A large Late Miocene cetotheriid (Cetacea, Mysticeti) from the Netherlands clarifies the status of Tranatocetidae
Cetotheriidae are a group of small baleen whales (Mysticeti) that evolved alongside modern rorquals. They once enjoyed a nearly global distribution, but then largely went extinct during the Plio-Pleistocene. After languishing as a wastebasket taxon for more than a century, the concept of Cetotheriidae is now well established. Nevertheless, the clade remains notable for its variability, and its scope remains in flux. In particular, the recent referral of several traditional cetotheriids to a new and seemingly unrelated family, Tranatocetidae, has created major phylogenetic uncertainty. Here, we describe a new species of Tranatocetus, the type of Tranatocetidae, from the Late Miocene of the Netherlands. Tranatocetus maregermanicum sp. nov. clarifies several of the traits previously ascribed to this genus, and reveals distinctive auditory and mandibular morphologies suggesting cetotheriid affinities. This interpretation is supported by a large phylogenetic analysis, which mingles cetotheriids and tranatocetids within a unified clade. As a result, we suggest that both groups should be reintegrated into the single family Cetotheriidae.
Marx et al. (2019) A large Late Miocene cetotheriid (Cetacea, Mysticeti) from the Netherlands clarifies the status of Tranatocetidae. PeerJ 7:e6426 https://doi.org/10.7717/peerj.6426
Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask)
The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.
Spatial and Geographic Information Science
Monteiro et al. (2019) Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask). PeerJ 7:e6446 https://doi.org/10.7717/peerj.6446
The value of diffusion tensor tractography delineating corticospinal tract in glioma in rat: validation via correlation histology
Background An assessment of the degree of white matter tract injury is important in neurosurgical planning for patients with gliomas. The main objective of this study was to assess the injury grade of the corticospinal tract (CST) in rats with glioma using diffusion tensor imaging (DTI). Methods A total 17 rats underwent 7.0T MRI on day 10 after tumor implantation. The apparent diffusion coefficient (ADC) and fractional anisotropy (FA) were acquired in the tumor, peritumoral and contralateral areas, and the ADC ratio (ipsilateral ADC/contralateral ADC) and rFA (relative FA = ipsilateral FA/contralateral FA) in the peritumoral areas were measured. The CST injury was divided into three grades and delineated by diffusion tensor tractography reconstruction imaging. The fiber density index (FDi) of the ipsilateral and contralateral CST and rFDi (relative FDi = ipsilateral FDi/contralateral FDi) in the peritumoral areas were measured. After the mice were sacrificed, the invasion of glioma cells and fraction of proliferating cells were observed by hematoxylin-eosin and Ki67 staining in the tumor and peritumoral areas. The correlations among the pathology results, CST injury grade and DTI parameter values were calculated using a Spearman correlation analysis. One-way analysis of variance was performed to compare the different CST injury grade by the rFA, rFDi and ADC ratio values. Results The tumor cells and proliferation index were positively correlated with the CST injury grade (r = 0.8857, 0.9233, P < 0.001). A negative correlation was demonstrated between the tumor cells and the rFA and rFDi values in the peritumoral areas (r = −0.8571, −0.5588), and the proliferation index was negatively correlated with the rFA and rFDi values (r = −0.8571, −0.5588), while the ADC ratio was not correlated with the tumor cells or proliferation index. The rFA values between the CST injury grades (1 and 3, 2 and 3) and the rFDi values in grades 1 and 3 significantly differed (P < 0.05). Conclusions Diffusion tensor imaging may be used to quantify the injury degrees of CST involving brain glioma in rats. Our data suggest that these quantitative parameters may be used to enhance the efficiency of delineating the relationship between fiber tracts and malignant tumor.
Jia et al. (2019) The value of diffusion tensor tractography delineating corticospinal tract in glioma in rat: validation via correlation histology. PeerJ 7:e6453 https://doi.org/10.7717/peerj.6453
Morphological identification and molecular confirmation of the deep-sea blue and red shrimp Aristeus antennatus larvae
The early life stages of the blue and red shrimp Aristeus antennatus (Decapoda: Dendrobranchiata: Penaeoidea: Aristeidae) were described by Heldt in 1955 based on plankton samples, larval rearing and assumptions of species habitat. Even with adequate keys, identification of its first larval stages remained a difficult task due to the lack of specific morphological characters which would differentiate them from other Penaeoidea species. Larvae of Aristeus antennatus were collected in the continental slope off the Spanish Mediterranean coast in August 2016 with a neuston net and preserved in ethanol 96%. DNA from the larvae was extracted and the molecular markers Cytochrome Oxidase I and 16S rDNA were sequenced and compared to that of adults with the objective of confirming the previous morphological description. Then, we present additional information to the morphological description of Aristeus antennatus larval stages through scanning electron microscopy and molecular analysis. This represents the first documented occurrence of Aristeus antennatus larvae off the Catalan coast and sets the grounds for further work on larval ecology and population connectivity of the species, which is an important contribution to a more sustainable fishery.
Carreton et al. (2019) Morphological identification and molecular confirmation of the deep-sea blue and red shrimp Aristeus antennatus larvae. PeerJ 7:e6063 https://doi.org/10.7717/peerj.6063
The running kinematics of free-roaming giraffes, measured using a low cost unmanned aerial vehicle (UAV)
The study of animal locomotion can be logistically challenging, especially in the case of large or unhandleable animals in uncontrolled environments. Here we demonstrate the utility of a low cost unmanned aerial vehicle (UAV) in measuring two-dimensional running kinematics from free-roaming giraffes (Giraffa camelopardalis giraffa) in the Free State Province, South Africa. We collected 120 Hz video of running giraffes, and calibrated each video frame using metatarsal length as a constant object of scale. We tested a number of methods to measure metatarsal length. The method with the least variation used close range photography and a trigonometric equation to spatially calibrate the still image, and derive metatarsal length. In the absence of this option, a spatially calibrated surface model of the study terrain was used to estimate topographical dimensions in video footage of interest. Data for the terrain models were collected using the same equipment, during the same study period. We subsequently validated the accuracy of the UAV method by comparing similar speed measurements of a human subject running on a treadmill, with treadmill speed. At 8 m focal distance we observed an error of 8% between the two measures of speed. This error was greater at a shorter focal distance, and when the subject was not in the central field of view. We recommend that future users maximise the camera focal distance, and keep the subject in the central field of view. The studied giraffes used a grounded rotary gallop with a speed range of 3.4–6.9 ms−1 (never cantering, trotting or pacing), and lower duty factors when compared with other cursorial quadrupeds. As this pattern might result in adverse increases in peak vertical limb forces with speed, it was notable to find that contralateral limbs became more in-phase with speed. Considering the latter pattern and the modest maximal speed of giraffes, we speculate that tissue safety factors are maintained within tolerable bounds this way. Furthermore, the angular kinematics of the neck were frequently isolated from the pitching of the body during running; this may be a result of the large mass of the head and neck. Further field experiments and biomechanical models are needed to robustly test these speculations.
Basu et al. (2019) The running kinematics of free-roaming giraffes, measured using a low cost unmanned aerial vehicle (UAV). PeerJ 7:e6312 https://doi.org/10.7717/peerj.6312
Responses of Phaseolus calcaltus to lime and biochar application in an acid soil
Introduction Rice bean (Phaseolus calcaltus), as an annual summer legume, is always subjected to acid soils in tropical to subtropical regions, limiting its growth and nodulation. However, little is known about its responses to lime and biochar addition, the two in improving soil fertility in acid soils. Materials and Methods In the current study, a pot experiment was conducted using rice bean on a sandy yellow soil (Orthic Acrisol) with a pH of 5.5. The experiment included three lime rates (0, 0.75 and 1.5 g kg−1) and three biochar rates (0, 5 and 10 g kg−1). The biochar was produced from aboveground parts of Solanum tuberosum using a home-made device with temperature of pyrolysis about 500 °C. Results and Discussion The results indicated that both lime and biochar could reduce soil exchange Al concentration, increase soil pH and the contents of soil microbial biomass carbon and microbial biomass nitrogen, and enhance urease and dehydrogenase activities, benefiting P. calcaltus growth and nodulation in acid soils. Lime application did decrease the concentrations of soil available phosphorus (AP) and alkali dispelled nitrogen (AN), whereas biochar application increased the concentrations of soil AP, AN and available potassium (AK). However, sole biochar application could not achieve as much yield increase as lime application did. High lime rate (1.5 g lime kg−1) incorporated with low biochar rate (5 g biochar kg−1) could obtain higher shoot biomass, nutrient uptake, and nodule number when compared with high lime rate and high biochar rate. Conclusion Lime incorporated with biochar application could achieve optimum improvement for P. calcaltus growing in acid soils when compared with sole lime or biochar addition.
Yao et al. (2019) Responses of Phaseolus calcaltus to lime and biochar application in an acid soil. PeerJ 7:e6346 https://doi.org/10.7717/peerj.6346
Nation-scale primary prevention to reduce newly incident adolescent drug use: the issue of lag time
Background There is limited evidence about the effects of United States (US) nation-level policy changes on the incidence of alcohol drinking and tobacco smoking. To investigate the potential primary prevention effects on precocious drug use and to clarify lag-time issues, we estimated incidence rates for specified intervals anticipating and lagging after drug policy enactment. Our hypotheses are (a) reductions in underage drinking or smoking onset and (b) increases of incidence at the legal age (i.e., 21 for drinking and 18 for smoking). Methods The study population is 12–23-year-old non-institutionalized US civilian residents. Estimates are from 30 community samples drawn to be nationally representative for the US National Surveys on Drug Use and Health 1979–2015. Estimates were year-by-year annual incidence rates for alcohol drinking and tobacco smoking by 12–23-year-olds, age by age. Meta-regressions estimate age-specific incidence over time. Results Incidence of underage alcohol drinking declined and followed a trend line that started before 1984 enactment of the National Minimum Drinking Age Act, but increased drinking incidence for 21 year olds was observed approximately 10 years after policy enactment. Eight years after the Synar amendment enactment, evidence of reduced smoking incidence started to emerge. Among 18 year olds, a slight increase in tobacco smoking incidence occurred about 10 years after the Synar amendment. Conclusion Once nation-level policies affecting drug sales to minors are enacted, one might have to wait almost a decade before seeing tangible policy effects on drug use incidence rates.
Cheng et al. (2019) Nation-scale primary prevention to reduce newly incident adolescent drug use: the issue of lag time. PeerJ 7:e6356 https://doi.org/10.7717/peerj.6356
Modeling the spatial structure of the endemic mara (Dolichotis patagonum) across modified landscapes
Across modified landscapes, anthropic factors can affect habitat selection by animals and consequently their abundance and distribution patterns. The study of the spatial structure of wild populations is crucial to gain knowledge on species’ response to habitat quality, and a key for the design and implementation of conservation actions. This is particularly important for a low-density and widely distributed species such as the mara (Dolichotis patagonum), a large rodent endemic to Argentina across the Monte and Patagonian drylands where extensive sheep ranching predominates. We aimed to assess the spatial variation in the abundance of maras and to identify the natural and anthropic factors influencing the observed patterns in Península Valdés, a representative landscape of Patagonia. We conducted ground surveys during the austral autumn from 2015 to 2017. We built density surface models to account for the variation in mara abundance, and obtained a map of mara density at a resolution of four km2. We estimated an overall density of 0.93 maras.km−2 for the prediction area of 3,476 km2. The location of ranch buildings, indicators of human presence, had a strong positive effect on the abundance of maras, while the significant contribution of the geographic longitude suggested that mara density increases with higher rainfall. Although human presence favored mara abundance, presumably by providing protection against predators, it is likely that the association could bring negative consequences for maras and other species. The use of spatial models allowed us to provide the first estimate of mara abundance at a landscape scale and its spatial variation at a high resolution. Our approach can contribute to the assessment of mara population abundance and the factors shaping its spatial structure elsewhere across the species range, all crucial attributes to identify and prioritize conservation actions.
Antún et al. (2019) Modeling the spatial structure of the endemic mara (Dolichotis patagonum) across modified landscapes. PeerJ 7:e6367 https://doi.org/10.7717/peerj.6367
Overexpression of OsFTL10 induces early flowering and improves drought tolerance in Oryza sativa L.
Flowering time control is critically important for the reproductive accomplishment of higher plants as floral transition can be affected by both environmental and endogenous signals. Flowering Locus T-like (FTL) genes are major genetic determinants of flowering in plants. In rice, 13 OsFTL genes have been annotated in the genome and amongst them, Hd3a (OsFTL2) and RFT1 (OsFTL3) have been studied extensively and their functions are confirmed as central florigens that control rice flowering under short day and long day environment, respectively. In this report, a rice OsFTL gene, OsFTL10, was characterized, and its function on flowering and abiotic stress was investigated. The expression level of OsFTL10 was high in young seedlings and shown to be induced by GA3 and drought stress. Overexpression of OsFTL10 resulted in earlier flowering in rice plants by up to 2 weeks, through up-regulation of the downstream gene OsMADS15. OsFTL10 also regulated Ehd1 and OsMADS51 through a feedback mechanism. The OsFTL10 protein was also detected in both nucleus and cytoplasm. Furthermore, yeast two hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) results show that OsFTL10 could interact with multiple 14-3-3s, suggesting that OsFTL10 might function in a similar way to Hd3a in promoting rice flowering by forming a FAC complex with 14-3-3, and OsFD1. Further experiments revealed that constitutive expression of OsFTL10 improved the drought tolerance of transgenic plants by stimulating the expression of drought responsive genes. These results suggest that rice FTL genes might function in flowering promotion and responses to environmental signals.
Fang et al. (2019) Overexpression of OsFTL10 induces early flowering and improves drought tolerance in Oryza sativa L.. PeerJ 7:e6422 https://doi.org/10.7717/peerj.6422
Production of eugenol from fungal endophytes Neopestalotiopsis sp. and Diaporthe sp. isolated from Cinnamomum loureiroi leaves
Endophytic fungi, which colonize within a host plant without causing any apparent diseases, have been considered as an important source of bioactive secondary metabolites containing antimicrobial and antioxidant activities. The aim of this research was to isolate the endophytic fungi of Cinnamomum loureiroi and then to screen their antimicrobial and antioxidant activities. A total of 11 fungal endophytes were isolated from healthy leaves of Cinnamomum loureiroi belonging to six genera: Botryosphaeria, Colletotrichum, Diaporthe, Fusarium, Neopestalotiopsis, and Pestalotiopsis. All isolated strains were cultured and further extracted with ethyl acetate solvent. Antimicrobial activity of all crude endophytic fungal extracts was analyzed using disc diffusion assay against six bacterial and two fungal pathogens. Crude extracts of strains MFLUCC15-1130 and MFLUCC15-1131 showed broad-spectrum antimicrobial activity against all tested pathogens. Activity against Bacillus cereus and Staphylococcus epidermidis was notable, showing the lowest minimum inhibitory concentration at 3.91 μg/mL. Antioxidant activity of all crude endophytic fungal extracts was also evaluated based on 2,2-diphenyl-1-picrylhydrazyl assay. Significant antioxidant activity was detected in the crude extracts of fungus MFLUCC15-1130 and MFLUCC15-1131 with IC50 of 22.92 ± 0.67 and 37.61 ± 0.49 μg/mL, respectively. Using molecular identification, MFLUCC15-1130 and MFLUCC15-1131 were identified as Neopestalotiopsis sp. and Diaporthe sp., respectively. The major chemical constituents produced by both crude extracts were identified by gas chromatography-mass spectrometry. Eugenol, myristaldehyde, lauric acid, and caprylic acid were the primary antimicrobial and antioxidant compounds in both crude extracts. This is the first report of eugenol being a biologically active compound of Neopestalotiopsis sp. and Diaporthe sp. fungal endophytes. Eugenol has been reported as antimicrobial and antioxidant agents with agronomic applications. Thus the two newly-isolated endophytes may be used for eugenol production, which in turn can be used in a variety of applications.
Tanapichatsakul et al. (2019) Production of eugenol from fungal endophytes Neopestalotiopsis sp. and Diaporthe sp. isolated from Cinnamomum loureiroi leaves. PeerJ 7:e6427 https://doi.org/10.7717/peerj.6427