Adaptation Research Articles

Whole Genome Analysis Reveals Evolutionary History and Introgression Events in Bale Monkeys

Background/Objective: The Bale monkey (Chlorocebus djamdjamensis) is a threatened primate species endemic to Ethiopia and, in contrast to other members of the genus Chlorocebus, lives at high altitudes and feeds mainly on bamboo. Two populations of the species are present, one in continuous bamboo forest (CF) in the eastern part of the species’ range, and the other in fragmented forest (FF) in the western part. Based on mitochondrial DNA and phenotypic characteristics, previous studies have suggested introgression by parapatric congeners into the FF population but not into the CF population. The objective of this study was to gain insights into the evolutionary history of Bale monkeys and their potential genetic adaptations to high altitudes and for bamboo consumption. Methods: We sequenced the whole genomes of individuals from both populations and compared their genomes with those of the other five Chlorocebus species. We applied phylogenetic methods and conducted population demographic simulations to elucidate their evolutionary history. A genome-wide analysis was conducted to assess gene flow and identify mutations potentially associated with adaptations to high altitudes and for bamboo metabolism. Results: Our analyses revealed Bale monkeys as the sister clade to Chlorocebus aethiops and showed that gene flow occurred between C. aethiops and FF but not between C. aethiops and CF. In addition, we detected non-synonymous mutations in genes potentially associated with the adaptation to high altitudes (EPAS1) in both populations and with the adaptation for bamboo metabolism (TAS2R16, MPST, and TST) mainly in the CF population. Conclusions: Our study provides insights into the evolutionary history of a threatened primate species and reveals the genetic basis for its adaptions to unique environments and for diet specialization.

Genetic Adaptations of Soybean to Cold Stress Reveal Key Insights Through Transcriptomic Analysis

Low temperatures greatly restrict the development, growth, and productivity of soybeans, with their effects differing across various cultivars. The present work investigated the transcriptome and physiological reactions of two soybean cultivars, namely “KD52” exhibiting cold tolerance and “DS17” displaying cold sensitivity, to cold stress across a precisely defined period. The soybean plants were subjected to cold treatment at 6 °C for durations of 0, 2, 4, and 8 h. A comparative physiological marker study revealed distinct reactions to cold stress in the two cultivars. The findings showed that increased malondialdehyde levels provided evidence of DS17’s heightened vulnerability to lipid peroxidation and membrane degradation. In contrast, the KD52 cultivar exhibited increased activities of antioxidant enzymes, including peroxidase and superoxide dismutase, in response to cold exposure, suggesting a strong antioxidant defense system against oxidative stress. The transcriptomic analysis revealed dynamic responses, mapping 54,532 genes. Within this group, a total of 234 differentially expressed genes (DEGs) were found to be consistently changed at several time intervals, showing unique expression patterns across the two cultivars. Analysis of the association between these important DEGs and the physiological indicators revealed candidate genes that may be involved in controlling oxidative damage and antioxidant defenses. Some key genes showed a progressive rise in expression over time in both cultivars, with a more significant acceleration in KD52, and are probably involved in promoting adaptation processes during extended periods of cold exposure. The identification of improved defense mechanisms in KD52, together with the identification of crucial genes, offers great prospects for enhancing the cold stress resilience of soybean.

Fermentative and Enological Features of Saccharomyces cerevisiae Populations Generated Through Adaptive Laboratory Evolution

Adaptive laboratory evolution (ALE) is a non-GMO technique utilized for the amelioration of wine yeast strains. Employing two-step ALE strategies, we recently acquired six evolved Saccharomyces cerevisiae populations with improved fermentative abilities compared to their parental strains in synthetic broths. Herein, we evaluated the qualities of the abovementioned evolved populations under real winemaking conditions, using the grape musts Assyrtiko and Roditis. The ethanol-tolerant populations evolved solely with glucose delayed to complete the fermentation due to slow fructose assimilation, albeit showing improved ethanol yields, compared to their parental strains. The volatile compounds of the evolved populations were significantly different from those of parental strains. Statistically significant differences were observed in the organoleptic profiles between the evolved populations’ and parental strains’ wines. Notably, wine from one evolved population (BLR200) was rated higher in overall aroma and quality. This study supports the magnitude of ALE strategies for the generation of novel wine yeasts.

Origin of Pressure Resistance in Deep-Sea Lactate Dehydrogenase.

High hydrostatic pressure has a dramatic effect on biochemical systems, as exposure to high pressure can result in structural perturbations ranging from dissociation of protein complexes to complete denaturation. The deep ocean presents an interesting paradox since it is teeming with life despite the high-pressure environment. This is due to evolutionary adaptations in deep-sea organisms, such as amino acid substitutions in their proteins, which aid in resisting the denaturing effects of pressure. However, the physicochemical mechanism by which these substitutions can induce pressure resistance remains unknown. Here, we use molecular dynamics simulations to study pressure-adapted lactate dehydrogenase from the deep-sea abyssal grenadier (Coryphaenoides armatus), in comparison with that of the shallow-water Atlantic cod (Gadus morhua). We examined structural, thermodynamic and volumetric contributions to pressure resistance, and report that the amino acid substitutions result in a decrease in volume of the deep-sea protein accompanied by a decrease in thermodynamic stability of the native protein. Our simulations at high pressure also suggest that differences in compressibility may be important for understanding pressure resistance in deep-sea proteins.

The cryptonephridial/rectal complex: an evolutionary adaptation for water and ion conservation.

Arthropods have integrated digestive and renal systems, which function to acquire and maintain homeostatically the substances they require for survival. The cryptonephridial complex (CNC) is an evolutionary novelty in which the renal organs and gut have been dramatically reorganised. Parts of the renal or Malpighian tubules (MpTs) form a close association with the surface of the rectum, and are surrounded by a novel tissue, the perinephric membrane, which acts to insulate the system from the haemolymph and thus allows tight regulation of ions and water into and out of the CNC. The CNC can reclaim water and solutes from the rectal contents and recycle these back into the haemolymph. Fluid flow in the MpTs runs counter to flow within the rectum. It is this countercurrent arrangement that underpins its powerful recycling capabilities, and represents one of the most efficient water conservation mechanisms in nature. CNCs appear to have evolved multiple times, and are present in some of the largest and most evolutionarily successful insect groups including the larvae of most Lepidoptera and in a major beetle lineage (Cucujiformia + Bostrichoidea), suggesting that the CNC is an important adaptation. Here we review the knowledge of this remarkable organ system gained over the past 200 years. We first focus on the CNCs of tenebrionid beetles, for which we have an in-depth understanding from physiological, structural and ultrastructural studies (primarily in Tenebrio molitor), which are now being extended by studies in Tribolium castaneum enabled by advances in molecular and microscopy approaches established for this species. These recent studies are beginning to illuminate CNC development, physiology and endocrine control. We then take a broader view of arthropod CNCs, phylogenetically mapping their reported occurrence to assess their distribution and likely evolutionary origins. We explore CNCs from an ecological viewpoint, put forward evidence that CNCs may primarily be adaptations for facing the challenges of larval life, and argue that their loss in many aquatic species could point to a primary function in conserving water in terrestrial species. Finally, by considering the functions of renal and digestive epithelia in insects lacking CNCs, as well as the typical architecture of these organs in relation to one another, we propose that ancestral features of these organs predispose them for the evolution of CNCs.

Evolution and maintenance of a large multidrug-resistant plasmid in a Salmonella enterica Typhimurium host under differing antibiotic selection pressures.

The dissemination of antibiotic resistance genes (ARGs) through plasmids is a major mechanism for the development of bacterial antimicrobial resistance. The adaptation and evolution mechanisms of multidrug-resistant (MDR) plasmids with their hosts are not fully understood. Herein, we conducted experimental evolution of a 244 kb MDR plasmid (pJXP9) under various conditions including no antibiotics and mono- or combinational drug treatments of colistin (CS), cefotaxime (CTX), and ciprofloxacin (CIP). Our results showed that long-term with or without positive selections for pJXP9, spanning approximately 600 generations, led to modifications of the plasmid-encoded MDR and conjugative transfer regions. These modifications could mitigate the fitness cost of plasmid carriage and enhance plasmid maintenance. The extent of plasmid modifications and the evolution of plasmid-encoded antibiotic resistance depended on treatment type, particularly the drug class and duration of exposure. Interestingly, prolonged exposure to mono- and combinational drugs of CS and CIP resulted in a substantial loss of the plasmid-encoded MDR region and antibiotic resistance, comparable to the selection condition without antibiotic. By contrast, combinational treatment with CTX contributed to the maintenance of the MDR region over a long period of time. Furthermore, drug selection was able to maintain and even amplify the corresponding plasmid-encoded ARGs, with co-selection of ARGs in the adjacent regions. In addition, parallel mutations in chromosomal arcA were also found to be associated with pJXP9 plasmid carriage among endpoint-evolved clones from diverse treatments. Meanwhile, arcA deletion improved the persistence of pJXP9 plasmid without drugs. Overall, our findings indicated that plasmid-borne MDR region deletion and chromosomal arcA inactivation mutation jointly contributed to co-adaptation and co-evolution between MDR IncHI2 plasmid and Salmonella Typhimurium under different drug selection pressure.IMPORTANCEThe plasmid-mediated dissemination of antibiotic resistance genes has become a significant concern for human health, even though the carriage of multidrug-resistant (MDR) plasmids is frequently associated with fitness costs for the bacterial host. However, the mechanisms by which MDR plasmids and bacterial pairs evolve plasmid-mediated antibiotic resistance in the presence of antibiotic selections are not fully understood. Herein, we conducted an experimental evolution of a large multidrug-resistant plasmid in a Salmonella enterica Typhimurium host under single and combinatorial drug selection pressures. Our results show the adaptive evolution of plasmid-encoded antibiotic resistance through alterations of the MDR region in the plasmid, in particular substantial loss of the MDR region, in response to different positive selections, especially mono- and combinational drugs of colistin and ciprofloxacin. In addition, strong parallel mutations in chromosomal arcA were associated with pJXP9 carriage in Salmonella Typhimurium from diverse treatments. Our results thus highlight promoting the loss of the plasmid's MDR region could offer an alternative approach for combating plasmid-encoded antibiotic resistance.

Demographic History and Adaptive Evolution of Indo-Pacific Bottlenose Dolphins (Tursiops aduncus) in Western Australia.

Demographic processes can substantially affect a species' response to changing ecological conditions, necessitating the combined consideration of genetic responses to environmental variables and neutral genetic variation. Using a seascape genomics approach combined with population demographic modelling, we explored the interplay of demographic and environmental factors that shaped the current population structure in Indo-Pacific bottlenose dolphins (Tursiops aduncus) along the Western Australian coastline. We combined large-scale environmental data gathered via remote sensing with RADseq genomic data from 133 individuals at 19 sampling sites. Using population genetic and outlier detection analyses, we identified three distinct genetic clusters, coinciding with tropical, subtropical and temperate provincial bioregions. In contrast to previous studies, our demographic models indicated that populations occupying the paleo-shoreline split into two demographically independent lineages before the last glacial maximum (LGM). A subsequent split after the LGM 12-15 kya gave rise to the Shark Bay population, thereby creating the three currently observed clusters. Although multi-locus heterozygosity declined from north to south, dolphins from the southernmost cluster inhabiting temperate waters had higher heterozygosity in potentially adaptive loci compared to dolphins from subtropical and tropical waters. These findings suggest ongoing adaptation to cold-temperate waters in the southernmost cluster, possibly linked to distinct selective pressures between the different bioregions. Our study demonstrated that in the marine realm, without apparent physical boundaries, only a combined approach can fully elucidate the intricate environmental and genetic interactions shaping the evolutionary trajectory of marine mammals.

The mitochondrial genomes of the reef-dwelling spiny lobsters Panulirus echinatus and Panulirus interruptus with insights into the phylogeny and adaptive evolution of protein-coding genes in the Achelata

AbstractTemperature and oxygen levels drive the evolution of morphological, behavioral, and physiological traits in marine invertebrates, including crustaceans. Environmental conditions are also expected to prompt the adaptive evolution of mitochondrial protein-coding genes (PCGs), which are vital for energy production via the oxidative phosphorylation pathway. We formally tested for adaptive evolution in mitochondrial protein-coding genes in representatives of the decapod infraorder Achelata, including two spiny lobsters, Panulirus echinatus and P. interruptus, for which we sequenced complete mitochondrial genomes (15,644 and 15,659 bp long, respectively). A phylomitogenomic analysis supported the monophyly of the genus Panulirus, the families Palinuridae and Scyllaridae, and the infraorder Achelata. Over the strong negative selection background observed for mitochondrial PCGs in the Achelata, signatures of positive selective pressure were detected within PCGs in equatorial Panulirus spp. and deepwater Scyllaridae. In Panulirus spp. inhabiting equatorial latitudes with consistently high temperatures, the Datamonkey analysis RELAX suggested intensified purifying selection strength in 9 of the 13 PCGs and relaxation in purifying selection strength in atp6, while aBSREL, BUSTED, and MEME recovered signatures of positive selection on PCGs within Complex I, III, and IV PCGs. Likewise, in Scyllaridae species inhabiting depths with low-oxygen levels, RELAX indicated relaxed selection strength in 6 of the 13 PCGs, while aBSREL, BUSTED, and MEME recovered signatures of positive selection on PCGs within Complexes I, III, IV, and V. The newly assembled mitochondrial genomes of P. echinatus and P. interruptus represent new genomic resources to aid with the conservation and management of lobsters targeted by major fisheries and contribute to our understanding of how environmental conditions drive adaptive evolution in spiny and slipper lobster mitochondrial PCGs.

Olfactory and gustatory chemical sensor systems in the African turquoise killifish: Insights from morphology.

Smell and taste are extensively studied in fish species as essential for finding food and selecting mates while avoiding toxic substances and predators. Depending on the evolutionary position and adaptation, a discrete variation in the morphology of these sense organs has been reported in numerous teleost species. Here, for the first time, we approach the phenotypic characterization of the olfactory epithelium and taste buds in the African turquoise killifish (Nothobranchius furzeri), a model organism known for its short lifespan and use in ageing research. Our observations indicate that the olfactory epithelium of N. furzeri is organized as a simple patch, lacking the complex folding into a rosette, with an average size of approximately 600µm in length, 300µm in width, and 70µm in thickness. Three main cytotypes, including olfactory receptor neurons (CalbindinD28K), supporting cells (β-tubulin IV), and basal cells (Ki67), were identified across the epithelium. Further, we determined the taste buds' distribution and quantification between anterior (skin, lips, oral cavity) and posterior (gills, pharynx, oesophagus) systems. We identified the key cytotypes by using immunohistochemical markers, i.e. CalbindinD28K, doublecortin, and neuropeptide Y (NPY) for gustatory receptor cells, glial fibrillary acidic protein (GFAP) for supporting cells, and Ki67, a marker of cellular proliferation for basal cells. Altogether, these results indicate that N. furzeri is a microsmatic species with unique taste and olfactory features and possesses a well-developed posterior taste system compared to the anterior. This study provides fundamental insights into the chemosensory biology of N. furzeri, facilitating future investigations into nutrient-sensing mechanisms and their roles in development, survival, and ageing.

Nematocyst Types and Characteristics in the Tentacles of Gershwinia thailandensis and Morbakka sp. (Cubozoa: Carybdeida) from the Gulf of Thailand.

Nematocysts, specialized stinging cells in cnidarians, play a crucial role in both defense and prey capture, containing venomous, coiled tubes within a capsule. While box jellyfish are recognized as a medical threat, information on the nematocysts of species like Gershwinia thailandensis and Morbakka sp. from Thai waters remains sparse. This study explores the types and morphology of nematocysts found in the tentacles of these species using light and scanning electron microscopy. We identified three nematocyst types: club-shaped microbasic p-mastigophores, oval isorhizas, and oval microbasic p-rhopaloids. Notably, significant differences in capsule sizes were observed, especially in the microbasic p-mastigophores and isorhizas. The discharge tubules tapered from the proximal to the distal ends, featuring arrow-shaped spines in a helical pattern. A distinct lancet structure was present in both microbasic p-mastigophores and p-rhopaloids. These findings suggest that variations in nematocyst size and morphology may be linked to evolutionary adaptations, functional roles, and venom toxicity. Further research into venom discharge mechanisms could offer valuable insights into the ecological and medical importance of these cnidarians.

Efficient Optimization: Unveiling the Application of Ensemble Learning Combined with the CMA-ES Algorithm in Hydraulic Fracturing Design

Optimizing fracturing parameters is crucial for enhancing production and reducing costs in oil and gas exploration and development. Effectively integrating geological and engineering parameters for the automated optimization of fracturing design continues to pose challenges. This study utilizes the cluster-based local outlier factor method for anomaly detection and removal from the dataset, significantly enhancing data quality. By integrating diverse models, including tree-based models and neural networks, an ensemble model for production prediction was developed. This approach successfully addresses the limitations of relying on a single model and achieves high-precision production forecasting. Furthermore, a Covariance Matrix Adaptation Evolution Strategy (CMA-ES)-based framework was established to comprehensively optimize the design parameters of fracturing projects. Optimization practices for two selected wells resulted in a 168.54% increase in production and identified the optimal design parameter configuration for all cases studied. The results of this study demonstrate the feasibility and effectiveness of the proposed ensemble prediction model and optimization framework in practical applications. Data-driven optimization strategies are expected to play a larger role in future oil and gas development, driving technological innovation and advancement in the field.

Genetic Adaptations of the Tibetan Pig to High-Altitude Hypoxia on the Qinghai-Tibet Plateau.

The Tibetan Plateau's distinctive high-altitude environment, marked by extreme cold and reduced oxygen levels, presents considerable survival challenges for both humans and mammals. Natural selection has led to the accumulation of adaptive mutations in Tibetan pigs, enabling them to develop distinctive adaptive phenotypes. Here, we aim to uncover the genetic mechanisms underlying the adaptation of Tibetan pigs to high-altitude hypoxia. Therefore, we conducted a systematic analysis of 140 whole-genome sequencing (WGS) data points from different representing pig populations. Our analysis identified a total of 27,614,561 mutations, including 22,386,319 single-nucleotide variants (SNVs) and 5,228,242 insertions/deletions (INDELs, size < 50 bp). A total of 11% (2,678,569) of the SNVs were newly identified in our project, significantly expanding the dataset of genetic variants in Tibetan pigs. Compared to other pig breeds, Tibetan pigs are uniquely adapted to high-altitude environments, exhibiting the highest genetic diversity and the lowest inbreeding coefficient. Employing the composite of multiple signals (CMS) method, we scanned the genome-wide Darwinian positive selection signals and identified 32,499 Tibetan pig positively selected SNVs (TBPSSs) and 129 selected genes (TBPSGs), including 213 newly discovered genes. Notably, we identified eight genes (PHACTR1, SFI1, EPM2A, SLC30A7, NKAIN2, TNNI3K, and PLIN2) with strong nature selection signals. They are likely to improve cardiorespiratory function and fat metabolism to help Tibetan pigs become adapted to the high-altitude environment. These findings provide new insights into the genetic mechanisms of high-altitude adaptation and the adaptive phenotypes of Tibetan pigs.

Evidence of Intraspecific Adaptive Variation in the American Pika (Ochotona princeps) on a Continental Scale Using a Target Enrichment and Mitochondrial Genome Skimming Approach.

Montane landscapes present an array of abiotic challenges that drive adaptive evolution amongst organisms. These adaptations can promote habitat specialisation, which may heighten the risk of extirpation from environmental change. For example, higher metabolic rates in an endothermic species may contribute to heightened cold tolerance, whilst simultaneously limiting heat tolerance. Here, using the climate-sensitive American pika (Ochotona princeps), we test for evidence of intraspecific adaptive variation amongst environmental gradients across the Intermountain West of North America. We leveraged results from previous studies on pika adaptation to generate a custom nuclear target enrichment design to sequence several hundred candidate genes related to cold, hypoxia and dietary detoxification. We also applied a 'genome skimming' approach to sequence mitochondrial DNA. Using genotype-environment association tests, we identified rare genomic variants associated with elevation and temperature variation amongst populations. Amongst mitochondrial genes, we identified intraspecific variation in selective signals and significant changes to the amino acid property equilibrium constant, which may relate to electron transport chain efficiency. These results illustrate a complex dynamic of adaptive variation amongst O. princeps where lineages and populations have adapted to unique regional conditions. Some of the clearest signals of selection were in a genetic lineage that includes pikas of the Great Basin region, which is also where recent localised extirpations have taken place and highlights the risk of losing adaptive alleles during environmental change.

Physicochemical and Structural Validation of Myxovirus Resistance 1 (Mx1) Protein of Three Strains of the Nigerian Indigenous (&amp;lt;i&amp;gt;Gallus Gallus domesticus&amp;lt;/i&amp;gt;) and Exotic Chickens

This research was conducted on three strains of Nigerian Indigenous (&amp;lt;i&amp;gt;gallus gallus domesticus&amp;lt;/i&amp;gt;) and Noiler (exotic) chickens. It examined the physicochemical and structural validation of Myxovirus resistance 1 (Mx1) protein on the three strains of Nigerian indigenous (naked neck, frizzle feather, normal feather) and noiler (exotic) chickens and also the prediction of the Physicochemical Analysis of protein. Nucleotide sequence were retrieved from National Center for Bio-Technology Information (NCBI) database and subjected to multiple sequence alignment, prediction of the physicochemical analysis of protein was done in the ProtParam web server. Modeling of 3D structural validation, Swiss modeling and Statistical analysis were all carried out. Software was used to align the sequences to find any Single Nucleotide Polymorphism (SNPS). The result of physicochemical analysis showed that the properties of the Mx1 protein fell within accepted threshold and predicted that the proteins were generally related. To validate the structure obtained from modeling, the obtained PDB files were ran on the Pro-check validation server and obtained Errat and Ramachandran plots. The study elucidates the unique features and potential functional implications of Mx1 protein across different strains of Nigerian indigenous and exotic chickens. This knowledge can inform the development of strategies to improve disease resistance in local chicken populations through selective breeding or genetic manipulation. Comparing the Mx1 protein among different strains of Nigerian indigenous chickens can reveal evolutionary adaptations and provide valuable information for understanding the molecular basis of immune defense mechanisms in poultry. Understanding the physicochemical properties and structural dynamics of Mx1 protein contributes to the broader understanding of innate immune responses in indigenous chicken breeds, offering insights into their disease resistance and adaptation mechanisms.

Abiotic factors that prompt major ecological transitions: Are fish on land to escape an intolerable aquatic environment?

Abstract Colonisation of novel habitats are important events in evolution, but the factors that initially prompt such ecological transitions are often unknown. The invasion of land by fish is an extreme habitat transition that offers an opportunity to empirically investigate the causes of major ecological transitions. The intertidal ecotone—and rock pools in particular—have been an important staging ground for transitions onto land. Classic hypotheses focus on the adverse abiotic conditions of rock pools at low tide as the instigator of fish voluntarily stranding themselves out of water, which can then lead to the evolution of an amphibious lifestyle. To test these hypotheses, we studied the abiotic conditions of 54 rock pools on the island of Guam where there are various species of aquatic, amphibious and terrestrial blenny fishes. We found little support for the expected deterioration of abiotic conditions in standing pools at low tide (salinity, pH and oxygen), and fish were not seen to be excluded from those pools that were found to exhibit poor abiotic conditions (temperature, salinity and pH). Hypoxia was the only factor that might account for the absence of blennies from certain rock pools. Next, we experimentally measured oxygen depletion by an aquatic, mildly amphibious and highly amphibious species of blenny found on Guam in a simulated rockpool to infer the proportion of rock pools at low tide outside the tolerable range of blennies. Rock pools were found to have oxygen levels within the requirements of most blennies and those of other marine fishes reported in the literature. We conclude that the abiotic environment of rock pools alone was unlikely to have instigated the evolution of amphibious behaviour in blennies, at least on Guam. Instead, the broad range of abiotic conditions experienced in rock pools suggests these conditions could have primed amphibious blennies to better endure the novel conditions on land. Any ecotone typified by fluctuations or gradients in abiotic conditions is likely a key transitional environment for the invasion of novel habitats and, as such, are an important location for adaptive evolution and species diversification. Read the free Plain Language Summary for this article on the Journal blog.

Comparative genomics provides insights into the evolutionary history of the phylum Ciliophora (Eukaryota, Alveolata) and uncovers the adaptive evolution of anaerobic ciliate classes

Comparative genomics provides insights into the evolutionary history of the phylum Ciliophora (Eukaryota, Alveolata) and uncovers the adaptive evolution of anaerobic ciliate classes

Adaptation of skin structures to environmental variations in anurans from southern and southwestern China.

Variations in skin structures can possibly reflect local adaptation to distinct environmental factors. As the primary interface with the surrounding environment, amphibian skin undergoes phenotypic innovations that play a key role in protection, water absorption, and respiration. However, the effects of environmental factors on skin structures have been examined in only a limited number of species. Here, we conducted a comparative analysis of the skin structures of 102 Chinese anuran species across varying geographical distributions and habitat types. Our results revealed that the total volume of granular glands and capillary density in the dorsal skin significantly increased with increasing latitude. We also found that the thickness of calcified layers in both dorsal and ventral skin was positively correlated with annual temperature and negatively correlated with humidity. Additionally, terrestrial species exhibited the largest dorsal granular gland, whereas arboreal species had the smallest one. Likewise, the largest dorsal mucous gland was observed in aquatic species, while the smallest was found in terrestrial species. These results highlighted the importance of understanding the relationship between skin phenotypes and environmental variables and thus providing conservation strategies based on the evolutionary adaptations in anurans. Our study can contribute to the broader knowledge of evolutionary biology in anurans by demonstrating how specific skin traits are linked to survival and fitness across various ecological contexts.

Enhancers in Plant Development, Adaptation, and Evolution.

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants. This review provides an overview of how enhancers function to control gene regulation, methods to predict DNA sequences that may have enhancer activity, methods utilized to functionally validate enhancers, and the current knowledge of enhancers in plants, including how they impact plant development, response to environment, and evolutionary adaptation.

Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies

Promiscuous enzymes often serve as the starting point for the evolution of novel functions. Yet, the extent to which the promiscuity of an individual enzyme can be harnessed several times independently for different purposes during evolution is poorly reported. Here, we present a case study illustrating how NAD(P)+-dependent succinate semialdehyde dehydrogenase of Escherichia coli (Sad) is independently recruited through various evolutionary mechanisms for distinct metabolic demands, in particular vitamin biosynthesis and central carbon metabolism. Using adaptive laboratory evolution (ALE), we show that Sad can substitute for the roles of erythrose 4-phosphate dehydrogenase in pyridoxal 5’-phosphate (PLP) biosynthesis and glyceraldehyde 3-phosphate dehydrogenase in glycolysis. To recruit Sad for PLP biosynthesis and glycolysis, ALE employs various mechanisms, including active site mutation, copy number amplification, and (de)regulation of gene expression. Our study traces down these different evolutionary trajectories, reports on the surprising active site plasticity of Sad, identifies regulatory links in amino acid metabolism, and highlights the potential of an ordinary enzyme as innovation reservoir for evolution.

The global distribution and drivers of wood density and their impact on forest carbon stocks.

The density of wood is a key indicator of the carbon investment strategies of trees, impacting productivity and carbon storage. Despite its importance, the global variation in wood density and its environmental controls remain poorly understood, preventing accurate predictions of global forest carbon stocks. Here we analyse information from 1.1 million forest inventory plots alongside wood density data from 10,703 tree species to create a spatially explicit understanding of the global wood density distribution and its drivers. Our findings reveal a pronounced latitudinal gradient, with wood in tropical forests being up to 30% denser than that in boreal forests. In both angiosperms and gymnosperms, hydrothermal conditions represented by annual mean temperature and soil moisture emerged as the primary factors influencing the variation in wood density globally. This indicates similar environmental filters and evolutionary adaptations among distinct plant groups, underscoring the essential role of abiotic factors in determining wood density in forest ecosystems. Additionally, our study highlights the prominent role of disturbance, such as human modification and fire risk, in influencing wood density at more local scales. Factoring in the spatial variation of wood density notably changes the estimates of forest carbon stocks, leading to differences of up to 21% within biomes. Therefore, our research contributes to a deeper understanding of terrestrial biomass distribution and how environmental changes and disturbances impact forest ecosystems.