Methylation of ELOVL2 gene as a new epigenetic marker of age

The discovery of biomarkers able to predict biological age of individuals is a crucial goal in aging research. Recently, researchers' attention has turn toward epigenetic markers of aging. Using the Illumina Infinium HumanMethylation450 BeadChip on whole blood DNA from a small cohort of 64 subjects of different ages, we identified 3 regions, the CpG islands of ELOVL2, FHL2, and PENK genes, whose methylation level strongly correlates with age. These results were confirmed by the Sequenom's EpiTYPER assay on a larger cohort of 501 subjects from 9 to 99 years, including 7 cord blood samples. Among the 3 genes, ELOVL2 shows a progressive increase in methylation that begins since the very first stage of life (Spearman's correlation coefficient = 0.92) and appears to be a very promising biomarker of aging.     

Geographic mosaic of symbiont selectivity in a genus of epiphytic cyanolichens

In symbiotic systems, patterns of symbiont diversity and selectivity are crucial for the understanding of fundamental ecological processes such as dispersal and establishment. The lichen genus Nephroma (Peltigerales, Ascomycota) has a nearly cosmopolitan distribution and is thus an attractive model for the study of symbiotic interactions over a wide range of spatial scales. In this study, we analyze the genetic diversity of Nephroma mycobionts and their associated Nostoc photobionts within a global framework. The study is based on Internal Transcribed Spacer (ITS) sequences of fungal symbionts and tRNA^Leu (UAA) intron sequences of cyanobacterial symbionts. The full data set includes 271 Nephroma and 358 Nostoc sequences, with over 150 sequence pairs known to originate from the same lichen thalli. Our results show that all bipartite Nephroma species associate with one group of Nostoc different from Nostoc typically found in tripartite Nephroma species. This conserved association appears to have been inherited from the common ancestor of all extant species. While specific associations between some symbiont genotypes can be observed over vast distances, both symbionts tend to show genetic differentiation over wide geographic scales. Most bipartite Nephroma species share their Nostoc symbionts with one or more other fungal taxa, and no fungal species associates solely with a single Nostoc genotype, supporting the concept of functional lichen guilds. Symbiont selectivity patterns within these lichens are best described as a geographic mosaic, with higher selectivity locally than globally. This may reflect specific habitat preferences of particular symbiont combinations, but also the influence of founder effects.     

Annual plants change in size over a century of observations

Studies have documented changes in animal body sizes over the last century, but very little is known about changes in plant sizes, even though reduced plant productivity is potentially responsible for declines in size of other organisms. Here, I ask whether warming trends in the Great Basin have affected plant size by measuring specimens preserved on herbarium sheets collected between 1893 and 2011. I asked how maximum and minimum temperatures, precipitation, and the Pacific Decadal Oscillation (PDO) in the year of collection affected plant height, leaf size, and flower number, and asked whether changes in climate resulted in decreasing sizes for seven annual forbs. Species had contrasting responses to climate factors, and would not necessarily be expected to respond in parallel to climatic shifts. There were generally positive relationships between plant size and increased minimum and maximum temperatures, which would have been predicted to lead to small increases in plant sizes over the observation period. While one species increased in size and flower number over the observation period, five of the seven species decreased in plant height, four of these decreased in leaf size, and one species also decreased in flower production. One species showed no change. The mechanisms behind these size changes are unknown, and the limited data available on these species (germination timing, area of occupancy, relative abundance) did not explain why some species shrank while others grew or did not change in size over time. These results show that multiple annual forbs are decreasing in size, but that even within the same functional group, species may have contrasting responses to similar environmental stimuli. Changes in plant size could have cascading effects on other members of these communities, and differential responses to directional change may change the composition of plant communities over time.     

Effects of floral resources on the efficacy of a primary parasitoid and a facultative hyperparasitoid

Resources added to agroecosystems to enhance biological control are potentially available to multiple members of the resident insect community—not only the biological control agents for which the resources are intended. Many studies have examined the effects of sugar feeding on the efficacy of biological control agents. However, such information is lacking for other, interacting species such as facultative hyperparasitoids, which may contribute to pest suppression but can also interfere with introduced biological control agents. Under greenhouse conditions, we tested the direct effects of sugar and nectar provisioning on the longevity, host‐killing impact and offspring production of two pupal parasitoids associated with leek moth, Acrolepiopsis assectella: the introduced biological control agent, Diadromus pulchellus, and the native facultative hyperparasitoid, Conura albifrons. Adding sucrose, buckwheat or a combination of buckwheat and common vetch to a sugar‐deprived system (potted leek plants in cages) increased parasitoid longevity and resulted in higher leek moth parasitism and mortality compared to water or common vetch treatments. However, the two parasitoid species exhibited a distinct temporal response to the treatments, likely influenced by differences in their life histories. This study provides insight into how integrating conservation biological control techniques could affect the success of a classical biological control programme.     

Phylogenetic Position of Parasitic Chytrids on Diatoms: Characterization of a Novel Clade in Chytridiomycota

Chytrids are true fungi that reproduce with posteriorly uniflagellate zoospores. In the last decade, environmental DNA surveys revealed a large number of uncultured chytrids as well as undescribed order‐level novel clades in Chytridiomycota. Although many species have been morphologically described, only some DNA sequence data of parasitic chytrids are available from the database. We herein discuss five cultures of parasitic chytrids on diatoms Aulacoseira spp. and Asterionella formosa. In order to identify the chytrids examined, thallus morphologies were observed using light microscopy. We also conducted a phylogenetic analysis using 18S, 5.8S, and 28S rDNA sequences to obtain their phylogenetic positions. Based on their morphological characteristics, two cultures parasitic on As. formosa were identified as Rhizophydium planktonicum and Zygorhizidium planktonicum. The other three cultures infecting Aulacoseira spp. (two on Aulacoseira ambigua and the other on Aulacoseira granulata) were regarded as Zygorhizidium aff. melosirae. The results of the molecular phylogenetic analysis revealed that R. planktonicum belonged to the known order Chytridiales, while the two species of Zygorhizidium were placed in a novel clade that was previously reported as an undescribed clade composed of only the environmental sequences of uncultured chytrids.     

Evaluating the Qualitative Effectiveness of a Novel Pollinator: a Case Study of Two Endemic Hawaiian Plants

In situations where native mutualists have become extinct, non‐native species may partner with remnant native species. However, non‐native mutualists may differ behaviorally from extinct native mutualists. In the case of pollination, novel relationships between natives and non‐natives could differ both quantitatively and qualitatively from native–native relationships. In Hawai'i, the non‐native Japanese White‐eye (Zosterops japonicus) has largely replaced endemic birds as pollinator of the endemic Clermontia parviflora and C. montis‐loa. We surveyed Clermontia patches and found that they ranged from 106 to 1198 m in diameter. We performed manual pollination of flowers with pollen taken from plants at five distance categories, ranging from 0 (self‐fertilization) to 20 km, and examined the germination of resulting seeds. We used radiotelemetry to estimate daily Japanese White‐eye movement distances. Percent germination of seeds after short‐ to intermediate‐distance pollination crosses (i.e., 20–1200 m, or intra‐patch pollen transfer distances) significantly exceeded germination of seeds from selfed trials for C. parviflora. No significant differences in germination rates among treatments were detected for C. montis‐loa. The maximum daily movement distances of radio‐tracked birds were generally <1 km. Together, these results suggest that this novel pollinator may be an effective mutualist for both Clermontia species. This study serves as an example of research examining qualitative components of novel mutualism, which are generally neglected relative to quantitative components.     

Phylogeography of the freshwater raphidophyte Gonyostomum semen confirms a recent expansion in northern Europe by a single haplotype

Gonyostmum semen is a freshwater raphidophyte that has increased in occurrence and abundance in several countries in northern Europe since the 1980s. More recently, the species has expanded rapidly also in north‐eastern Europe, and it is frequently referred to as invasive. To better understand the species history, we have explored the phylogeography of G. semen using strains from northern Europe, United States, and Japan. Three regions of the ribosomal RNA gene (small subunit [SSU], internal transcribed spacer [ITS] and large subunit [LSU]) and one mitochondrial DNA marker (cox1) were analyzed. The SSU and partial LSU sequences were identical in all strains, confirming that they belong to the same species. The ITS region differentiated the American from the other strains, but showed high intra‐strain variability. In contrast, the mitochondrial marker cox1 showed distinct differences between the European, American, and Japanese strains. Interestingly, only one cox1 haplotype was detected in European strains. The overall low diversity and weak geographic structure within northern European strains supported the hypothesis of a recent invasion of new lakes by G. semen. Our data also show that the invasive northern European lineage is genetically distinct from the lineages from the other continents. Finally, we concluded that the mitochondrial cox1 was the most useful marker in determining large‐scale biogeographic patterns in this species.     

A clever solution to a vexing problem

F_ST (as well as related measures such as G_ST) has long been used both as a measure of the relative amount of genetic variation between populations and as an indicator of the amount of gene flow among populations. Unfortunately, F_ST and its clones are also sensitive to mutation, particularly when the mutation rate per locus is greater than the migration rate among populations. Relatively high mutation rates cause estimates of F_ST and G_ST to be much lower than researchers sometimes expect, when migration rates are low in the studied species. Several recent suggestions for dealing with this problem have been unsatisfactory for one reason or another, and no general solution exists (if we are not to abandon these otherwise useful measures of differentiation). In an important article in this issue, Jinliang Wang (2015) shows that it is possible to identify whether the genetic markers in a given study are likely to give estimates of F_ST that are strongly affected by mutation. The proposed test is simple and elegant, and with it, molecular ecologists can determine whether the F_ST from their makers can be depended on for further inference about their species’ genome and the demographic forces which shaped its patterns.     

Depolarization‐induced suppression of a glycinergic synapse in the superior olivary complex by endocannabinoids

The neuronal endocannabinoid system is known to depress synaptic inputs retrogradely in an activity‐dependent manner. This mechanism has been generally described for excitatory glutamatergic and inhibitory GABAergic synapses. Here, we report that neurones in the auditory brainstem of the Mongolian gerbil (Meriones unguiculatus) retrogradely regulate the strength of their inputs via the endocannabinoid system. By means of whole‐cell patch‐clamp recordings, we found that retrograde endocannabinoid signalling attenuates both glycinergic and glutamatergic post‐synaptic currents in the same types of neurones. Accordingly, we detected the cannabinoid receptor 1 in excitatory and inhibitory pre‐synapses as well as the endocannabinoid‐synthesising enzymes (diacylglycerol lipase α/β, DAGLα/β) post‐synaptically through immunohistochemical stainings. Our study was performed with animals aged 10–15 days, that is, in the time window around the onset of hearing. Therefore, we suggest that retrograde endocannabinoid signalling has a role in adapting inputs during the functionally important switch from spontaneously generated to sound‐related signals.

     

The peculiar nemertean larva pilidium recurvatum belongs to Riserius sp., a basal heteronemertean that eats Carcinonemertes errans,a hoplonemertean parasite of Dungeness crab

A typical nemertean pilidium larva resembles a hat with ear flaps. But one type, called pilidium recurvatum, looks more like a sock, swimming heel first. This distinctive larva was discovered in 1883 off the coast of Rhode Island and subsequently found in plankton samples from other parts of the world. Despite the long time since discovery, and its significance in discussions of larval evolution, this larva remained unidentified even to the family level. We collected pilidium recurvatum larvae from plankton samples in Coos Bay, OR, and identified them as belonging to the heteronemertean genus Riserius based on juvenile morphology and DNA sequence data. Phylogenetic analysis suggests that two distinct types of pilidium recurvatum from Oregon represent two new species within this currently monotypic genus. We describe the morphology of pilidium recurvatum using confocal microscopy and compare it to that of the typical pilidium, discussing possible implications for larval feeding. We also report our surprising discovery that juveniles of Riserius sp. from Oregon prey on another nemertean, Carcinonemertes errans, an egg predator of Cancer magister (Dungeness crab), a commercially important species. We speculate that the species‐level diversity and geographic distribution of Riserius may be much greater than currently appreciated.     

Research Note: Observations on a terrestrial charophyte in a temperate environment

This study describes the unusual growth forms of Chara (Charales) in a natural terrestrial environment in a temperate region (southern Siberia). Chara vulgaris had a moss‐like habit and grew on wet soil in small compact turfs probably germinated from oospores. The upper branchlets were curved in a hook‐liked manner and convergent above the apex of the thallus. The lowest internode and branchlets of fertile plants were ecorticate, whereas all other parts were normally corticated; the completely ecorticate plants were sterile. The terrestrial growth of charophytes had an irregular appearance but was successfully maintained in culture, providing a potential model of the first steps of land colonization by the ancestors of embryophytes.     

Timing of flowering and intensity of attack by a butterfly herbivore in a polyploid herb

Timing of plant development both determines the abiotic conditions that the plant experiences and strongly influences the intensity of interactions with other organisms. Plants and herbivores differ in their response to environmental cues, and spatial and temporal variation in environmental conditions might influence the synchrony between host plants and herbivores, and the intensity of their interactions. We investigated whether differences in first day of flowering among and within 21 populations of the polyploid herb Cardamine pratensis influenced the frequency of oviposition by the butterfly Anthocharis cardamines during four study years. The proportion of plants that became oviposited upon differed among populations, but these differences were not related to mean flowering phenology within the population in any of the four study years. Attack rates in the field were also not correlated with resistance to oviposition estimated under controlled conditions. Within populations, the frequency of butterfly attack was higher in early‐flowering individuals in two of the four study years, while there was no significant relationship in the other 2 years. Larger plants were more likely to become oviposited upon in all 4 years. The effects of first flowering day and size on the frequency of butterfly attack did not differ among populations. The results suggest that differences in attack intensities among populations are driven mainly by differences in the environmental context of populations while mean differences in plant traits play a minor role. The fact that within populations timing of flowering influenced the frequency of herbivore attack only in some years and suggests that herbivore‐mediated selection on plant phenology differs among years, possibly because plants and herbivores respond differently to environmental cues.     

Genetic architecture of a body colour cline in Drosophila americana

Phenotypic variation within a species is often structured geographically in clines. In Drosophila americana, a longitudinal cline for body colour exists within North America that appears to be due to local adaptation. The tan and ebony genes have been hypothesized to contribute to this cline, with alleles of both genes that lighten body colour found in D. americana. These alleles are similar in sequence and function to the allele fixed in D. americana's more lightly pigmented sister species, Drosophila novamexicana. Here, we examine the frequency and geographic distribution of these D. novamexicana‐like alleles in D. americana. Among alleles from over 100 strains of D. americana isolated from 21 geographic locations, we failed to identify additional alleles of tan or ebony with as much sequence similarity to D. novamexicana as the D. novamexicana‐like alleles previously described. However, using genetic analysis of 51 D. americana strains derived from 20 geographic locations, we identified one new allele of ebony and one new allele of tan segregating in D. americana that are functionally equivalent to the D. novamexicana allele. An additional 5 alleles of tan also showed marginal evidence of functional similarity. Given the rarity of these alleles, however, we conclude that they are unlikely to be driving the pigmentation cline. Indeed, phenotypic distributions of the 51 backcross populations analysed indicate a more complex genetic architecture, with diversity in the number and effects of loci altering pigmentation observed both within and among populations of D. americana. This genetic heterogeneity poses a challenge to association studies and genomic scans for clinal variation, but might be common in natural populations.     

Ramularia coleosporii,a Hyperparasite on Coleosporium plumeriae in India

During a survey of fungal plant diseases, parasitized uredinial pustules of Coleosporium plumeriae were observed in Umiam, Meghalaya, India. Microscopic examination was conducted using light and scanning electron microscopy which revealed the occurrence of the hyperparasitic hyphomycete Ramularia coleosporii. Molecular characterization using the ITS1‐5.8S‐ITS2 region of nrDNA also confirmed our results. This is the first record of R. coleosporii on C. plumeriae from India.     

Clonal diversity driven by parasitism in a freshwater snail

One explanation for the widespread abundance of sexual reproduction is the advantage that genetically diverse sexual lineages have under strong pressure from virulent coevolving parasites. Such parasites are believed to track common asexual host genotypes, resulting in negative frequency‐dependent selection that counterbalances the population growth‐rate advantage of asexuals in comparison with sexuals. In the face of genetically diverse asexual lineages, this advantage of sexual reproduction might be eroded, and instead sexual populations would be replaced by diverse assemblages of clonal lineages. We investigated whether parasite‐mediated selection promotes clonal diversity in 22 natural populations of the freshwater snail Melanoides tuberculata. We found that infection prevalence explains the observed variation in the clonal diversity of M. tuberculata populations, whereas no such relationship was found between infection prevalence and male frequency. Clonal diversity and male frequency were independent of snail population density. Incorporating ecological factors such as presence/absence of fish, habitat geography and habitat type did not improve the predictive power of regression models. Approximately 11% of the clonal snail genotypes were shared among 2–4 populations, creating a web of 17 interconnected populations. Taken together, our study suggests that parasite‐mediated selection coupled with host dispersal ecology promotes clonal diversity. This, in return, may erode the advantage of sexual reproduction in M. tuberculata populations.     

Biodiversity of green algae covering artificial hard substrate surfaces in a suburban environment: a case study using molecular approaches

In Middle European suburban environments green algae often cover open surfaces of artificial hard substrates. Microscopy reveals the Apatococcus/Desmococcus morphotype predominant over smaller coccoid forms. Adverse conditions such as limited water availability connected with high PAR and UV irradiance may narrow the algal diversity to a few specialists in these subaerial habitats. We used rRNA gene cloning/sequencing from both DNA extracts of the biofilms without culturing as well as cultures, for the unambiguous determination of the algal composition and to assess the algal diversity more comprehensively. The culture independent approach revealed mainly just two genera (Apatococcus, Trebouxia) for all study sites and five molecular operational taxonomic units (OTUs) for a particular study site, which based on microscopic observation was the one with the highest morphological diversity. The culture approach, however, revealed seven additional OTUs from five genera (Chloroidium, Coccomyxa, Coenochloris, Pabia, Klebsormidium) and an unidentified trebouxiophyte lineage for that same site; only two OTUs were shared by both approaches. Two OTUs or species were recovered for which references have been isolated only from Antarctica so far. However, the internal transcribed spacer (ITS) sequence differences among them supported they are representing distinct populations of the same species. Within Apatococcus five clearly distinct groups of ITS sequences, each putatively representing a distinct species, were recovered with three or four such ITS types co‐occurring at the same study site. Except for the streptophyte Klebsormidium only members of Trebouxiophyceae were detected suggesting these algae may be particularly well‐adapted to subaerial habitats.     

Extreme protomeric development in a burlingiid trilobite from Cambrian glacial erratics of Denmark

Pengia Geyer & Corbacho is a Cambrian burlingiid trilobite with fused trunk segments devoid of any articulation in the anamorphic and epimorphic phases of development. The type species is Pengia fusilis (Peng et al.) from the Wanshania wanshanensis Zone of China. Here we describe a second species, Pengia palsgaardia sp. nov., from the Lejopyge laevigata Zone of the Paradoxides forchhammeri Superzone. It comes from a glacial erratic in Denmark which probably originated in the Alum Shale Formation of Västergötland, Sweden. Pengia palsgaardia is a large burlingiid (~10 mm in length), with 14 fused segments in the trunk whose boundaries are marked by ridges. The axis is narrow, with the axial furrows faintly indicated or effaced across the median. Laterally along the axis and the tapering glabella, symmetrical globular lobes are developed that are pinched at their base. During ontogeny the glabellar furrows are pit‐like adaxially but shallow towards the axial furrow as the globular lobes develop. Their pit‐like appearance in Pengia palsgaardia and some other burlingiid species is not considered similar to the condition seen in oryctocephalid trilobites. A median preglabellar ridge resembling that of Schmalenseeia Moberg develops late in ontogeny but in early ontogeny the preglabellar field resembles that of Burlingia Walcott, Alumenella Geyer & Corbacho and Niordilobites Geyer & Corbacho. This gives Pengia a more basal position in the schmalenseeid lineage, outside the derived Schmalenseeia. In mature specimens the facial sutures in P. palsgaardia are fused, but an ocular suture may have been present. During ontogeny Pengia would have gone through the anamorphic and protomeric protaspid segmental conditions, but articulation between either the cephalon and pygidium, or pygidium and thoracic segments of the trunk never developed so it did not progress beyond the protaspid phase. This extreme protomeric development is considered to be a derived feature in Pengia.     

Amplification of ABA biosynthesis and signaling through a positive feedback mechanism in seeds

Abscisic acid is an essential hormone for seed dormancy. Our previous study using the plant gene switch system, a chemically induced gene expression system, demonstrated that induction of 9‐cis‐epoxycarotenoid dioxygenase (NCED), a rate‐limiting ABA biosynthesis gene, was sufficient to suppress germination in imbibed Arabidopsis seeds. Here, we report development of an efficient experimental system that causes amplification of NCED expression during seed maturation. The system was created with a Triticum aestivum promoter containing ABA responsive elements (ABREs) and a Sorghum bicolor NCED to cause ABA‐stimulated ABA biosynthesis and signaling, through a positive feedback mechanism. The chimeric gene pABRE:NCED enhanced NCED and ABF (ABRE‐binding factor) expression in Arabidopsis Columbia‐0 seeds, which caused 9‐ to 73‐fold increases in ABA levels. The pABRE:NCED seeds exhibited unusually deep dormancy which lasted for more than 3 months. Interestingly, the amplified ABA pathways also caused enhanced expression of Arabidopsis NCED5, revealing the presence of positive feedback in the native system. These results demonstrated the robustness of positive feedback mechanisms and the significance of NCED expression, or single metabolic change, during seed maturation. The pABRE:NCED system provides an excellent experimental system producing dormant and non‐dormant seeds of the same maternal origin, which differ only in zygotic ABA. The pABRE:NCED seeds contain a GFP marker which enables seed sorting between transgenic and null segregants and are ideal for comparative analysis. In addition to its utility in basic research, the system can also be applied to prevention of pre‐harvest sprouting during crop production, and therefore contributes to translational biology.     

Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus

DNA barcoding aims to develop an efficient tool for species identification based on short and standardized DNA sequences. In this study, the DNA barcode paradigm was tested among the genera of the tribe Sisyrinchieae (Iridoideae). Sisyrinchium, with more than 77% of the species richness in the tribe, is a taxonomically complex genus. A total of 185 samples belonging to 98 species of Sisyrinchium, Olsynium, Orthrosanthus and Solenomelus were tested using matK, trnH‐psbA and internal transcribed spacer (ITS). Candidate DNA barcodes were analysed either as single markers or in combination. Detection of a barcoding gap, similarity‐based methods and tree‐based analyses were used to assess the discrimination efficiency of DNA barcodes. The levels of species identification obtained from plastid barcodes were low and ranged from 17.35% to 20.41% for matK and 5.11% to 7.14% for trnH‐psbA. The ITS provided better results with 30.61–38.78% of species identified. The analyses of the combined data sets did not result in a significant improvement in the discrimination rate. Among the tree‐based methods, the best taxonomic resolution was obtained with Bayesian inference, particularly when the three data sets were combined. The study illustrates the difficulties for DNA barcoding to identify species in evolutionary complex lineages. Plastid markers are not recommended for barcoding Sisyrinchium due to the low discrimination power observed. ITS gave better results and may be used as a starting point for species identification.