Evolution of the Dynein Heavy Chain Family in Ciliates

Dynein heavy chains are motor proteins that comprise a large gene family found across eukaryotes. We have investigated this gene family in four ciliate species: Ichthyophthirius, Oxytricha, Paramecium, and Tetrahymena. Ciliates appear to encode more dynein heavy chain genes than most eukaryotes. Phylogenetic comparisons demonstrated that the last common ancestor of the ciliates that were examined expressed at least 14 types of dynein heavy chains with most of the expansion coming from the single‐headed inner arm dyneins. Each of the dyneins most likely performed different functions within the cell.     

Modelling horse management in the Australian Alps

Management of the feral Horse (Equus caballus) in the Australian Alps bioregion is a difficult and emotive issue, with interested parties working from vastly differing perspectives. Compounding this, information regarding ecology and distribution of horses, and the cost and effectiveness of management strategies is often unknown or uncertain. Resolving these issues requires an objective approach with the flexibility to incorporate different potential scenarios. We used a spatially explicit population model to compare the potential effects of two different management strategies on populations of horses in the Australian Alps bioregion: culling from helicopters versus trapping and mustering. We populated the model using the results of population surveys conducted in 2014, vegetation data and cost estimates. We then provided an estimate of the effect of each strategy on population size across the Alps, and their corresponding costs, compared to no management. To account for uncertainties, we simulated different scenarios for horse population densities, dispersal rates and population growth rates. Management using aerial culling was more effective than mustering in every scenario modelled, and three to six times cheaper. Aerial culling was only slightly more effective within its control region. However, because mustering is necessarily restricted by road access, this translated to a substantial improvement in population control – up to 2000 horses where growth and dispersal rates were high. Our results unequivocally suggest aerial culling as the only strategy that could effectively control horses within the modelled range of scenarios; this result stands in addition to its other potential benefits of lower cost, animal stress and landscape disturbance. A major advantage of this modelling approach is that we can easily update it with new data, test different measures of effectiveness and add new scenarios to adapt to the rapidly changing situation on the ground, both in terms of the ecology and the political climate.     

Connectivity in the cold: the comparative population genetics of vent‐endemic fauna in the Scotia Sea,Southern Ocean

We report the first comparative population genetics study for vent fauna in the Southern Ocean using cytochrome C oxidase I and microsatellite markers. Three species are examined: the kiwaid squat lobster, Kiwa tyleri, the peltospirid gastropod, Gigantopelta chessoia, and a lepetodrilid limpet, Lepetodrilus sp., collected from vent fields 440 km apart on the East Scotia Ridge (ESR) and from the Kemp Caldera on the South Sandwich Island Arc, ~95 km eastwards. We report no differentiation for all species across the ESR, consistent with panmixia or recent range expansions. A lack of differentiation is notable for Kiwa tyleri, which exhibits extremely abbreviated lecithotrophic larval development, suggestive of a very limited dispersal range. Larval lifespans may, however, be extended by low temperature‐induced metabolic rate reduction in the Southern Ocean, muting the impact of dispersal strategy on patterns of population structure. COI diversity patterns suggest all species experienced demographic bottlenecks or selective sweeps in the past million years and possibly at different times. ESR and Kemp limpets are divergent, although with evidence of very recent ESR‐Kemp immigration. Their divergence, possibility indicative of incipient speciation, along with the absence of the other two species at Kemp, may be the consequence of differing dispersal capabilities across a ~1000 m depth range and/or different selective regimes between the two areas. Estimates of historic and recent limpet gene flow between the ESR and Kemp are consistent with predominantly easterly currents and potentially therefore, cross‐axis currents on the ESR, with biogeographic implications for the region.     

Chloroplast Genome Evolution in the Euglenaceae

Over the last few years multiple studies have been published outlining chloroplast genomes that represent many of the photosynthetic euglenid genera. However, these genomes were scattered throughout the euglenophyceaean phylogenetic tree, and focused on comparisons with Euglena gracilis. Here, we present a study exclusively on taxa within the Euglenaceae. Six new chloroplast genomes were characterized, those of Cryptoglena skujai, E. gracilis var. bacillaris, Euglena viridis, Euglenaria anabaena, Monomorphina parapyrum, and Trachelomonas volvocina, and added to six previously published chloroplast genomes to determine if trends existed within the family. With this study: at least one genome has now been characterized for each genus, the genomes of different strains from two taxa were characterized to explore intraspecific variability, and a second taxon has been characterized for the genus Monomorphina to examine intrageneric variability. Overall results showed a large amount of variability among the genomes, though a few trends could be identified both within Euglenaceae and within Euglenophyta. In addition, the intraspecific analysis indicated that the similarity of a genome sequence between strains was taxon dependent, and the intrageneric analysis indicated that the majority of the evolutionary changes within the Euglenaceae occurred intergenerically.     

How to deal with neglected tropical diseases in the light of an African ethic

Many countries in Africa, and more generally those in the Global South with tropical areas, are plagued by illnesses that the wealthier parts of the world (mainly ‘the West’) neither suffer from nor put systematic effort into preventing, treating or curing. What does an ethic with a recognizably African pedigree entail for the ways various agents ought to respond to such neglected diseases? As many readers will know, a characteristically African ethic prescribes weighty duties to aid on the part of those in a position to do so, and it therefore entails that there should have been much more contribution from the Western, ‘developed’ world. However, what else does it prescribe, say, on the part of sub‐Saharan governments and the African Union, and are they in fact doing it? I particularly seek to answer these questions here, by using the 2013‐16 Ebola crisis in West Africa to illustrate what should have happened but what by and large did not.     

Role of ethylene and related gene expression in the interaction between strawberry plants and the plant growth‐promoting bacterium Azospirillum brasilense

• Induced systemic resistance (ISR) is one of the indirect mechanisms of growth promotion exerted by plant growth‐promoting bacteria, and can be mediated by ethylene (ET). We assessed ET production and the expression of related genes in the Azospirillum–strawberry plant interaction.
• Ethylene production was evaluated by gas chromatography in plants inoculated or not with A. brasilense REC3. Also, plants were treated with AgNO₃, an inhibitor of ET biosynthesis; with 1‐aminocyclopropane‐1‐carboxylic acid (ACC), a precursor of ET biosynthesis; and with indole acetic acid (IAA). Plant dry biomass and the growth index were determined to assess the growth‐promoting effect of A. brasilense REC3 in strawberry plants. Quantitative real time PCR (qRT‐PCR) was performed to analyse relative expression of the genes Faetr1, Faers1 and Faein4, which encode ET receptors; Factr1 and Faein2, involved in the ET signalling pathway; Faacs1 encoding ACC synthase; Faaco1 encoding ACC oxidase; and Faaux1 and Faami1 for IAA synthesis enzymes.
• Results showed that ET acts as a rapid and transient signal in the first 12 h post‐treatment. A. brasilense REC3‐inoculated plants had a significantly higher growth index compared to control plants. Modulation of the genes Faetr1, Faers1, Faein4, Factr1, Faein2 and Faaco1 indicated activation of ET synthesis and signalling pathways. The up‐regulation of Faaux1 and Faami1 involved in IAA synthesis suggested that inoculation with A. brasilense REC3 induces production of this auxin, modulating ET signalling.
• Ethylene production and up‐regulation of genes associated with ET signalling in strawberry plants inoculated with A. brasilense REC3 support the priming activation characteristic of ISR. This type of resistance and the activation of systemic acquired resistance previously observed in this interaction indicate that both are present in strawberry plants, could act synergistically and increase protection against pathogens.

     

Circannual variation in blood parasitism in a sub‐Saharan migrant passerine bird,the garden warbler

Knowing the natural dynamics of pathogens in migratory birds is important, for example, to understand the factors that influence the transport of pathogens to and their transmission in new geographical areas, whereas the transmission of other pathogens might be restricted to a specific area. We studied haemosporidian blood parasites of the genera Plasmodium, Haemoproteus and Leucocytozoon in a migratory bird, the garden warbler Sylvia borin. Birds were sampled in spring, summer and early autumn at breeding grounds in Sweden, on migration at Capri, Italy and on arrival and departure from wintering staging areas in West Africa: mapping recoveries of garden warblers ringed in Fennoscandia and Capri showed that these sites are most probably on the migratory flyway of garden warblers breeding at Kvismaren. Overall, haemosporidian prevalence was 39%, involving 24 different parasite lineages. Prevalence varied significantly over the migratory cycle, with relatively high prevalence of blood parasites in the population on breeding grounds and at the onset of autumn migration, followed by marked declines in prevalence during migration both on spring and autumn passage. Importantly, we found that when examining circannual variation in the different lineages, significantly different prevalence profiles emerged both between and within genera. Our results suggest that differences in prevalence profiles are the result of either different parasite transmission strategies or coevolution between the host and the various parasite lineages. When separating parasites into common vs. rare lineages, we found that two peaks in the prevalence of rare parasites occur; on arrival at Swedish breeding grounds, and after the wintering period in Africa. Our results stress the importance of appropriate taxonomic resolution when examining host‐parasite interactions, as variation in prevalence both between and within parasite genera can show markedly different patterns.     

Expression of the purine biosynthetic enzyme phosphoribosyl formylglycinamidine synthase in neurons

Purines are metabolic building blocks essential for all living organisms on earth. De novo purine biosynthesis occurs in the brain and appears to play important roles in neural development. Phosphoribosyl formylglycinamidine synthase (FGAMS , also known as PFAS or FGARAT ), a core enzyme involved in the de novo synthesis of purines, may play alternative roles in viral pathogenesis. To date, no thorough investigation of the endogenous expression and localization of de novo purine biosynthetic enzymes has been conducted in human neurons or in virally infected cells. In this study, we characterized expression of FGAMS using multiple neuronal models. In differentiated human SH ‐SY 5Y neuroblastoma cells, primary rat hippocampal neurons, and in whole‐mouse brain sections, FGAMS immunoreactivity was distributed within the neuronal cytoplasm. FGAMS immunolabeling in vitro demonstrated extensive distribution throughout neuronal processes. To investigate potential changes in FGAMS expression and localization following viral infection, we infected cells with the human pathogen herpes simplex virus 1. In infected fibroblasts, FGAMS immunolabeling shifted from a diffuse cytoplasmic location to a mainly perinuclear localization by 12 h post‐infection. In contrast, in infected neurons, FGAMS localization showed no discernable changes in the localization of FGAMS immunoreactivity. There were no changes in total FGAMS protein levels in either cell type. Together, these data provide insight into potential purine biosynthetic mechanisms utilized within neurons during homeostasis as well as viral infection.

Cover Image for this Issue: doi: 10.1111/jnc.14169 .

     

Screening of natural products in the laboratory and the field for control of pollen beetles

Pollen beetles, Meligethes spp. (Coleoptera: Nitidulidae), are among the most damaging pests of oilseed rape (Brassica napus L.). Increasing populations of pyrethroid‐resistant pollen beetles coupled with the prohibition of synthetic pest control products in organic farming means that other direct control methods are needed. A laboratory study was therefore conducted to evaluate the effect of natural products, combinations of natural products and additives as well as natural and synthetic insecticides on mortality of pollen beetles. In addition, field trials under both integrated and organic production were conducted to evaluate the efficacy of six natural products, nine combinations of natural products, two synthetic insecticides (integrated‐production trials only), two natural insecticides and two additives to reduce pollen beetles. The laboratory trial, using both a curative and preventive approach, showed that two of the eight natural products (lavender oil and stone meal) caused a mortality of over 98% within the first day of application. The other natural products were only partially effective compared with the untreated control. In the field trials, the natural products reduced the number of pollen beetles 1 day after application compared with the untreated control in both trial years and production systems. Promising substances were stone meal, Silico‐Sec and liquid manure. Nevertheless, the efficacy was not consistent, and no effect on oilseed rape yield was observed. In spite of this, these products have the potential to control pollen beetles under field conditions with comparable effects to synthetic insecticides. Further research should therefore focus on timing and frequency of applications as well as on the formulation of the natural products to increase the persistency of the products under field conditions.     

The effect of Wolbachia on the lifetime reproductive success of its insect host in the field

Wolbachia is a widespread endosymbiont that induces dramatic manipulations of its host's reproduction. Although there has been substantial progress in the developing theory for Wolbachia–host interactions and in measuring the effects of Wolbachia on host fitness in the laboratory, there is a widely recognized need to quantify the effects of Wolbachia on the host fitness in the field. The wasp Anagrus sophiae, an egg parasitoid of planthoppers, carries a Wolbachia strain that induces parthenogenesis, but its effects on the fitness of its Anagrus host are unknown. We developed a method to estimate the realized lifetime reproductive success of female wasps by collecting them soon after they die naturally in the field, counting the number of eggs remaining in their ovaries and quantifying Wolbachia density in their body. We sampled from a highly infected A. sophiae population and found no evidence for Wolbachia virulence and possible evidence for positive effects of Wolbachia on realized reproductive success.     

Snake evolution in Melanesia: origin of the Hydrophiinae (Serpentes,Elapidae), and the evolutionary history of the enigmatic New Guinean elapid Toxicocalamus

The venomous snake subfamily Hydrophiinae includes more than 40 genera and approximately 200 species. Most members of this clade inhabit Australia, and have been well studied. But, because of poor taxon sampling of Melanesian taxa, basal evolutionary relationships have remained poorly resolved. The Melanesian genera Ogmodon, Loveridgelaps, and Salomonelaps have not been included in recent phylogenetic studies, and the New Guinean endemic, Toxicocalamus, has been poorly sampled and sometimes recovered as polyphyletic. We generated a multilocus phylogeny for the subfamily using three mitochondrial and four nuclear loci so as to investigate relationships among the basal hydrophiine genera and to determine the status of Toxicocalamus. We sequenced these loci for eight of the 12 described species within Toxicocalamus, representing the largest molecular data set for this genus. We found that a system of offshore island arcs in Melanesia was the centre of origin for terrestrial species of Hydrophiinae, and we recovered Toxicocalamus as monophyletic. Toxicocalamus demonstrates high genetic and morphological diversity, but some of the molecular diversity is not accompanied by diagnostic morphological change. We document at least five undescribed species that all key morphologically to Toxicocalamus loriae (Boulenger, 1898), rendering this species polyphyletic. Continued work on Toxicocalamus is needed to document the diversity of this genus, and is likely to result in the discovery of additional species. Our increased taxon sampling allowed us to better understand the evolution and biogeography of Hydrophiinae; however, several unsampled lineages remain, the later study of which may be used to test our biogeographic hypothesis.     

Differences in the Detection of BrdU/EdU Incorporation Assays Alter the Calculation for G1, S,and G2 Phases of the Cell Cycle in Trypanosomatids

Trypanosomatids are the etiologic agents of various infectious diseases in humans. They diverged early during eukaryotic evolution and have attracted attention as peculiar models for evolutionary and comparative studies. Here, we show a meticulous study comparing the incorporation and detection of the thymidine analogs BrdU and EdU in Leishmania amazonensis, Trypanosoma brucei, and Trypanosoma cruzi to monitor their DNA replication. We used BrdU‐ and EdU‐incorporated parasites with the respective standard detection approaches: indirect immunofluorescence to detect BrdU after standard denaturation (2 M HCl) and “click” chemistry to detect EdU. We found a discrepancy between these two thymidine analogs due to the poor detection of BrdU, which is reflected on the estimative of the duration of the cell cycle phases G1, S, and G2. To solve this discrepancy, we increase the exposure of incorporated BrdU using different concentrations of HCl. Using a new value for HCl concentration, we re‐estimated the phases G1, S, G2 + M, and cytokinesis durations, confirming the values found by this approach using EdU. In conclusion, we suggest that the studies using BrdU with standard detection approach, not only in trypanosomatids but also in others cell types, should be reviewed to ensure an accurate estimation of DNA replication monitoring.     

Branching the risks: architectural plasticity and bet‐hedging in Mediterranean annuals

It has been suggested that architectural plasticity in shoot size and number allows plants to manage environmental risks. Simpler structures require shorter development times and fewer resources, which secure minimal fitness even under risky and unfavourable conditions. Here we tested the hypothesis that the magnitude of such architectural plasticity depends on the species' developmental strategy. Specifically, species with late reproduction were expected to express the highest levels of architectural plasticity in response to environmental cues predicting high probability of abrupt deterioration in growth conditions. This hypothesis was tested by comparing Mediterranean and semi‐arid populations of three species, which differed in growth strategy: Trifolium purpureum, a determinate and late flowerer, and Emex spinosa and Hippocrepis unisiliquosa that flower indeterminately throughout the season. All plants were exposed to varying levels of water availability and competition, but only T. purpureum displayed plastic architectural responsiveness to the experimental manipulations. In contrast, the early and extended step‐by‐step flowering of both E. spinosa and H. unisiliquosa reflected a relatively deterministic bet‐hedging reproductive schedule, whereby minimum fitness is secured even under adverse conditions. These two opposing strategies gave contrasting results, with E. spinosa and H. unisiliquosa displaying reduced efficiency under favourable conditions under which T. purpureum had the highest reproductive efficiency. The evolutionary interplay between deterministic risk‐averse and plastic risk‐prone growth strategies might reflect contrasts in the probability and severity of environmental risks, and the costs of missed opportunities.     

Climate‐change refugia in the sheltered bays of Palau: analogs of future reefs

Coral bleaching and mortality are predicted to increase as climate change‐induced thermal‐stress events become more frequent. Although many studies document coral bleaching and mortality patterns, few studies have examined deviations from the expected positive relationships among thermal stress, coral bleaching, and coral mortality. This study examined the response of >30,000 coral colonies at 80 sites in Palau, during a regional thermal‐stress event in 2010. We sought to determine the spatial and taxonomic nature of bleaching and examine whether any habitats were comparatively resistant to thermal stress. Bleaching was most severe in the northwestern lagoon, in accordance with satellite‐derived maximum temperatures and anomalous temperatures above the long‐term averages. Pocillopora populations suffered the most extensive bleaching and the highest mortality. However, in the bays where temperatures were higher than elsewhere, bleaching and mortality were low. The coral‐community composition, constant exposure to high temperatures, and high vertical attenuation of light caused by naturally high suspended particulate matter buffered the corals in bays from the 2010 regional thermal‐stress event. Yet, nearshore reefs are also most vulnerable to land‐use change. Therefore, nearshore reefs should be given high conservation status because they provide refugia for coral populations as the oceans continue to warm.     

Identification of Intracellular Bacteria in the Ciliate Balantidium ctenopharyngodoni (Ciliophora,Litostomatea)

The ciliate Balantidium ctenopharyngodoni is the most prominent protist in the guts of grass carp, where it mainly inhabits the creamy luminal contents of the hindgut. Ciliates are generally colonized by microorganisms via phagotrophic feeding. In order to study the intracellular bacteria in this ciliate, we have successfully established it in in vitro culture. Herein, we investigated and compared the bacterial community structures of cultured and freshly collected B. ctenopharyngodoni. The results showed that these two groups exhibited different bacterial communities. The most abundant bacterial family in freshly collected samples was Enterobacteriaceae, while in cultured samples it was Fusobacteriaceae. In addition, a key intracellular bacterium, Cetobacterium somerae, was identified in the cytoplasm of cultured ciliates using fluorescence in situ hybridization (FISH). This study shows that ciliates can retain the intracellular bacteria acquired in the natural habitat for quite a long time, but the bacterial community structure of ciliates eventually changes after a long period of cultivation.