astrocyte differentiation in vivo. We could reproduce these effects by culturing retinal astrocytes in a low oxygen atmosphere, raising the possibility that blood-borne oxygen itself might induce astrocyte differentiation and indirectly prevent further elaboration of the vascular network.     

Forestry alters foraging efficiency and crop contents of aphid-tending red wood ants, Formica aquilonia

Forest management alters species behaviours, distributions and interactions. To evaluate forestry effects on ant foraging performance, we compared the quality and quantity of honeydew harvested by ants among clear-cuts, middle-aged and mature spruce-dominated stands in boreal forests in Sweden. Honeydew quality was examined using honeydew collected by squeezing the gasters of laden Formica aquilonia workers. We used fifteen laden individuals at each study site (four replicates of each stand age) and analysed honeydew chemical composition with gas chromatography-mass spectroscopy. To compare the quantity of honeydew collected by individual ants, we collected and weighed five ants moving up and five ants moving down each of ten trees at the twelve sites (totally 1200 ants). The concentration of trehalose in honeydew was lower in clear-cuts compared with middle aged and mature stands, and similar trends were shown for sucrose, raffinose and melezitose, indicating poorer honeydew quality on clear cuts. Concentrations of the amino acid serine were higher on clear-cuts. The same trend occurred for glutamine, suggesting that increased N-uptake by the trees after clear cutting is reflected in the honeydew of aphids. Ants in mature stands had larger heads and carried proportionally more honeydew and may therefore be more efficient foragers. Human alternation of habitats through clear-cutting thus affects food quality and worker condition in F. aquilonia. This is the first study to show that honeydew quality is affected by anthropogenic disturbances, likely contributing to the reduction in size and abundance of F. aquilonia workers and mounds after clear cutting.     

Micro and macro-habitat associations in saproxylic beetles: implications for biodiversity management

Restoration of habitats is critically important in preventing full realization of the extinction debt owed as a result of anthropogenic habitat destruction. Although much emphasis has been placed on macrohabitats, suitable microhabitats are also vital for the survival of most species. The aim of this large-scale field experiment was to evaluate the relative importance of manipulated microhabitats, i.e., dead wood substrates of spruce (snags, and logs that were burned, inoculated with wood fungi or shaded) and macrohabitats, i.e., stand types (clear-cuts, mature managed forests, and forest reserves) for species richness, abundance and assemblage composition of all saproxylic and red-listed saproxylic beetles. Beetles were collected in emergence traps in 30 forest stands in 2001, 2003, 2004 and 2006. More individuals emerged from snags and untreated logs than from burned and shaded logs, but species richness did not differ among substrates. Assemblage composition differed among substrates for both all saproxylics and red-listed saproxylic species, mainly attributed to different assemblage composition on snags. This suggests that the practise of leaving snags for conservation purposes should be complemented with log supplementation. Clear-cuts supported fewer species and different assemblages from mature managed forests and reserves. Neither abundance, nor species richness or assemblage composition differed between reserves and mature managed forests. This suggests that managed stands subjected to selective cutting, not clear-felling, maintain sufficient old growth characteristics and continuity to maintain more or less intact assemblages of saproxylic beetles. Thus, alternative management methods, e.g., continuity forestry should be considered for some of these stands to maintain continuity and conservation values. Furthermore, the significantly higher estimated abundance per ha of red-listed beetles in reserves underlines the importance of reserves for maintaining viable populations of rare red-listed species and as source areas for saproxylic species in boreal forest landscapes.     

Next-generation sequencing analyses of the emergence and maintenance of mutations in CTL epitopes in HIV controllers with differential viremia control

Background

Despite the low level of viral replication in HIV controllers (HICs), studies have reported viral mutations related to escape from cytotoxic T-lymphocyte (CTL) response in HIV-1 plasma sequences. Thus, evaluating the dynamics of the emergence of CTL-escape mutants in HICs reservoirs is important for understanding viremia control. To analyze the HIV-1 mutational profile and dynamics of CTL-escape mutants in HICs, we selected 11 long-term non-progressor individuals and divided them into the following groups: (1) viremic controllers (VCs; n?=?5) and (2) elite controllers (ECs; n?=?6). For each individual, we used HIV-1 proviral DNA from PBMCs related to earliest (V_E) and latest (V_L) visits to obtain gag and nef sequences using the Illumina HiSeq system. The consensus of each mapped gene was used to assess viral divergence, and next-generation sequencing data were employed to identify SNPs and variations within and flanking CTL epitopes.

Results

Divergence analysis showed higher values for nef compared to gag among the HICs. EC and VC groups showed similar divergence rates for both genes. Analysis of the number of SNPs showed that VCs present more variability in both genes. Synonymous/non-synonymous mutation ratios were?<?1 for gag among ECs and for nef among ECs and VCs, exhibiting a predominance of non-synonymous mutations. Such mutations were observed in regions encoding CTL-restricted epitopes in all individuals. All ECs presented non-synonymous mutations in CTL epitopes but generally at low frequency (<?1%); all VCs showed a high number of mutations, with significant frequency changes between V_E and V_L visits. A higher frequency of internal mutations was observed for gag epitopes, with significant changes across visits compared to Nef epitopes, indicating a pattern associated with differential genetic pressure.

Conclusions

The high genetic conservation of HIV-1 gag and nef among ECs indicates that the higher level of viremia control restricts the evolution of both genes. Although viral replication levels in HICs are low or undetectable, all individuals exhibited CTL epitope mutations in proviral gag and nef variants, indicating that potential CTL escape mutants are present in HIC reservoirs and that situations leading to a disequilibrium of the host-virus relationship can result in the spread of CTL-escape variants.