Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data
The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.
Panzera et al. (2017) Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data. PeerJ 5:e3941 https://doi.org/10.7717/peerj.3941
Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures
The fire blight pathogen Erwinia amylovora can be considered a psychrotrophic bacterial species since it can grow at temperatures ranging from 4 °C to 37 °C, with an optimum of 28 °C. In many plant pathogens the expression of virulence determinants is restricted to a certain range of temperatures. In the case of E. amylovora, temperatures above 18 °C are required for blossom blight epidemics under field conditions. Moreover, this bacterium is able to infect a variety of host tissues/organs apart from flowers, but it is still unknown how environmental temperatures, especially those below 18 °C, affect the pathogen ability to cause fire blight disease symptoms in such tissues/organs. There is also scarce information on how temperatures below 18 °C affect the E. amylovora starvation-survival responses, which might determine its persistence in the environment and probably contribute to the seasonal development of fire blight disease, as occurs in other pathogens. To characterize the virulence and survival of E. amylovora at temperate and low temperatures, we evaluated the effect of three temperatures (4 °C, 14 °C, 28 °C) on symptom development, and on different parameters linked to starvation and virulence. E. amylovora was pathogenic at the three assayed temperatures, with a slow-down of symptom development correlating with colder temperatures and slower growth rates. Siderophore secretion and motility also decreased in parallel to incubation temperatures. However, production of the exopolysaccharides amylovoran and levan was enhanced at 4 °C and 14 °C, respectively. Similarly, biofilm formation, and oxidative stress resistance were improved at 14 °C, with this temperature also favoring the maintenance of culturability, together with a reduction in cell size and the acquisition of rounded shapes in E. amylovora cells subjected to long-term starvation. However, starvation at 28 °C and 4 °C induced an enhanced viable but nonculturable (VBNC) response (to a lesser extent at 4 °C). This work reveals E. amylovora as a highly adaptable pathogen that retains its pathogenic potential even at the minimal growth temperatures, with an improved exopolysaccharide synthesis, biofilm formation or oxidative stress resistance at 14 °C, with respect to the optimal growth temperature (28 °C). Finally, our results also demonstrate the thermal modulation of starvation responses in E. amylovora, suggesting that the starvation-survival and the VBNC states are part of its life cycle. These results confirm the particular psychrotrophic adaptations of E. amylovora, revealing its pathogenic potential and survival at temperate and low environmental temperatures, which have probably contributed to its successful spread to countries with different climates. This knowledge might improve integrated control measures against fire blight.
Santander et al. (2017) Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures. PeerJ 5:e3931 https://doi.org/10.7717/peerj.3931
Evaluation of genetic variability among “Early Mature” Juglans regia using microsatellite markers and morphological traits
Limiting the juvenile phase and reducing tree size are the two main challenges for breeders to improve most fruit crops. Early maturation and dwarf cultivars have been reported for many fruit species. “Early mature” and low vigor walnut genotypes were found among seedlings of Persian walnut. Nine microsatellite markers were used to evaluate genetic diversity among “Early Mature” Persian walnut accessions and provide a comparison with “normal growth” accessions. Six maturation related characteristics were also measured in “Early Mature” samples. Phenotypic traits and diversity indices showed relatively high levels of genetic diversity in “Early Mature” seedlings and indicated high differentiation between individuals. Seedling height, the most diverse phenotypic trait, has an important role in the clustering of “Early Mature” accessions. The “Early Mature” type had higher number of alleles, number of effective allele, and Shannon index compared to the “Normal Growth” group. The two types of studied walnuts had different alleles, with more than half of produced alleles specific to a specific group. “Early Mature” and “Normal Growth” walnuts had 27 and 17 private alleles, respectively. Grouping with different methods separated “Early Mature” and “Normal Growth” samples entirely. The presence of moderate to high genetic diversity in “Early Mature” walnuts and high genetic differentiation with “Normal Growth” walnuts, indicated that “Early Mature” walnuts were more diverse and distinct from “Normal Growth” samples. Moreover, our results showed SSR markers were useful for differentiating between “Early Mature” and “Normal Growth” walnuts. A number of identified loci have potential in breeding programs for identification of “Early Mature” walnuts at the germination phase.
Ebrahimi et al. (2017) Evaluation of genetic variability among “Early Mature” Juglans regia using microsatellite markers and morphological traits. PeerJ 5:e3834 https://doi.org/10.7717/peerj.3834
Knowledge and beliefs regarding cervical cancer screening and HPV vaccination among urban and rural women in León, Nicaragua
Background In Nicaragua, cervical cancer is the leading cause of cancer-related death for women ages 15–44, yet access to the HPV vaccine is limited to those with financial resources to pay for it. Cervical cytology is provided free of charge in public clinics; however, only 10% of women receive Pap smears at the nationally recommended frequency. Previous studies have not investigated how beliefs regarding cervical cancer screening may differ for urban and rural populations in Nicaragua. Furthermore, no investigation has assessed Nicaraguan women’s beliefs about a potential HPV immunization campaign. Given beliefs’ influence on health behavior, we investigated the structural, sociocultural, and knowledge-based factors influencing women’s beliefs regarding cervical cancer screening among urban and rural women in León, Nicaragua, and assessed acceptance of a potential HPV immunization program. Methods Our sequential explanatory mixed-methods study consisted of two phases: (1) a close-ended questionnaire, followed by (2) a qualitative, in-depth interview. Our quantitative sample contained 117 urban and 112 rural participants aged 18–49. We assessed beliefs regarding cervical cancer screening using a 22-item scale, with higher scores indicating screening-promoting beliefs in simple linear and multiple linear regressions. Twenty qualitative interviews, exploring the sociocultural dimensions of knowledge and attitudes indicated by our quantitative findings, were conducted with a sample of 13 urban and 7 rural women aged 19–46. Results The multiple linear regression indicates that greater knowledge of Pap smears, HPV, and cervical cancer is significantly associated with screening-promoting beliefs after adjusting for other relevant factors. There was no significant difference in screening knowledge and beliefs for urban and rural women. Four recurrent themes representing determinants of knowledge, beliefs, and attitudes regarding cervical cancer screening arose from interviews and built on quantitative findings: (1) women’s embarrassment due to the intimate nature of the Pap smear and male gender of exam provider discourages screening; (2) women believe Pap smears and cervical cancer are associated with sexual promiscuity, and this association stigmatizes women with the disease; (3) knowledge of cervical cancer prevention is limited to those who regularly attend health centers; and (4) women find screening inconvenient, believing understaffed clinics increase patient wait time, limit time patients spend with clinicians, and delay Pap results. A fifth theme indicates (5) participants’ acceptance of a potential HPV immunization program. Discussion Future interventions should focus on increasing access to information about cervical cancer prevention for women who do not regularly attend health centers. Furthermore, our results suggest that if funding were allocated to make the HPV vaccine accessible in Nicaragua, it would be well received.
Rees et al. (2017) Knowledge and beliefs regarding cervical cancer screening and HPV vaccination among urban and rural women in León, Nicaragua. PeerJ 5:e3871 https://doi.org/10.7717/peerj.3871
Diversity of fish sound types in the Pearl River Estuary, China
Background Repetitive species-specific sound enables the identification of the presence and behavior of soniferous species by acoustic means. Passive acoustic monitoring has been widely applied to monitor the spatial and temporal occurrence and behavior of calling species. Methods Underwater biological sounds in the Pearl River Estuary, China, were collected using passive acoustic monitoring, with special attention paid to fish sounds. A total of 1,408 suspected fish calls comprising 18,942 pulses were qualitatively analyzed using a customized acoustic analysis routine. Results We identified a diversity of 66 types of fish sounds. In addition to single pulse, the sounds tended to have a pulse train structure. The pulses were characterized by an approximate 8 ms duration, with a peak frequency from 500 to 2,600 Hz and a majority of the energy below 4,000 Hz. The median inter-pulsepeak interval (IPPI) of most call types was 9 or 10 ms. Most call types with median IPPIs of 9 ms and 10 ms were observed at times that were exclusive from each other, suggesting that they might be produced by different species. According to the literature, the two section signal types of 1 + 1 and 1 + N10 might belong to big-snout croaker (Johnius macrorhynus), and 1 + N19 might be produced by Belanger’s croaker (J. belangerii). Discussion Categorization of the baseline ambient biological sound is an important first step in mapping the spatial and temporal patterns of soniferous fishes. The next step is the identification of the species producing each sound. The distribution pattern of soniferous fishes will be helpful for the protection and management of local fishery resources and in marine environmental impact assessment. Since the local vulnerable Indo-Pacific humpback dolphin (Sousa chinensis) mainly preys on soniferous fishes, the fine-scale distribution pattern of soniferous fishes can aid in the conservation of this species. Additionally, prey and predator relationships can be observed when a database of species-identified sounds is completed.
Wang et al. (2017) Diversity of fish sound types in the Pearl River Estuary, China. PeerJ 5:e3924 https://doi.org/10.7717/peerj.3924
Norwegian honey bees surviving Varroa destructor mite infestations by means of natural selection
Background Managed, feral and wild populations of European honey bee subspecies, Apis mellifera, are currently facing severe colony losses globally. There is consensus that the ectoparasitic mite Varroa destructor, that switched hosts from the Eastern honey bee Apis cerana to the Western honey bee A. mellifera, is a key factor driving these losses. For >20 years, breeding efforts have not produced European honey bee colonies that can survive infestations without the need for mite control. However, at least three populations of European honey bees have developed this ability by means of natural selection and have been surviving for >10 years without mite treatments. Reduced mite reproductive success has been suggested as a key factor explaining this natural survival. Here, we report a managed A. mellifera population in Norway, that has been naturally surviving consistent V. destructor infestations for >17 years. Methods Surviving colonies and local susceptible controls were evaluated for mite infestation levels, mite reproductive success and two potential mechanisms explaining colony survival: grooming of adult worker bees and Varroa Sensitive Hygiene (VSH): adult workers specifically detecting and removing mite-infested brood. Results Mite infestation levels were significantly lower in surviving colonies and mite reproductive success was reduced by 30% when compared to the controls. No significant differences were found between surviving and control colonies for either grooming or VSH. Discussion Our data confirm that reduced mite reproductive success seems to be a key factor for natural survival of infested A. mellifera colonies. However, neither grooming nor VSH seem to explain colony survival. Instead, other behaviors of the adult bees seem to be sufficient to hinder mite reproductive success, because brood for this experiment was taken from susceptible donor colonies only. To mitigate the global impact of V. destructor, we suggest learning more from nature, i.e., identifying the obviously efficient mechanisms favored by natural selection.
Oddie et al. (2017) Norwegian honey bees surviving Varroa destructor mite infestations by means of natural selection. PeerJ 5:e3956 https://doi.org/10.7717/peerj.3956
A massive update of non-indigenous species records in Mediterranean marinas
The Mediterranean Sea is home to over 2/3 of the world’s charter boat traffic and hosts an estimated 1.5 million recreational boats. Studies elsewhere have demonstrated marinas as important hubs for the stepping-stone transfer of non-indigenous species (NIS), but these unique anthropogenic, and typically artificial habitats have largely gone overlooked in the Mediterranean as sources of NIS hot-spots. From April 2015 to November 2016, 34 marinas were sampled across the following Mediterranean countries: Spain, France, Italy, Malta, Greece, Turkey and Cyprus to investigate the NIS presence and richness in the specialized hard substrate material of these marina habitats. All macroinvertebrate taxa were collected and identified. Additionally, fouling samples were collected from approximately 600 boat-hulls from 25 of these marinas to determine if boats host diverse NIS not present in the marina. Here, we present data revealing that Mediterranean marinas indeed act as major hubs for the transfer of marine NIS, and we also provide evidence that recreational boats act as effective vectors of spread. From this wide-ranging geographical study, we report here numerous new NIS records at the basin, subregional, country and locality level. At the basin level, we report three NIS new to the Mediterranean Sea (Achelia sawayai sensu lato, Aorides longimerus, Cymodoce aff. fuscina), and the re-appearance of two NIS previously known but currently considered extinct in the Mediterranean (Bemlos leptocheirus, Saccostrea glomerata). We also compellingly update the distributions of many NIS in the Mediterranean Sea showing some recent spreading; we provide details for 11 new subregional records for NIS (Watersipora arcuata, Hydroides brachyacantha sensu lato and Saccostrea glomerata now present in the Western Mediterranean; Symplegma brakenhielmi, Stenothoe georgiana, Spirobranchus tertaceros sensu lato, Dendostrea folium sensu lato and Parasmittina egyptiaca now present in the Central Mediterranean, and W. arcuata, Bemlos leptocheirus and Dyspanopeus sayi in the Eastern Mediterranean). We also report 51 new NIS country records from recreational marinas: 12 for Malta, 10 for Cyprus, nine for Greece, six for Spain and France, five for Turkey and three for Italy, representing 32 species. Finally, we report 20 new NIS records (representing 17 species) found on recreational boat-hulls (mobile habitats), not yet found in the same marina, or in most cases, even the country. For each new NIS record, their native origin and global and Mediterranean distributions are provided, along with details of the new record. Additionally, taxonomic characters used for identification and photos of the specimens are also provided. These new NIS records should now be added to the relevant NIS databases compiled by several entities. Records of uncertain identity are also discussed, to assess the probability of valid non-indigenous status.
Ulman et al. (2017) A massive update of non-indigenous species records in Mediterranean marinas. PeerJ 5:e3954 https://doi.org/10.7717/peerj.3954
Statins: antimicrobial resistance breakers or makers?
Introduction The repurposing of non-antibiotic drugs as adjuvant antibiotics may help break antimicrobial resistance (AMR). Statins are commonly prescribed worldwide to lower cholesterol. They also possess qualities of AMR “breakers”, namely direct antibacterial activity, synergism with antibiotics, and ability to stimulate the host immune system. However, statins’ role as AMR breakers may be limited. Their current extensive use for cardiovascular protection might result in selective pressures for resistance, ironically causing statins to be AMR “makers” instead. This review examines statins’ potential as AMR breakers, probable AMR makers, and identifies knowledge gaps in a statin-bacteria-human-environment continuum. The most suitable statin for repurposing is identified, and a mechanism of antibacterial action is postulated based on structure-activity relationship analysis. Methods A literature search using keywords “statin” or “statins” combined with “minimum inhibitory concentration” (MIC) was performed in six databases on 7th April 2017. After screening 793 abstracts, 16 relevant studies were identified. Unrelated studies on drug interactions; antifungal or antiviral properties of statins; and antibacterial properties of mevastatin, cerivastatin, antibiotics, or natural products were excluded. Studies involving only statins currently registered for human use were included. Results Against Gram-positive bacteria, simvastatin generally exerted the greatest antibacterial activity (lowest MIC) compared to atorvastatin, rosuvastatin, and fluvastatin. Against Gram-negative bacteria, atorvastatin generally exhibited similar or slightly better activity compared to simvastatin, but both were more potent than rosuvastatin and fluvastatin. Discussion Statins may serve as AMR breakers by working synergistically with existing topical antibiotics, attenuating virulence factors, boosting human immunity, or aiding in wound healing. It is probable that statins’ mechanism of antibacterial activity involves interference of bacterial cell regulatory functions via binding and disrupting cell surface structures such as wall teichoic acids, lipoteichoic acids, lipopolysaccharides, and/or surface proteins. The widespread use of statins for cardiovascular protection may favor selective pressures or co-selection for resistance, including dysbiosis of the human gut microbiota, sublethal plasma concentrations in bacteremic patients, and statin persistence in the environment, all possibly culminating in AMR. Conclusion Simvastatin appears to be the most suitable statin for repurposing as a novel adjuvant antibiotic. Current evidence better supports statins as potential AMR breakers, but their role as plausible AMR makers cannot be excluded. Elucidating the mechanism of statins’ antibacterial activity is perhaps the most important knowledge gap to address as this will likely clarify statins’ role as AMR breakers or makers.
Ko et al. (2017) Statins: antimicrobial resistance breakers or makers?. PeerJ 5:e3952 https://doi.org/10.7717/peerj.3952
Measuring language lateralisation with different language tasks: a systematic review
Language lateralisation refers to the phenomenon in which one hemisphere (typically the left) shows greater involvement in language functions than the other. Measurement of laterality is of interest both to researchers investigating the neural organisation of the language system and to clinicians needing to establish an individual’s hemispheric dominance for language prior to surgery, as in patients with intractable epilepsy. Recently, there has been increasing awareness of the possibility that different language processes may develop hemispheric lateralisation independently, and to varying degrees. However, it is not always clear whether differences in laterality across language tasks with fMRI are reflective of meaningful variation in hemispheric lateralisation, or simply of trivial methodological differences between paradigms. This systematic review aims to assess different language tasks in terms of the strength, reliability and robustness of the laterality measurements they yield with fMRI, to look at variability that is both dependent and independent of aspects of study design, such as the baseline task, region of interest, and modality of the stimuli. Recommendations are made that can be used to guide task design; however, this review predominantly highlights that the current high level of methodological variability in language paradigms prevents conclusions as to how different language functions may lateralise independently. We conclude with suggestions for future research using tasks that engage distinct aspects of language functioning, whilst being closely matched on non-linguistic aspects of task design (e.g., stimuli, task timings etc); such research could produce more reliable and conclusive insights into language lateralisation. This systematic review was registered as a protocol on Open Science Framework: https://osf.io/5vmpt/.
Bradshaw et al. (2017) Measuring language lateralisation with different language tasks: a systematic review. PeerJ 5:e3929 https://doi.org/10.7717/peerj.3929
The head turn paradigm to assess auditory laterality in cats: influence of ear position and repeated sound presentation
In most humans, speech is predominantly processed by the left hemisphere. This auditory laterality was formerly thought to be an exclusive human characteristic, but is now suggested to have pre-human origins. In studies on auditory laterality in nonhuman animals, the head turn paradigm has become very popular due to its non-invasive character. Although there are implications that the head turn direction indicates functional dominance of the contralateral hemisphere in processing a given sound, the validity of the paradigm is under debate. To validate the paradigm via comparison with imaging or electrophysiological methods, it is first necessary to establish turning biases at the individual level. Recently, the domestic cat, a common model in hearing research, has been found to show turning biases at the group level. To assess individual turning asymmetries in cats, we repeatedly presented kitten isolation calls and assessed whether differences in conveyed arousal changed the previously described left-wards lateralisation of conspecific vocalizations. Based on responses to 50 playback presentations (25 of high and 25 of low arousal), we calculated individual head turn indices. Based on the total data set, we found no consistent individual turning bias, irrespective of call category or sex of the receiver. Although the playback paradigm was chosen carefully to reduce any effects of lateralized loudness perception or changes in motivation due to habituation, individual head turn biases changed significantly in concordance with habituation to repeated playback-presentations and was predictable by small deflections in ear position prior to listening. When splitting the data set according to a decline in responsiveness after seven playback presentations, we revealed an initial left turning bias for most of our subjects (i.e., significant at the group level). We propose that this left turning bias is related to right hemisphere dominance in processes like vigilance behaviour or general arousal rather than on auditory processing, as such. Our findings suggest that both the experimental sequence and sound level differences, induced by asymmetric ear positions, strongly influence the outcome of the head turn paradigm and should be taken into account when evaluating auditory laterality at the behavioural level.
Konerding et al. (2017) The head turn paradigm to assess auditory laterality in cats: influence of ear position and repeated sound presentation. PeerJ 5:e3925 https://doi.org/10.7717/peerj.3925