Showing papers in "Philosophical Transactions of the Royal Society B in 1995"

A composite estimate of primate phylogeny

Abstract: This paper presents an estimate of the phylogeny of all 203 species of primate. The composite tree is derived by applying a parsimony algorithm to over a hundred previous estimates, and is well resolved, containing 160 nodes. The ages of over half the clades in the tree have been estimated from information in the literature. Bootstrapping has been used to indicate the degree of certainty associated with each clade. The tree will be a useful framework for comparative biologists and shows which areas of primate phylogeny are still only sketchily known.

Empirical Evidence that Declining Species Diversity May Alter the Performance of Terrestrial Ecosystems

Abstract: We examined experimentally the association between species diversity and ecosystem processes in a series of terrestrial mesocosms. We developed and maintained 14 mesocosms whose biota were assembled from a single pool of plant and animal species and whose environmental conditions were identically controlled. Each community contained four trophic levels: primary producers (annual herbs), consumers (herbivorous molluscs and phloem sucking insects), secondary consumers (parasitoids) and decomposers (earthworms, Collembola and microbes). All mesocosms received the same diurnal pattern of light, temperature, relative humidity and water. The initial volume of soil, soil structure, composition, nutrient content and inocula of both soil microbes and nematodes were also identical among replicates. The only experimentally manipulated factor was the number of plant and animal species within each trophic level. High, medium and low diversity communities had nine, 15 or 31 plant and animal species, respectively. We measured five ecosystem processes as response variables in these mesocosms over the course of 206 days: (i) community respiration; (ii) productivity; (iii) decomposition; (iv) nutrient retention; and (v) water retention. The manipulation of diversity produced communities that differed significantly in their ecosystem processes. Our results provide the first evidence (obtained by a direct manipulation of diversity under controlled environmental conditions) that ecosystem processes may be affected by loss of diversity.

The Evolutionary History of Sauropod Dinosaurs

Abstract: Most recent studies of dinosaur phylogeny have concentrated on theropods and ornithischians. As a result, the evolutionary relationships of sauropod dinosaurs are poorly understood. In this paper previous studies of sauropod phylogeny are reviewed and contrasted with the results of a recent cladistic analysis. This analysis forms the basis for a reconstruction of sauropod phylogeny. Sauropods diverged from other dinosaurs at some time in the Upper Triassic, but a large part of their early history is totally unknown. Vulcanodon is currently the most primitive sauropod. Many, but perhaps not all, of the Jurassic Chinese sauropods form a monophyletic radiation (the Euhelopodidae) which may reflect the geographic isolation of China during the Lower Jurassic. Members of the Euhelopodidae, such as Mamenchisaurus, are not considered to be closely related to the Diplodocidae. \`Forked' chevrons, which have played such an important role in previous studies of sauropod phylogeny, are here considered to have evolved twice within the Sauropoda. This convergence may reflect a correlation between chevron shape and the use of the tail as a weapon within these two sauropod families. The \`Neosauropoda' (sister group to the Euhelopodidae) contains the Brachiosauridae, Camara-sauridae and the new superfamilies Titanosauroidea and Diplodocoidea. The Cetiosauridae (here defined in a rather restricted sense) is also provisionally included within the Neosauropoda, but may be removed in future studies. The enigmatic Upper Cretaceous sauropod, Opisthocoelicaudia, is thought to be the sister taxon to the Titanosauridae and not a camarasaurid as previously suggested. The Diplodocoidea contains two well established families, the Dicraeosauridae and Diplodocidae, and the new family Nemegtosauridae. Finally, an overview of sauropod phylogeny is compared with recently published palaeogeographic reconstructions. There are many difficulties associated with the analysis of sauropod biogeographic distribution. Nevertheless, some aspects of sauropod phylogeny may be linked to the break-up of Laurasia and Gondwanaland during the Jurassic and Cretaceous.

Evolutionary radiation of visual and olfactory brain systems in primates, bats and insectivores

Abstract: How brains have evolved in response to particular selection pressures is illuminated by ecological correlates of differences in brain structure among contemporary species. The focus of most comparative studies has been on the overall size of brains relative to body size, hence ignoring the ways in which selection operates on specific neural systems. Here we investigate evolutionary radiations in the size of visual and olfactory brain structures within three orders of mammals: primates, bats and insectivores. The comparative relationships within these three orders show both similarities and differences. After removal of the allometric effect of overall brain size, the sizes of different structures within each sensory modality are positively correlated in all three orders. Correlations between visual and olfactory structures, however, are negative in primates, negative but non-significant in insectivores, and positive in bats. In both primates and insectivores, nocturnal lineages tend to have larger olfactory structures than do diurnal or partly diurnal lineages, and among the primates diurnal lineages have larger striate visual cortexes. Hence the apparent trade-off between vision and olfaction in primates seems to be related to the divergence of nocturnal and diurnal forms. However, negative correlations between visual and olfactory structures were also found when nocturnal strepsirhines and diurnal haplorhines were analysed separately, suggesting that ecological variables in addition to activity timing may be significant. Indeed, there were also associations with diet: frugivory was associated with enlargements of the geniculostriate visual system in diurnal primates, enlargements of olfactory structures in nocturnal primates, and possibly enlargements of both in bats. Further ecological associations were found within insectivores: aquatic lineages had smaller olfactory structures than in their non-aquatic counterparts, and fossorial lineages had smaller optic nerves than in non-fossorial forms. We conclude that activity timing, diet and habitat have each played a role in the evolutionary radiation of mammalian sensory systems, but with varying effects in the different taxa. Some of the associations between ecology and sensory systems suggest alternative explanations for correlates of overall brain size, which have in the past commonly been interpreted in terms of selection on intelligence.

Birds, body size and the threat of extinction

Abstract: A relation between body size and threat of extinction for animal species has often been hypothesized. However, evidence for the form of the relation is equivocal, and studies can be found reporting positive, negative, or no relation between body size and extinction risk. One way to assess this relation is to compare the body sizes of species considered to be globally threatened with those of species considered to be less at risk. We adopt this approach for birds, considering a bird to be in danger of global extinction if it was listed by Collar & Andrew (ICBP technical publication no. 8 (1988)). Threatened species of bird are, on average, larger-bodied than non-threatened species. This difference is not due to size differences between island endemic species and species with continental distributions. Island endemic and continental species show no consistent body size differences. The relation between body mass and threat of extinction is not due to differences between higher taxa: within taxa, there is still a relation between body size and extinction threat. We present evidence that the degree of threat faced by endangered species may also be related to body mass. We discuss possible explanations for the observed patterns, and conclude that a genuine tendency for large-bodied birds to be more at risk from extinction than small-bodied species is the most likely.

Dna-sequence evolution - the sounds of silence

Abstract: Silent sites (positions that can undergo synonymous substitutions) in protein-coding genes can illuminate two evolutionary processes First, despite being silent, they may be subject to natural selection Among eukaryotes this is exemplified by yeast, where synonymous codon usage patterns are shaped by selection for particular codons that are more efficiently and/or accurately translated by the most abundant tRNAs; codon usage across the genome, and the abundance of different tRNA species, are highly co-adapted Second, in the absence of selection, silent sites reveal underlying mutational patterns Codon usage varies enormously among human genes, and yet silent sites do not appear to be influenced by natural selection, suggesting that mutation patterns vary among regions of the genome At first, the yeast and human genomes were thought to reflect a dichotomy between unicellular and multicellular organisms However, it now appears that natural selection shapes codon usage in some multicellular species (eg Drosophila and Caenorhabditis), and that regional variations in mutation biases occur in yeast Silent sites (in serine codons) also provide evidence for mutational events changing adjacent nucleotides simultaneously

Articulated Halkieriids from the Lower Cambrian of North Greenland and their Role in Early Protostome Evolution

Abstract: Articulated halkieriids of Halkieria evangelista sp. nov. are described from the Sirius Passet fauna in the Lower Cambrian Buen Formation of Peary Land, North Greenland. Three zones of sclerites are recognizable: obliquely inclined rows of dorsal palmates, quincuncially inserted lateral cultrates and imbricated bundles of ventro-lateral siculates. In addition there is a prominent shell at both ends, each with radial ornamentation. Both sclerites and shells were probably calcareous, but increase in body size led to insertion of additional sclerites but marginal accretion of the shells. The ventral sole was soft and, in life, presumably muscular. Recognizable features of internal anatomy include a gut trace and possible musculature, inferred from imprints on the interior of the anterior shell. Halkieriids are closely related to the Middle Cambrian Wiwaxia, best known from the Burgess Shale: this clade appears to have played an important role in early protostome evolution. From an animal fairly closely related to Wiwaxia arose the polychaete annelids; the bundles of siculate sclerites prefigure the neurochaetae whereas the dorsal notochaetae derive from the palmates. Wiwaxia appears to have a relic shell and a similar structure in the sternaspid polychaetes may be an evolutionary remnant. The primitive state in extant polychaetes is best expressed in groups such as chrysopetalids, aphroditaceans and amphinomids. The homology between polychaete chaetae and the mantle setae of brachiopods is one line of evidence to suggest that the latter phylum arose from a juvenile halkieriid in which the posterior shell was first in juxtaposition to the anterior and rotated beneath it to provide the bivalved condition of an ancestral brachiopod. H. evangelista sp. nov. has shells which resemble those of a brachiopod; in particular the posterior one. From predecessors of the halkieriids known as siphogonuchitids it is possible that both chitons (polyplacophorans) and conchiferan molluscs arose. The hypothesis of halkieriids and their relatives having a key role in annelid-brachiopod-mollusc evolution is in accord with some earlier proposals and recent evidence from molecular biology. It casts doubt, however, on a number of favoured concepts including the primitive annelid being oligochaetoid and a burrower, the brachiopods being deuterostomes and the coelom being an archaic feature of metazoans. Rather, the annelid coelom arose as a functional consequence of the transition from a creeping halkieriid to a polychaete with stepping parapodial locomotion.

Space, persistence and dynamics of measles epidemics

Abstract: This paper explores the relations between persistence and dynamics in measles epidemics. Most current models, including the stochastic seasonally forced and age-structured models examined here, fail to capture simultaneously the observed dynamics and persistence characteristics of epidemics in large urban populations before vaccination. Summary measures of persistence and trienniality allow us to compare epidemics in England, New York and Copenhagen with results of non-spatial and spatial stochastic models. Spatial (metapopulation) structure allow persistence and triennial dynamics to coexist i this class of models. The spatial dynamics of measles, for which detailed spatiotemporal data are available, may serve as a useful test of ideas applicable to other epidemiological and ecological systems with an important spatial component.

Uses of molecular phylogenies for conservation

Abstract: Conservation requires the accurate targeting of resources together with information on population processes Molecular phylogenies can potentially contribute in both areas Interspecific molecular phylogenies can identify clades undergoing rapid diversification or extinction and can assess the contribution of individual lineages to overall genetic diversity Whether and how this should translate to conservation priorities is open to debate Within species, molecular phylogenies along with information on allele frequencies can be used to identify evolutionarily significant population units or areas In relation to population processes, molecular phylogenies may provide a perspective on population growth and connectivity over evolutionary time As threatened species typically have undergone rapid changes in population size an d/or migration rate, phylogeny-based estimates may be misleading about contemporary population processes However, the comparison between historical and current estimates may identify significant changes to long-term trends, thus identifying population in need of urgent management This information can potentially suggest strategies for managing declining or fragmented species, but this requires further theoretical and experimental study

The adaptive advantage of phenotypic memory in changing environments.

Abstract: The adaptive value of carry-over effects, the persistence of induced phenotypes for several generations despite the change in the conditions that first induced these phenotypes, is studied in the framework of a simple model. Three different organismal strategies-non-inducible (genetic), completely inducible (plastic), and intermediate (carry-over)-are compared in fitness terms within three different environments. Analytical results and numerical simulations show that carry-over effects can have an advantage in stochastic environments even over organisms with high adaptive plasticity. We argue that carry-over effects represent an adaptive mechanism on the ecological timescale that fills the gap between short-term individual adaptations and long-term evolutionary adaptations. An extension of the concept of plasticity to incorporate the time dimension and include the stability of induced phenotypes through both clonal and sexual generations, is suggested.

Optimal flight speed of birds

Abstract: The speed of birds in flapping flight is a behavioural attribute that, when interpreted in the light of optimization theory, may provide important implications about the limitations in time, energy and safety that affect birds in different situations. This study is an evaluation and review of optimal flight speeds of birds, based on foraging, migration and flight mechanical theory. Flight in different ecological contexts is considered, such as foraging flight, food transportation flight, migration flight and aerial display flight. Relevant optimization criteria and immediate currencies are identified for these flight situations, permitting the derivation of optimal flight speeds. Foraging birds are expected to maximize foraging gain ratio (the ratio of gross energy intake rate to the cost of foraging in excess of the resting metabolism) when energy minimization is of imminent importance or when they are constrained by a metabolic ceiling. In other circumstances they are expected to maximize the net energy intake rate. Generally, optimal flight speeds are faster in the latter than in the former case. Thus when the foraging gain ratio is maximized the optimal flight speed between foraging patches is V $\_{\text{mr}}$ (speed of minimum energy cost per unit of distance flown), whereas it is faster than this, to a variable degree depending on the quality of and distance between patches, when net energy intake rate is maximized. Birds should adapt their flight speed differently when transporting food or migrating as compared with flying in pure foraging situations. Cost of transport (energy/distance) or resulting speed of transport or of migration (distance/time) are the immediate currencies relevant for predicting optimal flight speeds depending on whether birds in food transportation flights are metabolically constrained or not and whether migrating birds are energy- or time-selected. Optimal flight speeds for maximizing the resulting speed of transport or of migration exceed V $\_{\text{mr}}$ to an increasing degree with an increasing rate of food/energy gain. Still other optimization criteria apply to further flight situations that are reviewed, and, in addition, flight speed is expected to vary with wind, load, altitude, climb rate and flock size. Optimal flight speed theory provides a possibility to use flight speed measurements of birds in widely different situations for obtaining insights about crucial time and energy limitations.

Shape vision in bees: innate preference for flower-like patterns

Abstract: The bees' spontaneous preferences toward various black-and-white patterns were studied using a multiple-choice test procedure. The patterns are presented on vertical planes, and the bees' choices at a fixed distance from the patterns are recorded. To exclude a possible influence of the bees' previous experience with natural flowers, the bees are trained to randomized checkerboard patterns prior to testing them with sets of other patterns. We find that, when the test patterns are of the same kind, but differ in their spatial frequencies, the bees prefer low over high frequencies. However, when the patterns differ in type, the bees express, regardless of spatial frequency, a positive preference for patterns containing radiating elements, and a negative preference for patterns containing circular elements or elements arranged at random. We find, in addition, that symmetrical patterns are more attractive than less symmetrical or non-symmetrical patterns. We propose that bees respond innately to some features of natural flowers, resulting in a spontaneous preference for radiating, as well as symmetrical patterns.

Molecular phylogenies and host-parasite cospeciation: gophers and lice as a model system.

Abstract: Recent methodological advances permit a rigorous comparison of phylogenetic trees for hosts and their parasites to determine the extent to which these groups have cospeciated through evolutionary time. In cases where significant levels of cospeciation are indicated, comparison of amounts of evolutionary change that have accumulated along analogous branches in the host and parasite trees provides a direct assessment of relative rates of evolution in the two groups. For such a comparison to be meaningful, the features compared in the hosts and parasites should be genetically based, evolutionarily homologous, and should evolve in a roughly time-dependent fashion within each group. Nucleotide sequences encoding homologous genes in hosts and parasites are an ideal source of data for comparative studies of evolutionary rates. Recent studies of pocket gophers and their lice are used to illustrate the variety of questions that can be addressed through phylogenetic study of host-parasite systems.

Leg design and jumping technique for humans, other vertebrates and insects

Abstract: Humans, bushbabies, frogs, locusts, fleas and other animals jump by rapidly extending a pair of legs. Mathematical models are used to investigate the effect muscle properties, leg design and jumping technique have on jump height. Jump height increases with increased isometric force exerted by leg muscles, their maximum shortening speeds and their series compliances. When ground forces are small multiples of body mass (as for humans), countermovement and catapult jumps are about equally high, and both are much better than squat jumps. Vertebrates have not evolved catapult mechanisms and use countermovement jumps instead. When ground forces are large multiples of body mass, catapult jumps (as used by locusts and fleas) are much higher than the other styles of jump could be. Increasing leg mass reduces jump height, but the proximal-to-distal distribution of leg mass has only a minor effect. Longer legs make higher jumps possible and additional leg segments, such as the elongated tarsi of bushbabies and frogs, increase jump height even if overall leg length remains unchanged. The effects of muscle moment arms that change as the leg extends, and of legs designed to work over different ranges of joint angle, are investigated.

Evolution of the cell cycle

Abstract: Cell proliferation involves duplication of all cell constituents and their more-or-less equal segregation to daughter cells. It seems probable that the performance of primitive cell-like structures would have been dogged by poor duplication and segregation fidelity, and by parasitism. This favoured evolution of the genome and with it the distinction between 'genomic' components like chromosomes whose synthesis is periodic and most other 'functional' components whose synthesis is continuous. Eukaryotic cells evolved from bacterial ancestors whose fused genome was replicated from a single origin and whose means of segregating sister chromatids depended on fixing their identity at replication. Evolution of an endo- or cytoskeleton, initially as means of consuming other bacteria, eventually enabled evolution of the mitotic spindle and a new means of segregating sister chromatids whose replication could be initiated from multiple origins. In this primitive eukaryotic cell, S and M phases might have been triggered by activation of a single cyclin-dependent kinase whose destruction along with that of other proteins would have triggered anaphase. Mitotic non-disjunction would have greatly facilitated genomic expansion, now possible due to multiple origins, and thereby accelerated the tempo of evolution when permitted by environmental conditions.

The genetic basis of XX-XY differences present before gonadal sex differentiation in the mouse.

Abstract: There is now a substantial body of data showing that in eutherian mammals (mouse, rat, cow and man) XY conceptuses are developmentally more advanced (and consequently larger) than XX conceptuses of equivalent gestational age. This developmental difference is already discernible in the preimplantation period and it has been suggested that the more advanced development of XY embryos may be a consequence of the preimplantation expression of Y chromosomal genes such as Sry or Zfy. In the present paper sex-chromosomally variant mice were used to analyse the genetic basis of XX-XY differences as manifest at 10.5 days post coitum. The results show that the XX-XY difference is due to a combination of a Y chromosome effect and an effect of the difference in X chromosome constitution (2X v 1X). The Y effect is not dependent on the presence of Sry. In the light of this and other studies, it is concluded that the Y chromosome of most mouse strains carries a factor which accelerates preimplantation development and that the resulting developmental advantage is carried over into the postimplantation period. The retarding effect of two X chromosomes is then superimposed on this Y effect subsequent to the blastocyst stage but prior to 9.5 days post coitum.

Inferring population history from molecular phylogenies.

Abstract: Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and applied to real data, illustrating ways of navigating through hypothesis space with two landmarks for reference: constant population size and exponentially growing population size.

The energy expenditure of free-ranging black-browed albatrosses

Abstract: As heart rate ( f H ) can be used to determine the energy expenditure of black-browed albatrosses ( Diomedea melanophrys ) (Bevan et al. 1994), data loggers - recording f H and abdominal temperature ( T ab ) -were implanted into free-ranging black-browed albatrosses breeding at South Georgia. Five birds also had salt water switches (sws) attached to one leg to record when the birds were on the water, and two others had satellite transmitters attached to their back to determine the birds’ position at sea. The birds were released into their natural environment and recaptured, on average, 23 days later when the data loggers were removed. The f H data were then converted into estimates of energy expenditure (ee) using a previously derived equation. The mean EE during incubation and brooding were 2.22 and 2.42 W kg -1 , respectively. When the birds were foraging at sea, EE increased to between 4.63 and 5.80 W kg -1 , depending on the phase of the reproductive cycle. As the birds spent approximately the same length of time at the nest and at sea during incubation and brooding, the overall mean ee during these phases were 3.63 and 3.54 W kg -1 respectively. These rates are significantly lower than that during the chick-rearing phase when a high level of foraging EE is maintained almost continuously. By combining information from the sws with the f H data, it was possible to determine the EE of the birds when on the water (5.77 W kg -1 ) and when flying (6.21 W kg -1 ). These values are approximately twice the estimated basal metabolic rate (BMR) for the species. The energy costs of flight are half previous values, estimated using the doubly labelled water technique, because of the previous assumption that birds on the water have an EE equivalent to BMR. When the birds were on the nest, T ab was 39.3 + 0.4 °C and this changed very little with time. However, when they were at sea, T ab showed large variations, depending on the behaviour of the bird. Information from the sws indicated that all large drops (> 0.5 °C) in Tab occurred when the birds were on water. The mean minimum value reached was 32.5 + 2.0 °C. It is likely that ingestion of prey or water are the major causes of this decrease. This is the first study to have used f H extensively to determine the EE of a free-ranging marine bird. The advantages of using this technique are that data can be obtained over long durations with high resolution, permitting the EE of different activities to be estimated.

Germ Cells and Germ Cell Sex

Abstract: Whether germ cells succeed in making eggs or sperm depends both on their genetic constitution and on the tissue environment in which they develop. The decision as to whether it is oogenesis or spermatogenesis on which they initially embark depends only on their environment, however, and not at all on their own chromosomes. The foetal testis of the mouse produces an inhibitor of meiosis: germ cells that are exposed to it develop as prospermatogonia. Germ cells in the foetal ovary enter meiosis and develop as oocytes: this may represent the default pathway for germ cell sexual differentiation, or there may exist a meiosis-inducing substance. Experimental evidence suggests that any such substance must be present ubiquitously, not just in the ovary. The stage of foetal development at which meiosis is initiated may be programmed in the germ cell lineage.

Cross-Species Transmission and Recombination of 'AIDS' Viruses

Abstract: Acquired Immune Deficiency Syndrome (AIDS) is caused by two different Human Immunodeficiency Viruses, HIV-1 and HIV-2. Closely related viruses (SIVs) are found in many species of non-human primates. Phylogenetic analyses indicate that cross-species transmission events have been quite frequent. Both HIV-1 and HIV-2 appear to have resulted from multiple transfers of lentiviruses naturally infecting other primates; the source of HIV-2 appears to have been sooty mangabeys, whereas for HIV-1 the source may have been chimpanzees. Phylogenetic analyses also provide evidence that recombination has occurred between divergent viruses in vivo. Evolutionary trees based on various regions of the viral genome generally have consistent branching orders. However, some isolates fall into significantly different phylogenetic positions, indicating that their genomes are mosaics of sequences with different evolutionary histories. This implies that co-infection with highly divergent viral strains can occur in HIV-infected humans and SIV-infected primates; this could lead to the generation of hybrid genomes with significantly altered biological properties, and also has important implications for HIV vaccine development programmes.

Site-Specific Recombination and Circular Chromosome Segregation

Abstract: The Xer site-specific recombination system functions in Escherichia coli to ensure that circular plasmids and chromosomes are in the monomeric state prior to segregation at cell division. Two recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome and to sites present in natural multicopy plasmids. In addition, recombination at the natural plasmid site cer, present in ColE1, requires the function of two additional accessory proteins, ArgR and PepA. These accessory proteins, along with accessory DNA sequences present in the recombination sites of plasmids are used to ensure that recombination is exclusively intramolecular, converting circular multimers to monomers. Wild-type and mutant recombination proteins have been used to analyse the formation of recombinational synapses and the catalysis of strand exchange in vitro. These experiments demonstrate how the same two recombination proteins can act with different outcomes, depending on the organization of DNA sites at which they act. Moreover, insight into the separate roles of the two recombinases is emerging.

A Combined Morphological and Molecular Phylogeny for Sea Urchins (Echinoidea: Echinodermata)

Abstract: Phylogenetic relationships of higher taxa of echinoids have been investigated using a 163 character morphological data base and molecular sequences from large and small subunit (LSU and SSU) ribosomal RNA (rRNA) genes. The complete SSU rRNA gene has been sequenced for 21 taxa, with representatives from nine of the 14 extant orders of Echinoidea. Partial LSU sequences, representing the first 400 base pairs (b.p.) from the 5' end were also sequenced for three taxa to complement an existing data base of ten taxa. The two molecular sequences provided a total of 371 variable sites, of which 143 were phylogenetically informative (compared to 145 phylogenetically informative sites from morphological data). Morphological, LSU and SSU data have been analysed separately and together. Morphological and SSU sequence data generate topologies that are not significantly in conflict (under Templeton's test), but the strong signal pairing arbaciids with clypeasteroids in the LSU derived tree marks the LSU sequence data as anomalous for this taxon. A 'total evidence' approach derived a tree very similar in topology to that derived from morphological data. Rooted on the stem group echinoid Archaeocidaris, our total evidence tree suggested relationships of higher taxa as follows: Cidaroida (Phormosomatidae (Echinothuriidae (Diadematidae ((Spatangoida (Clypeasteroida, Cassiduloida)) ((Calycina, Arbacioida) (Stomopneustidae (Glyphocidaridae (Temnopleuridae (Echinometridae (Echinidae, Stronglyocentridae)))))))))). Phylogenetic analyses run both with and without key fossil taxa yielded slightly different topologies. It is important to include fossil taxa in a phylogenetic analysis where there are long stem-group branches or where the crown group is highly derived.

Kinetic and equilibrium folding intermediates

Abstract: Our recent experiments on the molten globule state and other protein folding intermediates lead to following conclusions: (i) the molten globule is separated by intramolecular first-order phase transitions from the native and unfolded states and therefore is a specific thermodynamic state of protein molecules; (ii) the novel equilibrium folding intermediate (the 'pre-molten globule' state) exists which can be similar to the 'burst' kinetic intermediate of protein folding; (iii) proteins denature and release their non-polar ligands at moderately low pH and moderately low dielectric constant, i.e. under conditions which may be related to those near membranes.

Hox Genes and the Evolution of Diverse Body Plans

Abstract: Homeobox genes encode transcription factors that carry out diverse roles during development. They are widely distributed among eukaryotes, but appear to have undergone an extensive radiation in the earliest metazoa, to generate a range of homeobox subclasses now shared between diverse metazoan phyla. The Hox genes comprise one of these subfamilies, defined as much by conserved chromosomal organization and expression as by sequence characteristics. These Hox genes act as markers of position along the antero-posterior axis of the body in nematodes, arthropods, chordates, and by implication, most other triploblastic phyla. In the arthropods this role is visualized most clearly in the control of segment identity. Exactly how Hox genes control the structure of segments is not yet understood, but their differential deployment between segments provides a model for the basis of segment diversity. Within the arthropods, distantly related taxonomic groups with very different body plans (insects, crustaceans) may share the same set of Hox genes. The expression of these Hox genes provides a new character to define the homology of different body regions. Comparisons of Hox gene deployment between insects and a branchiopod crustacean suggest a novel model for the derivation of the insect body plan.

The evolution of mammalian sex chromosomes and the origin of sex determining genes

Abstract: Mammals have XX female: XY male chromosomal sex determination in which a small heterochromatic Y controls male development. Only a few active genes have been identified on the Y, including the testis determining factor SRY and candidate spermatogenesis genes. These genes, as well as several pseudogenes, have close relatives on the X, confirming that the Y was originally homologous to the X, but has been progressively degraded. We used comparative gene mapping of sex chromosomes from the three major groups of extant mammals (eutherians, marsupials and monotremes) to deduce how the X and Y evolved from a pair of autosomes, and how SRY assumed control of sex determination. We found that part of the X, and a corresponding region of the Y chromosome, is shared by all mammals and must be very ancient, but part of the X (and Y) was added quite recently. I propose that a small original X and Y were enlarged by cycles of autosomal addition to one partner, recombination onto the other and continuing attrition of the compound Y. This addition-attrition hypothesis predicts that the pseudoautosomal region of the human X is merely a relic of the last addition, and that the gene content of the pseudoautosomal region may well differ in different mammalian lineages. The only genes which remained active on the conserved or added regions of the Y were those, like SRY, that evolved functions in male sex determination and differentiation distinct from the general functions of their X-linked partners. Although the vertebrate gonadogenesis pathway is highly conserved, its control circuitry has probably changed radically and rapidly in evolution.

Models of cooperativity in protein folding

Abstract: What is the basis for the two-state cooperativity of protein folding? Since the 1950s, three main models have been put forward. 1. In \`helix-coil' theory, cooperativity is due to local interactions among near neighbours in the sequence. Helix-coil cooperativity is probably not the principal basis for the folding of globular proteins because it is not two-state, the forces are weak, it does not account for sheet proteins, and there is no evidence that helix formation precedes the formation of a hydrophobic core in the folding pathways. 2. In the \`sidechain packing' model, cooperativity is attributed to the jigsaw-puzzle-like complementary fits of sidechains. This too is probably not the basis of folding cooperativity because exact models and experiments on homopolymers with sidechains give no evidence that sidechain freezing is two-state, sidechain complementarities in proteins are only weak trends, and the molten globule model predicted by this model is far more native-like than experiments indicate. 3. In the `hydrophobic core collapse' model, cooperativity is due to the assembly of non-polar residues into a good core. Exact model studies show that this model gives two-state behaviour for some sequences of hydrophobic and polar monomers. It is based on strong forces. There is considerable experimental evidence for the kinetics this model predicts: the development of hydrophobic clusters and cores is concurrent with secondary structure formation. It predicts compact denatured states with sizes and degrees of disorder that are in reasonable agreement with experiments.

Anatomy and functional morphology of the largest marine reptile known, Mosasaurus hoffmanni (Mosasauridae, Reptilia) from the Upper Cretaceous, Upper Maastrichtian of The Netherlands

Abstract: Mosasaurus hoffmanni , one of the latest known mosasaurs, comes from the Upper Maastrichtian, Upper Cretaceous Chalk of The Netherlands. Although the first specimen was discovered over 200 years ago, it is here fully described for the first time to provide detailed insights into its anatomy, functional morphology and evolution. Many characters of the skull show that M. hoffmanni was among the most advanced mosasaurs. The skull is robustly constructed and is the least kinetic in the Mosasauridae and, with a tightly assembled palatal complex, provided greater cranial stability in this large-headed mosasaur. The cranial musculature is highly modified. The four-bar linkage system of lizards and early mosasaurs is non-functional in M. hoffmanni . The elements of the lower jaw are also more tightly united than in other mosasaurs. Tooth crowns are divided into several distinct, unique cutting surfaces or prisms. A functional analysis of the marginal teeth shows that they are particularly adapted to powerful bite forces although pterygoidal teeth are small and reduced in importance in ratchet feeding. Moderately large orbits and poorly developed olfactory organs suggest that Mosasaurus hoffmanni was a surface-swimming animal. A relatively lower level of binocular vision than in some other mosasaurs may indicate a somewhat uncomplicated habitat. Geological and palaeontological evidence indicates that M. hoffmanni lived in fairly deep nearshore waters of 40—50 m depth, with changing temperatures and rich vertebrate and invertebrate life. Several severely broken and healed mandibles suggest either a violent lifestyle in predation or in fighting.

The Use of Optimization Techniques to Model Marine Ecosystem Dynamics at the JGOFS Station at 47 degrees N 20 degrees W [and Discussion]

Abstract: A seven-compartment model of the mixed layer ecosystem was used to fit a time series of observations derived from data obtained during the 1989 JGOFS North Atlantic Bloom Experiment. A nonlinear optimization technique was used to obtain the best fit to the combined observation set. It was discovered that a solution which gave a good fit to primary production gave a bad fit to zooplankton and vice versa. The solution which fitted primary production also showed good agreement with a number of other independent data sets, but overestimated bacterial production. Further development is necessary to create a model capable of reproducing all the important features of the nitrogen flows within the mixed layer.

Insect-Crustacean Relationships: Insights from Comparative Developmental and Molecular Studies

Abstract: The phylogenetic relationships between the major arthropod groups are still far from being resolved. Phylogenetic analyses have usually relied on detailed morphological comparisons which are confounded by the extensive occurrence of convergence. We examine the available morphological evidence in the light of recent comparative developmental and molecular studies and suggest ways in which genetic-developmental information could help assess homology and overcome the problem of convergence. On the basis of such considerations we support the common origin of crustaceans and insects from a crustacean-like mandibulate ancestor. Focusing on the specific relationships between crustaceans, myriapods and insects, we suggest that insects could emerge from this crustacean-like ancestor independently from myriapods, and after the major crustacean radiations.

Genealogies and Geography

Abstract: Any sample of genes traces back to a single common ancestor. Each gene also has other properties: its sequence, its geographic location and the phenotype and fitness of the organism that carries it. With sexual reproduction, different genes have different genealogies, which gives us much more information, but also greatly complicates population genetic analysis. We review the close relation between the distribution of genealogies and the classic theory of identity by descent in spatially structured populations, and develop a simple diffusion approximation to the distribution of coalescence times in a homogeneous two-dimensional habitat. This shows that when neighbourhood size is large (as in most populations) only a small fraction of pairs of genes are closely related, and only this fraction gives information about current rates of gene flow. The increase of spatial dispersion with lineage age is thus a poor estimator of gene flow. The bulk of the genealogy depends on the long-term history of the population; we discuss ways of inferring this history from the concordance between genealogies across loci.