Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment
Although dragonflies are excellent environmental indicators for monitoring terrestrial water ecosystems, automatic monitoring techniques using digital tools are limited. We designed a novel camera trapping system with an original dragonfly detector based on the hypothesis that perching dragonflies can be automatically detected using inexpensive and energy-saving photosensors built in a perch-like structure. A trial version of the camera trap was developed and evaluated in a case study targeting red dragonflies (Sympetrum spp.) in Japan. During an approximately 2-month period, the detector successfully detected Sympetrum dragonflies while using extremely low power consumption (less than 5 mW). Furthermore, a short-term field experiment using time-lapse cameras for validation at three locations indicated that the detection accuracy was sufficient for practical applications. The frequency of false positive detection ranged from 17 to 51 over an approximately 2-day period. The detection sensitivities were 0.67 and 1.0 at two locations, where a time-lapse camera confirmed that Sympetrum dragonflies perched on the trap more than once. However, the correspondence between the detection frequency by the camera trap and the abundance of Sympetrum dragonflies determined by field observations conducted in parallel was low when the dragonfly density was relatively high. Despite the potential for improvements in our camera trap and its application to the quantitative monitoring of dragonflies, the low cost and low power consumption of the detector make it a promising tool.
Yoshioka et al. (2020) Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment. PeerJ 8:e9681 https://doi.org/10.7717/peerj.9681
Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing
Current projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world’s soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more “terrestrial” community in response to drought, in line with observed changes in the functioning of the ecosystem.
Reczuga et al. (2020) Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing. PeerJ 8:e9821 https://doi.org/10.7717/peerj.9821
Differences in small noncoding RNAs profile between bull X and Y sperm
The differences in small noncoding RNAs (sncRNAs), including miRNAs, piRNAs, and tRNA-derived fragments (tsRNAs), between X and Y sperm of mammals remain unclear. Here, we employed high-throughput sequencing to systematically compare the sncRNA profiles of X and Y sperm from bulls (n = 3), which may have a wider implication for the whole mammalian class. For the comparison of miRNA profiles, we found that the abundance of bta-miR-652 and bta-miR-378 were significantly higher in X sperm, while nine miRNAs, including bta-miR-204 and bta-miR-3432a, had greater abundance in Y sperm (p < 0.05). qPCR was then used to further validate their abundances. Subsequent functional analysis revealed that their targeted genes in sperm were significantly involved in nucleosome binding and nucleosomal DNA binding. In contrast, their targeted genes in mature oocyte were significantly enriched in 11 catabolic processes, indicating that these differentially abundant miRNAs may trigger a series of catabolic processes for the catabolization of different X and Y sperm components during fertilization. Furthermore, we found that X and Y sperm showed differences in piRNA clusters distributed in the genome as well as piRNA and tsRNA abundance, two tsRNAs (tRNA-Ser-AGA and tRNA-Ser-TGA) had lower abundance in X sperm than Y sperm (p < 0.05). Overall, our work describes the different sncRNA profiles of X and Y sperm in cattle and enhances our understanding of their potential roles in the regulation of sex differences in sperm and early embryonic development.
Zhou et al. (2020) Differences in small noncoding RNAs profile between bull X and Y sperm. PeerJ 8:e9822 https://doi.org/10.7717/peerj.9822
A new tiny toad species of Amazophrynella (Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil
The combination of different approaches has successfully delimited new species within many Neotropical species complexes traditionally classified as a single nominal organism. Recent studies have shown that the Amazonian endemic genus Amazophrynella, currently composed of 12 small-sized species, could harbor several additional species. Based on morphology and molecular data, we describe a new species of Amazophrynella from east of the Guiana Shield, in Pará state, Brazil. The new species is characterized by having one of the biggest size of the genus (SVL of males 16.0–17.8 mm and females 22.9–24.4 mm), presence of a large palmar tubercle (occupying 2/4 of the palmar surface), 5.6–8.1% uncorrected p-distance from its sister clade (including A. teko, A. sp.1, and A. manaos) for the 16S mitochondrial gene, and 8.8% for the COI. The new species described here represents a newly discovered lineage. Of the 12 Amazophrynella species currently recognized, two were describe in the last century (A. bokermanni and A. minuta) and the remaining species were recently discovered and described (in the last six years), which underscores the degree to which species richness of Amazophrynella is underestimated.
Mângia et al. (2020) A new tiny toad species of Amazophrynella (Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil. PeerJ 8:e9887 https://doi.org/10.7717/peerj.9887
Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function
Triceratops is one of the well-known Cretaceous ceratopsian dinosaurs. The ecology of Triceratops has been controversial because of its unique morphological features. However, arguments based on brain and inner ear structures have been scarce. In this study, two braincases (FPDM-V-9677 and FPDM-V-9775) were analyzed with computed tomography to generate three-dimensional virtual renderings of the endocasts of the cranial cavities and bony labyrinths. Quantitative analysis, including comparison of linear measurements of the degree of development of the olfactory bulb and inner ear, was performed on these virtual endocasts to acquire detailed neuroanatomical information. When compared with other dinosaurs, the olfactory bulb of Triceratops is relatively small, indicating that Triceratops had a reduced acuity in sense of smell. The lateral semicircular canal reveals that the basicranial axis of Triceratops is approximately 45° to the ground, which is an effective angle to display their horns as well as frill, and to graze. The semicircular canals of Triceratops are relatively smaller than those of primitive ceratopsians, such as Psittacosaurus and Protoceratops, suggesting that sensory input for the reflexive stabilization of gaze and posture of Triceratops was less developed than that of primitive ceratopsians. The cochlear length of Triceratops is relatively short when compared with other dinosaurs. Because cochlear length correlates with hearing frequency, Triceratops was likely adapted to hearing low frequencies.
Sakagami et al. (2020) Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function. PeerJ 8:e9888 https://doi.org/10.7717/peerj.9888
Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony
The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
Liu et al. (2020) Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony. PeerJ 8:e9889 https://doi.org/10.7717/peerj.9889
Native trees of Mexico: diversity, distribution, uses and conservation
Background Mexico is one of the most floristically rich countries in the world. Despite significant contributions made on the understanding of its unique flora, the knowledge on its diversity, geographic distribution and human uses, is still largely fragmented. Unfortunately, deforestation is heavily impacting this country and native tree species are under threat. The loss of trees has a direct impact on vital ecosystem services, affecting the natural capital of Mexico and people’s livelihoods. Given the importance of trees in Mexico for many aspects of human well-being, it is critical to have a more complete understanding of their diversity, distribution, traditional uses and conservation status. We aimed to produce the most comprehensive database and catalogue on native trees of Mexico by filling those gaps, to support their in situ and ex situ conservation, promote their sustainable use, and inform reforestation and livelihoods programmes. Methods A database with all the tree species reported for Mexico was prepared by compiling information from herbaria and reviewing the available floras. Species names were reconciled and various specialised sources were used to extract additional species information, i.e. endemic status, threat status, availability in seed collections, reports on plant uses and conservation actions currently in place. With this information, a comprehensive catalogue of native trees from Mexico was redacted. Available georeferenced records were used to map each species distribution and perform spatial analyses to identify gaps of information and priority areas for their conservation and exploration. Results Mexico has at least 2,885 native tree species, belonging to 612 genera and 128 families. Fabaceae is the most represented family and Quercus the most represented genus. Approximately 44% of tree species are endemic to the country. The southern part of the country showed the highest values of species richness. Six hundred and seventy-four species have at least one documented human use. In terms of conservation assessment, ca. 33% of species have been assessed by either the IUCN Red List (919) or the National protection catalogue “NORMA Oficial Mexicana NOM-059” (29) or both (45). Additionally, 98 species have been included in the CITES listing for protection. In terms of existing conservation efforts, 19% of species have ex situ protection in seed banks, while protected areas overlap with all the identified peaks of species richness, except for those in the states of Veracruz and Chiapas. This work constitutes a key milestone for the knowledge, management, and conservation of the Mexican native trees. The two areas with high density of tree species identified in Veracruz and Chiapas represent two priority areas for tree conservation in Mexico, where integrated in situ and ex situ conservation efforts should be focused.
Tellez et al. (2020) Native trees of Mexico: diversity, distribution, uses and conservation. PeerJ 8:e9898 https://doi.org/10.7717/peerj.9898
Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness
Cannibalism is considered one of the causes of intra-cohort size divergence in fish and is usually believed to result in increased fitness in terms of survival and reproduction, but direct evidence of this is lacking. Population demographics of the clearhead icefish (Protosalanx chinensis) from Lake Xingkai (Khanka) were investigated for one year. Size-frequencies exhibited a bimodal distribution from July through January, where the population diverged into an upper and a lower modal group based on size. Stomach content analysis confirmed the occurrence of cannibalism, where fish belonging to the larger, upper modal group preyed upon those of the smaller, lower modal group. We found P. chinensis does not spawn until all of the oocytes have reached maturity and then a single spawning event occurs although the oocytes may develope asynchronously in the ovary. Upper modal group females matured slightly earlier than those of the lower modal group, and reproductive investment was considerably greater in the upper modal group than the lower modal group. The lower modal males made up the majority of the population after the spawning period, which meant they may have few opportunities to participate in reproduction. Therefore, piscivory and cannibalism of P. chinensis appears to have increased fitness of the fish belonging to the upper modal group and greatly reduced the fitness of those belonging to the lower modal group.
Tang et al. (2020) Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness. PeerJ 8:e9900 https://doi.org/10.7717/peerj.9900
Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China
Nutrient resorption from senesced leaves is an important mechanism for nutrient conservation in plants. However, little is known about the effect of grazing on plant nutrient resorption from senesced leaves, especially in semiarid ecosystems. Here, we evaluated the effects of grazing on N and P resorption in the three most dominant grass species in a typical steppe in northern China. We identified the key pathways of grazing-induced effects on N and P resorption efficiency. Grazing increased N and P concentrations in the green leaves of Leymus chinensis and Stipa grandis but not in Cleistogenes squarossa. Both L. chinensis and S. grandis exhibited an increasing trend of leaf N resorption, whereas C. squarrosa recorded a decline in both leaf N and P resorption efficiency under grazing. Structural equation models showed that grazing is the primary driver of the changes in N resorption efficiency of the three dominant grass species. For L. chinensis, the P concentration in green and senesced leaves increased the P resorption efficiency, whereas the senesced leaf P concentration played an important role in the P resorption efficiency of C. squarrosa. Grazing directly drove the change in P resorption efficiency of S. grandis. Our results suggest that large variations in nutrient resorption patterns among plant species depend on leaf nutritional status and nutrient-use strategies under overgrazing, and indicate that overgrazing may have indirect effects on plant-mediated nutrient cycling via inducing shifts in the dominance of the three plant species.
Wang et al. (2020) Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China. PeerJ 8:e9915 https://doi.org/10.7717/peerj.9915
Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies
Dietary habits in extinct species cannot be directly observed; thus, in the absence of extraordinary evidence, they must be reconstructed with a combination of morphological proxies. Such proxies often include information on dental organization and function such as tooth formation time and tooth replacement rate. In extinct organisms, tooth formation times and tooth replacement rate are calculated, in part via extrapolation of the space between incremental lines in dental tissues representing daily growth (von Ebner Line Increment Width; VEIW). However, to date, little work has been conducted testing assumptions about the primary data underpinning these calculations, specifically, the potential impact of differential sampling and data extrapolation protocols. To address this, we tested a variety of intradental, intramandibular, and ontogentic sampling effects on calculations of mean VEIW, tooth formation times, and replacement rates using histological sections and CT reconstructions of a growth series of three specimens of the extant archosaurian Alligator mississippiensis. We find transect position within the tooth and transect orientation with respect to von Ebner lines to have the greatest impact on calculations of mean VEIW—a maximum number of VEIW measurements should be made as near to the central axis (CA) as possible. Measuring in regions away from the central axis can reduce mean VEIW by up to 36%, causing inflated calculations of tooth formation time. We find little demonstrable impact to calculations of mean VEIW from the practice of subsampling along a transect, or from using mean VEIW derived from one portion of the dentition to extrapolate for other regions of the dentition. Subsampling along transects contributes only minor variations in mean VEIW (<12%) that are dwarfed by the standard deviation (SD). Moreover, variation in VEIW with distance from the pulp cavity likely reflects idiosyncratic patterns related to life history, which are difficult to control for; however, we recommend increasing the number of VEIW measured to minimize this effect. Our data reveal only a weak correlation between mean VEIW and body length, suggesting minimal ontogenetic impacts. Finally, we provide a relative SD of mean VEIW for Alligator of 29.94%, which can be used by researchers to create data-driven error bars for tooth formation times and replacement rates in fossil taxa with small sample sizes. We caution that small differences in mean VEIW calculations resulting from non-standardized sampling protocols, especially in a comparative context, will produce inflated error in tooth formation time estimations that intensify with crown height. The same holds true for applications of our relative SD to calculations of tooth formation time in extinct taxa, which produce highly variable maximum and minimum estimates in large-toothed taxa (e.g., 718–1,331 days in Tyrannosaurus).
Kosch et al. (2020) Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies. PeerJ 8:e9918 https://doi.org/10.7717/peerj.9918