Surface Urban Energy and Water Balance Scheme (v2020a) in vegetated areas: parameter derivation and performance evaluation using FLUXNET2015 dataset

To compare the impact of surface–atmosphere exchanges from rural and urban areas, fully vegetated areas (e.g. deciduous trees, evergreen trees and grass) commonly found adjacent to cities need to be modelled. Here we provide a general workflow to derive parameters for SUEWS (Surface Urban Energy and Water Balance Scheme), including those associated with vegetation phenology (via leaf area index, LAI), heat storage and surface conductance. As expected, attribution analysis of bias in SUEWS-modelled QE finds that surface conductance (gs) plays the dominant role; hence there is a need for more estimates of surface conductance parameters. The workflow is applied at 38 FLUXNET sites. The derived parameters vary between sites with the same plant functional type (PFT), demonstrating the challenge of using a single set of parameters for a PFT. SUEWS skill at simulating monthly and hourly latent heat flux (QE) is examined using the site-specific derived parameters, with the default NOAH surface conductance parameters (Chen et al., 1996). Overall evaluation for 2 years has similar metrics for both configurations: median hit rate between 0.6 and 0.7, median mean absolute error less than 25Wm-2, and median mean bias error ~5Wm-2. Performance differences are more evident at monthly and hourly scales, with larger mean bias error (monthly: ~40Wm-2; hourly ~30Wm-2) results using the NOAH-surface conductance parameters, suggesting that they should be used with caution. Assessment of sites with contrasting QE performance demonstrates how critical capturing the LAI dynamics is to the SUEWS prediction skills of gs and QE. Generally gs is poorest in cooler periods (more pronounced at night, when underestimated by ~3mms-1). Given the global LAI data availability and the workflow provided in this study, any site to be simulated should benefit

Haematological characterization of loach Misgurnus anguillicaudatus: Comparison among diploid, triploid and tetraploid specimens

Abstract The purpose of this study was to determine whether diploid, triploid and tetraploid loach (Misgurnus anguillicaudatus) differed in terms of their main haematological and physiological characteristics. Diploid and tetraploid fish were produced by crossing of natural diploids (2n × 2n) and natural tetraploids (4n × 4n), respectively. Triploid fish were produced by hybridization between diploid males and tetraploid females. The blood cells were significantly larger in polyploids, and the volumetric ratios of erythrocytes and leucocytes (thrombocyte and neutrophil) in tetraploids, triploids and diploids were consistent with the ploidy level ratio of 4:3:2. No significant differences were observed in haematocrit among polyploids. The erythrocyte count decreased with increased ploidy level, while total haemoglobin, mean cell volume, mean cellular haemoglobin content, and mean cell haemoglobin concentration all increased with increase in ploidy level. Erythrocyte osmotic brittleness declined in polyploids so that polyploid erythrocytes were more resistant to osmotic stress than diploid ones. Overall, loach with higher ploidy levels showed evidence of some advantages in haematological characteristics

Correction to a Simple Biosphere Model 2 (SiB2) Simulation of Energy and Carbon Dioxide Fluxes over a Wheat Cropland in East China Using the Random Forest Model

Modeling the heat and carbon dioxide (CO2) exchanges in agroecosystems is critical for better understanding water and carbon cycling, improving crop production, and even mitigating climate change, in agricultural regions. While previous studies mainly focused on simulations of the energy and CO2 fluxes in agroecosystems on the North China Plain, their corrections, simulations and driving forces in East China are less understood. In this study, the dynamic variations of heat and CO2 fluxes were simulated by a standalone version of the Simple Biosphere 2 (SiB2) model and subsequently corrected using a Random Forest (RF) machine learning model, based on measurements from 1 January to 31 May 2015–2017 in eastern China. Through validation with direct measurements, it was found that the SiB2 model overestimated the sensible heat flux (H) and latent heat flux (LE), but underestimated soil heat flux (G0) and CO2 flux (Fc). Thus, the RF model was used to correct the results modeled by SiB2. The RF model showed that disturbances in temperature, net radiation, the G0 output of SiB2, and the Fc output of SiB2 were the key driving factors modulating the H, LE, G0, and Fc. The RF model performed well and significantly reduced the biases for H, LE, G0, and Fc simulated by SiB2, with higher R2 values of 0.99, 0.87, 0.75, and 0.71, respectively. The SiB2 and RF models combine physical mechanisms and mathematical correction to enable simulations with both physical meaning and accuracy

Evidence for the Growth Superiority and Delayed Ovarian Development in Tetraploid Loach Misgurnus anguillicaudatus

The diploids and tetraploids of cyprinid loach Misgurnus anguillicaudatus coexist in many natural habits. The tetraploids generally exhibit superior growth performance and delayed gonadal development compared with diploids. To investigate the regulation mechanism of growth superiority and ovarian development in tetraploids, we first conducted a long-term culture experiment and histological observation. The tetraploids exhibited a higher growth performance and delayed ovarian development. Meanwhile, at a genetic level, an average of 6891 differentially expressed genes (DEGs) between diploids and tetraploids were identified from the brain, pituitary, liver, gonad and muscle using the RNA-seq method. Among these DEGs, as expected, some candidate genes, including IGF family genes, somatostatin, leptin, cyp19a1b, gthα, lhβ and fshβ, were detected, which play critical roles in the regulation of growth and gonad development of fish. In particular, the genes related to GH/IGF axis and growth factors, signal transduction, gonadal hormone and appetite were significantly increased in tetraploids. The clustering analyses of the key candidate genes showed that most key genes were up-regulated in the pituitary and gonad of tetraploids instead of other tissues. The dynamics of these key genes provide valuable genetic evidence for clarifying the growth superiority and delayed gonadal development of tetraploids. Moreover, this study also provides some clues for unveiling the genetic superiority of polyploidy species in other phenotypes

Isolation of New 40 Microsatellite Markers in Mandarin Fish (Siniperca chuatsi)

In this study, 23 genomic microsatellite DNA markers and 17 express sequence tag (EST)-derived microsatellites were developed and characterized using the fast isolation by AFLP of sequences containing repeats (FIASCO) method and data mining from public EST databases of mandarin fish (Siniperca chuatsi). These polymorphic microsatellite markers were then tested for polymorphism in a wild S. chuatsi population. The number of alleles at 23 genomic SSRs varied from 2 to 19 with an average of 8.0 alleles per locus. The average observed and expected heterozygosities were 0.746 and 0.711, respectively. Of 5361 EST sequences examined, 3.9% (209) contain microsatellites, and di-nucleotide repeats are the most abundant (67.0%), followed by tri-nucleotide (29.7%) and tetra-nucleotide repeats (3.3%). The number of alleles at 17 EST-SSRs varied from 2 to 17 with an average of 8.4 alleles per locus. The average observed and expected heterozygosities were 0.789 and 0.685, respectively. No significant difference of loci polymorphism was found between genomic SSRs and EST-SSRs in terms of number of alleles and heterozygosities. Results of cross-species utility indicated that 13 (52.2%) of the genomic-SSRs and 13 (76.5%) of the EST-SSRs were successfully cross-amplified in a related species, the golden mandarin fish (Siniperca scherzeri)

Characteristics of SSRs in <i>H</i>. <i>erectus and H</i>. <i>mohnikei</i>.

<p>Characteristics of SSRs in <i>H</i>. <i>erectus and H</i>. <i>mohnikei</i>.</p

Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification

Abstract: Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The Ho ranged from 0.15 to 0.83, and He ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers fo

Leptin Genes in Blunt Snout Bream: Cloning, Phylogeny and Expression Correlated to Gonads Development

To investigate the leptin related genes expression patterns and their possible function during the gonadal development in fish, the cDNA and genomic sequences of leptin, leptin receptor (leptinR), and leptin receptor overlapping transcript like-1 (leprotl1) were cloned and their expression levels were quantified in the different gonadal development stages of Megalobrama amblycephala. The results showed that the full length cDNA sequences of leptin, leptinR and leprotl1 were 953, 3432 and 1676 bp, coding 168, 1082, and 131 amino acid polypeptides, and the genomic sequences were 1836, 28,528 and 5480 bp, which respectively had 3, 15 and 4 exons, respectively. The phylogenetic analysis revealed that three genes were relatively conserved in fish species. Quantitative real-time PCR results showed that the three genes were ubiquitously expressed in all examined tissues during the different gonadal development stages. The leptin and leptinR took part in the onset of puberty, especially in female M. amblycephala, by increasing the expression levels in brain during the stage I to III of ovary. The expression levels of leptin and leptinR had significant differences between male and female in hypothalamic-pituitary-gonadal (HPG) axis tissues (p &lt; 0.05). The leptinR had the same variation tendency with leptin, but the opposite changes of expression levels were found in leprotl1, which may resist the expression of leptinR for inhibiting the function of leptin in target organ. These findings revealed details about the possible role of these genes in regulating gonadal maturation in fish species