Integrative Analysis of the Metabolome and Transcriptome of a Cultivated Pepper and Its Wild Progenitor Chiltepin (Capsicum annuum L. var. glabriusculum) Revealed the Loss of Pungency During Capsicum Domestication

Pungency is a unique characteristic of chili peppers (Capsicum spp.) caused by capsaicinoids. The evolutionary emergence of pungency is thought to be a derived trait within the genus Capsicum. However, it is not well-known how pungency has varied during Capsicum domestication and specialization. In this study, we applied a comparative metabolomics along with transcriptomics analysis to assess various changes between two peppers (a mildly pungent cultivated pepper BB3 and its hot progenitor chiltepin) at four stages of fruit development, focusing on pungency variation. A total of 558 metabolites were detected in two peppers. In comparison with chiltepin, capsaicinoid accumulation in BB3 was almost negligible at the early stage. Next, 412 DEGs associated with the capsaicinoid accumulation pathway were identified through coexpression analysis, of which 18 genes (14 TFs, 3 CBGs, and 1 UGT) were deemed key regulators due to their high coefficients. Based on these data, we speculated that downregulation of these hub genes during the early fruit developmental stage leads to a loss in pungency during Capsicum domestication (from chiltepin to BB3). Of note, a putative UDP-glycosyltransferase, GT86A1, is thought to affect the stabilization of capsaicinoids. Our results lay the foundation for further research on the genetic diversity of pungency traits during Capsicum domestication and specialization.

On reappearance and complexity in musical calling

Music is especially valued in human societies, but music-like behavior in the form of song also occurs in a variety of other animal groups including primates. The calling of our primate ancestors may well have evolved into the music of modern humans via multiple selective scenarios. But efforts to uncover these influences have been hindered by the challenge of precisely defining musical behavior in a way that could be more generally applied across species. We propose an acoustic focused reconsideration of “musicality” that could help enable independent inquiry into potential ecological pressures on the evolutionary emergence of such behavior. Using published spectrographic images (n = 832 vocalizations) from the primate vocalization literature, we developed a quantitative formulation that could be used to help recognize signatures of human-like musicality in the acoustic displays of other species. We visually scored each spectrogram along six structural features from human music—tone, interval, transposition, repetition, rhythm, and syllabic variation—and reduced this multivariate assessment into a concise measure of musical patterning, as informed by principal components analysis. The resulting acoustic reappearance diversity index (ARDI) estimates the number of different reappearing syllables within a call type. ARDI is in concordance with traditional measures of bird song complexity yet more readily identifies shorter, more subtly melodic primate vocalizations. We demonstrate the potential utility of this index by using it to corroborate several origins scenarios. When comparing ARDI scores with ecological features, our data suggest that vocalizations with diversely reappearing elements have a pronounced association with both social and environmental factors. Musical calls were moderately associated with wooded habitats and arboreal foraging, providing partial support for the acoustic adaptation hypothesis. But musical calling was most strongly associated with social monogamy, suggestive of selection for constituents of small family-sized groups by neighboring conspecifics. In sum, ARDI helps construe musical behavior along a continuum, accommodates non-human musicality, and enables gradualistic co-evolutionary paths between primate taxa—ranging from the more inhibited locational calls of archaic primates to the more exhibitional displays of modern apes.

Evolution of Archaellum Rotation Involved Invention of a Stator Complex by Duplicating and Modifying a Core Component

Novelty in biology can arise from opportunistic repurposing of nascent characteristics of existing features. Understanding how this process happens at the molecular scale, however, suffers from a lack of case studies. The evolutionary emergence of rotary motors is a particularly clear example of evolution of a new function. The simplest of rotary motors is the archaellum, a molecular motor that spins a helical propeller for archaeal motility analogous to the bacterial flagellum. Curiously, emergence of archaellar rotation may have pivoted on the simple duplication and repurposing of a pre-existing component to produce a stator complex that anchors to the cell superstructure to enable productive rotation of the rotor component. This putative stator complex is composed of ArlF and ArlG, gene duplications of the filament component ArlB, providing an opportunity to study how gene duplication and neofunctionalization contributed to the radical innovation of rotary function. Toward understanding how this happened, we used electron cryomicroscopy to determine the structure of isolated ArlG filaments, the major component of the stator complex. Using a hybrid modeling approach incorporating structure prediction and validation, we show that ArlG filaments are open helices distinct to the closed helical filaments of ArlB. Curiously, further analysis reveals that ArlG retains a subset of the inter-protomer interactions of homologous ArlB, resulting in a superficially different assembly that nevertheless reflects the common ancestry of the two structures. This relatively simple mechanism to change quaternary structure was likely associated with the evolutionary neofunctionalization of the archaellar stator complex, and we speculate that the relative deformable elasticity of an open helix may facilitate elastic energy storage during the transmission of the discrete bursts of energy released by ATP hydrolysis to continuous archaellar rotation, allowing the inherent properties of a duplicated ArlB to be co-opted to fulfill a new role. Furthermore, agreement of diverse experimental evidence in our work supports recent claims to the power of new structure prediction techniques.

The role of potentiating mutations in the evolution of pandemic Escherichia coli clones

The Escherichia coli species exhibits a vast array of variable lifestyles, including environmental, commensal, and pathogenic organisms. Many of these E. coli contribute significantly to the global threat of antimicrobial resistance (AMR). Multidrug-resistant (MDR) clones of E. coli have arisen multiple times over varying timescales. The repeated emergence of successful pandemic clones, including the notorious ST131 lineage, highlights a desperate need to further study the evolutionary processes underlying their emergence and success. Here, we review the evolutionary emergence of E. coli ST131 pandemic clones and draw parallels between their evolutionary trajectories and those of other lineages. From colonization and expansion to the acquisition of multidrug resistance plasmids, potentiating mutations are present at each stage, leading to a proposed sequence of events that may result in the formation of an antimicrobial-resistant pandemic clone.

Building blocks of language

Articulate language is a form of communication unique to humans. Over time, a spectrum of researchers has proposed various frameworks attempting to explain the evolutionary acquisition of this distinctive human attribute, some deploring the apparent lack of direct evidence elucidating the phenomenon, whilst others have pointed to the contributions of palaeoanthropology, the social brain hypothesis and the fact that even amongst contemporary humans, social group sizes reflect brain size. Theologians have traditionally (largely) ignored evolutionary insights as an explanatory paradigm for the origin of humankind. However, an increasing number are, of late, contributing to a worldview of humanity which accommodates both the epistemological realities of evolutionary biology as well as insights from theology. This includes reviewing and assessing the origins of articulate language and the physiological attributes necessary for its development. It is in this sense that the evolution of language is relevant from a theological perspective. The association between mental capacity and articulate language, already noted by Darwin, is relevant in explaining the larger group sizes found amongst humans, as is the incipient role played by the evolution of laughter in triggering the neuroendocrine system promoting bonding, to the eventual development of articulate language. Our aim is to review a selection of contemporary perspectives on the evolution of language, amongst others, reasons for the ease with which young children acquire language competency, and whether we may be hardwired for language from birth. Further reading is suggested in the footnotes.Contribution: This article is part of a special collection reflecting on the evolutionary building blocks of our past, present and future. It is based on historical thought and contemporary research with regards to the evolutionary emergence of language. It fits well with the intersectional and trans-disciplinary nature of this collection and journal.

Ongoing Assessment of the Molecular Evolution of Peste Des Petits Ruminants Virus Continues to Question Viral Origins

Understanding the evolution of viral pathogens is critical to being able to define how viruses emerge within different landscapes. Host susceptibility, which is spread between different species and is a contributing factor to the subsequent epidemiology of a disease, is defined by virus detection and subsequent characterization. Peste des petits ruminants virus is a plague of small ruminant species that is a considerable burden to the development of sustainable agriculture across Africa and much of Asia. The virus has also had a significant impact on populations of endangered species in recent years, highlighting its significance as a pathogen of high concern across different regions of the globe. Here, we have re-evaluated the molecular evolution of this virus using novel genetic data to try and further resolve the molecular epidemiology of this disease. Viral isolates are genetically characterized into four lineages (I−IV), and the historic origin of these lineages is of considerable interest to the molecular evolution of the virus. Our re-evaluation of viral emergence using novel genome sequences has demonstrated that lineages I, II and IV likely originated in West Africa, in Senegal (I) and Nigeria (II and IV). Lineage III sequences predicted emergence in either East Africa (Ethiopia) or in the Arabian Peninsula (Oman and/or the United Arab Emirates), with a paucity of data precluding a more refined interpretation. Continual refinements of evolutionary emergence, following the generation of new data, is key to both understanding viral evolution from a historic perspective and informing on the ongoing genetic emergence of this virus.

The developmental biology of Charnia and the eumetazoan affinity of the Ediacaran rangeomorphs

Molecular timescales estimate that early animal lineages diverged tens of millions of years before their earliest unequivocal fossil evidence. The Ediacaran macrobiota (~574 to 538 million years ago) are largely eschewed from this debate, primarily due to their extreme phylogenetic uncertainty, but remain germane. We characterize the development of Charnia masoni and establish the affinity of rangeomorphs, among the oldest and most enigmatic components of the Ediacaran macrobiota. We provide the first direct evidence for the internal interconnected nature of rangeomorphs and show that Charnia was constructed of repeated branches that derived successively from pre-existing branches. We find homology and rationalize morphogenesis between disparate rangeomorph taxa, before producing a phylogenetic analysis, resolving Charnia as a stem-eumetazoan and expanding the anatomical disparity of that group to include a long-extinct bodyplan. These data bring competing records of early animal evolution into closer agreement, reformulating our understanding of the evolutionary emergence of animal bodyplans.

Pantomimic conceptions of language origins

Could pantomime have been the key step in the evolutionary emergence of symbolic communication? Such a possibility has been consistently present in the intellectual reflection on language origins. What makes pantomime interesting from this perspective is its rich expressive potential, since it can convey open-ended, semantically universal and displaced meanings without relying on semiotic conventions, so that spontaneous pantomimes can be recognized as such and successfully interpreted. Definitions are important in classifying a particular scenario as “pantomimic.” In this chapter, the authors employ a “rich” definition of pantomime: it is described as bodily-mimetic communication which is non-conventional, improvised, performed with the whole body, holistic, and communicatively and semantically complex. Based on this foundation, the authors review and evaluate pantomimic accounts of language origins, from the past to the present, and particularly focus on the contemporary pantomime accounts given by Michael Arbib, Michael Tomasello, and Jordan Zlatev.