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Heat shock transcription factors (HSFs) are crucial components in heat stress response. However, the contribution of the HSFs governing the inherent thermotolerance in Rhodomyrtus tomentosa has barely been investigated. We here compared the roles of RtHSFA9a, RtHSFA9b, and RtHSFA9c in heat stress tolerance. These three genes are the results of gene duplication events, but there exist vast variations in their amino acid sequences. They are all localized to the nucleus. Arabidopsis thaliana plants with overexpressed RtHSFA9a and RtHSFA9c outperformed the wild-type plants, while the over-accumulation of RtHSFA9b had little impact on plant thermotolerance. By transiently overexpressing RtHSFA9a, RtHSFA9b, and RtHSFA9c in R. tomentosa seedlings, the mRNA abundance of heat shock response genes, including RtHSFA2a, RtHSFA2b, RtHSP17.4, RtHSP21.8, RtHSP26.5, and RtHSP70, were upregulated. Transactivation assays confirmed that there exist regulatory divergences among these three genes, viz., RtHSFA9a has the highest transcription activity in regulating RtHSFA2a, RtHSFA2b, RtHSP21.8, and RtHSP70; RtHSFA9c can transcriptionally activate RtHSFA2b, RtHSP21.8, and RtHSP70; RtHSFA9b makes limited contributions to the accumulation of RtHSFA2b, RtHSP21.8, and RtHSP70. Our results indicate that the RtHSFA9 genes make crucial contributions to the thermal adaption of R. tomentosa by positively regulating the RtHSFA2a, RtHSFA2b, and RtHSP genes, which provides novel insights into the RtHSFA9 subfamily. [ABSTRACT FROM AUTHOR]

Brassinosteroids (BRs) are plant steroid hormones that control growth and stress responses. In the context of development, BRs play diverse roles in controlling cell differentiation and tissue patterning. The vascular system, which is essential for transporting water and nutrients throughout the plant body, initially establishes a tissue pattern during primary development and then dramatically increases the number of vascular cells during secondary development. This complex developmental process is properly regulated by a network consisting of various hormonal signaling pathways. Genetic studies have revealed that mutants that are defective in BR biosynthesis or the BR signaling cascade exhibit a multifaceted vascular development phenotype. Furthermore, BR crosstalk with other plant hormones, including peptide hormones, coordinately regulates vascular development. Recently, the involvement of BR in vascular development, especially in xylem differentiation, has also been suggested in plant species other than the model plant Arabidopsis thaliana. In this review, we briefly summarize the recent findings on the roles of BR in primary and secondary vascular development in Arabidopsis and other species. [ABSTRACT FROM AUTHOR]

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Semi‐natural grasslands are found predominantly in agricultural landscapes; however, their counterparts are also found in cities, referred to as urban grasslands. We sampled the most extensive patches of urban grasslands in Wrocław (Poland, Europe) in urban parks and along a river valley. We compared urban grasslands to broadly defined rural grasslands in terms of compositional gradients and both taxonomic and functional diversity. We also tested for relationships between rare species and different facets of diversity. Urban grasslands corresponded to three rural grassland habitat types: mesic pastures, mesic meadows, and alluvial meadows. We conducted analogous analyses, including and excluding habitat‐level assignment, to determine if emerging patterns between rural and urban grasslands are habitat‐dependent. Rural pastures and their urban counterparts showed high taxonomic and functional similarity, implying that short‐ and frequent‐cutting, applied in cities, mimics grazing management on agricultural sites. Rural mesic hay grasslands and alluvial meadows showed high taxonomic and functional dissimilarities from their urban counterparts. We found that rare species contribute to taxonomic diversity while only affecting functional diversity in a few cases. Varying patterns of taxonomic and functional similarity were observed across different habitats. Comparisons of grasslands without regard for habitat types mask diverging patterns in taxonomic and functional diversity. Despite high environmental and management pressures in urban areas (higher nutrient levels and temperatures, decreased moisture, and intensified management and soil disturbances), we showed that urban grasslands hold a considerable portion of the plant diversity found in rural grasslands. [ABSTRACT FROM AUTHOR]

Pancreatic ribonuclease (RNase1), a digestive enzyme produced by the pancreas, is associated with the functional adaptation of dietary habits and is regarded as an attractive model system for studies of molecular evolution. In this study, we identified 218 functional genes and 48 pseudogenes from 114 species that span all four Cetartiodactyla lineages: two herbivorous lineages (Ruminantia and Tylopoda) and two non‐herbivorous lineages (Cetancodonta and Suoidea). Multiple RNase1 genes were detected in all species of the two herbivorous lineages, and phylogenetic and genomic location analyses demonstrated that independent gene duplication events occurred in Ruminantia and Tylopoda. In Ruminantia, the gene duplication events occurred in the ancestral branches of the lineage in the Middle Eocene, a time of increasing climatic seasonality during which Ruminantia rapidly radiated. In contrast, only a single RNase1 gene was observed in the species of the two non‐herbivorous lineages (Cetancodonta and Suoidea), suggesting that the previous Cetacea‐specific loss hypothesis should be rejected. Moreover, the duplicated genes of RNase1 in the two herbivorous lineages (Ruminantia and Tylopoda) may have undergone functional divergence. In combination with the temporal coincidence between gene replication and the enhanced climatic seasonality during the Middle Eocene, this functional divergence suggests that RNase1 gene duplication was beneficial for Ruminantia to use the limited quantities of sparse fibrous vegetation and adapt to seasonal changes in climate. In summary, the findings indicate a complex and intriguing evolutionary pattern of RNase1 in Cetartiodactyla and demonstrate the molecular mechanisms by which organisms adapt to the environment. [ABSTRACT FROM AUTHOR]

Rubisco is assembled from large subunits (encoded by chloroplast gene rbcL) and small subunits (encoded by the nuclear rbcS multigene family), which are involved in the processes of carbon dioxide fixation in the Calvin cycle of photosynthesis. Although Rubisco has been studied in many plants, the evolutionary divergences among the different rbcS genes are still largely unknown. Here, using a rice closely related wild species, Oryza punctata Kotschy ex Steud, we investigated the differential properties of the rbcS genes in the species. We identified five rbcS genes (OprbcS1 through OprbcS5), OprbcS1 showed a different evolutionary pattern from the remaining four genes in terms of chromosome location, gene structure, and sequence homology. Phylogenetic analysis revealed that plant rbcS1 and other non‐rbcS1 genes originated from a common ancient duplication event that occurred at least in seed plants ancestor. RbcS1 was then retained in a few plant lineages, including Oryza, whereas non‐rbcS1 was mainly amplified in angiosperms. OprbcS1, OprbcS2–OprbcS4, and OprbcS5 were prominently expressed in stems and seeds, young leaves, and mature leaves, respectively. The yeast two‐hybrid assay detected a significant decrease in the interaction between OprbcS1 and OprbcL compared to the other four pairs of proteins (OprbcS2–OprbcS5 and OprbcL). We propose that OprbcS1 might be assigned a divergent function that was predominantly specific to nonphotosynthetic organs, whereas OprbcS2–OprbcS5, having different affinity in the assembly process of Rubisco, might be subfunctionalized in photosynthetic organs. This study not only deepens our understanding of the fine assembly of Rubisco, but also sheds some light on future de novo domestication of wild rice. [ABSTRACT FROM AUTHOR]

Cotton is one of the world's leading fiber crops, but climate change, drought, heat, and salinity have significantly decreased its production, consequently affecting the textile industries globally. To acclimate to these environmental challenges, a number of gene families involved in various molecular, physiological, and hormonal mechanisms play crucial roles in improving plants response to various abiotic stresses. One such gene family is the GhSRF, a Strubbelig-Receptor family (SRF), and member of the leucine-rich repeat (LRR-V) group. This family encodes leucine-rich repeat transmembrane receptor-like kinases (LRR-RLKs) and have not yet been explored in cotton. Arabidopsis thaliana Strubbelig-Receptor gene sequences were used as queries to identify the homologs in cotton, with subsequent support from the literature and functional prediction through online data. In the current study, a comprehensive genome-wide analysis of cotton was conducted, identifying 22 SRF putative proteins encoded by 22 genes. We performed the detailed analysis of these proteins, including phylogeny, motif and gene structure characterization, promoter analysis, gene mapping on chromosomes, gene duplication events, and chromosomal sub-cellular localization. Expression analysis of putative genes was performed under drought and heat stress conditions using publicly available RNAseq data. The qRT-PCR results showed elevated expression of GhSRF2, GhSRF3, GhSRF4, GhSRF10, and GhSRF22 under drought and heat stress. So, it could be speculated that these genes may play a role in drought and heat tolerance in cotton. These findings could be helpful in cotton breeding programs for the development of climate-resilient cultivars. [ABSTRACT FROM AUTHOR]

Aim: Quantify tree functional and phylogenetic richness and divergence at the global scale, and explore the drivers underpinning these biogeographic patterns. Location: Global. Time Period: Present. Major Taxa Studied: Trees. Methods: Using global tree occurrence data, we outlined species' observed ranges using individual alpha hulls to obtain per‐pixel tree species composition at a 0.83‐degree resolution. Using eight traits from a recent tree‐trait database and a vascular‐plant phylogeny we computed and mapped four pixel‐level biodiversity indices, including two metrics related to richness: phylogenetic richness and functional richness, and two related to divergence: mean pairwise phylogenetic distance and Rao's quadratic entropy. To account for the effect of species richness, we also calculated standardized effect sizes accounting for richness for each pixel. We then explored the relations between richness and divergence and the latitudinal patterns of divergence both globally and across biomes. Finally, we used a random forest modelling approach to test for drivers of the different dimensions of diversity in trees. Results: In contrast to the latitudinal gradient in species richness, functional and phylogenetic divergence both peak in mid‐latitude systems, exhibiting the highest values in temperate ecosystems and lowest values in boreal and tropical forests. This result holds for functional divergence when removing gymnosperms but the peak flattens for phylogenetic divergence. Phylogenetic richness is consistently lower than expected given the number of species, whereas functional richness has higher‐than‐expected values at mid‐latitudes, mimicking functional divergence patterns. When considering the drivers of these diversity patterns, temperature and historical speciation rates consistently emerge as the strongest forces driving divergence, with negligible effects of human influence, soils or historical climate stability. Main Conclusions: Collectively, these results reveal unique similarities and disparities across biomes that are not apparent in any single dimension of biodiversity, highlighting the importance of considering multiple aspects of biodiversity in the management of natural ecosystems. [ABSTRACT FROM AUTHOR]

Freshwater biodiversity has been declining in urban areas, which may threaten ecosystem functions. Although many studies have demonstrated a positive correlation between biodiversity and ecosystem functioning (BEF) in terrestrial and marine ecosystems, little is known about the BEF relationship in freshwater environments, especially in highly urbanized regions where water pollution is a major concern. Eutrophication in urban water bodies may trigger algae blooms, decreasing the evenness or functional divergence (FDiv) of phytoplankton communities, thus negatively affecting ecosystem functioning. Through an annual field investigation, we clarified the relationship between phytoplankton diversity and ecosystem functioning, represented as resource use efficiency (RUE), in an urban river in northern China. Results indicated that evenness in the phytoplankton community contributes most to driving ecosystem functioning compared to environmental factors. The relative abundance of dominant Bacillariophyta was positively correlated with the resource use efficiency of phytoplankton (RUEpp) but negatively correlated with the resource use efficiency of zooplankton (RUEzp). Both phytoplankton evenness and functional divergence were negatively linked to RUEpp but positively to RUEzp. Our findings suggest that the reduction of phytoplankton evenness and functional divergence may seriously threaten resource use efficiency (RUE), and its potential mechanism can provide a crucial reference for water quality protection and sustainable water resource utilization in the basin. [ABSTRACT FROM AUTHOR]

The study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel‐density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e. richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers. We propose the use of neighbor‐joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles. We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel‐density hypervolumes using both simulated and empirical datasets. Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree‐based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space. [ABSTRACT FROM AUTHOR]

The Transforming Growth Factor-β (TGF-β) cascade plays a critical role in insect metamorphosis and involves cell-surface receptors known as type I and II, respectively (TβRI and TβRII). In Drosophila melanogaster, the TβRI receptor, Baboon (Babo), consists of three variants (BaboA, BaboB, and BaboC), each with isoform-specific functions. However, the isoforms and functional specifications of Babo in non-Drosophilid insects have not been established. Here, we examined babo transcripts from seven coleopteran species whose genomes have been published and found that mutually exclusive alternative splicing of the third exon produces three babo isoforms, identical to the Drosophila babo gene. The same three transcript variants were accordingly recognized from the transcriptome data of a coleopteran Henosepilachna vigintioctopunctata. RNA interference (RNAi)-mediated knockdown of all three babo transcripts at the fourth-instar larval stage hindered gut modeling and arrested larval development in H. vigintioctopunctata. All the resultant larvae became arrested prepupae; they were gradually dried and darkened and, eventually, died. Depletion of HvbaboA rather than HvbaboB or HvbaboC is similar to the phenotypic alterations caused by simultaneous RNAi of all three babo isoforms. Therefore, our results established diverged roles of the three Babo isoforms and highlighted the regulatory role of BaboA during larval-pupal transition in a non-Drosophilid insect species. [ABSTRACT FROM AUTHOR]

The plant-specific homeodomain-leucine zipper I subfamily is involved in the regulation of various biological processes, particularly growth, development and stress response. In the present study, we characterized four BnaHB6 homologues from Brassica napus. All BnaHB6 proteins have transcriptional activation activity. Structural and functional data indicate the complex role of BnaHB6 genes in regulating biological processes, with some functions conserved and others diverged. Transcriptional analyzes revealed that they are induced in a similar manner in different tissues but show different expression patterns in response to stress and circadian rhythm. Only the BnaA09HB6 and BnaC08HB6 genes are expressed under dehydration and salt stress, and in darkness. The partial transcriptional overlap of BnaHB6s with the evolutionarily related genes BnaHB5 and BnaHB16 was also observed. Transgenic Arabidopsis thaliana plants expressing a single proBnaHB6::GUS partially confirmed the expression results. Bioinformatic analysis allowed the identification of TF-binding sites in the BnaHB6 promoters that may control their expression under stress and circadian rhythm. ChIP-qPCR analysis revealed that BnaA09HB6 and BnaC08HB6 bind directly to the promoters of the target genes BnaABF4 and BnaDREB2A. Comparison of their expression patterns in the WT plants and the bnac08hb6 mutant showed that BnaC08HB6 positively regulates the expression of the BnaABF4 and BnaDREB2A genes under dehydration and salt stress. We conclude that four BnaHB6 homologues have distinct functions in response to stress despite high sequence similarity, possibly indicating different binding preferences with BnaABF4 and BnaDREB2A. We hypothesize that BnaC08HB6 and BnaA09HB6 function in a complex regulatory network under stress. [ABSTRACT FROM AUTHOR]

ABSTRACT ClpXP is a protease complex that plays important roles in protein quality control and cell cycle regulation, but the functions of multiple ClpXs and multiple ClpPs in M. xanthus remain unknown. The genome of Myxococcus xanthus DK1622 contains two clpPs and three clpXs. The clpP1 and clpX1 genes are cotranscribed and are both essential, while the other copies are isolated in the genome and are deletable. The deletion of clpX2 caused the mutant to be deficient in fruiting body development, while the clpX3 gene is involved in resistance to thermal stress. Both ClpPs possess catalytic active sites, but only ClpP1 shows in vitro peptidase activity on the typical substrate Suc-LY-AMC. All of these clpP and clpX genes exhibit strong transcriptional upregulation in the stationary phase, and the transcription of the three clpX genes appears to be coordinated. Our results demonstrated that multiple ClpPs and multiple ClpXs are functionally divergent and may assist in the environmental adaptation and functional diversification of M. xanthus.IMPORTANCEClpXP is an important protease complex of bacteria and is involved in various physiological processes. Myxococcus xanthus DK1622 possesses two ClpPs and three ClpXs with unclear functions. We investigated the functions of these genes and demonstrated the essential roles of clpP1 and clpX1. Only ClpP1 has in vitro peptidase activity on Suc-LY-AMC, and the isolated clpX copies participate in distinct cellular processes. All of these genes exhibited significant transcriptional upregulation in the stationary phase. Divergent functions appear in multiple ClpPs and multiple ClpXs in M. xanthus DK1622.

Wintering birds serve as vital climate sentinels, yet they are often overlooked in studies of avian diversity change. Here, we provide a continental‐scale characterization of change in multifaceted wintering avifauna and examine the effects of climate change on these dynamics. We reveal a strong functional reorganization of wintering bird communities marked by a north–south gradient in functional diversity change, along with a superimposed mild east–west gradient in trait composition change. Assemblages in the northern United States saw contractions of the functional space and increases in functional evenness and originality, while the southern United States saw smaller contractions of the functional space and stasis in evenness and originality. Shifts in functional diversity were underlined by significant reshuffling in trait composition, particularly pronounced in the western and northern United States. Finally, we find strong contributions of climate change to this functional reorganization, underscoring the importance of wintering birds in tracking climate change impacts on biodiversity. [ABSTRACT FROM AUTHOR]

Biological diversity can be evaluated by the taxonomic and functional components. This study aimed to assess the relationship between taxonomic richness with the functional diversity components [functional richness (FRic), functional evenness (FEve) and functional divergence (FDiv)] and the functional trait dominance of polychaetes. In addition, we evaluated the environmental parameters that shape the functional structure in six tropical estuaries in north‐eastern Brazil. Three estuaries have a continuous environmental gradient (typical tropical), and the other three estuaries have no defined environmental gradient (semiarid tropical). We identified significant differences in the dominance of feeding strategy and habitat between estuaries, demonstrating that the functional space of the communities is not equally occupied. Also, the substrate particle size composition was correlated with the functional structure. FRic showed a positive relationship with taxonomic richness, regardless of the type of estuary. As taxonomic richness increases, the probability of different combinations of functional categories added to a community also increases. FEve and FDiv seem to be independent of taxonomic richness. Therefore, it is important to simultaneously evaluate diversity's taxonomic and functional components, considering the complementarity of the information provided by these diversity measures. [ABSTRACT FROM AUTHOR]

Gene duplication is a key biological process in the evolutionary history of plants and an important driving force for the diversification of genomic and genetic systems. Interactions between the calcium sensor calcineurin B-like protein (CBL) and its target, CBL-interacting protein kinase (CIPK), play important roles in the plant's response to various environmental stresses. As a food crop with important economic and research value, turnip (Brassica rapa var. rapa) has been well adapted to the environment of the Tibetan Plateau and become a traditional crop in the region. The BrrCIPK9 gene in turnip has not been characterized. In this study, two duplicated genes, BrrCIPK9.1 and BrrCIPK9.2, were screened from the turnip genome. Based on the phylogenetic analysis, BrrCIPK9.1 and BrrCIPK9.2 were found located in different sub-branches on the phylogenetic tree. Real-time fluorescence quantitative PCR analyses revealed their differential expression levels between the leaves and roots and in response to various stress treatments. The differences in their interactions with BrrCBLs were also revealed by yeast two-hybrid analyses. The results indicate that BrrCIPK9.1 and BrrCIPK9.2 have undergone Asparagine–alanine–phenylalanine (NAF) site divergence during turnip evolution, which has resulted in functional differences between them. Furthermore, BrrCIPK9.1 responded to high-pH (pH 8.5) stress, while BrrCIPK9.2 retained its ancestral function (low K+), thus providing further evidence of their functional divergence. These functional divergence genes facilitate turnip's good adaptation to the extreme environment of the Tibetan Plateau. In summary, the results of this study reveal the characteristics of the duplicated BrrCIPK9 genes and provide a basis for further functional studies of BrrCBLs–BrrCIPKs in turnip. [ABSTRACT FROM AUTHOR]

Key message: The BrrFT paralogues exhibit distinct expression patterns and play different roles in regulating flowering time, and BrrFT4 competes with BrrFT1 and BrrFT2 to interact with BrrFD proteins. Flowering time is an important agricultural trait for Brassica crops, and early bolting strongly affects the yield and quality of Brassica rapa ssp. rapa. Flowering Locus T paralogues play an important role in regulating flowering time. In this study, we identified FT-related genes in turnip by phylogenetic classification, and four BrrFT homoeologs that shared with high identities with BraFT genes were isolated. The different gene structures, promoter binding sites, and expression patterns observed indicated that these genes may play different roles in flowering time regulation. Further genetic and biochemical experiments showed that as for FT-like paralogues, BrrFT2 acted as the key floral inducer, and BrrFT1 seems to act as a mild ‘florigen’ protein. However, BrrFT4 acts as a floral repressor and antagonistically regulates flowering time by competing with BrrFT1 and BrrFT2 to bind BrrFD proteins. BrrFT3 may have experienced loss of function via base shift mutation. Our results revealed the potential roles of FT-related genes in flowering time regulation in turnip. [ABSTRACT FROM AUTHOR]

This study aimed to explore Cellulose synthase gene superfamily of teak, and its evolutionary relationship with homologous genes of other woody species. The incidence of evolutionary events like gene duplication and gene loss, influence of the selection pressure, and consequent adaptive functional divergence of the duplicated TgCes gene were assessed alongside it's role in wood coloration. This study identified 39 full-length non-redundant proteins belonging to CesA and Csl gene families. TgCesA and TgCsl proteins with Cellulose synthase domain repeats indicated tandem gene duplication and probable genetic variability, enabling local adaptation. Further, multi-domain protein (MYB-like DNA-binding domain and CesA domain) with maximum introns was also identified indicating gene fusion and formation of complex protein with novel functions. Phylogenetic analysis grouped the genes into seven subfamilies (CesA, CslA, CslC, CslD, CslE, CslG, and CslM) with each undergoing gene duplication and loss along their evolutionary history. Post-species gene duplications and probable neofunctionalization were identified in TgCesA and TgCsl gene families. Each subfamily was found to be under strong purifying selection with a few or no sites under positive selection. Functional divergence analysis further revealed site-specific selective constraints in CesA and Csl genes of the teak Cellulose synthase gene family. Furthermore, protein–protein interaction network analysis identified co-expression of Cellulose synthase gene with flavonoid 3′,5′-hydroxylase (F3′5′H, CYP75A), involved in the biosynthesis of xylem anthocyanin compounds, probably responsible for wood coloration. This study thus offers a foundation for future research in wood formation and wood property traits specific to teak and its provenances. [ABSTRACT FROM AUTHOR]

The Praja family is an E3 ubiquitin ligase, promoting polyubiquitination and subsequent degradation of substrates. It comprises two paralogs, praja1 and praja2. Prior research suggests these paralogs have undergone functional divergence, with examples, such as their distinct roles in neurite outgrowth. However, the specific evolutionary trajectories of each paralog remain largely unexplored preventing mechanistic understanding of functional differences between paralogs. Here, we investigated the phylogeny and divergence of the vertebrate Praja family through molecular evolutionary analysis. Phylogenetic examination of the vertebrate praja revealed that praja1 and praja2 originated from the common ancestor of placentals via gene duplication, with praja1 evolving at twice the rate of praja2 shortly after the duplication. Moreover, a unique evolutionary trajectory for praja1 relative to other vertebrate Praja was indicated, as evidenced by principal component analysis on GC content, codon usage frequency, and amino acid composition. Subsequent motif/domain comparison revealed conserved N terminus and C terminus in praja1 and praja2, together with praja1-specific motifs, including nuclear localization signal and Ala–Gly–Ser repeats. The nuclear localization signal was demonstrated to be functional in human neuroblastoma SH-SY5Y cells using deletion mutant, while praja2 was exclusively expressed in the nucleus. These discoveries contribute to a more comprehensive understanding of the Praja family's phylogeny and suggest a functional divergence between praja1 and praja2. Specifically, the shift of praja1 into the nucleus implies the degradation of novel substrates located in the nucleus as an evolutionary consequence. [ABSTRACT FROM AUTHOR]

The selective pressure from pathogens on individuals can have direct consequences on reproduction. Genes from the major histocompatibility complex (MHC) are central to the vertebrate adaptive immune system and pathogen resistance. In species with biparental care, each sex has distinct reproductive roles and levels of investment, and due to a trade‐off with immunity, one can expect different selective regimes acting upon the MHC of each parent. Here, we addressed whether couples combine each other's variation at MHC loci to increase their breeding success. Specifically, we used a 23‐year dataset from a barn owl population (Tyto alba) to understand how MHC class Iα and IIβ functional divergence and supertypes of each parent were associated with clutch size and fledging success. We did not detect associations between MHC diversity and supertypes with the clutch size or with the fledging success. In addition, to understand the relative contribution from the MHC of the genetic parents and the social parents, we analyzed the fledging success using only a cross‐fostered dataset. We found several associations of weak‐to‐moderate effect sizes between the father's MHC and fledging success: (i) lower MHC‐Iα divergence in the genetic father increases fledging success, which might improve paternal care during incubation, and (ii) one and two MHC‐IIβ DAB2 supertypes in the social father decrease and increase, respectively, fledging success, which may affect the paternal care after hatching. Furthermore, fledging success increased when both parents did not carry MHC‐IIβ DAB1 supertype 2, which could suggest conditional effects of this supertype. Although our study relied on a substantial dataset, we showed that the associations between MHC diversity and reproductive success remain scarce and of complex interpretation in the barn owl. Moreover, our results highlighted the need to incorporate more than one proxy of reproductive success and several MHC classes to capture more complex associations. [ABSTRACT FROM AUTHOR]

Apolipoprotein D (ApoD), a member of the lipocalin superfamily of proteins, is involved in lipid transport and stress resistance. Whereas only a single copy of the ApoD gene is found in humans and some other vertebrates, there are typically several ApoD‐like genes in insects. To date, there have been relatively few studies that have examined the evolution and functional differentiation of ApoD‐like genes in insects, particularly hemi‐metabolous insects. In this study, we identified 10 ApoD‐like genes (NlApoD1−10) with distinct spatiotemporal expression patterns in Nilaparvata lugens (BPH), which is an important pest of rice. NlApoD1−10 were found to be distributed on 3 chromosomes in a tandem array of NlApoD1/2, NlApoD3−5, and NlApoD7/8, and show sequence and gene structural divergence in the coding regions, indicating that multiple gene duplication events occurred during evolution. Phylogenetic analysis revealed that NlApoD1−10 can be clustered into 5 clades, with NlApoD3−5 and NlApoD7/8 potentially evolving exclusively in the Delphacidae family. Functional screening using an RNA interference approach revealed that only NlApoD2 was essential for BPH development and survival, whereas NlApoD4/5 are highly expressed in testes, and might play roles in reproduction. Moreover, stress response analysis revealed that NlApoD3−5/9, NlApoD3−5, and NlApoD9 were up‐regulated after treatment with lipopolysaccharide, H2O2, and ultraviolet‐C, respectively, indicating their potential roles in stress resistance. [ABSTRACT FROM AUTHOR]

Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S‐transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis‐like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site‐directed mutagenesis to replace amino acid residuals in different wild‐types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome. [ABSTRACT FROM AUTHOR]

PAMP-induced secreted peptide (PIP), one of the small post-translationally modified peptides (PTMPs), plays a crucial role in plant development and stress tolerance. However, little is known about functional divergence among this peptide family. Here, we studied the evolution of the PIP family in 23 plant species (10 monocotyledons and 13 dicotyledons from 7 families) and their functional divergence in Arabidopsis. A total of 128 putative PIP precursors were identified and classified into two subfamilies through phylogenetic analysis. Functional studies on AtPIP1 which represents Clade I family and AtPIP2 which represents Clade II family have shown that AtPIP2 displayed stronger immunity induction activity but weaker root growth inhibition than AtPIP1 in Arabidopsis. Transcriptome analysis of Arabidopsis seedlings treated with AtPIP1 and AtPIP2 showed that differential genes for both polypeptides were significantly enriched in similar plant defense pathways. However, Co-expression and Protein-protein interaction (PPI) analysis showed that the functions of AtprePIP2 co-expressed genes were more enriched in plant defense pathways than AtprePIP1. Molecular docking results show that AtPIP1 binds to RLK7 receptor with a more stable free energy and less binding area than AtPIP2, while hydrogen bond transfer occurs at the SGP motif position. The above results suggest that the PIP family have undergone functional divergence during evolution. Collectively, this work illustrates the relationship between PIP structure and function using Arabidopsis PIP as an example, and provides new insights into the current understanding between growth inhibition and immune responses which may be correlated but not fully coupled. [ABSTRACT FROM AUTHOR]

Understanding pathogen transmission and infection patterns at multiple biological scales is a central issue in disease ecology and evolution. Here, we suggest that functional traits of host species readily affect infection patterns of species, communities, and landscapes, and thus serve as a linkage for multilevel studies of infectious disease. [ABSTRACT FROM AUTHOR]

Mitogen-activated protein kinases (MAPKs) are crucial regulators in coping with abiotic and biotic stresses, including drought, salinity, fungi, and pathogens. However, little is known about the characteristics, evolution process, and functional divergence of the MAPK gene family in Rosaceae plants. A total of 97 MAPK members were identified in six Rosaceae species, including 12 genes in Fragaria vesca, 22 genes in Malus domestica, 23 genes in Pyrus bretschneideri, 12 genes in Prunus mume, 14 genes in Prunus persica, and 14 genes in Rosa chinensis. All MAPK members of six Rosaceae plants were categorized into four clusters by the phylogenetic relationship analysis. Collinearity analysis discovered that both segmental duplication and tandem duplication contributed to the expansion of MAPK family genes in Rosaceae plants. And the analysis of motifs and gene structures indicated that the evolution of the MAPK gene family was highly conserved among phylogenetic clusters in Rosaceae species. In addition, the dN/dS rates of MAPK paralogous gene pairs were below one, suggesting the MAPK gene family in Rosaceae was driven by purifying selective pressure. Furthermore, functional divergence analysis discovered that 14 amino acid residues were detected as potentially key sites for functional divergence of MAPK family genes between different cluster pairs, specifically Type I functional divergence. The analysis of functional distance indicated that cluster C retained more of the original functional features, while cluster B exhibited functional specialization. Moreover, the expression profiles revealed that PmMAPK8, PmMAPK9, and PmMAPK10 were both highly expressed under drought stress and low temperature conditions. This study aims to comprehensively analyze the evolutionary process and functional analyses of the MAPK gene family in Rosaceae plants, which will lay the foundation for future studies into MAPK genes of Rosaceae in response to drought and cold stress. [ABSTRACT FROM AUTHOR]

Climate change may potentially affect the biodiversity and functionality of forests globally. An understanding of the relationship between biodiversity and forest ecosystem functioning can be attained by evaluating variations in functional indices. The present study evaluated four taxonomic indicators: Species richness (SRic), Species evenness (SEve), Shannon index (H), and Simpson index (D), and three functional indices: Community Weighted Mean (CWM), Functional Diversity (FDiv), and Functional Regularity (FRO), in 17 temperate forest stands and their relationship with climatic factors in Western Himalaya. We evaluated the variation in the functioning of temperate forest stands and, the relationship between forest functioning and climatic parameters. We proposed an index for the evaluation of relative forest functionality by aggregating the three functional indices. The data were collected by randomly laying ten quadrats, each measuring 0.1 ha, in each of the seventeen forest stands. We found significant differences in the indices across the various forest stands. Structural equation modelling analysis found that maximum temperature, rainfall, SRic, D and FDiv were the main contributors to the temperate forest functionality. Therefore, the functionality of temperate forests in the region is being affected by changes in the rainfall and maximum temperature of the region. Consequently, there is a need for evaluations of forest resilience and adaptation under changing climate conditions to manage and conserve the forest. [ABSTRACT FROM AUTHOR]

The Transforming Growth Factor-β (TGF-β) cascade plays a critical role in insect metamorphosis and involves cell-surface receptors known as type I and II, respectively (TβRI and TβRII). In Drosophila melanogaster, the TβRI receptor, Baboon (Babo), consists of three variants (BaboA, BaboB, and BaboC), each with isoform-specific functions. However, the isoforms and functional specifications of Babo in non-Drosophilid insects have not been established. Here, we examined babo transcripts from seven coleopteran species whose genomes have been published and found that mutually exclusive alternative splicing of the third exon produces three babo isoforms, identical to the Drosophila babo gene. The same three transcript variants were accordingly recognized from the transcriptome data of a coleopteran Henosepilachna vigintioctopunctata. RNA interference (RNAi)-mediated knockdown of all three babo transcripts at the fourth-instar larval stage hindered gut modeling and arrested larval development in H. vigintioctopunctata. All the resultant larvae became arrested prepupae; they were gradually dried and darkened and, eventually, died. Depletion of HvbaboA rather than HvbaboB or HvbaboC is similar to the phenotypic alterations caused by simultaneous RNAi of all three babo isoforms. Therefore, our results established diverged roles of the three Babo isoforms and highlighted the regulatory role of BaboA during larval-pupal transition in a non-Drosophilid insect species.

ABSTRACT Picobirnaviruses (PBVs) are small, bi-segmented, double-stranded RNA viruses frequently associated with gastrointestinal and recently linked to respiratory infections. Detected in hosts from distant biological kingdoms, debate swirls as to their age and origins and whether they are prokaryotic or eukaryotic viruses. Our evolutionary analysis revealed a contemporaneous emergence for PBV, as PBV-R1&3 species arose ~350 years ago with both segments, whereas the more ancient species, PBV-R2, initially lacked capsid. Integrated phylogenetic reconstruction defined two origins for PBV, determining PBV-R1&3 species descended from Reovirus and PBV-R2 branched with Partitivirus ancestors. These results, coupled with the heterogeneity of Shine-Dalgarno motifs, argue against a prokaryotic origin. Epistatic interactions identified in the RdRp of PBV-R1&3 evidenced the constraints imposed by vertebrate host immunity, whereas its absence in PBV-R2 concurs with its fungal origin. After acquisition of capsid, PBV-R2 increased its adaptive and functional divergences in RdRp domains and the compactness of its RNA structure to enable encapsidation. While their pathogenicity remains an open question, picobirnaviruses likely originated from both fungal and avian hosts: parallel evolution mechanisms have driven the genetic similarities shared among present-day PBV species. IMPORTANCE Picobirnaviruses (PBVs) are highly heterogeneous viruses encoding a capsid and RdRp. Detected in a wide variety of animals with and without disease, their association with gastrointestinal and respiratory infections, and consequently their public health importance, has rightly been questioned. Determining the “true” host of Picobirnavirus lies at the center of this debate, as evidence exists for them having both vertebrate and prokaryotic origins. Using integrated and time-stamped phylogenetic approaches, we show they are contemporaneous viruses descending from two different ancestors: avian Reovirus and fungal Partitivirus. The fungal PBV-R2 species emerged with a single segment (RdRp) until it acquired a capsid from vertebrate PBV-R1 and PBV-R3 species. Protein and RNA folding analyses revealed how the former came to resemble the latter over time. Thus, parallel evolution from disparate hosts has driven the adaptation and genetic diversification of the Picobirnaviridae family.

Dkks have inhibitory effects on the Wnt signaling pathway, which is involved in the development of skin and its appendages and the regulation of hair growth. The nucleotide sequences were compared and analyzed to further investigate the relationship between the structure and function of the Dkk gene family and vertebrate epidermal hair. The analysis of the molecular evolution of the Dkk family revealed that the evolution rate of the genes changed significantly after speciation, with the Aves and Reptilia branches showing accelerated evolution. Additionally, positive selection was observed at specific sites. The tertiary structure of the protein was also predicted. The analysis of the functional divergence of the Dkk family revealed that the functional divergence coefficient of each gene was greater than 0, with most of the functional divergence sites were located in the Cys-2 domain and a few in the Cys-1 domain. This suggests that the amino acid and functional divergence sites may play a role in regulating the binding of the Dkk family to LRP5/6, and thus affect the inhibition of Wnt signaling, leading to different functions of Dkk1, Dkk2, and Dkk4 in the development of skin hair follicles. In addition, the Dkk families of Aves and Reptilia may have undergone adaptive evolution and functional divergence. [ABSTRACT FROM AUTHOR]

Functional diversity is regarded as a key concept for understanding the link between ecosystem function and biodiversity. The different and ecologically well‐defined aspects of the concept are reflected by the so‐called functional components, for example, functional richness and divergence. Many authors proposed that components be distinguished according to the multivariate technique on which they rely, but more recent studies suggest that several multivariate techniques, providing different functional representations (such as dendrograms and ordinations) of the community can in fact express the same functional component. Here, we review the relevant literature and find that (1) general ecological acceptance of the field is hampered by ambiguous terminology and (2) our understanding of the role of multivariate techniques in defining components is unclear. To address these issues, we provide new definitions for the three basic functional diversity components namely functional richness, functional divergence and functional regularity. In addition, we present a classification of presence‐/absence‐based approaches suitable for quantifying these components. We focus exclusively on the binary case for its relative simplicity. We find illogical, as well as logical but unused combinations of components and representations; and reveal that components can be quantified almost independently from the functional representation of the community. Finally, theoretical and practical implications of the new classification are discussed. [ABSTRACT FROM AUTHOR]

Species functional traits can influence pathogen transmission processes, and consequently affect species' host status, pathogen diversity, and community‐level infection risk. We here investigated, for 143 European waterbird species, effects of functional traits on host status and pathogen diversity (subtype richness) for avian influenza virus at species level. We then explored the association between functional diversity and HPAI H5Nx occurrence at the community level for 2016/17 and 2021/22 epidemics in Europe. We found that both host status and subtype richness were shaped by several traits, such as diet guild and dispersal ability, and that the community‐weighted means of these traits were also correlated with community‐level risk of H5Nx occurrence. Moreover, functional divergence was negatively associated with H5Nx occurrence, indicating that functional diversity can reduce infection risk. Our findings highlight the value of integrating trait‐based ecology into the framework of diversity–disease relationship, and provide new insights for HPAI prediction and prevention. [ABSTRACT FROM AUTHOR]

Duplicated genes show various degrees of functional diversification in plants. We previously identified 1,052 pairs of high diversified duplicates (HDDs) and 600 pairs of low diversified duplicates (LDDs) in Arabidopsis thaliana. Single knockdown of HDDs induced abnormal phenotypic changes because the other gene copy could not compensate for the knock-down effect, while single knock-down of LDDs did not induce abnormal phenotypic changes because of functional compensation by the copy gene. Here, focusing on one pair each of HDDs and LDDs, we performed transcriptome analyses in single-knock-down transgenic plants. The numbers of differentially expressed genes in single-knock-down transgenic plants were not different between HDDs and LDDs. Thus, functional compensation inferred by transcriptomics was similar between HDDs and LDDs. However, the trend of differentially expressed genes was similar in the pair of LDDs, while expression profiles were dissimilar in the pair of HDDs. This result indicates that a pair of LDDs tends to share similar functions but a pair of HDDs tends to have undergone functional divergence. Taking these findings together, as the reason for no phenotypic changes in single knock-down of LDDs but phenotypic changes in double knock-down of LDDs, we concluded that phenotypic changes of LDDs were induced by decreasing gene dosage. [ABSTRACT FROM AUTHOR]

BACKGROUND:Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstructed by mapping syntenic regions to the sorghum chromosomes. During evolution, maize has had uneven gene loss between each ancient subgenome. Fractionation and divergence between these genomes continue today, constantly changing genetic make-up and phenotypes and influencing agronomic traits. RESULTS:Here we regenerate the subgenome reconstructions for the most recent maize reference genome assembly. Based on both expression and abundance data for homeologous gene pairs across multiple tissues, we observed functional divergence of genes across subgenomes. Although the genes in the larger maize subgenome are often expressing more highly than their homeologs in the smaller subgenome, we observed cases where homeolog expression dominance switches in different tissues. We demonstrate for the first time that protein abundances are higher in the larger subgenome, but they also show tissue-specific dominance, a pattern similar to RNA expression dominance. We also find that pollen expression is uniquely decoupled from protein abundance. CONCLUSION:Our study shows that the larger subgenome has a greater range of functional assignments and that there is a relative lack of overlap between the subgenomes in terms of gene functions than would be suggested by similar patterns of gene expression and protein abundance. Our study also revealed that some reactions are catalyzed uniquely by the larger and smaller subgenomes. The tissue-specific, nonequivalent expression-level dominance pattern observed here implies a change in regulatory control which favors differentiated selective pressure on the retained duplicates leading to eventual change in gene functions.

Abstract Background In the riverine riparian ecosystem, particularly in India, the knowledge of the effects of habitat disturbance on taxonomic distinctness, functional diversity, and local contribution to β diversity (LCBD) of spider community is elusive. The present study examined the relationships between the index of taxonomic distinctness (Δ+), index of variation in taxonomic distinctness (λ+), functional evenness (FEve), functional divergence (FDiv), functional dispersion (FDis), and LCBD of spider community of the Ganga River and the effects of habitat disturbance on these indices. A total of 27 sampling sites were selected along the bank of the Ganga River. Based on the rating of the disturbance scores, the sites were classified into lowly, moderately, and highly disturbed sites. To understand the relationships between species richness, Δ+, λ+, FDis, FDiv, FEve, LCBD, and habitat disturbance score, Pearson’s correlation was calculated, followed by the linear regression model. The one-way multivariate analysis of variance was used to find differences in taxonomic distinctness and functional diversity in the different disturbed sites. Results Significant relationships were found between λ+ and Δ+, FDis and Δ+, FDis and λ+, FDiv and species richness, FEve and species richness, FEve and λ+, FEve and habitat disturbance, LCBD and FEve, and LCBD and habitat disturbance. A significant difference was present in the indices of functional diversity between the lowly, moderately, and highly disturbed sites. Agriculture, garbage dump, human settlement, and created embankment influenced the spider community's λ+, FEve, and LCBD. Conclusion Unrestrained anthropogenic activities exacerbate habitat disturbance by affecting ecological processes. Thus, understanding linkages between ecosystem disturbance, taxonomic, functional, and β diversity can be fundamental to managing and conserving natural resources. This work highlights the importance of including taxonomic and functional diversity to comprehend the impact of habitat disturbance on riverine riparian spiders beyond just the number of species. An integrated taxonomic and functional diversity approach coupled with β diversity can be used to support environmental assessment, restoration, and conservation planning of the biological resources of the Ganges River.

IntroductionEffective fisheries management requires monitoring and quantifying changes in exploited fish communities. Concerns about global fisheries sustainability have led to innovative approaches. Functional diversity, rooted in ecological theory, offers valuable insights into fishery activities and ecosystem processes. A trait-based approach was used to investigate the functional diversity of landed fish species in the Azores archipelago from 1980 to 2021.MethodsLandings data of exploited Actinopterygii and Elasmobranchii were provided by the Azores Fisheries Auction Services (LOTAÇOR/OKEANOS-UAc Fisheries Database). A trait matrix was built, incorporating 12 functional traits assigned to each species, capturing their importance in marine ecological processes. The Quickhull algorithm for convex hull was employed to calculate the volume occupied by the species in the four-dimensional functional space. Functional diversity (FD) was measured using three indices: functional richness (FRic), functional evenness (FEve), and functional divergence (FDiv). Trends in FD indices over the past 42 years were visualized using Generalized Additive Models (GAM) with interaction terms.Results and discussionGAM analysis revealed significant variations in the functional space and FD metrics over time. FRic exhibited peaks in the 1980s and 2010s, declining in the 1990s and from the 2010s onwards, indicating diversification in target species. The recent decrease in FRic can be attributed to the absence of catches of species with unique traits. The distribution of landings and trait combinations showed higher regularity in the functional space during the 1980s and 1990s (high FEve). Actinopterygii species targeted in the 1980s and 1990s had lower trait divergence (low FDiv) compared to those targeted from the 2000s onwards (high FDiv). Variability in FD can be linked to changes in fishing practices, species availability, market demand, environmental factors, and local regulations. This study underscores the importance of considering FD metrics alongside species richness and abundance when assessing the potential effects of fisheries on marine ecosystems and sustainable use of fishery resources.

There is increasing awareness that plant community functional properties can be an important driver of ecosystem functioning. However, major knowledge gaps exist about how environmental factors, especially climate and soil abiotic properties, shape plant functional diversity at a regional scale. Furthermore, at those scales the relationships between plant functional and taxonomic diversity have rarely been considered. Here, we used a large database of plant species and functional trait data from 180 temperate grasslands across England, covering a broad range of grassland types, climatic conditions and management intensities, the last having a strong influence on multiple soil variables. Our specific aims were to: (1) identify the dominant environmental factors explaining variation in different facets of plant community functional properties, including community weighted means (CWMs) of functional traits and various multi-trait functional diversity indices; and (2) test whether the relationship between plant functional and taxonomic diversity is mediated by environmental factors at a regional scale. We found that soil abiotic properties (pH and nutrient stocks), but not climate, were the main environmental factors explaining grassland plant functional diversity at a regional scale, with a significant contribution of soil nutrient stoichiometry (N/P ratio). Two indices of plant community functional properties, namely CWMs of specific leaf area and relative growth rate, were explained by interactions between soil pH and N and mean annual precipitation, soil pH soil N and soil N/P ratio. These indices were also negatively related to taxonomic diversity under certain soil abiotic conditions, specifically high soil clay content, pH and N/P. Together, our results indicate that soil abiotic properties rather than climate factors shape plant functional diversity across temperate grassland plant communities at a regional scale. They also suggest that interactions between environmental factors play a significant role in shaping patterns of plant community functional properties. Our findings are of importance for the design and interpretation of future studies using trait and diversity measures as proxies of ecosystem services at regional scales. [ABSTRACT FROM AUTHOR]

Riparian plant communities are key to ecosystem functioning and important providers of ecosystem services on which wildlife and people depend. Ecosystem functioning and stability depend on functional diversity and redundancy. Therefore, understanding which and how different drivers shape community assembly processes and functional patterns is crucial. However, there is limited knowledge of these processes at larger scales for the entire riparian vascular plant community.Two community assembly processes dominate: environmental filtering, where species living in similar environments have similar traits leading to trait convergence; and limiting similarity, where similar traits cause species to compete more strongly leading to trait divergence. We assessed functional diversity patterns of riparian vascular plant communities across an Atlantic–Mediterranean biogeographical gradient in north Portugal.We used functional diversity indices and null models to detect community assembly processes and whether these processes change along environmental gradients. We hypothesised that environmental filtering associated with precipitation and aridity would be the prevailing assembly process at a regional scale. We also expected a shift from environmental filtering to limiting similarity as precipitation‐related stress declined.As hypothesised, patterns of functional diversity were consistent with environmental filtering of species occurrences at the regional scale. Functional patterns were also consistent with a shift between environmental filtering and limiting similarity as cold and aridity stress declined. Under stressful environmental conditions, communities showed lower functional divergence and richness than expected by chance. Environmental filtering was more strongly associated with minimum temperatures than precipitation and aridity.Underlining the need for hierarchical approaches and the analysis of multiple climatic stressors, our results highlighted the relevance of large‐scale environmental stress gradients and the potential role of community assembly in influencing riparian functional diversity. Alterations in stress filters due to climate change will affect assembly processes and functional patterns, probably affecting ecosystem functioning and stability. [ABSTRACT FROM AUTHOR]

Dendroctonus-bark beetles are natural components and key ecological agents of coniferous forests. They spend most of their lives under the bark, where they are exposed to highly toxic terpenes present in the oleoresin. Cytochrome P450 (CYP) is a multigene family involved in the detoxification of these compounds. It has been demonstrated that CYP6DE and CYP6DJ subfamilies hydroxylate monoterpenes, whose derivatives can act as pheromone synergist compounds or be pheromones themselves in these insects. Given the diversity and functional role of CYPs, we investigated whether these cytochromes have retained their function throughout the evolution of these insects. To test this hypothesis, we performed a Bayesian phylogenetic analysis to determine phylogenetic subgroups of cytochromes in these subfamilies. Subgroups were mapped and reconciled with the Dendroctonus phylogeny. Molecular docking analyses were performed with the cytochromes of each subgroup and enantiomers of α-pinene and β-pinene, (+)-3-carene, β-myrcene and R-(+)-limonene. In addition, functional divergence analysis was performed to identify critical amino acid sites that influence changes in catalytic site conformation and/or protein folding. Three and two phylogenetic subgroups were recovered for the CYP6DE and CYP6DJ subfamilies, respectively. Mapping and reconciliation analysis showed different gain and loss patterns for cytochromes of each subgroup. Functional predictions indicated that the cytochromes analyzed are able to hydroxylate all monoterpenes; however, they showed preferential affinities to different monoterpenes. Functional divergence analyses indicated that the CYP6DE subfamily has experimented type I and II divergence, whereas the CYP6DJ subfamily has evolved under strong functional constraints. Results suggest cytochromes of the CYP6DE subfamily evolve to reinforce their detoxifying capacity hydroxylating mainly α- and β-pinene to (+) and (−)-trans-verbenol, being the negative enantiomer used as a pheromone by several Dendroctonus species; whereas cytochromes of the CYP6DJ subfamily appear to retain their original function related to the detoxification of these compounds.

Climate change impacts on freshwater ecosystems and freshwater biodiversity show strong spatial variability, highlighting the importance of a global perspective. While previous studies on biodiversity mostly focused on species richness, functional diversity, which is a better predictor of ecosystem functioning, has received much less attention. This study aims to comprehensively assess climate change threats to the functional diversity of freshwater fish across the world, considering three complementary metrics—functional richness, evenness and divergence. We built on existing spatially explicit projections of geographical ranges for 11,425 riverine fish species as affected by changes in streamflow and water temperature extremes at four warming levels (1.5°C, 2.0°C, 3.2°C and 4.5°C). To estimate functional diversity, we considered the following four continuous, morphological and physiological traits: relative head length, relative body depth, trophic level and relative growth rate. Together, these traits cover five ecological functions. We treated missing trait values in two different ways: we either removed species with missing trait values or imputed them. Depending on the warming level, 6%–25% of the locations globally face a complete loss of functional diversity when assuming no dispersal (6%–17% when assuming maximal dispersal), with hotspots in the Amazon and Paraná River basins. The three facets of functional diversity do not always follow the same pattern. Sometimes, functional richness is not yet affected despite species loss, while functional evenness and divergence are already reducing. Other times, functional richness reduces, while functional evenness and/or divergence increase instead. The contrasting patterns of the three facets of functional diversity show their complementarity among each other and their added value compared to species richness. With increasing climate change, impacts on freshwater communities accelerate, making early mitigation critically important. [ABSTRACT FROM AUTHOR]

Biological invasions remain one of the most pressing threats to biodiversity globally, with unprecedented rates of establishment that are unlikely to abate in the future. As such the occurrence of multiple interacting invasive non‐native species (INNS) is becoming more common. Despite this, much of the research on the interaction of multiple INNS is conducted within laboratory settings, with field studies remaining rare or being conducted as one‐off sampling. There is therefore a deficit of knowledge pertaining to the natural population trajectories of multiple INNS and the wider ecological implications for the structure and function of the native communities. Here we present multiple years of data collected from a reservoir in the United Kingdom, which has undergone invasion by three congener non‐native amphipods. We initially observed the coexistence of Dikerogammarus haemobaphes with Crangonyx pseudogracilis under habitat segregation in the reservoir. However, the following year saw complete displacement of C. pseudogracilis and reduced abundances of D. haemobaphes once the more competitive Dikerogammarus villosus established abundant populations in the reservoir. D. villosus exhibited strong effects for the structure and function of the wider macroinvertebrate community composition in addition to driving reductions in taxa and functional richness. Gastropoda taxa appeared to be unaffected by the invasion dynamics. Significant increases in functional divergence (and less so functional dispersion) values were also observed following D. villosus establishment, with this response metric possibly representing an important tool in detecting stress from biological invasions that we urge scientists to test more extensively. In contrast to D. villosus, D. haemobaphes implications for the wider ecological community appeared to be limited. Importantly, we observed evidence to suggest the presence of boom–bust cycles with the explosion of D. villosus leading to a dramatic drop in their abundances the following year. We believe that the wider ecological implications of their abundant populations were so great that resources were not sufficient within the reservoir to support their abundant populations, leading to the observed population collapses. We call for further studies that investigate the population trajectories and wider ecological implications of multiple non‐native species in field settings to further our limited knowledge base. [ABSTRACT FROM AUTHOR]

Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications. [ABSTRACT FROM AUTHOR]

Chitin is one of the most abundant polysaccharides in nature, forming important structures in insects, crustaceans, and fungal cell walls. Vertebrates on the other hand are generally considered "nonchitinous" organisms, despite having highly conserved chitin metabolismassociated genes. Recent work has revealed that the largest group of vertebrates, the teleosts, have the potential to both synthesize and degrade endogenous chitin. Yet, little is known about the genes and proteins responsible for these dynamic processes. Here, we used comparative genomics, transcriptomics, and chromatin accessibility data to characterize the repertoire, evolution, and regulation of genes involved in chitin metabolism in teleosts, with a particular focus on Atlantic salmon. Reconstruction of gene family phylogenies provides evidence for an expansion of teleost and salmonid chitinase and chitin synthase genes after multiple whole-genome duplications. Analyses of multi-tissue gene expression data demonstrated a strong bias of gastrointestinal tract expression for chitin metabolism genes, but with different spatial and temporal tissue specificities. Finally, we integrated transcriptomes from a developmental time series of the gastrointestinal tract with chromatin accessibility data to identify putative transcription factors responsible for regulating chitin metabolism gene expression (CDX1 and CDX2) as well as tissue-specific divergence in the regulation of gene duplicates (FOXJ2). The findings presented here support the hypothesis that chitin metabolism genes in teleosts play a role in developing and maintaining a chitin-based barrier in the teleost gut and provide a basis for further investigations into the molecular basis of this barrier. [ABSTRACT FROM AUTHOR]

Abstract Biological invasions remain one of the most pressing threats to biodiversity globally, with unprecedented rates of establishment that are unlikely to abate in the future. As such the occurrence of multiple interacting invasive non‐native species (INNS) is becoming more common. Despite this, much of the research on the interaction of multiple INNS is conducted within laboratory settings, with field studies remaining rare or being conducted as one‐off sampling. There is therefore a deficit of knowledge pertaining to the natural population trajectories of multiple INNS and the wider ecological implications for the structure and function of the native communities. Here we present multiple years of data collected from a reservoir in the United Kingdom, which has undergone invasion by three congener non‐native amphipods. We initially observed the coexistence of Dikerogammarus haemobaphes with Crangonyx pseudogracilis under habitat segregation in the reservoir. However, the following year saw complete displacement of C. pseudogracilis and reduced abundances of D. haemobaphes once the more competitive Dikerogammarus villosus established abundant populations in the reservoir. D. villosus exhibited strong effects for the structure and function of the wider macroinvertebrate community composition in addition to driving reductions in taxa and functional richness. Gastropoda taxa appeared to be unaffected by the invasion dynamics. Significant increases in functional divergence (and less so functional dispersion) values were also observed following D. villosus establishment, with this response metric possibly representing an important tool in detecting stress from biological invasions that we urge scientists to test more extensively. In contrast to D. villosus, D. haemobaphes implications for the wider ecological community appeared to be limited. Importantly, we observed evidence to suggest the presence of boom–bust cycles with the explosion of D. villosus leading to a dramatic drop in their abundances the following year. We believe that the wider ecological implications of their abundant populations were so great that resources were not sufficient within the reservoir to support their abundant populations, leading to the observed population collapses. We call for further studies that investigate the population trajectories and wider ecological implications of multiple non‐native species in field settings to further our limited knowledge base.

Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates. [ABSTRACT FROM AUTHOR]

The Fidgetin (FIGN) family, which comprises FIGN, Fidgetin-like 1 (FIGNL1), and Fidgetin-like 2 (FIGNL2), is a vital group of microtubule-severing proteins. These proteins feature a conserved AAA+ domain essential for ATPase activity and a hexameric assembly. This review provides an in-depth analysis of the evolution and functional divergence of the FIGN family members, highlighting their role in the dynamic organization of the cytoskeleton. We further explore their broader biological functions across various species, systems, and subcellular localization. Although the FIGN family is conserved, each member exhibits unique structural characteristics and functions that reflect their evolutionary adaptations. FIGNL1 is found across animal species, while FIGNL2 is specific to vertebrates, thereby indicating its more recent evolutionary origin. Moreover, synteny analysis has revealed that FIGN is located in a more conserved genomic region compared to FIGNL2, which has undergone substantial evolutionary changes. The expression patterns of the FIGN members also vary across organisms and tissues. For example, FIGNL2 shows a notably reduced expression in the mammalian nervous system compared to that in lower vertebrates. The FIGN family members have distinct roles in microtubule severing, cell division, and DNA repair. Specifically, FIGN is involved in cell division and neuronal regeneration, FIGNL1 in axonal growth and DNA repair, and FIGNL2 in cell migration and vascular development. Their involvement in these processes underscores their role as potential biomarkers for certain cancers as well as therapeutic targets for diseases affecting the nervous system and cardiovascular development. All these evolutionary insights and functional distinctions of the FIGN family offer a comprehensive framework for understanding cytoskeletal regulation and its implications in health and disease. • Fidgetin proteins are microtubule severing proteins with a conserved AAA+ domain. • Each Fidgetin family member has unique traits reflecting their evolutionary history. • Expression patterns of Fidgetin proteins vary widely across species and tissues. • Fidgetin proteins play key roles in cell division, DNA repair, and neuronal regeneration. • These proteins are potential biomarkers and therapeutic targets for diseases. [ABSTRACT FROM AUTHOR]

Mitogen-activated protein kinases (MAPKs) are crucial regulators in coping with abiotic and biotic stresses, including drought, salinity, fungi, and pathogens. However, little is known about the characteristics, evolution process, and functional divergence of the MAPK gene family in Rosaceae plants. A total of 97 MAPK members were identified in six Rosaceae species, including 12 genes in Fragaria vesca, 22 genes in Malus domestica, 23 genes in Pyrus bretschneideri, 12 genes in Prunus mume, 14 genes in Prunus persica, and 14 genes in Rosa chinensis. All MAPK members of six Rosaceae plants were categorized into four clusters by the phylogenetic relationship analysis. Collinearity analysis discovered that both segmental duplication and tandem duplication contributed to the expansion of MAPK family genes in Rosaceae plants. And the analysis of motifs and gene structures indicated that the evolution of the MAPK gene family was highly conserved among phylogenetic clusters in Rosaceae species. In addition, the dN/dS rates of MAPK paralogous gene pairs were below one, suggesting the MAPK gene family in Rosaceae was driven by purifying selective pressure. Furthermore, functional divergence analysis discovered that 14 amino acid residues were detected as potentially key sites for functional divergence of MAPK family genes between different cluster pairs, specifically Type I functional divergence. The analysis of functional distance indicated that cluster C retained more of the original functional features, while cluster B exhibited functional specialization. Moreover, the expression profiles revealed that PmMAPK8, PmMAPK9, and PmMAPK10 were both highly expressed under drought stress and low temperature conditions. This study aims to comprehensively analyze the evolutionary process and functional analyses of the MAPK gene family in Rosaceae plants, which will lay the foundation for future studies into MAPK genes of Rosaceae in response to drought and cold stress.

Unique to plants, growth regulatory factors (GRFs) play important roles in plant growth and reproduction. This study investigated the evolutionary and functional characteristics associated with plant growth. Using genome-wide analysis of 15 plant species, 173 members of the GRF family were identified and phylogenetically categorized into six groups. All members contained WRC and QLQ conserved domains, and the family’s expansion largely depended on segmental duplication. The promoter region of the GRF gene family mainly contained four types of cis-acting elements (light-responsive elements, development-related elements, hormone-responsive elements, and environmental stress-related elements) that are mainly related to gene expression levels. Functional divergence analysis revealed that changes in amino acid site evolution rate played a major role in the differentiation of the GRF gene family, with ten significant sites identified. Six significant sites were identified for positive selection. Moreover, the four groups of coevolutionary sites identified may play a key role in regulating the transcriptional activation of the GRF protein. Expression profiles revealed that GRF genes were generally highly expressed in young plant tissues and had tissue or organ expression specificity, demonstrating their functional conservation with distinct divergence. The results of these sequence and expression analyses are expected to provide molecular evolutionary and functional references for the plant GRF gene family.