Optimality models of phage life history and parallels in disease evolution

Optimality models constitute one of the simplest approaches to understanding phenotypic evolution. Yet they have shortcomings that are not easily evaluated in most organisms. Most importantly, the genetic basis of phenotype evolution is almost never understood, and phenotypic selection experiments are rarely possible. Both limitations can be overcome with bacteriophages. However, phages have such elementary life histories that few phenotypes seem appropriate for optimality approaches. Here we develop optimality models of two phage life history traits, lysis time and host range. The lysis time models show that the optimum is less sensitive to differences in host density than suggested by earlier analytical work. Host range evolution is approached from the perspective of whether the virus should avoid particular hosts, and the results match optimal foraging theory: there is an optimal "diet" in which host types are either strictly included or excluded, depending on their infection qualities. Experimental tests of both models are feasible, and phages provide concrete illustrations of many ways that optimality models can guide understanding and explanation. Phage genetic systems already support the perspective that lysis time and host range can evolve readily and evolve without greatly affecting other traits, one of the main tenets of optimality theory. The models can be extended to more general properties of infection, such as the evolution of virulence and tissue tropism.     

The curse of the pharaoh in space: free-living infectious stages and the evolution of virulence in spatially explicit populations

The idea that parasites with long-lived infective stages may evolve higher virulence has received considerable attention. This idea is called 'the curse of the pharaoh' because of the hypothesis that the death of Lord Carnavon was caused by very long-lived propagules of a highly virulent infectious disease. Here, we examined the evolution of diseases that transmit via free-living stages in a spatial context. We show that, if virulence evolves independently of transmission, long-lived infective stages can select for higher virulence. There is always the evolution of a finite transmission rate, which becomes higher when the infective stages are shorter lived. When a trade-off occurs between transmission and virulence, we show that there is no evidence for the curse of the pharaoh. Indeed, higher transmission and therefore virulence may be selected for by shorter rather than long-lived infective stages.     

Divergence and convergence in enzyme evolution

Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes.     

Relative Wulst volume is correlated with orbit orientation and binocular visual field in birds

In mammals, species with more frontally oriented orbits have broader binocular visual fields and relatively larger visual regions in the brain. Here, we test whether a similar pattern of correlated evolution is present in birds. Using both conventional statistics and modern comparative methods, we tested whether the relative size of the Wulst and optic tectum (TeO) were significantly correlated with orbit orientation, binocular visual field width and eye size in birds using a large, multi-species data set. In addition, we tested whether relative Wulst and TeO volumes were correlated with axial length of the eye. The relative size of the Wulst was significantly correlated with orbit orientation and the width of the binocular field such that species with more frontal orbits and broader binocular fields have relatively large Wulst volumes. Relative TeO volume, however, was not significant correlated with either variable. In addition, both relative Wulst and TeO volume were weakly correlated with relative axial length of the eye, but these were not corroborated by independent contrasts. Overall, our results indicate that relative Wulst volume reflects orbit orientation and possibly binocular visual field, but not eye size.     

Immunohistochemical evidence of cone-based ultraviolet vision in divergent bat species and implications for its evolution

We characterized Fos-like expression patterns in the primary visual cortex (V1) by binocular flicking stimulation with UV light to investigate cone-based UV vision in four bat species representing four lineages: Hipposideros armiger and Scotophilus kuhlii, insectivores using constant frequency (CF) or frequency modulation (FM) echolocation, respectively, and Rousettus leschenaultii and Cynopterus sphinx, cave-roosting and tree-roosting fruit bats, respectively. The optic centre processing the visual image, V1, appears more distinctly immunostaining in S. kuhlii and C. sphinx after 1 h of UV light stimuli while in H. armiger and R. leschenaultii, staining was no more distinct than in corresponding controls. Our immunohistochemical evidence supports differences in the distribution of cone-based UV vision in the order Chiroptera and supports our earlier postulate that due to possible sensory tradeoffs and roosting ecology, defects in the short wavelength opsin genes have resulted in loss of UV vision in CF but not in FM bats. In addition, fruit bats roosting in caves have lost UV vision but not those roosting in trees. Our results thus confirm that bats are a further mammalian taxon that has retained cone-based UV sensitivity in some species.     

Metal detoxification and homeostasis in Antarctic Notothenioids. A comparative survey on evolution, expression and functional properties of fish and mammal metallothioneins

Organisms from yeast to mammals contain cysteine-rich, heavy metal binding proteins termed metallothioneins. The putative roles of these proteins are trace metal homeostasis and detoxification of poisonous heavy metals. The highly conserved chemical composition and the structural constraints led to the conclusion that metallothioneins of different origin must display remarkably similar features. The present review aims at surveying the studies carried out on the metallothioneins of Antarctic Notothenioidei, a dominating fish group endowed of a number of striking adaptive characters, including reduced (or absent) hematocrit and presence of antifreeze glycoproteins. Given the unique peculiarities of the Antarctic environment, a comparative study of the features of notothenioid metallothioneins could provide new insights into the role of these proteins in physiology and toxicology. The results summarized here show that the metallothioneins of this fish group display a number of features at the level of evolution, expression pattern, structure and function remarkably different from those of mammal metallothioneins.     

Convergence rate estimation for the TKF91 model of biological sequence length evolution

The TKF91 model of biological sequence evolution describes changes in the sequence length via an infinite state-space birth-death process, which we term the TKF91-BD process. The TKF91 model assumes that, for any pair of modern sequences, the ancestral sequence has equilibrium length distribution, an assumption whose validity has not been rigorously investigated. We obtain explicit upper and lower bounds on the rate of convergence to equilibrium for the distribution of the TKF91-BD process. We show that the rate of convergence of the TKF91-BD process for protein sequences with parameter values inferred from sequence data on alpha and beta globins is too low to guarantee convergence to equilibrium on a reasonable timescale. For the analyzed nucleotide sequences, the convergence is faster, but the equilibrium sequence length is unrealistically small. The Jukes-Cantor model of nucleotide substitutions can converge considerably faster than the length evolution model for both amino acid and nucleotide sequences, while the speed of convergence for the Kimura model is close to that for the TKF91-BD process describing nucleotide sequences.     

Binocular vision: the eyes add and subtract

Our two eyes' views of the outside world are slightly different, providing the basis for stereopsis. A new study has found evidence that the human visual system has separately adaptable channels for adding and subtracting the neural signals from the two eyes, supporting an unconventional view of the initial stages of stereopsis.     

Ontogenetic mechanisms and the evolution of Cactaceae

Abstract

The ancestors of cacti were leafy trees that had hard, woody trunks. The development of the cactus body is controlled by ontogenetic mechanisms that have evolved, and now they produce a body that is leafless, succulent and has a photosynthetic cortex. Specific changes include: bark formation is postponed and the epidermis and stomata function for many years; the outer cortex is a palisade cortex with intercellular spaces; there are cortical bundles that resemble leaf veins but which have secondary xylem and phloem. Wood development has changed dramatically such that water storage is maximized (increased ray parenchyma) and danger of water stress is minimized (increased paratracheal parenchyma, loss of fibers). Several genera have polymorphic wood: the plants produce one type of wood for several years, then later they produce a different type. It is possible that the extensive evolutionary changes have resulted from mutations in the controller regions of genes, not in the structural regions.     

Developmental origins and evolution of jaws: new interpretation of "maxillary" and "mandibular"

Cartilage of the vertebrate jaw is derived from cranial neural crest cells that migrate to the first pharyngeal arch and form a dorsal "maxillary" and a ventral "mandibular" condensation. It has been assumed that the former gives rise to palatoquadrate and the latter to Meckel's (mandibular) cartilage. In anamniotes, these condensations were thought to form the framework for the bones of the adult jaw and, in amniotes, appear to prefigure the maxillary and mandibular facial prominences. Here, we directly test the contributions of these neural crest condensations in axolotl and chick embryos, as representatives of anamniote and amniote vertebrate groups, using molecular and morphological markers in combination with vital dye labeling of late-migrating cranial neural crest cells. Surprisingly, we find that both palatoquadrate and Meckel's cartilage derive solely from the ventral "mandibular" condensation. In contrast, the dorsal "maxillary" condensation contributes to trabecular cartilage of the neurocranium and forms part of the frontonasal process but does not contribute to jaw joints as previously assumed. These studies reveal the morphogenetic processes by which cranial neural crest cells within the first arch build the primordia for jaw cartilages and anterior cranium.     

Adaptive walks on behavioural landscapes and the evolution of optimal behaviour by natural selection

Summary One of the main challenges to the adaptationist programme in general and to the use of optimality models in behavioural and evolutionary ecology in particular is that natural selection need not optimise fitness. This challenge is addressed by considering the evolution of optimal patch choice by natural selection. The behavioural model is based on a state variable approach in which a strategy consists of a sequence denoting the patch to be visited as a function of the organism's state and time. The optimal strategy maximises expected terminal reproduction. The fitnesses of alternative strategies are computed by iteration of the associated equations for fitness; this characterises the adaptive behavioural landscape. There may be enormous numbers of strategies that have near optimal fitnesses. A population model is used to connect frequencies of behavioural types from one generation to the next. Theories on adaptive walks on fitness landscapes are considered in the context of behaviour. The main result is that within the context of optimality arguments at selective equilibrium, sub-optimal behaviours can persist. General implications for research in behavioural ecology, including tests of behavioural theories, are discussed.     

Predictors of orbital convergence in primates: a test of the snake detection hypothesis of primate evolution

Traditional explanations for the evolution of high orbital convergence and stereoscopic vision in primates have focused on how stereopsis might have aided early primates in foraging or locomoting in an arboreal environment. It has recently been suggested that predation risk by constricting snakes was the selective force that favored the evolution of orbital convergence in early primates, and that later exposure to venomous snakes favored further degrees of convergence in anthropoid primates. Our study tests this snake detection hypothesis (SDH) by examining whether orbital convergence among extant primates is indeed associated with the shared evolutionary history with snakes or the risk that snakes pose for a given species. We predicted that orbital convergence would be higher in species that: 1) have a longer history of sympatry with venomous snakes, 2) are likely to encounter snakes more frequently, 3) are less able to detect or deter snakes due to group size effects, and 4) are more likely to be preyed upon by snakes. Results based on phylogenetically independent contrasts do not support the SDH. Orbital convergence shows no relationship to the shared history with venomous snakes, likelihood of encountering snakes, or group size. Moreover, those species less likely to be targeted as prey by snakes show significantly higher values of orbital convergence. Although an improved ability to detect camouflaged snakes, along with other cryptic stimuli, is likely a consequence of increased orbital convergence, this was unlikely to have been the primary selective force favoring the evolution of stereoscopic vision in primates.     

Morphology and the evolution of cycadeoidales

OneCycadeoidea stem one cycadeoidalean gynoecium and a bisporangiate cone attached to a slender cycadeoidalean trunkCycadeoidella japonica Ogura from the Cretaceous of Japan shows well-preserved internal structure that provides evidence for a better understanding of the morphological architecture of the cycadeoidalean plant. Structural details of the cone were confirmed. The ovule has an intergument enclosing a free nucellus and a thin outer envelope. Both reproductive and vegetative structures support the medullosan affinity of Cycadeoidales. The cone is interpreted as a compressed fertile shoot. Axillary cones characterizing some Cretaceous genera such asCycadeoidea andMonanthesia consist of a lateral shoot subtended by a frond that is the first leaf of the cone shoot itself. The origin of axillary buds in the Cycadeoidales is discussed. Heterochrony may have mediated the morphological changes that resulted in the establishment of the Cycadeoidales.     

Organization and evolution of the mitochondrial genome of yeast

Summary The mitochondrial genome of yeast (S. cerevisiae orS. carlsbergensis) appears to be formed by 60–70 genetic units, each one of which is formed by (1) a GC-rich sequence, possibly having a regulatory role; (2) a gene, and (3) an AT-rich spacer, which probably is not transcribed. Recombination in this genome appears to underlie a number of important phenomena. The organization of the mitochondrial genome of yeast and these recombinational events are discussed in relationship with the organization and evolution of the nuclear genome of eukaryotes.     

The evolution of "deformed" brains in ant-like stone beetles (Scydmaeninae, Staphylinidae)

We present the first study of the central nervous system of adult representatives of Scydmaeninae. Histological staining, scanning electron microscopy and computer-based 3D reconstruction techniques were used to document the shape and configuration of the major cephalic elements of the central nervous system and to explain its anomalies compared to other Coleoptera. For the first time we report the presence of cephalic glands in ant-like stone beetles: in Scydmaenus (Cholerus) hellwigii openings of voluminous glands are located near the occipital constriction and their secretion accumulates in a large cavity of the dorsal head region. In Scydmaenus (Cholerus) perrisi the proto-, deuto-, tritocerebrum and the suboesophageal ganglion together form a large and compact ganglionic mass around the anterior foregut in the retracted neck region of the head. We exclude miniaturization as the driving force of the observed modifications. Comparative study of the head anatomy of S. perrisi, S. hellwigii, Scydmaenus (s. str.) tarsatus, Scydmaenus (Parallomicrus) rufus and Neuraphes elongatulus suggests a possible evolutionary scenario. We propose an evolutionary reversal hypothesis, involving a) the displacement and concentration of the cephalic central nervous system induced by the development of glandular cavities of the head, followed by b) a reduction of the glandular structures, without a secondary relocation of the cephalic CNS. The interpretation of head modifications in Scydmaeninae in the light of such a scenario may turn out as important for the reconstruction of the phylogeny and evolution of this highly successful group of beetles.     

Photoreceptor cells and eyes in Annelida

The evolution of photoreceptor cells and eyes in Metazoa is far from being resolved, although recent developmental and morphological studies provided strong evidence for a common origin of photoreceptor cells and existence of sister cell types in early metazoans. Photoreceptor cells are of two types, rhabdomeric and ciliary, depending on which part of the cells is involved in photoreception proper. A crucial point in understanding eye evolution is the explanation of the enormous structural diversity of photoreceptor cells and visual systems, given the general tendency for molecular conservation. One example of such diversity occurs in Annelida. In this taxon three types of photoreceptor cells exist: rhabdomeric, ciliary and phaosomous sensory cells. Whether the latter evolved independently or have been derived from one of the former cell types is still unresolved, since cilia and microvilli are found in these cells. These different photoreceptor cells are present in cerebral ocelli and eyes, in various ectopic ocelli and eyes situated in different places as well as in various photoreceptor-like sense organs. Whereas rhabdomeric cells mostly occur in connection with pigmented supportive cells, the other types are usually found with unpigmented supportive cells. Thus for the latter cells clear evidence for photoreception is still lacking in most cases. However, initial molecular-developmental investigations have shown that in fact ciliary photoreceptor cells exist within Annelida. Certain visual systems are only present during the larval phase and either replaced by the adult eyes or completely reduced during postlarval and adult stages. In the present paper the diversity of cerebral and extracerebral photoreceptor cells and ocelli as well as corresponding organs devoid of shading pigment is reviewed in Annelida.     

Chromosome evolution in the genus Ophioglossum L.

Cytological observations on eleven species of Ophioglossum revealed low gametic ( n ) chromosome numbers of 30, 34 and 60 in populations of O.eliminatum , contrasting with an earlier report of n = 90 in the same species. The rest of the species is based on n =120.Cytologically studied species of Ophioglossum exhibit a range of chromosome numbers from n = 30 in O.eliminatum to n =720 in O.reticulatum. The weighted highest common factor (HGF) from all the reported chromosome numbers in twelve species was found to be 30. This number is proposed as the palaeobasic chromosome number for the genuS. Reported chromosome numbers which are not multiples of 30 were subjected to sequential analysis, yielding three distinct ultimate base numbers, 4, 5 and 6, which can produce n = 30 in seven different ways. The neobasic number, n= 120, appears to have arisen through various combinations and permutations of these, theoretically 2401 routes; only a relatively few of these routes exist today, suggesting that extreme selection has been exerted against the majority, and further suggesting that Ophioglossum represents an evolutionary dead end through repeated cycles of polyploidy and is possibly at the verge of extinction. The stoichiometric model of evolution, which derives the various chromosome numbers possessed by the twelve species from the basic and ultimate basic chromosome numbers, is used to explain chromosomal evolution in the genus.     

Genomic view of the evolution of the complement system

The recent accumulation of genomic information of many representative animals has made it possible to trace the evolution of the complement system based on the presence or absence of each complement gene in the analyzed genomes. Genome information from a few mammals, chicken, clawed frog, a few bony fish, sea squirt, fruit fly, nematoda and sea anemone indicate that bony fish and higher vertebrates share practically the same set of complement genes. This suggests that most of the gene duplications that played an essential role in establishing the mammalian complement system had occurred by the time of the teleost/mammalian divergence around 500 million years ago (MYA). Members of most complement gene families are also present in ascidians, although they do not show a one-to-one correspondence to their counterparts in higher vertebrates, indicating that the gene duplications of each gene family occurred independently in vertebrates and ascidians. The C3 and factor B genes, but probably not the other complement genes, are present in the genome of the cnidaria and some protostomes, indicating that the origin of the central part of the complement system was established more than 1,000 MYA.     

Hominoid cytogenetics and evolution

Much of the literature on the chromosomes of the Hominoidea exists in virtual isolation from both evolutionary theory and physical anthropology. Several unjustified speculations about hominoid affinities in the literature of cytogenetics may be attributed to the effects of this isolation. In this paper, the literature of comparative hominoid cytogenetics is reviewed, and that on chromosomal band patterns and repetitive DNA distributions relative to current evolutionary theory is discussed. These data are critically analyzed and shown to be more consistent with an orthodox hominoid phylogeny than with heterodox phylogenies. Rates and modes of karyotypic evolution are also discussed in an attempt to begin to assimilate the study of hominoid chromosomes within the framework of physical anthropology.