Extreme heat and chronic water scarcity present formidable challenges to large desert-dwelling mammals.In addition to camels,antelopes within the Hippotraginae and Alcelaphinae subfamilies also exhibit remarkable phys...Extreme heat and chronic water scarcity present formidable challenges to large desert-dwelling mammals.In addition to camels,antelopes within the Hippotraginae and Alcelaphinae subfamilies also exhibit remarkable physiological and genetic specializations for desert survival.Among them,the critically endangered addax(Addax nasomaculatus)represents the most desert-adapted antelope species.However,the evolutionary and molecular mechanisms underlying desert adaptations remain largely unexplored.Herein,a high-quality genome assembly of the addax was generated to investigate the molecular evolution of desert adaptation in camels and desert antelopes.Comparative genomic analyses identified 136 genes harboring convergent amino acid substitutions implicated in crucial biological processes,including water reabsorption,fat metabolism,and stress response.Notably,a convergent R146S amino acid mutation in the prostaglandin EP2 receptor gene PTGER2 significantly reduced receptor activity,potentially facilitating large-mammal adaptation to arid environments.Lineage-specific innovations were also identified in desert antelopes,including previously uncharacterized conserved non-coding elements.Functional assays revealed that several of these elements exerted significant regulatory effects in vitro,suggesting potential roles in adaptive gene expression.Additionally,signals of introgression and variation in genetic load were observed,indicating their possible influence on desert adaptation.These findings provide insights into the sequential evolutionary processes that drive physiological resilience in arid environments and highlight the importance of convergent evolution in shaping adaptive traits in large terrestrial mammals.展开更多
High-altitude and marine mammals inhabit distinct ecosystems but share a common challenge:hypoxia.To survive in low-oxygen environments,these species have evolved similar phenotypic pulmonary adaptations,characterized...High-altitude and marine mammals inhabit distinct ecosystems but share a common challenge:hypoxia.To survive in low-oxygen environments,these species have evolved similar phenotypic pulmonary adaptations,characterized by a high density of elastic fibers.In this study,we explored the molecular mechanisms underlying these adaptations,focusing on pulmonary fibrosis and hypoxia tolerance through comparative genomics and convergent evolution analyses.We observed significant expansions and contractions in certain gene families across both high-altitude and marine mammals,closely associated with processes involved in pulmonary fibrosis.Notably,members of the keratin gene family,such as KRT17 and KRT14,appear to be associated with the development of the dense elastic fiber phenotype observed in the lungs of hypoxia-tolerant mammals.Through selection pressure and amino acid substitution analyses,we identified multiple genes exhibiting convergent accelerated evolution,positive selection,and amino acid substitution in these species,associated with adaptation to hypoxic environments.Specifically,the convergent evolution of ZFP36L1,FN1,and NEDD9 was found to contribute to the high density of elastic fibers in the lungs of both high-altitude and marine mammals,facilitating their hypoxia tolerance.Additionally,we identified convergent amino acid substitutions and gene loss events associated with sperm development,differentiation,and spermatogenesis,such as amino acid substitutions in SLC26A3 and pseudogenization of CFAP47,as confirmed by PCR.These genetic alterations may be linked to changes in the reproductive capabilities of these animals.Overall,this study offers novel perspectives on the genetic and molecular adaptations of high-altitude and marine mammals to hypoxic environments,with a particular emphasis on pulmonary fibrosis.展开更多
Convergent and parallel evolution occur more frequently than previously thought.Here,we focus on the evolutionary adaptations of angiosperms at sub-zero temperatures.We begin by introducing the history of research on ...Convergent and parallel evolution occur more frequently than previously thought.Here,we focus on the evolutionary adaptations of angiosperms at sub-zero temperatures.We begin by introducing the history of research on convergent and parallel evolution,defining all independent similarities as convergent evolu-tion.Our analysis reveals that frost zones(periodic or constant),which cover 49.1%of Earth’s land surface,host 137 angiosperm families,with over 90%of their species thriving in these regions.In this context,we revisit the global biogeography and evolutionary trajectories of plant traits,such as herbaceous form and deciduous leaves,that are thought to be evasion strategies for frost adaptation.At the physiological and mo-lecular levels,many angiosperms have independently evolved cold acclimation mechanisms through mul-tiple pathways in addition to the well-characterized C-repeat binding factor/dehydration-responsive element binding protein 1(CBF/DREB1)regulatory pathway.These convergent adaptations have occurred across various molecular levels,including amino acid substitutions and changes in gene duplication and expression within the same or similar functional pathways;however,identical amino acid changes are rare.Our results also highlight the prevalence of polyploidy in frost zones and the occurrence of paleopoly-ploidization events during global cooling.These patterns suggest repeated evolution in cold climates.Finally,we discuss plant domestication and predict climate zone shifts due to global warming and their ef-fects on plant migration and in situ adaptation.Overall,the integration of ecological and molecular perspec-tives is essential for understanding and forecasting plant responses to climate change.展开更多
Angraecum sesquipedale,also known as Darwin’s orchid,possesses an exceptionally long nectar spur.Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis,later identifi...Angraecum sesquipedale,also known as Darwin’s orchid,possesses an exceptionally long nectar spur.Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis,later identified as Xanthopan praedicta.In this plant-pollinator interaction,the A.sesquipedale flower emits a complex blend of scent compounds dominated by diurnally regulated oximes(R_(1)R_(2)C=N-OH)to attract crepuscular and nocturnal pollinators.The molecular mechanism of oxime biosynthesis remains unclear in orchids.Here,we present the chromosome-level genome of A.sesquipedale.The haploid genome size is 2.10 Gb and represents 19 pseudochromosomes.Cytochrome P450 encoding genes of the CYP79 family known to be involved in oxime biosynthesis in seed plants are not present in the A.sesquipedale genome nor the genomes of other members of the orchid family.Metabolomic analysis of the A.sesquipedale flower revealed a substantial release of oximes at dusk during the blooming stage.By integrating metabolomic and transcriptomic correlation approaches,flavin-containing monooxygenases(FMOs)encoded by six tandem-repeat genes in the A.sesquipedale genome are identified as catalyzing the formation of oximes present.Further in vitro and in vivo assays confirm the function of FMOs in the oxime biosynthesis.We designate these FMOs as orchid oxime synthases 1-6.The evolutionary aspects related to the CYP79 gene losses and neofunctionalization of FMO-catalyzed biosynthesis of oximes in Darwin’s orchid provide new insights into the convergent evolution of biosynthetic pathways.展开更多
The yellow boxfish(Ostracion cubicus)exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics,including a fused dermal plate.Contradictory evolutiona...The yellow boxfish(Ostracion cubicus)exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics,including a fused dermal plate.Contradictory evolutionary evidence hinders true classification of O.cubicus.To clarify its evolutionary position within Tetraodontiformes,a chromosome-level genome assembly was generated,representing the most contiguous and complete genome to date for this lineage.Notably,O.cubicus possessed the largest genome within the order Tetraodontiformes,primarily due to extensive transposable element expansion.Phylogenetic analysis based on 19 whole genomes and 131 mitochondrial genomes resolved Tetraodontiformes into three major sister groups(Ostraciidae-Molidae,Tetraodontidae,and Balistidae-Monacanthidae).Comparative genomic evidence indicated that O.cubicus diverged early from the common ancestor of modern Tetraodontiformes and retained the highest number of HOX genes among surveyed taxa.Although overall genomic architecture was largely conserved,certain genetic and environmental changes may have contributed to its phenotypic adaptations,including climate cooling during the Miocene-Pliocene Transition,recent DNA and long interspersed nuclear element(LINE)transposon bursts,lineage-specific chromosomal rearrangements,and gene family expansion.Many positively selected genes and rapidly evolving genes were associated with skeletal development,including bmp7,egf7,and bmpr2.Transcriptomic comparisons between carapace and tail skin revealed various candidate genes and pathways related to carapace formation,such as postn,scpp1,and components of the TGF-βsignaling pathway.A derived amino acid substitution in eda,coupled with protein structural modeling,suggested potential molecular convergence in dermal plate formation among teleosts.These findings provide novel insights into the genomic and developmental basis of carapace evolution and coral reef-adaptation in O.cubicus,offering a strong case for evolutionary balance between genomic conservation with regulatory innovation to achieve coral reef specialization.展开更多
Gut microbiota plays a critical role in host physiology and health.The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche.Multiple factors such as host die...Gut microbiota plays a critical role in host physiology and health.The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche.Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota.However,the relative contribution of each factor in shaping the structure of gut microbiota remains unclear.The giant(Ailuropoda melanoleuca)and red(Ailurus styani)pandas belong to different families of order Carnivora.They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution.Here,we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing.We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives.This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea.Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis.These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.展开更多
Azoreductases are involved in the bioremediation by bacteria of azo dyes found in waste water.In the gut flora,they activate azo pro-drugs,which are used for treatment of inflammatory bowel disease,releasing the activ...Azoreductases are involved in the bioremediation by bacteria of azo dyes found in waste water.In the gut flora,they activate azo pro-drugs,which are used for treatment of inflammatory bowel disease,releasing the active component 5-aminosalycilic acid.The bacterium P.aeruginosa has three azoreductase genes,paAzoR1,paAzoR2 and paAzoR3,which as recombinant enzymes have been shown to have different substrate specificities.The mechanism of azoreduction relies upon tautomerisation of the substrate to the hydrazone form.We report here the characterization of the P.aeruginosa azoreductase enzymes,including determining their thermostability,cofactor preference and kinetic constants against a range of their favoured substrates.The expression levels of these enzymes during growth of P.aeruginosa are altered by the presence of azo substrates.It is shown that enzymes that were originally described as azoreductases,are likely to act as NADH quinone oxidoreductases.The low sequence identities observed among NAD(P)H quinone oxidoreductase and azoreductase enzymes suggests convergent evolution.展开更多
Directed evolution(DE)inspired by natural evolution(NE)has been achieving tremendous successes in protein/enzyme engineering.However,the conventional"one-protein-for-one-task"DE cannot match the"multi-p...Directed evolution(DE)inspired by natural evolution(NE)has been achieving tremendous successes in protein/enzyme engineering.However,the conventional"one-protein-for-one-task"DE cannot match the"multi-proteins-for-multi-tasks"NE in terms of screening throughput and efficiency,thus often failing to meet the fast-growing demands for biocatalysts with desired properties.In this study,we design a novel"multi-enzymes-for-multi-substrates"(MEMS)DE model and establish the proof-ofconcept by running a NE-mimicking and higher-throughput screening on the basis of"two-P450 s-against-seven-substrates"(2P×7S)in one pot.With the multiplied throughput and improved hit rate,we witness a series of convergent evolution events of the two archetypal cytochrome P450 enzymes(P450 BM3 and P450 cam)in laboratory.It is anticipated that the new strategy of MEMS DE will find broader application for a larger repertoire of enzymes in the future.Furthermore,structural and substrate docking analysis of the two functionally convergent P450 variants provide important insights into how distinct P450 active-sites can reach a common catalytic goal.展开更多
Remarkable geometrical similarities are found in digging claws of soil burrowing animals,in spite of the fact that they evolved independently.Based on convergent evolution theory,this study innovatively proposed a bio...Remarkable geometrical similarities are found in digging claws of soil burrowing animals,in spite of the fact that they evolved independently.Based on convergent evolution theory,this study innovatively proposed a bionic engineering perspective that focuses on general and analogous geometrical characteristics of soil animals.It was observed that soil animals with powerful burrowing ability have analogous serrated structures on their digging claws.Taking soil imprinting toothed wheel as the research object,the hypothesis that special serrated structures have the potential of reducing penetrating resistance from soil and enhancing digging efficiency for soil engaging component was investigated.The convergent evolution inspired bionic serrated structures were utilized for the design of cutting edge on toothed wheel.Then,a toothed wheel that mounted with the conventional tooth and a bionic tooth were manufactured and tested in the soil bin.Results showed that special bionic serrated structure could reduce the required draft force for toothed wheel;meanwhile increase the depth and volume of prepared micro-basin.It was found that the soil-penetrating mechanism of the bionic toothed wheel behaved as saw cutting that similar to the digging behavior of soil burrowing animals.Geometry of serrated structure has the ability to maximum stress concentrations in soil,thus increased the tendency of soil material to fail.These results indicate that the convergent evolution inspired bionic approach is novel and advantageous for the design of new soil engaging implements for working quality optimization and forward resistance reduction.展开更多
The Ashy-headed Laughingthrush (Argya cinereifrons), a species endemic to Sri Lanka, has been historically considered a laughingthrush in the genus Garrulax. However, based on phylogenetic evidence, recent studies hav...The Ashy-headed Laughingthrush (Argya cinereifrons), a species endemic to Sri Lanka, has been historically considered a laughingthrush in the genus Garrulax. However, based on phylogenetic evidence, recent studies have suggested a new classification for the species under the genus Argya (true babblers). Despite the genetic signal showing affinity to true babblers Argya, as its common name suggests, the Ashy-headed Laughingthrush (AHLT) shows remarkable morphological similarities to other laughingthrushes of the Indo-Himalayan region. Here we attempted to address this incongruence in phenotypic and phylogenetic signals in this species by reconstructing the molecular phylogeny of babblers and comparing that with the key morphological, plumage, and vocal features of the two concerned groups. We hypothesized that the convergence of phenotype and vocalization of Garrulax in the wet evergreen forests of the Indian mainland and AHLT in the wet tropical rainforests of southern Sri Lanka has historically confused the taxonomists. The phylogenetic relationships were reconstructed using Bayesian inference using four mitochondrial and seven nuclear gene regions. The molecular phylogenetic tree placed the AHLT with India's Large Grey Babbler (A. malcolmi) as the sister taxon within the genus Argya. The hierarchical clustering based on body size, shape, plumage colour, and vocal properties resulted in the inconsistent placement of ALTH with babblers or laughingthrushes. Therefore, an incongruence in phenotype and genotype is observed. Our findings show that the convergent patterns of phenotypic evolution can confuse both historic and recent taxonomic delimitations in highly divergent groups such as Asian babblers.展开更多
In the tails of dromaeosaurid dinosaurs and rhamphorhynchid pterosaurs, elongate osteological rods extend anteriorly from the chevrons and the prezygapophyses. These caudal rods are positioned in parallel and are stac...In the tails of dromaeosaurid dinosaurs and rhamphorhynchid pterosaurs, elongate osteological rods extend anteriorly from the chevrons and the prezygapophyses. These caudal rods are positioned in parallel and are stacked dorsoventrally. The fully articulated and three-dimensionally preserved caudal series of some dromaeosaurid specimens show that individually these caudal rods were flexible, not rigid as previously thought. However, examination of the arrangement of the caudal rods in cross-section indicates that the combined effect of multiple caudal rods did provide substantial rigidity in the dorsoventral, but not in the lateral, plane. The results of digital muscle reconstructions confirm that dromaeosaurids and rhamphorhynchids also shared greatly reduced caudofemoral muscles in the anterior tail region. The striking similarities between the tails of dromaeosaurids and rhamphorhynchids suggest that both evolved under similar behavioral and biomechanical pressures. Combined with recent discoveries of primitive deinonychosaurs that phylogenetically bracket the evolution of dromaeosaurid caudal rods between two arboreal gliding/flying forms, these results are evidence that the unique caudal morphologies of dromaeosaurids and rhamphorhynchids were both adaptations for an aerial lifestyle.展开更多
Multiple primary lung cancer(MPLC)is an increasingly prevalent subtype of lung cancer.According to recent genomic studies,the different lesions of a single MPLC patient exhibit functional similarities that may reflect...Multiple primary lung cancer(MPLC)is an increasingly prevalent subtype of lung cancer.According to recent genomic studies,the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary convergence.We perform whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion found.Using our own and other relevant public data,evolutionary tree reconstruction reveals that cancer driver gene mutations occurred at the early trunk,indicating evolutionary contingency rather than adaptive convergence.Additionally,tumors from the same MPLC patient are as genetically diverse as those from different patients,while within-tumor genetic heterogeneity is significantly lower.Furthermore,the aberrant molecular functions enriched in mutated genes for a sample show a strong overlap with other samples from the same tumor,but not with samples from other tumors or other patients.Overall,there is no evidence of adaptive convergence during the evolution of MPLC.Most importantly,the similar between-tumor diversity and between-patient diversity suggest that personalized therapies may not adequately account for the genetic diversity among different tumors in an MPLC patient.To fully exploit the strategic value of precision medicine,targeted therapies should be designed and delivered on a per-lesion basis.展开更多
Morphological analyses are critical to quantify phenotypic variation,identify taxa,inform phylogenetic relationships,and shed light on evolutionary patterns.This work is particularly important in groups that display g...Morphological analyses are critical to quantify phenotypic variation,identify taxa,inform phylogenetic relationships,and shed light on evolutionary patterns.This work is particularly important in groups that display great morphological disparity.Such is the case in geomyoid rodents,a group that includes 2 of the most species-rich families of rodents in North America:the Geomyidae(pocket gophers)and the Heteromyidae(kangaroo rats,pocket mice,and their relatives).We assessed variation in skull morphology(including both shape and size)among geomyoids to test the hypothesis that there are statistically significant differences in skull measurements at the family,genus,and species levels.Our sample includes 886 specimens representing all geomyoid genera and 39 species.We used the geometric mean to compare size across taxa.We used 14 measurements of the cranium and lower jaw normalized for size to compare shape among and within taxa.Our results show that skull measurements enable the distinction of geomyoids at the family,genus,and species levels.There is a larger amount of size variation within Geomyidae than within Heteromyidae.Our phylomorphospace analysis shows that the skull shape of the common ancestor of all geomyoids was more similar to the common ancestor of heteromyids than that of geomyids.Geomyid skulls display negative allometry whereas heteromyid skulls display positive allometry.Within heteromyids,dipodomyines,and non-dipodomyines show significantly different allometric patterns.Future analyses including fossils will be necessary to test our evolutionary hypotheses.展开更多
Glutamate decarboxylase （GAD） has been found in animal and higher plant tissues as well as in yeasts and microorganisms. In animals the enzyme plays an important role in central nervous system activity because the e...Glutamate decarboxylase （GAD） has been found in animal and higher plant tissues as well as in yeasts and microorganisms. In animals the enzyme plays an important role in central nervous system activity because the enzyme substrate glutamic acid is a mediator of excitation process and the product, gamma-aminobutyric acid, is the most important mediator of inhibition process in the central nervous system. GAD65 is one form of the glutamate decarboxylases （GAD）, GAD65 has been identified as a major autoantigen in type 1 diabetes, so the GAD65 gene of porcine was cloned by RT-PCR method to construct phylogenetic tree, the homology of 13 glutamate decarboxylases （GAD） of different origin was analyzed by multiple alignment.展开更多
Examples of evolution,extinction and homoplasy of the larger benthic foraminifera(LBF)occur throughout their history.Since the Carboniferous,LBF have thrived in carbonate-rich tropical and subtropical shallow-marine s...Examples of evolution,extinction and homoplasy of the larger benthic foraminifera(LBF)occur throughout their history.Since the Carboniferous,LBF have thrived in carbonate-rich tropical and subtropical shallow-marine shelf environments.Their high abundance and diversity are due primarily to their extraordinary ability to inhabit a range of ecological niches and by hosting a variety of symbionts.Attaining relatively large,centimetre-scale sizes,made some forms very specialized and vulnerable to rapid ecological changes.For this reason,some LBF have shown a tendency to suffer periodically during major extinctions,especially when environmental conditions have changed rapidly and/or substantially.This,however,makes them valuable biostratigraphic microfossils and,in addition,gives invaluable insight into the spatial and temporal process of biological evolution,such as convergent/homoplasy and homology/iterative evolution.Here the evolutionary behavior of two important morphological types that occurred throughout the history of the LBF are discussed,namely the planispiral-fusiform test as typified by the fusulinids in the Late Paleozoic and the alveolinids in the Mid-Cretaceous and Neogene,and the three-layered discoid lenticular test as characterized by the orbitoids in the Mid-to Late Cretaceous,the orthophragminids in the Paleogene,and lepidocyclinids in the Oligocene to Quaternary.Understanding the propensity of these forms to convergent and iterative evolution,with the repeated re-occurrence of certain morphological features,is essential in understanding and constructing their phylogenetic relationships more generally within the main groups of the LBF.The insights gained from the history of these LBF have wider implications,and provide a more general understanding of the impacts of climate and ecological changes as driving forces for biological evolution.展开更多
Dormancy represents a fascinating adaptive strategy for organisms to survive in unforgiving environments.After a period of dormancy,organisms often exhibit exceptional resilience.This period is typically divided into ...Dormancy represents a fascinating adaptive strategy for organisms to survive in unforgiving environments.After a period of dormancy,organisms often exhibit exceptional resilience.This period is typically divided into hibernation and aestivation based on seasonal patterns.However,the mechanisms by which organisms adapt to their environments during dormancy,as well as the potential relationships between different states of dormancy,deserve further exploration.Here,we selected Perccottus glenii and Protopterus annectens as the primary subjects to study hibernation and aestivation,respectively.Based on histological and transcriptomic analysis of multiple organs,we discovered that dormancy involved a coordinated functional response across organs.Enrichment analyses revealed noteworthy disparities between the two dormant species in their responses to extreme temperatures.Notably,similarities in gene expression patterns pertaining to energy metabolism,neural activity,and biosynthesis were noted during hibernation,suggesting a potential correlation between hibernation and aestivation.To further explore the relationship between these two phenomena,we analyzed other dormancy-capable species using data from publicly available databases.This comparative analysis revealed that most orthologous genes involved in metabolism,cell proliferation,and neural function exhibited consistent expression patterns during dormancy,indicating that the observed similarity between hibernation and aestivation may be attributable to convergent evolution.In conclusion,this study enhances our comprehension of the dormancy phenomenon and offers new insights into the molecular mechanisms underpinning vertebrate dormancy.展开更多
Batesian mimics are harmless prey species that resemble dangerous ones （models）, and thus receive protection from predators. How such adaptive resemblances evolve is a classical problem in evolutionary biology. Mimi...Batesian mimics are harmless prey species that resemble dangerous ones （models）, and thus receive protection from predators. How such adaptive resemblances evolve is a classical problem in evolutionary biology. Mimicry is typically thought to be difficult to evolve, especially if the model and mimic produce the convergent phenotype through different proximate mecha- nisms. However, mimicry may evolve more readily if mimic and model share similar pathways for producing the convergent phenotype. In such cases, these pathways can be co-opted in ancestral mimic populations to produce high-fidelity mimicry with- out the need for major evolutionary innovations. Here, we show that a Batesian mimic, the scarlet kingsnake Larnpropeltis elap-soides, produces its coloration using the same physiological mechanisms as does its model, the eastern coral snake Micrurus fulvius. Therefore, precise color mimicry may have been able to evolve easily in this system. Generally, we know relatively little about the proximate mechanisms underlying mimicry .展开更多
Centromere positioning and organization are crucial for genome evolution;however,research on centro-mere biology is largely influenced by the quality of available genome assemblies.Here,we combined Oxford Nanopore and...Centromere positioning and organization are crucial for genome evolution;however,research on centro-mere biology is largely influenced by the quality of available genome assemblies.Here,we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum(TM-1)and Gossypium barbadense(3-79).Compared with previously published reference genomes,our assemblies show substantial improvements,with the contig N50 improved by 4.6-fold and 5.6-fold,respectively,and thus represent the most complete cotton genomes to date.These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G.hirsutum and G.barbadense,respectively.Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize(CRM)and Tekay long terminal repeat families,and the CRM family reshapes the centromere structure of the At subgenome after polyploidization.These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes,ensuring centromere function and genome stability.In addition,the reposi-tioning and high sequence divergence of centromeres between G.hirsutum and G.barbadense have contributed to speciation and centromere diversity.This study sheds light on centromere evolution in a sig-nificant crop and provides an alternative approach for exploring the evolution of polyploid plants.展开更多
For the last 40 years,the study of cooperative breeding(CB)in birds has proceeded primarily in the context of discovering the ecological,geographical,and behavioral drivers of helping.The advent of molecular tools in ...For the last 40 years,the study of cooperative breeding(CB)in birds has proceeded primarily in the context of discovering the ecological,geographical,and behavioral drivers of helping.The advent of molecular tools in the early 1990s assisted in clarifying the relatedness of helpers to those helped,in some cases,confirming predictions of kin selection theory.Methods for genome-wide analysis of sequence variation,gene expression,and epigenetics promise to add new dimensions to our understanding of avian CB,primarily in the area of molecular and developmental correlates of delayed breeding and dispersal,as well as the ontogeny of achieving parental status in nature.Here,we outline key ways in which modern-omics approaches,in particular genome sequencing,transcriptomics,and epigenetic profiling such as ATAC-seq,can be used to add a new level of ana-lysis of avian CB.Building on recent and ongoing studies of avian social behavior and sociogenom-ics,we review how high-throughput sequencing of a focal species or clade can provide a robust foundation for downstream,context-dependent destructive and non-destructive sampling of spe-cific tissues or physiological states in the field for analysis of gene expression and epigenetics.-Omics approaches have the potential to inform not only studies of the diversification of CB over evolutionary time,but real-time analyses of behavioral interactions in the field or lab.Sociogenomics of birds represents a new branch in the network of methods used to study CB,and can help clarify ways in which the different levels of analysis of CB ultimately interact in novel and unexpected ways.展开更多
基金supported by the National Key R&D Program of China(2022YFF1000100)Shaanxi Program for Support of Top-notch Young ProfessionalsFundamental Research Funds for the Central Universities。
文摘Extreme heat and chronic water scarcity present formidable challenges to large desert-dwelling mammals.In addition to camels,antelopes within the Hippotraginae and Alcelaphinae subfamilies also exhibit remarkable physiological and genetic specializations for desert survival.Among them,the critically endangered addax(Addax nasomaculatus)represents the most desert-adapted antelope species.However,the evolutionary and molecular mechanisms underlying desert adaptations remain largely unexplored.Herein,a high-quality genome assembly of the addax was generated to investigate the molecular evolution of desert adaptation in camels and desert antelopes.Comparative genomic analyses identified 136 genes harboring convergent amino acid substitutions implicated in crucial biological processes,including water reabsorption,fat metabolism,and stress response.Notably,a convergent R146S amino acid mutation in the prostaglandin EP2 receptor gene PTGER2 significantly reduced receptor activity,potentially facilitating large-mammal adaptation to arid environments.Lineage-specific innovations were also identified in desert antelopes,including previously uncharacterized conserved non-coding elements.Functional assays revealed that several of these elements exerted significant regulatory effects in vitro,suggesting potential roles in adaptive gene expression.Additionally,signals of introgression and variation in genetic load were observed,indicating their possible influence on desert adaptation.These findings provide insights into the sequential evolutionary processes that drive physiological resilience in arid environments and highlight the importance of convergent evolution in shaping adaptive traits in large terrestrial mammals.
基金supported by the National Natural Science Foundation of China(32270442,31872219,31370401,32030011,31630071,31772448)National Key Research and Development Program of China(2022YFF1301602)Postgraduate Research&Practice Innovation Program of Jiangsu Province(KYCX23_1747,KYCX23_1740)。
文摘High-altitude and marine mammals inhabit distinct ecosystems but share a common challenge:hypoxia.To survive in low-oxygen environments,these species have evolved similar phenotypic pulmonary adaptations,characterized by a high density of elastic fibers.In this study,we explored the molecular mechanisms underlying these adaptations,focusing on pulmonary fibrosis and hypoxia tolerance through comparative genomics and convergent evolution analyses.We observed significant expansions and contractions in certain gene families across both high-altitude and marine mammals,closely associated with processes involved in pulmonary fibrosis.Notably,members of the keratin gene family,such as KRT17 and KRT14,appear to be associated with the development of the dense elastic fiber phenotype observed in the lungs of hypoxia-tolerant mammals.Through selection pressure and amino acid substitution analyses,we identified multiple genes exhibiting convergent accelerated evolution,positive selection,and amino acid substitution in these species,associated with adaptation to hypoxic environments.Specifically,the convergent evolution of ZFP36L1,FN1,and NEDD9 was found to contribute to the high density of elastic fibers in the lungs of both high-altitude and marine mammals,facilitating their hypoxia tolerance.Additionally,we identified convergent amino acid substitutions and gene loss events associated with sperm development,differentiation,and spermatogenesis,such as amino acid substitutions in SLC26A3 and pseudogenization of CFAP47,as confirmed by PCR.These genetic alterations may be linked to changes in the reproductive capabilities of these animals.Overall,this study offers novel perspectives on the genetic and molecular adaptations of high-altitude and marine mammals to hypoxic environments,with a particular emphasis on pulmonary fibrosis.
基金supported by the National Natural Science Foundation of China(32470665)the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences(CI2023E002)+1 种基金the Innovation Team and Talents Cultivation Program of the National Administration of Traditional Chinese Medicine(ZYYCXTD-D-202005 and ZYYZDXK-2023244)the China Agriculture Research System of MOF and MARA(CARS-21).
文摘Convergent and parallel evolution occur more frequently than previously thought.Here,we focus on the evolutionary adaptations of angiosperms at sub-zero temperatures.We begin by introducing the history of research on convergent and parallel evolution,defining all independent similarities as convergent evolu-tion.Our analysis reveals that frost zones(periodic or constant),which cover 49.1%of Earth’s land surface,host 137 angiosperm families,with over 90%of their species thriving in these regions.In this context,we revisit the global biogeography and evolutionary trajectories of plant traits,such as herbaceous form and deciduous leaves,that are thought to be evasion strategies for frost adaptation.At the physiological and mo-lecular levels,many angiosperms have independently evolved cold acclimation mechanisms through mul-tiple pathways in addition to the well-characterized C-repeat binding factor/dehydration-responsive element binding protein 1(CBF/DREB1)regulatory pathway.These convergent adaptations have occurred across various molecular levels,including amino acid substitutions and changes in gene duplication and expression within the same or similar functional pathways;however,identical amino acid changes are rare.Our results also highlight the prevalence of polyploidy in frost zones and the occurrence of paleopoly-ploidization events during global cooling.These patterns suggest repeated evolution in cold climates.Finally,we discuss plant domestication and predict climate zone shifts due to global warming and their ef-fects on plant migration and in situ adaptation.Overall,the integration of ecological and molecular perspec-tives is essential for understanding and forecasting plant responses to climate change.
基金supported by grants from the Shanghai Landscaping and City Appearance Administrative Bureau(G222406,G232408)Sino-Africa Joint Research Center,CAS(SAJC201607)+4 种基金the Science and Technology Commission of Shanghai Municipality(19390743600)the National Wild Plant Germplasm Resource Centre for Shanghai Chenshan Botanical Garden(ZWGX2102)to W.C.H.and K.J.,and by a Distinguished Investigator grant(NNF190CO05456)from the Novo Nordisk Foundation to B.L.M.E.H.J.N.acknowledges funding from the Novo Nordisk Foundation(0054890)the Independent Research Fund Denmark(1131-00002B and 1051-00083 B).
文摘Angraecum sesquipedale,also known as Darwin’s orchid,possesses an exceptionally long nectar spur.Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis,later identified as Xanthopan praedicta.In this plant-pollinator interaction,the A.sesquipedale flower emits a complex blend of scent compounds dominated by diurnally regulated oximes(R_(1)R_(2)C=N-OH)to attract crepuscular and nocturnal pollinators.The molecular mechanism of oxime biosynthesis remains unclear in orchids.Here,we present the chromosome-level genome of A.sesquipedale.The haploid genome size is 2.10 Gb and represents 19 pseudochromosomes.Cytochrome P450 encoding genes of the CYP79 family known to be involved in oxime biosynthesis in seed plants are not present in the A.sesquipedale genome nor the genomes of other members of the orchid family.Metabolomic analysis of the A.sesquipedale flower revealed a substantial release of oximes at dusk during the blooming stage.By integrating metabolomic and transcriptomic correlation approaches,flavin-containing monooxygenases(FMOs)encoded by six tandem-repeat genes in the A.sesquipedale genome are identified as catalyzing the formation of oximes present.Further in vitro and in vivo assays confirm the function of FMOs in the oxime biosynthesis.We designate these FMOs as orchid oxime synthases 1-6.The evolutionary aspects related to the CYP79 gene losses and neofunctionalization of FMO-catalyzed biosynthesis of oximes in Darwin’s orchid provide new insights into the convergent evolution of biosynthetic pathways.
基金supported by the Basic and Applied Basic Research Foundation of Guangdong Province(2020A1515110882)National Science Fund for Distinguished Young Scholars(32225049)。
文摘The yellow boxfish(Ostracion cubicus)exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics,including a fused dermal plate.Contradictory evolutionary evidence hinders true classification of O.cubicus.To clarify its evolutionary position within Tetraodontiformes,a chromosome-level genome assembly was generated,representing the most contiguous and complete genome to date for this lineage.Notably,O.cubicus possessed the largest genome within the order Tetraodontiformes,primarily due to extensive transposable element expansion.Phylogenetic analysis based on 19 whole genomes and 131 mitochondrial genomes resolved Tetraodontiformes into three major sister groups(Ostraciidae-Molidae,Tetraodontidae,and Balistidae-Monacanthidae).Comparative genomic evidence indicated that O.cubicus diverged early from the common ancestor of modern Tetraodontiformes and retained the highest number of HOX genes among surveyed taxa.Although overall genomic architecture was largely conserved,certain genetic and environmental changes may have contributed to its phenotypic adaptations,including climate cooling during the Miocene-Pliocene Transition,recent DNA and long interspersed nuclear element(LINE)transposon bursts,lineage-specific chromosomal rearrangements,and gene family expansion.Many positively selected genes and rapidly evolving genes were associated with skeletal development,including bmp7,egf7,and bmpr2.Transcriptomic comparisons between carapace and tail skin revealed various candidate genes and pathways related to carapace formation,such as postn,scpp1,and components of the TGF-βsignaling pathway.A derived amino acid substitution in eda,coupled with protein structural modeling,suggested potential molecular convergence in dermal plate formation among teleosts.These findings provide novel insights into the genomic and developmental basis of carapace evolution and coral reef-adaptation in O.cubicus,offering a strong case for evolutionary balance between genomic conservation with regulatory innovation to achieve coral reef specialization.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)the National Natural Science Foundation of China(31821001,31471992,31970386)the project of Strategic Biological Resources Service Network of the Chinese Academy of Sciences(ZSSD003)。
文摘Gut microbiota plays a critical role in host physiology and health.The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche.Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota.However,the relative contribution of each factor in shaping the structure of gut microbiota remains unclear.The giant(Ailuropoda melanoleuca)and red(Ailurus styani)pandas belong to different families of order Carnivora.They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution.Here,we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing.We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives.This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea.Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis.These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.
文摘Azoreductases are involved in the bioremediation by bacteria of azo dyes found in waste water.In the gut flora,they activate azo pro-drugs,which are used for treatment of inflammatory bowel disease,releasing the active component 5-aminosalycilic acid.The bacterium P.aeruginosa has three azoreductase genes,paAzoR1,paAzoR2 and paAzoR3,which as recombinant enzymes have been shown to have different substrate specificities.The mechanism of azoreduction relies upon tautomerisation of the substrate to the hydrazone form.We report here the characterization of the P.aeruginosa azoreductase enzymes,including determining their thermostability,cofactor preference and kinetic constants against a range of their favoured substrates.The expression levels of these enzymes during growth of P.aeruginosa are altered by the presence of azo substrates.It is shown that enzymes that were originally described as azoreductases,are likely to act as NADH quinone oxidoreductases.The low sequence identities observed among NAD(P)H quinone oxidoreductase and azoreductase enzymes suggests convergent evolution.
基金supported by the National Key Research and Development Program of China(2019YFA0706900)the National Natural Science Foundation of China(32025001,31872729,31600045,32071266,31800664,82022066,and 31800041)+5 种基金the Natural Science Foundation of Shandong Province,China(ZR2019ZD20,ZR2016CQ05,and ZR2019QC009)the Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology(Qingdao)(LMDBKF-2019-01)the Tianjin Synthetic Biotechnology Innovation Capability Improvement Project(TSBICIP-KJGG-001)the State Key Laboratory of Bio-organic and Natural Products Chemistry(SKLBNPC18242)the Fundamental Research Funds of Shandong University(2019GN030 and 2019GN033)the Foundation of Qilu University of Technology of Cultivating Subject for Biology and Biochemistry(No.202014)。
文摘Directed evolution(DE)inspired by natural evolution(NE)has been achieving tremendous successes in protein/enzyme engineering.However,the conventional"one-protein-for-one-task"DE cannot match the"multi-proteins-for-multi-tasks"NE in terms of screening throughput and efficiency,thus often failing to meet the fast-growing demands for biocatalysts with desired properties.In this study,we design a novel"multi-enzymes-for-multi-substrates"(MEMS)DE model and establish the proof-ofconcept by running a NE-mimicking and higher-throughput screening on the basis of"two-P450 s-against-seven-substrates"(2P×7S)in one pot.With the multiplied throughput and improved hit rate,we witness a series of convergent evolution events of the two archetypal cytochrome P450 enzymes(P450 BM3 and P450 cam)in laboratory.It is anticipated that the new strategy of MEMS DE will find broader application for a larger repertoire of enzymes in the future.Furthermore,structural and substrate docking analysis of the two functionally convergent P450 variants provide important insights into how distinct P450 active-sites can reach a common catalytic goal.
基金Thank for the financial support for this research project by the National Natural Science Foundation of China for Young Scholars(Grant No.51605210)by Scientific Research Project of Yunnan Provincial Education Department(Grant No.2018Y018).
文摘Remarkable geometrical similarities are found in digging claws of soil burrowing animals,in spite of the fact that they evolved independently.Based on convergent evolution theory,this study innovatively proposed a bionic engineering perspective that focuses on general and analogous geometrical characteristics of soil animals.It was observed that soil animals with powerful burrowing ability have analogous serrated structures on their digging claws.Taking soil imprinting toothed wheel as the research object,the hypothesis that special serrated structures have the potential of reducing penetrating resistance from soil and enhancing digging efficiency for soil engaging component was investigated.The convergent evolution inspired bionic serrated structures were utilized for the design of cutting edge on toothed wheel.Then,a toothed wheel that mounted with the conventional tooth and a bionic tooth were manufactured and tested in the soil bin.Results showed that special bionic serrated structure could reduce the required draft force for toothed wheel;meanwhile increase the depth and volume of prepared micro-basin.It was found that the soil-penetrating mechanism of the bionic toothed wheel behaved as saw cutting that similar to the digging behavior of soil burrowing animals.Geometry of serrated structure has the ability to maximum stress concentrations in soil,thus increased the tendency of soil material to fail.These results indicate that the convergent evolution inspired bionic approach is novel and advantageous for the design of new soil engaging implements for working quality optimization and forward resistance reduction.
基金funded by the University of Colombo Research Grants,Sri Lanka(AP/3/2012/CG/15 and AP/3/2017/CG/27).
文摘The Ashy-headed Laughingthrush (Argya cinereifrons), a species endemic to Sri Lanka, has been historically considered a laughingthrush in the genus Garrulax. However, based on phylogenetic evidence, recent studies have suggested a new classification for the species under the genus Argya (true babblers). Despite the genetic signal showing affinity to true babblers Argya, as its common name suggests, the Ashy-headed Laughingthrush (AHLT) shows remarkable morphological similarities to other laughingthrushes of the Indo-Himalayan region. Here we attempted to address this incongruence in phenotypic and phylogenetic signals in this species by reconstructing the molecular phylogeny of babblers and comparing that with the key morphological, plumage, and vocal features of the two concerned groups. We hypothesized that the convergence of phenotype and vocalization of Garrulax in the wet evergreen forests of the Indian mainland and AHLT in the wet tropical rainforests of southern Sri Lanka has historically confused the taxonomists. The phylogenetic relationships were reconstructed using Bayesian inference using four mitochondrial and seven nuclear gene regions. The molecular phylogenetic tree placed the AHLT with India's Large Grey Babbler (A. malcolmi) as the sister taxon within the genus Argya. The hierarchical clustering based on body size, shape, plumage colour, and vocal properties resulted in the inconsistent placement of ALTH with babblers or laughingthrushes. Therefore, an incongruence in phenotype and genotype is observed. Our findings show that the convergent patterns of phenotypic evolution can confuse both historic and recent taxonomic delimitations in highly divergent groups such as Asian babblers.
基金the financial support of the Dinosaur Research Institute and the University of Alberta China Institute
文摘In the tails of dromaeosaurid dinosaurs and rhamphorhynchid pterosaurs, elongate osteological rods extend anteriorly from the chevrons and the prezygapophyses. These caudal rods are positioned in parallel and are stacked dorsoventrally. The fully articulated and three-dimensionally preserved caudal series of some dromaeosaurid specimens show that individually these caudal rods were flexible, not rigid as previously thought. However, examination of the arrangement of the caudal rods in cross-section indicates that the combined effect of multiple caudal rods did provide substantial rigidity in the dorsoventral, but not in the lateral, plane. The results of digital muscle reconstructions confirm that dromaeosaurids and rhamphorhynchids also shared greatly reduced caudofemoral muscles in the anterior tail region. The striking similarities between the tails of dromaeosaurids and rhamphorhynchids suggest that both evolved under similar behavioral and biomechanical pressures. Combined with recent discoveries of primitive deinonychosaurs that phylogenetically bracket the evolution of dromaeosaurid caudal rods between two arboreal gliding/flying forms, these results are evidence that the unique caudal morphologies of dromaeosaurids and rhamphorhynchids were both adaptations for an aerial lifestyle.
基金supported by the National Key Research and Development Program of China to J.-R. Y.(2021YFF1200904 and2021YFA1302500)the National Natural Science Foundation of China to J.-R. Y.(31871320 and 81830103)+1 种基金by Science and Technology Planning Project of ZhuHai,China to H. C.by Science and Technology Planning Project of Guangdong Province,China to X. Z.(2014A030304053)
文摘Multiple primary lung cancer(MPLC)is an increasingly prevalent subtype of lung cancer.According to recent genomic studies,the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary convergence.We perform whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion found.Using our own and other relevant public data,evolutionary tree reconstruction reveals that cancer driver gene mutations occurred at the early trunk,indicating evolutionary contingency rather than adaptive convergence.Additionally,tumors from the same MPLC patient are as genetically diverse as those from different patients,while within-tumor genetic heterogeneity is significantly lower.Furthermore,the aberrant molecular functions enriched in mutated genes for a sample show a strong overlap with other samples from the same tumor,but not with samples from other tumors or other patients.Overall,there is no evidence of adaptive convergence during the evolution of MPLC.Most importantly,the similar between-tumor diversity and between-patient diversity suggest that personalized therapies may not adequately account for the genetic diversity among different tumors in an MPLC patient.To fully exploit the strategic value of precision medicine,targeted therapies should be designed and delivered on a per-lesion basis.
基金This research was funded by a Paleontological Society Norman Newel Award,a College of Arts and Sciences Regional Campus Research and Creative Activity Grant from the Ohio State University,a research grant from the Ohio State University at Marion,startup funds from the Ohio State University to JC,and Summer Research Assistantship funds from the Ohio State University at Marion to LN.Some of the ideas for this project were developed while JC was supported by a Meaningful Inquiry grant from The Ohio State University library system.
文摘Morphological analyses are critical to quantify phenotypic variation,identify taxa,inform phylogenetic relationships,and shed light on evolutionary patterns.This work is particularly important in groups that display great morphological disparity.Such is the case in geomyoid rodents,a group that includes 2 of the most species-rich families of rodents in North America:the Geomyidae(pocket gophers)and the Heteromyidae(kangaroo rats,pocket mice,and their relatives).We assessed variation in skull morphology(including both shape and size)among geomyoids to test the hypothesis that there are statistically significant differences in skull measurements at the family,genus,and species levels.Our sample includes 886 specimens representing all geomyoid genera and 39 species.We used the geometric mean to compare size across taxa.We used 14 measurements of the cranium and lower jaw normalized for size to compare shape among and within taxa.Our results show that skull measurements enable the distinction of geomyoids at the family,genus,and species levels.There is a larger amount of size variation within Geomyidae than within Heteromyidae.Our phylomorphospace analysis shows that the skull shape of the common ancestor of all geomyoids was more similar to the common ancestor of heteromyids than that of geomyids.Geomyid skulls display negative allometry whereas heteromyid skulls display positive allometry.Within heteromyids,dipodomyines,and non-dipodomyines show significantly different allometric patterns.Future analyses including fossils will be necessary to test our evolutionary hypotheses.
基金Supported in part by Heilongjiang Province Tackle Key Problem Item (GB01B104)
文摘Glutamate decarboxylase （GAD） has been found in animal and higher plant tissues as well as in yeasts and microorganisms. In animals the enzyme plays an important role in central nervous system activity because the enzyme substrate glutamic acid is a mediator of excitation process and the product, gamma-aminobutyric acid, is the most important mediator of inhibition process in the central nervous system. GAD65 is one form of the glutamate decarboxylases （GAD）, GAD65 has been identified as a major autoantigen in type 1 diabetes, so the GAD65 gene of porcine was cloned by RT-PCR method to construct phylogenetic tree, the homology of 13 glutamate decarboxylases （GAD） of different origin was analyzed by multiple alignment.
文摘Examples of evolution,extinction and homoplasy of the larger benthic foraminifera(LBF)occur throughout their history.Since the Carboniferous,LBF have thrived in carbonate-rich tropical and subtropical shallow-marine shelf environments.Their high abundance and diversity are due primarily to their extraordinary ability to inhabit a range of ecological niches and by hosting a variety of symbionts.Attaining relatively large,centimetre-scale sizes,made some forms very specialized and vulnerable to rapid ecological changes.For this reason,some LBF have shown a tendency to suffer periodically during major extinctions,especially when environmental conditions have changed rapidly and/or substantially.This,however,makes them valuable biostratigraphic microfossils and,in addition,gives invaluable insight into the spatial and temporal process of biological evolution,such as convergent/homoplasy and homology/iterative evolution.Here the evolutionary behavior of two important morphological types that occurred throughout the history of the LBF are discussed,namely the planispiral-fusiform test as typified by the fusulinids in the Late Paleozoic and the alveolinids in the Mid-Cretaceous and Neogene,and the three-layered discoid lenticular test as characterized by the orbitoids in the Mid-to Late Cretaceous,the orthophragminids in the Paleogene,and lepidocyclinids in the Oligocene to Quaternary.Understanding the propensity of these forms to convergent and iterative evolution,with the repeated re-occurrence of certain morphological features,is essential in understanding and constructing their phylogenetic relationships more generally within the main groups of the LBF.The insights gained from the history of these LBF have wider implications,and provide a more general understanding of the impacts of climate and ecological changes as driving forces for biological evolution.
基金supported by the National Natural Science Foundation of China (32170480,31972866)Youth Innovation Promotion Association,Chinese Academy of Sciences (http://www.yicas.cn)+1 种基金Young Top-notch Talent Cultivation Program of Hubei ProvinceWuhan Branch,Supercomputing Center,Chinese Academy of Sciences,China。
文摘Dormancy represents a fascinating adaptive strategy for organisms to survive in unforgiving environments.After a period of dormancy,organisms often exhibit exceptional resilience.This period is typically divided into hibernation and aestivation based on seasonal patterns.However,the mechanisms by which organisms adapt to their environments during dormancy,as well as the potential relationships between different states of dormancy,deserve further exploration.Here,we selected Perccottus glenii and Protopterus annectens as the primary subjects to study hibernation and aestivation,respectively.Based on histological and transcriptomic analysis of multiple organs,we discovered that dormancy involved a coordinated functional response across organs.Enrichment analyses revealed noteworthy disparities between the two dormant species in their responses to extreme temperatures.Notably,similarities in gene expression patterns pertaining to energy metabolism,neural activity,and biosynthesis were noted during hibernation,suggesting a potential correlation between hibernation and aestivation.To further explore the relationship between these two phenomena,we analyzed other dormancy-capable species using data from publicly available databases.This comparative analysis revealed that most orthologous genes involved in metabolism,cell proliferation,and neural function exhibited consistent expression patterns during dormancy,indicating that the observed similarity between hibernation and aestivation may be attributable to convergent evolution.In conclusion,this study enhances our comprehension of the dormancy phenomenon and offers new insights into the molecular mechanisms underpinning vertebrate dormancy.
基金We thank Karin Pfennig, Ver6nica Rodriguez-Moncalvo, Lisa Bono, and three anonymous refe-rees for helpful comments. Antonio Serrato helped with specimen collection. Chris Willett and Erin Burch aided with spectroscopy, and Vicky Madden and Steven Ray provided TEM services. Ken Wray kindly furnished coral snake speci-mens. Animal research was conducted under UNC IACUC permit 11-108. Funding was provided by the National Science Foundation （DEB-1110385 and DEB - 1019479）.
文摘Batesian mimics are harmless prey species that resemble dangerous ones （models）, and thus receive protection from predators. How such adaptive resemblances evolve is a classical problem in evolutionary biology. Mimicry is typically thought to be difficult to evolve, especially if the model and mimic produce the convergent phenotype through different proximate mecha- nisms. However, mimicry may evolve more readily if mimic and model share similar pathways for producing the convergent phenotype. In such cases, these pathways can be co-opted in ancestral mimic populations to produce high-fidelity mimicry with- out the need for major evolutionary innovations. Here, we show that a Batesian mimic, the scarlet kingsnake Larnpropeltis elap-soides, produces its coloration using the same physiological mechanisms as does its model, the eastern coral snake Micrurus fulvius. Therefore, precise color mimicry may have been able to evolve easily in this system. Generally, we know relatively little about the proximate mechanisms underlying mimicry .
基金supported by the National Natural Science Foundation of China (32170645)the National Key Research and Development Program of China (2021YFF1000900).
文摘Centromere positioning and organization are crucial for genome evolution;however,research on centro-mere biology is largely influenced by the quality of available genome assemblies.Here,we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum(TM-1)and Gossypium barbadense(3-79).Compared with previously published reference genomes,our assemblies show substantial improvements,with the contig N50 improved by 4.6-fold and 5.6-fold,respectively,and thus represent the most complete cotton genomes to date.These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G.hirsutum and G.barbadense,respectively.Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize(CRM)and Tekay long terminal repeat families,and the CRM family reshapes the centromere structure of the At subgenome after polyploidization.These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes,ensuring centromere function and genome stability.In addition,the reposi-tioning and high sequence divergence of centromeres between G.hirsutum and G.barbadense have contributed to speciation and centromere diversity.This study sheds light on centromere evolution in a sig-nificant crop and provides an alternative approach for exploring the evolution of polyploid plants.
基金F.T.-G was supported by the Fundacion Mexico en Harvard and Consejo Nacional de Ciencia y Tecnologia(CONACYT,Mexico)Postdoctoral Fellowships.L.O.was supported by the National Science Foundation[IOS-1845651,IOS-1827333,and IOS-1822025]the Rita Allen Foundation,and the L'Oreal USA for Women in Science.C.N.B.was supported by the National Science Foundation[IOS-1456612 and DHB-1754406]Work in the lab of S.V.E.was supported by the National Science Foundation[DEB-1355343]and by Harvard University.
文摘For the last 40 years,the study of cooperative breeding(CB)in birds has proceeded primarily in the context of discovering the ecological,geographical,and behavioral drivers of helping.The advent of molecular tools in the early 1990s assisted in clarifying the relatedness of helpers to those helped,in some cases,confirming predictions of kin selection theory.Methods for genome-wide analysis of sequence variation,gene expression,and epigenetics promise to add new dimensions to our understanding of avian CB,primarily in the area of molecular and developmental correlates of delayed breeding and dispersal,as well as the ontogeny of achieving parental status in nature.Here,we outline key ways in which modern-omics approaches,in particular genome sequencing,transcriptomics,and epigenetic profiling such as ATAC-seq,can be used to add a new level of ana-lysis of avian CB.Building on recent and ongoing studies of avian social behavior and sociogenom-ics,we review how high-throughput sequencing of a focal species or clade can provide a robust foundation for downstream,context-dependent destructive and non-destructive sampling of spe-cific tissues or physiological states in the field for analysis of gene expression and epigenetics.-Omics approaches have the potential to inform not only studies of the diversification of CB over evolutionary time,but real-time analyses of behavioral interactions in the field or lab.Sociogenomics of birds represents a new branch in the network of methods used to study CB,and can help clarify ways in which the different levels of analysis of CB ultimately interact in novel and unexpected ways.
