From the Guiana Highlands to the Brazilian Atlantic Rain Forest: four new species of Selaginella (Selaginellaceae – Lycopodiophyta: S. agioneuma, S. magnafornensis, S. ventricosa, and S. zartmanii)
We describe four new species in the genus Selaginella (i.e., S. agioneuma, S. magnafornensis, S. ventricosa, and S. zartmanii) from Brazil, all presently classified in subg. Stachygynandrum. For each of the new taxa we discuss taxonomic affinities and provide information on habitat, distribution, and conservation status. In addition, line drawings and scanning electron microscope (SEM) images of stems sections, leaves, and spores (when present) are included. Selaginella agioneuma and S. magnafornensis are from the State of Espíritu Santo where they inhabit premontane to montane Atlantic rain forests in the Reserva Biológica Augusto Ruschi and Parque Estadual Forno Grande, respectively. Selaginella ventricosa was collected in upper montane forests at Parque Nacional Serra da Mocidade, State of Roraima and S. zartmanii in premontane Amazon rain forests on upper Rio Negro at Mpio. São Gabriel da Cachoeira, Amazonas State in both Serra Curicuriari and the Morro dos Seis Lagos Biological Reserve.
Valdespino et al. (2018) From the Guiana Highlands to the Brazilian Atlantic Rain Forest: four new species of Selaginella (Selaginellaceae – Lycopodiophyta: S. agioneuma, S. magnafornensis, S. ventricosa, and S. zartmanii). PeerJ 6:e4708 https://doi.org/10.7717/peerj.4708
Comparison of hoop-net trapping and visual surveys to monitor abundance of the Rio Grande cooter (Pseudemys gorzugi)
Abundance estimates play an important part in the regulatory and conservation decision-making process. It is important to correct monitoring data for imperfect detection when using these data to track spatial and temporal variation in abundance, especially in the case of rare and elusive species. This paper presents the first attempt to estimate abundance of the Rio Grande cooter (Pseudemys gorzugi) while explicitly considering the detection process. Specifically, in 2016 we monitored this rare species at two sites along the Black River, New Mexico via traditional baited hoop-net traps and less invasive visual surveys to evaluate the efficacy of these two sampling designs. We fitted the Huggins closed-capture estimator to estimate capture probabilities using the trap data and distance sampling models to estimate detection probabilities using the visual survey data. We found that only the visual survey with the highest number of observed turtles resulted in similar abundance estimates to those estimated using the trap data. However, the estimates of abundance from the remaining visual survey data were highly variable and often underestimated abundance relative to the estimates from the trap data. We suspect this pattern is related to changes in the basking behavior of the species and, thus, the availability of turtles to be detected even though all visual surveys were conducted when environmental conditions were similar. Regardless, we found that riverine habitat conditions limited our ability to properly conduct visual surveys at one site. Collectively, this suggests visual surveys may not be an effective sample design for this species in this river system. When analyzing the trap data, we found capture probabilities to be highly variable across sites and between age classes and that recapture probabilities were much lower than initial capture probabilities, highlighting the importance of accounting for detectability when monitoring this species. Although baited hoop-net traps seem to be an effective sampling design, it is important to note that this method required a relatively high trap effort to reliably estimate abundance. This information will be useful when developing a larger-scale, long-term monitoring program for this species of concern.
Mali et al. (2018) Comparison of hoop-net trapping and visual surveys to monitor abundance of the Rio Grande cooter (Pseudemys gorzugi). PeerJ 6:e4677 https://doi.org/10.7717/peerj.4677
Lighten up the dark: metazoan parasites as indicators for the ecology of Antarctic crocodile icefish (Channichthyidae) from the north-west Antarctic Peninsula
Due to its remote and isolated location, Antarctica is home to a unique diversity of species. The harsh conditions have shaped a primarily highly adapted endemic fauna. This includes the notothenioid family Channichthyidae. Their exceptional physiological adaptations have made this family of icefish the focus of many studies. However, studies on their ecology, especially on their parasite fauna, are comparatively rare. Parasites, directly linked to the food chain, can function as biological indicators and provide valuable information on host ecology (e.g., trophic interactions) even in remote habitats with limited accessibility, such as the Southern Ocean. In the present study, channichthyid fish (Champsocephalus gunnari: n = 25, Chaenodraco wilsoni: n = 33, Neopagetopsis ionah: n = 3, Pagetopsis macropterus: n = 4, Pseudochaenichthys georgianus: n = 15) were collected off South Shetland Island, Elephant Island, and the tip of the Antarctic Peninsula (CCAML statistical subarea 48.1). The parasite fauna consisted of 14 genera and 15 species, belonging to the six taxonomic groups including Digenea (four species), Nematoda (four), Cestoda (two), Acanthocephala (one), Hirudinea (three), and Copepoda (one). The stomach contents were less diverse with only Crustacea (Euphausiacea, Amphipoda) recovered from all examined fishes. Overall, 15 new parasite-host records could be established, and possibly a undescribed genotype or even species might exist among the nematodes.
Kuhn et al. (2018) Lighten up the dark: metazoan parasites as indicators for the ecology of Antarctic crocodile icefish (Channichthyidae) from the north-west Antarctic Peninsula. PeerJ 6:e4638 https://doi.org/10.7717/peerj.4638
Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications
The discovery of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka in 2006 was heralded as a major breakthrough of the decade in stem cell research. The ability to reprogram human somatic cells to a pluripotent embryonic stem cell-like state through the ectopic expression of a combination of embryonic transcription factors was greeted with great excitement by scientists and bioethicists. The reprogramming technology offers the opportunity to generate patient-specific stem cells for modeling human diseases, drug development and screening, and individualized regenerative cell therapy. However, fundamental questions have been raised regarding the molecular mechanism of iPSCs generation, a process still poorly understood by scientists. The efficiency of reprogramming of iPSCs remains low due to the effect of various barriers to reprogramming. There is also the risk of chromosomal instability and oncogenic transformation associated with the use of viral vectors, such as retrovirus and lentivirus, which deliver the reprogramming transcription factors by integration in the host cell genome. These challenges can hinder the therapeutic prospects and promise of iPSCs and their clinical applications. Consequently, extensive studies have been done to elucidate the molecular mechanism of reprogramming and novel strategies have been identified which help to improve the efficiency of reprogramming methods and overcome the safety concerns linked with iPSC generation. Distinct barriers and enhancers of reprogramming have been elucidated, and non-integrating reprogramming methods have been reported. Here, we summarize the progress and the recent advances that have been made over the last 10 years in the iPSC field, with emphasis on the molecular mechanism of reprogramming, strategies to improve the efficiency of reprogramming, characteristics and limitations of iPSCs, and the progress made in the applications of iPSCs in the field of disease modelling, drug discovery and regenerative medicine. Additionally, this study appraises the role of genomic editing technology in the generation of healthy iPSCs.
Omole et al. (2018) Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications. PeerJ 6:e4370 https://doi.org/10.7717/peerj.4370
Glycosylceramide modifies the flavor and metabolic characteristics of sake yeast
In the manufacture of sake, Japanese traditional rice wine, sake yeast is fermented with koji, which is steamed rice fermented with the non-pathogenic fungus Aspergillus oryzae. During fermentation, sake yeast requires lipids, such as unsaturated fatty acids and sterols, in addition to substances provided by koji enzymes for fermentation. However, the role of sphingolipids on the brewing characteristics of sake yeast has not been studied. In this study, we revealed that glycosylceramide, one of the sphingolipids abundant in koji, affects yeast fermentation. The addition of soy, A. oryzae, and Grifola frondosa glycosylceramide conferred a similar effect on the flavor profiles of sake yeast. In particular, the addition of A. oryzae and G. frondosa glycosylceramide were very similar in terms of the decreases in ethyl caprylate and ethyl 9-decenoate. The addition of soy glycosylceramide induced metabolic changes to sake yeast such as a decrease in glucose, increases in ethanol and glycerol and changes in several amino acids and organic acids concentrations. Tricarboxylic acid (TCA) cycle, pyruvate metabolism, starch and sucrose metabolism, and glycerolipid metabolism were overrepresented in the cultures incubated with sake yeast and soy glycosylceramide. This is the first study of the effect of glycosylceramide on the flavor and metabolic profile of sake yeast.
Ferdouse et al. (2018) Glycosylceramide modifies the flavor and metabolic characteristics of sake yeast. PeerJ 6:e4768 https://doi.org/10.7717/peerj.4768
Loss anticipation and outcome during the Monetary Incentive Delay Task: a neuroimaging systematic review and meta-analysis
Background Reward seeking and avoidance of punishment are key motivational processes. Brain-imaging studies often use the Monetary Incentive Delay Task (MIDT) to evaluate motivational processes involved in maladaptive behavior. Although the bulk of research has been done on the MIDT reward events, little is known about the neural basis of avoidance of punishment. Therefore, we conducted a meta-analysis of brain activations during anticipation and receipt of monetary losses in healthy controls. Methods All functional neuro-imaging studies using the MIDT in healthy controls were retrieved using PubMed, Google Scholar & EMBASE databases. Functional neuro-imaging data was analyzed using the Seed-based d Mapping Software. Results Thirty-five studies met the inclusion criteria, comprising 699 healthy adults. In both anticipation and loss outcome phases, participants showed large and robust activations in the bilateral striatum, (anterior) insula, and anterior cingulate gyrus relatively to Loss > Neutral contrast. Although relatively similar activation patterns were observed during the two event types, they differed in the pattern of prefrontal activations: ventro-lateral prefrontal activations were observed during loss anticipation, while medial prefrontal activations were observed during loss receipt. Discussion Considering that previous meta-analyses highlighted activations in the medial prefrontal cortex/anterior cingulate cortex, the anterior insula and the ventral striatum, the current meta-analysis highlighted the potential specificity of the ventro-lateral prefrontal regions, the median cingulate cortex and the amygdala in the loss events. Future studies can rely on these latter results to examine the neural correlates of loss processing in psychiatric populations characterized by harm avoidance or insensitivity to punishment.
Dugré et al. (2018) Loss anticipation and outcome during the Monetary Incentive Delay Task: a neuroimaging systematic review and meta-analysis. PeerJ 6:e4749 https://doi.org/10.7717/peerj.4749
Exotic lagomorph may influence eagle abundances and breeding spatial aggregations: a field study and meta-analysis on the nearest neighbor distance
The introduction of alien species could be changing food source composition, ultimately restructuring demography and spatial distribution of native communities. In Argentine Patagonia, the exotic European hare has one of the highest numbers recorded worldwide and is now a widely consumed prey for many predators. We examine the potential relationship between abundance of this relatively new prey and the abundance and breeding spacing of one of its main consumers, the Black-chested Buzzard-Eagle (Geranoaetus melanoleucus). First we analyze the abundance of individuals of a raptor guild in relation to hare abundance through a correspondence analysis. We then estimated the Nearest Neighbor Distance (NND) of the Black-chested Buzzard-eagle abundances in the two areas with high hare abundances. Finally, we performed a meta-regression between the NND and the body masses of Accipitridae raptors, to evaluate if Black-chested Buzzard-eagle NND deviates from the expected according to their mass. We found that eagle abundance was highly associated with hare abundance, more than with any other raptor species in the study area. Their NND deviates from the value expected, which was significantly lower than expected for a raptor species of this size in two areas with high hare abundance. Our results support the hypothesis that high local abundance of prey leads to a reduction of the breeding spacing of its main predator, which could potentially alter other interspecific interactions, and thus the entire community.
Barbar et al. (2018) Exotic lagomorph may influence eagle abundances and breeding spatial aggregations: a field study and meta-analysis on the nearest neighbor distance. PeerJ 6:e4746 https://doi.org/10.7717/peerj.4746
A new large-bodied thalattosuchian crocodyliform from the Lower Jurassic (Toarcian) of Hungary, with further evidence of the mosaic acquisition of marine adaptations in Metriorhynchoidea
Based on associated and three-dimensionally preserved cranial and postcranial remains, a new thalattosuchian crocodyliform, Magyarosuchus fitosi gen. et sp. nov. from the Lower Jurassic (Upper Toarcian) Kisgerecse Marl Formation, Gerecse Mountains, Hungary is described here. Phylogenetic analyses using three different datasets indicate that M. fitosi is the sister taxon of Pelagosaurus typus forming together the basal-most sub-clade of Metriorhynchoidea. With an estimated body length of 4.67–4.83 m M. fitosi is the largest known non-metriorhynchid metriorhynchoid. Besides expanding Early Jurassic thalattosuchian diversity, the new specimen is of great importance since, unlike most contemporaneous estuarine, lagoonal or coastal thalattosuchians, it comes from an ‘ammonitico rosso’ type pelagic deposit of the Mediterranean region of the Tethys. A distal caudal vertebra having an unusually elongate and dorsally projected neural spine implies the presence of at least a rudimentary hypocercal tail fin and a slight ventral displacement of the distal caudal vertebral column in this basal metriorhynchoid. The combination of retaining heavy dorsal and ventral armors and having a slight hypocercal tail is unique, further highlighting the mosaic manner of marine adaptations in Metriorhynchoidea.
Ősi et al. (2018) A new large-bodied thalattosuchian crocodyliform from the Lower Jurassic (Toarcian) of Hungary, with further evidence of the mosaic acquisition of marine adaptations in Metriorhynchoidea. PeerJ 6:e4668 https://doi.org/10.7717/peerj.4668
Development of a site fidelity index based on population capture-recapture data
Background Site fidelity is considered as an animal’s tendency to return to a previously occupied place; this is a component of animal behaviour that allows us to understand movement patterns and aspects related to the animal’s life history. Although there are many site fidelity metrics, the lack of standardisation presents a considerable challenge in terms of comparability among studies. Methods This investigation focused on the theoretical development of a standardised composite site fidelity index and its statistical distribution in order to obtain reliable population-level site fidelity comparisons. The arithmetic and harmonic means were used as mathematical structures in order to create different indexes by combining the most commonly used indicators for site fidelity such as Occurrence, Permanence and Periodicity. The index performance was then evaluated in simulated populations and one real population of Commerson’s dolphins (Cephalorhynchus commersonii (Lacépède 1804)). In the first case, the indexes were evaluated based on how they were affected by different probability values such as the occurrence of the individual within the study area (φ) and capture probability (p). As a precision measure for the comparison of the indexes, the Wald confidence interval (CI) and the mean square error were applied. Given that there was no previous data concerning the distribution parameters of this population, bootstrap CIs were applied for the study case. Results Eight alternative indexes were developed. The indexes with an arithmetic mean structure, in general, had a consistently inferior performance than those with a harmonic mean structure. The index IH4, in particular, achieved the best results in all of the scenarios and in the study case. Additionally, this index presented a normal distribution. As such, it was proposed as a standardised measure for site fidelity (Standardised Site Fidelity Index—SSFI). Discussion The SSFI is the first standardised metric that quantifies site fidelity at a populational level. It is an estimator that varies between zero and one and works in situations where detection is not perfect and effort can be constant or not. Moreover, it has an associated CI that allows users to make comparisons.
Tschopp et al. (2018) Development of a site fidelity index based on population capture-recapture data. PeerJ 6:e4782 https://doi.org/10.7717/peerj.4782
The performance of cleaner wrasse, Labroides dimidiatus, in a reversal learning task varies across experimental paradigms
Testing performance in controlled laboratory experiments is a powerful tool for understanding the extent and evolution of cognitive abilities in non-human animals. However, cognitive testing is prone to a number of potential biases, which, if unnoticed or unaccounted for, may affect the conclusions drawn. We examined whether slight modifications to the experimental procedure and apparatus used in a spatial task and reversal learning task affected performance outcomes in the bluestreak cleaner wrasse, Labroides dimidiatus (hereafter “cleaners”). Using two-alternative forced-choice tests, fish had to learn to associate a food reward with a side (left or right) in their holding aquarium. Individuals were tested in one of four experimental treatments that differed slightly in procedure and/or physical set-up. Cleaners from all four treatment groups were equally able to solve the initial spatial task. However, groups differed in their ability to solve the reversal learning task: no individuals solved the reversal task when tested in small tanks with a transparent partition separating the two options, whereas over 50% of individuals solved the task when performed in a larger tank, or with an opaque partition. These results clearly show that seemingly insignificant details to the experimental set-up matter when testing performance in a spatial task and might significantly influence the outcome of experiments. These results echo previous calls for researchers to exercise caution when designing methodologies for cognition tasks to avoid misinterpretations.
Gingins et al. (2018) The performance of cleaner wrasse, Labroides dimidiatus, in a reversal learning task varies across experimental paradigms. PeerJ 6:e4745 https://doi.org/10.7717/peerj.4745