Conflicting selection pressures on seed size and germination caused by carnivorous seed dispersers

Plants produce nutritious,fleshy fruits that attract various animals to facilitate seed dispersal and recruitment dynamic.Species-specific differential selection of seed size by multiple frugivorous disperser assemblages may affect the subsequent germination of the ingested seeds.However,there is little empirical evidence supporting this association.In the present study,we documented conflicting selection pressures exerted on seed size and germination by five frugivorous carnivores on a mammal-dispersed pioneer tree,the date-plum persimmon(Diospyros lotus),in a subtropical forest.Fecal analyses revealed that these carnivores acted as primary seed dispersers of D.lotus.We also observed that seed sizes were selected based on body mass and were species-specific,confirming the“gape limitation”hypothesis;three small carnivores(the masked palm civet Paguma larvata,yellow-throated marten Martes flavigula,and Chinese ferret-badger Melogale moschata)significantly preferred to disperse smaller seeds in comparison with control seeds obtained directly from wild plants whereas the largest Asiatic black bears(Ursus thibetanus)ingested larger seeds.Seeds dispersed by medium-sized hog badgers(Arctonyx albogularis)were not significantly different from control seeds.However,regarding the influence of gut passage on seed germination,three arboreal dispersal agents(martens,civets,and bears)enhanced germination success whereas terrestrial species(ferret-badgers and hog badgers)inhibited the germination process compared with undigested control seeds.These conflicting selection pressures on seed size and germination may enhance the heterogeneity of germination dynamics and thus increase species fitness through diversification of the regeneration niche.Our results advance our understanding of seed dispersal mechanisms and have important implications for forest recruitment and ecosystem dynamics.

G-quadruplexes in genomes of viruses infecting eukaryotes or prokaryotes are under different selection pressures from hosts

G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming sequences(PQSs) across the known viral genomes and analyzed the abundance, structural stability, and conservation of viral PQSs. A Viral Putative G-quadruplex Database(http://jsjds.hzau.edu.cn/MBPC/Vi PGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides guidance for selecting the desirable PQS. The PQS with two putative G-tetrads(G2-PQS) was significantly enriched in both eukaryotic viruses and prokaryotic viruses, whereas the PQSs with three putative G-tetrads(G3-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation analysis showed that the G2-PQS, instead of G3-PQS, was highly conserved within the genus. This suggested that the G2-quadruplex might play an important role in viral biology, and the difference in the occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the different selection pressures from hosts.

Genome-Wide Characterization of the Hyaluronidase Gene Family and Their Potential Roles in Viviparous Black Rockfish(Sebastes schlegeli)

Black rockfish(Sebastes schlegelii)has evolved viviparous reproduction mode.Different from the oviparous fishes,the spermatozoa of black rockfish are stored on the surface of ovarian follicle for over four months until the egg mature in ovary,while the adaptive evolution of fertilization-related genes remains to be studied.In the present study,based on the genome and transcriptome information of black rockfish,a total of 10 hyaluronidase genes were identified by phylogenetic and sequence analyses,including hyal1,hyal2,hyal3,hyal4,hyal6 and spam1a,spam1b,spam1c and spam1d.The spam1 subfamilies,including spam1a,spam1b,spam1c and spam1d,were significantly expanded compared to other species.The adaptive evolution of hyaluronidase was further investigated by selection pressure analysis of branch model and branch site model.The results showed that only spam1 subfamily was positively selected with a large number of positive selection sites,and the evolution rate was significantly higher thanthose of other teleosts.Two positively selected sites,LYS-171 and GLY-164,were located in the neutral hyaluronidase activity domain,which was pivotal for SPAM1 to participate in enzymatic hydrolysis of the extracellular hyaluronic acid matrix and mediate acrosome reaction in mammals.Furthermore,spam1 was mainly expressed in spermatocytes,secondary spermatocytes,and spermatids of testis,whereas it was not found in metamorphic sperm and mature sperm based on the spatiotemporal expression analysis.All results indicated that spam1 might originate from the testis and might be an adaptation of viviparous trait in black rockfish.

Genomic Landscape of Rare Codon Usage at Start Region in the Pacific Oyster Genome

Synonymous codons have different frequencies of usage in many species.Based on the frequency of usage,the codons can be divided into two groups,rare codons and abundant codons.Rare codons are found to be enriched at the start regions of genes,and it is assumed that these codons can reduce elongation speed of genes.However,the rare codon usage in different genomic regions of mollusks and their relationship with selective pressure has not been systematically investigated.In this study,the patterns of rare codon usage are characterized at whole genome level,and their relationship with selective pressures is investigated in Crassostrea gigas.The rare codons are enriched at the start regions of genes with high and medium expression levels,and their proportion is higher than those in the genes with low expression level.The genes with longer coding sequences and more exon numbers have lower fraction of rare codons at start regions.Rare codons have lower level of nucleotide diversity and higher frequency of rare mutations at start regions.This work is the first comprehensive investigation of the relationships between rare codon usage and some intrinsic genetic factors in mollusca species.The results suggest that the selective pressures play an important role in shaping the rare codon usage in the C.gigas genome.

Correlation between Climatic Factors and Genetic Diversity of Phrynocephalus forsythii

Global climate change is a threat to animals in nearly all biomes and ecosystems, especially for ectotherm whose life activities highly depend on environmental thermal regime. Population genetic diversity which is essential for adaptation to environmental change is a useful index for long-term species survival. In this paper, genetic diversity of eight Phrynocephalus forsythii population which distributed in Tarim Basin, China, were evaluated based on three mtDNA gene and its correlation with environment factors were investigated using RDA. Our result revealed that, the level of genetic diversity of P. forsythii populations was related to its location but there was no significant correlation between genetic distances and geographic distances in P. forsythii. However, we find that mtDNA of P. forsythii was subjected to selection pressure during evolution and population genetic diversity was significantly positively related to variation coefficient of rainfall(VCR) and altitude(AL), while significantly negatively related to longitude(N) and annual average temperature(AAT). Our result supported the previous prediction that excessive ambient heat is a threat to P. forsythii.

Hybrid Multipopulation Cellular Genetic Algorithm and Its Performance

The selection pressure of genetic algorithm reveals the degree of balance between the global exploration and local optimization.A novel algorithm called the hybrid multi-population cellular genetic algorithm(HCGA)is proposed,which combines population segmentation with particle swarm optimization(PSO).The control parameters are the number of individuals in the population and the number of subpopulations.By varying these control parameters,changes in selection pressure can be investigated.Population division is found to reduce the selection pressure.In particular,low selection pressure emerges in small and highly divided populations.Besides,slight or mild selection pressure reduces the convergence speed,and thus a new mutation operator accelerates the system.HPCGA is tested in the optimization of four typical functions and the results are compared with those of the conventional cellular genetic algorithm.HPCGA is found to significantly improve global convergence rate,convergence speed and stability.Population diversity is also investigated by HPCGA.Appropriate numbers of subpopulations not only achieve a better tradeoff between global exploration and local exploitation,but also greatly improve the optimization performance of HPCGA.It is concluded that HPCGA can elucidate the scientific basis for selecting the efficient numbers of subpopulations.

Functional structure analysis and genome‑wide identification of CNX gene family in cotton

Background:Under abiotic stress conditions,cotton growth is inhibited and yield losses are severe.Identification of calnexin family members and function analysis under abiotic stress laid the foundation for the screening of stressrelated candidate genes.Results:A total of 60 CNX family members have been identified in Gossypium hirsutum,G.barbadense,G.arboreum,and G.raimondii,and they were divided into two categories:CNX and CRT genes.Through the construction of a phylogenetic tree,they were subdivided into three classes.Further analysis of chromosome localization,conserved promoters,gene structure and selection under pressure showed that the family members were highly conserved in the evolution process.Analysis of cis-acting elements in the promoter regions showed that CNX family genes contain regulatory elements for growth and development,anaerobic,drought,defense and stress response,and plant hormones.Using RNA-seq data to study the expression pattern of GhCNX genes under cold,hot,salt stress and Polyethylene glycol,it was observed that the gene expression levels changed by different degrees under different stress conditions,indicating that GhCNX members were involved in the regulation of multiple biological stresses.Conclusion:This study provides an insight into the members of cotton CNX genes.The results of this study suggested that CNX family members play a role in defense against adversity and provide a foundation for the discovery of stress-related genes.

Isolation and phylogenetic analysis of feline calicivirus strains from various region of China

Feline calicivirus(FCV)is an important feline pathogen mainly causing upper respiratory tract disease,conjunctivitis,and stomatitis,and it is classifed into genotype I and genotype II.To investigate the prevalence and molecular characteristics of FCV,this study collected 337 cat swab samples from animal hospitals in diferent regions of China from 2019 to 2021.The positive detection rate of FCV was 29.9%(101/337)by RT-PCR.Statistical analysis showed that FCV prevalence was signifcantly associated with living environment(p=0.0004),age(p=0.031)and clinical symptoms(p=0.00),but not with sex(p=0.092)and breed(p=0.171).The 26 strains of FCV were isolated using F81 cells.Phylogenetic analysis showed that 10 isolates belonged to genotype I,and 16 isolates belonged to genotype II.These 26 isolates were highly genetically diverse,of which HB7 isolate had three same virulence-related amino acid loci with VSD strains.Potential loci distinguishing diferent genotypes were identifed from 26 isolates,suggesting the genetic relationship between diferent genotypes.In addition,selection pressure analysis based on capsid protein of 26 isolates revealed that the protein is under diversifying selection.This study reveals the genetic diversity of FCV and provides a reference for the screening of vaccine candidate strains and the development of vaccines with better cross-protection efects.

Complete Genome Sequence Analysis of Guangdong Isolates of Cymbidium Mosaic Virus

[Objectives]The paper was to explore the genetic information and evolution of CymMV,and to provide an important scientific basis for monitoring and early warning of orchid virus disease and anti-virus genetic engineering of orchid in Guangdong Province.[Methods]RT-PCR and DASELISA were used to detect and identify CymMV from leaves with suspected virus disease of Cymbidium sinense collected from Guangzhou area.The genome sequence assembly,annotation,phylogeny and selection pressure analysis of CymMV isolates were performed with related molecular biology software.[Results]Two CymMV isolates(GZV013 and ZC29)were found in Guangdong Province for the first time in this study.The genome of both GZV013 and ZC29 were 6227 nt in length,encoding 5 functional proteins.The similarity analysis of the full sequence showed that the nucleotide sequence identity of GZV013 and Taiwan isolate M2 was 97.03% and that of ZC29 and Nanjing isolate NJ-1 was 97.11%.The complete genome sequence identity among CymMV isolates ranged from 86.85% to 98.31%,and the differentiation of diverse populations was closely related to host species and geographical isolation.Each region of CymMV genome was affected by negative selection and conformed to the neutral evolution model.The genes encoding RdRp,TGB1 and TGB2 had the highest mutation rates in the genome.[Conclusions]GZV013 was most closely related to Taiwan isolate M2,and ZC29 was most closely related to Nanjing isolate NJ-1,belonging to the same branch of a family.

Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

Mutants lacking wild-type MLO(Mildew resistance Locus O)proteins show broad-spectrum resistance to the powdery mildew fungus,and dysregulated cell death control,with spontaneous cell death in response to developmental or abiotic stimuli.In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants,we analysed systematically genome-wide data from Fragaria vesca,Prunus persica,Prunus mume,Malus domestica,Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods.Using three phylogenetic methods(the neighbour-joining,maximum likelihood,and Bayesian methods),we identified 117 MLO genes from 6 Rosaceae species.The results of all three phylogenetic analysis methods supported that these genes were divided into six clades.Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues.The findings indicated that motif 2 might be shared by the MLO gene family.The structural features of these genes showed large variations in sequence length among different species,although the lengths and the numbers of exons exhibited high degrees of similarity.Selective pressure analysis showed extremely significant differences in all 6 clades,with 2,1,and 1 site(s)under significant positive selection detected in clades III,IV,and VI,respectively.These positive selection sites were important driving forces for the promotion of the functional differentiation of the MLO genes.Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes.Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process.However,clade I may have undergone extensive altered functional constraints as a specialised functional role.Moreover,the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew,which then gradually evolved into functions such as the regulation of flower development,the control of root morphology,and seed evolution due to the different evolutionary rates after gene duplication.These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.

Efficacy of selective laser trabeculoplasty following incisional glaucoma surgery

AIM： To evaluate the efficacy of selective laser trabeculoplasty（SLT） in glaucomatous eyes with previous incisional glaucoma surgery. METHODS： A retrospective cohort of eyes that underwent SLT at a single institution from 2013-2015 were followed for 1 y. Reduction in intraocular pressure（IOP） following SLT was evaluated in eyes with prior trabeculectomy with Ex Press mini shunt（Alcon, Ft Worth, TX, USA）, Ahmed valve（New World Medical, Cucamonga, CA, USA）, or combined phacoemulsification-trabeculectomy. A control group was included with eyes without prior surgery that underwent SLT. Success was defined as 〉20% drop in IOP from pre-SLT baseline. RESULTS： One-hundred and six eyes were included with 53 in both the prior glaucoma surgery（PGS） and no prior glaucoma surgery（NPGS） groups. Mean pre-SLT IOP was 19.2±4.3 and 20.6±6.0 mm Hg for PGS and NPGS groups, respectively（P=0.17）. Both groups produced statistically significant IOP reductions at 1 and 6 mo（P〈0.04）. At 6 mo, mean IOP reduction reached 7.3% and 10.8% for the PGS and NPGS groups, respectively（P=0.42）. Overall, 27.9% and 31.7% of eyes in PGS and NPGS groups met success criteria at 1 y（P=0.70）. In the PGS group, eyes with baseline IOP ≥21 mm Hg had IOP reductions of 18.1%（P〈0.001）, 16.7%（P〈0.01）, and 8.4%（P=0.31） compared to eyes with baseline IOP 〈21 mm Hg who had IOP reductions of 2.3%（P=0.39）, 3.4%（P=0.19）, and 1.1%（P=0.72） at 1, 6 mo, and 1 y, respectively. CONCLUSION： SLT is efficacious in eyes with prior incisional glaucoma surgery and results in similar IOP reductions compared to eyes without PGS. A larger IOP reduction is observed following SLT in eyes with higher pre-SLT IOP.

Evolution of Phenotype and Mitochondrial Genome Reveals Limbless and Body-elongated Squamates may Change Their Energy Basis for Locomotion

Limb reduction in Squamata present the dramatic characteristic to focus and usually accompanied with particularly morphological modifications, impacting tremendous locomotion changing and might generate different energy requirement. Herein, we combined both morphological and mitochondrial genomic data to explore the evolution of phenotypic transformation and mitochondrial genome of limbless and body-elongated squamates. We collected phenotypic measurements of 503 individuals, representing limbed or limbless taxa across all major lineages in Squama ta to investiga te the morphological correla tions with limb-reduction. Furthermore, we provided the mitochondrial genome of the representative limbless and elongated species Dibamus bourreti(Angel, 1935) to detect selective constraints on limbless clades with published mitogenomes of other squa ma te reptiles. Our results evidenced tha t body elongation had certain negative relationship with limbreduction in Squamata lineage and Lacertilia lineage(R = –0.495, P < 2.2 e-16;R= –0.332, P = 1.1 e-13, respectively), while tail length showed slight correlation in both clades(R = 0.156, P = 4.3 e-04;R= 0.192, P = 2.1 e-05, respectively). Besides, detection demonstrated that ATP6 has experienced accelerated evolution among limbless lineages, suggesting selective pressure on mitogenomes may play an essential role in energy disparity for locomotion of limbed and limbless squamates.

Novel differential evolution algorithm with spatial evolution rules

In order to reduce the pressure of parameter selection and avoid trapping into the local optimum,a novel differential evolution( DE) algorithm without crossover rate is proposed. Through embedding cellular automata into the DE algorithm,those interactions among vectors are restricted within cellular structure of neighbors while the cell own evolution,which may be used to balance the tradeoff between exploration and exploitation and then tune the selection pressure. And further more,the orthogonal crossover without crossover rate is used instead of the binomial crossover,which can maintain the population diversity and accelerate the convergence rate. Experimental studies are carried out on a suite of 7 bound-constrained numerical benchmark functions. The results show that the proposed algorithm has better capability of maintaining the population diversity and faster convergence than the classical differential evolution and several classic differential evolution variants.

Quantification of perfluorinated compounds in atmospheric particulate shows potential connection with environmental event

A method of quantification of perfluorinated compounds(PFCs)from atmospheric particulate matter(APM)is described.A single step pretreatment method,selective pressurized liquid extraction(SPLE),was developed to reduce the high matrix background and avoid contamination from commonly used multiple sample pretreatment steps.An effective sorbent was selected to purify the PFCs during SPLE,followed by liquid chromatography-tandem mass spectrometry(LC–MS/MS),for quantification of PFCs.Conditions affecting the SPLE efficiency,including temperature,static extraction time,and number of extraction cycles used,were studied.The optimum conditions were found to be 120℃,10 min,and 3 cycles,respectively.LC-MS/MS method was developed to obtain the optimal sensitivity specific to PFCs.The method detection limits(MDLs)were 0.006 to 0.48 ng/g for the PFCs studied and the linear response range was from 0.1 to 100 ng/g.To ensure accurate values were obtained,each step of the experiment was evaluated and controlled to prevent contamination.The optimized method was tested by performing spiking experiments in natural particulate matter matrices and good rates of recovery and reproducibility were obtained for all target compounds.Finally,the method was successfully used to measure 16 PFCs in the APM samples collected in Beijing over five years from 2015 to 2019.It is observed that some PFCs follow the trend of total PFC changes,and can be attributed to the environment influencing events and policy enforcement,while others don't seem to change as much with time of the year or from year to year.

KaKs_Calculator 3.0:Calculating Selective Pressure on Coding and Non-coding Sequences

KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences.Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences,selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences.As testified on empirical data,KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of selection operated on molecular sequences,accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at a whole-genome scale.The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.

Aerobic granules cultivated and operated in continuous-flow bioreactor under particle-size selective pressure

A novel method based on the selective pressure of particle size （particle-size cultivation method, PSCM） was developed for the cultivation and operation of aerobic granular sludge in a continuous-flow reactor, and compared with the conventional method based on the selective pressure of settling velocity （settling-velocity cultivation method, SVCM）. Results indicated that aerobic granules could be cultivated in continuous operation mode by this developed method within 14 days. Although in the granulation process, under particle-size selective pressure, mixed liquor suspended solids （MLSS） in the reactor fluctuated greatly and filamentous bacteria dominated the sludge system during the initial operation days, no obvious difference in profile was found between the aerobic granules cultivated by PSCM and SVCM. Moreover, aerobic granules cultivated by PSCM presented larger diameter, lower water content and higher specific rates of nitrification, denitrifieation and phosphorus removal, but lower settling velocity. Under long term operation of more than 30 days, aerobic granules in the continuous-flow reactor could remain stable and obtain good chemical oxygen demand （COD）, NH4^＋-N, total nitrogen （TN） and total phosphorus （TP） removal. The results indicate that PSCM was dependent on the cultivation and maintenance of the stability of aerobic granules in continuous-flow bioreactors.

The mechanism shaping the logistic growth of mutation proportion in epidemics at population scale

Virus evolution is a common process of pathogen adaption to host population and environment.Frequently,a small but important fraction of virus mutations are reported to contribute to higher risks of host infection,which is one of the major determinants of infectious diseases outbreaks at population scale.The key mutations contributing to transmission advantage of a genetic variant often grow and reach fixation rapidly.Based on classic epidemiology theories of disease transmission,we proposed a mechanistic explanation of the process that between-host transmission advantage may shape the observed logistic curve of the mutation proportion in population.The logistic growth of mutation is further generalized by incorporating time-varying selective pressure to account for impacts of external factors on pathogen adaptiveness.The proposed model is implemented in real-world data of COVID-19 to capture the emerging trends and changing dynamics of the B.1.1.7 strains of SARS-CoV-2 in England.The model characterizes and establishes the underlying theoretical mechanism that shapes the logistic growth of mutation in population.

Global dispersal and adaptive evolution of domestic cattle:a genomic perspective

Domestic cattle have spread across the globe and inhabit variable and unpredictable environments.They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions,including UV exposure,diseases,and stall-feeding systems.These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations.Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations,along with the growing availability of ancient bovid DNA data,have significantly advanced our understanding of the genomic architecture,recent evolution of complex traits,common diseases,and local adaptation in cattle.Here,we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.

Isolation and Characterization of a Putative Class E Gene from Taihangia rupestris

Studies In model plants showed that SEPALLATA （SEP） genes are required for the Identification of floral organs and the determination of floral meristems In Arabidopsis. In this paper a SEP homolog, TrSEP3, was Isolated from a China-specific species, Taihangla rupestrisi Yü et LI. Phylogenetlc analysis showed that the gene belongs to the SEP3-clade of SEP （previous AGL2） subfamily. In situ hybridization was used to reveal the potential functional specification, and the results showed that TrSEP3 expression was first observed in floral meristems and then confined to the floral primordla of the three inner whorls. In the matured flower, TrSEP3 was strongly expressed In the tips of pistils and weak In stamens and petals. The evolution force analysis shows that TrSEP3 might undergo a relaxed negative selection. These results suggested that TrSEP3 may not only function In determining the identity of floral merlstems and the primordia of three inner whorls, but also function In matured reproductive organs.

Size-dependent flight capacity and propensity in a range-expanding invasive insect

For capital-breeding insects,all resources available for adult metabolic needs are accumulated during larval feeding.Therefore,body size at adult eclosion represents the total energetic capacity of the individual.For female capital breeders,body size is strongly correlated with lifetime fecundity,while in males,body size,which correlates with fitness,is less understood.In capital-breeding species with wingless,flightless,or dispersal-limited females,flight potential for male Lepidoptera has important implications for mate-finding and may be correlated with body size.At low population densities,failure to mate has been identified as an important Allee effect and can drive the success or failure of invasive species at range edges and in species of conservation concern.Th capital-breeding European subspecies of Lymantria dispar(L.),was introduced to North America in 1869 and now ranges across much of eastern North America.In L.dispar,females are flightless and mate-finding is entirely performed by males.We quantified male L.dispar flight capacity and propensity relative to morphological and physiological characteristics using fixed-arm flight mills.A range of male body sizes was produced by varying the protein content of standard artificial diets while holding other dietary components constant.Wing length,a proxy for body size,relative thorax mass,and forewing aspect were all important predictors of total flight distance and maximum speed.These results have important implications for mate-finding and invasion dynamics in L.dispar and may apply broadly to other capital-breeding insects.