Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA
Mine tailing disasters have occurred worldwide and contemporary release of tailings of large proportions raise concerns of the chronic impacts that trace metals may have on the aquatic biodiversity. Environmental metabarcoding (eDNA) offers an as yet poorly explored opportunity for biological monitoring of impacted aquatic ecosystems from mine tailings and contaminated sediments. eDNA has been increasingly recognized to be an effective method to detect previously unrecognized small-sized Metazoan taxa, but their ecological responses to environmental pollution has not been assessed by metabarcoding. Here, we evaluated chronic effects of trace metal contamination from sediment eDNA of the Rio Doce estuary, 1.7 years after the Samarco mine tailing disaster, which released over 40 million m3 of iron tailings in the Rio Doce river basin. We identified 123 new sequence variants environmental taxonomic units (eOTUs) of benthic taxa and an assemblage composition dominated by Nematoda, Crustacea and Platyhelminthes; typical of other estuarine ecosystems. We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary. This was in contrast to environmental filtering of meiofaunal assemblages of non-polluted estuaries. Here, we suggest that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content.
Bernardino et al. (2019) Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA. PeerJ 7:e8042 https://doi.org/10.7717/peerj.8042
Effects of afforestation on water resource variations in the Inner Mongolian Plateau
Afforestation is a key approach used to effectively prevent ecosystem degradation, which in itself is a key reason for the obstruction of sustainable societal development. In order to suppress sand and dust storms as a result of ecological environmental degradation in North China, the Government of China has sanctioned the planting of a large number of trees in Inner Mongolia. However, water resources in the Inner Mongolian Plateau are insufficient to sustain this effort because such a large number of trees consume a large amount of water, which also significantly increases evapotranspiration. This study uses spatiotemporal trend analyses and abrupt change analyses to determine the effects of afforestation on water resource variations in the Inner Mongolian Plateau. Results show that even though water resources in Inner Mongolia fluctuate, this resource has generally exhibited a declining trend from 1980 to 2015, corresponding to the NDVI trend. On spatial-temporal scales, water resources decreased significantly in the eastern section of the plateau, especially in the Horqin District and the Hulunbuir Plateau. By contrast, water resources increased as a whole in the western section of the plateau (Alxa Plateau). Driving analysis results show that water resource variation is mainly due to the contribution of change in precipitation (positive effect), which accounted for 39.35% of total changes in water resources, followed by the evapotranspiration (negative effect). In other words, afforestation with the primary aim of improving ecosystem has effectually upset the water resource balance of Inner Mongolia Plateau.
Xiao et al. (2019) Effects of afforestation on water resource variations in the Inner Mongolian Plateau. PeerJ 7:e7525 https://doi.org/10.7717/peerj.7525
Neck mobility in the Jurassic plesiosaur Cryptoclidus eurymerus: finite element analysis as a new approach to understanding the cervical skeleton in fossil vertebrates
The sauropterygian clade Plesiosauria arose in the Late Triassic and survived to the very end of the Cretaceous. Plesiosauria evolved the greatest species diversity of any marine reptile clade, attaining a global distribution. Plesiosauria consist of two clades, Rhomaleosauridae and Neoplesiosauria. Basal Neoplesiosauria have long necks with at least 30 cervicals, but show qualitative osteological evidence for a stiff neck. Here we quantify neck mobility in lateral, ventral, and dorsal directions based on finite element modeling of neck vertebrae from the Middle Jurassic plesiosaur Cryptoclidus eurymerus. We model the mobility in a single motion segment, consisting of two adjacent cervical vertebrae and the joints connecting them. Based on the model with a maximum intervertebral spacing of 3 mm, we find that in Cryptoclidus, the maximum angle of lateral deflection in the motion segment was 2°. The maximum angle of ventral deflection was 5° and of dorsal deflection was 5°. When these values are multiplied by the number of cervical vertebrae, it becomes apparent that neck mobility was limited in all directions. The maximum angle of total lateral deflection in the neck was 67°. The maximum angle of total ventral deflection was 148° and of total dorsal deflection was 157°. This raises the question of the function of such a long, multi-segment but immobile neck. We posit that the long neck served in hydrodynamic and visual camouflage, hiding the bulk of the body from the small but abundant prey, such as schooling fish and squid. Neck immobility may have been advantageous in withstanding strong hydrodynamic forces acting on the neck during predatory strikes.
Wintrich et al. (2019) Neck mobility in the Jurassic plesiosaur Cryptoclidus eurymerus: finite element analysis as a new approach to understanding the cervical skeleton in fossil vertebrates. PeerJ 7:e7658 https://doi.org/10.7717/peerj.7658
Short-term vasoactive agent treatment driven by physicians’ preference in acute esophageal variceal bleeding in a tertiary center
Background Vasoactive drugs are frequently used in combination with endoscopic variceal ligation (EVL) in treatment of acute esophageal variceal bleeding (EVB). The aim of study was to assess physicians’ preference of vasoactive agents in acute EVB, their reasons of preference and efficacy and safety of these short course regimens. Methods Cirrhotic patients with suspected EVB were screened (n = 352). Eligible patients were assigned based on the physician’s preference to either somatostatin (group S) or terlipressin (group T) followed by EVL. In group S, intravenous bolus (250 µg) of somatostatin followed by 250 µg/hour was continued for three days. In group T, 2 mg bolus injection of terlipressin was followed by 1 mg infusion every 6 h for three days. Results A total of 150 patients were enrolled; 41 in group S and 109 in group T. Reasons for physician preference was convenience in administration (77.1%) for group T and good safety profile (73.2%) for group S. Very early rebleeding within 49–120 h occurred in one patient in groups S and T (p = 0.469). Four patients in group S and 14 patients in group T have variceal rebleeding episodes within 6–42 d (p = 0.781). Overall treatment-related adverse effects were compatible in groups S and T (p = 0.878), but the total cost of terlipressin and somatostatin differed i.e., USD 621.32 and USD 496.43 respectively. Conclusions Terlipressin is the preferred vasoactive agent by physicians in our institution for acute EVB. Convenience in administration and safety profile are main considerations of physicians. Safety and hemostatic effects did not differ significantly between short-course somatostatin or terlipressin, although terlipressin is more expensive.
Chuah et al. (2019) Short-term vasoactive agent treatment driven by physicians’ preference in acute esophageal variceal bleeding in a tertiary center. PeerJ 7:e7913 https://doi.org/10.7717/peerj.7913
Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico
Background Spatial genetic structure (SGS) analysis is a powerful approach to quantifying gene flow between trees, thus clarifying the functional connectivity of trees at population and landscape scales. The findings of SGS analysis may be useful for conservation and management of natural populations and plantations. Pinus cembroides is a widely distributed tree species, covering an area of about 2.5 million hectares in Mexico. The aim of this study was to examine five natural seed stands of P. cembroides in the Sierra Madre Occidental to determine the SGS at population (within the seed stand) and landscape (among seed stands) levels in order to establish guidelines for the conservation and management of the species. We hypothesized that P. cembroides, in which the seeds are dispersed by birds and mammals, creates weaker SGS than species with wind-dispersed seeds. Methods DNA fingerprinting was performed using the amplified fragment length polymorphism (AFLP) technique. In order to estimate the SGS at population and landscape levels, we measured the geographical (spatial) distance as the Euclidean distance. We also estimated the genetic distances between individuals using the pairwise kinship coefficient. Results The results showed non-significant autocorrelation in four out of five seed stands studied (i.e., a mainly random distribution in the space of the genetic variants of P. cembroides at population level). Discussion SGS was detected at the landscape scale, supporting the theory of isolation by distance as a consequence of restricted pollen and seed dispersal. However, the SGS may also have been generated by our sampling strategy. We recommended establishing a close network of seed stands of P. cembroides to prevent greater loss of local genetic variants and alteration of SGS. We recommend seed stands of P. cembroides of a minimum width of 225 m.
García-Zubia et al. (2019) Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico. PeerJ 7:e8002 https://doi.org/10.7717/peerj.8002
Enforced symmetry: the necessity of symmetric waxing and waning
A fundamental question in ecology is how the success of a taxon changes through time and what drives this change. This question is commonly approached using trajectories averaged over a group of taxa. Using results from probability theory, we show analytically and using examples that averaged trajectories will be more symmetric as the number of averaged trajectories increases, even if none of the original trajectories they were derived from is symmetric. This effect is not only based on averaging, but also on the introduction of noise and the incorporation of a priori known origination and extinction times. This implies that averaged trajectories are not suitable for deriving information about the processes driving the success of taxa. In particular, symmetric waxing and waning, which is commonly observed and interpreted to be linked to a number of different paleobiological processes, does not allow drawing any conclusions about the nature of the underlying process.
Hohmann et al. (2019) Enforced symmetry: the necessity of symmetric waxing and waning. PeerJ 7:e8011 https://doi.org/10.7717/peerj.8011
A new alligatoroid from the Eocene of Vietnam highlights an extinct Asian clade independent from extant Alligator sinensis
During systematic paleontological surveys in the Na Duong Basin in North Vietnam between 2009 and 2012, well-preserved fossilized cranial and postcranial remains belonging to at least 29 individuals of a middle to late Eocene (late Bartonian to Priabonian age (39–35 Ma)) alligatoroid were collected. Comparative anatomical study of the material warrants the diagnosis of a new taxon, Orientalosuchus naduongensis gen. et sp. nov. The combined presence of an enlarged fifth maxillary tooth, prominent preorbital ridges, a large supraoccipital exposure on the skull table, a palatine-pterygoid suture anterior to the posterior end of the suborbital fenestra, and a pterygoid forming a neck surrounding the choana is unique to this species. Unlike previous phylogenies, our parsimony analysis recovers a monophyletic Late Cretaceous to Paleogene East to Southeastern Asian alligatoroid group, here named Orientalosuchina. The group includes Orientalosuchus naduongensis, Krabisuchus siamogallicus, Eoalligator chunyii, Jiangxisuchus nankangensis and Protoalligator huiningensis, all of them sharing a medial shifted quadrate foramen aerum. The recognition of this clade indicates at least two separate dispersal events from North America to Asia: one during the Late Cretaceous by Orientalosuchina and one by the ancestor of Alligator sinensis during the Paleogene or Neogene, the timing of which is poorly constrained.
Massonne et al. (2019) A new alligatoroid from the Eocene of Vietnam highlights an extinct Asian clade independent from extant Alligator sinensis. PeerJ 7:e7562 https://doi.org/10.7717/peerj.7562
L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus
Phenotypic differences between Campylobacter fetus fetus and C. fetus venerealis subspecies allow the differential diagnosis of bovine genital campylobacteriosis. The hydrogen sulfide production, for example, is a trait exclusive to C. fetus fetus and C. fetus venerealis biovar intermedius. This gas that can be biochemically tested can be produced from L-cysteine (L-Cys). Herein, we report a novel multiplex-PCR to differentiate C. fetus based on the evaluation of a deletion of an ATP-binding cassette-type L-Cys transporter that could be involved in hydrogen sulfide production, as previously described. A wet lab approach combined with an in silico whole genome data analysis showed complete agreement between this L-Cys transporter-PCR and the hydrogen sulfide production biochemical test. This multiplex-PCR may complement the tests currently employed for the differential diagnosis of C. fetus.
Farace et al. (2019) L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus. PeerJ 7:e7820 https://doi.org/10.7717/peerj.7820
Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin
Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as “blue crab” and “Product of the USA” may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as “Product of the USA” and “Product of Venezuela.” In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise Fst values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.
Windsor et al. (2019) Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin. PeerJ 7:e7827 https://doi.org/10.7717/peerj.7827
Prey selectivity and the effect of diet on growth and development of a dragonfly, Sympetrum sanguineum
Despite a long tradition of research, our understanding of mechanisms driving prey selectivity in predatory insects is limited. According to optimal foraging theory, predators should prefer prey which provides the highest amount of energy per unit time. However, prey selectivity may also depend on previous diet and specific nutritional demands of the predator. From the long-term perspective, diet composition affects predator fitness. An open question is whether short-term selectivity of predators provides a diet which is optimal in the long-term. To shed more light on these issues, we conducted laboratory experiments on prey selectivity and its long-term consequences in larvae of the dragonfly Sympetrum sanguineum. We conditioned the larvae to one of two prey types, the cladoceran Daphnia magna and larvae of a non-biting midge Chironomus sp., and then exposed them to various combinations of the two prey types. We found that dragonfly larvae conditioned to Chironomus larvae consumed the same amount of D. magna, but significantly less Chironomus larvae compared to dragonfly larvae conditioned to D. magna. However, there was no effect of previous diet on their success of capture and handling time, suggesting a limited role of learning in their ability to process prey. We then tested the long-term effects of diets with different proportions of both prey for survival and growth of the dragonfly larvae. Individuals fed Chironomus-only diet had higher mortality and slower growth than dragonflies fed D. magna, while larvae fed a mixed diet had the highest survival and growth rate. In conclusion, we show that dragonfly larvae fed by Chironomus larvae performed poorly and compensated by preferring D. magna when both prey types were available. The superiority of the mixed diet suggests that a diverse diet may be needed to satisfy nutritional demands in S. sanguineum larvae. We demonstrate that merging short-term predation experiments with relevant data on predator fitness may provide better understanding of predator-prey interactions and conclude that detailed information on the (mis)matches between prey composition and predator nutritional demands is needed for further progress.
Dudová et al. (2019) Prey selectivity and the effect of diet on growth and development of a dragonfly, Sympetrum sanguineum. PeerJ 7:e7881 https://doi.org/10.7717/peerj.7881