An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.     

Natural and Regenerated Saltmarshes Exhibit Similar Soil and Belowground Organic Carbon Stocks,Root Production and Soil Respiration

Ecosystems - Saltmarshes provide many valuable ecosystem services including storage of a large amount of ‘blue carbon’ within their soils. To date, up to 50% of the world’s...     

Antileishmanial activity and cytotoxicity of ent-beyerene diterpenoids

We describe the in vitro activity of two natural isomeric ent-beyerene diterpenes, several derivatives and synthetic intermediates. Beyerenols 1 and 2 showed EC₅₀ of 4.6?±?9.4 and 5.3?±?9.4?μg/mL against amastigotes of L. (V) brazilensis, with SI of 5.1 and 7.7, respectively. Beyerenol 1 was synthesized from stevioside. In vivo experiments with bereyenols showed cure in 50% of hamsters infected with L. (V) brazilensis topically applied as Cream I (beyerenol 1, 0.81%, w/w) and Cream III (beyerenol 2, 1.96%, w/w). These results suggest that beyerenols are potential candidates for cutaneous leishmaniasis chemotherapy by topical application. In vitro assays of amastigotes of L. (V) brazilensis showed EC₅₀ of 1.1?±?0.1 and 1.3?±?0.04?μg/mL, with SI of 3.1 and 3.5 for hydrazone intermediates 10 and 11, respectively.     

A gene for resistance to the Varroa mite (Acari) in honey bee (Apis mellifera) pupae

Social insect colonies possess a range of defences which protect them against highly virulent parasites and colony collapse. The host–parasite interaction between honey bees (Apis mellifera) and the mite Varroa destructor is unusual, as honey bee colonies are relatively poorly defended against this parasite. The interaction has existed since the mid‐20th Century, when Varroa switched host to parasitize A. mellifera. The combination of a virulent parasite and relatively naïve host means that, without acaricides, honey bee colonies typically die within 3 years of Varroa infestation. A consequence of acaricide use has been a reduced selective pressure for the evolution of Varroa resistance in honey bee colonies. However, in the past 20 years, several natural‐selection‐based breeding programmes have resulted in the evolution of Varroa‐resistant populations. In these populations, the inhibition of Varroa's reproduction is a common trait. Using a high‐density genome‐wide association analysis in a Varroa‐resistant honey bee population, we identify an ecdysone‐induced gene significantly linked to resistance. Ecdysone both initiates metamorphosis in insects and reproduction in Varroa. Previously, using a less dense genetic map and a quantitative trait loci analysis, we have identified Ecdysone‐related genes at resistance loci in an independently evolved resistant population. Varroa cannot biosynthesize ecdysone but can acquire it from its diet. Using qPCR, we are able to link the expression of ecdysone‐linked resistance genes to Varroa's meals and reproduction. If Varroa co‐opts pupal compounds to initiate and time its own reproduction, mutations in the host's ecdysone pathway may represent a key selection tool for honey bee resistance and breeding.     

Bare soil cover and arbuscular mycorrhizal community in the first montane forest restoration in Central Argentina

Soil erosion affects extensive areas worldwide and must be urgently reduced promoting plant cover and beneficial microorganisms associated with plants, including arbuscular mycorrhizal fungi (AMF). In mountain environments, plant cover is difficult to enhance due to harsh conditions during the dry season and steep slopes. Our objective was to evaluate the percentage of the soil surface covered by plants and the AMF community associated with trees 12.5 years after planting during forest restoration efforts in microsites at different levels of soil degradation. The study was performed in the first montane forest restoration initiative of Central Argentina, where one of the trials consisted of planting Polylepis australis saplings at microsites with different levels of soil degradation: high, intermediate, and low. After 12.5 years, percentage of bare soil cover was significantly reduced by 36 and 37% in the high and intermediate degradation microsites, respectively. Low degradation microsites were initially very low in bare soil and did not significantly change. Mycorrhizal colonization, hyphae, vesicles, arbuscules, AMF diversity, and community structure were similar among microsite types. Percentage of hyphal entry points was higher at microsites with low degradation, number of spores was higher in high and intermediate degradation, and species richness was higher in high degradation. Acaulospora and Glomus were the most abundant genera in all microsites. We conclude that even in the most degraded microsites around 2.8% of the bare soil is covered by vegetation each year and that the arbuscular mycorrhizal community is highly tolerant and adapted to soils with different disturbance types.     

Incomplete datasets obscure associations between traits affecting dispersal ability and geographic range size of reef fishes in the Tropical Eastern Pacific

Dispersal is thought to be an important process determining range size, especially for species in highly spatially structured habitats, such as tropical reef fishes. Despite intensive research efforts, there is conflicting evidence about the role of dispersal in determining range size. We hypothesize that traits related to dispersal drive range sizes, but that complete and comprehensive datasets are essential for detecting relationships between species’ dispersal ability and range size. We investigate the roles of six traits affecting several stages of dispersal (adult mobility, spawning mode, pelagic larval duration (PLD), body size, aggregation behavior, and circadian activity), in explaining range size variation of reef fishes in the Tropical Eastern Pacific (TEP). All traits, except for PLD (148 species), had data for all 497 species in the region. Using a series of statistical models, we investigated which traits were associated with large range sizes, when analyzing all TEP species or only species with PLD data. Furthermore, using null models, we analyzed whether the PLD‐subset is representative of the regional species pool. Several traits affecting dispersal ability were strongly associated with range size, although these relationships could not be detected when using the PLD‐subset. Pelagic spawners (allowing for passive egg dispersal) had on average 56% larger range sizes than nonpelagic spawners. Species with medium or high adult mobility had on average a 25% or 33% larger range, respectively, than species with low mobility. Null models showed that the PLD‐subset was nonrepresentative of the regional species pool, explaining why model outcomes using the PLD‐subset differed from the ones based on the complete dataset. Our results show that in the TEP, traits affecting dispersal ability are important in explaining range size variation. Using a regionally complete dataset was crucial for detecting the theoretically expected, but so far empirically unresolved, relationship between dispersal and range size.     

Adaptable mesocosm facility to study oil spill impacts on corals

Although numerous studies have been carried out on the impacts of oil spills on coral physiology, most have relied on laboratory assays. This scarcity is partly explained by the difficulty of reproducing realistic conditions in a laboratory setting or of performing experiments with toxic compounds in the field. Mesocosm systems provide the opportunity to carry out such studies with safe handling of contaminants while reproducing natural conditions required by living organisms. The mesocosm design is crucial and can lead to the development of innovative technologies to mitigate environmental impacts. Therefore, this study aimed to develop a mesocosm system for studies simulating oil spills with several key advantages, including true replication and the use of gravity to control flow‐through that reduces reliance on pumps that can clog thereby decreasing errors and costs. This adaptable system can be configured to (a) have continuous flow‐through; (b) operate as an open or closed system; (c) be fed by gravity; (d) have separate mesocosm sections that can be used for individual and simultaneous experiments; and (e) simulate the migration of oil from ocean oil spills to the nearby reefs. The mesocosm performance was assessed with two experiments using the hydrocoral Millepora alcicornis and different configurations to simulate two magnitudes of oil spills. With few exceptions, physical and chemical parameters remained stable within replicates and within treatments throughout the experiments. Physical and chemical parameters that expressed change during the experiment were still within the range of natural conditions observed in Brazilian marine environments. The photosynthetic potential (F_v/F_m) of the algae associated with M. alcicornis decreased in response to an 1% crude‐oil contamination, suggesting a successful delivery of the toxic contaminant to the targeted replicates. This mesocosm is customizable and adjustable for several types of experiments and proved to be effective for studies of oil spills.     

Species composition of semi-natural mesic grasslands as a factor influencing the methane yield of plant biomass (Central Europe)

Semi-natural lowland and mountain mesic meadows are grasslands rich in species, and their conservation status depends on treatments such as mowing or grazing livestock. In many countries, the condition of grasslands is deteriorating because of their inappropriate use or abandonment. This study aimed to determine the effects of the species composition of plant communities and functional plant groups on the methane yield from biomass harvested from mesic grasslands in the Sudetes Mountains. Biogas potential analysis was performed based on biomass samples collected from Poland and the Czech Republic. The biogas potential was determined in 40 day-long batch anaerobic digestion tests. The average methane yield obtained from the biomass was 246 ± 16 NL CH₄ kg^?1 VS, whereas the methane yield per hectare was 870 ± 203 m³ CH₄ ha^?1. Plant communities comprising different dominant species had no effect on the methane yield but affected the methane yield per hectare. Additionally, the species composition of grasslands with a higher percentage of forbs had lower biomass yield, resulting in lower methane yields per hectare. The continuity of the low-intensity management of mountain grassland, which can be provided by the utilization of their biomass for bioenergy production, sustains high biodiversity and ensures appropriate meadow conservation.     

Fallen Branches as Part of Leaf-Cutting Ant Trails: Their Role in Resource Discovery and Leaf Transport Rates in Atta cephalotes

Fallen branches, logs, and exposed roots (fallen branches hereafter) commonly form part of the trunk trail system of leaf-cutting ants that inhabit the tropical rain forest. We studied the role of fallen branches on resource discovering and on leaf transport rates in Atta cephalotes . Fallen branches were common components of the A. cephalotes trail system; they were present in all the nests, and in the majority of the trunk trails examined (13/16). A field experiment revealed that, at the beginning of their foraging activity, ants discovered food sources located at the end of fallen branches earlier than those located on the leaf litter. Additionally, laden ants walked faster along a fallen branch than along soil tracks of the trunk trails. This increment in speed was higher in slow-walking ants ( e.g. , with larger loads) than in fast-walking ants ( e.g. , with smaller loads). These results suggest that the presence of fallen branches may direct the searching effort of leaf-cutters and increase the foraging speed of laden ants when these structures are part of the trunk trail system. The advantages of using fallen branches as part of a trail system, and their potential consequences in the spatial foraging pattern of leaf-cutting ants, are discussed.