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PubMed2001

Earliest evidence for efficient oral processing in a terrestrial herbivore.

Herbivores can increase their digestion rate by mechanically reducing particle size through oral trituration. Groups of terrestrial vertebrates with the greatest capacity to reduce tough plant foods orally are also the most abundant and diverse, as exemplified by ornithopod dinosaurs during the Mesozoic and extant artiodactyl and perissodactyl mammals. Thus, the effective oral processing of high-fibre plant material seems to represent an evolutionary innovation of both functional and macroevolutionary significance. However, evidence for oral processing is poorly documented in the fossil record, especially during the initial stages of terrestrial vertebrate diversification. Here we report on the basal anomodont Suminia getmanovi, the only known Palaeozoic vertebrate in which unequivocal specializations in its cranium and teeth for high-fibre herbivory are well preserved. We propose that the capacity to comminute tough plant foods was critical to the diversification of anomodonts, the most diverse, widely dispersed and abundant group of Palaeozoic terrestrial vertebrates, and to the onset of modern terrestrial ecosystems.

Animals↗
PubMed2002

Snake circumvents constraints on prey size.

For animals who are unable to take bites out of their food, the size of the food item that can be consumed is constrained by the maximal size of the mouth opening (gape)--snakes are an example of gape-limited predators and they usually swallow their prey whole. Here we describe unique feeding behaviours in two closely related species of snake, which circumvent their gape limitation by removing and consuming pieces from newly moulted crabs that are too large to be swallowed intact. This evolutionary innovation is surprising, as the needle-like teeth and highly mobile bones that facilitate the capture and engulfment of large, whole prey by snakes are ill-suited both to cutting and to generating large bite forces.

Animals↗
PubMed2004

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.

Whole-genome duplication followed by massive gene loss and specialization has long been postulated as a powerful mechanism of evolutionary innovation. Recently, it has become possible to test this notion by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. The two genomes are related by a 1:2 mapping, with each region of K. waltii corresponding to two regions of S. cerevisiae, as expected for whole-genome duplication. This resolves the long-standing controversy on the ancestry of the yeast genome, and makes it possible to study the fate of duplicated genes directly. Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions.

Codon↗
PubMed2006

Evidence that mechanisms of fin development evolved in the midline of early vertebrates.

The origin of paired appendages was a major evolutionary innovation for vertebrates, marking the first step towards fin- (and later limb-) driven locomotion. The earliest vertebrate fossils lack paired fins but have well-developed median fins, suggesting that the mechanisms of fin development were assembled first in the midline. Here we show that shark median fin development involves the same genetic programs that operate in paired appendages. Using molecular markers for different cell types, we show that median fins arise predominantly from somitic (paraxial) mesoderm, whereas paired appendages develop from lateral plate mesoderm. Expression of Hoxd and Tbx18 genes, which specify paired limb positions, also delineates the positions of median fins. Proximodistal development of median fins occurs beneath an apical ectodermal ridge, the structure that controls outgrowth of paired appendages. Each median fin bud then acquires an anteroposteriorly-nested pattern of Hoxd expression similar to that which establishes skeletal polarity in limbs. Thus, despite their different embryonic origins, paired and median fins utilize a common suite of developmental mechanisms. We extended our analysis to lampreys, which diverged from the lineage leading to gnathostomes before the origin of paired appendages, and show that their median fins also develop from somites and express orthologous Hox and Tbx genes. Together these results suggest that the molecular mechanisms for fin development originated in somitic mesoderm of early vertebrates, and that the origin of paired appendages was associated with re-deployment of these mechanisms to lateral plate mesoderm.

Animals↗
PubMed2005

Modularity and evolutionary constraint on proteins.

Modularity, which has been found in the functional and physical protein interaction networks of many organisms, has been postulated to affect both the mode and tempo of evolution. Here I show that in the yeast Saccharomyces cerevisiae, protein interaction hubs situated in single modules are highly constrained, whereas those connecting different modules are more plastic. This pattern of change could reflect a tendency for evolutionary innovations to occur by altering the proteins and interactions between rather than within modules, in a manner somewhat similar to the evolution of new proteins through the shuffling of conserved protein domains.

Computer Simulation↗
PubMed2026

Zebrafish relatives as models for functional comparative genetics and genomics.

Closely related species, such as danionin fishes of the Danio, Danionella and Devario genera, often differ in their biology despite their shared evolutionary history, providing a platform for defining the molecular basis for the divergence of phenotypic traits. Such an approach requires the availability of large-scale genomic data, which have been provided by recent reports detailing the genomes of several danionins. Facilitated by the large number of genetic tools that are available for manipulation of the most studied member of this subgroup - the zebrafish, Danio rerio - the danionins have emerged as a useful comparative model system. Here we review their phylogeny and outline the phenotypic traits that are distinct to individual species or genera. We highlight how functional genetic tools such as interspecies hybridization, mutagenesis and transgenesis, as well as the recently reported genome assemblies, have enabled new avenues for hypothesis-driven and technology-driven exploration that collectively establish danionins as important genetic models for understanding a wide range of evolutionary innovations.

Journal Article↗
PubMed2006

Robustness and evolution: concepts, insights and challenges from a developmental model system.

Robustness, the persistence of an organismal trait under perturbations, is a ubiquitous property of complex living systems. We here discuss key concepts related to robustness with examples from vulva development in the nematode Caenorhabditis elegans. We emphasize the need to be clear about the perturbations a trait is (or is not) robust to. We discuss two prominent mechanistic causes of robustness, namely redundancy and distributed robustness. We also discuss possible evolutionary causes of robustness, one of which does not involve natural selection. To better understand robustness is of paramount importance for understanding organismal evolution. Part of the reason is that highly robust systems can accumulate cryptic variation that can serve as a source of new adaptations and evolutionary innovations. We point to some key challenges in improving our understanding of robustness.

Animals↗
PubMedDate not supplied

Comparative development of fiber in wild and cultivated cotton.

One of the most striking examples of plant hairs is the single-celled epidermal seed trichome of cultivated cotton. The developmental morphology of these commercial "fibers" has been well-characterized in Gossypium hirsutum, but little is known about the pattern and tempo of fiber development in wild Gossypium species, all of which have short, agronomically inferior fiber. To identify developmental differences that account for variation in fiber length, and to place these differences in a phylogenetic context, we conducted SEM studies of ovules at and near the time of flowering, and generated growth curves for cultivated and wild diploid and tetraploid species. Trichome initiation was found to be similar in all taxa, with few notable differences in trichome density or early growth. Developmental profiles of the fibers of most wild species are similar, with fiber elongation terminating at about two weeks post-anthesis. In contrast, growth is extended to three weeks in the A- and F-genome diploids. This prolonged elongation period is diagnosed as a key evolutionary event in the origin of long fiber. A second evolutionary innovation is that absolute growth rate is higher in species with long fibers. Domestication of species is associated with a further prolongation of elongation at both the diploid and allopolyploid levels, suggesting the effects of parallel artificial selection. Comparative analysis of fiber growth curves lends developmental support to previous quantitative genetic suggestions that genes for fiber "improvement" in tetraploid cotton were contributed by the agronomically inferior D-genome diploid parent.

Agriculture↗
PubMedDate not supplied

Early evolution of a homeobox gene: the parahox gene Gsx in the Cnidaria and the Bilateria.

Homeobox transcription factors are commonly involved in developmental regulation in diverse eukaryotes, including plants, animals, and fungi. The origin of novel homeobox genes is thought to have contributed to many evolutionary innovations in animals. We perform a molecular phylogenetic analysis of cnox2, the best studied homeobox gene from the phylum Cnidaria, a very ancient lineage of animals. Among three competing hypotheses, our analysis decisively favors the hypothesis that cnox2 is orthologous to the gsx gene of Bilateria, thereby establishing the existence of this specific homeobox gene in the eumetazoan stem lineage, some 650-900 million years ago. We assayed the expression of gsx in the planula larva and polyp of the sea anemone Nematostella vectensis using in situ hybridization and reverse transcriptase polymerase chain reaction. The gsx ortholog of Nematostella, known as anthox2, is expressed at high levels in the posterior planula and the corresponding "head" region of the polyp. It cannot be detected in the anterior planula or the corresponding "foot" region of the polyp. We have attempted to reconstruct the evolution of gsx spatiotemporal expression in cnidarians and bilaterians using a phylogenetic framework. Because of the surprisingly high degree of variability in gsx expression within the Cnidaria, it is currently not possible to infer unambiguously the ancestral cnidarian condition or the ancestral eumetazoan condition for gsx expression.

Amino Acid Sequence↗
PubMed1990

Haplodiploidy in the Oxyurida: decoupling the evolutionary processes of adaptation and speciation.

Host distribution and life history variation in the Oxyurida are discussed in the context of haplodiploidy. The Oxyurida have the broadest host distribution of any zooparasitic nematode group but have retained a virtually unchanged life cycle. Like other haplodiploids, oxyuridians have life histories that maintain viscous population structures. It is postulated that this has facilitated speciation but may have discouraged major evolutionary innovation in the group.

Adaptation, Physiological↗
PubMed2001

Evolution of sociality in a primitively eusocial lineage of bees.

Eusociality is a major evolutionary innovation involving alterations in life history, morphology, and behavior. Advanced eusocial insects, such as ants, termites, and corbiculate bees, cannot provide insights into the earliest stages of eusocial evolution because eusociality in these taxa evolved long ago (in the Cretaceous) and close solitary relatives are no longer extant. In contrast, primitively eusocial insects, such as halictid bees, provide insights into the early stages of eusocial evolution because eusociality has arisen recently and repeatedly. By mapping social behavior onto well-corroborated phylogenies, I show that eusociality has arisen only three times within halictid bees (contrary to earlier estimates of six or more origins). Reversals from eusocial to solitary behavior have occurred as many as 12 times, indicating that social reversals are common in the earliest stages of eusocial evolution. Important attributes of social complexity (e.g., colony size, queen/worker dimorphism) show no obvious association with phylogeny, and some reversals to solitary nesting are related to host-plant switches (from polylecty to oligolecty). These results provide a glimpse of social evolution in its earliest stages and provide insights into the early evolution of advanced eusocial organisms.

Animals↗
PubMed2003

Dynamics of the Neoproterozoic carbon cycle.

The existence of unusually large fluctuations in the Neoproterozoic (1,000-543 million years ago) carbon-isotopic record implies strong perturbations to the Earth's carbon cycle. To analyze these fluctuations, we examine records of both the isotopic content of carbonate carbon and the fractionation between carbonate and marine organic carbon. Together, these are inconsistent with conventional, steady-state models of the carbon cycle. The records can be well understood, however, as deriving from the nonsteady dynamics of two reactive pools of carbon. The lack of a steady state is traced to an unusually large oceanic reservoir of organic carbon. We suggest that the most significant of the Neoproterozoic negative carbon-isotopic excursions resulted from increased remineralization of this reservoir. The terminal event, at the Proterozoic-Cambrian boundary, signals the final diminution of the reservoir, a process that was likely initiated by evolutionary innovations that increased export of organic matter to the deep sea.

Animals↗
PubMed1974

Three flies and three islands: parallel evolution in Drosophila.

Most organisms are evolutionary conservatives; they may subdivide their niches but tend to remain within them. Yet the fossil record shows many cases of breakthrough to a new mode of life. How may such evolutionary innovation be recognized at this time level? Three species of Drosophila have accomplished an innovation in that they breed as obligate commensals on tropical land crabs. This could be dismissed as a curious aberration were it not for the fact that the three flies concerned represent three different phyletic lines of the family. Although Drosophila is abundant on the continents, these three parallel innovative evolutions have occurred on islands. The proposal is made that the genetic systems of many conservative groups of organisms carry variability that would permit them to evolve in a novel direction. The realization of this capacity, however, is possible only under special environmental conditions.

Adaptation, Biological↗
PubMed1998

Identification and characterization of amelogenin genes in monotremes, reptiles, and amphibians.

Two features make the tooth an excellent model in the study of evolutionary innovations: the relative simplicity of its structure and the fact that the major tooth-forming genes have been identified in eutherian mammals. To understand the nature of the innovation at the molecular level, it is necessary to identify the homologs of tooth-forming genes in other vertebrates. As a first step toward this goal, homologs of the eutherian amelogenin gene have been cloned and characterized in selected species of monotremes (platypus and echidna), reptiles (caiman), and amphibians (African clawed toad). Comparisons of the homologs reveal that the amelogenin gene evolves quickly in the repeat region, in which numerous insertions and deletions have obliterated any similarity among the genes, and slowly in other regions. The gene organization, the distribution of hydrophobic and hydrophilic segments in the encoded protein, and several other features have been conserved throughout the evolution of the tetrapod amelogenin gene. Clones corresponding to one locus only were found in caiman, whereas the clawed toad possesses at least two amelogenin-encoding loci.

Alligators and Crocodiles↗
PubMed2006

Pereskia and the origin of the cactus life-form.

The cactus life-form is cited as an example of a tight relationship between organism form and function: a succulent, long-lived, photosynthetic stem allows cacti to survive long periods of drought while maintaining a positive tissue water status. Pereskia (Cactaceae) comprises 17 species of leafy shrubs and trees that are thought to represent the original cactus condition. Recent phylogenetic work has shown that there are two separate clades of Pereskia species, which are basal and paraphyletic with respect to the rest of the cacti. We selected seven Pereskia species, representing both clades, and characterized their water relations by measuring a suite of physiological traits in wild populations. Additionally, we estimated basic climate parameters from collection localities for all 17 Pereskia species. Extant Pereskia species exhibit ecological water use patterns that are very similar to those of the leafless, stem-succulent cacti. Ancestral trait reconstruction for the physiological and environmental data provides a preliminary assessment of the ecology and water relations of the earliest cacti and suggests that several key elements of the cactus ecological niche were established before the evolution of the cactus life-form. We interpret these ecological traits as potentially important drivers of evolutionary innovation in the cacti.

Biological Evolution↗
PubMed2026

De Novo Genome Sequence Assembly of the Algal Endosymbiont Micractinium conductrix Derived From Its Host Paramecium bursaria 186b.

Endosymbiosis is a major driver of evolutionary innovation and underpins the function of diverse ecosystems. The origins and evolution of endosymbiosis are challenging to study experimentally due to the short-lived culturability of many microbial strains derived from endosymbiotic interactions. The facultative endosymbiosis between the ciliate, Paramecium bursaria, and the green alga, Micractinium conductrix (Chlorellaceae, Trebouxiophyceae), is ecologically widespread and has emerged as a powerful lab-tractable model system. This endosymbiosis is founded upon a reciprocal nutrient exchange, but each of the species can be cultured independently enabling quantification of symbiotic fitness effects, new partnerships to be generated in the lab, and co-associations to be subject to experimental evolution. To date, evolve-and-resequence approaches have been limited due to a lack of high-quality genome assemblies enabling gene variants to be identified. Here, we report a near telomere-to-telomere genome assembly for M. conductrix 186b, using a range of sequencing technologies. Comparative analysis shows that this is one of the most complete Chlorellaceae algal genome assemblies available to date. To aid accurate gene calling and annotation, we conducted both RNAseq and Iso-Seq transcriptome sequencing experiments. Collectively, these 'omics datasets will facilitate: (i) comparative genomics studies of endosymbiont evolution, (ii) evolve-and-resequence experiments, (iii) genome-scale metabolic modeling studies, and (iv) identification of targets for genetic modification experiments and biotechnological applications.

Symbiosis↗
PubMed2000

Natural selection, infectious transfer and the existence conditions for bacterial plasmids.

Despite the near-ubiquity of plasmids in bacterial populations and the profound contribution of infectious gene transfer to the adaptation and evolution of bacteria, the mechanisms responsible for the maintenance of plasmids in bacterial populations are poorly understood. In this article, we address the question of how plasmids manage to persist over evolutionary time. Empirical studies suggest that plasmids are not infectiously transmitted at a rate high enough to be maintained as genetic parasites. In part i, we present a general mathematical proof that if this is the case, then plasmids will not be able to persist indefinitely solely by carrying genes that are beneficial or sometimes beneficial to their host bacteria. Instead, such genes should, in the long run, be incorporated into the bacterial chromosome. If the mobility of host-adaptive genes imposes a cost, that mobility will eventually be lost. In part ii, we illustrate a pair of mechanisms by which plasmids can be maintained indefinitely even when their rates of transmission are too low for them to be genetic parasites. First, plasmids may persist because they can transfer locally adapted genes to newly arriving strains bearing evolutionary innovations, and thereby preserve the local adaptations in the face of background selective sweeps. Second, plasmids may persist because of their ability to shuttle intermittently favored genes back and forth between various (noncompeting) bacterial strains, ecotypes, or even species.

Bacterial Physiological Phenomena↗
PubMedDate not supplied

Male pregnancy in seahorses and pipefishes (family Syngnathidae): rapid diversification of paternal brood pouch morphology inferred from a molecular phylogeny.

In contrast to the majority of vertebrate species, primary male parental care is common in fishes and encompasses a remarkable diversity of adaptations. Seahorses and pipefishes (Family Syngnathidae) exhibit some of the most specialized forms of paternal care in animals and so are ideally suited to the study of the evolution of male parental care. During mating, female syngnathids transfer eggs to specialized morphological structures that are located on either the abdomen or tail of the male. The male provides all postfertilization parental care and has morphological and physiological adaptations to osmoregulate, aerate, and even nourish the developing embryos. While all syngnathid species are adapted for paternal care, the brooding structure with which this is accomplished varies between species, from simple ventral gluing areas to much more complex structures such as the completely enclosed pouches of the seahorses. Our combined cytochrome b-, 12S rDNA-, and 16S rDNA-based molecular phylogeny of syngnathid fishes demonstrates that rapid diversification of male brooding structures has been associated with the major evolutionary radiation of the group, suggesting that development and diversification of structures involved in paternal care may have been key evolutionary innovations of the Syngnathidae. Molecular analyses also highlight geographical centers of biodiversity and suggest interoceanic migration of Syngnathus pipefishes from their center of origin in the Pacific.

Animals↗