Basis Of Evolution Research Articles

Complex Hybridization in a Clade of Polytypic Salamanders (Plethodontidae: Desmognathus) Uncovered by Estimating Higher-Level Phylogenetic Networks.

Reticulation between incipient lineages is a common feature of diversification. We examine these phenomena in the Pisgah clade of Desmognathus salamanders from the southern Appalachian Mountains of the eastern United States. The group contains four to seven species exhibiting two discrete phenotypes, aquatic "shovel-nosed" and semi-aquatic "black-bellied" forms. These ecomorphologies are ancient and have apparently been transmitted repeatedly between lineages through introgression. Geographically proximate populations of both phenotypes exhibit admixture, and at least two black-bellied lineages have been produced via reticulations between shovel-nosed parentals, suggesting potential hybrid speciation dynamics. However, computational constraints currently limit our ability to reconstruct network radiations from gene-tree data. Available methods are limited to level-1 networks wherein reticulations do not share edges, and higher-level networks may be non-identifiable in many cases. We present a heuristic approach to recover information from higher-level networks across a range of potentially identifiable empirical scenarios, supported by theory and simulation. When extrinsic information indicates the location and direction of reticulations, our method can successfully estimate a reduced possible set of non-level-1 networks. Phylogenomic data support a single backbone topology with up to five overlapping hybrid edges in the Pisgah clade. These results suggest an unusual mechanism of ecomorphological hybrid speciation, wherein a binary threshold trait causes some hybrid populations to shift between microhabitat niches, promoting ecological divergence between sympatric hybrids and parentals. This contrasts with other well-known systems in which hybrids exhibit intermediate, novel, or transgressive phenotypes. The genetic basis of these phenotypes is unclear and further data are needed to clarify the evolutionary basis of morphological changes with ecological consequences.

The evolutionary basis of elevated testosterone in women with polycystic ovary syndrome: an overview of systematic reviews of the evidence.

Polycystic ovary syndrome (PCOS) exhibits high prevalence and heritability despite causing negative impacts on fertility and fecundity. Previous hypotheses have postulated that some PCOS-associated traits, especially above-average levels of testosterone, were associated with benefits in ancestral environments. As such, PCOS would represent, in part, a maladaptive extreme of adaptations related to relatively high testosterone. To evaluate this hypothesis, we conducted a series of systematic literature reviews on the associations of testosterone levels, and prenatal testosterone metrics, with measures of strength, robustness, muscularity, and athleticism in females. We also systematically reviewed the literature on associations of testosterone with dominance in females and reviewed archaeological evidence concerning female strength and muscularity and its correlates. The main findings were fivefold: (1) elevated testosterone levels were generally associated with higher strength, muscularity and athleticism in females; (2) females with PCOS showed notable evidence of increased strength, muscularity, and athleticism compared to controls; (3) females with higher testosterone levels exhibited clear evidence of high dominance, (4) despite evidence that higher testosterone is linked with higher bone mineral density in healthy females, PCOS was not clearly associated with this phenotype; and (5) archaeological evidence from osteology, and data from some current small-scale societies, indicated that females often exhibit substantial levels of muscularity. Overall, the hypothesis that relatively high levels of testosterone are associated with benefits to females in some contexts was largely supported. These results provide evidence for the "maladaptive extremes of adaptation" model, with implications for treatment of females with PCOS and for future research.

Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster

Accuracy and efficiency are fundamental to mRNA translation. Codon usage bias is widespread across species. Despite the long-standing association between optimized codon usage and improved translation, our understanding of its evolutionary basis and functional effects remains limited. Drosophila is widely used to study codon usage bias, but genome-scale experimental data are scarce. Using high-resolution mass spectrometry data from Drosophila melanogaster, we show that optimal codons have lower translation errors than nonoptimal codons after accounting for these biases. Genomic-scale analysis of ribosome profiling data shows that optimal codons are translated more rapidly than nonoptimal codons. Although we find no long-term selection favoring synonymous mutations in D. melanogaster after diverging from D. simulans, we identify signatures of positive selection driving codon optimization in the D. melanogaster population. These findings expand our understanding of the functional consequences of codon optimization and serve as a foundation for future investigations.

Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains

Dynamic ADP-ribosylation signalling is a crucial pathway that controls fundamental cellular processes, in particular, the response to cellular stresses such as DNA damage, reactive oxygen species and infection. In some pathogenic microbes the response to oxidative stress is controlled by a SirTM/zinc-containing macrodomain (Zn-Macro) pair responsible for establishment and removal of the modification, respectively. Targeting this defence mechanism against the host’s innate immune response may lead to novel approaches to support the fight against emerging antimicrobial resistance. Earlier studies suggested that Zn-Macros play a key role in the activation of this defence. Therefore, we used phylogenetic, biochemical, and structural approaches to elucidate the functional properties of these enzymes. Using the substrate mimetic asparagine-ADP-ribose as well as the ADP-ribose product, we characterise the catalytic role of the zinc ion in the removal of the ADP-ribosyl modification. Furthermore, we determined structural properties that contribute to substrate selectivity within the different Zn-Macro branches. Together, our data not only give new insights into the Zn-Macro family but also highlight their distinct features that may be exploited for the development of future therapies.

Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases

Protein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches – tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory folded conformation, due to intrinsic sequence effects. Here we investigate the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a thermodynamic cycle involving many (n = 108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation DFG-out Activation Loop Folded, is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modes in trans and additional modes of regulation in cis for TKs.

Evolution of glucuronoxylan side chain variability in vascular plants and the compensatory adaptations of cell wall-degrading hydrolases.

Polysaccharide structural complexity not only influences cell wall strength and extensibility but also hinders pathogenic and biotechnological attempts to saccharify the wall. In certain species and tissues, glucuronic acid side groups on xylan exhibit arabinopyranose or galactose decorations whose genetic and evolutionary basis is completely unknown, impeding efforts to understand their function and engineer wall digestibility. Genetics and polysaccharide profiling were used to identify the responsible loci in Arabidopsis and Eucalyptus from proposed candidates, while phylogenies uncovered a shared evolutionary origin. GH30-family endo-glucuronoxylanase activities were analysed by electrophoresis, and their differing specificities were rationalised by phylogeny and structural analysis. The newly identified xylan arabinopyranosyltransferases comprise an overlooked subfamily in the GT47-A family of Golgi glycosyltransferases, previously assumed to comprise mainly xyloglucan galactosyltransferases, highlighting an unanticipated adaptation of both donor and acceptor specificities. Further neofunctionalisation has produced a Myrtaceae-specific xylan galactosyltransferase. Simultaneously, GH30 endo-glucuronoxylanases have convergently adapted to overcome these decorations, suggesting a role for these structures in defence. The differential expression of glucuronoxylan-modifying genes across Eucalyptus tissues, however, hints at further functions. Our results demonstrate the rapid adaptability of biosynthetic and degradative carbohydrate-active enzyme activities, providing insight into plant-pathogen interactions and facilitating plant cell wall biotechnological utilisation.

The evolution of exceptional diversity in parental care and fertilization modes in ray-finned fishes.

Among vertebrates, ray-finned fishes (Actinopterygii) display the highest diversity in parental care, and their diversification has been hypothesized to be related to phylogenetic changes in fertilization modes. Using the most comprehensive, sex-specific data from 7,600 species of 62 extant orders of ray-finned fishes, we inferred ancestral states and transitions among care types and caring episodes (i.e., the stage of offspring development). Our work has uncovered 3 novel findings. First, transitions among different care types (i.e., male-only care, female-only care, biparental care, and no care) are common, and the frequencies of these transitions show unusually diverse patterns concerning fertilization modes (external, or internal via oviduct, mouth, or brood pouch). Second, both oviduct and mouth fertilization are selected for female-biased care, whereas fertilization in a brood pouch is selected for male-biased care. Importantly, internal fertilization without parental care is extremely unstable phylogenetically. Third, we show that egg care in both sexes is associated with nest building (which is male-biased) and fry care (which is female-biased). Taken together, the aquatic environment, which supports considerable flexibility in care, facilitated the diversification of parenting behavior, creating the evolutionary bases for more comprehensive parenting to protect offspring in semiterrestrial or terrestrial environments.

The allatotropin/orexin system as an example of immunomodulatory properties of neuropeptides

The central nervous system (CNS) plays a critical role in signal integration in animals and allows the orchestration of life processes to maintain homeostasis. Current research clearly shows that inflammatory processes can also be modulated by the CNS via the neuroendocrine system. One of the neuropeptide families that participate in vertebrates in this process is orexins (OXs). Interestingly, our previous results suggested that a similar dependency may also exist between neuropeptides and immune system activity in insects. Due to the structural homology of orexin and allatotropin receptors and the functional similarity between these two neuropeptide families, the main aim of this research was to perform a complex analysis of the relationships between allatotropin (AT) and the insect immune response. Our results revealed functional similarities between vertebrate OXs and insect ATs. Similar effects were observed in the profile of the expression level of the gene encoding the AT precursor in the Tenebrio molitor nervous system and in the general action of Tenmo-AT on selected immune parameters of the tested beetles. Moreover, for the first time in insects, we confirmed the role of cytokines in the modulation of neuroendocrine system by determining the effect of Spätzle-like protein injection on the expression of genes encoding AT precursor and receptor. All these results are important for understanding the evolutionary basis of hormonal regulation of the immune response.

Analysis of bone structure in PEROMYSCUS: Effects of burrowing behavior.

We compare the effects of burrowing behavior on appendicular bone structure in two Peromyscus (deer mouse) species. P. polionotus creates complex burrows in their territories, while P. eremicus is a non-burrowing nesting mouse. We examined museum specimens' bones of wild-caught mice of the two species and lab-reared P. polionotus not given the opportunity to burrow. Bones were scanned using micro-computed tomography, and cortical and trabecular bone structural properties were quantified. Wild P. polionotus mice had a larger moment of area in the ulnar and tibial cortical bone compared with their lab-reared counterparts, suggesting developmental adaptation to bending resistance. Wild P. polionotus had a larger normalized second moment of area and cross-sectional area in the tibia compared with P. eremicus. Tibial trabecular analysis showed lower trabecular thickness and spacing in wild P. polionotus than in P. eremicus and femoral analysis showed wild P. polionotus had lower thickness than P. eremicus and lower spacing than lab-reared P. polionotus, suggesting adaptation to high loads from digging. Results lay the groundwork for future exploration of the ontogenetic and evolutionary basis of mechanoadaptation in Peromyscus.

Reforming the structure and models of privatization

The article is devoted to the monitoring of the economic situation in Ukraine, the activities of control bodies and the coverage of approaches to reforming the ownership structure based on privatization processes. The analysis of the situation occurring in the field of privatization characterizes their complexity, which is caused by the state of war and instability in the state, the spread of illegal possession of state property and other destabilizing factors used by the structures of the aggressor country to achieve their own goals. The need for further localization of shadow privatization schemes is determined by the growth of the share of foreign capital in strategic sectors of the economy and in critical infrastructure facilities, which is one of the greatest modern threats to the economic sphere of Ukraine, which is dangerous for the economic independence of Ukraine. In the framework of stabilization privatization, the need to take into account not only national legislation, but also international norms, in particular the provisions of the OECD Declaration «On International Investments and Multinational Enterprises», which deals with the national regime, conflicting requirements for corporations and international investments, which should be applied in current conditions and in the post- war period of Ukraine. In this regard, it is worth defining a state body that will competently and competently manage Russian assets that are subject to sanctions and that will be transferred by partner countries after they are unfrozen for the restoration of our state according to the standards of sovereign funds or national welfare funds. Post-war privatization should contain an evolutionary basis and attention to national assets, especially in basic industries and relatively non-renewable resources that belong to the citizens of Ukraine. Thus, a clear balance is necessary between the needs of the country in the person of its institutions and the rights and freedoms of a person and a citizen, which are guaranteed and narrowing of their content is not allowed when adopting new laws or making changes to existing laws. It is worth preserving the foundations of Article 41 of the Constitution of Ukraine, which stipulates that everyone has the right to own, use and dispose of their property, and no one can be unlawfully deprived of the right to property, which is inviolable and guaranteed by Article 1 of the «First Protocol to the Convention on the Protection of Human Rights and fundamental freedoms». Thus, the design of the future privatization should also take into account the elements of the historical privatization part, which began with the recognition of Ukraine’s independence and is regulated by the provisions of the Decree of the President of Ukraine «On the procedure for allocating lands transferred to collective ownership to agricultural enterprises and organizations» dated August 8, 1995 No. 720, which are still in force today remain relevant in view of today’s challenges (focusing on threats to food security) and sometimes require the intervention of regulatory and law enforcement agencies, since without the past there is no future.

Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria

BackgroundAscetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea.ResultsUsing a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12–36 Mb) and gene-sparse (~ 2300–5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70–90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group.ConclusionsWe present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.

REGIONAL PRODUCTION PROFILE AND SUSTAINABILITY: CASE STUDY OF PORTUGAL

Objective: The study of Portugal's productive profile, at the level of the NUT III regions and on an evolutionary basis, in order to obtain a picture of the country at two different times 20 years apart. We also sought to establish a relationship between these profiles and productivity. Theoretical Framework: Review of the literature on productive specialisation and development, as well as other empirical work already carried out. Method: Construction of location indicators for productive activities, regional specialisation and relational analysis with productivity indicators. The data used, namely GVA and Employment relating to 10 activity branches/25 NUT III, has been made available by STATISTICS PORTUGAL through request. Results and Discussion: The results show a profile of Portugal in which the primary sector predominates in the interior of northern Portugal and in Alentejo, the secondary sector in the north coast and in the centre, and the tertiary sector is strongly represented in Lisbon and Porto. This profile is associated with different productivities and in evolutive terms there are signs of some changes, but still not significant. Research Implications: The sustainability of regions depends, among others, on their productive profile. As a matter of fact it is the productive sector that generates income and employment, the key variables in the socioeconomic components of sustainability. The way in which economic activities are concentrated and in which agglomeration economies can be generated are factors that can influence this development. Originality/Value: Knowledge of the evolution of a country's productive profile and how activities with different productivities fit in could contribute to a more efficient policy of intelligent specialisation and guarantee a path to sustainable development.

Unveiling the vulnerability of the human abducens nerve: insights from comparative cranial base anatomy in mammals and primates.

The topographic anatomy of the abducens nerve has been the subject of research for more than 150 years. Although its vulnerability was initially attributed to its length, this hypothesis has largely lost prominence. Instead, attention has shifted toward its intricate anatomical relations along the cranial base. Contrary to the extensive anatomical and neurosurgical literature on abducens nerve anatomy in humans, its complex anatomy in other species has received less emphasis. The main question addressed here is why the human abducens nerve is predisposed to injury. Specifically, we aim to perform a comparative analysis of the basicranial pathway of the abducens nerve in mammals and primates. Our hypothesis links its vulnerability to cranial base flexion, particularly around the sphenooccipital synchondrosis. We examined the abducens nerve pathway in various mammals, including primates, humans (N = 40; 60% males; 40% females), and human fetuses (N = 5; 60% males; 40% females). The findings are presented at both the macroscopic and histological levels. To associate our findings with basicranial flexion, we measured the cranial base angles in the species included in this study and compared them to data in the available literature. Our findings show that the primitive state of the abducens nerve pathway follows a nearly flat (unflexed) cranial base from the pontomedullary sulcus to the superior orbital fissure. Only the gulfar segment, where the nerve passes through Dorello's canal, demonstrates some degree of variation. We present evidence indicating that the derived state of the abducens pathway, which is most pronounced in humans from an early stage of development, is characterized by following the significantly more flexed basicranium. Overall, the present study elucidates the evolutionary basis for the vulnerability of the abducens nerve, especially within its gulfar and cavernous segments, which are situated at the main synchondroses between the anterior, middle, and posterior cranial fossae-a unique anatomical relation exclusive to the abducens nerve. The principal differences between the pathways of this nerve and those of other cranial nerves are discussed. The findings suggest that the highly flexed human cranial base plays a pivotal role in the intricate anatomical relations and resulting vulnerability of the abducens nerve.

Evolutionary history and biological adaptation of Han Chinese people on the Mongolian Plateau

Complex demographic processes and natural selection pressures are critical to resolving patterns of the molecular genetic basis of adaptive traits or complex diseases. Recent ancient genome data allow us to trace how key traits evolved in different human populations over time, connecting ancient population history with disease susceptibility in western Eurasians. To fill this gap in eastern Eurasians and provide deep insights into the evolutionary history of the population-specific genetic basis of complex biological traits, we explored the evolutionary basis of adaptive traits in one integrative modern and ancient genomic database, including 225 out of 5583 genomes first reported here. We comprehensively characterized the demographic history and biological adaptation of Han Chinese individuals on the Mongolian Plateau based on the allele frequency spectrum and haplotype-resolved fragments. We found strong genetic homogeneity among geographically different Han populations from Inner Mongolia (IMH). We reconstructed their admixture models and demographic events, revealing that IMH had a close genetic relationship with ancient millet farmers and obtained additional gene flow from Altaic-speaking populations. The enrichment of selected candidate genes suggested that essential metabolism-related genes promoted the rapid adaptation of eastern Eurasians to ancient environmental shifts and dietary changes during agricultural innovations. Evolutionary trajectory reconstruction of metabolism-related genes of methylenetetrahydrofolate reductase (MTHFR) and fatty acid desaturase 1 (FADS1) suggested that ancient dietary shifts during the Neolithic transition period promoted the differentiated metabolic rate of folate and fatty acid. We revealed the polygenicity of biological adaptation traits and the pleiotropy of adaptive genes, indicating that complex recent polygenic adaptations, genetic interactions, and genotype–phenotype correlations have contributed to the genetic architecture of complex traits in eastern Eurasians.

Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction.

Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.

A fitness landscape instability governs the morphological diversity of tip-growing cells

Cellular morphology affects many aspects of cellular and organismal physiology. This makes it challenging to dissect the evolutionary basis for specific morphologies since various cellular functions may exert competing selective pressures on this trait, and the influence of these pressures will depend on the specific mechanisms of morphogenesis. In this light, we combined experiment and theory to investigate the complex basis for morphological diversity among tip-growing cells from across the tree of life. We discovered that an instability in the widespread mechanism of "inflationary" tip growth leads directly to a bifurcation in the common fitness landscape of tip-growing cells, which imposes a strict global constraint on their morphologies. This result rationalizes the morphology of an enormous diversity of important fungal, plant, protistan, and bacterial systems. More broadly, our study elucidates the principle that strong evolutionary constraints on complex traits, like biological form, may emerge from emergent instabilities within developmental systems.

Decryption of the survival "black box": gene family expansion promotes the encystment in ciliated protists.

Encystment is an important survival strategy extensively employed by microbial organisms to survive unfavorable conditions. Single-celled ciliated protists (ciliates) are popular model eukaryotes for studying encystment, whereby these cells degenerate their ciliary structures and develop cyst walls, then reverse the process under more favorable conditions. However, to date, the evolutionary basis and mechanism for encystment in ciliates is largely unknown. With the rapid development of high-throughput sequencing technologies, genome sequencing and comparative genomics of ciliates have become effective methods to provide insights into above questions. Here, we profiled the MAC genome of Pseudourostyla cristata, a model hypotrich ciliate for encystment studies. Like other hypotrich MAC genomes, the P. cristata MAC genome is extremely fragmented with a single gene on most chromosomes, and encodes introns that are generally small and lack a conserved branch point for pre-mRNA splicing. Gene family expansion analyses indicate that multiple gene families involved in the encystment are expanded during the evolution of P. cristata. Furthermore, genomic comparisons with other five representative hypotrichs indicate that gene families of phosphorelay sensor kinase, which play a role in the two-component signal transduction system that is related to encystment, show significant expansion among all six hypotrichs. Additionally, cyst wall-related chitin synthase genes have experienced structural changes that increase them from single-exon to multi-exon genes during evolution. These genomic features potentially promote the encystment in hypotrichs and enhance their ability to survive in adverse environments during evolution. We systematically investigated the genomic structure of hypotrichs and key evolutionary phenomenon, gene family expansion, for encystment promotion in ciliates. In summary, our results provided insights into the evolutionary mechanism of encystment in ciliates.

The genomic and enzymatic basis for iridoid biosynthesis in cat thyme (Teucrium marum).

Iridoids are non-canonical monoterpenoids produced by both insects and plants. An example is the cat-attracting and insect-repelling volatile iridoid nepetalactone, produced by Nepeta sp. (catmint) and aphids. Recently, both nepetalactone biosynthetic pathways were elucidated, showing a remarkable convergent evolution. The iridoid, dolichodial, produced by Teucrium marum (cat thyme) and multiple insect species, has highly similar properties to nepetalactone but its biosynthetic origin remains unknown. We set out to determine the genomic, enzymatic, and evolutionary basis of iridoid biosynthesis in T. marum. First, we generated a de novo chromosome-scale genome assembly for T. marum using Oxford Nanopore Technologies long reads and proximity-by-ligation Hi-C reads. The 610.3 Mb assembly spans 15 pseudomolecules with a 32.9 Mb N50 scaffold size. This enabled identification of iridoid biosynthetic genes, whose roles were verified via activity assays. Phylogenomic analysis revealed that the evolutionary history of T. marum iridoid synthase, the iridoid scaffold-forming enzyme, is not orthologous to typical iridoid synthases but is derived from its conserved paralog. We discovered an enzymatic route from nepetalactol to diverse iridoids through the coupled activity of an iridoid oxidase cytochrome P450 and acetyltransferases, via an inferred acylated intermediate. This work provides a genomic resource for specialized metabolite research in mints and demonstration of the role of acetylation in T. marum iridoid diversity. This work will enable future biocatalytic or biosynthetic production of potent insect repellents, as well as comparative studies into iridoid biosynthesis in insects.

Genome evolution and divergence in cis-regulatory architecture is associated with condition-responsive development in horned dung beetles.

Phenotypic plasticity is thought to be an important driver of diversification and adaptation to environmental variation, yet the genomic mechanisms mediating plastic trait development and evolution remain poorly understood. The Scarabaeinae, or true dung beetles, are a species-rich clade of insects recognized for their highly diversified nutrition-responsive development including that of cephalic horns-evolutionarily novel, secondary sexual weapons that exhibit remarkable intra- and interspecific variation. Here, we investigate the evolutionary basis for horns as well as other key dung beetle traits via comparative genomic and developmental assays. We begin by presenting chromosome-level genome assemblies of three dung beetle species in the tribe Onthophagini (> 2500 extant species) including Onthophagus taurus, O. sagittarius, and Digitonthophagus gazella. Comparing these assemblies to those of seven other species across the order Coleoptera identifies evolutionary changes in coding sequence associated with metabolic regulation of plasticity and metamorphosis. We then contrast chromatin accessibility in developing head horn tissues of high- and low-nutrition O. taurus males and females and identify distinct cis-regulatory architectures underlying nutrition- compared to sex-responsive development, including a large proportion of recently evolved regulatory elements sensitive to horn morph determination. Binding motifs of known and new candidate transcription factors are enriched in these nutrition-responsive open chromatin regions. Our work highlights the importance of chromatin state regulation in mediating the development and evolution of plastic traits, demonstrates gene networks are highly evolvable transducers of environmental and genetic signals, and provides new reference-quality genomes for three species that will bolster future developmental, ecological, and evolutionary studies of this insect group.

The Roots of Science, Technology, Engineering, and Mathematics: What Are the Evolutionary and Neural Bases of Human Mathematics and Technology?

Introduction: Neural exaptations represent descent via transitions to novel neural functions. A primary transition in human cognitive and neural evolution was from a predominantly socially oriented primate brain to a brain that also instantiates and subserves science, technology, and engineering, all of which depend on mathematics. Upon what neural substrates and upon what evolved cognitive mechanisms did human capacities for science, technology, engineering, and mathematics (STEM), and especially its mathematical underpinnings, emerge? Previous theory focuses on roles for tools, language, and arithmetic in the cognitive origins of STEM, but none of these factors appears sufficient to support the transition. Methods: In this article, I describe and evaluate a novel hypothesis for the neural origins and substrates of STEM-based cognition: that they are based in human kinship systems and human maximizing of inclusive fitness. Results: The main evidence for this hypothesis is threefold. First, as demonstrated by anthropologists, human kinship systems exhibit complex mathematical and geometrical structures that function under sets of explicit rules, and such systems and rules pervade and organize all human cultures. Second, human kinship underlies the core algebraic mechanism of evolution, maximization of inclusive fitness, quantified as personal reproduction plus the sum of all effects on reproduction of others, each multiplied by their coefficient of relatedness to self. This is the only “natural” equation expected to be represented in the human brain. Third, functional imaging studies show that kinship-related cognition activates frontal-parietal regions that are also activated in STEM-related tasks. In turn, the decision-making that integrates kinship levels with costs and benefits from alternative behaviors has recently been shown to recruit the lateral septum, a hub region that combines internal (from the prefrontal cortex, amygdala, and other regions) and external information relevant to social behavior, using a dedicated subsystem of neurons specific to kinship. Conclusions: Taken together, these lines of evidence suggest that kinship systems and kin-associated behaviors may represent exaptations for the origin of human STEM.