Evolutionary Transitions Research Articles

An Equus-Dominated Middle Pleistocene (Irvingtonian) Vertebrate Fauna from Northcentral Florida, USA

A newly discovered deposit on the bed of the Steinhatchee River produced a moderately diverse assemblage of 15 vertebrate taxa herein designated the Steinhatchee River 2A (STR 2A) local fauna. Mammalian taxa isotopically shown from other sites to be either grazers or grazing-dominated mixed-feeders numerically dominate the fauna, especially a species of Equus. About 75% of the 552 identifiable fossils from STR 2A, representing a minimum of nine individuals, are referred to the informally named Equus (Equus) sp. A. The site produced the first known examples of associated upper and lower cheekteeth and lower incisors for this species, and also one of just two records outside of central and southern peninsular Florida. Like most Pleistocene sites in Florida, xenarthrans are diverse, with two cingulates, Dasypus and Holmesina, and two pilosans, Paramylodon and Megalonyx. An astragalus and several metatarsals of Holmesina are within the size range of H. septentrionalis, but also have some characteristics found in the older species H. floridanus. These finds corroborate that an evolutionary transition between these two species occurred in Florida during the Irvingtonian. The age of STR 2A is most likely middle Irvingtonian, ca. 0.5–0.7 Ma, an interval poorly known in Florida and the rest of the southeastern USA.

Seasonal evolution modes of tropical sea surface temperature anomalies and their links to antarctic sea ice anomalies

Abstract Previous studies have explored the teleconnections between variability of Antarctic sea ice cover and tropical sea surface temperature (SST) across the Pacific, Atlantic, and Indian Ocean basins, typically focusing on each basin individually. However, there has been limited investigation into the impact of tropical SSTs—particularly from a seasonal evolution perspective—on Antarctic sea ice cover. In this study, we employ the self-organizing map method to identify and analyze the primary modes of seasonal SST evolution in the tropical oceans from 1854 to 2022. We also project changes in the frequency of these modes through the 21st century. Moreover, we examine the seasonal variability of Antarctic sea ice concentration in relation to these tropical SST modes over the past four decades. Our results reveal that tropical SST anomalies display both uniform and shifted seasonal evolution patterns. Notably, the frequency of switched modes—namely, transitions from La Niña to El Niño (node 8) and from El Niño to La Niña (node 3)—is expected to increase in future climate. Interestingly, nearly mirrored SST seasonal evolution patterns do not lead to entirely opposite atmospheric circulation anomalies in the southern mid-high latitudes, nor do they result in completely inverse Antarctic sea ice cover anomalies.

Multimodal signalling in manakins: lack of correlated evolution between acoustic, visual and behavioural traits

Sexual traits, such as visual adornments, sound‐based cues and courtship dances, are frequently displayed in combination as multimodal signals. Some hypotheses propose that different signals trade‐off with each other, potentially due to resource limitations (‘trade‐off’ or transfer hypothesis) or that these develop simultaneously to enhance communication effectiveness (‘joint evolution’ hypothesis). Alternatively, multiple cues may evolve independently to serve distinct functions or convey different information (‘multiple messages’ hypothesis). Here, we explored the interdependence between different signal modalities in manakins (Pipridae), which are known for great interspecific diversity in the degree of elaboration in courtship dance, song and plumage coloration. We also used comparative methods to explore the mode of evolution and the degree of conservatism of these signals. We found that song, plumage coloration and courtship dance evolved independently as there was no correlation between these traits. Song evolution in manakins was attracted to a single optimum and exhibited a weak phylogenetic signal in comparison with those of colour and behavioural diversity. The high support found for the speciational and κ models when analysing the multivariate estimates of trait variability suggests that these signals (especially colour and behaviour attributes) may have evolved in a punctuated manner, with large evolutionary changes at speciation events and minimal subsequent changes along the branches. Our results show that song, colour and dance diversity are each associated (or marginally associated) with different ecological factors, indicating that sexual signals in manakins might convey different information and/or respond to different selection pressures. Larger species and those with lower dispersal capacity tend to exhibit higher colour richness, which in turn differed among lek categories, being higher in species with ‘classic’ leks and lower in non‐lekking species. Overall, the present study supports the idea that correlation between signal modalities does not constitute a widespread pattern in songbirds.

Evolution of 3D Chromatin Folding.

Studies examining the evolution of genomes have focused mainly on sequence conservation. However, the inner working of a cell implies tightly regulated crosstalk between complex gene networks controlled by small dispersed regulatory elements of physically contacting DNA regions. How these different levels of chromatin organization crosstalk in different species underpins the potential for genome evolutionary plasticity. We review the evolution of chromatin organization across the Animal Tree of Life. We introduce general aspects of the mode and tempo of genome evolution to later explore the multiple layers of genome organization. We argue that both genome and chromosome size modulate patterns of chromatin folding and that chromatin interactions facilitate the formation of lineage-specific chromosomal reorganizations, especially in germ cells. Overall, analyzing the mechanistic forces involved in the maintenance of chromatin structure and function of the germ line is critical for understanding genome evolution, maintenance, and inheritance.

Genome dynamics across the evolutionary transition to endosymbiosis.

Endosymbiosis-where a microbe lives and replicates within a host-is an important contributor to organismal function that has accelerated evolutionary innovations and catalyzed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we leverage the wide diversity of host-associated lifestyles of the genus Arsenophonus to reveal the complex evolutionary processes that occur during the transition to a vertically transmitted endosymbiotic lifestyle from strains maintained solely by horizontal (infectious) transmission. We compared the genomes of 38 strains spanning diverse lifestyles from horizontally transmitted pathogens to obligate interdependent endosymbionts. Among culturable strains, we observed those with vertical transmission had larger genome sizes than closely related horizontally transmitting counterparts, consistent with evolutionary innovation and the rapid gain of new functions. Increased genome size was a consequence of prophage and plasmid acquisition, including a cargo of type III effectors, alongside the concomitant loss of CRISPR-Cas genome defense systems, enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, which we hypothesize to be a consequence of reduced microbe-microbe competition. Thereafter, the transition to endosymbiosis with strict vertical inheritance was associated with the expected relaxation of purifying selection, gene pseudogenization, metabolic degradation, and genome reduction. We argue that reduced phage predation in endosymbiotic niches drives the loss of genome defense systems driving rapid genome expansion upon the adoption of endosymbiosis and vertical transmission. This remodeling enables rapid horizontal gene transfer-mediated evolutionary innovation and precedes the reductive evolution traditionally associated with adaptation to endosymbiosis.

Approaching the adiabatic infimum of topological pumps on thin-film lithium niobate waveguides.

Topological pumps reveal topological insights of adiabatic mode evolution, in which adiabaticity plays a crucial role. However, the adiabatic infimum, i.e., the possible shortest evolution duration of an adiabatic topological pumping process, has remained elusive. In this study, we report the approach of adiabatic infimum in topological pumps in photonic waveguides based on the lithium niobate-on-insulator (LNOI) platform. Besides the most common way to achieve adiabaticity by slowing down the evolution of the system, the adiabaticity of a topological pump is also contingent on an effective Berry connection between instant eigenstates, which can be controlled by the selection of specific pump loops. Specifically, we develop a strategy to identify a pump loop with a minimized effective Berry connection, corresponding to the adiabatic infimum of a topological pump. As such, it is experimentally demonstrated that topological pumps can happen even with rapid evolution speed, at which the conventional pump would completely fail. The adiabatic infimum accelerates the topological pumps from the constraints of slow evolution and facilitates the design of compact topological devices.

Charged atomization characteristics and influencing factors analysis of aviation kerosene/ethanol blended fuel

ABSTRACT In this study, an experimental apparatus for charged atomization was established to explore the charged atomization modes of blended aviation kerosene/ethanol fuels and the corresponding evolution of atomization modes for E0 (100% aviation kerosene), E10 (10% ethanol + 90% aviation kerosene), E30 (30% ethanol + 70% aviation kerosene), and E50 (50% ethanol + 50% aviation kerosene) blends with varying applied voltages. Furthermore, the influence of the ethanol blending ratio, electrode separation distance, fuel flow rate, nozzle diameter, and other influencing factors on the charged atomization characteristics was investigated. Experimental results within the 0 to 10 kV voltage range revealed that as the voltage increased, the E0 fuel transitioned from droplet formation to spindle shape without exhibiting atomization, while the E10, E30, and E50 fuels displayed a sequential progression of atomization modes including droplet, micro-droplet, pulsed-jet, cone-jet, deflected-jet, and multi-jet configurations. As the ethanol blending ratio increases, the critical voltage required for the transition to atomization mode decreases, while the atomization cone angle gradually increases. The average atomization cone angles are 38.98°, 49.97°, and 66.83° for E10, E30, and E50, respectively. When the nozzle diameter is reduced from 1.05 mm to 0.3 mm, the charged atomization cone angle does not change significantly. With increasing fuel flow, the critical voltage for the atomization mode transition increases progressively, and the charged atomization cone angle also increases. The average atomization cone angles are 65.80°, 88.45°, 93.04°, 103.63°, and 110.97°, respectively.

Orientation-dependent strain and dislocation in HVPE-grown α -Ga2O3 epilayers on sapphire substrates

Orientation-dependent substrates provide effective platforms for achieving α-Ga2O3 with low dislocation densities, whereas the associated strain and dislocation dynamics have not been fully explored. Herein, we investigated the evolution of growth mode, interfacial strain, and dislocation propagation in the α-Ga2O3 epitaxial layer with various orientations, grown by the halide vapor-phase epitaxy. Strain tensor theory and geometric phase analysis indicate that the m-plane α-Ga2O3 epitaxial layer exhibits the lowest misfit tensile strain, measured at εxx = 1.46% and εyy = 1.81%, resulting in the lowest edge dislocation density. The m-plane lattice exhibits an inclination of 33.60°, while the c-plane lattice is horizontally aligned and the a-plane lattice oriented perpendicularly. The orientation-dependent growth significantly influences stress relaxation through the generation of misfit dislocations, originating from either basal or prismatic slip. Edge dislocations, induced by misfit dislocations, favor the c-axis, remaining well confined within the in-plane interfacial layer of the m-plane α-Ga2O3, leading to reduced low edge dislocation density in the subsequent thick epitaxial layer. These findings shed light on the epitaxial dynamics of α-Ga2O3 heteroepitaxy, paving the way for the development of high-performance power devices.

The brain atlas of a subsocial bee reflects that of eusocial Hymenoptera.

The evolutionary transition from solitary life to group-living in a society with cooperative brood care, reproductive division of labor and morphological castes is associated with increased cognitive demands for task-specialization. Associated with these demands, the brains of eusocial Hymenoptera divide transcriptomic signatures associated with foraging and reproduction to different populations of cells and also show diverse astrocyte and Kenyon cell types compared with solitary non-hymenopteran insects. The neural architecture of subsocial bees, which represent evolutionary antecedent states to eusocial Hymenoptera, could then show how widely this eusocial brain is conserved across aculeate Hymenoptera. Using single-nucleus transcriptomics, we have created an atlas of neuron and glial cell types from the brain of a subsocial insect, the small carpenter bee (Ceratina calcarata). The proportion of C. calcarata neurons related to the metabolism of classes of neurotransmitters is similar to that of other insects, whereas astrocyte and Kenyon cell types show highly similar gene expression patterns to those of eusocial Hymenoptera. In the winter, the transcriptomic signature across the brain reflected diapause. When the bee was active in the summer, however, genes upregulated in neurons reflected foraging, while the gene expression signature of glia associated with reproductive functions. Like eusocial Hymenoptera, we conclude that neural components for foraging and reproduction in C. calcarata are compartmentalized to different parts of its brain. Cellular examination of the brains of other solitary and subsocial insects can show the extent of neurobiological conservation across levels of social complexity.

Fracture Mode and Thermal Damage Evolution of Sandstone Under the Coupling Effect of Thermal Treatment and Impact Load

The dynamic properties of high-temperature sandstone quickly deteriorate with different cooling methods, which leads to the instability of underground engineering rock structures. Therefore, it is of great significance to quantify the changes in the dynamic characteristics of high-temperature cooled sandstone under impact loads. Therefore, the sandstone is heated to different temperatures and cooled using three methods. A dynamic tensile test is performed using the Splitting Hopkinson Pressure Bar (SHPB) test set for high-temperature cooled sandstone. At the same time, the transient process of rock failure was examined using high-speed cameras. The influence of different temperatures and cooling methods on the thermal damage value of sandstone was analyzed, and the prediction equation was formed. The change in rock energy during rock failure under impact load was calculated.

«Прикладная» геймификация в креолизованном медиатексте как один из способов продуцирования и восприятия информационного контента

The article considers gamification as a variant of infotainment in line with the trends of visualization and multimedia of modern media. The relevance of the proposed work lies in the fact that the author draws attention to the applied nature of gaming technologies, as well as their educational and training functions. Due to the evolutionary transition of gaming in the media from entertainment to information and training, the contingent to which games can be addressed is changing. Gaming technologies are diverse, from epistolary forms and comics that are leaving us to immersive games, stimulating the process of effective production and perception of information content in creolized media texts.

Repeat-based holocentromeres of the woodrush Luzula sylvatica reveal insights into the evolutionary transition to holocentricity

In most studied eukaryotes, chromosomes are monocentric, with centromere activity confined to a single region. However, the rush family (Juncaceae) includes species with both monocentric (Juncus) and holocentric (Luzula) chromosomes, where centromere activity is distributed along the entire chromosome length. Here, we combine chromosome-scale genome assembly, epigenetic analysis, immuno-FISH and super-resolution microscopy to study the transition to holocentricity in Luzula sylvatica. We report repeat-based holocentromeres with an irregular distribution of features along the chromosomes. Luzula sylvatica holocentromeres are predominantly associated with two satellite DNA repeats (Lusy1 and Lusy2), while CENH3 also binds satellite-free gene-poor regions. Comparative repeat analysis suggests that Lusy1 plays a crucial role in centromere function across most Luzula species. Furthermore, synteny analysis between L. sylvatica (n = 6) and Juncus effusus (n = 21) suggests that holocentric chromosomes in Luzula could have arisen from chromosome fusions of ancestral monocentric chromosomes, accompanied by the expansion of CENH3-associated satellite repeats.

Ancient Secretory Pathways Contributed to the Evolutionary Origin of an Ecologically Impactful Bioluminescence System.

Evolutionary innovations in chemical secretion-such as the production of secondary metabolites, pheromones, and toxins-profoundly impact ecological interactions across a broad diversity of life. These secretory innovations may involve a "legacy-plus-innovation" mode of evolution, whereby new biochemical pathways are integrated with conserved secretory processes to create novel products. Among secretory innovations, bioluminescence is important because it evolved convergently many times to influence predator-prey interactions, while often producing courtship signals linked to increased rates of speciation. However, whether or not deeply conserved secretory genes are used in secretory bioluminescence remains unexplored. Here, we show that in the ostracod Vargula tsujii, the evolutionary novel c-luciferase gene is co-expressed with many conserved genes, including those related to toxin production and high-output protein secretion. Our results demonstrate that the legacy-plus-innovation mode of secretory evolution, previously applied to sensory modalities of olfaction, gustation, and nociception, also encompasses light-producing signals generated by bioluminescent secretions. This extension broadens the paradigm of secretory diversification to include not only chemical signals but also bioluminescent light as an important medium of ecological interaction and evolutionary innovation.

Phylogeny and evolution of larval feeding mode in the megadiverse superfamily Sciaroidea (Diptera)

Abstract Sciaroidea is a megadiverse clade within Diptera that exhibits diverse larval feeding modes. In this study, we explored the phylogenetic relationships and evolution of larval feeding modes within the superfamily using a fossil-calibrated time tree. We found that filtering out potentially fast-evolving sites altered the family-level tree topology, and that species within Sciaroidea incertae sedis might be crucial in determining the general tree topology. The most recent common ancestor of Sciaroidea was inferred to have originated in the Upper Triassic (~225 Ma). A major radiation of families occurred from the Uppermost Triassic to the Lowermost Jurassic (190–200 Ma). The ancestral larval feeding mode was inferred to be mycophagy. Most families retained this feature with only minor transitions occurring in some clades; however, Cecidomyiidae and Keroplatidae went through notable shifts in larval feeding mode. Cecidomyiidae underwent a transition from mycophagy to phytophagy in the Lower Cretaceous, in line with angiosperm radiation as suggested in previous studies. The larvae of stem Keroplatidae were inferred to be predators since the Jurassic. A transition back to mycophagy occurred within the subfamily Keroplatinae during the Paleogene to Uppermost Cretaceous, coinciding with the origin and radiation of species-rich mycophagous clades of other sciaroid families. Our study highlights the importance of taxon sampling and sequence filtering in phylogenetic analyses of Sciaroidea. We suggest, based on temporal patterns of lineage diversification, that the evolution of larval feeding modes within the group might be correlated with the diversification of mushroom-forming fungi and angiosperms.

Spread of yellow-bill-color alleles favored by selection in the long-tailed finch hybrid system

Carotenoid pigments produce the yellow and red colors of birds and other vertebrates. Despite their importance in social signaling and sexual selection, our understanding of how carotenoid ornamentation evolves in nature remains limited. Here, we examine the long-tailed finch Poephila acuticauda, an Australian songbird with a yellow-billed western subspecies acuticauda and a red-billed eastern subspecies hecki, which hybridize where their ranges overlap. We found that yellow bills can be explained by the loss of C(4)-oxidation, thus preventing yellow dietary carotenoids from being converted to red. Combining linked-read genomic sequencing and reflectance spectrophotometry measurements of bill color collected from wild-sampled finches and laboratory crosses, we identify four loci that together explain 53% of variance in this trait. The two loci of largest effect contain the genes CYP2J19, an essential enzyme for producing red carotenoids, and TTC39B, an enhancer of carotenoid metabolism. A paucity of protein-coding changes and an enrichment of associated upstream variants suggest that the loss of C(4)-oxidation results from cis-regulatory evolution. Evolutionary genealogy reconstruction indicates that the red-billed phenotype is ancestral and that yellow alleles at CYP2J19 and TTC39B first arose and fixed in acuticauda approximately 100 kya. Yellow alleles subsequently introgressed into hecki less than 5 kya. Across all color loci, acuticauda-derived variants show evidence of selective sweeps, implying that yellow bill coloration has been favored by natural selection. Our study illustrates how evolutionary transitions between yellow and red coloration can be achieved by successive selective events acting on regulatory changes at a few interacting genes.

Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee.

Comparative genomic studies of social insects suggest that changes in gene regulation are associated with evolutionary transitions in social behavior, but the activity of predicted regulatory regions has not been tested empirically. We used self-transcribing active regulatory region sequencing, a high-throughput enhancer discovery tool, to identify and measure the activity of enhancers in the socially variable sweat bee, Lasioglossum albipes. We identified over 36,000 enhancers in the L. albipes genome from 3 social and 3 solitary populations. Many enhancers were identified in only a subset of L. albipes populations, revealing rapid divergence in regulatory regions within this species. Population-specific enhancers were often proximal to the same genes across populations, suggesting compensatory gains and losses of regulatory regions may preserve gene activity. We also identified 1,182 enhancers with significant differences in activity between social and solitary populations, some of which are conserved regulatory regions across species of bees. These results indicate that social trait variation in L. albipes is associated with the fine-tuning of ancient enhancers as well as lineage-specific regulatory changes. Combining enhancer activity with population genetic data revealed variants associated with differences in enhancer activity and identified a subset of differential enhancers with signatures of selection associated with social behavior. Together, these results provide the first empirical map of enhancers in a socially flexible bee and highlight links between cis-regulatory variation and the evolution of social behavior.

Mode decomposition to identify oscillation patterns of flexible aeroshell

Flexible aeroshells, featuring deformable membrane surfaces supported by pressurized gas, offer a novel re-entry system for high-altitude deceleration during re-entry. The flexibility of structural components introduces unique challenges in predicting aerodynamic behavior, as deformations can significantly alter the flow field, affecting pressure distribution and potentially causing aerodynamic instabilities. Therefore, coupled analysis is crucial to ensure the performance reliability of inflatable aeroshells. This study investigates the unsteady aerodynamic behavior, considering structural deformation in a two-way partitioned coupled manner in transonic flow. The dominant deformation patterns are identified using dynamic mode decomposition and the greedy compressive sensing algorithm. The findings reveal that the primary deformation pattern combines axial deformation and swing oscillation. The dominant oscillation frequencies remain different from the eigenfrequencies, indicating that the aerodynamic force is the primary driving force of such oscillations. The time evolution of these dominant modes indicates purely oscillatory behavior rather than increasing or decreasing trends. These insights are critical for the design and reliability assessment of inflatable aeroshells in varying aerodynamic environments.

Impact of continuously extending/retracting wall on Mack-mode evolution in hypersonic boundary layers

Structural morphing is regarded as a potential solution for future space transportation systems, necessitating aircraft capable of extensive altitude ranges, wide speed ranges, and multi-regime operations. The investigation of laminar-turbulent transition incorporating morphing effects aims to compensate for the lack of physical mechanisms in aircraft designs. This paper particularly focuses on the impact of a continuously extending or retracting wall in the chordwise direction on the evolution of inviscid Mack modes in a Mach 5.92 hypersonic boundary layer. Using the high-Reynolds-number asymptotic technique, a model is developed to quantify the morphing effect by an amplification factor, which includes both the scattering effect at the rigid-morphing junction and the successive modification of the Mack growth rate by the morphing velocity in the downstream region. Such a model enables us to conduct a comprehensive investigation across a wide parameter space defined by morphing speed and flow parameters. A critical frequency is identified near the most unstable second-mode frequency. For an extending wall, the oncoming Mack modes are suppressed for frequencies above this critical frequency and enhanced for frequencies below it. Conversely, the retracting-wall effect exhibits an inverse impact on the Mack modes. To validate the accuracy of the asymptotic predictions, the harmonic linearized Navier–Stokes calculations are performed, resulting in favorable agreements. This research sheds light on the complex interplay between wall morphing and the Mack-mode evolution, offering informative contributions to the understanding of the aerodynamic behaviors in hypersonic boundary layers.

A new and large monofenestratan reveals the evolutionary transition to the pterodactyloid pterosaurs

A new and large monofenestratan reveals the evolutionary transition to the pterodactyloid pterosaurs

Discharge modes evolution characteristics of metal particle on the spacer surface in AC gas insulated switchgear

Abstract Flashover faults on gas insulated switchgear (GIS) insulators induced by metal particles occur frequently. Previous studies have obtained the characteristics of partial discharges (PDs) induced by metal particles on spacer surfaces, but these characteristics cannot explain the detection failure of ultra-high frequency (UHF) online monitoring. To enable further study of the PD characteristics induced by surface metal particles, the space electric field and a very-high-sensitivity pulse current (PC) measurement system were established. The electric field and PC characteristics of a PD induced by metal particle on the spacer surface of a 126 kV GIS were obtained. Two PD modes were found to be induced by surface metal particles. In addition to the typical pulse discharge (TP), there is a micro-discharge group (MG) mode with low apparent charge and long duration. The average apparent charge of the MG mode is approximately one-tenth of that of the TP at 0.4 pC. Its duration may extend to the millisecond level, causing significant distortion of the spatial electric field while hardly producing UHF signals. Moreover, increasing the applied voltage will increase the proportion of the MG within the total discharge, where this proportion can reach more than 90% before flashover, and the proportion of the discharge pulses that generates UHF signals is as low as 1%. The MG generation mechanism is analysed, the ion group stranded on the spacer surface by the TP changes the local electric field at the tip of the metal particle, which reduces the development length and apparent charge of the MG. Low apparent charge is cleared easily by the background electric field and thus the discharge interval is very short. This paper can provide an important basis for revealing the mechanism of GIS spacer surface discharge induced by metal particles and solving the effectiveness of PD monitoring devices.