Harsh environmental conditions often impose strong selection on the phenotype of natural populations through impacts on their fitness.For overwintering birds,winter is an important period for survival because the weat...Harsh environmental conditions often impose strong selection on the phenotype of natural populations through impacts on their fitness.For overwintering birds,winter is an important period for survival because the weather conditions in winter is usually severer than in other seasons and birds often suffer more thermoregulation costs while food is in short supply.Thus,the selective effect of weather conditions on phenotype in winter is expected to be strong.In this study,we examined the relationship of overwinter survival of Silver-throated Tits(Aegithalos glaucogularis)with their morphological traits under different levels of winter conditions(winters with and without snowstorms)to explore the differential selective effect of winter weather on their morphology.We found that regardless of whether the winter experienced a snowstorm,the female Silver-throated Tits with a smaller bill surface area or smaller bill depth and a smaller surface area:volume ratio were more likely to survive during the winter,which supported the hypothesis of selection for heat retention.Furthermore,the females with a smaller body length survived better than the larger females,indicating that the lesser food requirements for smaller body sizes may confer advantages during the winter when food availability was reduced.In addition,in agreement with the finding in many short-lived birds that survival rate increases with the increase of age,older(≥2-year-old)female Silver-throated Tits had higher overwinter survival than 1-year-old females.However,we did not find any correlation of morphological traits and age with survival in male Silver-throated Tits.These results illustrate differential selective effects of winter weather on female and male Silver-throated Tits and contribute to the knowledge of sex-specific selection on the phenotype of natural populations.展开更多
Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and hap...Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.展开更多
Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes...Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula. In present study, 39 531 available coding sequences (CDSs) from M. truncatula were examined for codon usage bias (CUB). Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.展开更多
Endothelial PAS domain protein 1(EPAS1), also called hypoxia-inducible factor-2, is a key regulatory factor of hypoxic responses and plays an essential role in high-altitude adaptation in mammalian species. In this ...Endothelial PAS domain protein 1(EPAS1), also called hypoxia-inducible factor-2, is a key regulatory factor of hypoxic responses and plays an essential role in high-altitude adaptation in mammalian species. In this study, polymorphisms of EPAS1 were detected in 217 individuals from 2 Tibetan pig populations and 3 low-altitude pig breeds by DNA pooling, PCR-SSCP, PCR-RFLP and DNA sequencing methods. A total of 14 synonymous polymorphisms were identified in the coding region. The analysis suggested that SNP1(G963A), SNP7(C1632T), SNP10(G1929A) and SNP11(G1947A) showed potential association with high-altitude environment because of their particular variation patterns in Tibetan pigs. Linkage disequilibrium(LD) of these SNPs was analyzed. One common LD block including 5 SNPs clustering in exon 12 was identified in all studied pig populations. Haplotype H1(AGGTC) in LD block was dominant in Tibetan pigs(76.6 and 74.2% in Linzhi(LZ) and Chayu(CY) pigs, respectively) and segregated at higher frequency than that in low-altitude pig breeds(52.3, 58.7 and 56.2% in Wuzhishan(WZS), Min(M) and Laiwu(LW) pigs, respectively), indicating that H1 may relate to adaptation to high altitude in Tibetan pigs. These findings raise hope that EPAS1 gene can be a candidate gene that involved in adaptation of high altitude in Tibetan pigs.展开更多
Darwin’s theory of evolution believes that biological evolution is a process of natural selection. This theory has been supported by much evidence, but the internal biological mechanism is not clear. Here, I elaborat...Darwin’s theory of evolution believes that biological evolution is a process of natural selection. This theory has been supported by much evidence, but the internal biological mechanism is not clear. Here, I elaborate on the cycle of potassium resources on the earth and the biological utilization and efficiency, which may be the core mechanism of natural selection and affect the evolution of organisms and the development of human society.展开更多
A proposition based on the fluctuation theorem in thermodynamics is formulated to quantitatively describe molecular evolution processes in biology. Although we cannot give full proof of its generality, we demonstrate ...A proposition based on the fluctuation theorem in thermodynamics is formulated to quantitatively describe molecular evolution processes in biology. Although we cannot give full proof of its generality, we demonstrate via computer simulation its applicability in an example of DNA in vitro evolution. According to this theorem, the evolution process is a series of exponentially rare fluctuations fixed by the force of natural selection展开更多
This paper presents the development process relating to the conceptual design of glass/renewable natural fibrereinforced polymer hybrid composite motorcycle side cover.Motorcycle side cover is a component frequently m...This paper presents the development process relating to the conceptual design of glass/renewable natural fibrereinforced polymer hybrid composite motorcycle side cover.Motorcycle side cover is a component frequently made from plastic or steel that functions on covering the motorcycle parts,components and systems such as frame,battery,electrical systems and mechanical systems.Function Analysis Systems Techniques(FAST)is used to identify the functions of motorcycle side cover.The right-side cover of motorcycle model SYM E-Bonus 110 has been physically studied to identify the competitive benchmarking criteria.The functions and competitive benchmarking criteria are then compiled and integrated with the environmental requirements to identify the Product Design Specifications(PDS).The coir fibre has been selected from six identified dominant renewable natural fibre used for automotive component through integration of Ranking Method and Quality Based Selection(QBS).Then the polypropylene matrix is selected after shortlisting the existing thermoplastic that is used with coir fibre and has high suitability for injection moulding manufacturing.The polypropylene matrix is then evaluated using Weighted Evaluation Matrix(WEM)by comparing to benchmark material which is Acrylonitrile Butadiene Styrene(ABS).After that,the conceptual design development of glass/renewable coir fibre-reinforced polypropylene motorcycle side cover is carried out using an integrated Theory of Inventive Problem Solving(TRIZ)and Morphological Chart,followed by final conceptual design selection using integration of Pugh Scoring Method and QBS.The conceptual design development intended on improving the biodegradability to reduce pollution to the environment.However,the usage of glass/coir fibre-reinforced polypropylene hybrid composite may increase the weight due to higher density.Four innovative design concepts have been developed and the selected final concept design has the most minimum number of ribs and minimum thickness with the same ratio of glass fibre and natural fibre composition.展开更多
1 Technology of natural materials Early man used conveniently shaped stones as tools. "Workshop" areas have been found with large numbers of stones, some showing signs of being worked. However, organic materials li...1 Technology of natural materials Early man used conveniently shaped stones as tools. "Workshop" areas have been found with large numbers of stones, some showing signs of being worked. However, organic materials like wood will decay under normal wet conditions in the presence of oxygen, so we won't find the same sort of evidence for wooden tools. It is safe to assume that early man used sticks as probes and clubs, and maybe even for making some sort of nestlike protection against the elements and predators, since we see chimpanzees and other animals doing this sort of thing. So wood, and ahnost certainly other plant materials such as fibrous leaves, and bone and other materials gleaned from dead animals, would be used from the earliest times. We need to know this in order to establish the idea that Man can be expected to have a long history of the use and manipulation of natural materials. This needs skills in choosing materials for certain uses on the basis of their mechanical properties, whether those properties are to do with the ease of shaping the material or the effectiveness of that material in use. Occasionally the material was chosen simply because it was readily available. If we find that a particular material was always used for a certain job, it's reasonable to deduce that Man was exerting materials selection criteria through experience.展开更多
Jack London is one of the most outstanding naturalistic writers in America who composed many renowned full-length novels.Jack London’s short story,"To Build a Fire"is a good reflection of naturalistic tende...Jack London is one of the most outstanding naturalistic writers in America who composed many renowned full-length novels.Jack London’s short story,"To Build a Fire"is a good reflection of naturalistic tendencies.It chooses"To Build a Fire"so as to fully understand his perspective of naturalism.First,it provides a brief introduction to Jack London and this short story.Second,it specifically displays naturalism in this short story from four aspects.Among them,objective authenticity is the most distinctive feature in naturalistic elements.Meanwhile,his literature creation is also deeply influenced by Darwin’s theory of evolution.It aims to investigate gold seeker’s failure that reflects natural selection and theory of survival of the fittest.Finally,it concludes that only by respecting nature can human beings survive in natural selection.Through the analysis of gold seeker’s tragic fate,it warns that the readers should master wild survival skills and live in harmony with nature.展开更多
The evolution of light-skin pigmentation among Eurasians is considered as an adaptation to the high-latitude environments.East Asians are ideal populations for studying skin color evolution because of the complex envi...The evolution of light-skin pigmentation among Eurasians is considered as an adaptation to the high-latitude environments.East Asians are ideal populations for studying skin color evolution because of the complex environment of East Asia.Here,we report a strong selection signal for the pigmentation gene phenylalanine hydroxylase(PAH)in light-skinned Han Chinese individuals.The intron mutation rs10778203 in PAH is enriched in East Asians and is significantly associated with skin color of the back of the hand in Han Chinese males(P<0.05).In vitro luciferase and transcription factor binding assays show that the ancestral allele of rs10778203 could bind to SMAD2 and has a significant enhancer activity for PAH.However,the derived T allele(the major allele in East Asians)of rs10778203 decreases the binding activity of transcription factors and enhancer activity.Meanwhile,the derived T allele of rs10778203 shows a weaker ultraviolet radiation response in A375 cells and zebrafish embryos.Furthermore,rs10778203 decreases melanin production in transgenic zebrafish embryos after ultraviolet B(UVB)treatment.Collectively,PAH is a potential pigmentation gene that regulates skin tanning ability.Natural selection has enriched the adaptive allele,resulting in weakened tanning ability in East Asians,suggesting a unique genetic mechanism for evolutionary skin lightening in East Asians.展开更多
Tibeto-Burman(TB)people have endeavored to adapt to the hypoxic,cold,and high-UV high-altitude environments in the Tibetan Plateau and complex disease exposures in lowland rainforests since the late Paleolithic period...Tibeto-Burman(TB)people have endeavored to adapt to the hypoxic,cold,and high-UV high-altitude environments in the Tibetan Plateau and complex disease exposures in lowland rainforests since the late Paleolithic period.However,the full landscape of genetic history and biological adaptation of geographically diverse TB-speaking people,as well as their interaction mechanism,remain unknown.Here,we generate a whole-genome meta-database of 500 individuals from 39 TB-speaking populations and present a comprehensive landscape of genetic diversity,admixture history,and differentiated adaptative features of geographically different TB-speaking people.We identify genetic differentiation related to geography and language among TB-speaking people,consistent with their differentiated admixture process with incoming or indigenous ancestral source populations.A robust genetic connection between the Tibetan-Yi corridor and the ancient Yellow River people supports their Northern China origin hypothesis.We finally report substructure-related differentiated biological adaptative signatures between highland Tibetans and Loloish speakers.Adaptative signatures associated with the physical pigmentation(EDAR and SLC24A5)and metabolism(ALDH9A1)are identified in Loloish people,which differed from the high-altitude adaptative genetic architecture in Tibetan.TB-related genomic resources provide new insights into the genetic basis of biological adaptation and better reference for the anthropologically informed sampling design in biomedical and genomic cohort research.展开更多
The evolution and maintenance of color clines is a classic topic of research in evolutionary ecology.However,studies analyzing the temporal dynamics of such clines are much less frequent,due to the difficulty of obtai...The evolution and maintenance of color clines is a classic topic of research in evolutionary ecology.However,studies analyzing the temporal dynamics of such clines are much less frequent,due to the difficulty of obtaining reliable data about past color distributions along environmen-tal gradients.In this article,we describe a case of decades-long temporal stability and directional change in a color cline of the marine snail Littorina saxatilis along the coastal inlet of the Ria de Vigo(NW Spain).L.saxatilis from this area shows a clear color cline with 3 distinct areas from the innermost to the more wave-exposed localities of the Ria:the inner,protected localities show an abundance of fawn-like individuals;the intermediate localities show a high diversity of colors;and the outer,wave-exposed localities show populations with a high frequency of a black and lineated morph.We compare data from the 1970s and 2022 in the same localities,showing that the cline has kept relatively stable for at least over half a century,except for some directional change and local variability in the frequency of certain morphs.Multiple regression analyses and biodiversity measures are presented to provide clues into the selective pressures that might be involved in the maintenance of this color cline.Future research avenues to properly test the explanatory power of these selective agents as well as the possible origins of the cline are discussed.展开更多
Solar energy,which is essential for the origin and evolution of all life forms on Earth,can be objectively recorded through attributes such as climatic ambient temperature(CAT),ultraviolet radiation(UVR),and sunlight ...Solar energy,which is essential for the origin and evolution of all life forms on Earth,can be objectively recorded through attributes such as climatic ambient temperature(CAT),ultraviolet radiation(UVR),and sunlight duration(SD).These attributes have specific geographical variations and may cause different adaptation traits.However,the adaptation profile of each attribute and the selective role of solar energy as a whole during human evolution remain elusive.Here,we performed a genome-wide adaptation study with respect to CAT,UVR,and SD using the Human Genome Diversity Project-Centre Etude Polymorphism Humain(HGDP-CEPH)panel data.We singled out CAT as the most important driving force with the highest number of adaptive loci(6 SNPs at the genome-wide 1×10^(-7)level;401 at the suggestive 1×10^(-5)level).Five of the six genomewide significant adaptation SNPs were successfully replicated in an independent Chinese population(N=1395).The corresponding 316 CAT adaptation genes were mostly involved in development and immunity.In addition,265(84%)genes were related to at least one genome-wide association study(GWAS)-mapped human trait,being significantly enriched in anthropometric loci such as those associated with body mass index(χ^(2);P<0.005),immunity,metabolic syndrome,and cancer(χ^(2);P<0.05).For these adaptive SNPs,balancing selection was evident in Euro-Asians,whereas obvious positive and/or purifying selection was observed in Africans.Taken together,our study indicates that CAT is the most important attribute of solar energy that has driven genetic adaptation in development and immunity among global human populations.It also supports the non-neutral hypothesis for the origin of disease-predisposition alleles in common diseases.展开更多
With the support by the National Natural Science Foundation of China,a study by the research group led by Prof.Tu Pengfei(屠鹏飞)from the School of Pharmaceutical Sciences,Peking University demonstrates that natural s...With the support by the National Natural Science Foundation of China,a study by the research group led by Prof.Tu Pengfei(屠鹏飞)from the School of Pharmaceutical Sciences,Peking University demonstrates that natural small-molecule sappanone A directly targets IMPDH2to block its activity,展开更多
Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.I...Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.In this study,by combining whole-genome resequencing and genome-wide association studies we identified a novel locus,Time of Flowering 5(Tof5),which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean.By genomic,genetic and transgenic analyses we showed that Tof5 en-codes a homolog of Arabidopsis thaliana FRUITFULL(FUL).Importantly,further analyses suggested that different alleles of Tof5 have undergone parallel selection.The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean,while Tof5H2 allele was naturally selected in wild soybean,and in each case facilitating adaptation to high latitudes.Moreover,we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter.In turn,Tof5 physically associates with the promoters of two important FLOWERING LOCUS T(FT),FT2a and FT5a,to upregulate their transcription and promote flowering under long photoperiods.Collectively,ourfindings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.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
One of the main topics in population genetics is identi- fication of adaptive selection among populations. For this purpose, population history should be correctly inferred to evaluate the effect of random drift and e...One of the main topics in population genetics is identi- fication of adaptive selection among populations. For this purpose, population history should be correctly inferred to evaluate the effect of random drift and exclude it in selection identification. With the rapid progress in genomics in the past decade, vast genome- scale variations are available for population genetic analysis, which however requires more sophisticated models to infer species' demographic history and robust methods to detect local adaptation. Here we aim to review what have been achieved in the fields of demographic modeling and selection detection. We summarize their rationales, implementations, and some classical applications. We also propose that some widely-used methods can be improved in both theoreti- cal and practical aspects in near future.展开更多
In the field of anthropology, the uniparerttally inherited Y chromosome has long been used to trace the paternal lineage of the populations and to understand differences in migration and population genetics between ma...In the field of anthropology, the uniparerttally inherited Y chromosome has long been used to trace the paternal lineage of the populations and to understand differences in migration and population genetics between males and females, with additional advantages of small effective population size, suf- ficient markers, and population-specific haplotype distribution (Jobling and Tyler-Smith, 1995; Jin and Su, 2000; Underhill et al., 2000). Many such population studies have rested on the assumption that all the Y chromosome markers in the non- recombination regions are selectively neutral (Jobling and Tyler-Smith, 2003).展开更多
Motivated by recent understandings in the stochastic natures of gene expression, biochemical signaling, and spontaneous reversible epigenetic switchings, we study a simple deterministic cell population dynamics in whi...Motivated by recent understandings in the stochastic natures of gene expression, biochemical signaling, and spontaneous reversible epigenetic switchings, we study a simple deterministic cell population dynamics in which subpopulations grow with different rates and individual cells can bi-directionally switch between a small number of different epigenetic phenotypes. Two theories in the past, the population dynamics and thermodynamics of master equations, separately defined two important concepts in mathematical terms: thefitness in the former and the (non- adiabatic) entropy production in the latter. Both of them play important roles in the evolution of the cell population dynamics. The switching sustains the variations among the subpopulation growth, thus sustains continuous natural selection. As a form of Price's equation, the fitness increases with (i) natural selection through variations and (ii) a positive covariance between the per capita growth and switching, which represents a Lamarchian-like behavior. A negative covariance balances the natural selection in a fitness steady state —— "the red queen" scenario. At the same time the growth keeps the proportions of subpopulations away from the "intrinsic" switching equilibrium of individual cells, thus leads to a continuous entropy production. A covariance, between the per capita growth rate and the "chemical potential" of subpopulation, counteracts the entropy production. Analytical results are obtained for the limiting cases of growth dominating switching and vice versa.展开更多
There is increasing awareness of biocomplexity as a field of study,although there are some disagreements about its definition among biologists.The science of biocomplexity has been influenced greatly by the emergence ...There is increasing awareness of biocomplexity as a field of study,although there are some disagreements about its definition among biologists.The science of biocomplexity has been influenced greatly by the emergence of the science of complexity,which aims to solve complicated problems in complex systems.In this paper,I review the basic concepts and scientific problems of biocomplexity.I argue that biological systems are adaptive complex systems that tend to become more complicated over time.I hypothesize that complexity is favored by natural selection.There are two relatively independent evolutionary templates for complexity in biological systems:gene-guided and neural-guided systems.In general,biology has been overly influenced by gene-dominant evolution theory,which cannot account for the complex behaviors,social structures,and ecosystems that exist.Sustained energy intake,non-polynomial(NP)-hard problems and stability(e.g.thermodynamic,non-linear and evolutionary stability)are probably the three most important properties of biological systems.Total work is not equivalent to the energy input(non-equivalence rule)in biological systems because the input energy is re-used.The total work can be measured using the order energy(ordergy),a function of energy input and the efficiency of energy transformation.Hierarchy may be essential in solving NP-hard problems and in reducing the instability of non-linearity in biological systems.展开更多
基金supported by the National Natural Science Foundation of China(31970421,31472011,31101644)。
文摘Harsh environmental conditions often impose strong selection on the phenotype of natural populations through impacts on their fitness.For overwintering birds,winter is an important period for survival because the weather conditions in winter is usually severer than in other seasons and birds often suffer more thermoregulation costs while food is in short supply.Thus,the selective effect of weather conditions on phenotype in winter is expected to be strong.In this study,we examined the relationship of overwinter survival of Silver-throated Tits(Aegithalos glaucogularis)with their morphological traits under different levels of winter conditions(winters with and without snowstorms)to explore the differential selective effect of winter weather on their morphology.We found that regardless of whether the winter experienced a snowstorm,the female Silver-throated Tits with a smaller bill surface area or smaller bill depth and a smaller surface area:volume ratio were more likely to survive during the winter,which supported the hypothesis of selection for heat retention.Furthermore,the females with a smaller body length survived better than the larger females,indicating that the lesser food requirements for smaller body sizes may confer advantages during the winter when food availability was reduced.In addition,in agreement with the finding in many short-lived birds that survival rate increases with the increase of age,older(≥2-year-old)female Silver-throated Tits had higher overwinter survival than 1-year-old females.However,we did not find any correlation of morphological traits and age with survival in male Silver-throated Tits.These results illustrate differential selective effects of winter weather on female and male Silver-throated Tits and contribute to the knowledge of sex-specific selection on the phenotype of natural populations.
基金This study was supported by the Ministry of Higher Education,Malaysia(FRGS0322-SG-1/2013)Universiti Malaysia Sabah(GUG0521-2/2020).
文摘Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.
基金supported by the National Basic Research Program of China (2014CB138702)the National Natural Science Foundation of China (31502001)
文摘Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula. In present study, 39 531 available coding sequences (CDSs) from M. truncatula were examined for codon usage bias (CUB). Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.
基金supported by the National Natural Science Foundation of China(31272403)the Determination of Molecular Characterization for Genetically Modified Organism,China(2013ZX08012-002)the Livestock and Poultry Sharing Platform in China(2013)
文摘Endothelial PAS domain protein 1(EPAS1), also called hypoxia-inducible factor-2, is a key regulatory factor of hypoxic responses and plays an essential role in high-altitude adaptation in mammalian species. In this study, polymorphisms of EPAS1 were detected in 217 individuals from 2 Tibetan pig populations and 3 low-altitude pig breeds by DNA pooling, PCR-SSCP, PCR-RFLP and DNA sequencing methods. A total of 14 synonymous polymorphisms were identified in the coding region. The analysis suggested that SNP1(G963A), SNP7(C1632T), SNP10(G1929A) and SNP11(G1947A) showed potential association with high-altitude environment because of their particular variation patterns in Tibetan pigs. Linkage disequilibrium(LD) of these SNPs was analyzed. One common LD block including 5 SNPs clustering in exon 12 was identified in all studied pig populations. Haplotype H1(AGGTC) in LD block was dominant in Tibetan pigs(76.6 and 74.2% in Linzhi(LZ) and Chayu(CY) pigs, respectively) and segregated at higher frequency than that in low-altitude pig breeds(52.3, 58.7 and 56.2% in Wuzhishan(WZS), Min(M) and Laiwu(LW) pigs, respectively), indicating that H1 may relate to adaptation to high altitude in Tibetan pigs. These findings raise hope that EPAS1 gene can be a candidate gene that involved in adaptation of high altitude in Tibetan pigs.
文摘Darwin’s theory of evolution believes that biological evolution is a process of natural selection. This theory has been supported by much evidence, but the internal biological mechanism is not clear. Here, I elaborate on the cycle of potassium resources on the earth and the biological utilization and efficiency, which may be the core mechanism of natural selection and affect the evolution of organisms and the development of human society.
基金Project supported by the National Natural Science Foundation of China (Grant No. 10721403)the National Basic Research Program of China (Grant No. 2007CB814802)the Jun-Zheng Foundation at Peking University
文摘A proposition based on the fluctuation theorem in thermodynamics is formulated to quantitatively describe molecular evolution processes in biology. Although we cannot give full proof of its generality, we demonstrate via computer simulation its applicability in an example of DNA in vitro evolution. According to this theorem, the evolution process is a series of exponentially rare fluctuations fixed by the force of natural selection
文摘This paper presents the development process relating to the conceptual design of glass/renewable natural fibrereinforced polymer hybrid composite motorcycle side cover.Motorcycle side cover is a component frequently made from plastic or steel that functions on covering the motorcycle parts,components and systems such as frame,battery,electrical systems and mechanical systems.Function Analysis Systems Techniques(FAST)is used to identify the functions of motorcycle side cover.The right-side cover of motorcycle model SYM E-Bonus 110 has been physically studied to identify the competitive benchmarking criteria.The functions and competitive benchmarking criteria are then compiled and integrated with the environmental requirements to identify the Product Design Specifications(PDS).The coir fibre has been selected from six identified dominant renewable natural fibre used for automotive component through integration of Ranking Method and Quality Based Selection(QBS).Then the polypropylene matrix is selected after shortlisting the existing thermoplastic that is used with coir fibre and has high suitability for injection moulding manufacturing.The polypropylene matrix is then evaluated using Weighted Evaluation Matrix(WEM)by comparing to benchmark material which is Acrylonitrile Butadiene Styrene(ABS).After that,the conceptual design development of glass/renewable coir fibre-reinforced polypropylene motorcycle side cover is carried out using an integrated Theory of Inventive Problem Solving(TRIZ)and Morphological Chart,followed by final conceptual design selection using integration of Pugh Scoring Method and QBS.The conceptual design development intended on improving the biodegradability to reduce pollution to the environment.However,the usage of glass/coir fibre-reinforced polypropylene hybrid composite may increase the weight due to higher density.Four innovative design concepts have been developed and the selected final concept design has the most minimum number of ribs and minimum thickness with the same ratio of glass fibre and natural fibre composition.
文摘1 Technology of natural materials Early man used conveniently shaped stones as tools. "Workshop" areas have been found with large numbers of stones, some showing signs of being worked. However, organic materials like wood will decay under normal wet conditions in the presence of oxygen, so we won't find the same sort of evidence for wooden tools. It is safe to assume that early man used sticks as probes and clubs, and maybe even for making some sort of nestlike protection against the elements and predators, since we see chimpanzees and other animals doing this sort of thing. So wood, and ahnost certainly other plant materials such as fibrous leaves, and bone and other materials gleaned from dead animals, would be used from the earliest times. We need to know this in order to establish the idea that Man can be expected to have a long history of the use and manipulation of natural materials. This needs skills in choosing materials for certain uses on the basis of their mechanical properties, whether those properties are to do with the ease of shaping the material or the effectiveness of that material in use. Occasionally the material was chosen simply because it was readily available. If we find that a particular material was always used for a certain job, it's reasonable to deduce that Man was exerting materials selection criteria through experience.
文摘Jack London is one of the most outstanding naturalistic writers in America who composed many renowned full-length novels.Jack London’s short story,"To Build a Fire"is a good reflection of naturalistic tendencies.It chooses"To Build a Fire"so as to fully understand his perspective of naturalism.First,it provides a brief introduction to Jack London and this short story.Second,it specifically displays naturalism in this short story from four aspects.Among them,objective authenticity is the most distinctive feature in naturalistic elements.Meanwhile,his literature creation is also deeply influenced by Darwin’s theory of evolution.It aims to investigate gold seeker’s failure that reflects natural selection and theory of survival of the fittest.Finally,it concludes that only by respecting nature can human beings survive in natural selection.Through the analysis of gold seeker’s tragic fate,it warns that the readers should master wild survival skills and live in harmony with nature.
基金supported by the National Natural Science Foundation of China(32070579 and 32370664 to Z.Y.,31871449 and 32170813 to J.C.)the Natural Science Foundation of Henan(222300420067 to Z.Y.)+3 种基金State Key Laboratory of Genetic Resources and Evolution Grant(GREKF20-13 to Z.Y)Innovation and Entrepreneurship Training Program(2022cxcy568,2022cxcy717 and 2023cxcy475 to Z.Y.)the 1.3·5 project for disciplines of excellence of West China Hospital,Sichuan University(ZYGD23026 and 2024HXFH035)Science and Technologyy Department of Sichuan province(2024NSFSC0651).
文摘The evolution of light-skin pigmentation among Eurasians is considered as an adaptation to the high-latitude environments.East Asians are ideal populations for studying skin color evolution because of the complex environment of East Asia.Here,we report a strong selection signal for the pigmentation gene phenylalanine hydroxylase(PAH)in light-skinned Han Chinese individuals.The intron mutation rs10778203 in PAH is enriched in East Asians and is significantly associated with skin color of the back of the hand in Han Chinese males(P<0.05).In vitro luciferase and transcription factor binding assays show that the ancestral allele of rs10778203 could bind to SMAD2 and has a significant enhancer activity for PAH.However,the derived T allele(the major allele in East Asians)of rs10778203 decreases the binding activity of transcription factors and enhancer activity.Meanwhile,the derived T allele of rs10778203 shows a weaker ultraviolet radiation response in A375 cells and zebrafish embryos.Furthermore,rs10778203 decreases melanin production in transgenic zebrafish embryos after ultraviolet B(UVB)treatment.Collectively,PAH is a potential pigmentation gene that regulates skin tanning ability.Natural selection has enriched the adaptive allele,resulting in weakened tanning ability in East Asians,suggesting a unique genetic mechanism for evolutionary skin lightening in East Asians.
基金the National Natural Science Foundation of China(82202078)the Center for Archaeological Science of Sichuan University(23SASA01).
文摘Tibeto-Burman(TB)people have endeavored to adapt to the hypoxic,cold,and high-UV high-altitude environments in the Tibetan Plateau and complex disease exposures in lowland rainforests since the late Paleolithic period.However,the full landscape of genetic history and biological adaptation of geographically diverse TB-speaking people,as well as their interaction mechanism,remain unknown.Here,we generate a whole-genome meta-database of 500 individuals from 39 TB-speaking populations and present a comprehensive landscape of genetic diversity,admixture history,and differentiated adaptative features of geographically different TB-speaking people.We identify genetic differentiation related to geography and language among TB-speaking people,consistent with their differentiated admixture process with incoming or indigenous ancestral source populations.A robust genetic connection between the Tibetan-Yi corridor and the ancient Yellow River people supports their Northern China origin hypothesis.We finally report substructure-related differentiated biological adaptative signatures between highland Tibetans and Loloish speakers.Adaptative signatures associated with the physical pigmentation(EDAR and SLC24A5)and metabolism(ALDH9A1)are identified in Loloish people,which differed from the high-altitude adaptative genetic architecture in Tibetan.TB-related genomic resources provide new insights into the genetic basis of biological adaptation and better reference for the anthropologically informed sampling design in biomedical and genomic cohort research.
基金support from the Ministerio de Ciencia e Innovacion(PID2021-124930NB-I00)Xunta de Galicia(GRC,ED431C 2020-05)+2 种基金Centro singular de Investigacion de Galicia accreditation 2019-2022,and the European Union(European Regional Development Fund-ERDF)Juan Galindo was funded by a JIN project(Jovenes Investigadores,Ministerio de Ciencia,Innovacion y Universidades,RTI2018-101274-J-100)Juan Gefaell was funded by a Xunta de Galicia Predoctoral Research Contract(ED481A-2021/274).
文摘The evolution and maintenance of color clines is a classic topic of research in evolutionary ecology.However,studies analyzing the temporal dynamics of such clines are much less frequent,due to the difficulty of obtaining reliable data about past color distributions along environmen-tal gradients.In this article,we describe a case of decades-long temporal stability and directional change in a color cline of the marine snail Littorina saxatilis along the coastal inlet of the Ria de Vigo(NW Spain).L.saxatilis from this area shows a clear color cline with 3 distinct areas from the innermost to the more wave-exposed localities of the Ria:the inner,protected localities show an abundance of fawn-like individuals;the intermediate localities show a high diversity of colors;and the outer,wave-exposed localities show populations with a high frequency of a black and lineated morph.We compare data from the 1970s and 2022 in the same localities,showing that the cline has kept relatively stable for at least over half a century,except for some directional change and local variability in the frequency of certain morphs.Multiple regression analyses and biodiversity measures are presented to provide clues into the selective pressures that might be involved in the maintenance of this color cline.Future research avenues to properly test the explanatory power of these selective agents as well as the possible origins of the cline are discussed.
基金supported by grants from the National Key R&D Program of China(Grant No.2018YFE0203700)the National Natural Science Foundation of China(Grant No.81402747)+2 种基金the Applied Research Project on Nonprofit Technology of Zhejiang Province(Grant No.LGF20H260009)the KC Wong Magna Fund in Ningbo University,Chinasupported by CUHK VC discretionary fund,China。
文摘Solar energy,which is essential for the origin and evolution of all life forms on Earth,can be objectively recorded through attributes such as climatic ambient temperature(CAT),ultraviolet radiation(UVR),and sunlight duration(SD).These attributes have specific geographical variations and may cause different adaptation traits.However,the adaptation profile of each attribute and the selective role of solar energy as a whole during human evolution remain elusive.Here,we performed a genome-wide adaptation study with respect to CAT,UVR,and SD using the Human Genome Diversity Project-Centre Etude Polymorphism Humain(HGDP-CEPH)panel data.We singled out CAT as the most important driving force with the highest number of adaptive loci(6 SNPs at the genome-wide 1×10^(-7)level;401 at the suggestive 1×10^(-5)level).Five of the six genomewide significant adaptation SNPs were successfully replicated in an independent Chinese population(N=1395).The corresponding 316 CAT adaptation genes were mostly involved in development and immunity.In addition,265(84%)genes were related to at least one genome-wide association study(GWAS)-mapped human trait,being significantly enriched in anthropometric loci such as those associated with body mass index(χ^(2);P<0.005),immunity,metabolic syndrome,and cancer(χ^(2);P<0.05).For these adaptive SNPs,balancing selection was evident in Euro-Asians,whereas obvious positive and/or purifying selection was observed in Africans.Taken together,our study indicates that CAT is the most important attribute of solar energy that has driven genetic adaptation in development and immunity among global human populations.It also supports the non-neutral hypothesis for the origin of disease-predisposition alleles in common diseases.
文摘With the support by the National Natural Science Foundation of China,a study by the research group led by Prof.Tu Pengfei(屠鹏飞)from the School of Pharmaceutical Sciences,Peking University demonstrates that natural small-molecule sappanone A directly targets IMPDH2to block its activity,
基金supported by the National Natural Science Foundation of China(grant nos.32090065 and 32001508 to L.D.,32090064 and 31725021 to F.K.,31930083 to B.L,31901568 to Q.C,32022062 to S.Lu.,32001502 to Y,Z)and also supported by the Major Program of Guangdong Basic and Applied FResearch(grant no.2019B030302006 to F.K.andB.L).
文摘Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor.In particular,the genetic basis of the adaptation in wild soybean remains poorly understood.In this study,by combining whole-genome resequencing and genome-wide association studies we identified a novel locus,Time of Flowering 5(Tof5),which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean.By genomic,genetic and transgenic analyses we showed that Tof5 en-codes a homolog of Arabidopsis thaliana FRUITFULL(FUL).Importantly,further analyses suggested that different alleles of Tof5 have undergone parallel selection.The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean,while Tof5H2 allele was naturally selected in wild soybean,and in each case facilitating adaptation to high latitudes.Moreover,we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter.In turn,Tof5 physically associates with the promoters of two important FLOWERING LOCUS T(FT),FT2a and FT5a,to upregulate their transcription and promote flowering under long photoperiods.Collectively,ourfindings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.
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.
文摘One of the main topics in population genetics is identi- fication of adaptive selection among populations. For this purpose, population history should be correctly inferred to evaluate the effect of random drift and exclude it in selection identification. With the rapid progress in genomics in the past decade, vast genome- scale variations are available for population genetic analysis, which however requires more sophisticated models to infer species' demographic history and robust methods to detect local adaptation. Here we aim to review what have been achieved in the fields of demographic modeling and selection detection. We summarize their rationales, implementations, and some classical applications. We also propose that some widely-used methods can be improved in both theoreti- cal and practical aspects in near future.
基金supported by the National Excellent Youth Science Foundation of China (No. 31222030)the National Natural Science Foundation of China (Nos. 31071098 and 91131002)+2 种基金the Shanghai Rising-Star Program (No. 12QA1400300)the Shanghai Commission of Education Research Innovation Key Project (No. 11zz04)the Shanghai Professional Development Funding (No. 2010001)
文摘In the field of anthropology, the uniparerttally inherited Y chromosome has long been used to trace the paternal lineage of the populations and to understand differences in migration and population genetics between males and females, with additional advantages of small effective population size, suf- ficient markers, and population-specific haplotype distribution (Jobling and Tyler-Smith, 1995; Jin and Su, 2000; Underhill et al., 2000). Many such population studies have rested on the assumption that all the Y chromosome markers in the non- recombination regions are selectively neutral (Jobling and Tyler-Smith, 2003).
文摘Motivated by recent understandings in the stochastic natures of gene expression, biochemical signaling, and spontaneous reversible epigenetic switchings, we study a simple deterministic cell population dynamics in which subpopulations grow with different rates and individual cells can bi-directionally switch between a small number of different epigenetic phenotypes. Two theories in the past, the population dynamics and thermodynamics of master equations, separately defined two important concepts in mathematical terms: thefitness in the former and the (non- adiabatic) entropy production in the latter. Both of them play important roles in the evolution of the cell population dynamics. The switching sustains the variations among the subpopulation growth, thus sustains continuous natural selection. As a form of Price's equation, the fitness increases with (i) natural selection through variations and (ii) a positive covariance between the per capita growth and switching, which represents a Lamarchian-like behavior. A negative covariance balances the natural selection in a fitness steady state —— "the red queen" scenario. At the same time the growth keeps the proportions of subpopulations away from the "intrinsic" switching equilibrium of individual cells, thus leads to a continuous entropy production. A covariance, between the per capita growth rate and the "chemical potential" of subpopulation, counteracts the entropy production. Analytical results are obtained for the limiting cases of growth dominating switching and vice versa.
文摘There is increasing awareness of biocomplexity as a field of study,although there are some disagreements about its definition among biologists.The science of biocomplexity has been influenced greatly by the emergence of the science of complexity,which aims to solve complicated problems in complex systems.In this paper,I review the basic concepts and scientific problems of biocomplexity.I argue that biological systems are adaptive complex systems that tend to become more complicated over time.I hypothesize that complexity is favored by natural selection.There are two relatively independent evolutionary templates for complexity in biological systems:gene-guided and neural-guided systems.In general,biology has been overly influenced by gene-dominant evolution theory,which cannot account for the complex behaviors,social structures,and ecosystems that exist.Sustained energy intake,non-polynomial(NP)-hard problems and stability(e.g.thermodynamic,non-linear and evolutionary stability)are probably the three most important properties of biological systems.Total work is not equivalent to the energy input(non-equivalence rule)in biological systems because the input energy is re-used.The total work can be measured using the order energy(ordergy),a function of energy input and the efficiency of energy transformation.Hierarchy may be essential in solving NP-hard problems and in reducing the instability of non-linearity in biological systems.