Functional Divergence Research Articles

In silico comparative analysis of cestode and human NPC1 provides insights for ezetimibe repurposing to visceral cestodiases treatment

Visceral cestodiases, like cysticercoses and echinococcoses, are caused by cystic larvae from parasites of the Cestoda class and are endemic or hyperendemic in many areas of the world. Current therapeutic approaches for these diseases are complex and present limitations and risks. Therefore, new safer and more effective treatments are urgently needed. The Niemann-Pick C1 (NPC1) protein is a cholesterol transporter that, based on genomic data, would be the solely responsible for cholesterol uptake in cestodes. Considering that human NPC1L1 is a known target of ezetimibe, used in the treatment of hypercholesterolemia, it has the potential for repurposing for the treatment of visceral cestodiases. Here, phylogenetic, selective pressure and structural in silico analyses were carried out to assess NPC1 evolutive and structural conservation, especially between cestode and human orthologs. Two NPC1 orthologs were identified in cestode species (NPC1A and NPC1B), which likely underwent functional divergence, leading to the loss of cholesterol transport capacity in NPC1A. Comparative interaction analyses performed by molecular docking of ezetimibe with human NPC1L1 and cestode NPC1B pointed out to similarities that consolidate the idea of cestode NPC1B as a target for the repurposing of ezetimibe as a drug for the treatment of visceral cestodiases.

ELUCIDATING THE DIFFERENTIAL IMPACTS OF EQUIVALENT GATING-CHARGE MUTATIONS IN VOLTAGE-GATED SODIUM CHANNELS.

Voltage-gated sodium (Nav) channels are pivotal for cellular signaling and mutations in Nav channels can lead to excitability disorders in cardiac, muscular, and neural tissues. A major cluster of pathological mutations localizes in the voltage-sensing domains (VSDs), resulting in either gain-of-function (GoF), loss-of-function (LoF) effects, or both. However, the mechanism behind this functional divergence of mutations at equivalent positions remains elusive. Through hotspot analysis, we identified three gating charges (R1, R2, and R3) as major mutational hotspots in VSDs. The same amino-acid substitutions at equivalent gating-charge positions in VSDI and VSDII of the cardiac sodium channel Nav1.5 show differential gating-property impacts in electrophysiology measurements. We conducted 120 μs molecular dynamics (MD) simulations on wild-type and six mutants to elucidate the structural basis of their differential impacts. Our μs-scale MD simulations with applied external electric fields captured VSD state transitions and revealed the differential structural dynamics between equivalent R-to-Q mutants. Notably, we observed transient leaky conformations in some mutants during structural transitions, offering a detailed structural explanation for gating-pore currents. Our salt-bridge network analysis uncovered VSD-specific and state-dependent interactions among gating charges, countercharges, and lipids. This detailed analysis elucidated how mutations disrupt critical electrostatic interactions, thereby altering VSD permeability and modulating gating properties. By demonstrating the crucial importance of considering the specific structural context of each mutation, our study represents a significant leap forward in understanding structure-function relationships in Nav channels. Our work establishes a robust framework for future investigations into the molecular basis of ion channel-related disorders.

Diversity, functional redundancy, and vulnerability of reef fish communities of the Saudi Arabian coast, in the northern Red Sea

In light of the current development of several giga-projects along the Saudi Red Sea coast, understanding the health status of coral reefs is paramount to developing baselines and management strategies to minimize the human impact on these ecosystems. Here, we present an assessment of the diversity, functional redundancy, and vulnerability for coral reef fish communities in the northern Red Sea. The focus area of our study falls within the marine jurisdiction of the NEOM giga-project. We performed fish surveys with three different methods aiming to cover a wide set of habitats and thus capture a comprehensive picture of the regional diversity: i) standardized belt transects, ii) roving diviersity surveys, and iii) collection of cryptobenthic fish. Our results showed a highly variable community composition along the ten surveyed sites highlighting Sindalah as an essential site for piscivore species, Al Muwaileh as an important site for herbivores, and Sanafir-Tiran as the most diverse site. Functional diversity analysis revealed similar levels of redundancy, over-redundancy, and vulnerability among sites. Functional richness, evenness, and divergence did not vary substantially between sites and, in general, indicated that the fish communities in the selected sites present mid to low levels of functional diversity. We further compare regional-scale and site-specific functional assessments. Notably, some of the species groups that are functionally redundant at the regional scale represented vulnerable functions at the site level. These results call to attention the need to create site-specific conservation strategies and not to solely rely on regional diviersity assessments as the basis for management decisions.

Biochemical Characterisation of the Short Isoform of Histone N-Terminal Acetyltransferase NAA40.

N-alpha-acetyltransferase 40 (NAA40) is an evolutionarily conserved N-terminal acetyltransferase (NAT) linked to oncogenesis and chemoresistance. A recent study reported the generation of a second, shorter NAA40 isoform (NAA40S) through alternative translation, which we proceeded to further characterise. Notably, recombinant NAA40S had a greater in vitro enzymatic activity and affinity towards its histone H2A/H4 substrates compared to full-length NAA40 (NAA40L). Within cells, NAA40S was enzymatically active, based on its ability to suppress the H2A/H4S1Ph antagonistic mark in CRISPR-generated NAA40 knockout cells. Finally, we show that in addition to alternative translation, the NAA40S isoform could be derived from a primate and testis-specific transcript, which may align with the "out-of-testis" origin of recently evolved genes and isoforms. To summarise, our data reveal an even greater functional divergence between the two NAA40 isoforms than had been previously recognised.

SUPERMAN genes: uncovering a new function in the development of complex inflorescences.

The Arabidopsis SUPERMAN (SUP) gene and its orthologs in eudicots are crucial in regulating the number of reproductive floral organs. In Medicago truncatula, in addition to this function, a novel role in controlling meristem activity during compound inflorescence development was assigned to the SUP-ortholog (MtSUP). These findings led us to investigate whether the role of SUP genes in inflorescence development was legume-specific or could be extended to other eudicots. To assess that, we used Solanum lycopersicum as a model system with a cymose complex inflorescence and Arabidopsis thaliana as the best-known example of simple inflorescence. We conducted a detailed comparative expression analysis of SlSUP and SUP from vegetative stages to flower transition. In addition, we performed an exhaustive phenotypic characterisation of two different slsup and sup mutants during the plant life cycle. Our findings reveal that SlSUP is required for precise regulation of the meristems that control shoot and inflorescence architecture in tomato. In contrast, in Arabidopsis, SUP performs no meristematic function, but we found a role of SUP in floral transition. Our findings suggest that the functional divergence of SUP-like genes contributed to the modification of inflorescence architecture during angiosperm evolution.

Rice BARENTSZ genes are required to maintain floral developmental stability against temperature fluctuations.

BARENTSZ (BTZ), a core component of the exon junction complex, regulates diverse developmental processes in animals. However, its evolutionary and developmental roles in plants remain elusive. Here, we revealed that three groups of paralogous BTZ genes existed in Poaceae, and Group 2 underwent loss-of-function mutations during evolution. They showed surprisingly low (~33%) sequence identities, implying functional divergence. Two genes retained in rice, OsBTZ1 and OsBTZ3, were edited; however, the resultant osbtz1 and osbtz3 mutants showed similar floral morphological and functional defects at a low frequency. When growing under low-temperature conditions, developmental abnormalities became pronounced, and new floral variations were induced. In particular, stamen and carpel functionality was impaired in these rice btz mutants. The double-gene mutant osbtz1/3 shared these floral defects with an increased frequency, which was further induced under low-temperature conditions. OsBTZs interacted with OsMADS7 and OsMADS8, and the floral expressions of the OsTGA10 and MADS-box genes were correlatively altered in these osbtz mutants and responded to low-temperature treatment. These novel findings demonstrate that two highly diverged OsBTZs are required to maintain floral developmental stability under low-temperature conditions, and play an integral role in male and female fertility, thus providing new insights into the indispensable roles of BTZ genes in plant development and adaptive evolution.

The MAP4 kinase NbM4K3 regulates immune responses in Nicotiana benthamiana

The mitogen-activated protein kinase kinase kinase kinase (M4K) family is evolutionarily conserved across plants and animals. In Arabidopsis, the protein kinase SIK1, an M4K member, is known to positively modulate reactive oxygen species (ROS) production during pattern-triggered immunity (PTI) by stabilizing BIK1, a key receptor-like cytoplasmic kinase (RLCK). While homologs of SIK1 exhibit conserved protein domain architectures across a range of land plants, their functional conservation remains incompletely understood. This study investigates the functional conservation and divergence of SIK1 homologs, focusing particularly on NbM4K3 in Nicotiana benthamiana. Silencing NbM4K3 resulted in an impairment of the flg22-induced ROS burst and expression of PTI marker genes. Additionally, silencing NbM4K3 led to diminished protein accumulation of RLCKs, while overexpression of the RLCKs prominently enhanced the flg22-induced ROS burst in NbM4K3-silenced plants. Furthermore, NbM4K3-silenced plants exhibited a compromised hypersensitive response (HR), reduced ROS accumulation, and diminished expression of effector-triggered immunity (ETI) marker genes when challenged with the avirulent strains Ralstonia solanacearum GMI1000 and Pseudomonas syringae DC3000, suggesting that NbM4K3 is a positive regulator of ETI. The attenuated HR phenotype observed in NbM4K3-silenced plants upon expression of RipP1 or RipE1, two avirulent type III effectors of GMI1000, further supports the affirmative role of NbM4K3 in ETI. In summary, our data indicate that the M4K NbM4K3 positively regulates both PTI and ETI in N. benthamiana, potentially by stabilizing RLCKs. These findings not only strengthen the role of M4K family in plant immunity but also suggest its potential in improving disease resistance in plants.

Intercropping outweighs straw incorporation driving community and functional diversity of microarthropods after 5 years of tillage practices

Crop-leguminous intercropping and straw incorporation are considerable approaches to sustainable agriculture and have been widely used as a coping strategy to mitigate the negative effects caused by intensive agriculture. Yet, as a sustainable agriculture requires a deeper understanding of the impacts of conservation tillage practices on soil fauna, such as collembolans and acarid mites. These organisms are considered the most abundant and functionally critical soil fauna in many terrestrial natural, agricultural, and urban systems. In the present study, we assessed the responses of the community and functional diversity of collembolan and acarid mite assemblages to long-term intercropping and straw incorporation practices in a temperate farming land, in China. The experimental site was established with a full-factorial design of conservation managements (maize monocropping, maize-peanut intercropping, without maize straw addition, and with maize straw addition) over five consecutive years. Results showed that intercropping doubled collembolan and acarid density. Most of the enriched species in the intercropping field were euedaphic collembolans and cleptoparasitic mites. Nonetheless, the density of most phoretic species decreased, resulting in a negative effect of intercropping on acarid diversity. Despite straw incorporation additionally boosting the intercropping-induced increases in biomass, richness, and density of the collembolan community, the effects of straw incorporation on the community structure of collembolans and acarid mites were negligible. Similarly, intercropping affected the functional composition of collembolans and mites differently. Intercropping favored euedaphic collembolans characterized by less-developed furca, ocelli and sexual reproduction, but fungivorous, and benefited the cleptoparasitic mites that might be transported by their provisional hosts during pollinating peanut flowers. Moreover, intercropping decreased the functional dispersion of acarid mites, resulting in an acarid community with a homogenized ecological niche of acarid mites. In contrast, the ecological niche was more differentiated. Similar to intercropping, the ecological niche of collembolans in the field with straw was relatively higher, as well as the functional divergence, suggesting more intense resource competition between collembolans. In conclusion, intercropping has species-specific effects on the community and functional diversity of collembolans and mites and is relatively beneficial to collembolans, whereas straw incorporation has a marginal advantage on collembolans and acarid mites.

Functional investigation of the two ClpPs and three ClpXs in Myxococcus xanthus DK1622.

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.

Drp1 splice variants regulate ovarian cancer mitochondrial dynamics and tumor progression

Aberrant mitochondrial fission/fusion dynamics are frequently associated with pathologies, including cancer. We show that alternative splice variants of the fission protein Drp1 (DNM1L) contribute to the complexity of mitochondrial fission/fusion regulation in tumor cells. High tumor expression of the Drp1 alternative splice variant lacking exon 16 relative to other transcripts is associated with poor outcome in ovarian cancer patients. Lack of exon 16 results in Drp1 localization to microtubules and decreased association with mitochondrial fission sites, culminating in fused mitochondrial networks, enhanced respiration, changes in metabolism, and enhanced pro-tumorigenic phenotypes in vitro and in vivo. These effects are inhibited by siRNAs designed to specifically target the endogenously expressed transcript lacking exon 16. Moreover, lack of exon 16 abrogates mitochondrial fission in response to pro-apoptotic stimuli and leads to decreased sensitivity to chemotherapeutics. These data emphasize the pathophysiological importance of Drp1 alternative splicing, highlight the divergent functions and consequences of changing the relative expression of Drp1 splice variants in tumor cells, and strongly warrant consideration of alternative splicing in future studies focused on Drp1.

Protein phosphatase 2A regulates blood cell proliferation and differentiation in Drosophila larval lymph glands.

Protein phosphatase 2A (PP2A), one of the most abundant protein phosphatases, has divergent functions in multiple types of cells. Its inactivation has been closely associated with leukemia diseases. However, the physiological function of PP2A for hematopoiesis has been poorly understood in organisms. Drosophila hematopoiesis parallels the vertebrate counterpart in developmental and functional features but involves a much simpler hematopoietic system. Here, utilizing the Drosophila major larval hematopoietic organ lymph gland, we studied the function of PP2A for hematopoiesis in vivo. By knocking down the expression of Pp2A-29B that encodes the scaffold subunit of the PP2A holoenzyme complex, we found that PP2A silencing in the differentiating hemocytes resulted in their excessive proliferation. Furthermore, this PP2A inhibition downregulated the expression of Smoothened (Smo), a crucial component in the Hedgehog pathway, and smo overexpression was able to rescue the phenotypes of PP2A depletion, indicating that Smo functions as a downstream effector of PP2A to restrict the hemocyte proliferation. PDGF/VEGF-receptor (Pvr) overexpression also restored the Smo expression and lymph gland morphology of PP2A silencing, suggesting a PP2A-Pvr-Smo axis to regulate lymph gland growth and hemocyte proliferation. Moreover, inhibiting PP2A activity in the blood progenitor cells promoted their differentiation, but which was independent with Smo. Together, our data suggested that PP2A plays a dual role in the Drosophila lymph gland by preserving the progenitor population and restraining the hemocyte proliferation, to properly regulate the hematopoietic process.

Potential Roles of the GRF Transcription Factors in Sorghum Internodes during Post-Reproductive Stages.

Growth-regulating factor (GRF) is a plant-specific family of transcription factors crucial for meristem development and plant growth. Sorghum (Sorghum bicolor L. Moench) is a cereal species widely used for food, feed and fuel. While sorghum stems are important biomass components, the regulation of stem development and the carbohydrate composition of the stem tissues remain largely unknown. Here, we identified 11 SbGRF-encoding genes and found the SbGRF expansion driven by whole-genome duplication events. By comparative analyses of GRFs between rice and sorghum, we demonstrated the divergence of whole-genome duplication (WGD)-derived OsGRFs and SbGRFs. A comparison of SbGRFs' expression profiles supports that the WGD-duplicated OsGRFs and SbGRFs experienced distinct evolutionary trajectories, possibly leading to diverged functions. RNA-seq analysis of the internode tissues identified several SbGRFs involved in internode elongation, maturation and cell wall metabolism. We constructed co-expression networks with the RNA-seq data of sorghum internodes. Network analysis discovered that SbGRF1, 5 and 7 could be involved in the down-regulation of the biosynthesis of cell wall components, while SbGRF4, 6, 8 and 9 could be associated with the regulation of cell wall loosening, reassembly and/or starch biosynthesis. In summary, our genome-wide analysis of SbGRFs reveals the distinct evolutionary trajectories of WGD-derived SbGRF pairs. Importantly, expression analyses highlight previously unknown functions of several SbGRFs in internode elongation, maturation and the potential involvement in the metabolism of the cell wall and starch during post-anthesis stages.

Hidden results of functional diversity in macroinvertebrates: Trait-groups specific response to flow intermittency in lowland streams

As global flow intermittency increases, understanding how macroinvertebrates respond at a functional level in streams becomes crucial for effective water management. This study investigates the functional response of macroinvertebrates to flow intermittency in Hungarian lowland streams over a 10-month period, comparing intermittent and perennial streams across the entire community, trait groups, and trait states. We aimed to demonstrate differences in functional diversity using metrics such as functional richness, evenness, divergence, dispersion, and Rao's quadratic entropy. For trait groups, we focused on both response and stable traits, anticipating greater differences in response traits. Additionally, we identified which trait states, as indicated by community-weighted means, contribute significantly to variations between streams. Our findings indicate that functional diversity in intermittent streams is generally lower or equivalent to that in perennial streams, suggesting disparities in functional trait composition. Significant differences were observed within trait groups, indicating specific responses of trait groups to intermittency. We identified resilience trait states—including current velocity, reproduction, respiration, female length, locomotion, substrate relation, aquatic stages, and resistance forms—that contributed to these differences. The three-level analysis revealed a hidden relationship: differences at the state level do not consistently manifest at the trait group or whole community levels. Investigating functional changes at the trait group or trait state level can serve as an early indicator of community shifts. Incorporating trait groups as indices into assessment frameworks could facilitate early detection of functional changes during bioassessment. We recommend considering trait groups when evaluating functional responses to flow intermittency in future studies.

Ancestral duplication of MADS-box genes in land plants empowered the functional divergence between sporophytes and gametophytes.

Ancestral duplication of MADS-box genes in land plants empowered the functional divergence between sporophytes and gametophytes.

All of Us diversity and scale improve polygenic prediction contextually with greatest improvements for under-represented populations.

Recent studies have demonstrated that polygenic risk scores (PRS) trained on multi-ancestry data can improve prediction accuracy in groups historically underrepresented in genomic studies, but the availability of linked health and genetic data from large-scale diverse cohorts representative of a wide spectrum of human diversity remains limited. To address this need, the All of Us research program (AoU) generated whole-genome sequences of 245,388 individuals who collectively reflect the diversity of the USA. Leveraging this resource and another widely-used population-scale biobank, the UK Biobank (UKB) with a half million participants, we developed PRS trained on multi-ancestry and multi-biobank data with up to ∼750,000 participants for 32 common, complex traits and diseases across a range of genetic architectures. We then compared effects of ancestry, PRS methodology, and genetic architecture on PRS accuracy across a held out subset of ancestrally diverse AoU participants. Due to the more heterogeneous study design of AoU, we found lower heritability on average compared to UKB (0.075 vs 0.165), which limited the maximal achievable PRS accuracy in AoU. Overall, we found that the increased diversity of AoU significantly improved PRS performance in some participants in AoU, especially underrepresented individuals, across multiple phenotypes. Notably, maximizing sample size by combining discovery data across AoU and UKB is not the optimal approach for predicting some phenotypes in African ancestry populations; rather, using data from only AoU for these traits resulted in the greatest accuracy. This was especially true for less polygenic traits with large ancestry-enriched effects, such as neutrophil count ( R 2 : 0.055 vs. 0.035 using AoU vs. cross-biobank meta-analysis, respectively, because of e.g. DARC ). Lastly, we calculated individual-level PRS accuracies rather than grouping by continental ancestry, a critical step towards interpretability in precision medicine. Individualized PRS accuracy decays linearly as a function of ancestry divergence, but the slope was smaller using multi-ancestry GWAS compared to using European GWAS. Our results highlight the potential of biobanks with more balanced representations of human diversity to facilitate more accurate PRS for the individuals least represented in genomic studies.

Modulation of cell differentiation and growth underlies the shift from bud protection to light capture in cauline leaves.

Plant organs have evolved into diverse shapes for specialized functions despite emerging as simple protrusions at the shoot apex. Cauline leaves serve as photosynthetic organs and protective structures for emerging floral buds. However, the growth patterns underlying this dual function remain unknown. Here, we investigate the developmental dynamics shaping Arabidopsis (Arabidopsis thaliana) cauline leaves underlying their functional diversification from other laminar organs. We show that cauline leaves display a significant delay in overall elongation compared to rosette leaves. Using live imaging, we reveal that their functional divergence hinges on early modulation of the timing of cell differentiation and cellular growth rates. In contrast to rosette leaves and sepals, cell differentiation is delayed in cauline leaves, fostering extended proliferation, prolonged morphogenetic activity, and growth redistribution within the organ. Notably, cauline leaf growth is transiently suppressed during the early stages, keeping the leaf small and unfolded during the initiation of the first flowers. Our findings highlight the unique developmental timing of cauline leaves, underlying their shift from an early protective role to a later photosynthetic function.

Multi-modal incomplete label information three-way bidirectional decision-making: Applications of disease assessment

Disease assessment involves two stages of decision-making process. The first process is to infer the development trend of the disease through the existing judgment conditions, which is to make a positive estimation (prediction) decision. The second process is to update the judgment conditions for different disease states and optimize the clinical assessment evidence by fusing disease progression data, that is, to make a reverse evaluation (optimization) decision by reviewing historical diagnostic and treatment data to summarize the best judgment conditions for the disease characteristics. Therefore, we construct a three-way bidirectional decision method for multi-modal incomplete labeling information, considering the mixed data features with no labels and labels, and the bidirectional decision features of positive prediction and reverse optimization. Specifically, the method first introduces semi-supervised learning (SSL) into the rough sets, constructs a rough sets model based on cosine similarity relation, generates pseudo-labels for incomplete information, and explains the positive prediction decision process principle. Second, the gradient space is constructed on the predictive information system by the three-way decision-making principle, the loss function formed by the combination of KL divergence and cross entropy loss function is used to find the direction of the fastest decline in attribute information value, and the optimal decision rule and the automatic updating strategy of the threshold value are obtained. At the same time, the principle of the reverse optimization decision process is explained. Finally, multimodal information from pathological tissue images is used to evaluate clinical progress problem. A pathological tissue images dataset includes 2000 colorectal cancer and 300 kidney disease cases used for simulation experiments. The proposed three-way bidirectional decision-making model can be widely applied to actual decision-making scenarios for evaluating clinical progress of different diseases. Compared with previous studies, this method can realize objective calculation and automatic update of threshold and loss values and effectively solve complex prediction and optimization decision-making problems.

Functional trait mismatch between native and introduced bee pollinators servicing a global fruit crop

BackgroundUnderstanding connections between biodiversity and ecosystem services can be enhanced by shifting focus from species richness to functional trait-based approaches, that when paired with comparative phylogenetic methods can provide even deeper insights. We investigated the functional ecology and phylogenetic diversity of pollination services provided by hymenopteran insects visiting apple flowers in orchards surrounded by either ‘natural’ or ‘disturbed’ landscapes in New South Wales, Australia. We assessed whether morphological and behavioural traits (hairiness, body size, glossa length, pollen load purity, and probability of loose pollen) exhibited non-random phylogenetic patterns. Then, explored whether bees, the primary pollinators in this system, filled unique or overlapping functional entities (FEs). For each landscape, we calculated phylogenetic diversity and used FEs to assess functional richness, evenness, and diversion.ResultsA phylogenomic matrix based on ultraconserved elements (UCEs; 1,382,620 bp from 1,969 loci) was used to infer a fully-resolved and well-supported maximum likelihood phylogeny for 48 hymenopteran morphospecies. There was no significant difference in species richness between landscape categories. Pollinator communities at natural sites had higher phylogenetic complexity (X = 2.37) and functional divergence (x̄ = 0.74 ± 0.02 s.e.) than disturbed sites (X = 1.65 and x̄ = 0.6 ± 0.01 s.e.). Hairiness showed significant phylogenetic clustering (K = 0.94), whereas body size, glossa length, and loose pollen showed weaker non-random phylogenetic patterns (K between 0.3–0.5). Pollen load purity showed no association with phylogeny. The assemblage of 17 bee morphospecies comprised nine FEs: eight FEs consisted of native bees with three containing 65% of all native bee taxa. The introduced honey bee (Apis mellifera) occupied a unique FE, likely due to its different evolutionary history. Both landscape types supported six FEs each with three overlapping: two native bee FEs and the honey bee FE.ConclusionsBee hairiness was the only functional trait to exhibit demonstrable phylogenetic signal. Despite differences in species richness, and functional and phylogenetic diversity between orchard landscape types, both maintained equal bee FE numbers. While no native bee taxon was analogous to the honey bee FE, four native bee FEs shared the same hairiness level as honey bees. Health threats to honey bee populations in Australia will likely disrupt pollination services to apple, and other pollination-dependent food crops, given the low level of functional redundancy within the investigated pollinator assemblages.

Widespread convergence towards functional optimization in the lower jaws of crocodile-line archosaurs.

Extant crocodilian jaws are subject to functional demands induced by feeding and hydrodynamics. However, the morphological and ecological diversity of extinct crocodile-line archosaurs is far greater than that of living crocodilians, featuring repeated convergence towards disparate ecologies including armoured herbivores, terrestrial macropredators and fully marine forms. Crocodile-line archosaurs, therefore, present a fascinating case study for morphological and functional divergence and convergence within a clade across a wide range of ecological scenarios. Here, we build performance landscapes of two-dimensional theoretical jaw shapes to investigate the influence of strength, speed and hydrodynamics in the morphological evolution of crocodile-line archosaur jaws, and test whether ecologically convergent lineages evolved similarly optimal jaw function. Most of the 243 sampled jaw morphologies occupy optimized regions of theoretical morphospace for either rotational efficiency, resistance to Von Mises stress, hydrodynamic efficiency or a trade-off between multiple functions, though some seemingly viable shapes remain unrealized. Jaw speed is optimized only in a narrow region of morphospace whereas many shapes possess optimal jaw strength, which may act as a minimum boundary rather than a strong driver for most taxa. This study highlights the usefulness of theoretical morphology in assessing functional optimality, and for investigating form-function relationships in diverse clades.

Molecular mechanism of distinct chemokine engagement and functional divergence of the human Duffy antigen receptor

The Duffy antigen receptor is a seven-transmembrane (7TM) protein expressed primarily at the surface of red blood cells and displays strikingly promiscuous binding to multiple inflammatory and homeostatic chemokines. It serves as the basis of the Duffy blood group system in humans and also acts as the primary attachment site for malarial parasite Plasmodium vivax and pore-forming toxins secreted by Staphylococcus aureus. Here, we comprehensively profile transducer coupling of this receptor, discover potential non-canonical signaling pathways, and determine the cryoelectron microscopy (cryo-EM) structure in complex with the chemokine CCL7. The structure reveals a distinct binding mode of chemokines, as reflected by relatively superficial binding and a partially formed orthosteric binding pocket. We also observe a dramatic shortening of TM5 and 6 on the intracellular side, which precludes the formation of the docking site for canonical signal transducers, thereby providing a possible explanation for the distinct pharmacological and functional phenotype of this receptor.