The spatial regulation of meiotic recombination hotspots: Are all DSB hotspots crossover hotspots?

A key step for the success of meiosis is programmed homologous recombination, during which crossovers, or exchange of chromosome arms, take place. Crossovers increase genetic diversity but their main function is to ensure accurate chromosome segregation. Defects in crossover number and position produce aneuploidies that represent the main cause of miscarriages and chromosomal abnormalities such as Down's syndrome. Recombination is initiated by the formation of programmed double strand breaks (DSBs), which occur preferentially at places called DSB hotspots. Among all DSBs generated, only a small fraction is repaired by crossover, the other being repaired by other homologous recombination pathways. Crossover maps have been generated in a number of organisms, defining crossover hotspots. With the availability of genome-wide maps of DSBs as well as the ability to measure genetically the repair outcome at several hotspots, it is becoming more and more clear that not all DSB hotspots behave the same for crossover formation, suggesting that chromosomal features distinguish different types of hotspots.     

Biodiversity hotspots: hot for what?

In complex areas of international policy, such as biodiversity conservation, there is a risk that well-promoted strategies will be received by decision makers as a cure-all. The U.S.-based Conservation International is promoting biodiversity hotspots as a 'silver bullet' strategy for conserving most species for least cost. We assess the degree to which this goal is compatible with four social values that characterize the conservation movement. We find that biodiversity hotspots provide only a partial response because conservation does not treat all species as equal. We argue that explicit recognition of such values is fundamental to a structured debate contributing to the development of a common strategy for biodiversity conservation.     

Hidden structural heterogeneity enhances marine hotspots’ biodiversity

Studies in terrestrial and shallow-water ecosystems have unravelled the key role of interspecific interactions in enhancing biodiversity, but important knowledge gaps persist for the deep sea. Cold-water coral reefs are hotspots of biodiversity, but the role of interspecific interactions and “habitat cascades” (i.e. positive effects on focal organisms mediated by biogenic habitat formation) in shaping their biodiversity is unknown. Associations between macrofaunal hosts and epifauna were examined in 47 stations at the Mingulay Reef Complex (northeast Atlantic). In total, 101 (group level) and 340 (species level) unique types of facultative associations formed by 43 hosts and 39 epifaunal species were found. Molluscs and empty polychaete tubes had higher values for the type and number of host-epifaunal associations, the Shannon–Wiener (H) and Margalef (d) indices of the epifauna than the rest of the taxonomic groups (p < 0.05). Hosts’ body size, orientation, surface smoothness, and growth form explained a significant amount of variability (32.96%) in epifauna community composition. Epifaunal species richness (S), H and d were 27.4 (± 2.2%), 56.2 (± 2.8%) and 39.9 (± 2.3%) of the respective values for the total sessile communities living on coral framework. This is intriguing as coral framework is orders of magnitude larger than the size of macrofaunal hosts. It is suggested that bivalves, tunicates and empty polychaete tubes increase habitat heterogeneity and enhance biodiversity through “habitat cascades”, in a similar way that epiphytes do in tropical rainforests. Most macrofaunal habitat suppliers in the studied cold-water coral reef are calcified species and likely susceptible to ocean acidification. This indicates that the impacts of climate change on the total biodiversity, structure and health of cold-water coral reefs may potentially be more severe than previously thought.

     

Can we detect oceanic biodiversity hotspots from space?

Understanding the variability of marine biodiversity is a central issue in microbiology. Current observational programs are based on in situ studies, but their implementation at the global scale is particularly challenging, owing to the ocean extent, its temporal variability and the heterogeneity of the data sources on which compilations are built. Here, we explore the possibility of identifying phytoplanktonic biodiversity hotspots from satellite. We define a Shannon entropy index based on patchiness in ocean color bio-optical anomalies. This index provides a high resolution (1 degree) global coverage. It shows a relation to temperature and mid-latitude maxima in accordance with those previously evidenced in microbiological biodiversity model and observational studies. Regional maxima are in remarkable agreement with several known biodiversity hotspots for plankton organisms and even for higher levels of the marine trophic chain, as well as with some in situ planktonic biodiversity estimates (from Atlantic Meridional Transect cruise). These results encourage to explore marine biodiversity with a coordinated effort of the molecular, ecological and remote sensing communities.     

Double-chain-cut sites are recombination hotspots in the red pathway of phage λ

The Red recombination pathway of phage λ is shown to target recombination to doublechain ends of DNA. A double-chain cut, delivered in vivo to only one of two parents participating in a λ lytic cross by a type II restriction endonuclease, increases the proportion of crossing over in the interval containing the cut compared with other intervals. The stimulating effect of a cut is evident whether replication is inhibited or permitted. Cut stimulation can move away from the initial cut-site, presumably by doublechain degradation. Movement of the stimulating effect of a cut is dependent on the Escherichia coli gene recA when the cross is carried out under conditions that inhibit phage replication. When replication is permitted, all aspects of cut-stimulated recombination are independent of recA. Evidence is presented to show that the reaction that is stimulated by cutting is often non-reciprocal at the molecular level.     

What and where? Predicting invasion hotspots in the Arctic marine realm

The risk of aquatic invasions in the Arctic is expected to increase with climate warming, greater shipping activity and resource exploitation in the region. Planktonic and benthic marine aquatic invasive species (AIS) with the greatest potential for invasion and impact in the Canadian Arctic were identified and the 23 riskiest species were modelled to predict their potential spatial distributions at pan‐Arctic and global scales. Modelling was conducted under present environmental conditions and two intermediate future (2050 and 2100) global warming scenarios. Invasion hotspots—regions of the Arctic where habitat is predicted to be suitable for a high number of potential AIS—were located in Hudson Bay, Northern Grand Banks/Labrador, Chukchi/Eastern Bering seas and Barents/White seas, suggesting that these regions could be more vulnerable to invasions. Globally, both benthic and planktonic organisms showed a future poleward shift in suitable habitat. At a pan‐Arctic scale, all organisms showed suitable habitat gains under future conditions. However, at the global scale, habitat loss was predicted in more tropical regions for some taxa, particularly most planktonic species. Results from the present study can help prioritize management efforts in the face of climate change in the Arctic marine ecosystem. Moreover, this particular approach provides information to identify present and future high‐risk areas for AIS in response to global warming.     

Use of prey hotspots by an avian predator: purposeful unpredictability?

The use of space by predators in relation to their prey is a poorly understood aspect of predator-prey interactions. Classic theory suggests that predators should focus their efforts on areas of abundant prey, that is, prey hotspots, whereas game-theoretical models of predator and prey movement suggest that the distribution of predators should match that of their prey's resources. If, however, prey are spatially anchored to one location and these prey have particularly strong antipredator responses that make them difficult to capture with frequent attacks, then predators may be forced to adopt alternative movement strategies to hunt behaviorally responsive prey. We examined the movement patterns of bird-eating sharp-shinned hawks (Accipiter striatus) in an attempt to shed light on hotspot use by predators. Our results suggest that these hawks do not focus on prey hotspots such as bird feeders but instead maintain much spatial and temporal unpredictability in their movements. Hawks seldom revisited the same area, and the few frequently used areas were revisited in a manner consistent with unpredictable returns, giving prey little additional information about risk.     

Can biodiversity hotspots protect more than tropical forest plants and vertebrates?

Conservation International's biodiversity hotspots are areas of high vascular plant endemism combined with high levels of habitat destruction and land use change. Although such hotspots have also been shown to be centres for terrestrial vertebrate endemism, much less is known about how well these areas function as hotspots for other less well‐studied groups, including the hyperdiverse arthropods, other invertebrates and fungi. Because there is a close evolutionary and ecological relationship between insects and plants, we suggest that the potential role of plants as umbrella species for herbivorous insects, potentially herbivorous fungi and nematodes, and parasitic insects should be explored. Finally, we reflect on the increasing social, economic, human conflict and governance issues and the impacts of increasing land use change and global climate change that threaten the biodiversity hotspot system.     

Fiddling in biodiversity hotspots while deserts burn? Collapse of the Sahara's megafauna

Biodiversity hotspots understandably attract considerable conservation attention. However, deserts are rarely viewed as conservation priority areas, due to their relatively low productivity, yet these systems are home to unique species, adapted to harsh and highly variable environments. While global attention has been focused on hotspots, the world's largest tropical desert, the Sahara, has suffered a catastrophic decline in megafauna. Of 14 large vertebrates that have historically occurred in the region, four are now extinct in the wild, including the iconic scimitar‐horned oryx (Oryx dammah). The majority has disappeared from more than 90% of their Saharan range, including addax (Addax nasomaculatus), dama gazelle (Nanger dama) and Saharan cheetah (Acinonyx jubatus hecki) – all now on the brink of extinction. Greater conservation support and scientific attention for the region might have helped to avert these catastrophic declines. The Sahara serves as an example of a wider historical neglect of deserts and the human communities who depend on them. The scientific community can make an important contribution to conservation in deserts by establishing baseline information on biodiversity and developing new approaches to sustainable management of desert species and ecosystems. Such approaches must accommodate mobility of both people and wildlife so that they can use resources most efficiently in the face of low and unpredictable rainfall. This is needed to enable governments to deliver on their commitments to halt further degradation of deserts and to improve their status for both biodiversity conservation and human well‐being. Only by so‐doing will deserts be able to support resilient ecosystems and communities that are best able to adapt to climate change.     

Is reproduction of endemic plant species particularly pollen limited in biodiversity hotspots?

Current evidence suggests that plants in biodiversity hotspots suffer more from pollen limitation of reproduction than those in lower diversity regions, primarily due to the response of self‐incompatible species. Species in biodiversity hotspots may thus be more at risk of limited reproduction and subsequent population decline. Should these species have restricted ranges (i.e. be endemics to a certain region), pollen limitation within highly diverse regions may pose an important threat to global plant biodiversity. We further dissect the global pattern by exploring whether pollen limitation of range‐restricted (endemic) species is distinctive and/or relates differently to species diversity than that of widespread (non‐endemic) species. To provide a preliminary test of this prediction we conducted both cross‐species and comparative phylogenetic meta‐analyses to determine the effect of endemism on the magnitude of pollen limitation and its relationship with regional species richness. Our data set included 287 plant species belonging to 78 families distributed world‐wide. Our results revealed that endemism and self‐compatibility contribute to the global association between pollen limitation and species richness. Self‐incompatible species were more pollen limited than self‐compatible ones, and the PICs analysis indicated that transitions to endemism were associated with transitions to self‐compatibility. The relationship between pollen limitation and species richness was significant only for the self‐incompatible species, and was monotonically increasing in non‐endemic species but accelerating in the endemic species. Thus, self‐incompatible endemic species from biodiversity hotspots are at the greatest risk of pollination failure, a previously unknown aspect suggesting this group of species as a top priority for future development of conservation strategies. In contrast, reproduction of self‐compatible species appears to be unrelated to plant diversity, although we caution that current data do not account for the reproductive limitation due to the quality of pollen received. Understanding the mechanisms underlying these patterns requires further investigation into plant–plant pollinator mediated interactions and the dynamics of pollen transfer in communities differing in species diversity.     

How do predators and scavengers locate resource hotspots within a tropical forest?

In many parts of the world, wildlife species congregate at ‘hotspot’ locations that offer feeding opportunities unmatched in the wider landscape. But to exploit those resource‐rich sites, animals must first locate them. In tropical Australia, predators and scavengers (especially dingos, scrub turkeys, snakes, and invasive toads) gather beneath large canopy‐emergent trees that house breeding colonies of metallic starlings (Aplonis metallica). Some wildlife species feed on fallen nestlings whereas others consume the rich insect fauna supported by bird detritus, or the other species attracted to those resources. Those congregations largely cease as soon as colony trees fall, suggesting that wildlife aggregations are responses to bird‐associated cues rather than to specific locations. To identify the proximate cues that elicit congregation of wildlife under such trees, we deployed sound cues (starling‐chatter) and two types of scent cues (soil from beneath a starling tree, and complete nests on broken branches). We recorded visitations by animals with camera‐traps. Starling‐chatter did not attract significant numbers of animals, but soil from beneath colony trees attracted many animals (mostly scrub turkeys). Complete nests attracted nest‐predators (dingos, snakes). Our experiments suggest that faunal aggregations beneath colony trees are driven by proximate responses to distinctive scent cues in the soil, especially for species that obtain their food from that bird‐fertilized substrate; but predators that feed directly on fallen nestlings key in specifically on that resource.     

Identity of a Chi site of Escherichia coli and Chi recombinational hotspots of bacteriophage λ

Chi sites in bacteriophage λ stimulate recombination promoted by the RecBC pathway of Escherichia coli. We have located a Chi site within the E. coli lacZ gene by deletion mapping and have isolated a mutation inactivating this Chi. Sequence analysis showed that the mutation arose by a single base-pair transition $\text{G}\text{C}\text{?}\text{→}\text{A}\text{T}\text{?}$ within an eight base-pair sequence (5′ G-C-T-G-G-T-G-G 3′) identical to that found at Chi sites in λ and in plasmid pBR322.     

Diversity of mammals in the tropical–temperate Neotropics: hotspots on a regional scale

The tropical–temperate interface of the southern Neotropics harbours an interdigitating array of biomes (Puna, Monte, Chaco, Yungas). This topographic and climatically complex region needs urgent conservation efforts, as it is being transformed by human activities at an accelerating pace. We analyse georeferenced field records of mammal species in northwestern Argentina (provinces: Catamarca, Jujuy, Salta, Tucuman) in order to define biodiversity hotspots on the basis of 0.5°× 0.5° grid cells within northwestern Argentina according to total richness of mammal species, richness of megaspecies (species above 10 kg), and endemic species (species restricted to Argentina or neighbouring countries with shared biomes). The mammal fauna of northwestern Argentina is fairly well known (176 species). The biomes differ considerably in species richness (Puna low, Yungas high) and species composition. We found no significant difference between endemic and non-endemic species regarding cell occupancy or body size. Cell occupancy was not correlated to body size. Across grids, species richness, number of megaspecies as well as richness of endemics are all correlated to sampling effort. More than 50% of the species in the region are restricted to one or two biomes. Overall, the species turn-over between biomes in northwestern Argentina is high. Using a simple algorithm we identified 10 grid cells which covered 90% of the total number of recorded species, and contrast them with the protected areas. While the Puna and Yungas biomes are rather well protected, the arid and semiarid Monte and Chaco are in need of urgent attention in biodiversity conservation.     

Detecting biodiversity hotspots using species–area and endemics–area relationships: the case of butterflies

Using data of the Red Data Book of European Butterflies we establish the species–area relationship (S = 8.5 A^0.23) and the endemics–area relationship (S = 0.5 A^0.18) of European butterflies. Applying confidence limits as tools for the identification of hotspot countries we show that in the case of butterflies hotspots of endemism and hotspots of overall species richness do not coincide. We introduce plots of residuals from species–area relationships shifted upwards by the 95% confidence limits of the intercept (α-values) as a new tool for identifying and ranking of hotspots.     

Differentiated free-living and sediment-attached bacterial community structure inside and outside denitrification hotspots in the river–groundwater interface

This study assessed the functional significance of attached and free-living bacterial communities involved in the process of denitrification in a shallow aquifer of a riparian zone (Garonne River, SW France). Denitrification enzyme activity (DEA), bacterial density (BD) and bacterial community composition (BCC) were measured in two aquifer compartments: the groundwater and the sandy fraction of the sediment deposit. Samples were collected in wells located inside (IHD) and outside (OHD) identified hotspots of denitrification. Despite high BD values (up to 1.14 × 10¹² cells m⁻³), DEA was not detected in the water compartment (< 0.32 mg N–N₂O m⁻³ d⁻¹). The sandy fraction showed detectable DEA (up to 1,389 mg N–N₂O m⁻³ d⁻¹) and, consistent with BD pattern, higher DEA values were measured in IHD zones than in OHD zones. The BCC assessed by 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) partly supported this result: attached and free-living communities were significantly different (< 30% similarity) but patterns of BCC did not cluster according to IHD and OHD zones. Targeting the denitrifying communities by means of a culture enrichment step prior to 16S rDNA PCR-DGGE showed that the free-living and sediment attached communities differed. Most sequences obtained from DGGE profiles of denitrifying communities were affiliated to Proteobacteria and showed low genetic distance with taxa that have already been detected in aquifers (e.g., Azoarcus sp., Acidovorax sp. and Pseudomonas spp.). This study confirms that in the aquifer the sediment-attached fraction exhibits different functions (DEA) from free-living communities and suggests that this functional difference is related to the communities’ structure.     

Decomposition ‘hotspots’ in a rewetted peatland: implications for water quality and carbon cycling

The hypothesis that specific components of seawater, such as particulate, dissolved and colloidal organic and inorganic material, render virions non-infective has long been postulated, but never rigorously tested. To address this hypothesis, the plaque assay method was used to derive infective decay rates, k, of two bacteriophages—P1 (marine host: PWH3a) and T4 (enteric host: E. coli B). We compared k values of bacteriophage suspended in serial filtrations of seawater, with and without autoclaving and UV oxidation. Both phages exhibited reduced decay rates in particle-free water (<0.2 μm) compared to <10 μm filtrate. The largest decrease in virion decay rates was achieved by autoclaving the 0.2 μm filtrate. UV oxidation of <0.2 μm filtrate, however, yielded higher decay rates than observed in autoclaved treatments. The lowest k values were seen in ultra-filtered seawater (<10 kDa). Exposure to a wide range of concentrations of Pronase E (a proteolytic enzyme), inorganic clay (kaolinite or montmorillonite), and organic particles (phytoplankton debris) did not promote phage inactivation. P1 infective titers were also not consistently reduced by exposures to axenic cultures of a resistant host mutant (PWH3a-R) and a non-host marine bacterium (MB-5). Finally, phage were exposed to a range of temperatures to derive activation energies required for phage inactivation. Application of the Arrhenius model to inactivation of T4 and P1 yielded activation energies (E _a) of 49 and 40 kJ mol⁻¹, respectively. This is the first comprehensive analysis in which specific seawater components were assayed for their ability to inactivate bacteriophage. Inactivation of these phage does not appear to depend on capsomere denaturation, proteolytic extracellular enzymes, sorption to non-host bacteria, clay particles or particulate organic debris, but is accelerated by naturally occurring particles, which include living organisms, and heat-labile colloids and macromolecules >10 kDa.     

Rational design of thermostability in bacterial 1,3-1,4-β-glucanases through spatial compartmentalization of mutational hotspots

Higher thermostability is required for 1,3-1,4-β-glucanase to maintain high activity under harsh conditions in the brewing and animal feed industries. In this study, a comprehensive and comparative analysis of thermostability in bacterial β-glucanases was conducted through a method named spatial compartmentalization of mutational hotspots (SCMH), which combined alignment of homologous protein sequences, spatial compartmentalization, and molecular dynamic (MD) simulation. The overall/local flexibility of six homologous β-glucanases was calculated by MD simulation and linearly fitted with enzyme optimal enzymatic temperatures. The calcium region was predicted to be the crucial region for thermostability of bacterial 1,3-1,4-β-glucanases, and optimization of four residue sites in this region by iterative saturation mutagenesis greatly increased the thermostability of a mesophilic β-glucanase (BglT) from Bacillus terquilensis. The E46P/S43E/H205P/S40E mutant showed a 20 °C increase in optimal enzymatic temperature and a 13.8 °C rise in protein melting temperature (T _m) compared to wild-type BglT. Its half-life values at 60 and 70 °C were 3.86-fold and 7.13-fold higher than those of wild-type BglT. The specific activity of E46P/S43E/H205P/S40E mutant was increased by 64.4 %, while its stability under acidic environment was improved. The rational design strategy used in this study might be applied to improve the thermostability of other industrial enzymes.

     

Do hotspots fall within protected areas? A Geographic Approach to Planning analysis of regional freshwater biodiversity

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Systematic conservation assessment for the Mesoamerica, Chocó, and Tropical Andes biodiversity hotspots: a preliminary analysis

Using IUCN Red List species as biodiversity surrogates, supplemented with additional analyses based on ecoregional diversity, priority areas for conservation in Mesoamerica, Chocó, and the Tropical Andes were identified using the methods of systematic conservation planning. Species’ ecological niches were modeled from occurrence records using a maximum entropy algorithm. Niche models for 78 species were refined to produce geographical distributions. Areas were prioritized for conservation attention using a complementarity-based algorithm implemented in the ResNet software package. Targets of representation for Red List species were explored from 10 to 90% of the modeled distributions at 10% increments; for the 53 ecoregions, the target was 10% for each ecoregion. Selected areas were widely dispersed across the region, reflecting the widespread distribution of Red List species in Mesoamerica, Chocó, and the Tropical Andes, which underscores the region’s importance for biodiversity. In general, existing protected areas were no more representative of biodiversity than areas outside them. Among the countries in the region, the protected areas of Belize performed best and those of Colombia and Ecuador worst. A high representation target led to the selection of a very large proportion of each country except Colombia and Ecuador (for a 90% target, 83–95% of each country was selected). Since such large proportions of land cannot realistically be set aside as parks or reserves, biodiversity conservation in Mesoamerica, Chocó, and the Tropical Andes will require integrative landscape management which combines human use of the land with securing the persistence of biota. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.