Density dependent attributes of fish aggregative behaviour
Grouping behaviour, as fascinating as it is unclear, has lately drawn the attention of numerous researchers. While most of the authors focused their work on a mechanistic approach to the matter of schooling, this study explores the issue from a population point of view. Present camera observation study on the fish community carried out in the epipelagic habitat of a European temperate reservoir in the Czech Republic explored the relationship between density and aggregative features of predominantly cyprinid fish stock. Results demonstrated that schooling behaviour is triggered by the ‘critical density’ of fish in the habitat. School size as well as counts of schools and proportion of schooling individuals increased with the density of fish. Counts of clusters (observed units in time, including singletons, pairs and schools) and cluster size, on the other hand, showed a slowing tendency to increase. The slower increase implies the tendency of fish for not being frequent but rather to create larger groups. Altogether, our findings suggest that fish density is a triggering factor in the formation of large fish schools. As the tendency of cyprinid species for school formation could be an evolutional advantage responsible for dominance in later succession phases of water bodies, we suggest that more in situ studies should be encouraged for the proper understanding of the ecological interactions that drive the structure of aquatic ecosystems and for ensuring unbiased assessment.
Holubová et al. (2019) Density dependent attributes of fish aggregative behaviour. PeerJ 7:e6378 https://doi.org/10.7717/peerj.6378
Recent dating of extinct Atlantic gray whale fossils, (Eschrichtius robustus), Georgia Bight and Florida, western Atlantic Ocean
The Atlantic gray whale (Eschrichtius robustus) presents an interesting case study of climate related dispersal and extinction. While (limited) fossil records confirm its presence in the Atlantic up until the 18th Century, its abundance and distribution within the Eastern and Western basins are still not well understood. The discovery of presumed gray whale fossil remains from the Georgia Bight and the Atlantic coast of Florida, from the mid-1980s to late-2000s, provides a new opportunity to recover additional data regarding their chronology within the Western basin. Here, we apply accelerator mass spectrometry radiocarbon techniques to six fossil whale finds, identifying dates within marine isotope stage 3 (59–24 ka) and the late Holocene, ∼2,000 yr BP. We additionally confirm the taxonomic identification of two fossil bone samples as E. robustus using collagen peptide mass fingerprinting (ZooMS). The obtained dates, when combined with a larger corpus of previously published Atlantic gray whale fossil dates, support the hypothesis for the decline of the Atlantic gray whale in the late Pleistocene and the late Holocene. These new data augment the findings of the Eastern Atlantic Basin and better incorporate the Western Atlantic Basin into a pan-ocean understanding for the species.
Garrison et al. (2019) Recent dating of extinct Atlantic gray whale fossils, (Eschrichtius robustus), Georgia Bight and Florida, western Atlantic Ocean. PeerJ 7:e6381 https://doi.org/10.7717/peerj.6381
The rise of feathered dinosaurs: Kulindadromeus zabaikalicus, the oldest dinosaur with ‘feather-like’ structures
Diverse epidermal appendages including grouped filaments closely resembling primitive feathers in non-avian theropods, are associated with skeletal elements in the primitive ornithischian dinosaur Kulindadromeus zabaikalicus from the Kulinda locality in south-eastern Siberia. This discovery suggests that “feather-like” structures did not evolve exclusively in theropod dinosaurs, but were instead potentially widespread in the whole dinosaur clade. The dating of the Kulinda locality is therefore particularly important for reconstructing the evolution of “feather-like” structures in dinosaurs within a chronostratigraphic framework. Here we present the first dating of the Kulinda locality, combining U-Pb analyses (LA-ICP-MS) on detrital zircons and monazites from sedimentary rocks of volcaniclastic origin and palynological observations. Concordia ages constrain the maximum age of the volcaniclastic deposits at 172.8 ± 1.6 Ma, corresponding to the Aalenian (Middle Jurassic). The palynological assemblage includes taxa that are correlated to Bathonian palynozones from western Siberia, and therefore constrains the minimum age of the deposits. The new U-Pb ages, together with the palynological data, provide evidence of a Bathonian age—between 168.3 ± 1.3 Ma and 166.1 ± 1.2 Ma—for Kulindadromeus. This is older than the previous Late Jurassic to Early Cretaceous ages tentatively based on local stratigraphic correlations. A Bathonian age is highly consistent with the phylogenetic position of Kulindadromeus at the base of the neornithischian clade and suggests that cerapodan dinosaurs originated in Asia during the Middle Jurassic, from a common ancestor that closely looked like Kulindadromeus. Our results consequently show that Kulindadromeus is the oldest known dinosaur with “feather-like” structures discovered so far.
Cincotta et al. (2019) The rise of feathered dinosaurs: Kulindadromeus zabaikalicus, the oldest dinosaur with ‘feather-like’ structures. PeerJ 7:e6239 https://doi.org/10.7717/peerj.6239
African savanna elephants (Loxodonta africana) as an example of a herbivore making movement choices based on nutritional needs
Background The increasing human population and global intensification of agriculture have had a major impact on the world’s natural ecosystems and caused devastating effects on populations of mega-herbivores such as the African savanna elephants, through habitat reduction and fragmentation and increased human–animal conflict. Animals with vast home ranges are forced into increasingly smaller geographical areas, often restricted by fencing or encroaching anthropogenic activities, resulting in huge pressures on these areas to meet the animals’ resource needs. This can present a nutritional challenge and cause animals to adapt their movement patterns to meet their dietary needs for specific minerals, potentially causing human–animal conflict. The aim of this review is to consolidate understanding of nutritional drivers for animal movement, especially that of African savanna elephants and focus the direction of future research. Peer reviewed literature available was generally geographically specific and studies conducted on isolated populations of individual species. African savanna elephants have the capacity to extensively alter the landscape and have been more greatly studied than other herbivores, making them a good example species to use for this review. Alongside this, their movement choices, potentially linked with nutritional drivers could be applicable to a range of other species. Relevant case study examples of other herbivores moving based on nutritional needs are discussed. Methods Three databases were searched in this review: Scopus, Web of Science and Google Scholar, using identified search terms. Inclusion and exclusion criteria were determined and applied as required. Additional grey literature was reviewed as appropriate. Results Initial searches yielded 1,870 records prior to application of inclusion and exclusion criteria. A less detailed review of grey literature, and additional peer-reviewed literature which did not meet the inclusion criteria but was deemed relevant by the authors was also conducted to ensure thorough coverage of the subject. Discussion A review of peer reviewed literature was undertaken to examine nutritional drivers for African elephant movement, exploring documented examples from free-ranging African savanna elephants and, where relevant, other herbivore species. This could help inform prediction or mitigation of human–elephant conflict, potentially when animals move according to nutritional needs, and related drivers for this movement. In addition, appropriate grey literature was included to capture current research.
Sach et al. (2019) African savanna elephants (Loxodonta africana) as an example of a herbivore making movement choices based on nutritional needs. PeerJ 7:e6260 https://doi.org/10.7717/peerj.6260
Suppression of hesA mutation on nitrogenase activity in Paenibacillus polymyxa WLY78 with the addition of high levels of molybdate or cystine
The diazotrophic Paenibacillus polymyxa WLY78 possesses a minimal nitrogen fixation gene cluster consisting of nine genes (nifB nifH nifD nifK nifE nifN nifX hesA and nifV). Notably, the hesA gene contained within the nif gene cluster is also found within nif gene clusters among diazotrophic cyanobacteria and Frankia. The predicted product HesA is a member of the ThiF-MoeB-HesA family containing an N-terminal nucleotide binding domain and a C-terminal MoeZ/MoeB-like domain. However, the function of hesA gene in nitrogen fixation is unknown. In this study, we demonstrate that the hesA mutation of P. polymyxa WLY78 leads to nearly complete loss of nitrogenase activity. The effect of the mutation can be partially suppressed by the addition of high levels of molybdate or cystine. However, the nitrogenase activity of the hesA mutant could not be restored by Klebsiella oxytoca nifQ or Escherichia coli moeB completely. In addition, the hesA mutation does not affect nitrate reductase activity of P. polymyxa WLY78. Our results demonstrate hesA is a novel gene specially required for nitrogen fixation and its role is related to introduction of S and Mo into the FeMo-co of nitrogenase.
Liu et al. (2019) Suppression of hesA mutation on nitrogenase activity in Paenibacillus polymyxa WLY78 with the addition of high levels of molybdate or cystine. PeerJ 7:e6294 https://doi.org/10.7717/peerj.6294
Wild edible fool’s watercress, a potential crop with high nutraceutical properties
Background Fool’s watercress (Apium nodiflorum) is an edible vegetable with potential as a new crop. However, little information is available regarding the antioxidant properties of the plant and the individual phenolics accounting for this capacity are unknown. Methods The antioxidant properties of twenty-five wild populations were analysed and individual phenolics present in the species reported and compared with celery and parsley. The antioxidant activity was measured as the 2,2-diphenyl-1-picrylhydrazyl hydrate (DPPH) free radical scavenging capacity, and the total phenolics content (TPC) via the Folin-Ciocalteu procedure. The individual phenolics constituents were determined via high performance liquid chromatography (HPLC) as aglycones. Results The average DPPH and TPC of fool’s watercress were 28.1 mg Trolox g−1 DW and 22.3 mg of chlorogenic acid equivalents g−1 DW, respectively, much higher than those of celery and parsley. Significant differences for both DPPH and TPC, which may be explained by either genotype or environmental factors, were detected among groups established according to geographical origin. Quercetin was identified as the major phenolic present in the leaves of the species, unlike parsley and celery, in which high amounts of apigenin and luteolin were determined. Quercetin represented 61.6% of the phenolics targeted in fool’s watercress, followed by caffeic acid derivatives as main hydroxycinnamic acids. Discussion The study reports the high antioxidant properties of fool’s watercress based on a large number of populations. Results suggest that quercetin accounts for an important share of the antioxidant capacity of this potential new crop. The study also provides a basis for future breeding programs, suggesting that selection by geographical locations may result in differences in the antioxidant properties.
Guijarro-Real et al. (2019) Wild edible fool’s watercress, a potential crop with high nutraceutical properties. PeerJ 7:e6296 https://doi.org/10.7717/peerj.6296
Total incombustible (mineral) content of Cherax quadricarinatus differs between feral populations in Central-Eastern Australia
Cherax quadricarinatus has been widely translocated within Australia, and a number of self-sustaining feral populations have established, and persisted, in central-eastern Australia for over 20 years: however, the biology and ecology of feral populations remain poorly understood. Using the loss-by-ignition method, this study investigated differences in the total content of incombustible material (as a proxy for total mineral content), between feral C. quadricarinatus populations in southeast Queensland and northeastern New South Wales. A total of 102 C. quadricarinatus were ignited, and percent total incombustible material was not proportional to the body size, or gender of the crayfish. Incombustible content was however, significantly different between some locations of capture (i.e., waterbodies). The site where incombustible content in crayfish was atypical, Lake Ainsworth, is a naturally acidic coastal lake, and we suggest that acidity and low concentration of calcium in that waterbody are likely responsible for the difference in mineral content detected in that population. Mechanism(s) driving the difference detected in the Lake Ainsworth population are unknown, but we suggest the acidic environment could directly impact maintenance of internal calcium reserves in the crayfish (intermoult), during recalcification of the cuticle (postmoult), or both. Limited calcium availability in the lake may also be a direct, or indirect, contributing factor. The ability of C. quadricarinatus to occupy acidic habitats while managing biomineralization challenges possibly could enable additional range-expansion of the species, and potential impacts on both endangered ecological communities and other biota occupying the acidic coastal habitats of Eastern Australia.
Tierney et al. (2019) Total incombustible (mineral) content of Cherax quadricarinatus differs between feral populations in Central-Eastern Australia. PeerJ 7:e6351 https://doi.org/10.7717/peerj.6351
New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east–west lineage split and genetic mixture within western subtropical China
Background Subtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species. Liriodendron chinense is a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern of L. chinense and to explore the role of mountains in the conservation of L. chinense genetic resources. Methods Three chloroplast regions (psbJ-petA, rpl32-ndhF, and trnK5’-matK) were sequenced in 40 populations of L. chinense for phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods. Results Obvious phylogeographic structure was found in L. chinense. SAMOVA revealed seven groups matching the major landscape features of the L. chinense distribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin of L. chinense in the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage. Discussion The clear geographical distributions of haplotypes suggested multiple mountainous refugia of L. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots of haplotype diversity in the Dalou Mountains and Wuling Mountains likely benefited from gene flow from the Wu Mountains and Yungui Plateau. Collectively, these results indicate that mountain regions should be the main units for conserving and collecting genetic resources of L. chinense and other similar species in subtropical China.
Yang et al. (2019) New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east–west lineage split and genetic mixture within western subtropical China. PeerJ 7:e6355 https://doi.org/10.7717/peerj.6355
Identification of species and materia medica within Saussurea subg. Amphilaena based on DNA barcodes
Saussurea is one of the most species-rich genera in the family Asteraceae, where some have a complex evolutionary history, including radiation and convergent evolution, and the identification of these species is notoriously difficult. This genus contains many plants with medical uses, and thus an objective identification method is urgently needed. Saussurea subg. Amphilaena is one of the four subgenera of Saussurea and it is particularly rich in medical resources, where 15/39 species are used in medicine. To test the application of DNA barcodes in this subgenus, five candidates were sequenced and analyzed using 131 individuals representing 15 medical plants and four additional species from this subgenus. Our results suggested that internal transcribed spacer (ITS) + rbcL or ITS + rbcL + psbA-trnH could distinguish all of the species, while the ITS alone could identify all of the 15 medical plants. However, the species identification rates based on plastid barcodes were low, i.e., 0% to 36% when analyzed individually, and 63% when all four loci were combined. Thus, we recommend using ITS + rbcL as the DNA barcode for S. subg. Amphilaena or the ITS alone for medical plants. Possible taxonomic problems and substitutes for medicinal plant materials are also discussed.
Chen et al. (2019) Identification of species and materia medica within Saussurea subg. Amphilaena based on DNA barcodes. PeerJ 7:e6357 https://doi.org/10.7717/peerj.6357
A gelatin/collagen/polycaprolactone scaffold for skin regeneration
Background A tissue-engineered skin substitute, based on gelatin (“G”), collagen (“C”), and poly(ε-caprolactone) (PCL; “P”), was developed. Method G/C/P biocomposites were fabricated by impregnation of lyophilized gelatin/collagen (GC) mats with PCL solutions, followed by solvent evaporation. Two different GC:PCL ratios (1:8 and 1:20) were used. Results Differential scanning calorimetry revealed that all G/C/P biocomposites had characteristic melting point of PCL at around 60 °C. Scanning electron microscopy showed that all biocomposites had similar fibrous structures. Good cytocompatibility was present in all G/C/P biocomposites when incubated with primary human epidermal keratinocytes (PHEK), human dermal fibroblasts (PHDF) and human adipose-derived stem cells (ASCs) in vitro. All G/C/P biocomposites exhibited similar cell growth and mechanical characteristics in comparison with C/P biocomposites. G/C/P biocomposites with a lower collagen content showed better cell proliferation than those with a higher collagen content in vitro. Due to reasonable mechanical strength and biocompatibility in vitro, G/C/P with a lower content of collagen and a higher content of PCL (GCLPH) was selected for animal wound healing studies. According to our data, a significant promotion in wound healing and skin regeneration could be observed in GCLPH seeded with adipose-derived stem cells by Gomori’s trichrome staining. Conclusion This study may provide an effective and low-cost wound dressings to assist skin regeneration for clinical use.
Wei et al. (2019) A gelatin/collagen/polycaprolactone scaffold for skin regeneration. PeerJ 7:e6358 https://doi.org/10.7717/peerj.6358