Diversification of plant chemical phenotypes is typically associated with spatially and temporally variable plant-insect interactions. Floral scent is often assumed to be the target of pollinator-mediated selection, whereas foliar compounds are considered targets of antagonist-mediated selection. However, floral and vegetative phytochemicals can be biosynthetically linked and may thus evolve as integrated phenotypes. Utilizing a common garden of 28 populations of the perennial herb Arabis alpina (Brassicaceae), we investigated integration within and among floral scent compounds and foliar defense compounds (both volatile compounds and tissue-bound glucosinolates). Within floral scent volatiles, foliar volatile compounds, and glucosinolates, phytochemicals were often positively correlated, and correlations were stronger within these groups than between them. Thus, we found no evidence of integration between compound groups indicating that these are free to evolve independently. Relative to self-compatible populations, self-incompatible populations experienced stronger correlations between floral scent compounds, and a trend toward lower integration between floral scent and foliar volatiles. Our study serves as a rare test of integration of multiple, physiologically related plant traits that each are potential targets of insect-mediated selection. Our results suggest that independent evolutionary forces are likely to diversify different axes of plant chemistry without major constraints.

The evolution of the hominoid lineage is characterized by pervasive homoplasy, notably in regions such as the vertebral column, which plays a central role in body support and locomotion. Few isolated and fewer associated vertebrae are known for most fossil hominoid taxa, but identified specimens indicate potentially high levels of convergence in terms of both form and number. Homoplasy thus complicates attempts to identify the anatomy of the last common ancestor of hominins and other taxa and stymies reconstructions of evolutionary scenarios. One way to clarify the role of homoplasy is by investigating constraints via phenotypic integration, which assesses covariation among traits, shapes evolutionary pathways, and itself evolves in response to selection. We assessed phenotypic integration and evolvability across the subaxial (cervical, thoracic, lumbar, sacral) vertebral column of macaques (n = 96), gibbons (n = 77), chimpanzees (n = 92), and modern humans (n = 151). We found a mid-cervical cluster that may have shifted cranially in hominoids, a persistent thoracic cluster that is most marked in chimpanzees, and an expanded lumbosacral cluster in hominoids that is most expanded in gibbons. Our results highlight the highly conserved nature of the vertebral column. Taxa appear to exploit existing patterns of integration and ontogenetic processes to shift, expand, or reduce cluster boundaries. Gibbons appear to be the most highly derived taxon in our sample, possibly in response to their highly specialized locomotion.

BACKGROUND: Alternative splicing (AS) is a principal mode of genetic regulation and one of the most widely used mechanisms to generate structurally and functionally distinct mRNA and protein variants. Dysregulation of AS may result in aberrant transcription and protein products, leading to the emergence of human diseases. Although considered important for regulating gene expression, genome-wide AS dysregulation, underlying mechanisms, and clinical relevance in knee osteoarthritis (OA) remain unelucidated. Therefore, in this study, we elucidated and validated AS events and their regulatory mechanisms during OA progression.
RESULTS: In this study, we identified differentially expressed genes between human OA and healthy meniscus samples. Among them, the OA-associated genes were primarily enriched in biological pathways such as extracellular matrix organization and ossification. The predominant OA-associated regulated AS (RAS) events were found to be involved in apoptosis during OA development. The expression of the apoptosis-related gene BCL2L13, XAF1, and NF2 were significantly different between OA and healthy meniscus samples. The construction of a covariation network of RNA-binding proteins (RBPs) and RAS genes revealed that differentially expressed RBP genes LAMA2 and CUL4B may regulate the apoptotic genes XAF1 and BCL2L13 to undergo AS events during OA progression. Finally, RT-qPCR revealed that CUL4B expression was significantly higher in OA meniscus samples than in normal controls and that the AS ratio of XAF1 was significantly different between control and OA samples; these findings were consistent with their expected expression and regulatory relationships.
CONCLUSIONS: Differentially expressed RBPs may regulate the AS of apoptotic genes during knee OA progression. XAF1 and its regulator, CUL4B, may serve as novel biomarkers and potential therapeutic targets for this disease.

The modular organization of tetrapod paired limbs and girdles, influenced by the expression of Hox genes is one of the primary driving forces of the evolution of animal locomotion. The increased morphological diversification of the paired limbs is correlated with reduced between-limb covariation, while correlation within the elements is usually higher than between the elements. The tailed amphibians, such as Lissotriton newts, have a biphasic lifestyle with aquatic and terrestrial environments imposing different constraints on limb skeleton. By employing the methods of computerized microtomography and 3D geometric morphometrics, we explored the pattern of morphological variation, disparity, modularity and morphological integration in the proximal parts of the anterior limbs of six species of Eurasian small bodied newts. Although the species significantly differ in limb shape, there is a great overlap in morphology of scapula and humerus, and there are no differences in morphological disparity. For the scapula, the shape differences related to the duration of the aquatic period are in length, depth and curvature. The shape of the humerus is not affected by the length of aquatic period, and shape differences between the species are related to robustness of the body. The length of aquatic period has statistically supported phylogenetic signal. The scapula and humerus are structures of varying modularity. For the humerus, the strongest support on the phylogenetic level was for the capitulum/shaft hypothesis, which can also be interpreted as functional modularity. For the scapula, the greatest support was for the antero-posterior hypothesis of modularity in case of Lissotriton vulgaris, which can be explained by different functional roles and muscle insertion patterns, while there was no phylogenetic modularity. The modularity patterns seem to correspond with the general tetrapod pattern, with modularity being more pronounced in the distal structure. The future research should include more salamandrid taxa with different habitat preferences and both adult and larval stages, in order to explore how size, phylogeny and ecology affect the morphology and covariation patterns of limbs.

An important pathogen of concern for Pacific oyster growers in the USA is ostreid herpesvirus 1 (OsHV-1). Currently, oyster stocks exist that are tolerant to OsHV-1; however, it is uncertain if a trade-off exists between their tolerance to OsHV-1 and their growth in different environments. To investigate any potential trade-offs, Pacific oyster families with varying levels of OsHV-1 tolerance were grown in a bay where OsHV-1 is endemic (Tomales Bay, CA) and in a bay where OsHV-1 is absent (Willapa Bay, WA). In Tomales Bay, we found that oysters from OsHV-1 tolerant families grew faster than oysters from OsHV-1 susceptible families, while in Willapa Bay, no statistically significant difference in growth was found between oyster families with different levels of OsHV-1 tolerance observed in Tomales Bay. These findings indicate that Pacific oysters bred to be tolerant to OsHV-1 would not be expected to have a longer time-to-market regardless of the presence of OsHV-1 in the growing environment.

The biological significance of behavioural predictability (environment-independent within-individual behavioural variation) became accepted recently as an important part of an individual\'s behavioural strategy besides behavioural type (individual mean behaviour). However, we do not know how behavioural type and predictability evolve. Here, we tested different evolutionary scenarios: (i) the two traits evolve independently (lack of correlations) and (ii) the two traits\' evolution is constrained (abundant correlations) due to either (ii/a) proximate constraints (direction of correlations is similar) or (ii/b) local adaptations (direction of correlations is variable). We applied a set of phylogenetic meta-analyses based on 93 effect sizes across 44 vertebrate and invertebrate species, focusing on activity and risk-taking. The general correlation between behavioural type and predictability did not differ from zero. Effect sizes for correlations showed considerable heterogeneity, with both negative and positive correlations occurring. The overall absolute (unsigned) effect size was high (Zr = 0.58), and significantly exceeded the null expectation based on randomized data. Our results support the adaptive scenario: correlations between behavioural type and predictability are abundant in nature, but their direction is variable. We suggest that the evolution of these behavioural components might be constrained in a system-specific way.

Facial approximation (FA) provides a promising means of generating the possible facial appearance of a deceased person. It facilitates exploration of the evolutionary forces driving anatomical changes in ancestral humans and can capture public attention. Despite the recent progress made toward improving the performance of FA methods, a limited understanding of detailed quantitative craniofacial relationships between facial bone and soft tissue morphology may hinder their accuracy, and hence subjective experience and artistic interpretation are required. In this study, we explored craniofacial relationships among human populations based upon average facial soft tissue thickness depths (FSTDs) and covariations between hard and soft tissues of the nose and mouth using geometric morphometrics. Furthermore, we proposed a computerized method to assign the learned craniofacial relationships to generate a probable facial appearance of Homo sapiens, reducing human intervention. A smaller resemblance comparison (an average Procrustes distance was 0.0258 and an average Euclidean distance was 1.79 mm) between approximated and actual faces and a greater recognition rate (91.67%) tested by a face pool indicated that average dense FSTDs contributed to raising the accuracy of approximated faces. Results of partial least squares (PLS) analysis showed that nasal and oral hard tissues have an effect on their soft tissues separately. However, relatively weaker RV correlations (<0.4) and greater approximation errors suggested that we need to be cautious about the accuracy of the approximated nose and mouth soft tissue shapes from bony structures. Overall, the proposed method can facilitate investigations of craniofacial relationships and potentially improve the reliability of the approximated faces for use in numerous applications in forensic science, archaeology, and anthropology.

Spatial growth constraints in the head region can lead to coordinated patterns of morphological variation that pleiotropically modify genetically defined phenotypes as the tissues compete for space. Here we test for such architectural modifications during rhesus macaque (Macaca mulatta) postnatal ontogeny. We captured cranium and brain shape from 153 MRI datasets spanning 13 to 1090 postnatal days and tested for patterns of covariation with measurements of relative brain, eyeball, and masseter muscle size as well as callosal tract length. We find that the shape of the infant (<365 days) macaque cranium was most closely aligned to masseter muscle and brain size measured relative to face size. Infant brain and juvenile (365-1090 days) cranium shape were more closely linked with brain size relative to basicranium and face size. Meanwhile, the juvenile macaque brain shape was dominated by the size of the brain relative to that of the basicranium. Associations with relative eyeball size and commissural tract lengths were weaker. Our results are consistent with a spatial-packing regime operating during postnatal macaque ontogeny, in which relative growth of the masseter, face and basicranium have a greater influence than brain growth on the overall shape of the cranium and brain.

Few studies of angiosperms have focused on androecial evolution in conjunction with evolutionary shifts in corolla morphology and pollinator relationships. The Western Hemisphere clade of Justiciinae (Acanthaceae) presents the rare opportunity to examine remarkable diversity in staminal morphology. We took a phylogenetically informed approach to examine staminal diversity in this hypervariable group and asked whether differences in anther thecae separation is associated with phylogenetically informed patterns of variation in corolla morphology. We further discuss evidence for associations between anther diversity and pollinators in this lineage.
For the Dianthera/Sarotheca/Plagiacanthus (DSP) clade of Western Hemisphere Justiciinae, we characterized floral diversity based on a series of corolla measurements and using a model-based clustering approach. We then tested for correlations between anther thecae separation and corolla traits, and for shifts in trait evolution, including evidence for convergence.
There is evolutionary vagility in corolla and anther traits across the DSP clade with little signal of phylogenetic constraint. Floral morphology clusters into four distinct groups that are, in turn, strongly associated with anther thecae separation, a novel result in Acanthaceae and, to our knowledge, across flowering plants. These cluster groups are marked by floral traits that strongly point to associations with pollinating animals. Specifically, species that are known or likely to be hummingbird pollinated have stamens with parallel thecae, whereas those that are likely bee or fly pollinated have stamens with offset, divergent thecae.
Our results suggest that anther thecae separation is likely under selection in concert with other corolla characters. Significant morphological shifts detected by our analyses corresponded to putative shifts from insect to hummingbird pollination. Results from this study support the hypothesis that floral structures function in an integrated manner and are likely subject to selection as a suite. Further, these changes can be hypothesized to represent adaptive evolution.

Specific interactions between transcription factors (TFs) and substrate DNA constitute the fundamental basis of gene expression. Unlike in TFs like basic helix-loop-helix or basic leucine zippers, prediction of substrate DNA is extremely challenging for helix-turn-helix (HTH). Experimental techniques like chromatin immunoprecipitation combined with massively parallel DNA sequencing remains a viable option. We characterize the molecular basis of heterogeneity in HTH-DNA interaction using in silico tools and thence validate them experimentally. Given the profound functional diversity in HTH, we focus primarily on winged-HTH (wHTH). We consider 180 wHTH TFs, whose experimental three-dimensional structures are available in DNA bound/unbound conformations. Starting with PDB-wide scanning and curation of data, we construct a phylogenetic tree, which distributes 180 wHTH sequences under multiple sub-groups. Structure-sequence alignment followed by detailed intra/intergroup analysis, covariation studies and extensive network theory analysis help us to gain deep insight into heterogeneous wHTH-substrate DNA interactions. A central aim of this study is to find a consensus to predict the substrate DNA sequence for wHTH, amidst heterogeneity. The strength of our exhaustive theoretical investigations including molecular docking are successfully tested through experimental characterization of wHTH TF from Sulfurimonas denitrificans.