Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera)
Ensign wasps (Hymenoptera: Evaniidae) develop as predators of cockroach eggs (Blattodea), have a wide distribution and exhibit numerous interesting biological phenomena. The taxonomy of this lineage has been the subject of several recent, intensive efforts, but the lineage lacked a robust phylogeny. In this paper we present a new phylogeny, based on increased taxonomic sampling and data from six molecular markers (mitochondrial 16S and COI, and nuclear markers 28S, RPS23, CAD, and AM2), the latter used for the first time in phylogenetic reconstruction. Our intent is to provide a robust phylogeny that will stabilize and facilitate revision of the higher-level classification. We also show the continued utility of molecular motifs, especially the presence of an intron in the RPS23 fragments of certain taxa, to diagnose evaniid clades and assist with taxonomic classification. Furthermore, we estimate divergence times among evaniid lineages for the first time, using multiple fossil calibrations. Evaniidae radiated primarily in the Early Cretaceous (134.1–141.1 Mya), with and most extant genera diverging near the K-T boundary. The estimated phylogeny reveals a more robust topology than previous efforts, with the recovery of more monophyletic taxa and better higher-level resolution. The results facilitate a change in ensign wasp taxonomy, with Parevania, and Papatuka, syn. nov. becoming junior synonyms of Zeuxevania, and Acanthinevania, syn. nov. being designated as junior synonym of Szepligetella. We transfer 30 species to Zeuxevania, either reestablishing past combinations or as new combinations. We also transfer 20 species from Acanthinevania to Szepligetella as new combinations.
Sharanowski et al. (2019) Multi-gene phylogeny and divergence estimations for Evaniidae (Hymenoptera). PeerJ 7:e6689 https://doi.org/10.7717/peerj.6689
Spiders did not repeatedly gain, but repeatedly lost, foraging webs
Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10–14 times, and that the orb web evolved at least three times. These findings in fact result from a particular phylogenetic character coding strategy, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e., not absent) web architectures. “Absence” of webs should be regarded as inapplicable data. To be analyzed properly by character optimization algorithms, it should be coded as “?” because these codes—or their equivalent—are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (misspellings cause some optimization algorithms to drop terminals, which affects taxon sampling and results), and mistakes in spider natural history. In sum, the method causes character optimization algorithms to produce counter-intuitive results, and does not distinguish absence from secondary loss. Proper treatment of missing entries and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ∼5–7 times, not gained 10–14 times. The orb web, specifically, may be homologous (originated only once) although lost 2–6 times.
Coddington et al. (2019) Spiders did not repeatedly gain, but repeatedly lost, foraging webs. PeerJ 7:e6703 https://doi.org/10.7717/peerj.6703
Prehemodialysis arteriovenous access creation is associated with better cardiovascular outcomes in patients receiving hemodialysis: a population-based cohort study
Background Cardiovascular (CV) disease contributes to nearly half of the mortalities in patients with end-stage renal disease. Patients who received prehemodialysis arteriovenous access (pre-HD AVA) creation had divergent CV outcomes. Methods We conducted a population-based cohort study by recruiting incident patients receiving HD from 2001 to 2012 from the Taiwan National Health Insurance Research Database. Patients’ characteristics, comorbidities, and medicines were analyzed. The primary outcome of interest was major adverse cardiovascular events (MACEs), defined as hospitalization due to acute myocardial infarction, stroke, or congestive heart failure (CHF) occurring within the first year of HD. Secondary outcomes included MACE-related mortality and all-cause mortality in the same follow-up period. Results The patients in the pre-HD AVA group were younger, had a lower burden of underlying diseases, were more likely to use erythropoiesis-stimulating agents but less likely to use renin–angiotensin–aldosterone system blockers. The patients with pre-HD AVA creation had a marginally lower rate of MACEs but a significant 35% lower rate of CHF hospitalization than those without creation (adjusted hazard ratio (HR) 0.65, 95% confidence interval (CI) [0.48–0.88]). In addition, the pre-HD AVA group exhibited an insignificantly lower rate of MACE-related mortality but a significantly 52% lower rate of all-cause mortality than the non-pre-HD AVA group (adjusted HR 0.48, 95% CI [0.39–0.59]). Sensitivity analyses obtained consistent results. Conclusions Pre-HD AVA creation is associated with a lower rate of CHF hospitalization and overall death in the first year of dialysis.
Yen et al. (2019) Prehemodialysis arteriovenous access creation is associated with better cardiovascular outcomes in patients receiving hemodialysis: a population-based cohort study. PeerJ 7:e6680 https://doi.org/10.7717/peerj.6680
A longitudinal study of the faecal microbiome and metabolome of periparturient mares
Background Periparturient mares are at increased risk of colic including large colon volvulus, which has a high mortality rate. Alterations in colonic microbiota related to either physiological or management changes, or both, that occur at this time have been suggested as potential causes for increased colic risk in this population of horses. Although the effect of management changes on the horse faecal microbiota has been investigated, limited work has been conducted to investigate changes in faecal microbiota structure and function in the periparturient period. The objectives of the current study were to investigate temporal stability of the faecal microbiota and volatile organic compounds (VOCs) of the faecal metabolome in periparturient mares. Methods Faecal samples were collected weekly from five pregnant mares from 3 weeks pre-foaling to 7 weeks post-foaling. The microbiome data was generated by PCR amplification and sequencing of the V1–V2 regions of the bacterial 16S rRNA genes, while the VOC profile was characterised using headspace solid phase microextraction gas chromatography mass spectrometry. Results The mare faecal microbiota was relatively stable over the periparturient period and most variation was associated with individual mares. A small number of operational taxonomic units were found to be significantly differentially abundant between samples collected before and after foaling. A total of 98 VOCs were identified. The total number of VOCs did not vary significantly between individual mares, weeks of sample collection and feeds available to the mares. Three VOCs (decane, 2-pentylfuran, and oct-2-ene) showed significant increase overtime on linear mixed effects modelling analysis. These results suggest that the mare faecal microbiota is structurally and functionally stable during the periparturient period. The findings also suggest that if changes in the gut microbiota are related to development of colic postpartum, altered risk may be due to inherent differences between individual mares. VOCs offer a cost-effective means of looking at the functional changes in the microbiome and warrant further investigation in mares at risk of colic.
Salem et al. (2019) A longitudinal study of the faecal microbiome and metabolome of periparturient mares. PeerJ 7:e6687 https://doi.org/10.7717/peerj.6687
Density of intertidal barnacles along their full elevational range of distribution conforms to the abundant-centre hypothesis
The abundant-centre hypothesis (ACH) predicts that the density of a species should peak at its distribution centre and decrease similarly towards distribution margins. The ACH has been deduced from a theory that postulates that environmental conditions should be most favourable for a species at the centre of its distribution. This idealised density pattern, however, has been supported by limited field studies, as natural patterns are often more complex. It is thus of interest to examine under what conditions compliance with the ACH could be favoured. Such conditions could be smooth environmental gradients with limited habitat patchiness throughout the distribution range of a species. Thus, we tested the ACH by measuring the density of an intertidal barnacle (Semibalanus balanoides) across its full vertical distribution range (from low to high elevations) on a rocky shore with similar substrate properties across elevations. To do a reliable test, we surveyed eight elevation zones applying an equal sampling effort in each zone. Average barnacle density conformed to the ACH, as it peaked at the middle of the vertical distribution range of this species. The same underlying theory predicts a similar unimodal pattern for maximum body size, but this trait was decoupled from density, as maximum barnacle size increased from low to high elevations. Overall, although the ACH is not a universal predictive tool as once envisioned, it may predict some cases well, as shown by this study. Therefore, the ACH should not be discarded completely, and its domain of application should be further evaluated.
Scrosati et al. (2019) Density of intertidal barnacles along their full elevational range of distribution conforms to the abundant-centre hypothesis. PeerJ 7:e6719 https://doi.org/10.7717/peerj.6719
Environmental modulation of the proteomic profiles from closely phylogenetically related populations of the red seaweed Plocamium brasiliense
The genus Plocamium encompasses seaweeds that are widely distributed throughout the world’s oceans, with Plocamium brasiliense found along the tropical and subtropical coasts of the Western Atlantic. This wide distribution can lead to structured populations due to environmental differences (e.g., light levels or temperature), restricted gene flow, and the presence of cryptic species. Abiotic variation can also affect gene expression, which consequently leads to differences in the seaweeds protein profile. This study aimed to analyze the genetic and proteomic profiles of P. brasiliense sampled in two geographically distinct sites on the coastline of Rio de Janeiro state, Brazil: Arraial do Cabo (P1) and Búzios (P2). The genetic profiles of macroalgal specimens from these two sites were indistinguishable as assessed by the markers UPA/23S, rbcL, and COI-5P; however, the protein profiles varied significantly between populations from the two sites. At both sites the ribulose-1,5-biphosphate carboxylase/oxygenase was the most abundant protein found in P. brasiliense specimens. The number of phycobiliproteins differed between both sites with the highest numbers being found at P1, possibly due to water depth. The differences in proteomic profiles of the two nearly identical populations of P. brasiliense suggest that environmental parameters such as light availability and desiccation might induce distinct protein expression, probably as a result of the phenotypic plasticity within this population of seaweed.
Calegario et al. (2019) Environmental modulation of the proteomic profiles from closely phylogenetically related populations of the red seaweed Plocamium brasiliense. PeerJ 7:e6469 https://doi.org/10.7717/peerj.6469
Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico
The aim of this study was to describe the reproductive dynamic of Euthynnus alletteratus in the southwest Gulf of Mexico. The annual variation of the volume fraction occupied by gametes and tissues in gonads were related with main body indexes, such as the gonadosomatic index (IG), the hepatosomatic index (IH), and the nutrition index (IN), and compared with the sea surface temperature. A total of 951 E. alletteratus individuals were sampled, where a sex ratio of 1:1 and a size interval strongly skewed towards organisms with a fork length (LF) of 36–40 cm were observed. The IG showed an increase from March to September with maximum values in April and July. Two clearly defined peaks were observed, and they were consistent with the histological analysis, where the percentage of ripe gametes predominated from April to September. The optimum thermal window for reproductive activity was from 24 to 28 °C. The size of first sex maturity was 34.35 cm of LF for males and 34.60 (LF) for females, without significant difference between sexes.
Cruz-Castán et al. (2019) Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico. PeerJ 7:e6558 https://doi.org/10.7717/peerj.6558
Comparison of shallow-water seston among biogenic habitats on tidal flats
Aquatic structure-formers have the potential to establish mosaics of seston in shallow water if they modify the relative amounts of deposition (or filtration) and resuspension of particles. By sampling surface water adjacent to Lagrangian drifters traveling 0.1 to 2 m above the bottom, we tested the modification of seston in water masses flowing over two biogenic marine species (native eelgrass, Zostera marina; introduced oysters, Crassostrea gigas) in comparison to unstructured tidal flats. Water properties were examined at five intertidal sites in Washington State, USA, each with 27 drifts (three drifts at different stages of the tidal cycle in each of three patches of three habitat types; drift distance 116 m (109SD), duration 24 min (15SD)). At the initiation of each drift, habitat differences in water properties were already apparent: chlorophyll-a and total suspended solid (TSS) concentrations were greater in structured habitats than bare, and TSS was also inversely related to water depth. Water flowed more slowly across eelgrass than other habitat types. As water flowed across each habitat type, TSS generally increased, especially in shallow water, but without habitat differences; chlorophyll-a in these surface-water samples showed no consistent change during drifts. At higher TSS concentrations, quality in terms of organic content declined, and this relationship was not habitat-specific. However, quality in terms of chlorophyll-a concentration increased with TSS, as well as being greater in water over eelgrass than over other habitat types. These results support widespread mobilization of seston in shallow water ebbing or flooding across Washington State’s tidal flats, especially as water passes into patches of biogenic species.
Ruesink et al. (2019) Comparison of shallow-water seston among biogenic habitats on tidal flats. PeerJ 7:e6616 https://doi.org/10.7717/peerj.6616
Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China
Background Epidemiological data on malocclusion among Chinese children are scant. The aim of this study was to provide detailed information on the prevalence of malocclusion in early mixed dentition children in Shanghai, China. Methods A cross-sectional survey was conducted from September 2016 to April 2017, and 2,810 children aged 7- to 9- years were selected from 10 primary schools by cluster random sampling. Several occlusal parameters, including Angle molar relationship, overjet, overbite, open bite, anterior and posterior crossbite, midline displacement, scissors bite, and teeth crowding and spacing, were clinically registered by five calibrated orthodontic dentists. Results We found that 79.4% children presented one or more occlusal anomalies. Angle Class I, Class II and Class III molar relationship were recorded in 42.3%, 50.9% and 5.9% of the sample, respectively. The proportion of Class III increased from 5.0% at age 7 to 7.8% at age 9. In the sagittal plane, increased overjet >3 mm was observed in 40.8% subjects, while the prevalence of severe overjet (>8 mm), anterior edge-to-edge (zero overjet) and anterior crossbite were 5.2%, 8.1% and 10.5%, respectively. Vertically, deep overbite >2/3 overlap was found in 6.2% of the children and open bite in 4.3%. Boys exhibited a higher rate of overbite than girls. For the transversal occlusal anomalies, 36.1% of the children had a midline displacement, which was followed by posterior crossbite (2.6%) and scissors bite (1.0%). Teeth space discrepancies were also common anomalies and anterior crowding (>2 mm) affecting 28.4% of the children, while anterior spacing (>4 mm) affecting 9.5%. Girls showed a higher prevalence of anterior crowding and a lower frequency of teeth spacing than boys. Conclusions Our study demonstrated that malocclusion is prevalent among children in the early mixed dentition, and more health resources should be warranted to meet the challenge of prevention or early intervention of malocclusion.
Yu et al. (2019) Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China. PeerJ 7:e6630 https://doi.org/10.7717/peerj.6630
On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection
The illegal practice of using cyanide (CN) as a stunning agent to collect fish for both the marine aquarium and live fish food trades has been used throughout the Indo-Pacific for over 50 years. CN fishing is destructive to all life forms within the coral reef ecosystems where it is used and is certainly one of many anthropogenic activities that have led to 95% of the reefs in the Indo-Pacific being labeled at risk for degradation and loss. A field-deployable test for detecting fish caught using CN would assist in combating the use of this destructive practice, however, no reliable and robust test exists. Further, there is little toxicokinetic data available on marine fish to support the development of such a test, yet such data is critical to establishing the concentration range and time scale over which such a test would be viable. This study presents the first direct measurement of the half-life of the metabolite thiocyanate (SCN) after pulsed exposure to CN in a marine fish. SCN was measured in the plasma of Amphiprion ocellaris after exposure to 50 ppm CN for three exposure times (20, 45, and 60 s) using HPLC-UV and a C30 column pre-treated with polyethylene glycol. Plasma SCN levels observed are dose-dependent, reflecting a longer time for conversion of CN to SCN as the dose of CN increases. SCN plasma levels reached a maximum concentration (1.2–2.3 ppm) 12–20 h after exposure to CN. The half-life for the elimination of SCN was 1.01 ± 0.26 days for 45 s exposure and 0.44 ± 0.15 days for 20 s exposure. Fish were also directly exposed to SCN (100 ppm for 11 days) and the observed half-life for SCN elimination was 0.35 ± 0.07 days. Plasma SCN levels did not return to control levels, even after 41 days when exposed to CN but did return to control levels after 48 days when exposed to SCN. The similar half-lives observed for CN and SCN exposure suggests that SCN exposure can be used as a proxy for measuring the rate of SCN elimination following CN exposure. In order for plasma SCN to be used as a marker for CN exposure, these results must be extended to other species and endogenous levels of SCN in wild caught fish must be established.
Breen et al. (2019) On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection. PeerJ 7:e6644 https://doi.org/10.7717/peerj.6644