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Convergence is considered powerful evidence for adaptation to similar natural selection pressures. However, for many ecologically and morphologically convergent species, it remains unclear whether convergence extends to reproductive strategies, which are particularly important because of their tight connection to fitness. Here, by measuring key life-history traits (e.g. reproductive status, egg size, oviposition frequency, reproductive effort) across a full annual cycle comprising both reproductive and non-reproductive seasons, we discover divergence in reproductive strategies in two Anolis lizards that are otherwise strikingly convergent in ecology, morphology, and behaviour. The Cuban brown anole (Anolis sagrei) rapidly produces many small eggs during a concentrated summer reproductive season, whereas the Puerto Rican crested anole (Anolis cristatellus) produces comparatively fewer, larger eggs over a longer period. Thus, despite evolving highly convergent ecomorphological phenotypes and both being constrained to a single-egg clutch, these species exhibit marked divergence in life-history trade-off strategies along the fast–slow continuum. Our results indicate that ecomorphological convergence evolved uncoupled from life-history pathways in these species. [ABSTRACT FROM AUTHOR]

Carangidae is an economically important fish family comprised of 32 genera with more than 140 circumglobally distributed species. Its members exhibit vast differences in morphology and lifestyle, thus making them compelling subjects for evolutionary studies. Recently, more works on carangids have detected the presence of cryptic lineages through molecular and/or non-molecular techniques. Credited for its inherent amplification efficiency, mitophylogenomics became effective in opening avenues to further understand higher-level interrelationships in many fish groups. However, the mitophylogenomic approach has not yet been widely applied to infer evolutionary history at the lower-level interrelationships, especially on cryptic representatives. In this study, we evaluated the diagnostic applicability of mitogenomes in detecting population-level divergences within Carangidae. Using the mitogenomes, we detected intraspecific divergences on some taxa, namely Caranx melampygus, Selaroides leptolepis, Seriola lalandi, Decapterus maruadsi, and Trachurus trachurus, with divergences highly correspondent to that of their geographic origins. Additionally, a widespread Pacific arrangement was also detected for S. rivoliana. Our discoveries were highly corroborative with findings from other Carangidae studies which utilized different diagnostic markers (e.g., SNPs, microsatellites, morphometrics, parasites). Dated phylogeny also suggested that intraspecific diversifications occurred during the Late Neogene. Likewise, we characterized two mitogenomes from different cryptic lineages of Selaroides leptolepis and revealed that the two mitogenomes were K2P pairwise = 5.58% different from each other. Its genetic compositions included 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. These findings paved way for future evolutionary insights into the divergence histories of other fish populations. [ABSTRACT FROM AUTHOR]

Subterranean and surface habitats are in stark contrast in several environmental factors. Therefore, adaptation to the subterranean environment typically impedes the (re)colonisation of surface habitats. The genus Niphargus includes amphipod crustaceans that primarily occupy subterranean habitats. All its species show typical adaptations to the subterranean environment. However, some Niphargus species occur in surface‐subterranean ecotones. To understand whether (i) habitat‐based phenotypic divergence is present between the cave and the ecotone species and (ii) similar phenotypes emerge independently in each ecotone, we studied morphological divergence between four cave and four ecotone Niphargus species based on 13 functional morphological traits. To account for different selection acting on the sexes, we included both males (N = 244) and females (N = 222). Nine out of 13 traits showed habitat‐divergence. Traits related to feeding and crawling were shorter, while traits related to oxygenation were larger in ecotone species. Eleven out of 13 traits were sexually dimorphic. Traits related to oxygenation and crawling were larger in females, while the trait related to swimming was larger in males. We found that the extent of sexual dimorphism differs between the habitats in eight traits related to sensing, feeding, oxygenation and crawling. Additionally, we found that in certain traits related to sensing and oxygenation, habitat‐related differences are only present in one sex, but not the other. We conclude that the detected differences between the cave and the ecotone species indicate divergent evolution, where similarities among the different species within habitat type indicate convergent evolution. The high degree of sexual dimorphism paired with differences in sexual dimorphism between the habitats in certain traits suggest that sexual and fecundity selections have comparable effects to environmental selection. Thus, studies of habitat‐dependent adaptations investigating one sex only, or not considering sexual dimorphism, can lead to erroneous conclusions. [ABSTRACT FROM AUTHOR]

Phenotypic differences among populations stem from the interaction between neutral and adaptive processes, and phenotypic plasticity. Although clinal trait variation along climatic gradients often evolves in widely distributed species, it is unknown whether substrate specialization, such as that of Mediterranean gypsum plants, has constrained adaptation to climate.Using a common garden experiment with two contrasting watering treatments, we quantified phenotypic plasticity, assessed evidence for footprints of selection using FST – QST comparisons, and evaluated the ecological factors driving genetically based phenotypic differentiation of 11 populations encompassing the full environmental range of the gypsum shrub Lepidium subulatum.We found evidence for genetic differentiation among populations related to climatic differences, with populations from warmer and drier sites showing lower specific leaf area and leaf N, earlier phenology, greater water use efficiency and greater fitness. Multiple lines of evidence suggest that this differentiation was driven by past divergent selection rather than neutral processes. All populations showed high phenotypic plasticity, indicating that plasticity has not been selected against, even in populations from sites with harsher climatic conditions.Synthesis. Our results indicate that despite strong substrate specialization, adaptive differentiation related to climatic gradients occurs in this species. However, we also found that populations from mesic sites may be particularly vulnerable to future climate change given their relatively lower fitness under both wet and dry conditions. [ABSTRACT FROM AUTHOR]

The Atlantic dog whelk, Nucella lapillus, is a marine snail that exhibits divergent evolution in response to habitat adaptation, resulting in distinct populations at the phenotypic, genotypic, and karyotypic levels. In this study, we utilized short- and long-read NGS data to perform a de novo assembly of the entire mitochondrial genome of N. lapillus and developed a multiplex PCR protocol to sequence most of its length using ONT sequencing. Our analysis revealed a typical circular configuration of 16,474 bp in length with 13 protein-coding genes, 22 different tRNA genes, 2 of them showing two copies, 2 rRNA genes, and a control region. Long-read sequencing enabled us to identify a 1826 bp perfect inverted repeat within the control region. Comparative analysis of the mitogenomes of related species in the Muricidae family revealed a conserved gene configuration for N. lapillus. We found a low genetic diversity, as well as a moderate genetic differentiation among the studied populations. Interestingly, there was no observed differentiation between the two chromosomal races, suggesting either introgression and permanent incorporation of the mitochondrial DNA haplotype from one of the chromosomal races into the other or a slower evolutionary rate of the mtDNAs with respect to that of the karyotypes. Our study serves as a foundation for comparative genomics and evolutionary investigations in this species. [ABSTRACT FROM AUTHOR]

The evolution of microRNAs (miRNAs) has been studied extensively to understand their roles in gene regulation and evolutionary processes. This review focuses on how miRNA‐mediated regulation has evolved in bilaterian animals, highlighting both convergent and divergent evolution. Since animals and plants display significant differences in miRNA biogenesis and target recognition, the 'independent origin' hypothesis proposes that miRNA pathways in these groups independently evolved from the RNA interference (RNAi) pathway, leading to modern miRNA repertoires through convergent evolution. However, recent evidence raises the alternative possibility that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and that the differences in miRNA pathway and miRNA repertoires among animal and plant lineages arise from lineage‐specific innovations and losses of miRNA pathways, miRNA acquisition, and loss of miRNAs after eukaryotic divergence. The repertoire of miRNAs has considerably expanded during bilaterian evolution, primarily through de novo creation and duplication processes, generating new miRNAs. Although ancient functionally established miRNAs are rarely lost, many newly emerged miRNAs are transient and lineage specific, following a birth–death evolutionary pattern aligning with the 'out‐of‐the‐testis' and 'transcriptional control' hypotheses. Our focus then shifts to the convergent molecular evolution of miRNAs. We summarize how miRNA clustering and seed mimicry contribute to this phenomenon, and we review how miRNAs from different sources converge to degrade maternal messenger RNAs (mRNAs) during animal development. Additionally, we describe how miRNAs evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, which can result in variations in target sites among orthologous miRNAs across distant strains or species. We also provide a summary of the current understanding regarding how the target sites of orthologous miRNAs can vary across strains or distantly related species. Although many paralogous miRNAs retain their seed or mature sequences after duplication, alterations can occur in the seed or mature sequences or expression patterns of paralogous miRNAs, leading to functional diversification. We discuss our current understanding of the functional divergence between duplicated miRNAs, and illustrate how the functional diversification of duplicated miRNAs impacts target site evolution. By investigating these topics, we aim to enhance our current understanding of the functions and evolutionary dynamics of miRNAs. Additionally, we shed light on the existing challenges in miRNA evolutionary studies, particularly the complexity of deciphering the role of miRNA‐mediated regulatory network evolution in shaping gene expression divergence and phenotypic differences among species. [ABSTRACT FROM AUTHOR]

Noise pollution, one of the most prominent features of urbanization, is an important factor influencing the vocal behavior of urban wildlife. Studies have reported that many songbirds raise their song minimum frequencies in response to urban noise. It has been proposed that this increased minimum frequency (IMF) of songs is an adaptation that allows urban populations to cope with the masking effect of noise pollution. However, urban populations of some songbirds do not exhibit significant IMF compared with non‐urban populations; thus, the notion that IMF is an adaptation to urban noise has been questioned. Furthermore, the effects of IMF might be influenced by both noise levels and the acoustic structures of songs. Here, we employed dichotomous and gradient effect size approaches to investigate IMF regarding two distinct acoustic structures (whistled and harmonic) in songs of six grey‐cheeked fulvetta Alcippe morrisonia morrisonia populations in Taiwan, three with high noise pollution and three with low noise pollution. We found that when using the dichotomous approach, paired populations with significant divergence in noise levels exhibited weak or insignificant divergence in the minimum frequencies for both whistled and harmonic phrases. In contrast, we found that when using the gradient approach, the effect size of noise‐level divergence was strongly correlated with the effect size of divergence in the minimum frequency of the harmonic phrase and only moderately correlated with the effect size of divergence in the minimum frequency of the whistled phrase. These findings suggest that noise pollution has a more pronounced effect on the divergence in the minimum frequency of harmonic phrases used in short‐range communication, compared to the whistled phrases used in long‐range communication. For population comparisons on the IMF, adopting a gradient approach could provide insights into the impact of noise pollution on the acoustic structures of songs across various communication ranges. [ABSTRACT FROM AUTHOR]

Abstract Subterranean and surface habitats are in stark contrast in several environmental factors. Therefore, adaptation to the subterranean environment typically impedes the (re)colonisation of surface habitats. The genus Niphargus includes amphipod crustaceans that primarily occupy subterranean habitats. All its species show typical adaptations to the subterranean environment. However, some Niphargus species occur in surface‐subterranean ecotones. To understand whether (i) habitat‐based phenotypic divergence is present between the cave and the ecotone species and (ii) similar phenotypes emerge independently in each ecotone, we studied morphological divergence between four cave and four ecotone Niphargus species based on 13 functional morphological traits. To account for different selection acting on the sexes, we included both males (N = 244) and females (N = 222). Nine out of 13 traits showed habitat‐divergence. Traits related to feeding and crawling were shorter, while traits related to oxygenation were larger in ecotone species. Eleven out of 13 traits were sexually dimorphic. Traits related to oxygenation and crawling were larger in females, while the trait related to swimming was larger in males. We found that the extent of sexual dimorphism differs between the habitats in eight traits related to sensing, feeding, oxygenation and crawling. Additionally, we found that in certain traits related to sensing and oxygenation, habitat‐related differences are only present in one sex, but not the other. We conclude that the detected differences between the cave and the ecotone species indicate divergent evolution, where similarities among the different species within habitat type indicate convergent evolution. The high degree of sexual dimorphism paired with differences in sexual dimorphism between the habitats in certain traits suggest that sexual and fecundity selections have comparable effects to environmental selection. Thus, studies of habitat‐dependent adaptations investigating one sex only, or not considering sexual dimorphism, can lead to erroneous conclusions.

Noise pollution, one of the most prominent features of urbanization, is an important factor influencing the vocal behavior of urban wildlife. Studies have reported that many songbirds raise their song minimum frequencies in response to urban noise. It has been proposed that this increased minimum frequency (IMF) of songs is an adaptation that allows urban populations to cope with the masking effect of noise pollution. However, urban populations of some songbirds do not exhibit significant IMF compared with non‐urban populations; thus, the notion that IMF is an adaptation to urban noise has been questioned. Furthermore, the effects of IMF might be influenced by both noise levels and the acoustic structures of songs. Here, we employed dichotomous and gradient effect size approaches to investigate IMF regarding two distinct acoustic structures (whistled and harmonic) in songs of six grey‐cheeked fulvetta Alcippe morrisonia morrisonia populations in Taiwan, three with high noise pollution and three with low noise pollution. We found that when using the dichotomous approach, paired populations with significant divergence in noise levels exhibited weak or insignificant divergence in the minimum frequencies for both whistled and harmonic phrases. In contrast, we found that when using the gradient approach, the effect size of noise‐level divergence was strongly correlated with the effect size of divergence in the minimum frequency of the harmonic phrase and only moderately correlated with the effect size of divergence in the minimum frequency of the whistled phrase. These findings suggest that noise pollution has a more pronounced effect on the divergence in the minimum frequency of harmonic phrases used in short‐range communication, compared to the whistled phrases used in long‐range communication. For population comparisons on the IMF, adopting a gradient approach could provide insights into the impact of noise pollution on the acoustic structures of songs across various communication ranges.

FAD‐independent methylene‐tetrahydrofolate (methylene‐H4F) reductase (Mfr), recently identified in mycobacteria, catalyzes the reduction of methylene‐H4F to methyl‐H4F with NADH as hydride donor by a ternary complex mechanism. This biochemical reaction corresponds to that of the ubiquitous FAD‐dependent methylene‐H4F reductase (MTHFR), although the latter uses a ping‐pong mechanism with the prosthetic group as intermediate hydride carrier. Comparative genomics and genetic analyses indicated that Mfr is indispensable for the growth of Mycobacterium tuberculosis, which lacks the MTHFR encoding gene. Therefore, Mfr appears to be an excellent target for the design of antimycobacterial drugs. Here, we report the heterologous production, enzymological characterization, and the crystal structure of Mfr from the thermophilic mycobacterium Mycobacterium hassiacum (hMfr), which shows 78% sequence identity to Mfr from M. tuberculosis. Although hMfr and MTHFR have minor sequence identity and different catalytic mechanisms, their structures are highly similar, thus suggesting a divergent evolution of Mfr and MTHFR from a common ancestor. Most of the important active site residues of MTHFR are conserved and equivalently positioned in the tertiary structure of hMfr. The Glu9Gln variant of hMfr exhibits a drastic reduction of the catalytic activity, which supports the predicted function of the glutamate residue as proton donor in both hMfr and MTHFR. Thus, highly similar binding modes for the C1‐carriers and the reducing agents in hMfr and MTHFR are assumed. [ABSTRACT FROM AUTHOR]

The Severe Acute Respiratory Syndrome 2 (COVID-19/SARS-CoV-2) has become the pandemic of the century due to its drastically infectious nature. SARS & MERS are the most notable of past coronaviruses infecting merely thousands compared to COVID-19s gigantic magnitude. COVID-19s global spread has been attributed to its high asymptotic transmission and explosive infectious nature, mainly due to mutational changes in the spike glycoprotein. The purpose of this research is to comprehend & evaluate the divergent evolution of the spike glycoprotein in COVID-19, and other coronaviruses, at the molecular level via bioinformatic analysis. A phylogenetic tree was constructed using spike glycoprotein sequences from viral genomes using MEGA X program. Nucleotide composition analysis and genome organization study were carried out. Dot plot comparisons were performed using EMBOSS Dot Matcher program. Phylogenetic analysis produced four distinct clades for each coronavirus genera with a common ancestral origin sometime in recent history. More importantly, COVID-19 and SARS formed their own subclade suggesting that evolution of sequence has taken place in the spike glycoprotein over the period time. Genome organization and nucleotide composition provided further evidence of mutational changes in the spike glycoprotein. The results from this study demonstrated the divergent evolution of coronaviruses. Mutational changes in the spike glycoprotein have resulted in more virulent forms of COVID-19. [Med-Science 2022; 11(1.000): 171-5]

The inflation of SARS-CoV-2 lineages with a high number of accumulated mutations (such as the recent case of Omicron) has risen concerns about the evolutionary capacity of this virus. Here, we propose a computational study to examine non-synonymous mutations gathered within genomes of SARS-CoV-2 from the beginning of the pandemic until February 2022. We provide both qualitative and quantitative descriptions of such corpus, focusing on statistically significant co-occurring and mutually exclusive mutations within single genomes. Then, we examine in depth the distributions of mutations over defined lineages and compare those of frequently co-occurring mutation pairs. Based on this comparison, we study mutations’ convergence/divergence on the phylogenetic tree. As a result, we identify 1,818 co-occurring pairs of non-synonymous mutations showing at least one event of convergent evolution and 6,625 co-occurring pairs with at least one event of divergent evolution. Notable examples of both types are shown by means of a tree-based representation of lineages, visually capturing mutations’ behaviors. Our method confirms several well-known cases; moreover, the provided evidence suggests that our workflow can explain aspects of the future mutational evolution of SARS-CoV-2.

Two types of nitrogen-fixing root nodule symbioses are known, rhizobial and actinorhizal symbioses. The latter involve plants of three orders, Fagales, Rosales, and Cucurbitales. To understand the diversity of plant symbiotic adaptation, we compared the nodule transcriptomes of Datisca glomerata (Datiscaceae, Cucurbitales) and Ceanothus thyrsiflorus (Rhamnaceae, Rosales); both species are nodulated by members of the uncultured Frankia clade, cluster II. The analysis focused on various features. In both species, the expression of orthologs of legume Nod factor receptor genes was elevated in nodules compared to roots. Since arginine has been postulated as export form of fixed nitrogen from symbiotic Frankia in nodules of D. glomerata, the question was whether the nitrogen metabolism was similar in nodules of C. thyrsiflorus. Analysis of the expression levels of key genes encoding enzymes involved in arginine metabolism revealed up-regulation of arginine catabolism, but no up-regulation of arginine biosynthesis, in nodules compared to roots of D. glomerata, while arginine degradation was not upregulated in nodules of C. thyrsiflorus. This new information corroborated an arginine-based metabolic exchange between host and microsymbiont for D. glomerata, but not for C. thyrsiflorus. Oxygen protection systems for nitrogenase differ dramatically between both species. Analysis of the antioxidant system suggested that the system in the nodules of D. glomerata leads to greater oxidative stress than the one in the nodules of C. thyrsiflorus, while no differences were found for the defense against nitrosative stress. However, induction of nitrite reductase in nodules of C. thyrsiflorus indicated that here, nitrite produced from nitric oxide had to be detoxified. Additional shared features were identified: genes encoding enzymes involved in thiamine biosynthesis were found to be upregulated in the nodules of both species. Orthologous nodule-specific subtilisin-like proteases that have been linked to the infection process in actinorhizal Fagales, were also upregulated in the nodules of D. glomerata and C. thyrsiflorus. Nodule-specific defensin genes known from actinorhizal Fagales and Cucurbitales, were also found in C. thyrsiflorus. In summary, the results underline the variability of nodule metabolism in different groups of symbiotic plants while pointing at conserved features involved in the infection process.

Understanding the mechanisms that drive community assembly in species‐rich tropical forest remains a fundamental challenge in ecology. Here, we integrated multivariate functional trait dimensions, phylogeny and metabolomics to test fundamental predictions concerning the role of differentiation with respect to abiotic and biotic niche axes in the maintenance of high local diversity of woody plants in the Euphorbiaceae.We measured 40 functional traits related to resource acquisition, photosynthetic capacity, hydraulic efficiency and secondary‐metabolite profiles generated using untargeted metabolomics in all 26 Euphorbiaceae species in a 20‐ha forest dynamics plot in tropical southwestern China. We examined the correlation structure of 40 traits using a trait networking approach. We coupled these traits with variation in soil nutrients, light environment, soil water content and herbivore pressure within the plot to assess niche differentiation in space. We compared phylogenetic signal among multivariate trait dimensions and secondary metabolites to assess niche differentiation in evolutionary time.Network analysis revealed that a small number of traits with high network centrality reflected variation in ecological strategy among the Euphorbiaceae. Using these high‐centrality traits, we observed significant functional turnover along environmental gradients defined by light, soil moisture, soil nutrients and leaf herbivory, respectively. Most resource utilization traits showed significant phylogenetic signal, whereas almost all defensive traits lacked phylogenetic signal, including species similarity with respect to plant secondary metabolites.Synthesis. Our results suggest that resource‐utilization traits and the habitat associations play a significant role in the niche segregation of co‐occurring woody plants in the Euphorbiaceae. Secondary metabolites, however, may enhance diversity at a finer spatial scale by allowing closely related species with similar functional traits to partition biotic niche space within shared habitats in tropical rainforest. [ABSTRACT FROM AUTHOR]

Abstract Background Sexual selection has been considered to promote diversification and speciation. Sexually dimorphic species have been used to explore the supposed effect, however, with mixed results. In dwarf spiders (Erigoninae), many species are sexually dimorphic—males possess marked prosomal modifications. These male traits vary from moderate elevations to bizarre shapes in various prosomal regions. Previous studies established that male dwarf spiders produce substances in these prosomal modifications that are taken up by the females. These substances can act as nuptial gifts, which increase the mating probability of males and the oviposition rate in females. Therefore, these dimorphic traits have evolved in the context of sexual selection. Here, we explore the evolutionary lability of this gustatory trait complex with the aim of assessing the role of this trait complex in species divergence by investigating (1) if erigonine modified prosomata are inherently linked to nuptial-gift-producing glands, (2) if the evolution of the glands evolution preceded that of the modified prosomal shapes, and by assessing (3) the occurrence of convergent/divergent evolution and cryptic differentiation. Results We reconstructed the position and extent of the glandular tissue along with the muscular anatomy in the anterior part of the prosoma of 76 erigonine spiders and three outgroup species using X-ray micro-computed tomography. In all but one case, modified prosomata are associated with gustatory glands. We incorporated the location of glands and muscles into an existing matrix of somatic and genitalic morphological traits of these taxa and reanalyzed their phylogenetic relationship. Our analysis supports that the possession of glandular equipment is the ancestral state and that the manifold modifications of the prosomal shape have evolved convergently multiple times. We found differences in gland position between species with both modified and unmodified prosomata, and reported on seven cases of gland loss. Conclusions Our findings suggest that the occurrence of gustatory glands in sexually monomorphic ancestors has set the stage for the evolution of diverse dimorphic external modifications in dwarf spiders. Differences among congeners suggest that the gland position is highly susceptible to evolutionary changes. The multiple incidences might reflect costs of glandular tissue maintenance and nuptial feeding. Our results indicate divergent evolutionary patterns of gustatory-courtship-related traits, and thus a likely facilitating effect of sexual selection on speciation.

The allotetraploid Solanaceae plant Nicotiana benthamiana contains two closely related receptor-like proteins (RLPs), NbEIX2 and NbRXEG1, which regulate the recognition of VdEIX3 and PsXEG1, respectively. VdEIX3, PsXEG1, and their homologs represent two types of microbe-associated molecular patterns (MAMPs) that are widespread in diverse pathogens. Here, we report that NbRXEG1 also participates in VdEIX3 recognition. Both eix2 and rxeg1 single mutants exhibited significantly impaired but not abolished ability to mediate VdEIX3-triggered immune responses, which are nearly abolished in eix2 rxeg1 double mutants. Moreover, a dominant negative mutant of eix2 that contains a 60 bp deletion failed to respond to VdEIX3 and could suppress VdEIX3-induced cell death in the wild-type N. benthamiana. Further phylogenetic analyses showed that NbEIX2 and NbRXEG1 are obtained from different diploid ancestors by hybridization. These results demonstrate that the allotetraploid N. benthamiana recognizes two types of MAMPs by two homologous but diverged RLPs, which provides a model in which an allopolyploid plant probably exhibits defense hybrid vigor by acquiring divergent immune receptors from different ancestors. [ABSTRACT FROM AUTHOR]

Summary: Resource‐use strategies are hypothesized to evolve along climatic gradients. However, our understanding of the environmental factors driving divergent evolution of resource‐use strategies and the relationship between trait genetic variation and phenotypic plasticity is far from complete. Using the Mediterranean tree Quercus faginea as study system, we tested the hypothesis that a conservative resource‐use strategy with increased drought tolerance and reduced phenotypic plasticity has evolved in areas with longer and more severe dry seasons.We conducted a glasshouse experiment in which we measured leaf morphological, physiological, growth and allocation traits in seedlings from 10 range‐wide climatically contrasting populations, grown under two different watering treatments.Both univariate and multivariate analyses revealed a genetic gradient of resource‐use strategies and phenotypic plasticity associated with provenance climate. In particular, populations from harsher (drier and colder) environments had more sclerophyllous leaves, lower growth rates, better physiological performance under dry conditions and reduced multi‐trait phenotypic plasticity compared to populations from more mesic and milder environments.Our results suggest that contrasting precipitation and temperature regimes play an important role in the adaptive intraspecific evolution of multivariate phenotypes and their plasticity, resulting in coordinated morphology, physiology, growth and allometry according to alternative resource‐use strategies. [ABSTRACT FROM AUTHOR]

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced‐representation sequencing of native samples collected recently in northwestern Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid‐19th century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges. [ABSTRACT FROM AUTHOR]

The Severe Acute Respiratory Syndrome 2 (COVID-19/SARS-CoV-2) has become the pandemic of the century due to its drastically infectious nature. SARS & MERS are the most notable of past coronaviruses infecting merely thousands compared to COVID-19's gigantic magnitude. COVID-19's global spread has been attributed to its high asymptotic transmission and explosive infectious nature, mainly due to mutational changes in the spike glycoprotein. The purpose of this research is to comprehend & evaluate the divergent evolution of the spike glycoprotein in COVID-19, and other coronaviruses, at the molecular level via bioinformatic analysis. A phylogenetic tree was constructed using spike glycoprotein sequences from viral genomes using MEGA X program. Nucleotide composition analysis and genome organization study were carried out. Dot plot comparisons were performed using EMBOSS Dot Matcher program. Phylogenetic analysis produced four distinct clades for each coronavirus genera with a common ancestral origin sometime in recent history. More importantly, COVID-19 and SARS formed their own subclade suggesting that evolution of sequence has taken place in the spike glycoprotein over the period time. Genome organization and nucleotide composition provided further evidence of mutational changes in the spike glycoprotein. The results from this study demonstrated the divergent evolution of coronaviruses. Mutational changes in the spike glycoprotein have resulted in more virulent forms of COVID-19. [ABSTRACT FROM AUTHOR]

ABSTRACT Carbapenem-resistant Klebsiella pneumoniae (CRKp) is an urgent public health threat. Worldwide dissemination of CRKp has been largely attributed to clonal group (CG) 258. However, recent evidence indicates the global emergence of a CRKp CG307 lineage. Houston, TX, is the first large city in the United States with detected cocirculation of both CRKp CG307 and CG258. We sought to characterize the genomic and clinical factors contributing to the parallel endemic spread of CG258 and CG307. CRKp isolates were collected as part of the prospective, Consortium on Resistance against Carbapenems in Klebsiella and other Enterobacterales 2 (CRACKLE-2) study. Hybrid short-read and long-read genome assemblies were generated from 119 CRKp isolates (95 originated from Houston hospitals). A comprehensive characterization of phylogenies, gene transfer, and plasmid content with pan-genome analysis was performed on all CRKp isolates. Plasmid mating experiments were performed with CG307 and CG258 isolates of interest. Dissection of the accessory genomes suggested independent evolution and limited horizontal gene transfer between CG307 and CG258 lineages. CG307 contained a diverse repertoire of mobile genetic elements, which were shared with other non-CG258 K. pneumoniae isolates. Three unique clades of Houston CG307 isolates clustered distinctly from other global CG307 isolates, indicating potential selective adaptation of particular CG307 lineages to their respective geographical niches. CG307 strains were often isolated from the urine of hospitalized patients, likely serving as important reservoirs for genes encoding carbapenemases and extended-spectrum β-lactamases. Our findings suggest parallel cocirculation of high-risk lineages with potentially divergent evolution. IMPORTANCE The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKp) infections in nosocomial settings remains a public health challenge. High-risk clones such as clonal group 258 (CG258) are particularly concerning due to their association with blaKPC carriage, which can severely complicate antimicrobial treatments. There is a recent emergence of clonal group 307 (CG307) worldwide with little understanding of how this successful clone has been able to adapt while cocirculating with CG258. We provide the first evidence of potentially divergent evolution between CG258 and CG307 with limited sharing of adaptive genes. Houston, TX, is home to the largest medical center in the world, with a large influx of domestic and international patients. Thus, our unique geographical setting, where two pandemic strains of CRKp are circulating, provides an indication of how differential accessory genome content can drive stable, endemic populations of CRKp. Pan-genomic analyses such as these can reveal unique signatures of successful CRKp dissemination, such as the CG307-associated plasmid (pCG307_HTX), and provide invaluable insights into the surveillance of local carbapenem-resistant Enterobacterales (CRE) epidemiology.

Abstract Background EP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy. Danio rerio is a promising model organism to study EP300 related diseases and drugs; however, the effect of EP300 duplicates derived from teleost-specific whole genome duplication should not just be neglected. Results In this study, we obtained EP300 protein sequences of representative teleosts, mammals and sauropsids, with which we inferred a highly supported maximum likelihood tree. We observed that Ep300 duplicates (Ep300a and Ep300b) were widely retained in teleosts and universally expressed in a variety of tissues. Consensus sequences of Ep300a and Ep300b had exactly the same distribution of conserved domains, suggesting that their functions should still be largely overlapped. We analyzed the molecular evolution of Ep300 duplicates in teleosts, using branch-site models, clade models and site models. The results showed that both duplicates were subject to strong positive selection; however, for an extant species, generally at most one copy was under positive selection. At the clade level, there were evident positive correlations between evolutionary rates, the number of positively selected sites and gene expression levels. In Ostariophysi, Ep300a were under stronger positive selection than Ep300b; in Neoteleostei, another species-rich teleost clade, the contrary was the case. We also modeled 3D structures of zf-TAZ domain and its flanking regions of Ep300a and Ep300b of D. rerio and Oryzias latipes and found that in either species the faster evolving copy had more short helixes. Conclusions Collectively, the two copies of Ep300 have undoubtedly experienced directional divergence in main teleost clades. The divergence of EP300 between teleosts and mammals should be greater than the divergence between different teleost clades. Further studies are needed to clarify to what extent the EP300 involved regulatory network has diverged between teleosts and mammals, which would also help explain the huge success of teleosts.

Abstract Background The alignment of character sequences is important in bioinformatics. The quality of this procedure is determined by the substitution matrix and parameters of the insertion-deletion penalty function. These matrices are derived from sequence alignment and thus reflect the evolutionary process. Currently, in addition to evolutionary matrices, a large number of different background matrices have been obtained. To make an optimal choice of the substitution matrix and the penalty parameters, we conducted a numerical experiment using a representative sample of existing matrices of various types and origins. Results We tested both the classical evolutionary matrix series (PAM, Blosum, VTML, Pfasum); structural alignment based matrices, contact energy matrix, and matrix based on the properties of the genetic code. This study presents results for two test set types: first, we simulated sequences that reflect the divergent evolution; second, we performed tests on Balibase sequences. In both cases, we obtained the dependences of the alignment quality (Accuracy, Confidence) on the evolutionary distance between sequences and the evolutionary distance to which the substitution matrices correspond. Optimization of a combination of matrices and the penalty parameters was carried out for local and global alignment on the values of penalty function parameters. Consequently, we found that the best alignment quality is achieved with matrices corresponding to the largest evolutionary distance. These matrices prove to be universal, i.e. suitable for aligning sequences separated by both large and small evolutionary distances. We analysed the correspondence of the correlation coefficients of matrices to the alignment quality. It was found that matrices showing high quality alignment have an above average correlation value, but the converse is not true. Conclusions This study showed that the best alignment quality is achieved with evolutionary matrices designed for long distances: Gonnet, VTML250, PAM250, MIQS, and Pfasum050. The same property is inherent in matrices not only of evolutionary origin, but also of another background corresponding to a large evolutionary distance. Therefore, matrices based on structural data show alignment quality close enough to its value for evolutionary matrices. This agrees with the idea that the spatial structure is more conservative than the protein sequence.

Mycoplasmas are a group of prokaryotes without cell walls that have evolved through several rounds of degenerative evolution. With a low cell DNA G + C content and definitively long genetic lineages, mycoplasmas are thought to be in a state of rapid evolution. However, little associated evidence has been provided. Enolase is a key enzyme in glycolysis that is widely found in all species from the three domains, and it is evolutionarily conserved. In our previous studies, enolase acted as a virulence factor and participated in cell-surface adhesion in Mycoplasma hyopneumoniae. Furthermore, unique loop regions were first found in the crystal structure of Mhp Eno. Here, enolase structures from Mycoplasma pneumoniae and Mycoplasma bovis were determined. An extra helix 7 is specific and conservatively found in almost all mycoplasma enolases, as confirmed by crystal structures and sequence alignment. Particular motifs for helix 7, which is composed of F-K/G-K-L/F-K-X-A-I, have been proposed and could be regarded as molecular markers. To our surprise, the genetic distances between any two mycoplasma enolases were obviously longer than those between the two corresponding species themselves, indicating divergent evolution of mycoplasma enolases, whereas no horizontal gene transfer was detected in mycoplasma enolase genens. Furthermore, different evolutionary patterns were adopted by different loop regions of mycoplasma enolase. Enolases from different Mycoplasma species also showed different affinities for PLG and fibronectin. Our results indicate the rapid and divergent evolution of mycoplasma enolase and mycoplasmas. This study will also aid understanding the independent evolution of Mycoplasma species after separation from their common ancestor.

True sea snakes (Hydrophiini) are among the last and most successful clades of vertebrates that show secondary marine adaptation, exhibiting diverse phenotypic traits and lethal venom systems. To better understand their evolution, we generated the first chromosome-level genomes of two representative Hydrophiini snakes, Hydrophis cyanocinctus and H. curtus. Through comparative genomics we identified a great expansion of the underwater olfaction-related V2R gene family, consisting of more than 1,000 copies in both snakes. A series of chromosome rearrangements and genomic structural variations were recognized, including large inversions longer than 30 megabase (Mb) on sex chromosomes which potentially affect key functional genes associated with differentiated phenotypes between the two species. By integrating multiomics we found a significant loss of the major weapon for elapid predation, three-finger toxin genes, which displayed a dosage effect in H. curtus. These genetic changes may imply mechanisms that drove the divergent evolution of adaptive traits including prey preferences between the two closely related snakes. Our reference-quality sea snake genomes also enrich the repositories for addressing important issues on the evolution of marine tetrapods, and provide a resource for discovering marine-derived biological products. [ABSTRACT FROM AUTHOR]

Background: Sexual selection has been considered to promote diversification and speciation. Sexually dimorphic species have been used to explore the supposed effect, however, with mixed results. In dwarf spiders (Erigoninae), many species are sexually dimorphic—males possess marked prosomal modifications. These male traits vary from moderate elevations to bizarre shapes in various prosomal regions. Previous studies established that male dwarf spiders produce substances in these prosomal modifications that are taken up by the females. These substances can act as nuptial gifts, which increase the mating probability of males and the oviposition rate in females. Therefore, these dimorphic traits have evolved in the context of sexual selection. Here, we explore the evolutionary lability of this gustatory trait complex with the aim of assessing the role of this trait complex in species divergence by investigating (1) if erigonine modified prosomata are inherently linked to nuptial-gift-producing glands, (2) if the evolution of the glands evolution preceded that of the modified prosomal shapes, and by assessing (3) the occurrence of convergent/divergent evolution and cryptic differentiation. Results: We reconstructed the position and extent of the glandular tissue along with the muscular anatomy in the anterior part of the prosoma of 76 erigonine spiders and three outgroup species using X-ray micro-computed tomography. In all but one case, modified prosomata are associated with gustatory glands. We incorporated the location of glands and muscles into an existing matrix of somatic and genitalic morphological traits of these taxa and reanalyzed their phylogenetic relationship. Our analysis supports that the possession of glandular equipment is the ancestral state and that the manifold modifications of the prosomal shape have evolved convergently multiple times. We found differences in gland position between species with both modified and unmodified prosomata, and reported on seven cases of gland loss. Conclusions: Our findings suggest that the occurrence of gustatory glands in sexually monomorphic ancestors has set the stage for the evolution of diverse dimorphic external modifications in dwarf spiders. Differences among congeners suggest that the gland position is highly susceptible to evolutionary changes. The multiple incidences might reflect costs of glandular tissue maintenance and nuptial feeding. Our results indicate divergent evolutionary patterns of gustatory-courtship-related traits, and thus a likely facilitating effect of sexual selection on speciation. [ABSTRACT FROM AUTHOR]

The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes—the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni.

Ecological character displacement is a prominent hypothesis for the maintenance of ecological differences between species that are critical to stable coexistence. Models of character displacement often ascribe interspecific competitive interactions to a single character, but multiple characters contribute to competition, and their effects on selection can be nonadditive. Focusing on one character, we ask if other characters that affect competition alter evolutionary outcomes for the focal character. We address this question using the variable environment seed bank model for two species with two traits. The focal trait is the temporal pattern of germination, which is evolutionary labile. The other trait is the temporal pattern of plant growth, which is assumed fixed. We ask whether evolutionary divergence of germination patterns between species depends on species differences in plant growth. Patterns of growth can affect selection on germination patterns in two ways. First, cues present at germination can provide information about future growth. Second, germination and growth jointly determine the biomass of plants, which determines demand for resources. Germination and growth contribute to the selection gradient in distinct components, one density-independent and the other density-dependent. Importantly, the relative strengths of the components are key. When the density-dependent component is stronger, displacement in germination patterns between species is larger. Stronger cues at germination strengthen the density-independent component by increasing the benefits of germinating in years of favorable growth. But cues also affect the density-dependent component by boosting a species' biomass, and hence its competitive effect, in good years. Consequently, cues weaken character displacement when growth patterns are similar for two competitors, but favor displacement when growth patterns are species-specific. Understanding how these selection components change between contexts can help understand the origin and maintenance of species differences in germination patterns in temporally fluctuating environments. [ABSTRACT FROM AUTHOR]

The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes—the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni. [ABSTRACT FROM AUTHOR]

Abstract Background Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. Results Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case study, taxonomic reclassifications of many isolates provides novel insights into their phylogenetic lineage. Whole-genome-based comparisons were attempted to investigate the intra- and inter-species divergence. Recent studies clarified that functional and structural specificities of bacterial strains might provide opportunities for adaptive evolution responding to local environmental conditions. Acidophilic microorganisms play a key role in the acidification of natural waters and thus the formation of extremely acidic environments, and the feedbacks of the latter might confer the distinct evolutionary patterns of Acidithiobacillus spp. Varied horizontal gene transfer events occurred in different bacterial strains, probably resulting in the expansion of Acidithiobacillus genomes. Gene loss as another evolutionary force might cause the adaptive phenotypic diversity. A conceptual model for potential community-dependent evolutionary adaptation was thus proposed to illustrate the observed genome differentiation. Conclusions Collectively, the findings shed light on the phylogeny and divergent evolution of Acidithiobacillus strains, and provided a useful reference for evolutionary studies of other extremophiles.

Over the last two decades, a trend of multiculturalism in world history has enjoyed a largely uncontested rise to prominence. Its main aim has been to challenge Eurocentrism. Its main achievement is to have issued a corrective in early modern economic history: prior to the industrial revolution, there were numerous economic parallels between Europe and Asia, particularly China. But multicultural world history is now under greater scrutiny and challenge for marginalizing the West and downplaying numerous non-economic divergences of the West. In response, a post-multicultural world history is now emerging. Its most important work so far is Ricardo Duchesne’s The Uniqueness of Western Civilization (2011). The main achievement of post-multicultural world history is to have established that there were numerous critical non-economic divergences between Europe and other regions. The West was both peculiar and inventive across many domains.

There was a wave of whole genome duplications (WGD) during and subsequent to the K-Pg interface, which was followed by an increase in the proportion of species that were polyploid. I consider why this wave of polyploid speciation has continued to rise through the divergent evolution of polyploid lineages, and through rounds of homoploid and heteroploid chromosomal change. I also consider why the polyploid speciation wave is likely to rise in the next millennium. I propose that the speed of polyploid genesis through ploidal increase and through diversification among polyploids likely will be greater than the speed of diploid speciation. The increase in polyploid diversity is expected to lag well behind episodes of WGD, owing to the very long period required for species diversification either by lineage splitting or additional rounds of polyploidy, in addition to the long period of genomic adjustment to higher ploidal levels in neopolyploids.

Summary: It is hypothesised that tree distributions in Europe are largely limited by their ability to cope with the summer drought imposed by the Mediterranean climate in the southern areas and by their competitive potential in central regions with more mesic conditions.We investigated the extent to which leaf and plant morphology, gas exchange, leaf and stem hydraulics and growth rates have evolved in a coordinated way in oaks (Quercus) as a result of adaptation to contrasting environmental conditions in this region. We implemented an experiment in which seedlings of 12 European/North African oaks were grown under two watering treatments, a well‐watered treatment and a drought treatment in which plants were subjected to three cycles of drought.Consistent with our hypothesis, species from drier summers had traits conferring more tolerance to drought such as small sclerophyllous leaves and lower percent loss of hydraulic conductivity. However, these species did not have lower growth rates as expected by a trade‐off with drought tolerance.Overall, our results revealed that climate is an important driver of functional strategies in oaks and that traits have evolved along two coordinated functional axes to adapt to different precipitation and temperature regimes. See also the Commentary on this article by Cavender‐Bares et al., (2020) 227: 659–663. [ABSTRACT FROM AUTHOR]

There was a wave of whole genome duplications (WGD) during and subsequent to the K-Pg interface, which was followed by an increase in the proportion of species that were polyploid. I consider why this wave of polyploid speciation has continued to rise through the divergent evolution of polyploid lineages, and through rounds of homoploid and heteroploid chromosomal change. I also consider why the polyploid speciation wave is likely to rise in the next millennium. I propose that the speed of polyploid genesis through ploidal increase and through diversification among polyploids likely will be greater than the speed of diploid speciation. The increase in polyploid diversity is expected to lag well behind episodes of WGD, owing to the very long period required for species diversification either by lineage splitting or additional rounds of polyploidy, in addition to the long period of genomic adjustment to higher ploidal levels in neopolyploids. [ABSTRACT FROM AUTHOR]

An undescribed species of Microcambeva , a genus of small psammophilic catfishes from the Atlantic Forest of south-eastern Brazil, was found together the congener Microcambeva ribeirae inhabiting the same sand stretch of a stream, in the Rio Ribeira do Iguape basin. The new species and its sympatric congener exhibit highly divergent morphological features, but a multigene phylogeny support them as sister taxa. The new species, M. filamentosa sp. nov., is readily distinguished from all other congeners by the presence of long barbels, long filamentous first pectoral-fin ray and a hypertrophied predorsal adipose fold. Microcambeva filamentosa and M. ribeirae share two unique apomorphic features: a single supraorbital pore s6 situated on the centre of the dorsal surface of the head and a deep concavity between the dorsal process of the opercle and the opercular odontode patch, conditions that are independently acquired in other psammophilic trichomycterids. A comparative context, involving other trichomycterid lineages exhibiting similar morphological adaptations, highly suggests that morphological differences between M. filamentosa and M. ribeirae are related to different strategies to exploit their habitat. In M. ribeirae , the short and thickened first pectoral-fin ray is interpreted as an adaptation to the fish posing propped on the substratum while visually detecting potential preys, what is reinforced by the unique possession in this taxon of a relatively large eye positioned on the top of the head. On the other hand, the relatively small eye and long barbels of M. filamentosa highly suggest the use of a predominantly chemosensory and tactile detection of food, indicating possible nocturnal habits. [ABSTRACT FROM AUTHOR]

Mammals inhabit a wide variety of ecological niches, which in turn can be affected by various ecological factors, especially in relation to immunity. The canonical TRC repertoire (TRAC, TRBC, TRGC, and TRDC) codes C regions of T cell receptor chains that form the primary antigen receptors involved in the activation of cellular immunity. At present, little is known about the correlation between the evolution of mammalian TRC genes and ecological factors. In this study, four types canonical of TRC genes were identified from 37 mammalian species. Phylogenetic comparative methods (phyANOVA and PGLS) and selective pressure analyses among different groups of ecological factors (habitat, diet, and sociality) were carried out. The results showed that habitat was the major ecological factor shaping mammalian TRC repertoires. Specifically, trade-off between TRGC numbers and positive selection of TRAC and the balanced evolutionary rates between TRAC and TRDC genes were speculated as two main mechanisms in adaption to habitat and sociality. Overall, our study suggested divergent mechanisms for the evolution of TRCs, prompting mammalian immunity adaptions within diverse niches.

Dry forests characterize many of the biomes of southern South America and the Andes, such as the Chaco and the inter-Andean valley forests, which form a continuous belt (Chaco–Andes dry forest belt). Some of the taxa that inhabit this forest belt present genetic and phenotypic differentiation between edges of the region, which suggests the action of divergent evolutionary processes between forests (i.e., parapatric divergence). In order to test this hypothesis, we studied the morphological and phylogeographic variation of the White-tipped Plantcutter Phytotoma rutila (Cotingidae) and evaluated predictions of genetic and morphological evolutionary processes (e.g., local adaptation). The results supported that the environmental gradient along the Chaco–Andes dry forests might be promoting diversification because we found that body size of the White-tipped Plantcutter varied according to a step cline related to altitude, and thus parapatric processes might be responsible for this pattern. There are other taxa co-distributed across the study region presenting similar patterns of geographic variation, which suggests the action of concerted evolutionary phenomena in the Chaco–Andes dry forest. [ABSTRACT FROM AUTHOR]

A major goal of evolutionary science is to understand how biological diversity is generated and altered. Despite considerable advances, we still have limited insight into how phenotypic variation arises and is sorted by natural selection. Here we argue that an integrated view, which merges ecology, evolution and developmental biology (eco evo devo) on an equal footing, is needed to understand the multifaceted role of the environment in simultaneously determining the development of the phenotype and the nature of the selective environment, and how organisms in turn affect the environment through eco evo and eco devo feedbacks. To illustrate the usefulness of an integrated eco evo devo perspective, we connect it with the theory of resource polymorphism (i.e. the phenotypic and genetic diversification that occurs in response to variation in available resources). In so doing, we highlight fishes from recently glaciated freshwater systems as exceptionally well‐suited model systems for testing predictions of an eco evo devo framework in studies of diversification. Studies on these fishes show that intraspecific diversity can evolve rapidly, and that this process is jointly facilitated by (i) the availability of diverse environments promoting divergent natural selection; (ii) dynamic developmental processes sensitive to environmental and genetic signals; and (iii) eco evo and eco devo feedbacks influencing the selective and developmental environments of the phenotype. We highlight empirical examples and present a conceptual model for the generation of resource polymorphism – emphasizing eco evo devo, and identify current gaps in knowledge. [ABSTRACT FROM AUTHOR]

Summary: Glycyrrhizin, a sweet triterpenoid saponin found in the roots and stolons of Glycyrrhiza species (licorice), is an important active ingredient in traditional herbal medicine. We previously identified two cytochrome P450 monooxygenases, CYP88D6 and CYP72A154, that produce an aglycone of glycyrrhizin, glycyrrhetinic acid, in Glycyrrhiza uralensis. The sugar moiety of glycyrrhizin, which is composed of two glucuronic acids, makes it sweet and reduces its side‐effects. Here, we report that UDP‐glycosyltransferase (UGT) 73P12 catalyzes the second glucuronosylation as the final step of glycyrrhizin biosynthesis in G. uralensis; the UGT73P12 produced glycyrrhizin by transferring a glucuronosyl moiety of UDP‐glucuronic acid to glycyrrhetinic acid 3‐O‐monoglucuronide. We also obtained a natural variant of UGT73P12 from a glycyrrhizin‐deficient (83‐555) strain of G. uralensis. The natural variant showed loss of specificity for UDP‐glucuronic acid and resulted in the production of an alternative saponin, glucoglycyrrhizin. These results are consistent with the chemical phenotype of the 83‐555 strain, and suggest the contribution of UGT73P12 to glycyrrhizin biosynthesis in planta. Furthermore, we identified Arg32 as the essential residue of UGT73P12 that provides high specificity for UDP‐glucuronic acid. These results strongly suggest the existence of an electrostatic interaction between the positively charged Arg32 and the negatively charged carboxy group of UDP‐glucuronic acid. The functional arginine residue and resultant specificity for UDP‐glucuronic acid are unique to UGT73P12 in the UGT73P subfamily. Our findings demonstrate the functional specialization of UGT73P12 for glycyrrhizin biosynthesis during divergent evolution, and provide mechanistic insights into UDP‐sugar selectivity for the rational engineering of sweet triterpenoid saponins. Significance Statement: Glycyrrhizin, a licorice‐derived sweet triterpenoid diglycoside, is one of the most important phytoconstituents in the pharmaceutical and food industries. Here, we identified UGT73P12 as the enzyme catalyzing the sugar–sugar linkage to produce glycyrrhizin from its less glycosylated precursor in the presence of UDP‐glucuronic acid, and found that Arg32 of UGT73P12 is essential for the high specificity for UDP‐glucuronic acid, which was probably acquired during evolution to enable the functional specialization of UGT73P12 for glycyrrhizin biosynthesis. [ABSTRACT FROM AUTHOR]

Water pores and stomata play roles in water regulation through guttation and transpiration, respectively. On the Ficus formosana leaves, water pores are present in the hydathodes on the upper surface, whereas stomata are randomly distributed on the abaxial epidermis of non-vein regions. Here, we investigate the development and physiological functions of water pores and stomata from the same leaves and explore their evolutionary relationships. We compare their structures using optical and electron microscope, and establish their functions through physiological experiments. Ficus formosana Maxim. f. shimadae Hayata water pores are almost circular, whereas its stomata are elliptical. Water pores are clustered and occur at a higher density than stomata, with these latter being anomocytic. Our ultrastructural analysis shows that F. formosana f. shimadae water pores contain amyloplasts and have thickened walls around the pores, with many plasmodesmata observed during their development. The chloroplasts of the stomatal guard cells possess typical plant cell grana and thylakoids, and the inner walls around the stomatal space are thickened. The differentiation and developmental processes of water pores and stomata are similar. Stomatal apertures were regulated by light/dark, fusicoccin, ABA, or mannitol treatments, but water pores were not. Our findings indicate that water pores and stomata on the F. formosana f. shimadae leaves evolved divergently. [ABSTRACT FROM AUTHOR]

Mammals inhabit a wide variety of ecological niches, which in turn can be affected by various ecological factors, especially in relation to immunity. The canonical TRC repertoire (TRAC, TRBC, TRGC , and TRDC) codes C regions of T cell receptor chains that form the primary antigen receptors involved in the activation of cellular immunity. At present, little is known about the correlation between the evolution of mammalian TRC genes and ecological factors. In this study, four types canonical of TRC genes were identified from 37 mammalian species. Phylogenetic comparative methods (phyANOVA and PGLS) and selective pressure analyses among different groups of ecological factors (habitat, diet, and sociality) were carried out. The results showed that habitat was the major ecological factor shaping mammalian TRC repertoires. Specifically, trade-off between TRGC numbers and positive selection of TRAC and the balanced evolutionary rates between TRAC and TRDC genes were speculated as two main mechanisms in adaption to habitat and sociality. Overall, our study suggested divergent mechanisms for the evolution of TRCs, prompting mammalian immunity adaptions within diverse niches. [ABSTRACT FROM AUTHOR]

The goat's rue rhizobia (Neorhizobium galegae) represent a convenient model to study the evolution and speciation of symbiotic bacteria. This rhizobial species is composed of two biovars (bv. orientalis and bv. officinalis), which form N2-fixing nodules with certain species of goat's rue (Galega orientalis and G. officinalis). The cross-inoculation between them results in the formation of nodules unable to fix nitrogen. On the basis of the data on the whole-genome sequencing, we studied the nucleotide polymorphism of 11 N. galegae strains isolated from the North Caucasus ecosystems, where G. orientalis has higher diversity than G. officinalis. The low level of differences in the polymorphism within the group of the sym genes in comparison with the nonsymbiotic genes can be associated with the active participation of host plants in the evolution of rhizobia. The intragenic polymorphism of bv. orientalis proved to be significantly higher than that of bv. officinalis. The level of polymorphism of nonsymbiotic genes was lower than that of the symbiotic genes, which are functionally more homogeneous. The divergence of the nitrogen fixation genes (nif/fix) is more pronounced than that of the nodule formation genes (nod) in the N. galegae biovars. These facts indicate the leading role of the host-specific nitrogen fixation in the evolution of the studied rizhobial species. [ABSTRACT FROM AUTHOR]

Members of the Aconitum genus within the Ranunculaceae family are known to accumulate a broad array of medicinal and toxic diterpenoid alkaloids (DAs). Historically, ent -copalyl diphosphate (ent -CPP) was considered the sole precursor in DAs biosynthesis. However, the recent discovery of ent -8,13-CPP synthase in A. gymnandrum Maxim., which participates in ent -atiserene biosynthesis, raises the question of whether this gene is conserved throughout the Aconitum genus. In this study, RNA sequencing and PacBio Iso-sequencing were employed to identify diterpene synthases (diTPSs) in four additional Aconitum species with distinct DA compositions. In vitro and in vivo analyses functionally characterized a diverse array of 10 class II and 9 class I diTPSs. In addition to the identification of seven class II diTPSs as ent -CPP synthases, three other synthases generating ent -8,13-CPP, 8,13-CPP, and 8 α -hydroxy-CPP were also discovered. Four class I kaurene synthases-like (KSLs) were observed to react with ent -CPP to yield ent -kaurene. Three KSLs not only reacted with ent -CPP but also ent -8,13-CPP to produce ent -atiserene. AsiKSL2-1 was found to react with 8 α -hydroxy-CPP to produce Z -abienol and AsiKSL2-2 exhibited no activity with any of the four intermediates. This research delineates the known diterpene biosynthesis pathways in six Aconitum species and explores the highly divergent diterpene synthases within the genus, which are consistent with their phylogeny and may be responsible for the differential distribution of diterpenoid alkaloids in root and aerial parts. These findings contribute valuable insights into the diversification of diterpene biosynthesis and establish a solid foundation for future investigation into DA biosynthetic pathways in Aconitum. [Display omitted] • Eighteen diterpene synthase genes were identified from four Aconitum species with characteristic diterpenoid alkaloids. • 8,13-CPP, 8 α -hydroxy-CPP and Z -abienol synthase were identified for the first time in Aconitum species. • Class II diterpene synthases were highly diverged within the genus. [ABSTRACT FROM AUTHOR]

Two types of nitrogen-fixing root nodule symbioses are known, rhizobial and actinorhizal symbioses. The latter involve plants of three orders, Fagales, Rosales, and Cucurbitales. To understand the diversity of plant symbiotic adaptation, we compared the nodule transcriptomes of Datisca glomerata (Datiscaceae, Cucurbitales) and Ceanothus thyrsiflorus (Rhamnaceae, Rosales); both species are nodulated by members of the uncultured Frankia clade, cluster II. The analysis focused on various features. In both species, the expression of orthologs of legume Nod factor receptor genes was elevated in nodules compared to roots. Since arginine has been postulated as export form of fixed nitrogen from symbiotic Frankia in nodules of D. glomerata, the question was whether the nitrogen metabolism was similar in nodules of C. thyrsiflorus. Analysis of the expression levels of key genes encoding enzymes involved in arginine metabolism revealed up-regulation of arginine catabolism, but no up-regulation of arginine biosynthesis, in nodules compared to roots of D. glomerata, while arginine degradation was not upregulated in nodules of C. thyrsiflorus. This new information corroborated an arginine-based metabolic exchange between host and microsymbiont for D. glomerata, but not for C. thyrsiflorus. Oxygen protection systems for nitrogenase differ dramatically between both species. Analysis of the antioxidant system suggested that the system in the nodules of D. glomerata leads to greater oxidative stress than the one in the nodules of C. thyrsiflorus, while no differences were found for the defense against nitrosative stress. However, induction of nitrite reductase in nodules of C. thyrsiflorus indicated that here, nitrite produced from nitric oxide had to be detoxified. Additional shared features were identified: genes encoding enzymes involved in thiamine biosynthesis were found to be upregulated in the nodules of both species. Orthologous nodule-specific subtilisin-like proteases that have been linked to the infection process in actinorhizal Fagales, were also upregulated in the nodules of D. glomerata and C. thyrsiflorus. Nodule-specific defensin genes known from actinorhizal Fagales and Cucurbitales, were also found in C. thyrsiflorus. In summary, the results underline the variability of nodule metabolism in different groups of symbiotic plants while pointing at conserved features involved in the infection process.