How fish traits and functional diversity respond to environmental changes and species invasion in the largest river in Southeastern China
Background Freshwater fish populations are facing multiple stressors, including climate change, species invasion, and anthropogenic interference. Temporal studies of fish functional diversity and community assembly rules based on trait-environment relationships provide insights into fish community structure in riverine ecosystems. Methods Fish samples were collected in 2015 in the Min River, the largest freshwater riverine system in Southeastern China. Fish functional diversity was compared with the background investigation in 1979. Changes in functional richness, functional evenness, functional divergence, and functional beta diversity were analyzed. Relationships between functional diversity and environmental factors were modeled by random forest regression. Correlations between fish functional traits and environmental factors were detected by fourth-corner combined with RLQ analysis. Results Functional richness was significantly reduced in 2015 compared with 1979. Functional beta diversity in 2015 was significantly higher than that in 1979, with functional nestedness being the driving component. Reduction of functional richness and domination of functional nestedness is associated with species loss. Trait convergence was the dominant mechanism driving the temporal changes of functional diversity. Precipitation, temperature, species invasion, and human population were the most significant factors driving fish functional diversity. Higher precipitation, higher temperature, and presence of invasive species were significantly associated with higher swimming factor and higher relative eye diameter, while the opposite environmental conditions were significantly associated with higher pectoral fin length and eurytopic water flow preference. Conclusions Environmental filtering is the dominant temporal assembly mechanism shaping fish community structure. This work contributes to the understanding of temporal freshwater fish community assembly and the associations between fish functional structure and local environmental conditions, which will be informative for future freshwater fish conservation.
Lin et al. (2021) How fish traits and functional diversity respond to environmental changes and species invasion in the largest river in Southeastern China. PeerJ 9:e11824 https://doi.org/10.7717/peerj.11824
Assessing the quantitative relationships between the impervious surface area and surface heat island effect during urban expansion
As an important component of underlying urban surfaces, the distribution pattern and density of the impervious surface area (ISA) play an important role in the generation of surface urban heat island (SUHI) effects. However, the quantitative and localized exploration of the ISA’s influence on SUHIs in the process of urban expansion from the perspective of temporal and spatial changes is still not clear. Based on multisource remote sensing data, the SUHI effect of urban expansion is revealed by using geospatial analysis methods such as profile, difference and regression analysis. The results show the following: (1) urban expansion plays a significant role in aggravating SUHIs. Overall, the ISA and land surface temperature (LST) have obvious consistency in terms of spatial distribution patterns. However, local spatial differentiation is significant. The areas with the highest LST were not concentrated in the downtown area with the highest ISA but were scattered in the cultivated land and exposed surface areas under development in the northern part of the city. (2) In general, the ISA can explain the spatial distribution of LST well, there is an obvious positive correlation between them, and the quadratic polynomial function is the best fitting model between them. (3) The density and spatial allocation of ecological elements, such as green space and water bodies, play an important role in alleviating SUHIs. This study found that the urban center with the highest ISA coverage rate has no significant SUHI due to the reasonable allocation of green space and water bodies. The research results can provide a scientific basis for future urban planning and ecological environment construction.
Spatial and Geographic Information Science
Ma et al. (2021) Assessing the quantitative relationships between the impervious surface area and surface heat island effect during urban expansion. PeerJ 9:e11854 https://doi.org/10.7717/peerj.11854
Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat (Triticum aestivum)
Background Alcohol dehydrogenase (ADH) plays an important role in plant survival under anaerobic conditions. Although some research about ADH in many plants have been carried out, the bioinformatics analysis of the ADH gene family from Triticum aestivum and their response to abiotic stress is unclear. Methods A total of 22 ADH genes were identified from the wheat genome, and these genes could be divided into two subfamilies (subfamily I and subfamily II). All TaADH genes belonged to the Medium-chain ADH subfamily. Sequence alignment analysis showed that all TaADH proteins contained a conservative GroES-like domain and Zinc-binding domain. A total of 64 duplicated gene pairs were found, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these genes were relatively conservative and did not change greatly in the process of duplication. Results The organizational analysis showed that nine TaADH genes were highly expressed in all organs, and the rest of TaADH genes had tissue specificity. Cis-acting element analysis showed that almost all of the TaADH genes contained an anaerobic response element. The expression levels of ADH gene in waterlogging tolerant and waterlogging sensitive wheat seeds were analyzed by quantitative real-time PCR (qRT-PCR). This showed that some key ADH genes were significantly responsive to waterlogging stress at the seed germination stage, and the response of waterlogging tolerant and waterlogging sensitive wheat seeds to waterlogging stress was regulated by different ADH genes. The results may be helpful to further study the function of TaADH genes and to determine the candidate gene for wheat stress resistance breeding.
Shen et al. (2021) Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat (Triticum aestivum). PeerJ 9:e11861 https://doi.org/10.7717/peerj.11861
Effects of step length and cadence on hip moment impulse in the frontal plane during the stance phase
Background An excessive daily cumulative hip moment in the frontal plane (determined as the product of hip moment impulse in the frontal plane during the stance phase and mean number of steps per day) is a risk factor for the progression of hip osteoarthritis. Moreover, walking speed and step length decrease, whereas cadence increases in patients with hip osteoarthritis. However, the effects of step length and cadence on hip moment impulse in the frontal plane during the stance phase are not known. Therefore, this study aimed to examine the effects of step length and cadence on hip moment impulse in the frontal plane during the stance phase. Methods We used a public dataset (kinetic and kinematic data) of over-ground walking and selected 31 participants randomly from the full dataset of 57 participants. The selected participants walked at a self-selected speed and repeated the exercise 15 times. We analyzed the data for all 15 trials for each participant. Multiple regression analysis was performed with the hip moment impulse in the frontal plane during the stance phase as the dependent variable and step length and cadence as independent variables. Results The adjusted R2 in this model was 0.71 (p < 0.001). The standardized partial regression coefficients of step length and cadence were 0.63 (t = 5.24; p < 0.001) and −0.60 (t = − 4.58; p < 0.001), respectively. Conclusions Our results suggest that low cadence, not short step length, increases the hip moment impulse in the frontal plane. Our findings help understand the gait pattern with low hip moment impulse in the frontal plane.
Inai et al. (2021) Effects of step length and cadence on hip moment impulse in the frontal plane during the stance phase. PeerJ 9:e11870 https://doi.org/10.7717/peerj.11870
Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach
Background A significant proportion of perinatal losses in pigs occurs due to congenital malformations. The purpose of this study is the identification of genomic loci associated with fetal malformations in piglets. Methods The malformations were divided into two groups: associated with limb defects (piglet splay leg) and associated with other congenital anomalies found in newborn piglets. 148 Landrace and 170 Large White piglets were selected for the study. A genome-wide association study based on the gradient boosting machine algorithm was performed to identify markers associated with congenital anomalies and piglet splay leg. Results Forty-nine SNPs (23 SNPs in Landrace pigs and 26 SNPs in Large White) were associated with congenital anomalies, 22 of which were localized in genes. A total of 156 SNPs (28 SNPs in Landrace; 128 in Large White) were identified for piglet splay leg, of which 79 SNPs were localized in genes. We have demonstrated that the gradient boosting machine algorithm can identify SNPs and their combinations associated with significant selection indicators of studied malformations and productive characteristics. Data availability Genotyping and phenotyping data are available at http://www.compubioverne.group/data-and-software/.
Bakoev et al. (2021) Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach. PeerJ 9:e11580 https://doi.org/10.7717/peerj.11580
Variation in the skulls of Elgaria and Gerrhonotus (Anguidae, Gerrhonotinae) and implications for phylogenetics and fossil identification
Background There are limited data on intra- and interspecific osteological variation for many squamate clades. Those data are relevant for phylogenetic analyses that use osteological characters and for apomorphic identifications of fossils. We investigate whether morphological features in the skulls of extant gerrhonotine lizards can be used to distinguish taxa at the species- and genus-level and assess whether newly discovered intra- and interspecific osteological variation alters the utility of previously reported apomorphic features. We examined skulls of species belonging to the gerrhonotine genera Elgaria and Gerrhonotus. These genera contain 17 extant species, but the cranial osteology of only a few species was previously examined. As a result, intra- and interspecific osteological variation of these gerrhonotines is poorly understood. Methods We employed high-resolution x-ray computed tomography (CT) to scan 25 alcohol-preserved specimens. We provide data on the skulls of all eight species of Elgaria, four for the first time, and five species of Gerrhonotus, three for the first time. We examined 3-D reconstructed skulls of the scanned specimens as well as dry, traditionally prepared skeletons (when they were available). Results We found that the purported diagnostic utility of many previously described morphological features is impacted because of substantial morphological variation between and within species. We present an assessment of osteological differences that may be useful to differentiate species of Elgaria and Gerrhonotus, many of which are present on isolated cranial elements commonly recovered as fossils, including the premaxilla, maxilla, parietal, pterygoid, prootic, dentary, and surangular. We demonstrate the importance of documenting patterns of osteological variation using large sample sizes, and the utility of examining disarticulated cranial elements of the squamate skull to identify diagnostic morphology. This study adds to a growing body of literature suggesting that extensive documentation of morphological variation is needed to further our understanding of the phylogenetic and diagnostic utility of morphological features across vertebrate clades. Efforts in that direction likely will benefit from examination of disarticulated skeletal elements.
Ledesma et al. (2021) Variation in the skulls of Elgaria and Gerrhonotus (Anguidae, Gerrhonotinae) and implications for phylogenetics and fossil identification. PeerJ 9:e11602 https://doi.org/10.7717/peerj.11602
Comparative anatomy of the middle ear in some lizard species with comments on the evolutionary changes within Squamata
The skeleton of the middle ear of lizards is composed of three anatomical elements: columella, extracolumella, and tympanic membrane, with some exceptions that show modifications of this anatomy. The main function of the middle ear is transforming sound waves into vibrations and transmitting these to the inner ear. Most middle ear studies mainly focus on its functional aspects, while few describe the anatomy in detail. In lizards, the morphology of the columella is highly conservative, while the extracolumella shows variation in its presence/absence, size, and the number of processes present on the structure. In this work, we used diaphanized and double-stained specimens of 38 species of lizards belonging to 24 genera to study the middle ear’s morphology in a comparative framework. Results presented here indicate more variation in the morphology of the extracolumella than previously known. This variation in the extracolumella is found mainly in the pars superior and anterior processes, while the pars inferior and the posterior process are more constant in morphology. We also provide new information about the shape of gekkotan extracolumella, including traits that are diagnostic for the iguanid and gekkonid middle ear types. The data collected in this study were combined with information from published descriptive works. The new data included here refers to the length of the columella relative to the extracolumella central axis length, the general structure of the extracolumella, and the presence of the internal process. These characters were included in ancestral reconstruction analysis using Bayesian and parsimony approaches. The results indicate high levels of homoplasy in the variation of the columella-extracolumella ratio, providing a better understanding of the ratio variation among lizards. Additionally, the presence of four processes in the extracolumella is the ancestral state for Gekkota, Pleurodonta, and Xantusiidae, and the absence of the internal processes is the ancestral state for Gekkota, Gymnophthalmidae, and Scincidae; despite the fact that these groups convergently develop these character states, they could be used in combination with other characters to diagnose these clades. The posterior extension in the pars superior and an anterior process with some small and sharp projections is also a diagnostic trait for Gekkota. A more accurate description of each process of the extracolumella and its variation needs to be evaluated in a comprehensive analysis, including a greater number of species. Although the number of taxa sampled in this study is small considering the vast diversity of lizards, the results provide an overall idea of the amount of variation of the middle ear while helping to infer the evolutionary history of the lizard middle ear.
Sánchez-Martínez et al. (2021) Comparative anatomy of the middle ear in some lizard species with comments on the evolutionary changes within Squamata. PeerJ 9:e11722 https://doi.org/10.7717/peerj.11722
Change in mental health, physical health, and social relationships during highly restrictive lockdown in the COVID-19 pandemic: evidence from Australia
Background A novel coronavirus first reported in Wuhan City in China in 2019 (COVID-19) developed into a global pandemic throughout 2020. Many countries around the world implemented strict social distancing policies to curb the spread of the virus. In this study we aimed to examine potential change in mental/physical health and social relationships during a highly restrictive COVID-19 lockdown period in Australia during April 2020. Methods Our survey (n = 1, 599) included questions about concerns, social behaviour, perceived change in relationship quality, social media use, frequency of exercise, physical health, and mental health during COVID-19 lockdown (April, 2020). Results When estimating their mental health for the previous year 13% of participants reported more negative than positive emotion, whereas this increased to 41% when participants reflected on their time during COVID-19 lockdown. A substantial proportion (39–54%) of participants reported deterioration in mental health, physical health, financial situation, and work productivity. However, most of these participants reported ’somewhat’ rather than ’a lot’ of deterioration, and many others reported ’no change’ (40–50%) or even ’improvement’ (6–17%). Even less impact was apparent for social relationships (68% reported ’no change’) as participants compensated for decreased face-to-face interaction via increased technology-mediated interaction. Conclusions The psychological toll of COVID-19 on Australians may not have been as large as other parts of the world with greater infection rates. Our findings highlight how technology-mediated communication can allow people to adequately maintain social relationships during an extreme lockdown event.
Rogers et al. (2021) Change in mental health, physical health, and social relationships during highly restrictive lockdown in the COVID-19 pandemic: evidence from Australia. PeerJ 9:e11767 https://doi.org/10.7717/peerj.11767
Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)
Background The YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo. Methods In the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments. Results Based on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress.
Ma et al. (2021) Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz). PeerJ 9:e11780 https://doi.org/10.7717/peerj.11780
Alterations to arbuscular mycorrhizal fungal community composition is driven by warming at specific elevations
Background Global warming can alter plant productivity, and community composition which has consequences for soil-plant associated microorganisms. Arbuscular mycorrhizal fungi (AMF) are distributed widely and form symbiotic relationships with more than 80% of vascular plants and play a key role in nutrient cycling processes at the ecosystem scale. Methods A simulated warming experiment at multiple elevations (3,000, 3,500, 3,800, and 4,170 m) was conducted utilizing an in-situ open-top chamber (OTC) for exploring the effect of global warming on AMF community structure in the Qinghai-Tibet Plateau (QTP). This region has been identified as one of the most sensitive areas to climatic changes. Soil DNA was extracted and sequenced using next the Mi-Seq platform for diversity profiling. Results AMF richness was higher under the simulated warming chamber, however this only occurred in the elevation of 3,500 m. Warming did not alter other AMF alpha diversity indices (e.g. Shannon, Ace, and Simpson evenness index). Glomus and Acaulospora were the dominate AMF genera as assessed through their relative abundance and occurrence in control and warming treatments at the different elevations. Conclusion Warming changed significantly AMF community. The effects of warming on AMF community structure varied depend on elevations. Moreover, the occurrences of AMF in different genera were also presented the different responses to warming in four elevations.
Yang et al. (2021) Alterations to arbuscular mycorrhizal fungal community composition is driven by warming at specific elevations. PeerJ 9:e11792 https://doi.org/10.7717/peerj.11792