Diet drives convergent evolution of gut microbiomes in bamboo-eating species

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.

Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases

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.

Development of MEMS directed evolution strategy for multiplied throughput and convergent evolution of cytochrome P450 enzymes

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.

Convergent evolution inspired serrated structure for improving efficiency of soil imprinting and its mechanism investigation

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.

Comparative transcriptomic evidence of physiological changes and potential relationships in vertebrates under different dormancy states

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.

Dragon Tails:Convergent Caudal Morphology in Winged Archosaurs

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.

Cloning and molecular evolution research of porcine GAD65 gene

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.

High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres

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.

A chromosome-level genome of electric catfish(Malapterurus electricus)provided new insights into order Siluriformes evolution

The electric catfish(Malapterurus electricus),belonging to the family Malapteruridae,order Siluriformes(Actinopterygii:Ostariophysi),is one of the six branches that has independently evolved electrical organs.We assembled a 796.75 Mb M.electricus genome and anchored 88.72%sequences into 28 chromosomes.Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors.Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like(arhgef4),which is associated with G-protein coupled receptor(GPCR)signaling pathway,underwent adaptive parallel evolution.Gene identification suggests visual degradation in catfishes,and an important role for taste in environmental adaptation.Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes.

Molecular mechanisms of adaptive evolution in wild animals and plants

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution,an important strategy for species survival and persistence.Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification,phenotypic convergence,and inter-species interaction.As the genome sequences of more and more non-model organisms are becoming available,the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning.In this study,we reviewed the latest research advances in wild animals and plants,focusing on adaptive traits,convergent evolution,and coevolution.Firstly,we focused on the adaptive evolution of morphological,behavioral,and physiological traits.Secondly,we reviewed the phenotypic convergences of life history traits and responding to environmental pressures,and the underlying molecular convergence mechanisms.Thirdly,we summarized the advances of coevolution,including the four main types:mutualism,parasitism,predation and competition.Overall,these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction,demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies.Finally,we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

Lack of evolutionary convergence in multiple primary lung cancer suggests insufficient specificity of personalized therapy

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.

Explaining patterns of species dominance in the shrub steppe systems of the Junggar Basin(China) and Great Basin(USA)

Natural scientists have long recognized that regions with similar climate tend to have similar vegetation.Preliminary observations suggest that shrub steppe communities of the western US and western China may be two such regions with similar annual precipitation,temperature,land use,and vegetation.These cold dry shrub steppes have traditionally been grazed.Despite these similarities,patterns of species dominance are different.Annual species that are rare in China become dominant when introduced to the United States.The objective of this study was to investigate how climate,land use and community structure may explain these patterns of species dominance.Community structure and grazing intensity were measured at 5 sites in each region.This information was combined with a broader review of the literature describing the history of grazing in both basins.Climate was analyzed based on a spatially-gridded,interpolated weather time series （monthly records） and climatological summary （1961-1990 mean conditions） data set from the Climate Research Unit.We found that differences in summer precipitation and winter minimum temperature,land use intensity,and shrub size may all contribute to the dominance of annual species in the Great Basin,particularly Bromus tectorum.In particular,previous work indicates that summer precipitation and winter temperature drive the distribution of Bromus tectorum in the Great Basin.As a result,sites with wet summers and cold springs,similar to the Chinese sites,would not be expected to be dominated by Bromus tectorum.A history of more intense grazing of the Chinese sites,as described in the literature,also is likely to decrease fire frequency,and decreases litter and shrub dominance,all of which have been demonstrated to be important in Bromus tectorum establishment and ultimate dominance.Further research is necessary to determine if other annuals that follow the same pattern of scarcity in the Junggar Basin and dominance in the Great Basin are responding to the same influences.

Morphology and Histochemistry of Infralabial Glands of Two Species in the Slug-Eating Family Pareidae(Reptilia:Serpentes)

Pareidae and Dipsadidae,two independently evolved taxa in the Serpentes lineage,both feed exclusively on terrestrial mollusks(snails and slugs).Dipsadid snakes developed hypertrophic infralabial glands in their lower jaw,which are thought to be associated with their specialized feeding behaviors.However,whether a similar gland exists in pareid snakes is unknown.In this study,we examined the morphological characteristics of the infralabial glands in Pareas berdmorei and Pareas chinensis based on comparative anatomical,histochemical,and histopathological analysis.Our results demonstrated that both Pareas species had similar hypertrophied infralabial glands in the lower jaw,which consisted of tubules with mucinous properties and seromucous acini.The secretory granules of the seromucous cells also showed high electron density.The cytoplasm was rich in rough endoplasmic reticulum,mitochondria,and Golgi apparatus,suggesting that these cells may secrete protein substances,and play an important role in digesting mollusks.This study provides evidence of morphological convergence between Pareidae and Dipsadidae due to specialized diet adaptation,which will be the foundation for prospective functional research.

Multivariate analyses of skull morphology inform the taxonomy and evolution of geomyoid rodents

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.

Plant cytochrome P450 plasticity and evolution

The superfamily of cytochrome P450(CYP)enzymes plays key roles in plant evolution and metabolic diversification.This review provides a status on the CYP Iandscape within green algae and land plants.The 11 conserved CYP clans known from vascular plants are all present in green algae and several green algaespecific clans are recognized.Clan 71,72,and 85 remain the largest CYP clans and include many taxaspecific CYP(sub)families reflecting emergence of linage-specific pathways.Molecular features and dynamics of CYP plasticity and evolution are discussed and exemplified by selected biosynthetic pathways.High substrate promiscuity is commonly observed for CYPs from large families,favoring retention of gene duplicates and neofunctionalization,thus seeding acquisition of new functions.Elucidation of biosynthetic pathways producing metabolites with sporadic distribution across plant phylogeny reveals multiple exampies of convergent evolution where CYPs have been independently recruited from the same or different CYP families,to adapt to similar environmental challenges or ecological niches.Sometimes only a single or a few mutations are required for functional interconversion.A compilation of functionally characterized plant CYPs is provided online through the Plant P450 Database(erda.dk/public/vgrid/PlantP450/).

Genome-wide signatures of mammalian skin covering evolution

Animal body coverings provide protection and allow for adaptation to environmental pressures such as heat,ultraviolet radiation,water loss,and mechanical forces.Here,using a comparative genomics analysis of 39 mammal species spanning three skin covering types(hairless,scaly and spiny),we found some genes(e.g.,UVRAG,POLH,and XPC)involved in skin inflammation,skin innate immunity,and ultraviolet radiation damage repair were under selection in hairless ocean mammals(e.g.,whales and manatees).These signatures might be associated with a high risk of skin diseases from pathogens and ultraviolet radiation.Moreover,the genomes from three spiny mammal species shared convergent genomic regions(EPHB2,EPHA4,and NIN)and unique positively selected genes(FZD6,INVS,and CDC42)involved in skin cell polarity,which might be related to the development of spines.In scaly mammals,the shared convergent genomic regions(e.g.,FREM2)were associated with the integrity of the skin epithelium and epidermal adhesion.This study identifies potential convergent genomic features among distantly related mammals with the same skin covering type.

Phylogeny of the Acarosporaceae(Lecanoromycetes,Ascomycota,Fungi)and the evolution of carbonized ascomata

The phylogeny of the Acarosporaceae(Lecanoromycetes,Acarosporomycetidae,Acarosporales)is investigated using data from three molecular markers;nuclear ITS-LSU rDNA,mitochondrial SSU andβ-tubulin.Acarosporaceae is shown to be constituted by six main clades;Myriospora,Timdalia,Pleopsidium,a clade composed by BAcarospora^rhizobola and BA.^terricola,the poorly supported Sarcogyne clade(including several Polysporina and Acarospora species)and the Acarospora clade(including the type of Polysporina,P.simplex,and several other Polysporina species).The common ancestor of the Acarosporaceae did not produce strongly black pigmented(carbonized or melanized)ascomata,but this trait has arisen secondarily and independently numerous times in the evolution of the group.The number of changes in character states of both carbonized epihymenium and carbonized exciple are considerably more than the minimum number.The genera Sarcogyne and Polysporina—largely circumscribed based on the presence of black pigmented ascomata—are shown to be distinctly non-monophyletic.The presence of green algae in the ascoma margin(lecanorine or lecideine ascomata)may vary even within single species.

Evolution,Extinction,Homology and Homoplasy of the Larger Benthic Foraminifera from the Carboniferous to the Present Day,as Exemplified by Planispiral-Fusiform and Discoidal Forms

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.

Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesis

Crassulacean acid metabolism(CAM)has high water-use efficiency(WUE)and is widely recognized to have evolved from C3 photosynthesis.Different plant lineages have convergently evolved CAM,but the molecular mechanism that underlies C3-to-CAM evolution remains to be clarified.Platycerium bifurcatum(elkhorn fern)provides an opportunity to study the molecular changes underlying the transition from C3 to CAM photosynthesis because both modes of photosynthesis occur in this species,with sporotrophophyll leaves(SLs)and cover leaves(CLs)performing C3 and weak CAM photosynthesis,respectively.Here,we report that the physiological and biochemical attributes of CAM in weak CAM-performing CLs differed from those in strong CAM species.We investigated the diel dynamics of the metabolome,proteome,and transcriptome in these dimorphic leaves within the same genetic background and under identical environmental conditions.We found that multi-omic diel dynamics in P.bifurcatum exhibit both tissue and diel effects.Our analysis revealed temporal rewiring of biochemistry relevant to the energy-producing pathway(TCA cycle),CAM pathway,and stomatal movement in CLs compared with SLs.We also confirmed that PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE(PPCK)exhibits convergence in gene expression among highly divergent CAM lineages.Gene regulatory network analysis identified candidate transcription factors regulating the CAM pathway and stomatal movement.Taken together,our results provide new insights into weak CAM photosynthesis and new avenues for CAM bioengineering.

Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts

Although most fishes are ectothermic,some,including tuna and billfish,achieve endothermy through specialized heat producing tissues that are modified muscles.How these heat producing tissues evolved,and whether they share convergent molecular mechanisms,remain unresolved.Here,we generated a high-quality genome from the mackerel tuna(Euthynnus affinis)and investigated the heat producing tissues of this fish by single-nucleus and bulk RNA sequencing.Compared with other teleosts,tuna-specific genetic variation is strongly associated with muscle differentiation.Single-nucleus RNA-seq revealed a high proportion of specific slow skeletal muscle cell subtypes in the heat producing tissues of tuna.Marker genes of this cell subtype are associated with the relative sliding of actin and myosin,suggesting that tuna endothermy is mainly based on shivering thermogenesis.In contrast,cross-species transcriptome analysis indicated that endothermy in billfish relies mainly on nonshivering thermogenesis.Nevertheless,the heat producing tissues of the different species do share some tissue-specific genes,including vascular-related and mitochondrial genes.Overall,although tunas and billfishes differ in their thermogenic strategies,they share similar expression patterns in some respects,highlighting the complexity of convergent evolution.