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PubMed2006

"Evolutionist and missionary," The Reverend John Thomas Gulick (1832-1923). Part I: cumulative segregation--geographical isolation.

During the late 19th and early 20th centuries, the American missionary and naturalist John Thomas Gulick (1832-1923) was one of the most well-known and influential evolutionists, anticipating in his research and writing, later proposals of geographical isolation, population genetics, genetic drift, and the founder principle in speciation. In over 20 publications based on studies of non-adaptive geographical variation in several hundred species of snails in the genus Achatinella, collected in the valleys of Oahu in the Sandwich Islands (Hawaii), Gulick provided evidence for the formation of new species from varieties and the importance of geographical (non-adaptive) isolation in species diversification. Gulick's theory of the species-differentiating effects of isolation was regarded by many as a more complete theory of speciation than Darwin's, and by others as correcting a fundamental deficiency in Darwin's theory, namely how groups of organisms diversify one from another. Gulick also saw organisms as active participants in, and in interaction with, their environment, for which he coined the term coincident selection, anticipating the Baldwin effect/organic selection. With his concepts of cumulative segregation (geographical isolation), indiscriminate isolation (the Founder effect) and coincident selection (the Baldwin effect), we should recognize Gulick as one of the earliest and most original and innovative evolutionary biologists.

Animals↗
PubMed2006

Origin of dental occlusion in tetrapods: signal for terrestrial vertebrate evolution?

Evolutionary changes of the dentition in tetrapods can be associated with major events in the history of terrestrial vertebrates. Dental occlusion, the process by which teeth from the upper jaw come in contact with those in the lower jaw, appears first in the fossil record in amniotes and their close relatives near the Permo-Carboniferous boundary approximately 300 million years ago. This evolutionary innovation permitted a dramatic increase in the level of oral processing of food in these early tetrapods, and has been generally associated with herbivory. Whereas herbivory in extinct vertebrates is based on circumstantial evidence, dental occlusion provides direct evidence about feeding strategies because jaw movements can be reconstructed from the wear patterns of the teeth. Examination of the evolution of dental occlusion in Paleozoic tetrapods within a phylogenetic framework reveals that this innovation developed independently in several lineages of amniotes, and is represented by a wide range of dental and mandibular morphologies. Dental occlusion also developed within diadectomorphs, the sister taxon of amniotes. The independent, multiple acquisition of this feeding strategy represents an important signal in the evolution of complex terrestrial vertebrate communities, and the first steps in the profound changes in the pattern of trophic interactions in terrestrial ecosystems.

Animals↗
PubMed1996

When neural crest and placodes collide: interactions between melanophores and the lateral lines that generate stripes in the salamander Ambystoma tigrinum tigrinum (Ambystomatidae).

A prominent element of the early larval pigment pattern in the salamander Ambystoma tigrinum tigrinum (family Ambystomatidae) is a horizontal stripe over the lateral surface of the myotomes where otherwise abundant, neural crest-derived melanophores are not found. This study examines the formation of this "melanophore-free region". When the trunk lateral lines were ablated (by removing cranial lateral line placodes), the melanophore-free region did not form; instead, melanophores populated the middle of the flank and the distribution of yellow, neural chest-derived zanthophores was perturbed. Time-lapse videomicrography demonstrated that during normal development, the melanophore-free region is established because melanophores retreat from the midbody lateral line primordium as it migrates caudally along the inner side of the epidermis. Melanophores do not repopulate the middle of the flank after primordium migration and heterochronic grafting experiments suggest that extracellular factors contribute to maintaining the melanophore-free region during these later stages. Finally, photographic series, microsurgical manipulations, electron microscopy, and staining for molecules of the extracellular matrix (peanut agglutinin-binding components, tenascin, chondroitin sulfate proteoglycans, fibronectin, laminin) suggest that several factors contribute to establishing and maintaining the melanophore-free region, including steric effects of the lateral lines, interactions between melanophores and xanthophores, lateral line-dependent alterations of the subepidermal basement membrane, and a general elaboration of the extracellular matrix. Lateral line effects on melanophores are inferred to be a shared, ancestral feature of pigment pattern development for the families Ambystomatidae and Salamandridae (D.M. Parichy, Dev. Biol. 174, 265-282. 1996). The results of this study thus provide insights into a phylogenetically primitive mechanism for stripe formation, and a context for interpreting evolutionary innovations in pattern-forming mechanisms.

Ambystoma↗
PubMed1995

The origin of synergistic symbiosis.

A dominant theme in the history of life has been the evolutionary innovations of cooperative symbioses: the first genomes near the origin of life, integrated prokaryotic cells, the complex symbiotic communities that evolved into modern eukaryotic cells, lichens, mycorrhizae, and so on. In this paper, a model of cooperative symbiosis that shows a threshold condition for the evolution of cooperation is analyzed. The threshold is not easily passed, but cooperative evolution proceeds rapidly once a symbiosis overcomes the threshold. In the model presented here, each species has genetic variability for a symbiotic trait. The trait imposes a reproductive cost on its bearer but enhances the reproduction of its partner species. For example, in the origin of genetic systems, the trait may cause biochemical synergism for the rate of replication of primitive RNA strands as in Eigen and Schuster's hypercycle model. Models of growth are contrasted with synergism, which are most appropriate for the evolution of genetic systems and for mutualisms such as lichens, with the strategic and psychological applications of the Prisoner's Dilemma model.

Biological Evolution↗
PubMed1995

The tympanal hearing organ of a fly: phylogenetic analysis of its morphological origins.

A key adaptation for any parasitoid insect is the sensory modality that it uses to locate its host insect. All members of the speciose family Tachinidae (Diptera) are parasitoids, but only flies of the tribe Ormiini use acoustic cues to find their hosts. Ormiine flies are parasitoids of various genera of crickets and katydids. Gravid females of one ormiine species, Ormia ochracea, hear the reproductive calling song of male field crickets and home in on those calls to locate their hosts. While many flies possess various kinds of "ears" to detect airborne sounds, only ormiine flies have been reported to possess true tympanal hearing organs. Such organs are well-known to occur in their cricket and katydid hosts. The ormiine ear is an evolutionary innovation within Diptera. Our objective was to trace the phylogenetic origins of the tympanal hearing organ among higher flies. Since the ormiine hearing organ is a complex organ within the prothorax, we examined possible precursor structures in the prothoraces of selected Diptera. We have uncovered a suite of characters that define the ormiine ear. These characters in the prothorax include a pair of prosternal tympanal membranes, a pair of chordotonal sensory organs, and modifications of the tracheal system. We have been able to identify and trace the presumptive homologs of these ormiine characters through selected species of related Diptera, using the method of outgroup comparison.

Animals↗
PubMed1999

On the possibility of constructive neutral evolution.

The neutral theory often is presented as a theory of "noise" or silent changes at an isolated "molecular level," relevant to marking the steady pace of divergence, but not to the origin of biological structure, function, or complexity. Nevertheless, precisely these issues can be addressed in neutral models, such as those elaborated here with regard to scrambled ciliate genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate genes. All of these are instances of a more general scheme of "constructive neutral evolution" that invokes biased variation, epistatic interactions, and excess capacities to account for a complex series of steps giving rise to novel structures or operations. The directional and constructive outcomes of these models are due not to neutral allele fixations per se, but to these other factors. Neutral models of this type may help to clarify the poorly understood role of nonselective factors in evolutionary innovation and directionality.

Amino Acid Sequence↗
PubMed2001

First description of an apical epidermis cone in Paratenuisentis ambiguus (Acanthocephala: Eoacanthocephala) and its phylogenetic implications.

The proboscis apex of the eoacanthocephalan parasite Paratenuisentis ambiguus was studied, using electron and light microscopy, for a better understanding of the parasite's attachment at the intestinal wall of its definitive hosts (Anguilla rostrata and A. anguilla). The results suggest the presence of an epidermis cone with three nuclei at the proboscis apex of P. ambiguus instead of an apical sense organ, as has been previously supposed. Dendritic terminations, sensory nerves and secretory ducts were absent. The existence of many fibres suggests a mechanical function of the epidermis cone. Probably, it presses the proboscis apex and the anterior hooks into the intestinal wall of the definitive host. The presence of an epidermis cone in other eoacanthocephalan species can be derived from data in the literature. The absence of an epidermis cone outside the Eoacanthocephala suggests that it is an evolutionary innovation, supporting the monophyly of the Eoacanthocephala.

Acanthocephala↗
PubMed2002

Ontogenetic data and the evolutionary origin of the mammalian scapula.

One of the most useful diagnostic therian features is the division of the lateral surface of the scapula into two fossae separated by a scapular spine. A new model to describe this evolutionary innovation based on ontogenetic data is provided, consistent with information provided by recent fossil discoveries. The development of the scapula in three didelphid and one dasyurid marsupials using histological sections was studied. Only the ventral, acromial portion of the scapular spine, which originates from the anterior margin of the scapular blade, is preformed in cartilage. The major dorsal portion is formed at a later stage by appositional bone, which expands from the perichondral ossification of the scapula into an intermuscular aponeurosis between the supra-and infraspinatus muscles. This intermuscular aponeurosis inserts more or less in the middle of the lateral surface of the developing scapula. Thus, the floor of the supraspinous fossa is already present at the beginning of scapular development, simultaneous with the infraspinous fossa. The portion of the scapular spine that is situated dorsal to the acromial process is hypothesized to be a neomorphic structure of therians. The dorsal portion of the scapular spine evolved as additional attachment for powerful supraspinatus and infraspinatus muscles meeting near the middle of the lateral scapula.

Animals↗
PubMed2003

Isolation of a neurotoxin (alpha-colubritoxin) from a nonvenomous colubrid: evidence for early origin of venom in snakes.

The evolution of venom in advanced snakes has been a focus of long-standing interest. Here we provide the first complete amino acid sequence of a colubrid toxin, which we have called alpha-colubritoxin, isolated from the Asian ratsnake Coelognathus radiatus (formerly known as Elaphe radiata), an archetypal nonvenomous snake as sold in pet stores. This potent postsynaptic neurotoxin displays readily reversible, competitive antagonism at the nicotinic receptor. The toxin is homologous with, and phylogenetically rooted within, the three-finger toxins, previously thought unique to elapids, suggesting that this toxin family was recruited into the chemical arsenal of advanced snakes early in their evolutionary history. LC-MS analysis of venoms from most other advanced snake lineages revealed the widespread presence of components of the same molecular weight class, suggesting the ubiquity of three-finger toxins across advanced snakes, with the exclusion of Viperidae. These results support the role of venom as a key evolutionary innovation in the early diversification of advanced snakes and provide evidence that forces a fundamental rethink of the very concept of nonvenomous snake.

Amino Acid Sequence↗
PubMed2026

Regulatory Evolution and the Genetic Basis of Human Brain Expansion.

The evolution of the human brain is characterized by profound changes in structure and function, despite relatively limited divergence in protein-coding genes compared to other primates. This paradox has led to increasing recognition of gene regulatory elements (GREs) as primary drivers of evolutionary innovation. In this review, we synthesize current knowledge on the role of conserved noncoding elements (CNEs), human accelerated regions (HARs), and transposable element (TE)-derived sequences in shaping gene regulatory networks (GRNs) underlying brain development. Comparative analyses across humans and closely related primates, including the chimpanzee, gorilla, and orangutan, reveal that while core regulatory architectures are highly conserved, subtle changes in regulatory elements drive species-specific gene expression patterns. We highlight how CNEs provide a stable regulatory framework, whereas HARs and TE-derived elements introduce lineage-specific modifications that fine-tune neurodevelopmental processes. Advances in functional genomics, including CRISPR-based perturbations, massively parallel reporter assays, and single-cell multi-omics, have enabled direct interrogation of regulatory function, linking sequence variation to cellular phenotypes. Furthermore, we discuss how regulatory evolution contributes to both cognitive innovation and susceptibility to neurological disorders. Despite significant progress, challenges remain in establishing causal relationships between regulatory variation and phenotypic outcomes. Future integration of multi-omics data and comparative models will be essential for resolving these complexities. Together, this review provides a comprehensive framework for understanding the molecular basis of primate brain evolution through the lens of gene regulation.

Brain evolution↗
PubMed1990

Parasitoids, polydnaviruses and endosymbiosis.

Symbiotic associations traditionally have been treated as evolutionary curios rather than as a major source of evolutionary innovation. Recent research on a wide variety of organisms is changing this view and is breaking down the barriers between the traditional categories of parasitism, commensalism and mutualism, to produce a more flexible view of multispecific interactions. An especially abundant, but little discussed, mutualism exists between parasitoid wasps in the superfamily Ichneumonoidea and a novel form of DNA viruses known as polydnaviruses. Mutualisms between viruses and eukaryotes are not often reported, although as many as 100 000 species of organisms may exhibit this unusual association. In this review Jim Whitfield considers what is known about the parasitoid-polydnavirus relationship and how (and from what) it might have arisen.

Journal Article↗
PubMed2004

The evolutionary development of the protein complement of photosystem 2.

During the transition from anoxygenic to oxygenic photosynthesis, the Type 2 reaction center underwent many changes, none so dramatic as the remarkable increase in complexity at the protein level, from only three or four subunits in the anoxygenic reaction center to possibly more than 25 in Photosystem 2 (PS2). The evolutionary source of most of these proteins is enigmatic, as they have no apparent homology to any other proteins in existing databases. However, some of the proteins in PS2 have apparent homologies to each other, suggesting ancient gene duplications have played an important role in the development of the complex. These homologies include the well-known examples of the D1 and D2 reaction center core proteins and the CP43 and CP47 core antenna proteins. In addition, PsbE and PsbF, the two subunits comprising cytochrome b-559, show homology to each other, suggesting that a homodimeric cytochrome preceded the heterodimeric one. Other potential homologies that appear to be statistically significant include PsbV with the N-terminal part of D1 and PsbT with PsbI. Most of the proteins that make up the photosynthetic apparatus bear no relation to any other proteins from any source. This suggests that a period of remarkable evolutionary innovation took place when the ability to make oxygen was invented. This was probably a response to the production of highly toxic oxygen and these new proteins served to protect and repair the photosynthetic apparatus from the harmful effects of oxygen.

Cyanobacteria↗
PubMed2005

A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis.

Sexual reproduction in eukaryotes is accomplished by meiosis, a complex and specialized process of cell division that results in haploid cells (e.g., gametes). The stereotypical reductive division in meiosis is a major evolutionary innovation in eukaryotic cells, and delineating its history is key to understanding the evolution of sex. Meiosis arose early in eukaryotic evolution, but when and how meiosis arose and whether all eukaryotes have meiosis remain open questions. The known phylogenetic distribution of meiosis comprises plants, animals, fungi, and numerous protists. Diplomonads including Giardia intestinalis (syn. G. lamblia) are not known to have a sexual cycle; these protists may be an early-diverging lineage and could represent a premeiotic stage in eukaryotic evolution. We surveyed the ongoing G. intestinalis genome project data and have identified, verified, and analyzed a core set of putative meiotic genes-including five meiosis-specific genes-that are widely present among sexual eukaryotes. The presence of these genes indicates that: (1) Giardia is capable of meiosis and, thus, sexual reproduction, (2) the evolution of meiosis occurred early in eukaryotic evolution, and (3) the conserved meiotic machinery comprises a large set of genes that encode a variety of component proteins, including those involved in meiotic recombination.

Animals↗
PubMed2024

Molecular mechanisms of the specialization of human synapses in the neocortex.

Synapses of the neocortex specialized during human evolution to develop over extended timescales, process vast amounts of information and increase connectivity, which is thought to underlie our advanced social and cognitive abilities. These features reflect species-specific regulations of neuron and synapse cell biology. However, despite growing understanding of the human genome and the brain transcriptome at the single-cell level, linking human-specific genetic changes to the specialization of human synapses has remained experimentally challenging. In this review, we describe recent progress in characterizing divergent morphofunctional and developmental properties of human synapses, and we discuss new insights into the underlying molecular mechanisms. We also highlight intersections between evolutionary innovations and disorder-related dysfunctions at the synapse.

Humans↗
PubMed2026

A duplicated female pathway gene figla-like evolves as the male sex-determining gene in tilapia.

As the largest group of vertebrates, fish exhibit frequent turnover of sex-determining (SD) genes. Here, we assemble a chromosome-level YY red tilapia genome and identify figla-like (figlal) as the SD gene on tilapia linkage group (LG) 1. Integrative phylogenetic and genomic evidence suggests that figlal originated from a tilapia-specific duplication and transposition of the ancestral bHLH family gene figla from LG12 to LG1. Fluorescence in situ hybridization reveals expression divergence between figla and figlal, with figla expressed in female oocytes and figlal expressed in male gonadal somatic cells during early gonadal differentiation. The shift in expression after duplication might be driven by the insertion of cis-regulatory elements mediated by transposable elements. Knockout of figlal in XY fish results in male-to-female sex reversal as indicated by ovarian morphology, down-regulation of the male pathway gene dmrt1, and up-regulation of the female pathway gene cyp19a1a in the gonads. In contrast, overexpression of figlal in XX fish induces female-to-male sex reversal. These findings implicate figlal as an SD gene on tilapia LG1 and reveal the history of a unique evolutionary innovation in which a female oocyte gene evolved into a male SD gene via duplication, transposition, and cis-regulatory rewiring.

Animals↗
PubMed2005

War is peace--dispatches from the bacterial and phage killing fields.

Large-scale sequence analyses of phage and bacteria have provided new insights into the diverse and multifaceted interactions of these genomes. Such interactions are important because they determine the partitioning of a large fraction of global biomass. Furthermore, the struggle between phage and bacteria has had a significant impact on the evolution of the biosphere. This competition for resources has created an enormous pool of genetic diversity. Eons of horizontal genetic transfer have permitted the entire biosphere to directly benefit from a bargain-basement source of evolutionary innovation.

Bacteria↗
PubMed2006

Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity.

The ubiquity of mobile elements in mammalian genomes poses considerable challenges for the maintenance of genome integrity. The predisposition of mobile elements towards participation in genomic rearrangements is largely a consequence of their interspersed homologous nature. As tracts of nonallelic sequence homology, they have the potential to interact in a disruptive manner during both meiotic recombination and DNA repair processes, resulting in genomic alterations ranging from deletions and duplications to large-scale chromosomal rearrangements. Although the deleterious effects of transposable element (TE) insertion events have been extensively documented, it is arguably through post-insertion genomic instability that they pose the greatest hazard to their host genomes. Despite the periodic generation of important evolutionary innovations, genomic alterations involving TE sequences are far more frequently neutral or deleterious in nature. The potentially negative consequences of this instability are perhaps best illustrated by the >25 human genetic diseases that are attributable to TE-mediated rearrangements. Some of these rearrangements, such as those involving the MLL locus in leukemia and the LDL receptor in familial hypercholesterolemia, represent recurrent mutations that have independently arisen multiple times in human populations. While TE-instability has been a potent force in shaping eukaryotic genomes and a significant source of genetic disease, much concerning the mechanisms governing the frequency and variety of these events remains to be clarified. Here we survey the current state of knowledge regarding the mechanisms underlying mobile element-based genetic instability in mammals. Compared to simpler eukaryotic systems, mammalian cells appear to have several modifications to their DNA-repair ensemble that allow them to better cope with the large amount of interspersed homology that has been generated by TEs. In addition to the disruptive potential of nonallelic sequence homology, we also consider recent evidence suggesting that the endonuclease products of TEs may also play a key role in instigating mammalian genomic instability.

Animals↗