Timing and ecological priority shaped the diversification of sedges in the Himalayas
Background Diversification patterns in the Himalayas have been important to our understanding of global biodiversity. Despite recent broad-scale studies, the most diverse angiosperm genus of the temperate zone—Carex L. (Cyperaceae), with ca. 2100 species worldwide—has not yet been studied in the Himalayas, which contains 189 Carex species. Here the timing and phylogenetic pattern of lineage and ecological diversification were inferred in this ecologically significant genus. We particularly investigated whether priority, adaptation to ecological conditions, or both explain the highly successful radiation of the Kobresia clade (ca. 60 species, of which around 40 are present in the Himalayas) of Himalayan Carex. Methods Phylogenetic relationships were inferred using maximum likelihood analysis of two nuclear ribosomal DNA (nrDNA) regions (ITS and ETS) and one plastid gene (matK); the resulting tree was time-calibrated using penalized likelihood and a fossil calibration at the root of the tree. Biogeographical reconstruction for estimation of historical events and ancestral ranges was performed using the dispersal-extinction-cladogenesis (DEC) model, and reciprocal effects between biogeography and diversification were inferred using the geographic state speciation and extinction (GeoSSE) model. Climatic envelopes for all species for which mapped specimen data available were estimated using climatic data from WORLDCLIM, and climatic niche evolution was inferred using a combination of Ornstein-Uhlenbeck models of shifting adaptive optima and maximum likelihood inference of ancestral character states under a Brownian motion model. Results The Himalayan Carex flora represents three of the five major Carex clades, each represented by multiple origins within the Himalayas. The oldest Carex radiation in the region, dating to ca. 20 Ma, near the time of Himalayan orogeny, gave rise to the now abundant Kobresia clade via long-distance dispersal from the Nearctic. The Himalayan Carex flora comprises a heterogeneous sample of diversifications drawn from throughout the cosmopolitan, but mostly temperate, Carex radiation. Most radiations are relatively recent, but the widespread and diverse Himalayan Kobresia radiation arose at the early Miocene. The timing and predominance of Kobresia in high-elevation Himalayan meadows suggests that Kobresia may have excluded other Carex lineages: the success of Kobresia in the Himalayas, in other words, appears to be a consequence largely of priority, competitive exclusion and historical contingency.
Uzma et al. (2019) Timing and ecological priority shaped the diversification of sedges in the Himalayas. PeerJ 7:e6792 https://doi.org/10.7717/peerj.6792
A behavioral and genetic study of multiple paternity in a polygamous marine invertebrate, Octopus oliveri
Octopus oliveri is a widespread and common rocky intertidal cephalopod that mates readily in the laboratory, but for which mating behavior has not been reported previously. Four sets of behavioral experiments were recorded wherein three males, small, medium & large in varying order, were introduced to each of six females, for a total of 24 individual females and 12 individual males utilized in the experiments. Video analysis shows that successful mating occurred in each of the mount, reach and beak-to-beak positions. Mating was observed for all males, regardless of size relative to the female, or order of introduction. Females showed preference for the first male to which they were introduced in experimental pairings rather than any specific male trait, and mating time increased significantly with increasing female size. Five novel microsatellite markers were developed and used to test paternity in the eleven broods resulting from these experimental pairings. We found skewed paternity in each brood, with early male precedence and male size being the best predictors of parentage. Multiple paternity was observed in every experimental cross but was estimated to be comparatively low in the field, suggesting that sperm limitation might be common in this species. We saw no evidence of direct sperm competition in Octopus oliveri, but larger males produced significantly more offspring. This study contributes to the growing research on cephalopod mating systems and indicates that octopus mating dynamics might be more variable and complex than thought previously.
Ylitalo et al. (2019) A behavioral and genetic study of multiple paternity in a polygamous marine invertebrate, Octopus oliveri. PeerJ 7:e6927 https://doi.org/10.7717/peerj.6927
The cutting-edge morphology of the mole snake’s dental apparatus
The mole snake (Pseudaspis cana) is capable of inflicting unusual bites in defence and during male combat that present as two parallel lacerations. We investigated the dental morphology of the mole snake by making SEM images, and by CT-scanning and digitally reconstructing the skulls of 14 specimens comprising both sexes. The lengths, volumes, shapes and positions of maxillary and dentary teeth were compared within individuals, between individuals, and between sexes. CT reconstructions show the occurrence of large, flat triangular teeth at the posterior end of the maxilla that are angled to point towards the posterior of the skull. SEM imagery highlights the presence of sharp ridges (carinae) on the posterior edges of the posterior dentary and maxillary teeth. Males have greater dental specialization, maxillary tooth variation, enlargement of the posterior-most maxillary teeth, and dentary teeth with posterior carinae. We hypothesize that mole snake dental specializations are adaptations for their particular form of male combat and possibly for subduing prey in the confines of underground burrows. Our findings reveal a complex dental morphology in mole snakes and provide impetus for further studies on the functional morphology of snake teeth.
Evans et al. (2019) The cutting-edge morphology of the mole snake’s dental apparatus. PeerJ 7:e6943 https://doi.org/10.7717/peerj.6943
Move it or lose it: interspecific variation in risk response of pond-breeding anurans
Changes in behavior are often the proximate response of animals to human disturbance, with variability in tolerance levels leading some species to exhibit striking shifts in life history, fitness, and/or survival. Thus, elucidating the effects of disturbance on animal behavior, and how this varies among taxonomically similar species with inherently different behaviors and life histories is of value for management and conservation. We evaluated the risk response of three anuran species—southern leopard frog (Lithobates sphenocephalus), Blanchard’s cricket frog (Acris blanchardi), and green tree frog (Hyla cinerea)—to determine how differences in microhabitat use (arboreal vs ground-dwelling) and body size (small vs medium) may play a role in response to a potential threat within a human-altered subtropical forest. Each species responded to risk with both flight and freeze behaviors, however, behaviors were species- and context-specific. As distance to cover increased, southern leopard frogs increased freezing behavior, green tree frogs decreased freezing behavior, and Blanchard’s cricket frogs increased flight response. The propensity of green tree frogs to use the canopy of vegetation as refugia, and the small body size of Blanchard’s cricket frogs likely led to greater flight response as distance to cover increased, whereas innate reliance on camouflage among southern leopard frogs may place them at greater risk to landscaping, agricultural, and transportation practices in open terrain. As such, arboreal and small-bodied species may inherently be better suited in human altered-landscapes compared to larger, ground-dwelling species. As land-use change continues to modify habitats, understanding how species respond to changes in their environment continues to be of importance, particularly in ecosystems where human-wildlife interactions are expected to increase in frequency.
Matich et al. (2019) Move it or lose it: interspecific variation in risk response of pond-breeding anurans. PeerJ 7:e6956 https://doi.org/10.7717/peerj.6956
Chronic intake of high-dose of blueberry leaf extract does not augment the harmful effects of ethanol in rats
Excessive alcohol consumption is a risk factor for liver diseases. Enhancement of alcohol metabolism could be an effective strategy to prevent these adverse effects since it promotes the clearance of ethanol and acetaldehyde from the serum. Polyphenol-rich products have shown to protect against alcohol-related liver damage. Blueberry leaves have attracted attention as they are rich polyphenols such as proantocyanidins and chlorogenic acid. In this study, we investigated the effects of a high dose of blueberry leaf extract (BLEx) on alcohol metabolism during chronic intake of ethanol. Seven-week old Sprague-Dawley (SD) rats were divided into four groups: normal liquid diet group (NLD), normal liquid diet + BLEx group (NLD + BLEx), alcohol liquid diet group (ALD), and alcohol liquid diet + BLEx (ALD + BLEx). Then, rats were fed experimental diet for 5 weeks and at the end of feeding period, body weight, food intake, liver weight, indices of liver injury, expression and activity of alcohol metabolism-related and anti-oxidative enzymes, and levels of carbonyl protein, triglyceride (TG), and total cholesterol (T-Chol) were measured. Body weight and food intake decreased, whereas liver aldehyde dehydrogenase (ALDH) activity, liver microsomal cytochrome P450 2E1 (CYP2E1) protein and mRNA expression, and heme oxygenase 1 (HO-1) mRNA expression were upregulated by ethanol intake. Dietary BLEx, however, did not affect any of these ethanol-related changes. Indices of liver injury, expression and activity of other alcohol metabolism-related enzymes, liver carbonyl protein, TG, and T-Chol levels were not altered by ethanol and BLEx. Thus, chronic BLEx intake does not ameliorate the harmful effects of ethanol.
Yamasaki et al. (2019) Chronic intake of high-dose of blueberry leaf extract does not augment the harmful effects of ethanol in rats. PeerJ 7:e6989 https://doi.org/10.7717/peerj.6989
Digital dissection of the pelvis and hindlimb of the red-legged running frog, Phlyctimantis maculatus, using Diffusible Iodine Contrast Enhanced computed microtomography (DICE μCT)
Background The current study applies both traditional and Diffusible Iodine Contrast Enhanced computed microtomography (DICE µCT) techniques to reveal the musculoskeletal anatomy of Phlyctimantis maculatus. DICE µCT has emerged as a powerful tool to visualise intricate musculoskeletal anatomy. By generating 3D digital models, anatomical analyses can be conducted non-destructively, preserving the in situ 3D topography of the system, therefore eliminating some of the drawbacks associated with traditional methods. We aim to describe the musculature of the spine, pelvis, and hindlimb, compare the musculoskeletal anatomy and pelvic morphology of P. maculatus with functionally diverse frogs, and produce 3D digital anatomy reference data. Method An adult frog was stained using an aqueous Lugol’s solution and scanned in a SkyScan1176 in vivo µCT scanner. Scan images were reconstructed, resampled, and digitally segmented to produce a 3D model. A further adult female frog was dissected traditionally for visualisation of tendinous insertions. Results Our work revealed three main findings: (1) P. maculatus has similar gross muscular anatomy to Rana catesbeiana (bullfrog) but is distinct from those species that exhibit ancestral traits (leopelmids) and those that are highly specialised (pipids), (2) P. maculatus’s pelvic anatomy best fits the description of Emerson’s walking/hopping pelvic morphotype IIA, and (3) a split in the semimembranosus and gracilis major muscles is consistent with the reported myology in other anuran species. Discussion While DICE µCT methods were instrumental in characterising the 3D anatomy, traditional dissection was still required to visualise important structures such as the knee aponeurosis, tendinous insertions, and fasciae. Nonetheless, the anatomical data presented here marks the first detailed digital description of an arboreal and terrestrial frog. Further, our digital model presents P. maculatus as a good frog model system and as such has formed a crucial platform for further functional analysis within the anuran pelvis and hindlimb.
Collings et al. (2019) Digital dissection of the pelvis and hindlimb of the red-legged running frog, Phlyctimantis maculatus, using Diffusible Iodine Contrast Enhanced computed microtomography (DICE μCT). PeerJ 7:e7003 https://doi.org/10.7717/peerj.7003
Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach
The genome-scale metabolic model of a lipid-overproducing strain of Mucor circinelloides WJ11 was developed. The model (iNI1159) contained 1,159 genes, 648 EC numbers, 1,537 metabolites, and 1,355 metabolic reactions, which were localized in different compartments of the cell. Using flux balance analysis (FBA), the iNI1159 model was validated by predicting the specific growth rate. The metabolic traits investigated by phenotypic phase plane analysis (PhPP) showed a relationship between the nutrient uptake rate, cell growth, and the triacylglycerol production rate, demonstrating the strength of the model. A putative set of metabolic reactions affecting the lipid-accumulation process was identified when the metabolic flux distributions under nitrogen-limited conditions were altered by performing fast flux variability analysis (fastFVA) and relative flux change. Comparative analysis of the metabolic models of the lipid-overproducing strain WJ11 (iNI1159) and the reference strain CBS277.49 (iWV1213) using both fastFVA and coordinate hit-and-run with rounding (CHRR) showed that the flux distributions between these two models were significantly different. Notably, a higher flux distribution through lipid metabolisms such as lanosterol, zymosterol, glycerolipid and fatty acids biosynthesis in iNI1159 was observed, leading to an increased lipid production when compared to iWV1213. In contrast, iWV1213 exhibited a higher flux distribution across carbohydrate and amino acid metabolisms and thus generated a high flux for biomass production. This study demonstrated that iNI1159 is an effective predictive tool for the pathway engineering of oleaginous strains for the production of diversified oleochemicals with industrial relevance.
Isarankura Na Ayudhya et al. (2019) Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach. PeerJ 7:e7015 https://doi.org/10.7717/peerj.7015
Antioxidant enzyme cycling over reproductive lunar cycles in Pocillopora damicornis
The impacts of continued degradation of watersheds on coastal coral reefs world-wide is alarming, and action addressing anthropogenic stressors and subsequent rehabilitation of watersheds and adjacent reefs is an urgent priority. The aim of this study is to develop and improve the use of antioxidant enzymes as bioindicators of stress in coral species. In order to fully develop such tools, it is necessary to first understand baseline cycling of these enzymes within coral tissues. Due to inherent links between reproduction and oxidative stress, these aims may be facilitated by sampling coral tissues over reproductively-linked lunar cycles to determine variations from baseline. By developing a greater understanding of biochemical markers of stress in corals, specifically antioxidant defense enzymes catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx), and superoxide dismutase (SOD) in Hawaiian Pocillopora damicornis, we have provided molecular tools that identify thresholds of stress on coral reefs. Our results suggest that the coral reproductive state is a significant factor affecting the activity of antioxidant enzymes. Specifically, CAT and GR display maximum activity during peak reproductive state. Whereas significant maximal Se-independent GPx and SOD activity was measured during off-peak reproductive cycles. Such insight into the cyclical variation of the activity of these enzymes should be applied towards differentiating the influence of natural biological activity cycling in diagnostic tests identifying the effects of different physical environmental factors and chemical pollutants on coral health. Through the development and application of these molecular biomarkers of stress, we look to improve our ability to identify problems at the sub-lethal level, when action can be taken to mitigate a/biotic impacts.
Murphy et al. (2019) Antioxidant enzyme cycling over reproductive lunar cycles in Pocillopora damicornis. PeerJ 7:e7020 https://doi.org/10.7717/peerj.7020
The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)
This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.
Worth et al. (2019) The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana). PeerJ 7:e7026 https://doi.org/10.7717/peerj.7026
The influence of pharmacologically-induced affective states on attention bias in sheep
When an individual attends to certain types of information more than others, the behavior is termed an attention bias. The occurrence of attention biases in humans and animals can depend on their affective states. Based on evidence from the human literature and prior studies in sheep, we hypothesized that an attention bias test could discriminate between pharmacologically-induced positive and negative affective states in sheep. The test measured allocation of attention between a threat and a positive stimulus using key measures of looking time and vigilance. Eighty 7-year-old Merino ewes were allocated to one of four treatment groups; Anxious (m-chlorophenylpiperazine), Calm (diazepam), Happy (morphine) and Control (saline). Drugs were administered 30 min prior to attention bias testing. The test was conducted in a 4 × 4.2 m arena with high opaque walls. An approximately life-size photograph of a sheep was positioned on one wall of the arena (positive stimulus). A small window with a retractable opaque cover was positioned on the opposite wall, behind which a dog was standing quietly (threat). The dog was visible for 3 s after a single sheep entered the arena, then the window was covered and the dog was removed. Sheep then remained in the arena for 3 min while behaviors were recorded. Key behaviors included time looking toward the dog wall or photo wall, duration of vigilance behavior and latency to become non-vigilant. In contrast with our hypothesis, no significant differences were found between treatment groups for duration of vigilance or looking behaviors, although Anxious sheep tended to be more vigilant than Control animals (P < 0.1) and had a longer latency to become non-vigilant (P < 0.001). A total of 24 of 80 animals were vigilant for the entire test duration. This censoring of data may explain why no differences were detected between groups for vigilance duration. Overall, a lack of difference between groups may suggest the test cannot discriminate positive and negative states in sheep. We suggest that the censoring of vigilance duration data, the use of insufficient drug doses, the potential influence of background noise and the age of the sheep may explain a lack of difference between groups. Due to these potential effects, it remains unclear whether the attention bias test can detect positive states in sheep.
Monk et al. (2019) The influence of pharmacologically-induced affective states on attention bias in sheep. PeerJ 7:e7033 https://doi.org/10.7717/peerj.7033