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PubMed2005

Evolution of the morphological innovations of feathers.

Feathers are complex assemblages of multiple morphological innovations. Recent research on the development and evolution of feathers has produced new insights into the origin and diversification of the morphological innovations in feathers. In this article, I review and discuss the contribution of three different factors to the evolution of morphological innovations in feathers: feather tubularity, hierarchical morphological modularity, and the co-option molecular signaling modules. The developing feather germ is a tube of epidermis with a central dermal pulp. The tubular organization of the feather germ and follicle produces multiple axes over which morphological differentiation can be organized. Feather complexity is organized into a hierarchy of morphological modules. These morphological modules evolved through the innovative differentiation along multiple different morphological axes created by the tubular feather germ. Concurrently, many of the morphological innovations of feathers evolved through the evolutionary co-option of plesiomorphic molecular signaling modules. Gene co-option also reveals a role for contingency in the evolution of hierarchical morphological innovations.

Animals↗
PubMed2005

An alternative approach for neural network evolution with a genetic algorithm: crossover by combinatorial optimization.

In this work we present a new approach to crossover operator in the genetic evolution of neural networks. The most widely used evolutionary computation paradigm for neural network evolution is evolutionary programming. This paradigm is usually preferred due to the problems caused by the application of crossover to neural network evolution. However, crossover is the most innovative operator within the field of evolutionary computation. One of the most notorious problems with the application of crossover to neural networks is known as the permutation problem. This problem occurs due to the fact that the same network can be represented in a genetic coding by many different codifications. Our approach modifies the standard crossover operator taking into account the special features of the individuals to be mated. We present a new model for mating individuals that considers the structure of the hidden layer and redefines the crossover operator. As each hidden node represents a non-linear projection of the input variables, we approach the crossover as a problem on combinatorial optimization. We can formulate the problem as the extraction of a subset of near-optimal projections to create the hidden layer of the new network. This new approach is compared to a classical crossover in 25 real-world problems with an excellent performance. Moreover, the networks obtained are much smaller than those obtained with classical crossover operator.

Algorithms↗
PubMed2005

Maternal expression relaxes constraint on innovation of the anterior determinant, bicoid.

The origin of evolutionary novelty is believed to involve both positive selection and relaxed developmental constraint. In flies, the redesign of anterior patterning during embryogenesis is a major developmental innovation and the rapidly evolving Hox gene, bicoid (bcd), plays a critical role. We report evidence for relaxation of selective constraint acting on bicoid as a result of its maternal pattern of gene expression. Evolutionary theory predicts 2-fold greater sequence diversity for maternal effect genes than for zygotically expressed genes, because natural selection is only half as effective acting on autosomal genes expressed in one sex as it is on genes expressed in both sexes. We sample an individual from ten populations of Drosophila melanogaster and nine populations of D. simulans for polymorphism in the tandem gene duplicates bcd, which is maternally expressed, and zerknüllt (zen), which is zygotically expressed. In both species, we find the ratio of bcd to zen nucleotide diversity to be two or more in the coding regions but one in the noncoding regions, providing the first quantitative support for the theoretical prediction of relaxed selective constraint on maternal-effect genes resulting from sex-limited expression. Our results suggest that the accelerated rate of evolution observed for bcd is owing, at least partly, to variation generated by relaxed selective constraint.

Animals↗
PubMed2004

Memetic algorithms for the unconstrained binary quadratic programming problem.

This paper presents a memetic algorithm, a highly effective evolutionary algorithm incorporating local search for solving the unconstrained binary quadratic programming problem (BQP). To justify the approach, a fitness landscape analysis is conducted experimentally for several instances of the BQP. The results of the analysis show that recombination-based variation operators are well suited for the evolutionary algorithms with local search. Therefore, the proposed approach includes--besides a highly effective randomized k-opt local search--a new variation operator that has been tailored specially for the application in the hybrid evolutionary framework. The operator is called innovative variation and is fundamentally different from traditional crossover operators, since new genetic material is included in the offspring which is not contained in one of the parents. The evolutionary heuristic is tested on 35 publicly available BQP instances, and it is shown experimentally that the algorithm is capable of finding best-known solutions to large BQPs in a short time and with a high frequency. In comparison to other approaches for the BQP, the approach appears to be much more effective, particularly for large instances of 1000 or 2500 binary variables.

Algorithms↗
PubMed2003

Cephalopod Hox genes and the origin of morphological novelties.

Cephalopods are a diverse group of highly derived molluscs, including nautiluses, squids, octopuses and cuttlefish. Evolution of the cephalopod body plan from a monoplacophoran-like ancestor entailed the origin of several key morphological innovations contributing to their impressive evolutionary success. Recruitment of regulatory genes, or even pre-existing regulatory networks, may be a common genetic mechanism for generating new structures. Hox genes encode a family of transcriptional regulatory proteins with a highly conserved role in axial patterning in bilaterians; however, examples highlighting the importance of Hox gene recruitment for new developmental functions are also known. Here we examined developmental expression patterns for eight out of nine Hox genes in the Hawaiian bobtail squid Euprymna scolopes, by whole-mount in situ hybridization. Our data show that Hox orthologues have been recruited multiple times and in many ways in the origin of new cephalopod structures. The manner in which these genes have been co-opted during cephalopod evolution provides insight to the nature of the molecular mechanisms driving morphological change in the Lophotrochozoa, a clade exhibiting the greatest diversity of body plans in the Metazoa.

Animals↗
PubMed2003

A computational model of symbiotic composition in evolutionary transitions.

Several of the major transitions in evolutionary history, such as the symbiogenic origin of eukaryotes from prokaryotes, share the feature that existing entities became the components of composite entities at a higher-level of organization. This composition of pre-adapted extant entities into a new whole is a fundamentally different source of variation from the gradual accumulation of small random variations, and it has some interesting consequences for issues of evolvability. Intuitively, the pre-adaptation of sets of features in reproductively independent specialists suggests a form of 'divide and conquer' decomposition of the adaptive domain. Moreover, the compositions resulting from one level may become the components for compositions at the next level, thus scaling-up the variation mechanism. In this paper, we explore and develop these concepts using a simple abstract model of symbiotic composition to examine its impact on evolvability. To exemplify the adaptive capacity of the composition model, we employ a scale-invariant fitness landscape exhibiting significant ruggedness at all scales. Whilst innovation by mutation and by conventional evolutionary algorithms becomes increasingly more difficult as evolution continues in this landscape, innovation by composition is not impeded as it discovers and assembles component entities through successive hierarchical levels.

Adaptation, Physiological↗
PubMed2026

Venomous Lepidoptera: defensive toxin systems, venom composition, and clinical significance.

Venomous Lepidoptera constitute an underrecognized yet medically significant group of toxin-producing arthropods that employ contact-mediated defensive envenomation through specialized integumentary structures such as setae, spines, and scoli. Unlike actively stinging arthropods, these insects deliver venom passively upon contact, eliciting a diverse spectrum of clinical manifestations collectively termed lepidopterism. Clinical outcomes range from localized pain and dermatitis to severe systemic effects, including hemorrhagic syndromes, complement activation, and chronic inflammatory disorders. Recent advances in proteomic and transcriptomic technologies have transformed our understanding of lepidopteran venoms, revealing unexpectedly complex toxin repertoires comprising serine proteases, phospholipases, pore-forming proteins, disulfide-rich peptides, neuroactive RF-amide peptides, and immune-modulating components. These findings have provided new insights into the molecular basis of toxicity, host-pathogen interactions, and the evolutionary diversification of venom systems within Lepidoptera. This review synthesizes current knowledge on the morphology of venom-delivery structures, venom composition, mechanisms of action, and associated clinical manifestations, while highlighting medically important taxa, particularly species of the genus Lonomia. The successful development of antivenom against Lonomia envenomation underscores the translational relevance of lepidopteran toxin research and its potential for therapeutic innovation. By integrating molecular, clinical, and evolutionary perspectives, this review repositions venomous Lepidoptera as a legitimate and important component of arthropod toxinology. Furthermore, it identifies critical methodological limitations and key knowledge gaps, providing a framework for future investigations aimed at advancing our understanding of toxin biology, immunopathology, and the development of novel biomedical applications.

Animals↗
PubMed2006

Exploiting protein structure data to explore the evolution of protein function and biological complexity.

New directions in biology are being driven by the complete sequencing of genomes, which has given us the protein repertoires of diverse organisms from all kingdoms of life. In tandem with this accumulation of sequence data, worldwide structural genomics initiatives, advanced by the development of improved technologies in X-ray crystallography and NMR, are expanding our knowledge of structural families and increasing our fold libraries. Methods for detecting remote sequence similarities have also been made more sensitive and this means that we can map domains from these structural families onto genome sequences to understand how these families are distributed throughout the genomes and reveal how they might influence the functional repertoires and biological complexities of the organisms. We have used robust protocols to assign sequences from completed genomes to domain structures in the CATH database, allowing up to 60% of domain sequences in these genomes, depending on the organism, to be assigned to a domain family of known structure. Analysis of the distribution of these families throughout bacterial genomes identified more than 300 universal families, some of which had expanded significantly in proportion to genome size. These highly expanded families are primarily involved in metabolism and regulation and appear to make major contributions to the functional repertoire and complexity of bacterial organisms. When comparisons are made across all kingdoms of life, we find a smaller set of universal domain families (approx. 140), of which families involved in protein biosynthesis are the largest conserved component. Analysis of the behaviour of other families reveals that some (e.g. those involved in metabolism, regulation) have remained highly innovative during evolution, making it harder to trace their evolutionary ancestry. Structural analyses of metabolic families provide some insights into the mechanisms of functional innovation, which include changes in domain partnerships and significant structural embellishments leading to modulation of active sites and protein interactions.

Algorithms↗
PubMed2002

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms: Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translation-arrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids; flagellar shaft of glycoprotein, not flagellin; DNA-binding protein lob; specially modified tRNA; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution: the fact that, during major evolutionary transformations, some organismal characters are highly innovative and change remarkably swiftly, whereas others are largely static, remaining conservatively ancestral in nature. This phenotypic mosaicism creates character distributions among taxa that are puzzling to those mistakenly expecting uniform evolutionary rates among characters and lineages. The mixture of novel (neomuran or archaebacterial) and ancestral eubacteria-like characters in archaebacteria primarily reflects such vertical mosaic evolution, not chimaeric evolution by lateral gene transfer. No symbiogenesis occurred. Quantum evolution of the basic neomuran characters, and between sister paralogues in gene duplication trees, makes many sequence trees exaggerate greatly the apparent age of archaebacteria. Fossil evidence is compelling for the extreme antiquity of eubacteria [over 3500 million years (My)] but, like their eukaryote sisters, archaebacteria probably arose only 850 My ago. Negibacteria are the most ancient, radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria.

Archaea↗
PubMed2004

Exploiting human--fish genome comparisons for deciphering gene regulation.

Comparative genomics has served as an essential guide in the identification of functional coding and non-coding sequences in vertebrate genomes. Human-mouse pair-wise comparisons have limited utility for identifying functional conserved non-coding sequences, owing to the large number of sequences shared between these species. In searching for more stringent filters to uncover non-coding elements more likely to be of functional importance in the human genome, human-fish sequence comparisons have emerged as an important strategy, leading to the efficient identification of enhancer elements. These sequences are unevenly distributed in the genome, tending to cluster around genes involved in key developmental processes, with recent studies suggesting that they represent genomic segments in which sequence variation can result in morphological changes and innovation. These elements, conserved over long evolutionary time, emerge as primary candidates that are likely to harbor sequence variation contributing to susceptibility of human disease phenotypes.

Animals↗
PubMed2005

Conserved versus innovative features in animal body organization.

The origin of evolutionary novelties is a central topic in evolutionary developmental biology (evo-devo) studies. In any new feature, there is a conserved component that is either structural or related to the underlying genetic control, but it is not always obvious what is really new and what is conserved. Nevertheless, disentangling this blending of old and new features is basic to understanding mechanisms of evolutionary change. The origin of arthropod appendages illustrates the complexity in tracing the origin of evolutionary novelties. At the base of the lineage, the main body axis was already segmented and antero-posteriorly patterned, and the genetic tool kit required to form lateral outgrowths was already available. The novelty was possibly the developmental decision to "read" the available axial information and to exploit it for differentiating segmentally patterned and axially segmented appendages. Some important novelties bridge the gap between what have been traditionally distinguished as systemic and local changes. For example, the origin of the body cavities evolved by several animal groups may have been initiated by simple changes in cell-to-cell adhesive properties. Any possible change in an existing ontogenetic pathway has the potential to generate novelties.

Animals↗
PubMed2025

SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution.

The reconstruction of human evolutionary history has undergone repeated advances, each made possible by methodological innovations. In recent decades, genetic and genomic data played a central role in the reconstruction of major evolutionary events such as the out-of-Africa migration, and genetic simulations of human evolutionary history have come to play a major role in testing more specific hypotheses including proposed patterns of migration and admixture with archaic hominins. Increasing computational power has allowed human evolutionary history to be modeled at ever-larger scales, but simulations that encompass the complete human genome, including sex chromosomes and mitochondrial DNA, have been difficult due to the lack of support for whole-genome models in commonly used evolutionary simulation frameworks. With the recent introduction of SLiM 5 such simulations are now straightforward to construct, allowing the easy simulation of humans at whole-genome scale under different demographic models and evolutionary dynamics. We here present three versions of a reusable, customizable, open-source SLiM 5 model for simulating the molecular evolution of the full human genome. We also show some simple analyses of results from the model, to illustrate its utility. We hope this model, which we have nicknamed "SimHumanity" in jest, will facilitate further progress in the field of human evolutionary simulations.

SLiM↗
PubMed2026

The convergent evolution of the pelvic suction cup: A unique key innovation in spiny-finned fishes.

Key innovations open ecological opportunities and can redirect evolutionary trajectories. In spiny-finned fishes, the pelvic suction cup-a fused adhesive structure formed from the pelvic fins and supported by a modified girdle-appears to be one such trait. Using a novel 960-species phylogeny spanning 940 exons and 67 newly sequenced snailfish genomes, we show that the suction cup evolved independently three times across lineages separated by over 100 million years. By enabling adhesion in high-energy habitats such as tide pools and waterfalls, the suction cup set the stage for body depression and accompanying shifts in scales, teeth, and clade-specific ecofunctional profiles. Comparative analyses reveal convergence in a distinctive region of morphospace and body-shape evolution accelerated two- to fivefold. Diversification analyses uncover heterogeneous but elevated rates, with a clear burst in rock-climbing gobies associated with suction cup evolution. By opening novel habitats and fostering phenotypic novelty, the suction cup emerges as a key innovation that reshaped spiny-finned fish evolution.

Animals↗
PubMed2005

Consideration of the neural crest and its skeletal derivatives in the context of novelty/innovation.

I examine the neural crest and skeletal tissues derived from neural crest cells in the context of novelty/innovation by asking whether the neural crest is a novel tissue and whether the evolutionary origin of the neural crest required innovative developmental processes. As a vertebrate autapomorphy, the neural crest is a novel structure. I equate novelty with innovation and take a hierarchical approach. Some other workers separate the two, using novelty for new structures not found in an ancestor and not homologous with a feature in an ancestor, and innovation for the new processes required to generate the novel structure. While development clearly evolves, I do not separate those processes that result in the production of novel features from those that lead to change in existing structures, whether that change is a transition or transformation from one homologous feature to another (fins-->tetrapod limbs or locomotory appendages-->crustacean maxilliped feeding appendages). The existence of novelties causes us to consider the concept of latent homology. Neural crest cells form cartilage, dentine and bone. Cartilage is found in invertebrates and so is not a vertebrate innovation. No invertebrate cartilage mineralizes in vivo, although some can be induced to mineralize in vitro. Mineralization of cartilage in vivo is a vertebrate innovation. Dentine is a novel tissue that only forms from neural crest cells. Bone is a vertebrate innovation but not one exclusive to the neural crest. The developmental processes responsible for the neural crest and for these skeletal tissues did not arise de novo with the vertebrates. Novelty/innovation results from tinkering with existing processes, from the flexibility that arises from modifications of existing gene networks, and from the selective advantage provided by gene duplications or modifications.

Animals↗
PubMed2002

Bioactive components in milk.

Milk is the only biomaterial that evolved under the Darwinian selective pressure to nourish growing mammals. The purpose of this article is to review the scientific research that is using new techniques of integrating biological sequence, structure and function, to understand the innovative biology underlying the products of that evolutionary pressure. As it emerges that milk is actively communicating between the maternal mammary epithelia and the infant's gastrointestinal system, actively directing and educating the immune, metabolic and microflora systems within the infant, enhancing nutrient absorption and delivery, and conferring multiple means of protection, nutritionists are gaining a host of new molecular targets towards which to build scientific strategies for future foods and clinical applications. As new components and functions are being discovered in milk by using traditional methods and modern genomic tools, the complexities of demonstrating, and particularly in humans, the functional mechanisms behind milk's newly observed physiological benefits are becoming the next challenge of this rapidly growing field.

Animals↗
PubMed2006

Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice.

In Arabidopsis, tandemly arrayed genes (TAGs) comprise >10% of the genes in the genome. These duplicated genes represent a rich template for genetic innovation, but little is known of the evolutionary forces governing their generation and maintenance. Here we compare the organization and evolution of TAGs between Arabidopsis and rice, two plant genomes that diverged ~150 million years ago. TAGs from the two genomes are similar in a number of respects, including the proportion of genes that are tandemly arrayed, the number of genes within an array, the number of tandem arrays, and the dearth of TAGs relative to single copy genes in centromeric regions. Analysis of recombination rates along rice chromosomes confirms a positive correlation between the occurrence of TAGs and recombination rate, as found in Arabidopsis. TAGs are also biased functionally relative to duplicated, nontandemly arrayed genes. In both genomes, TAGs are enriched for genes that encode membrane proteins and function in "abiotic and biotic stress" but underrepresented for genes involved in transcription and DNA or RNA binding functions. We speculate that these observations reflect an evolutionary trend in which successful tandem duplication involves genes either at the end of biochemical pathways or in flexible steps in a pathway, for which fluctuation in copy number is unlikely to affect downstream genes. Despite differences in the age distribution of tandem arrays, the striking similarities between rice and Arabidopsis indicate similar mechanisms of TAG generation and maintenance.

Arabidopsis↗
PubMed2005

Origin and rapid diversification of a tropical moss.

Molecular sequences rarely evolve at a constant rate. Yet, even in instances where a clock can be assumed or approximated for a particular set of sequences, fossils or clear patterns of vicariance are rarely available to calibrate the clock. Thus, obtaining absolute timing for diversification of natural lineages can prove difficult. Unfortunately, without absolute time we cannot develop a complete understanding of important evolutionary processes, including adaptive radiations and key innovations. In the present study, the coding sequence of the nuclear gene, glyceraldehyde 3-phosphate dehydrogenase (gpd), extracted from the paleotropical moss, Mitthyridium, was found to exhibit clocklike behavior and used to reconstruct the history of 80 distinct molecular lineages that cover the full geographic range of Mitthyridium. Two separate clades endemic to two geographically distinct oceanic archipelagos were revealed by this phylogenetic analysis. This allowed the use of island age (as derived from potassium-argon dating) as a maximum age of origin of each monophyletic group, providing two independent time anchors for the clock found in gpd, the final piece needed to study absolute time. Based on results from both maximum age calibrations, which separately yielded highly consistent estimates, the ancestor of this moss group arose approximately 8 million years ago, and then diversified at the rapid rate of 0.56 +/- 0.004 new lineages per million years. Such a rate is on par with the highest diversification rates reported in the literature including rapidly radiating insular groups like the Hawaiian silversword alliance, a classic example of an adaptive radiation. Using independent sources of data, it was found that neither the age nor diversification estimates were affected by the use of molecular lineages rather than species as the operational taxonomic units. Identifying the cause for this rapid diversification requires further testing, but it appears to be related to a general shift in reproductive strategy from sexual to asexual, which may be a key innovation for this young group.

Asia, Southeastern↗
PubMed2006

Formation of the Arabidopsis pentatricopeptide repeat family.

In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus.

Arabidopsis↗