Candidate gene polymorphisms for behavioural adaptations during urbanization in blackbirds

Successful urban colonization by formerly rural species represents an ideal situation in which to study adaptation to novel environments. We address this issue using candidate genes for behavioural traits that are expected to play a role in such colonization events. We identified and genotyped 16 polymorphisms in candidate genes for circadian rhythms, harm avoidance and migratory and exploratory behaviour in 12 paired urban and rural populations of the blackbird Turdus merula across the Western Palaearctic. An exonic microsatellite in the SERT gene, a candidate gene for harm avoidance behaviour, exhibited a highly significant association with habitat type in an analysis conducted across all populations. Genetic divergence at this locus was consistent in 10 of the 12 population pairs; this contrasts with previously reported stochastic genetic divergence between these populations at random markers. Our results indicate that behavioural traits related to harm avoidance and associated with the SERT polymorphism experience selection pressures during most blackbird urbanization events. These events thus appear to be influenced by homogeneous adaptive processes in addition to previously reported demographic founder events.     

Risk analysis reveals global hotspots for marine debris ingestion by sea turtles

Plastic marine debris pollution is rapidly becoming one of the critical environmental concerns facing wildlife in the 21st century. Here we present a risk analysis for plastic ingestion by sea turtles on a global scale. We combined global marine plastic distributions based on ocean drifter data with sea turtle habitat maps to predict exposure levels to plastic pollution. Empirical data from necropsies of deceased animals were then utilised to assess the consequence of exposure to plastics. We modelled the risk (probability of debris ingestion) by incorporating exposure to debris and consequence of exposure, and included life history stage, species of sea turtle and date of stranding observation as possible additional explanatory factors. Life history stage is the best predictor of debris ingestion, but the best‐fit model also incorporates encounter rates within a limited distance from stranding location, marine debris predictions specific to the date of the stranding study and turtle species. There is no difference in ingestion rates between stranded turtles vs. those caught as bycatch from fishing activity, suggesting that stranded animals are not a biased representation of debris ingestion rates in the background population. Oceanic life‐stage sea turtles are at the highest risk of debris ingestion, and olive ridley turtles are the most at‐risk species. The regions of highest risk to global sea turtle populations are off of the east coasts of the USA, Australia and South Africa; the east Indian Ocean, and Southeast Asia. Model results can be used to predict the number of sea turtles globally at risk of debris ingestion. Based on currently available data, initial calculations indicate that up to 52% of sea turtles may have ingested debris.     

An ecological genetic delineation of local seed‐source provenance for ecological restoration

An increasingly important practical application of the analysis of spatial genetic structure within plant species is to help define the extent of local provenance seed collection zones that minimize negative impacts in ecological restoration programs. Here, we derive seed sourcing guidelines from a novel range‐wide assessment of spatial genetic structure of 24 populations of Banksia menziesii (Proteaceae), a widely distributed Western Australian tree of significance in local ecological restoration programs. An analysis of molecular variance (AMOVA) of 100 amplified fragment length polymorphism (AFLP) markers revealed significant genetic differentiation among populations (Φ_PT = 0.18). Pairwise population genetic dissimilarity was correlated with geographic distance, but not environmental distance derived from 15 climate variables, suggesting overall neutrality of these markers with regard to these climate variables. Nevertheless, Bayesian outlier analysis identified four markers potentially under selection, although these were not correlated with the climate variables. We calculated a global R‐statistic using analysis of similarities (ANOSIM) to test the statistical significance of population differentiation and to infer a threshold seed collection zone distance of ~60 km (all markers) and 100 km (outlier markers) when genetic distance was regressed against geographic distance. Population pairs separated by >60 km were, on average, twice as likely to be significantly genetically differentiated than population pairs separated by <60 km, suggesting that habitat‐matched sites within a 30‐km radius around a restoration site genetically defines a local provenance seed collection zone for B. menziesii. Our approach is a novel probability‐based practical solution for the delineation of a local seed collection zone to minimize negative genetic impacts in ecological restoration.     

The Lactoperoxidase System: a Natural Biochemical Biocontrol Agent for Pre‐ and Postharvest Applications

Controlling pests in pre‐ and postharvest crops using natural and low‐impact products is a major challenge. The lactoperoxidase system is an enzymatic system that exists in all external secretions in mammals and is part of the non‐immune system. We tested its efficacy in in vitro microplates on Phytophthora infestans, Penicillium digitatum, Penicillium italicum, Penicillium expansum and Botrytis cinerea to determine the most suitable concentrations for use. Then, we verified its efficacy in planta under controlled conditions. Solutions prepared with 5.4 mm iodide and 1.2 mm thiocyanate and diluted threefold inhibited pathogen growth in vitro by 63–100%. Twofold‐diluted solutions protected potato plants against P. infestans by 60–74% under controlled conditions. Undiluted solution inhibited orange's and apple's postharvest pathogens in curative application with efficacy levels ranging between 84 and 95% in orange and between 63 and 74% in apple. 1.5‐fold concentrated solutions inhibited postharvest pathogens of apple in curative application with efficacy levels ranging between 84 and 92%. Our results also show that the oxidative stress response of fruit following wounding could interfere with ion efficiency. Our tests demonstrate for the first time that this biochemical method is as efficient as a conventional synthetic chemical method under controlled conditions.     

A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidum ssp. durum)

Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi‐allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd‐B1, while the latter overlapped with the vernalization locus VRN‐A3. Additionally, 21 QTL with environment‐specific effects were found. Our results indicated a prevalence of environment‐specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes.     

Clumping behavior and byssus production as strategies for substrate competition in Mytilus edulis

Laboratory experiments showed that the mussel Mytilus edulis aggregated more intensely around living organisms (the bivalve Hiatella arctica and the solitary ascidian Styela rustica, which commonly co‐occur with mussels in fouling communities) than around inanimate objects. When exposed to an inanimate object, mussels attached their byssal threads primarily to the substrate, close to the object, but when exposed to a living organism, they attached their byssal threads directly to the organism. The ascidian was more intensely covered with byssal threads than was the bivalve. Mussel attachment to the ascidians was apparently determined by the physical characteristics of the tunic and to a lesser extent by the excretion‐secretion products released by S. rustica. This study indicates that mussels can use byssus threads as a means of entrapment of potential competitors for space. It remains unclear why mussels preferentially attached to ascidians compared to the bivalve. This can be explained either by competitive interactions, or by attractiveness of the ascidian tunic as an attachment substratum.     

Phylogenetics of tribe Sabiceeae (Ixoroideae,Rubiaceae) revisited,with a new subgeneric classification for Sabicea

Tribe Sabiceeae (Ixoroideae, Rubiaceae) has undergone recent taxonomical changes with the incorporation of the related genera Ecpoma, Pseudosabicea and Stipularia into the type genus Sabicea. We use phylogenetic analysis and morphological data to verify the relationships among members of the tribe, including the most comprehensive taxon sampling of the tribe to date with 74 of 145 species. Sequence data from the nuclear internal transcribed spacer (ITS) and three plastid markers (petD, rps16, trnT–F) were used to infer relationships among the members of the tribe. Individual analyses using maximum likelihood, parsimony and Bayesian approaches reveal several supported clades: the former genus Stipularia is resolved as a monophyletic unit, but Ecpoma is monophyletic only if Sabicea urbaniana and Sabicea xanthotricha are included (corresponding to Sabicea subgenus Stipulariopsis sensu Wernham). Pseudosabicea is biphyletic, with one clade corresponding to section Anisophyllae of Hallé (1964) and the other one to the other sections (Floribundae and Sphaericae) of the genus. Eleven morphological characteristics were recorded for all species studied and seven have been mapped onto the phylogenetic tree to study their evolution in the group and assess their value for the classification of Sabicea s.l. Finally, our study shows that a combination of diagnostic characteristics should be used to differentiate each group and we propose to recognise four subgenera in Sabicea.     

A Screen for Swainsonine in Select North American Astragalus Species

Swainsonine is found in several plant species worldwide, and causes severe toxicosis in livestock grazing these plants, leading to a chronic condition characterized by weight loss, altered behavior, depression, decreased libido, infertility, and death. Swainsonine has been detected in 13 North American Astragalus species of which eight belong to taxa in four taxonomic sections, the Densifolii, Diphysi, Inflati, and Trichopodi. These sections belong to two larger groups representing several morphologically related species, the Pacific Piptolobi and the small‐flowered Piptolobi. The objective of this study was to screen the other 31 species for swainsonine in sections Densifolii, Diphysi, Inflati, and Trichopodi previously not known to contain swainsonine. Furthermore, to broaden the scope further, 21 species within the 8 sections of the Pacific Piptolobi and the small flowered Piptolobi were screened for swainsonine. Swainsonine was detected for the first time in 36 Astragalus taxa representing 29 species using liquid and gas chromatography coupled with mass spectrometry. Several taxonomic sections were highly enriched in species that contain swainsonine while others were not. A systematic examination for swainsonine in these species will provide important information on the toxic risk of these species and may be a valuable reference for diagnosticians and land managers.     

Functionally Similar Species Confer Greater Resistance to Invasion: Implications for Grassland Restoration

Plant community functional composition can be manipulated in restored ecosystems to reduce the establishment potential of invading species. This study was designed to compare invasion resistance among communities with species functionally similar or dissimilar to yellow starthistle (Centaurea solstitialis), a late‐season annual. A field experiment was conducted in the Central Valley of California with six experimental plant communities that included (1) six early‐season native annual forbs (AF); (2) five late‐season native perennials and one summer annual forb (NP); (3) a combination of three early‐season native annual forbs and three late‐season native perennials (FP); (4) six early‐season non‐native annual grasses (AG); (5) monoculture of the late‐season native perennial grass Elymus glaucus (EG); and (6) monoculture of the late‐season native perennial Grindelia camporum (GC). Following establishment, C. solstitialis seed was added to half of the plots, and a monoculture of C. solstitialis (CS) was established as a control. Over a 5‐year period, the AF and AG communities were ineffective at preventing C. solstitialis invasion. Centaurea solstitialis cover remained less than 10% in the FP and NP communities, except in year 1. By the fourth year, E. glaucus cover was greater than 50% in NP and FP communities and had spread to all other communities (e.g., 27% cover in CS in year 5). Communities containing E. glaucus, which is functionally similar to C. solstitialis, better resisted invasion than communities lacking a functional analog. In contrast, G. camporum, which is also functionally similar to C. solstitialis, failed to survive. Consequently, species selection for restored communities must consider not only functional similarity to the invader but also establishment success, competitiveness, and survivorship.     

Salicylic and jasmonic acid pathways are necessary for defence against Dickeya solani as revealed by a novel method for Blackleg disease screening of in vitro grown potato

Potato is major crop ensuring food security in Europe, and blackleg disease is increasingly causing losses in yield and during storage. Recently, one blackleg pathogen, Dickeya solani has been shown to be spreading in Northern Europe that causes aggressive disease development. Currently, identification of tolerant commercial potato varieties has been unsuccessful; this is confounded by the complicated etiology of the disease and a strong environmental influence on disease development. There is currently a lack of efficient testing systems. Here, we describe a system for quantification of blackleg symptoms on shoots of sterile in vitro potato plants, which saves time and space compared to greenhouse and existing field assays. We found no evidence for differences in infection between the described in vitro‐based screening method and existing greenhouse assays. This system facilitates efficient screening of blackleg disease response of potato plants independent of other microorganisms and variable environmental conditions. We therefore used the in vitro screening method to increase understanding of plant mechanisms involved in blackleg disease development by analysing disease response of hormone‐ related (salicylic and jasmonic acid) transgenic potato plants. We show that both jasmonic (JA) and salicylic (SA) acid pathways regulate tolerance to blackleg disease in potato, a result unlike previous findings in Arabidopsis defence response to necrotrophic bacteria. We confirm this by showing induction of a SA marker, pathogenesis‐related protein 1 (StPR1), and a JA marker, lipoxygenase (StLOX), in Dickeya solani infected in vitro potato plants. We also observed that tubers of transgenic potato plants were more susceptible to soft rot compared to wild type, suggesting a role for SA and JA pathways in general tolerance to Dickeya.     

Optimization of growth conditions and fatty acid analysis for three freshwater diatom isolates

Diatoms are a group of highly abundant and diverse aquatic algae species. They contain high lipid content along with many bioactive compounds that can be exploited for biotechnological applications. Despite these attractive attributes, diatoms are underrepresented in production projects due to difficulties in their cultivation. To optimize the growth of three freshwater diatom isolates, Cyclotella sp., Synedra sp. and Navicula sp., an orthogonal assay on N, P, Si and Fe, as well as temperature and pH, was designed using traditional single‐factor tests. We also studied the effect of using nanosilica as an alternate Si source on growth and found that the diatom isolates studied achieved their highest growth rates under different combinations of nutrient and environmental conditions. Silica had the greatest influence on growth, followed by phosphate and iron. The optimized growth conditions for Synedra sp. were N: 30 mg L^?1, P: 3 mg L^?1, Si: 14.8 mg L^?1, Fe: 0.448 mg L^?1, temperature 25°C and pH 8. For Navicula sp.: N: 20 mg L^?1, P: 2.5 mg L^?1, Si: 19.7 mg L^?1, Fe: 0.112 mg L^?1, temperature 30°C and pH 7.5–8. For Cyclotella sp.: N: 20 mg L^?1, P: 2.5 mg L^?1, Si: 19.7 mg L^?1, Fe: 0.448 mg L^?1, temperature 30°C and pH 7.5–8. Nano silica negatively affected growth in Navicula sp. and Cyclotella sp., but no such effect was observed in Synedra sp. Fatty acid profiling showed C16:0, C16:1(n ? 7), C18:0 and C20:5(n ? 3) as major fatty acids, with no significant differences in fatty acid methyl ester profiles between traditional and modified media. This work gives us a new insight into the growth requirements of freshwater diatom species, which are less studied than marine species.     

State‐of‐the‐art CRISPR/Cas9 Technology for Genome Editing in Trypanosomatids

CRISPR/Cas9 technology has revolutionized biology. This prokaryotic defense system against foreign DNA has been repurposed for genome editing in a broad range of cell tissues and organisms. Trypanosomatids are flagellated protozoa belonging to the order Kinetoplastida. Some of its most representative members cause important human diseases affecting millions of people worldwide, such as Chagas disease, sleeping sickness and different forms of leishmaniases. Trypanosomatid infections represent an enormous burden for public health and there are no effective treatments for most of the diseases they cause. Since the emergence of the CRISPR/Cas9 technology, the genetic manipulation of these parasites has notably improved. As a consequence, genome editing is now playing a key role in the functional study of proteins, in the characterization of metabolic pathways, in the validation of alternative targets for antiparasitic interventions, and in the study of parasite biology and pathogenesis. In this work we review the different strategies that have been used to adapt the CRISPR/Cas9 system to Trypanosoma cruzi, Trypanosoma brucei, and Leishmania spp., as well as the research progress achieved using these approaches. Thereby, we will present the state‐of‐the‐art molecular tools available for genome editing in trypanosomatids to finally point out the future perspectives in the field.     

Substrate modification for enhanced native forest restoration,Reefton

Restoration of postmining substrates to native forest is a standard requirement of resource consents for mine sites located within areas of native forest in New Zealand. Unweathered waste rock presents significant challenges for plant growth, and past research highlights the importance of replacing soil as part of restoration. However, replacing soil with its horizon structure intact or even obtaining sufficient soil for restoration can be a challenge in some situations. In this paper, we describe the results of two trials undertaken at the OceanaGold Ltd. open‐cast gold mine in Reefton to explore the influence of substrate conditions on the growth of native forest seedlings. We show that beech (Nothofagus) seedlings grown on A‐horizon soil grew significantly better than those grown on soil mixed with waste rock, and both grew significantly better than plants grown just on waste rock. In the second trial, we show that bark chips are not a good substitute for soil. These results confirm the importance of having the correct substrate for successful native forest restoration.     

Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size

Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long‐term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome‐wide ROH coverage (S_ROH) within the range of 237.4–284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity (S_ROH from 176.4–180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size (ZFAT, LASP1 and LCORL/NCAPG), coat color (MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis (HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.     

A dual role for integrin‐linked kinase and β1‐integrin in modulating cardiac aging

Cardiac performance decreases with age, which is a major risk factor for cardiovascular disease and mortality in the aging human population, but the molecular mechanisms underlying cardiac aging are still poorly understood. Investigating the role of integrin‐linked kinase (ilk) and β1‐integrin (myospheroid, mys) in Drosophila, which colocalize near cardiomyocyte contacts and Z‐bands, we find that reduced ilk or mys function prevents the typical changes of cardiac aging seen in wildtype, such as arrhythmias. In particular, the characteristic increase in cardiac arrhythmias with age is prevented in ilk and mys heterozygous flies with nearly identical genetic background, and they live longer, in line with previous findings in Caenorhabditis elegans for ilk and in Drosophila for mys. Consistent with these findings, we observed elevated β1‐integrin protein levels in old compared with young wild‐type flies, and cardiac‐specific overexpression of mys in young flies causes aging‐like heart dysfunction. Moreover, moderate cardiac‐specific knockdown of integrin‐linked kinase (ILK)/integrin pathway‐associated genes also prevented the decline in cardiac performance with age. In contrast, strong cardiac knockdown of ilk or ILK‐associated genes can severely compromise cardiac integrity, including cardiomyocyte adhesion and overall heart function. These data suggest that ilk/mys function is necessary for establishing and maintaining normal heart structure and function, and appropriate fine‐tuning of this pathway can retard the age‐dependent decline in cardiac performance and extend lifespan. Thus, ILK/integrin‐associated signaling emerges as an important and conserved genetic mechanism in longevity, and as a new means to improve age‐dependent cardiac performance, in addition to its vital role in maintaining cardiac integrity.     

Comparative study of sequence aligners for detecting antibiotic resistance in bacterial metagenomes

We aim to compare the performance of Bowtie2 , bwa‐mem , blastn and blastx when aligning bacterial metagenomes against the Comprehensive Antibiotic Resistance Database (CARD). Simulated reads were used to evaluate the performance of each aligner under the following four performance criteria: correctly mapped, false positives, multi‐reads and partials. The optimal alignment approach was applied to samples from two wastewater treatment plants to detect antibiotic resistance genes using next generation sequencing. blastn mapped with greater accuracy among the four sequence alignment approaches considered followed by Bowtie2 . blastx generated the greatest number of false positives and multi‐reads when aligned against the CARD. The performance of each alignment tool was also investigated using error‐free reads. Although each aligner mapped a greater number of error‐free reads as compared to Illumina‐error reads, in general, the introduction of sequencing errors had little effect on alignment results when aligning against the CARD. Given each performance criteria, blastn was found to be the most favourable alignment tool and was therefore used to assess resistance genes in sewage samples. Beta‐lactam and aminoglycoside were found to be the most abundant classes of antibiotic resistance genes in each sample.

Significance and Impact of the Study

Antibiotic resistance genes (ARGs) are pollutants known to persist in wastewater treatment plants among other environments, thus methods for detecting these genes have become increasingly relevant. Next generation sequencing has brought about a host of sequence alignment tools that provide a comprehensive look into antimicrobial resistance in environmental samples. However, standardizing practices in ARG metagenomic studies is challenging since results produced from alignment tools can vary significantly. Our study provides sequence alignment results of synthetic, and authentic bacterial metagenomes mapped against an ARG database using multiple alignment tools, and the best practice for detecting ARGs in environmental samples.     

Antibodies to Pseudogymnoascus destructans are not sufficient for protection against white‐nose syndrome

White‐nose syndrome (WNS) is a fungal disease caused by Pseudogymnoascus destructans (Pd) that affects bats during hibernation. Although millions of bats have died from WNS in North America, mass mortality has not been observed among European bats infected by the fungus, leading to the suggestion that bats in Europe are immune. We tested the hypothesis that an antibody‐mediated immune response can provide protection against WNS by quantifying antibodies reactive to Pd in blood samples from seven species of free‐ranging bats in North America and two free‐ranging species in Europe. We also quantified antibodies in blood samples from little brown myotis (Myotis lucifugus) that were part of a captive colony that we injected with live Pd spores mixed with adjuvant, as well as individuals surviving a captive Pd infection trial. Seroprevalence of antibodies against Pd, as well as antibody titers, was greater among little brown myotis than among four other species of cave‐hibernating bats in North America, including species with markedly lower WNS mortality rates. Among little brown myotis, the greatest titers occurred in populations occupying regions with longer histories of WNS, where bats lacked secondary symptoms of WNS. We detected antibodies cross‐reactive with Pd among little brown myotis naïve to the fungus. We observed high titers among captive little brown myotis injected with Pd. We did not detect antibodies against Pd in Pd‐infected European bats during winter, and titers during the active season were lower than among little brown myotis. These results show that antibody‐mediated immunity cannot explain survival of European bats infected with Pd and that little brown myotis respond differently to Pd than species with higher WNS survival rates. Although it appears that some species of bats in North America may be developing resistance to WNS, an antibody‐mediated immune response does not provide an explanation for these remnant populations.