Soil warming opens the nitrogen cycle at the alpine treeline

Climate warming may alter ecosystem nitrogen (N) cycling by accelerating N transformations in the soil, and changes may be especially pronounced in cold regions characterized by N‐poor ecosystems. We investigated N dynamics across the plant–soil continuum during 6 years of experimental soil warming (2007–2012; +4 °C) at a Swiss high‐elevation treeline site (Stillberg, Davos; 2180 m a.s.l.) featuring Larix decidua and Pinus uncinata. In the soil, we observed considerable increases in the pool size in the first years of warming (by >50%), but this effect declined over time. In contrast, dissolved organic nitrogen (DON) concentrations in soil solutions from the organic layer increased under warming, especially in later years (maximum of +45% in 2012), suggesting enhanced DON leaching from the main rooting zone. Throughout the experimental period, foliar N concentrations showed species‐specific but small warming effects, whereas δ¹⁵N values showed a sustained increase in warmed plots that was consistent for all species analysed. The estimated total plant N pool size at the end of the study was greater (+17%) in warmed plots with Pinus but not in those containing Larix, with responses driven by trees. Irrespective of plot tree species identity, warming led to an enhanced N pool size of Vaccinium dwarf shrubs, no change in that of Empetrum hermaphroditum (dwarf shrub) and forbs, and a reduction in that of grasses, nonvascular plants, and fine roots. In combination, higher foliar δ¹⁵N values and the transient response in soil inorganic N indicate a persistent increase in plant‐available N and greater cumulative plant N uptake in warmer soils. Overall, greater N availability and increased DON concentrations suggest an opening of the N cycle with global warming, which might contribute to growth stimulation of some plant species while simultaneously leading to greater N losses from treeline ecosystems and possibly other cold biomes.     

Polymorphism at the Clock gene predicts phenology of long‐distance migration in birds

Dissecting phenotypic variance in life history traits into its genetic and environmental components is at the focus of evolutionary studies and of pivotal importance to identify the mechanisms and predict the consequences of human‐driven environmental change. The timing of recurrent life history events (phenology) is under strong selection, but the study of the genes that control potential environmental canalization in phenological traits is at its infancy. Candidate genes for circadian behaviour entrained by photoperiod have been screened as potential controllers of phenological variation of breeding and moult in birds, with inconsistent results. Despite photoperiodic control of migration is well established, no study has reported on migration phenology in relation to polymorphism at candidate genes in birds. We analysed variation in spring migration dates within four trans‐Saharan migratory species (Luscinia megarhynchos; Ficedula hypoleuca; Anthus trivialis; Saxicola rubetra) at a Mediterranean island in relation to Clock and Adcyap1 polymorphism. Individuals with larger number of glutamine residues in the poly‐Q region of Clock gene migrated significantly later in one or, respectively, two species depending on sex and whether the within‐individual mean length or the length of the longer Clock allele was considered. The results hinted at dominance of the longer Clock allele. No significant evidence for migration date to covary with Adcyap1 polymorphism emerged. This is the first evidence that migration phenology is associated with Clock in birds. This finding is important for evolutionary studies of migration and sheds light on the mechanisms that drive bird phenological changes and population trends in response to climate change.     

A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata

Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering and, in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life history traits as it perceives changes in daylength. We asked whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57‐kb region from a German (Plech) and a Norwegian (Spiterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4‐kb region around PHYA in the northern Spiterstulen population. The overall level of linkage disequilibrium (LD) was higher in Spiterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.     

Nitrogen retention and partitioning at the initiation of lipid accumulation in nitrogen‐deficient algae

Nitrogen (N) deficiency promotes lipid accumulation in many oleaginous algae, but we have a poor understanding of the associations between the initiation of lipid accumulation and algal N retention and partitioning. Here, we report on total cell N, five bulk pools of N in the cell (protein, free amino acids, DNA, RNA, chl), and lipids from N saturation to growth cessation in three species. While the maximum level of N uptake differed among species, the ratio of minimum retained N to N retained at the initiation of lipid accumulation was consistent among species at 0.5 ± 0.04. This suggests that the cellular initiation of lipid accumulation was associated with a common magnitude of N deficiency among species. Concerning the partitioning of N, the concentration of RNA and the protein to RNA ratio were most similar among species at the initiation of lipid accumulation with averages of 3.2 ± 0.26 g · L^?1 (8.2% variation) and 16 ± 1.5 (9.2% variation), respectively. All other pools and physiologically relevant ratios were considerably more variable. The species commonalities in RNA and protein show a similar reduction in general cellular function due to N deficiency before cellular initiation of lipid accumulation. These results provide insight into the physiological drivers for lipid accumulation in N‐deficient algae and data for modeling these associations.     

Nuclear locus divergence at the early stages of speciation in the Orchard Oriole complex

As two lineages diverge from one another, mitochondrial DNA should evolve fixed differences more rapidly than nuclear DNA due to its smaller effective population size and faster mutation rate. As a consequence, molecular systematists have focused on the criteria of reciprocal monophyly in mitochondrial DNA for delimiting species boundaries. However, mitochondrial gene trees do not necessarily reflect the evolutionary history of the taxa in question, and even mitochondrial loci are not expected to be reciprocally monophyletic when the speciation event happened very recently. The goal of this study was to examine mitochondrial paraphyly within the Orchard Oriole complex, which is composed of Icterus spurius (Orchard Oriole) and Icterus fuertesi (Fuertes' Oriole). We increased the geographic sampling, added four nuclear loci, and used a range of population genetic and coalescent methods to examine the divergence between the taxa. With increased taxon sampling, we found evidence of clear structure between the taxa for mitochondrial DNA. However, nuclear loci showed little evidence of population structure, indicating a very recent divergence between I. spurius and I. fuertesi. Another goal was to examine the genetic variation within each taxon to look for evidence of a past founder event within the I. fuertesi lineage. Based on the high amounts of genetic variation for all nuclear loci, we found no evidence of such an event – thus, we found no support for the possible founding of I. fuertesi through a change in migratory behavior, followed by peripheral isolates speciation. Our results demonstrate that these two taxa are in the earliest stages of speciation, at a point when they have fixed differences in plumage color that are not reflected in monophyly of the mitochondrial or nuclear DNA markers in this study. This very recent divergence makes them ideal for continued studies of species boundaries and the earliest stages of speciation.     

Genetic demography at the leading edge of the distribution of a rabies virus vector

The common vampire bat, Desmodus rotundus, ranges from South America into northern Mexico in North America. This sanguivorous species of bat feeds primarily on medium to large‐sized mammals and is known to rely on livestock as primary prey. Each year, there are hotspot areas of D. rotundus‐specific rabies virus outbreaks that lead to the deaths of livestock and economic losses. Based on incidental captures in our study area, which is an area of high cattle mortality from D. rotundus transmitted rabies, it appears that D. rotundus are being caught regularly in areas and elevations where they previously were thought to be uncommon. Our goal was to investigate demographic processes and genetic diversity at the north eastern edge of the range of D. rotundus in Mexico. We generated control region sequences (441 bp) and 12‐locus microsatellite genotypes for 602 individuals of D. rotundus. These data were analyzed using network analyses, Bayesian clustering approaches, and standard population genetic statistical analyses. Our results demonstrate panmixia across our sampling area with low genetic diversity, low population differentiation, loss of intermediate frequency alleles at microsatellite loci, and very low mtDNA haplotype diversity with all haplotypes being very closely related. Our study also revealed strong signals of population expansion. These results follow predictions from the leading‐edge model of expanding populations and supports conclusions from another study that climate change may allow this species to find suitable habitat within the U.S. border.     

Development of the gregarious ectoparasitoid Nasonia vitripennis using five species of necrophagous flies as hosts and at various developmental temperatures

The utility of five species of necrophagous flies (Diptera) as pupal hosts for Nasonia vitripennis (Walker) (Hymenoptera: Pteromalidae) was examined by comparing incidences of parasitism, fecundity, and several features of wasp development at three rearing temperatures. Species differences in host suitability were evident in all life history features examined, with the highest incidences of parasitism, largest clutches and adult body sizes, and shortest periods of development occurring when the sarcophagid Sarcophaga bullata Parker served as hosts, regardless of temperature in which the wasps developed. Puparia of the calliphorids Lucilia illustris Meigen, Phormia regina Meigen, and Protophormia terraenovae Robineau‐Desvoidy were also accepted as hosts by the female parasitoids, albeit not equally so, and each yielded large, female‐biased broods. By contrast, pupae of the calliphorid Chrysomya rufifacies (Macquart) were not well suited to serve as an oviposition site or support the development of N. vitripennis. When successful parasitism did occur on any host species, duration of parasitoid development increased, adult body sizes were truncated, male‐biased sex ratios were produced, and mortality from egg hatch to adult emergence elevated with increasing rearing temperature. Unlike with the four other fly species, C. rufifacies did not yield any adult parasitoids when the rearing temperature was 35 °C. The results argue that developmental data determined for this wasp derived from a single host species is not sufficient for applying to all scenarios in which wasp development is necessary to estimate a postmortem interval or periods of insect activity.     

Genetic differentiation of the pine processionary moth at the southern edge of its range: contrasting patterns between mitochondrial and nuclear markers

The pine processionary moth (Thaumetopoea pityocampa) is an important pest of coniferous forests at the southern edge of its range in Maghreb. Based on mitochondrial markers, a strong genetic differentiation was previously found in this species between western (pityocampa clade) and eastern Maghreb populations (ENA clade), with the contact zone between the clades located in Algeria. We focused on the moth range in Algeria, using both mitochondrial (a 648 bp fragment of the tRNA‐cox2) and nuclear (11 microsatellite loci) markers. A further analysis using a shorter mtDNA fragment and the same microsatellite loci was carried out on a transect in the contact zone between the mitochondrial clades. Mitochondrial diversity showed a strong geographical structure and a well‐defined contact zone between the two clades. In particular, in the pityocampa clade, two inner subclades were found whereas ENA did not show any further structure. Microsatellite analysis outlined a different pattern of differentiation, with two main groups not overlapping with the mitochondrial clades. The inconsistency between mitochondrial and nuclear markers is probably explained by sex‐biased dispersal and recent afforestation efforts that have bridged isolated populations.     

High power line collision mortality of threatened bustards at a regional scale in the Karoo,South Africa

Quantifying avian collisions with power lines at large spatial scales is difficult, but such mortality is of serious conservation concern for many bird species worldwide. To investigate effects on the Endangered Ludwig's Bustard Neotis ludwigii and two other bustard species, mortality surveys were conducted quarterly along high‐voltage transmission lines at five sites (total length 252 km) across the Karoo for 2 years and one low‐voltage distribution line site (95 km) for 1 year. Thirty bird species were found, with Ludwig's Bustards constituting 69% and other bustards a further 18% of carcasses (n = 679 birds). Significant explanatory variables of Ludwig's Bustard collisions were season (collisions more likely in winter), rainfall (less likely in drier areas) and year on transmission lines (highlighting variability between years). Season and proximity to roads were significant variables on distribution lines, with collisions more likely during winter and away from roads. Ludwig's Bustard collision rates (corrected for survey biases) were higher on transmission (1.12; 95% confidence interval (CI) 0.40–2.58 bustards/km/year) than on distribution lines (0.86; 95% CI 0.30–1.96), but these smaller lines are four times as extensive in South Africa and so probably kill more birds. Despite being much less abundant, Kori Bustards Ardeotis kori were the second most commonly recovered species, with collision rates of 0.10 (95% CI 0.05–0.19) on transmission lines in the Nama Karoo alone. Collision rates are highly variable but suggest mortality suffered by these two species is worryingly high. This adds to growing concern about the impacts of power lines on bustards globally, so given ongoing expansion to the power grid, collision mitigation measures should be implemented at all new power lines.     

Feeding patterns of elephants at the Atherstone Collaborative Nature Reserve

The African savannah elephant (Loxodonta africana Blumenbach) is a generalist herbivore that relies on widely distributed resources. Vegetation decline, aggravated by these elephants, can compromise local conservation efforts. Thus it imperative to understand the factors that drive them to consume specific plant species and plant parts. The objective of our study was to investigate the feeding patterns of African savannah elephants in the enclosed bushveld savannah at the Atherstone Collaborative Nature Reserve in South Africa. For 1 year, we examined elephant selection of woody versus herbaceous vegetation, and identified which plant species and parts were preferentially consumed. We accomplished this by directly observing feeding elephants, and by utilizing data collected on elephant footprints, dung piles, stripped bark and broken branches. We further conducted vegetation surveys to determine selection frequency relative to species abundance. Elephants showed a preference for different plant parts consumption in the feeding plots. In total, leaves, branches and bark contributed mostly to their diet. Seasonal selection patterns showed an increasing proportion of bark and branch consumption during the dry season.     

Autumn growth of three perennial weeds at high latitude benefits from climate change

In autumn, agricultural perennial weeds prepare for winter and can store reserves into creeping roots or rhizomes. Little is known about influence of climate change in this period. We tested the effect of simulated climate change in autumn on three widespread and noxious perennial weeds, Elymus repens (L.) Gould, Cirsium arvense (L.) Scop. and Sonchus arvensis L. We divided and combined simulated climate change components into elevated CO₂ concentration (525 ppm), elevated temperatures (+2–2.5°C), treatments in open‐top chambers. In addition, a control in the open‐top chamber without any increase in CO₂ and temperature, and a field control outside the chambers were included. Two geographically different origins and three pre‐growth periods prior to the exposure to climate change factors were included for each species. All species increased leaf area under elevated temperature, close to doubling in E. repens and quadrupling in the dicot species. E. repens kept leaves green later in autumn. C. arvense did not benefit in below‐ground growth from more leaf area or leaf dry mass. S. arvensis had low levels of leaf area throughout the experiment and withered earlier than the two other species. Below‐ground plant parts of S. arvensis were significantly increased by elevated temperature. Except for root:shoot ratio of C. arvense, the effects of pure elevated CO₂ were not significant for any variables compared to the open‐top chamber control. There was an additive, but no synergistic, effect of enhanced temperature and CO₂. The length of pre‐growth period was highly important for autumn plant growth, while origin had minor effect. We conclude that the small transfer of enhanced above‐ground growth into below‐ground growth under climate change in autumn does not favour creeping perennial plants per se, but more leaf area may offer more plant biomass to be tackled by chemical or physical weed control.     

Low host specificity of root‐associated fungi at an Arctic site

In High Arctic ecosystems, plant growth and reproduction are limited by low soil moisture and nutrient availability, low soil and air temperatures, and a short growing season. Mycorrhizal associations facilitate plant nutrient acquisition and water uptake and may therefore be particularly ecologically important in nutrition‐poor and dry environments, such as parts of the Arctic. Similarly, endophytic root associates are thought to play a protective role, increasing plants' stress tolerance, and likely have an important ecosystem function. Despite the importance of these root‐associated fungi, little is known about their host specificity in the Arctic. We investigated the host specificity of root‐associated fungi in the common, widely distributed arctic plant species Bistorta vivipara, Salix polaris and Dryas octopetala in the High Arctic archipelago Svalbard. High‐throughput sequencing of the internal transcribed spacer 1 (ITS1) amplified from whole root systems generated no evidence of host specificity and no spatial autocorrelation within two 3 m × 3 m sample plots. The lack of spatial structure at small spatial scales indicates that Common Mycelial Networks (CMNs) are rare in marginal arctic environments. Moreover, no significant differences in fungal OTU richness were observed across the three plant species, although their root system characteristics (size, biomass) differed considerably. Reasons for lack of host specificity could be that association with generalist fungi may allow arctic plants to more rapidly and easily colonize newly available habitats, and it may be favourable to establish symbiotic relationships with fungi possessing different physiological attributes.     

Genetic variation at KIT locus may predispose to melanoma

As loss of KIT frequently occurs in melanoma progression, we hypothesized that KIT is implicated in predisposition to melanoma (MM). Thus, we sequenced the KIT coding region in 112 familial MM cases and 143 matched controls and genotyped tag single‐nucleotide polymorphisms (SNPs) in two cohorts of melanoma patients and matched controls. Five rare KIT substitutions, all predicted possibly or probably deleterious, were identified in five patients, but none in controls [RR = 2.26 (1.26–2.26)]. Expressed in melanocyte lines, three substitutions inhibited KIT signaling. Comparison with exomes database (7020 alleles) confirmed a significant excess of rare deleterious KIT substitutions in patients. Additionally, a common SNP, rs2237028, was associated with MM risk, and 6 KIT variants were associated with nevus count. Our data strongly suggest that rare KIT substitutions predispose to melanoma and that common variants at KIT locus may also impact nevus count and melanoma risk.     

Population viability analysis of Walia ibex (Capra walie) at Simien Mountains National Park (SMNP), Ethiopia

Population viability analysis (PVA) has been applied to the management of many threatened populations. The objective of this study was, therefore, to estimate the PVA of Walia ibex at the Simen Mountains National Park, in the north‐central highlands of Ethiopia, with respect to population growth parameters, the probability of the population reaching a lower extinction threshold and the mean time to extinction. Direct census of the population was carried out in 2009. Secondary census data were also collected from park authorities and the literature reviews. The result revealed that the estimates of the infinitesimal mean, μ (0.04117) was greater than the infinitesimal variance, σ² (0.0219). The probability that the population reaches the extinction threshold was very low (0.15%). The mean time required for the counts to decline from the existing population size to one individual animal was 160 years. But threatened species are adversely affected by changes in landscape. These changes can be brought by short‐ and long‐term human and climate change impacts, respectively. Therefore, with the absence of environmental and demographic stochasticity and, with the application of appropriate reproductions and habitat management, the population of Walia ibex will be viable and reaches its mean time of extinctions after 160 years.     

Combining hyperspectral imaging and chemometrics to assess and interpret the effects of environmental stressors on zebrafish eye images at tissue level

Changes on an organism by the exposure to environmental stressors may be characterized by hyperspectral images (HSI), which preserve the morphology of biological samples, and suitable chemometric tools. The approach proposed allows assessing and interpreting the effect of contaminant exposure on heterogeneous biological samples monitored by HSI at specific tissue levels. In this work, the model example used consists of the study of the effect of the exposure of chlorpyrifos‐oxon on zebrafish tissues. To assess this effect, unmixing of the biological sample images followed by tissue‐specific classification models based on the unmixed spectral signatures is proposed. Unmixing and classification are performed by multivariate curve resolution‐alternating least squares (MCR‐ALS) and partial least squares‐discriminant analysis (PLS‐DA), respectively. Crucial aspects of the approach are: (1) the simultaneous MCR‐ALS analysis of all images from 1 population to take into account biological variability and provide reliable tissue spectral signatures, and (2) the use of resolved spectral signatures from control and exposed populations obtained from resampling of pixel subsets analyzed by MCR‐ALS multiset analysis as information for the tissue‐specific PLS‐DA classification models. Classification results diagnose the presence of a significant effect and identify the spectral regions at a tissue level responsible for the biological change.      

Temporal Variation in Infection Prevalence by the Amphibian Chytrid Fungus in Three Species of Frogs at La Selva,Costa Rica

The emerging infectious disease chytridiomycosis, caused by the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), is implicated in widespread population declines, extirpations, and extinctions of amphibians throughout the world. In the Neotropics, most amphibian declines have occurred in cool mid‐ to high‐elevation sites (> 400 m asl), and it is hypothesized that high temperatures limit the growth of Bd in lowland tropical sites, despite few data available on the distribution of Bd in lowland forests. Here, we report the results of a 12‐mo pathogen surveillance program for three common species of frogs at a warm lowland site in northeastern Costa Rica. We combine standard non‐invasive skin swabbing techniques with a quantitative polymerase chain reaction assay to analyze the infection prevalence and Bd load across a 1‐yr period. Our data indicate an overall Bd infection rate of 6.1 percent, but prevalence varies from < 5 percent in warmer months to a peak of 34.7 percent in the coolest months of the year. Despite very little seasonal variation in temperature (< 4°C), our data indicate strong seasonal variation in the prevalence of Bd, with highest prevalence of infection in months with coolest air temperatures. While it has been suggested that Bd is primarily a riparian fungus, we find no difference in prevalence of infection among our species despite considerable differences in affiliation of these species with water. Our study provides further evidence that infection by Bd is regulated by temperature and shows that warm temperatures in lowland forests may restrict, but not prevent, infection by Bd.