Multiphoton microscopy is the enabling tool for biomedical research,but the aberrations of biological tissues have limited its imaging performance.Adaptive optics(AO)has been developed to partially overcome aberration...Multiphoton microscopy is the enabling tool for biomedical research,but the aberrations of biological tissues have limited its imaging performance.Adaptive optics(AO)has been developed to partially overcome aberration to restore imaging performance.For indirect AO,algorithm is the key to its successful implementation.Here,based on the fact that indirect AO has an analogy to the black-box optimization problem,we successfully apply the covariance matrix adaptation evolution strategy(CMA-ES)used in the latter,to indirect AO in multiphoton microscopy(MPM).Compared with the traditional genetic algorithm(GA),our algorithm has a greater improvement in convergence speed and convergence accuracy,which provides the possibility of realizing real-time dynamic aberration correction for deep in vivo biological tissues.展开更多
Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundan...Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Until now,the Ulva mutabilis genome is the only Ulva genome to have been sequenced.To obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from U.mutabilis,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in U.mutabilis.We detected 63 orthologs in U.mutabilis that were considered to be under positive selection.Functional analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.展开更多
Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wil...Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.展开更多
The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins...The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins(Hbs)serve as a paradigm of this process,with structural and functional canalization underpinning their exceptional aerobic capacity and elevational diversification.Despite significant advances of globins in our understanding of avian aerobic adaptation,a comprehensive synthesis of functional diversity,molecular evolution,and structural innovation is essential to fully elucidate their canalized roles in O_(2)homeostasis.Integrating perspectives on globin functional diversity and structural evolution,this review examines how chance(mutation/fixation biases)and contingency(historical genetic/epistatic constraints)shape Hb divergence and parallelism,thereby bridging molecular mechanisms with physiological adaptation in birds.We highlight how avian Hbs,canalized through compensatory substitutions and allosteric regulation,achieves a balance between evolutionary robustness and adaptive plasticity.However,critical gaps remain persist:the roles of understudied globins(e.g.,neuroglobin,globin E)and the mechanisms of genetic assimilation in migratory taxa.We propose an integrative framework that incorporates ecological divergence(elevation,flight endurance),phylogenetic timescales,and systems biology to unravel how canalization directs adaptive compromise.By focusing on birds within the amniotes,this synthesis advances a cohesive model for vertebrate evolution,wherein canalized globins reconcile metabolic precision with ecological innovation.Ultimately,this review refines hypotheses of O_(2)cascade evolution and calls for cross-disciplinary studies to decode the genetic and physiological architecture underlying adaptive canalization in extreme environments.展开更多
Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer project...Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer projects.The habitat transfers from brackish water to freshwater zones of Taenioides sp.have caused severe damage to Chinese aquatic ecosystems in recent years.Unfortunately,the molecular mechanism underlying freshwater invasion remains poorly understood.Considering changes of environmental factors,especially salinity,are bound to adjust the demands for energy affected by mitochondria via oxidative phosphorylation,13 Amblyopinae mitogenomes were compared,including the newly assembled Taenioides sp.mitogenome in this study.Comparative mitogenomic analyses revealed a highly conserved structure,composition and arrangements,with the exception of variable control region(CR).All of the CRs possessed tandem repeat sequences except Trypauchenopsis sp.G341,differing in motifs and number of copies,which was the dominant factor resulting in length heterogeneity of CR.The phylogenetic trees reconfirmed the paraphyletic origin of Amblyopinae with respect to Oxudercinae,supporting that these two subfamilies should be merged as an expansion of phenotypic variation within the“terrestrial goby”clade.Furthermore,four protein coding genes(COI,ND3,ND5 and Cyt b)in Taenioides sp.mitogenome have experienced adaptive evolution,indicating their important roles in enhancing the efficiency of ATP production to cope with the osmotic regulation adjustment and reach its current widespread distribution in multiple inland freshwaters of China.These results revealed the functional importance of mitochondrial genes,and provided fresh insights into the molecular mechanisms underlying the freshwater invasion.Also,our results may provide critical reference value for the future control of other invasive species.展开更多
Understanding how ecological processes affect phenotypic evolution has been and continues to be an important goal of ecology and evolutionary biology. Interspecific competition for resources can be a selective force d...Understanding how ecological processes affect phenotypic evolution has been and continues to be an important goal of ecology and evolutionary biology. Interspecific competition for resources can be a selective force driving phenotypic differentiation that reduces competition among sympatric species (character divergence), enabling closely-related species to coexist. However, although patterns of character divergence are well documented in both empirical and theoretical researches, how local adaptation to abiotic environment affects trait evolution in the face of interspecific competition is less known. Here, we investigate how patterns in morphological traits of 2 parapatric frog species, Feirana quadranus and F. taihangnica, vary among allopatric and sympatric regions using range-wide data derived from extensive field surveys. Feirana quadranus was overall larger than F. taihangnica in body size (i.e., snout-vent length [SVL]), and the difference between SVL of both species in sympatry was larger than that in allopatry. From allopatry to sympatry, the 2 species diverged in foot and hand traits, but converged in eye size and interorbital span, even when we controlled for the effects of geographic gradients. Sympatric divergence in SVL, hand and foot traits is likely acting as a case of evolutionary shift caused by interspecific competition. In contrast, sympatric convergence of eye-related traits may derive at least partly from adaptation to local environments. These results imply the relative roles of interspecific competition and local adaptation in shaping phenotypic diversification. Our findings illustrate how traits evolve in parapatric species pair due to sympatric divergent and convergent evolution. It thus provides insights into understanding underlying evolutionary processes of parapatric species, that is, competition and local adaptation.展开更多
For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bron...For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.展开更多
Figs and fig pollinators are one of the few classic textbook examples of obligate pollination mutualism.The specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources...Figs and fig pollinators are one of the few classic textbook examples of obligate pollination mutualism.The specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat changes.However,there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig pollinators.In fig syconia,there are also non-pollinator species.The non-pollinator species differ in their evolutionary and life histories from pollinators.We conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published genome.The pollinators colonized the figs approximately 66.9 million years ago,consistent with the origin of host figs.Compared with nonpollinators,many more genes in pollinators were subject to relaxed selection.Seven genes were absent in pollinators in response to environmental stress and immune activation.Pollinators had more streamlined gene repertoires in the innate immune system,chemosensory toolbox,and detoxification system.Our results provide genomic evidence for the differentiation between pollinators and nonpollinators.The data suggest that owing to the long-term adaptation to the fig,some genes related to functions no longer required are absent in pollinators.展开更多
Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas...Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information.We also sequenced the genome of 81specimens,representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera,i.e.,Alienauroa,Conothoa,Lagotona,Ochotona,and Pika,consistent with morphometric data.Morphologically,Alienauroa and Ochotona had similar traits,including smaller size and earlier divergence time compared to other pikas.Consistently,the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera.Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics,including several visual and hearingrelated genes.Analysis of shared amino acid substitutions and positively selected genes(PSGs)in Alienauroa and Ochotona identified two genes,i.e.,mitochondrial function-related TSFM(p.Q155E)and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas,and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake.Alienauroa and Ochotona individuals mostly inhabit different environments(e.g.,subtropical forests)than other pikas,suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments.This study increases our understanding of the evolutionary history of pikas.展开更多
Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa.However,genome-wide recombination landscape has not been reported in ciliates and it remains unkn...Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa.However,genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates:the synaptonemal complex(SC)-independent meiosis and the nuclear dimorphism.Here,we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid progeny.We detect 1021 crossover(CO)events(35.8 per meiosis),corresponding to an overall CO rate of 9.9 cM/Mb.However,gene conversion by non-crossover is rare(1.03 per meiosis)and not biased towards G or C alleles.Consistent with the reported roles of SC in CO interference,we find no obvious sign of CO interference.CO tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric regions.Gene ontology analyses show that CO hotspots are strongly associated with genes responding to environmental changes.We discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.展开更多
Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topograp...Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topographical map,and an improved adaptive differential evolution(IADE)algorithm is proposed for single UAV multitasking.As an optimized problem,the efficiency of using standard differential evolution to obtain the global optimal solution is very low to avoid this problem.Therefore,the algorithm adopts the mutation factor and crossover factor into dynamic adaptive functions,which makes the crossover factor and variation factor can be adjusted with the number of population iteration and individual fitness value,letting the algorithm exploration and development more reasonable.The experimental results implicate that the IADE algorithm has better performance,higher convergence and efficiency to solve the multitasking problem compared with other algorithms.展开更多
In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most ...In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most terrestrial plants, has been considered to be conserved; however, recent controversy regarding rbcL conservation has appeared since it was proposed to be under natural selection within all principal lineages of land plants. In this study, by examining the variation of DNA and protein sequences among 17 species in the family Tamaricaceae, three nonsynonymous mutations were identified to be under positive selection. The favored sites were located in the alph-helix domains of Rubisco, with decreased hydrophobicity and increased entropy, which could facilitate C〇 2 penetration into the active site of Rubisco. We also found that the expression level of rbcL in different genotypes of Reaumuria soongarica shifted in response to various stresses such as drought, temperature, salt, and light. This study not only sheds light on the functional/structural features of Rubisco in the evolution scenarios from 〇 3-like into C4 in Tamaricaceae but also provides useful information on directing genetic performance to enhance photosynthesis efficiency of desert plants for sustaining fragile desert ecosystems; fur-thermore, it promotes the ability to cope with desert aridification and global warming.展开更多
基金supported by the National Natural Science Foundation of China(Nos.62075135 and 61975126)the Science,Technology and Innovation Commission of Shenzhen Municipality(Nos.JCYJ20190808174819083 and JCYJ20190808175201640)。
文摘Multiphoton microscopy is the enabling tool for biomedical research,but the aberrations of biological tissues have limited its imaging performance.Adaptive optics(AO)has been developed to partially overcome aberration to restore imaging performance.For indirect AO,algorithm is the key to its successful implementation.Here,based on the fact that indirect AO has an analogy to the black-box optimization problem,we successfully apply the covariance matrix adaptation evolution strategy(CMA-ES)used in the latter,to indirect AO in multiphoton microscopy(MPM).Compared with the traditional genetic algorithm(GA),our algorithm has a greater improvement in convergence speed and convergence accuracy,which provides the possibility of realizing real-time dynamic aberration correction for deep in vivo biological tissues.
基金Foundation item:The National Key Research and Development Program of China under contract No.2016YFC1402102the Central Public-interest Scientific Institution Basal Research Fund,CAFS under contract Nos 2020TD19 and 2020TD27+3 种基金the Major Scientific and Technological Innovation Project of Shandong Provincial Key Research and Development Program under contract No.2019JZZY020706the National Natural Science Foundation of China under contract No.31770393the Earmarked Fund for China Agriculture Research System under contract No.CARS-50the Taishan Scholars Funding of Shandong Province.
文摘Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Until now,the Ulva mutabilis genome is the only Ulva genome to have been sequenced.To obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from U.mutabilis,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in U.mutabilis.We detected 63 orthologs in U.mutabilis that were considered to be under positive selection.Functional analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.
基金funded by the National Natural Science Foundation of China(grant no.32270238 and 31870311).
文摘Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.
基金supported by the National Natural Science Foundation of China(NSFC 31900313)to X.Z.the Central guide local science and technology development funds(XZ202301YD0007C)to L.Y.+1 种基金NSFC(32471572)National Key Research and Development Program of China(2024YFC2310303)to D.L。
文摘The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins(Hbs)serve as a paradigm of this process,with structural and functional canalization underpinning their exceptional aerobic capacity and elevational diversification.Despite significant advances of globins in our understanding of avian aerobic adaptation,a comprehensive synthesis of functional diversity,molecular evolution,and structural innovation is essential to fully elucidate their canalized roles in O_(2)homeostasis.Integrating perspectives on globin functional diversity and structural evolution,this review examines how chance(mutation/fixation biases)and contingency(historical genetic/epistatic constraints)shape Hb divergence and parallelism,thereby bridging molecular mechanisms with physiological adaptation in birds.We highlight how avian Hbs,canalized through compensatory substitutions and allosteric regulation,achieves a balance between evolutionary robustness and adaptive plasticity.However,critical gaps remain persist:the roles of understudied globins(e.g.,neuroglobin,globin E)and the mechanisms of genetic assimilation in migratory taxa.We propose an integrative framework that incorporates ecological divergence(elevation,flight endurance),phylogenetic timescales,and systems biology to unravel how canalization directs adaptive compromise.By focusing on birds within the amniotes,this synthesis advances a cohesive model for vertebrate evolution,wherein canalized globins reconcile metabolic precision with ecological innovation.Ultimately,this review refines hypotheses of O_(2)cascade evolution and calls for cross-disciplinary studies to decode the genetic and physiological architecture underlying adaptive canalization in extreme environments.
基金The National Natural Science Foundation of China under contract Nos 42171069 and 41976121.
文摘Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer projects.The habitat transfers from brackish water to freshwater zones of Taenioides sp.have caused severe damage to Chinese aquatic ecosystems in recent years.Unfortunately,the molecular mechanism underlying freshwater invasion remains poorly understood.Considering changes of environmental factors,especially salinity,are bound to adjust the demands for energy affected by mitochondria via oxidative phosphorylation,13 Amblyopinae mitogenomes were compared,including the newly assembled Taenioides sp.mitogenome in this study.Comparative mitogenomic analyses revealed a highly conserved structure,composition and arrangements,with the exception of variable control region(CR).All of the CRs possessed tandem repeat sequences except Trypauchenopsis sp.G341,differing in motifs and number of copies,which was the dominant factor resulting in length heterogeneity of CR.The phylogenetic trees reconfirmed the paraphyletic origin of Amblyopinae with respect to Oxudercinae,supporting that these two subfamilies should be merged as an expansion of phenotypic variation within the“terrestrial goby”clade.Furthermore,four protein coding genes(COI,ND3,ND5 and Cyt b)in Taenioides sp.mitogenome have experienced adaptive evolution,indicating their important roles in enhancing the efficiency of ATP production to cope with the osmotic regulation adjustment and reach its current widespread distribution in multiple inland freshwaters of China.These results revealed the functional importance of mitochondrial genes,and provided fresh insights into the molecular mechanisms underlying the freshwater invasion.Also,our results may provide critical reference value for the future control of other invasive species.
基金the National Natural Science Foundation of China(31572290,31770568,and 31270568)National Key Research and Development Plan(2016YFC 0503303).The funding bodies had no role in the design of the study and collection,analysis,and interpretation of data and in writing the manuscript.
文摘Understanding how ecological processes affect phenotypic evolution has been and continues to be an important goal of ecology and evolutionary biology. Interspecific competition for resources can be a selective force driving phenotypic differentiation that reduces competition among sympatric species (character divergence), enabling closely-related species to coexist. However, although patterns of character divergence are well documented in both empirical and theoretical researches, how local adaptation to abiotic environment affects trait evolution in the face of interspecific competition is less known. Here, we investigate how patterns in morphological traits of 2 parapatric frog species, Feirana quadranus and F. taihangnica, vary among allopatric and sympatric regions using range-wide data derived from extensive field surveys. Feirana quadranus was overall larger than F. taihangnica in body size (i.e., snout-vent length [SVL]), and the difference between SVL of both species in sympatry was larger than that in allopatry. From allopatry to sympatry, the 2 species diverged in foot and hand traits, but converged in eye size and interorbital span, even when we controlled for the effects of geographic gradients. Sympatric divergence in SVL, hand and foot traits is likely acting as a case of evolutionary shift caused by interspecific competition. In contrast, sympatric convergence of eye-related traits may derive at least partly from adaptation to local environments. These results imply the relative roles of interspecific competition and local adaptation in shaping phenotypic diversification. Our findings illustrate how traits evolve in parapatric species pair due to sympatric divergent and convergent evolution. It thus provides insights into understanding underlying evolutionary processes of parapatric species, that is, competition and local adaptation.
文摘For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.
基金supported by the National Natural Science Foundation of China(31830084,31970440 and 32070466)supported by“the Fundamental Research Funds for the Central Universities”,Nankai University(96172158,96173250 and 91822294)。
文摘Figs and fig pollinators are one of the few classic textbook examples of obligate pollination mutualism.The specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat changes.However,there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig pollinators.In fig syconia,there are also non-pollinator species.The non-pollinator species differ in their evolutionary and life histories from pollinators.We conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published genome.The pollinators colonized the figs approximately 66.9 million years ago,consistent with the origin of host figs.Compared with nonpollinators,many more genes in pollinators were subject to relaxed selection.Seven genes were absent in pollinators in response to environmental stress and immune activation.Pollinators had more streamlined gene repertoires in the innate immune system,chemosensory toolbox,and detoxification system.Our results provide genomic evidence for the differentiation between pollinators and nonpollinators.The data suggest that owing to the long-term adaptation to the fig,some genes related to functions no longer required are absent in pollinators.
基金supported by the National Natural Science Foundation of China(31470110,31970399)China National GeneBank(CNGB)。
文摘Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information.We also sequenced the genome of 81specimens,representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera,i.e.,Alienauroa,Conothoa,Lagotona,Ochotona,and Pika,consistent with morphometric data.Morphologically,Alienauroa and Ochotona had similar traits,including smaller size and earlier divergence time compared to other pikas.Consistently,the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera.Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics,including several visual and hearingrelated genes.Analysis of shared amino acid substitutions and positively selected genes(PSGs)in Alienauroa and Ochotona identified two genes,i.e.,mitochondrial function-related TSFM(p.Q155E)and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas,and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake.Alienauroa and Ochotona individuals mostly inhabit different environments(e.g.,subtropical forests)than other pikas,suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments.This study increases our understanding of the evolutionary history of pikas.
基金supported by the Wuhan Branch,Supercomputing Center,Chinese Academy of Sciences,Chinasupported by the National Aquatic Biological Resource Center(NABRC)+4 种基金supported by the Bureau of Frontier Sciences and Education,Chinese Academy of Sciences(ZDBS-LY-SM026)the National Natural Science Foundation of China(32370457,32122015,32130011,31900316,and 31900339)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB0480000)PJA3 grant of ARC Foundation(ARCPJA2021060003830)Equipes 2022 grant of Foundation Recherche Medicale(EQU202203014651).
文摘Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa.However,genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates:the synaptonemal complex(SC)-independent meiosis and the nuclear dimorphism.Here,we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid progeny.We detect 1021 crossover(CO)events(35.8 per meiosis),corresponding to an overall CO rate of 9.9 cM/Mb.However,gene conversion by non-crossover is rare(1.03 per meiosis)and not biased towards G or C alleles.Consistent with the reported roles of SC in CO interference,we find no obvious sign of CO interference.CO tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric regions.Gene ontology analyses show that CO hotspots are strongly associated with genes responding to environmental changes.We discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.
文摘Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topographical map,and an improved adaptive differential evolution(IADE)algorithm is proposed for single UAV multitasking.As an optimized problem,the efficiency of using standard differential evolution to obtain the global optimal solution is very low to avoid this problem.Therefore,the algorithm adopts the mutation factor and crossover factor into dynamic adaptive functions,which makes the crossover factor and variation factor can be adjusted with the number of population iteration and individual fitness value,letting the algorithm exploration and development more reasonable.The experimental results implicate that the IADE algorithm has better performance,higher convergence and efficiency to solve the multitasking problem compared with other algorithms.
基金supported by the National Natural Science Foundation of China(NSFC,Grant Nos.31370395 and 31500266)the"One Hundred Talents"project of the Chinese Academy of Sciences(Grant No.29Y127E71)
文摘In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most terrestrial plants, has been considered to be conserved; however, recent controversy regarding rbcL conservation has appeared since it was proposed to be under natural selection within all principal lineages of land plants. In this study, by examining the variation of DNA and protein sequences among 17 species in the family Tamaricaceae, three nonsynonymous mutations were identified to be under positive selection. The favored sites were located in the alph-helix domains of Rubisco, with decreased hydrophobicity and increased entropy, which could facilitate C〇 2 penetration into the active site of Rubisco. We also found that the expression level of rbcL in different genotypes of Reaumuria soongarica shifted in response to various stresses such as drought, temperature, salt, and light. This study not only sheds light on the functional/structural features of Rubisco in the evolution scenarios from 〇 3-like into C4 in Tamaricaceae but also provides useful information on directing genetic performance to enhance photosynthesis efficiency of desert plants for sustaining fragile desert ecosystems; fur-thermore, it promotes the ability to cope with desert aridification and global warming.
