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PubMed2026

A spatiotemporal resolution to genetic redundancy: MIR164 diversification coordinates development and metabolism in Brassica.

Whole-genome duplication (WGD) events create genetic redundancy, posing the evolutionary challenge of how paralogs escape functional overlap to drive innovation. Here, we demonstrate that the MIR164 family in Brassica oleracea resolves this redundancy through spatiotemporal niche partitioning. Following WGD, the family expanded to eight members, which subsequently underwent divergent selection-some preserved under purifying selection, while others showed signals of positive selection. This led to expression divergence, with Bol-MIR164a1 emerging as a key universally expressed paralog. CRISPR-Cas9 mutagenesis of Bol-MIR164a1 revealed its essential role in coordinating two pivotal traits: leaf serration and leaf coloration. Mutants exhibited enhanced leaf serration due to spatial deregulation of CUC2 at organ boundaries, concurrently with yellow-green leaves and elevated flavonoid accumulation. We mechanistically linked the metabolic phenotype to direct transactivation of the anthocyanidin reductase (ANR) promoter by NAC100, alongside its upregulation of chlorophyll catabolism genes. Our findings establish a paradigm in which spatial segregation of target gene expression domains enables a single, widely expressed miRNA paralog to resolve genetic redundancy by independently orchestrating distinct regulatory programs. This provides a fundamental framework for understanding complex trait evolution in polyploids. This allows a single miRNA locus to independently orchestrate both morphological patterning and metabolic programming, providing a fundamental framework for understanding complex trait evolution in polyploid crops.

MicroRNAs↗
PubMed2005

The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure.

BACKGROUND: The origin of the nuclear compartment has been extensively debated, leading to several alternative views on the evolution of the eukaryotic nucleus. Until recently, too little phylogenetic information was available to address this issue by using multiple characters for many lineages. RESULTS: We analyzed 65 proteins integral to or associated with the nuclear pore complex (NPC), including all the identified nucleoporins, the components of their anchoring system and some of their main partners. We used reconstruction of ancestral sequences of these proteins to expand the detection of homologs, and showed that the majority of them, present all over the nuclear pore structure, share homologs in all extant eukaryotic lineages. The anchoring system, by contrast, is analogous between the different eukaryotic lineages and is thus a relatively recent innovation. We also showed the existence of high heterogeneity of evolutionary rates between these proteins, as well as between and within lineages. We show that the ubiquitous genes of the nuclear pore structure are not strongly conserved at the sequence level, and that only their domains are relatively well preserved. CONCLUSION: We propose that an NPC very similar to the extant one was already present in at least the last common ancestor of all extant eukaryotes and it would not have undergone major changes since its early origin. Importantly, we observe that sequences and structures obey two very different tempos of evolution. We suggest that, despite strong constraints that froze the structural evolution of the nuclear pore, the NPC is still highly adaptive, modern, and flexible at the sequence level.

Adaptation, Physiological↗
PubMed2006

New species in evolving networks--stochastic theory of sensitive networks and applications on the metaphorical level.

In this paper we develop a theory to describe stochastic influences on the fate of new species with non-linear growth rates in evolutionary processes. We develop a theoretical framework based on notions of species, network, innovation, competition, survival and fitness. We introduce a stochastic picture describing the role of fluctuations in the survival of new species in non-linear systems. In particular we consider the fate of new species with non-linear growth. As an application of the general model framework we consider the fate of 'rare species' in early biological evolution. We show that hypercycle systems do not represent the end of the evolutionary process as they may evolve further in small niches. This has implications for different types of applications ranging from biological systems on one level to socio-technological systems on a more metaphoric level.

Biological Evolution↗
PubMed2006

FAST and the arms race: the interaction of group aggression and the families and schools together program in the aggressive and delinquent behaviors of inner-city elementary school students.

This study applies a multi-player arms race model to peer contagion in the aggressive and delinquent behaviors of inner-city elementary school students. Because this model of peer contagion differs from the usual model based on positive reinforcement of delinquent behavior, it raises the possibility that the persistent finding of iatrogenic effects of group treatment might not apply to group treatment of elementary school children if the possibility of aggressive behavior in the group is limited. One way of limiting aggressive behavior is to include parents in the groups. The study therefore applies the model to groups of elementary school students assigned to Families and Schools Together (FAST; a group treatment that includes parental participation) or to an intervention focused on individual families. The model effectively describes the relationship between group averages of aggressive behavior in the classroom and aggressive and delinquent behavior outside the classroom for those students assigned to the individual intervention. The model fits those children assigned to FAST less well, suggesting that FAST may make it less likely that aggressive and delinquent behavior is generalized outside of aggressive classroom settings. Editors' Strategic Implications: The authors draw on evolutionary biology, developmental psychology, sociology, and learning theory to present an innovative prevention model and test the promising FAST program. Using longitudinal data from 403 children, their parents, and their teachers, the authors describe how FAST may interfere with the process of escalating aggression.

Aggression↗
PubMedDate not supplied

Differential regulation of msx genes in the development of the gonopodium, an intromittent organ, and of the "sword," a sexually selected trait of swordtail fishes (Xiphophorus).

The possession of a conspicuous extension of colored ventral rays of the caudal fin in male fish of swordtails (genus Xiphophorus) is a prominent example for a trait that evolved by sexual selection. To understand the evolutionary history of this so-called sword molecularly, it is of interest to unravel the developmental pathways responsible for extended growth of sword rays during development of swordtail males. We isolated two msx genes and showed that they are differentially regulated during sword outgrowth. During sword growth in juvenile males, as well as during testosterone-induced sword development and fin ray regeneration in the sword after amputation, expression of msxC is markedly up-regulated in the sword forming fin rays. In contrast, msxE/1 is not differentially expressed in ventral and dorsal male fin rays, suggesting a link between the development of male secondary sexual characters in fins and up-regulation of msxC expression. In addition, we showed that msx gene expression patterns differ significantly between Xiphophorus and zebrafish. We also included in our study the gonopodium, a testosterone-dependent anal fin modification that serves as a fertilization organ in males of live-bearing fishes. Our finding that increased levels of msxC expression are associated with the testosterone-induced outgrowth of the gonopodium might suggest either that at least parts of the signaling pathways that pattern the evolutionary older gonopodium have been coopted to evolve a sexually selected innovation such as the sword or that increased msxC expression may be inherent to the growth process of long fin rays in general.

Amino Acid Sequence↗
PubMed2001

The origin and evolution of the woolly mammoth.

The mammoth lineage provides an example of rapid adaptive evolution in response to the changing environments of the Pleistocene. Using well-dated samples from across the mammoth's Eurasian range, we document geographical and chronological variation in adaptive morphology. This work illustrates an incremental (if mosaic) evolutionary sequence but also reveals a complex interplay of local morphological innovation, migration, and extirpation in the origin and evolution of a mammalian species. In particular, northeastern Siberia is identified as an area of successive allopatric innovations that apparently spread to Europe, where they contributed to a complex pattern of stasis, replacement, and transformation.

Africa↗
PubMed2001

Origin and evolution of the neural crest: a hypothetical reconstruction of its evolutionary history.

The neural crest has long been regarded as one of the key novelties in vertebrate evolutionary history. Indeed, the vertebrate characteristic of a finely patterned craniofacial structure is intimately related to the neural crest. It has been thought that protochordates lacked neural crest counterparts. However, recent identification and characterization of protochordate genes such as Pax3/7, Dlx and BMP family members challenge this idea, because their expression patterns suggest remarkable similarity between the vertebrate neural crest and the ascidian dorsal midline epidermis, which gives rise to both epidermal cells and sensory neurons. The present paper proposes that the neural crest is not a novel vertebrate cell population, but may have originated from the protochordate dorsal midline epidermis. Therefore, the evolution of the vertebrate neural crest should be reconsidered in terms of new cell properties such as pluripotency, delamination-migration and the carriage of an anteroposterior positional value, key innovations leading to development of the complex craniofacial structure in vertebrates. Molecular evolutionary events involved in the acquisitions of these new cell properties are also discussed. Genome duplications during early vertebrate evolution may have played an important role in allowing delamination of the neural crest cells. The new regulatory mechanism of Hox genes in the neural crest is postulated to have developed through the acquisition of new roles by coactivators involved in retinoic acid signaling.

Animals↗
PubMed2004

Molecular phylogeny and morphological change in the Psittacula parakeets.

We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that extends from the chin to the cheek. We examine the extent of sexual dimorphism in tail length across the phylogeny and reveal large differences between closely related forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. An ancestral Psittacula form appears to have evolved during the late Miocene-early Pliocene (3.4-9.7MYA), a time when regional geological processes on the Asian continent may have promoted subsequent diversity at the species level, and many forms diverged relatively early on in the evolutionary history of Psittacula (between 2.5 and 7.7MYA). However, others, such as the derbyan and moustached parakeets, diverged as recently as 0.2MYA. Our phylogeny also suggests that the echo parakeet from Mauritius diverged from the Indian ringneck parakeet as opposed to the African ringneck, and may have done so relatively recently. The molecular results indicate support for a southwards radiation from India across the Indian Ocean to Mauritius, where the arrival-date of the echo parakeet appears consistent with the island's volcanic formation.

Africa↗
PubMed2005

Horizontal gene transfer, genome innovation and evolution.

To what extent is the tree of life the best representation of the evolutionary history of microorganisms? Recent work has shown that, among sets of prokaryotic genomes in which most homologous genes show extremely low sequence divergence, gene content can vary enormously, implying that those genes that are variably present or absent are frequently horizontally transferred. Traditionally, successful horizontal gene transfer was assumed to provide a selective advantage to either the host or the gene itself, but could horizontally transferred genes be neutral or nearly neutral? We suggest that for many prokaryotes, the boundaries between species are fuzzy, and therefore the principles of population genetics must be broadened so that they can be applied to higher taxonomic categories.

Evolution, Molecular↗
PubMed1985

Climacteric in women: an evolutionary defect?

This is a theoretical paper. Climacteric in women has two basic consequences: (i) Sterility, which is interpreted here as a positive feature, because it protects the older woman from the hardships of pregnancy. (ii) Hormonal deficiency, which is interpreted here as a negative feature, because it leads to deleterious changes in various parts of the body. Can these negative features be regarded as evolutionary defects? The answer is no, if the following points are considered. Through human innovations, women's natural lifespan of less than 30 years has been extended to almost 80 years. Had the lifespan not been manipulated, most women would not reach climacteric, which normally does not begin before the fourth decade of life. When interpreting climacteric as a phenomenon precipitated by man rather then by Nature, it follows that the negative features of climacteric should not be regarded as evolutionary defects.

Adult↗
PubMed2001

Acne: a biopsychosocial and evolutionary perspective with a focus on shame.

PURPOSE: Hypotheses regarding the psychological factors implicated in the development and maintenance of acne first emerged in the middle of the eighteenth century. However, the psychodermatological literature from this date relating to acne has variously been described as confusing, overly prone to conjecture and, in particular, atheoretical. The current paper has two key objectives; first, to present a biopsychosocial model of acne development and maintenance and, secondly, to understand the psychosocial strain imposed by acne from an evolutionary perspective with a particular emphasis on body shame reactions. METHODS: The psychodermatological literature relating to acne is reviewed with the data analysed for potential biopsychosocial interactions and shame eliciting responses. RESULTS: The review indicates that acne can be reconceptualized as a biopsychosocial phenomena which, in turn, provides the field with innovative hypotheses for empirical inquiry and the potential for expanding and evaluating treatment options. The evolutionary analysis illustrates that acne provides the potential for distressing body shame reactions due to the skin disease's potential for damaging self-other evaluations of attractiveness. CONCLUSIONS: Acne has tended to be viewed as a minor dermatological complaint which imposes minimal psychological distress upon sufferers. The paper concludes that acne has the ability to elicit in some sufferers significant mental health concerns due to a heightened sense of shame relating to appearance.

Journal Article↗
PubMed2006

Predator-induced phenotypic plasticity in tadpoles: extension or innovation?

Phenotypic plasticity, the ability of a trait to change as a function of the environment, is central to many ideas in evolutionary biology. A special case of phenotypic plasticity observed in many organisms is mediated by their natural predators. Here, we used a predator-prey system of dragonfly larvae and tadpoles to determine if predator-mediated phenotypic plasticity provides a novel way of surviving in the presence of predators (an innovation) or if it represents a simple extension of the way noninduced tadpoles survive predation. Tadpoles of Limnodynastes peronii were raised in the presence and absence of predation, which then entered a survival experiment. Induced morphological traits, primarily tail height and tail muscle height, were found to be under selection, indicating that predator-mediated phenotypic plasticity may be adaptive. Although predator-induced animals survived better, the multivariate linear selection gradients were similar between the two tadpole groups, suggesting that predator-mediated phenotypic plasticity is an extension of existing survival strategies. In addition, nonlinear selection gradients indicated a cost of predator-induced plasticity that may limit the ability of phenotypic plasticity to enhance survival in the presence of predators.

Animals↗
PubMed2026

Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.

Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. However, the evolutionary trajectories and functional implications of these landscapes remain largely unexplored. Using chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis revealed that 56% of lineage-specific eRNAs originated from TE expansions, indicating that TEs serve as major reservoirs of species-specific regulatory innovation in cereals. Notably, we identified remarkable conservation in defense-related functions, root-specific expression, and TE-derived origins of eRNAs across both ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived, root-associated regulatory elements throughout Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibited pronounced root specificity and coordinated expression, suggesting targeted amplification and refinement of successful ancestral regulatory strategies established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our findings suggest that TE-mediated innovation of root-specific eRNAs may contribute to Triticeae adaptation and provide a foundational resource for exploiting regulatory variation in cereal crop breeding.

Enhancer RNAs↗
PubMed2005

Hemiascomycetous yeasts at the forefront of comparative genomics.

With more than a dozen species fully sequenced, as many as this partially sequenced, and more in development, yeasts are now used to explore the frontlines of comparative genomics of eukaryotes. Innovative procedures have been developed to compare and annotate genomes at various evolutionary distances, to identify short cis-acting regulatory elements, to map duplications, or to align syntenic blocks. Human and plant pathogens, in addition to yeasts that show a variety of interesting physiological properties, are included in this multidimensional comparative survey, which encompasses a very broad evolutionary range. As major steps of the evolutionary history of hemiascomycetous genomes emerge, precise questions on the general mechanisms of their evolution can be addressed, using both experimental and in silico methods.

Adaptation, Physiological↗
PubMed2004

Evolution of xylem lignification and hydrogel transport regulation.

In vascular plants, the polysaccharide-based walls of water-conducting cells are strengthened by impregnation with the polyphenolic polymer lignin. The fine-scale patterning of lignin deposition in water-conducting cells is shown here to vary phylogenetically across vascular plants. The extent to which water transport in xylem cells can be modified in response to changes in the ionic content of xylem sap also is shown to vary in correlation with variation in lignification patterns, consistent with the proposed mechanism for hydraulic response through size change of middle-lamella pectins. This covariation suggests that the fine-scale distribution of hydrophilic polysaccharides and hydrophobic lignin can affect hydraulic as well as mechanical properties, and that the evolutionary diversification of vascular cells thus reflects biochemical as well as morphological innovations evolved to fulfill opposing cell functions of transport and structural support.

Biological Evolution↗
PubMed2006

The genome of the sea urchin Strongylocentrotus purpuratus.

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Animals↗
PubMed2005

Brain size, innovative propensity and migratory behaviour in temperate Palaearctic birds.

The evolution of migration in birds remains an outstanding, unresolved question in evolutionary ecology. A particularly intriguing question is why individuals in some species have been selected to migrate, whereas in other species they have been selected to be sedentary. In this paper, we suggest that this diverging selection might partially result from differences among species in the behavioural flexibility of their responses to seasonal changes in the environment. This hypothesis is supported in a comparative analysis of Palaearctic passerines. First, resident species tend to rely more on innovative feeding behaviours in winter, when food is harder to find, than in other seasons. Second, species with larger brains, relative to their body size, and a higher propensity for innovative behaviours tend to be resident, while less flexible species tend to be migratory. Residence also appears to be less likely in species that occur in more northerly regions, exploit temporally available food sources, inhabit non-buffered habitats and have smaller bodies. Yet, the role of behavioural flexibility as a response to seasonal environments is largely independent of these other factors. Therefore, species with greater foraging flexibility seem to be able to cope with seasonal environments better, while less flexible species are forced to become migratory.

Analysis of Variance↗
PubMed2002

MalariaSphere: a greenhouse-enclosed simulation of a natural Anopheles gambiae (Diptera: Culicidae) ecosystem in western Kenya.

BACKGROUND: The development and implementation of innovative vector control strategies for malaria control in Africa requires in-depth ecological studies in contained semi-field environments. This particularly applies to the development and release of genetically-engineered vectors that are refractory to Plasmodium infection. Here we describe a modified greenhouse, designed to simulate a natural Anopheles gambiae Giles ecosystem, and the first successful trials to complete the life-cycle of this mosquito vector therein. METHODS: We constructed a local house, planted crops and created breeding sites to simulate the natural ecosystem of this vector in a screen-walled greenhouse, exposed to ambient climate conditions, in western Kenya. Using three different starting points for release (blood-fed females, virgin females and males, or eggs), we allowed subsequent stages of the life-cycle to proceed under close observation until one cycle was completed. RESULTS: Completion of the life-cycle was observed in all three trials, indicating that the major life-history behaviours (mating, sugar feeding, oviposition and host seeking) occurred successfully. CONCLUSION: The system described can be used to study the behavioural ecology of laboratory-reared and wild mosquitoes, and lends itself to contained studies on the stability of transgenes, fitness effects and phenotypic characteristics of genetically-engineered disease vectors. The extension of this approach, to enable continuous maintenance of successive and overlapping insect generations, should be prioritized. Semi-field systems represent a promising means to significantly enhance our understanding of the behavioural and evolutionary ecology of African malaria vectors and our ability to develop and evaluate innovative control strategies. With regard to genetically-modified mosquitoes, development of such systems is an essential prerequisite to full field releases.

Animals↗