Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions
Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models). Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude) were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species) and taxonomy (amphibians and reptiles). Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural parks.
Muñoz et al. (2016) Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions. PeerJ 4:e2405 https://doi.org/10.7717/peerj.2405
Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator
Background Talitrus saltator is an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean. T. saltator exhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species. Methods We harvested brain tissue from animals expressing robust circadian activity rhythms and used homology cloning and Illumina RNAseq approaches to sequence and identify the core circadian clock and clock-related genes in these samples. We assessed the temporal expression of these genes in time-course samples from rhythmic animals using RNAseq. Results We identified a comprehensive suite of circadian clock gene homologues in T. saltator including the ‘core’ clock genes period (Talper), cryptochrome 2 (Talcry2), timeless (Taltim), clock (Talclk), and bmal1 (Talbmal1). In addition we describe the sequence and putative structures of 23 clock-associated genes including two unusual, extended isoforms of pigment dispersing hormone (Talpdh). We examined time-course RNAseq expression data, derived from tissues harvested from behaviourally rhythmic animals, to reveal rhythmic expression of these genes with approximately circadian period in Talper and Talbmal1. Of the clock-related genes, casein kinase IIβ (TalckIIβ), ebony (Talebony), jetlag (Taljetlag), pigment dispensing hormone (Talpdh), protein phosphatase 1 (Talpp1), shaggy (Talshaggy), sirt1 (Talsirt1), sirt7 (Talsirt7) and supernumerary limbs (Talslimb) show temporal changes in expression. Discussion We report the sequences of principle genes that comprise the circadian clock of T. saltator and highlight the conserved structural and functional domains of their deduced cognate proteins. Our sequencing data contribute to the growing inventory of described comparative clocks. Expression profiling of the identified clock genes illuminates tantalising targets for experimental manipulation to elucidate the molecular and cellular control of clock-driven phenotypes in this crustacean.
O’Grady et al. (2016) Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator. PeerJ 4:e2555 https://doi.org/10.7717/peerj.2555
Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda)
We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10−5 per site per year or μ = 1.99 × 10−4 mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne = 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.
Fourdrilis et al. (2016) Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda). PeerJ 4:e2549 https://doi.org/10.7717/peerj.2549
The ethnobotany of psychoactive plant use: a phylogenetic perspective
Psychoactive plants contain chemicals that presumably evolved as allelochemicals but target certain neuronal receptors when consumed by humans, altering perception, emotion and cognition. These plants have been used since ancient times as medicines and in the context of religious rituals for their various psychoactive effects (e.g., as hallucinogens, stimulants, sedatives). The ubiquity of psychoactive plants in various cultures motivates investigation of the commonalities among these plants, in which a phylogenetic framework may be insightful. A phylogeny of culturally diverse psychoactive plant taxa was constructed with their psychotropic effects and affected neurotransmitter systems mapped on the phylogeny. The phylogenetic distribution shows multiple evolutionary origins of psychoactive families. The plant families Myristicaceae (e.g., nutmeg), Papaveraceae (opium poppy), Cactaceae (peyote), Convolvulaceae (morning glory), Solanaceae (tobacco), Lamiaceae (mints), Apocynaceae (dogbane) have a disproportionate number of psychoactive genera with various indigenous groups using geographically disparate members of these plant families for the same psychoactive effect, an example of cultural convergence. Pharmacological traits related to hallucinogenic and sedative potential are phylogenetically conserved within families. Unrelated families that exert similar psychoactive effects also modulate similar neurotransmitter systems (i.e., mechanistic convergence). However, pharmacological mechanisms for stimulant effects were varied even within families suggesting that stimulant chemicals may be more evolutionarily labile than those associated with hallucinogenic and sedative effects. Chemically similar psychoactive chemicals may also exist in phylogenetically unrelated lineages, suggesting convergent evolution or differential gene regulation of a common metabolic pathway. Our study has shown that phylogenetic analysis of traditionally used psychoactive plants suggests multiple ethnobotanical origins and widespread human dependence on these plants, motivating pharmacological investigation into their potential as modern therapeutics for various neurological disorders.
Alrashedy et al. (2016) The ethnobotany of psychoactive plant use: a phylogenetic perspective. PeerJ 4:e2546 https://doi.org/10.7717/peerj.2546
A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
Background Understanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients. Methods To better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn, Macrobrachium australiense using Illumina deep sequencing technology. This species was targeted because it can complete its life cycle totally in freshwater but, like many Macrobrachium sp., can also tolerate brackish water conditions and hence should have genes associated with tolerance of both FW and saline conditions. Results We obtained between 55.4 and 65.2 million Illumina read pairs from four cDNA libraries. Overall, paired end sequences assembled into a total of 125,196 non-redundant contigs (≥200 bp) with an N50 length of 2,282 bp and an average contig length of 968 bp. Transcriptomic analysis of M. australiense identified 32 different gene families that were potentially involved with osmoregulatory capacity. A total of 32,597 transcripts were specified with gene ontology (GO) terms identified on the basis of GO categories. Abundance estimation of expressed genes based on TPM (transcript per million) ≥20 showed 1625 transcripts commonly expressed in all four libraries. Among the top 10 genes expressed in four tissue libraries associated with osmoregulation, arginine kinase and Na+/K+- ATPase showed the highest transcript copy number with 7098 and 660, respectively in gill which is considered to be the most important organ involved in osmoregulation. Discussion The current study provides the first broad transcriptome from M. australiense using next generation sequencing and identifies potential candidate genes involved in salinity tolerance and osmoregulation that can provide a foundation for investigating osmoregulatory capacity in a wide variety of freshwater crustaceans.
Moshtaghi et al. (2016) A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense). PeerJ 4:e2520 https://doi.org/10.7717/peerj.2520
Antibacterial and anti-adherence effects of a plant extract mixture (PEM) and its individual constituent extracts (Psidium sp., Mangifera sp., and Mentha sp.) on single- and dual-species biofilms
Background Plant extracts mixture (PEM) and its individual constituent plant extracts(Psidium sp., Mangifera sp., Mentha sp.) are known to have an anti-adhering effect towards oral bacteria in the single-species biofilm. To date, the adhering ability of the early and late plaque colonisers (Streptococcus sanguinis and Streptococcus mutans) to PEM-treated experimental pellicle have not been investigated in dual-species biofilms. Methods Fresh leaves of these plants were used in the preparation of the respective aqueous extract decoctions. The minimum inhibitory concentration (MIC) of the extracts towards S. sanguinis ATCC BAA-1455 and S. mutans ATCC 25175 was determined using a two-fold serial microdilution method. The sum of fractional inhibitory concentration (ΣFIC) index of PEM and its constituent plant extracts was calculated using the MIC values of the plants. The minimum bactericidal concentration (MBC) of the plant extracts was also determined. The anti-adherence effect of the plant extracts (individually and mixed) was carried out by developing simulated S. sanguinis and S. mutans respectively in single- and dual-species of biofilms in the Nordini’s Artificial Mouth (NAM) model system in which the experimental pellicle was pretreated with the plant extract before bacterial inoculation. The bacterial population in the respective biofilms was quantified using ten-fold serial dilutions method and expressed as colony forming unit per ml (CFU/ml). The bacterial population was also viewed using Scanning Electron Microscope (SEM). All experiments were done in triplicate. Results The PEM compared with its respective constituent plants showed the lowest MIC towards S. sanguinis (3.81 mg/ml) and S. mutans (1.91 mg/ml) and exhibited a synergistic effect. The Psidium sp. (15.24 mg/ml) and, PEM and Psidium sp. (30.48 mg/ml) showed the lowest MBC towards S. sanguinis and S. mutans respectively. The anti-adherence effect of the PEM and its respective constituent plants (except Psidium sp.) was different for the two bacteria in the single-species biofilm. In the dual-species biofilms, PEM demonstrated similar anti-adherence effect towards S. sanguinis and S. mutans. The proportions of the bacterial population viewed under SEM appeared to be in agreement with the quantified population. Discussion The combination of the active constituents of the individual plant extracts in PEM may contribute to its low MIC giving rise to the synergistic effect. The different anti-adherence effect towards S. sanguinis and S. mutans in both single- and dual-species biofilms could be due to the different proportion of the active constituents of the extracts and the interaction between different bacteria. The better adhering ability of S. sanguinis towards the PEM-treated pellicle when present together with S. mutans in the dual-species biofilms may suggest the potential of PEM in controlling the balance between the early and late colonisers in biofilms.
Shafiei et al. (2016) Antibacterial and anti-adherence effects of a plant extract mixture (PEM) and its individual constituent extracts (Psidium sp., Mangifera sp., and Mentha sp.) on single- and dual-species biofilms. PeerJ 4:e2519 https://doi.org/10.7717/peerj.2519
Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae
Background The rice receptor kinase XA21 confers robust resistance to the bacterial pathogen Xanthomonas oryzaepv. oryzae(Xoo). We previously reported that XA21 is cleaved in transgenic plants overexpressing XA21 with a GFP tag (Ubi-XA21-GFP) and that the released C-terminal domain is localized to the nucleus. XA21 carries a predicted nuclear localization sequence (NLS) that directs the C-terminal domain to the nucleus in transient assays, whereas alanine substitutions in the NLS disrupt the nuclear localization. Methods To determine if the predicted NLS is required for XA21-mediated immunity in planta, we generated transgenic plants overexpressing an XA21 variant carrying the NLS with the same alanine substitutions (Ubi-XA21nls-GFP). Results Ubi-XA21nls-GFP plants displayed slightly longer lesion lengths, higher Xoobacterial populations after inoculation and lower levels of reactive oxygen species production compared with the Ubi-XA21-GFP control plants. However, the Ubi-XA21nls-GFP plants express lower levels of protein than that observed in Ubi-XA21-GFP. Discussion These results demonstrate that the predicted NLS is not required for XA21-mediated immunity.
Wei et al. (2016) Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae. PeerJ 4:e2507 https://doi.org/10.7717/peerj.2507
The effect of CO2 enrichment on net photosynthesis of the red alga Furcellaria lumbricalis in a brackish water environment
Anthropogenic carbon dioxide (CO2) emissions to the atmosphere are causing reduction in the global ocean pH, also known as ocean acidification. This change alters the equilibrium of different forms of dissolved inorganic carbon in seawater that macroalgae use for their photosynthesis. In the Baltic Sea, benthic macroalgae live in a highly variable environment caused by seasonality and rapid changes in meteorological conditions. The effect of increasing water CO2 concentration on the net photosynthesis of the red macroalgae Furcellaria lumbricalis (Hudson) Lamouroux was tested in short-term mesocosm experiments conducted in Kõiguste Bay (N Gulf of Riga) in June–July 2012 and 2013. Separate mesocosms were maintained at different pCO2 levels: ca. 2,000, ca. 1,000 and ca. 200 µatm. In parallel, different environmental factors were measured such as nutrients, light and water temperature. Thus, the current study also investigated whether elevated pCO2 and different environmental factors exerted interactive effects on the photosynthetic rate of F. lumbricalis. In addition, laboratory experiments were carried out to determine the optimal temperature for photosynthesis of F. lumbricalis. The results of our field experiments demonstrated that elevated pCO2 levels may remarkably enhance the photosynthetic rate of F. lumbricalis. However, the magnitude of this effect is altered by different environmental factors, mainly by changes in water temperature.
Pajusalu et al. (2016) The effect of CO2 enrichment on net photosynthesis of the red alga Furcellaria lumbricalis in a brackish water environment. PeerJ 4:e2505 https://doi.org/10.7717/peerj.2505
A new hynobiid-like salamander (Amphibia, Urodela) from Inner Mongolia, China, provides a rare case study of developmental features in an Early Cretaceous fossil urodele
A new fossil salamander, Nuominerpeton aquilonaris (gen. et sp. nov.), is named and described based on specimens from the Lower Cretaceous Guanghua Formation of Inner Mongolia, China. The new discovery documents a far northern occurrence of Early Cretaceous salamanders in China, extending the geographic distribution for the Mesozoic fossil record of the group from the Jehol area (40th–45th parallel north) to near the 49th parallel north. The new salamander is characterized by having the orbitosphenoid semicircular in shape; coracoid plate of the scapulocoracoid greatly expanded with a convex ventral and posterior border; ossification of two centralia in carpus and tarsus; and first digit being about half the length of the second digit in both manus and pes. The new salamander appears to be closely related to hynobiids, although this inferred relationship awaits confirmation by research in progress by us on a morphological and molecular combined analysis of cryptobranchoid relationships. Comparison of adult with larval and postmetamorphic juvenile specimens provides insights into developmental patterns of cranial and postcranial skeletons in this fossil species, especially resorption of the palatine and anterior portions of the palatopterygoid in the palate and the coronoid in the mandible during metamorphosis, and postmetamorphic ossification of the mesopodium in both manus and pes. Thus, this study provides a rare case study of developmental features in a Mesozoic salamander.
Jia et al. (2016) A new hynobiid-like salamander (Amphibia, Urodela) from Inner Mongolia, China, provides a rare case study of developmental features in an Early Cretaceous fossil urodele. PeerJ 4:e2499 https://doi.org/10.7717/peerj.2499
Prevention of necrotizing enterocolitis with probiotics: a systematic review and meta-analysis
Context Necrotizing enterocolitis (NEC) is the most frequent gastrointestinal emergency in neonates. The microbiome of the preterm gut may regulate the integrity of the intestinal mucosa. Probiotics may positively contribute to mucosal integrity, potentially reducing the risk of NEC in neonates. Objective To perform an updated systematic review and meta-analysis on the efficacy and safety of probiotics for the prevention of NEC in premature infants. Data Sources Structured searches were performed in: Medline, Embase, and the Cochrane Central Register of Controlled Trials (all via Ovid, from 2013 to January 2015). Clinical trial registries and electronically available conference materials were also searched. An updated search was conducted June 3, 2016. Study Selection Randomized trials including infants less than 37 weeks gestational age or less than 2,500 g on probiotic vs. standard therapy. Data Extraction Data extraction of the newly-identified trials with a double check of the previously-identified trials was performed using a standardized data collection tool. Results Thirteen additional trials (n = 5,033) were found. The incidence of severe NEC (RR 0.53 95% CI [0.42–0.66]) and all-cause mortality (RR 0.79 95% CI [0.68–0.93]) were reduced. No difference was shown in culture-proven sepsis RR 0.88 95% CI [0.77–1.00]. Limitations Heterogeneity of organisms and dosing regimens studied prevent a species-specific treatment recommendation from being made. Conclusions Preterm infants benefit from probiotics to prevent severe NEC and death.
Sawh et al. (2016) Prevention of necrotizing enterocolitis with probiotics: a systematic review and meta-analysis. PeerJ 4:e2429 https://doi.org/10.7717/peerj.2429