Selection rules for rovibronic transitions in symmetric top molecules

A simple diagrammatic rule is presented for determining the rotational selection rules governing transitions between any pair of vibronic states in electric dipole spectra of symmetric top molecules. The rule is useful in cases where degenerate vibronic levels with first-order Coriolis splittings occur, because it gives immediately the selection rule for the (+l) and (-l) components in any degenerate state. The rule is also helpful in determining the symmetry species and the effective zeta constants in overtone and combination levels involving degenerate vibrations. Particular attention is devoted to the conventions concerning the signs of zeta constants.

Raman selection rules for vibration-rotation transitions in symmetric top molecules

Symmetry restrictions on Raman selection rules can be obtained, quite generally, by considering a Raman allowed transition as the result of two successive dipole allowed transitions, and imposing the usual symmetry restrictions on the dipole transitions. This leads to the same results as the more familiar polarizability theory, but the vibration-rotation selection rules are easier to obtain by this argument. The selection rules for symmetric top molecules involving the (+l) and (-l) components of a degenerate vibrational level with first-order Coriolis splitting are derived in this paper. It is shown that these selection rules depend on the order of the highest-fold symmetry axis Cn, being different for molecules with n=3, n=4, or n ≧ 5; moreover the selection rules are different again for molecules belonging to the point groups Dnd with n even, and Sm with 1/2m even, for which the highest-fold symmetry axes Cn and Sm are related by m=2n. Finally it is shown that an apparent anomaly between the observed Raman and infra-red vibration-rotation spectra of the allene molecule is resolved when the correct selection rules are used, and a value for the A rotational constant of allene is derived without making use of the zeta sum rule.

Evolutionary bi-stability in pathogen transmission mode

Many pathogens transmit to new hosts by both infection (horizontal transmission) and transfer to the infected host's offspring (vertical transmission). These two transmission modes require speci®c adap- tations of the pathogen that can be mutually exclusive, resulting in a trade-off between horizontal and vertical transmission. We show that in mathematical models such trade-offs can lead to the simultaneous existence of two evolutionary stable states (evolutionary bi-stability) of allocation of resources to the two modes of transmission. We also show that jumping between evolutionary stable states can be induced by gradual environmental changes. Using quantitative PCR-based estimates of abundance in seed and vege- tative parts, we show that the pathogen of wheat, Phaeosphaeria nodorum, has jumped between two distinct states of transmission mode twice in the past 160 years, which, based on published evidence, we interpret as adaptation to environmental change. The ®nding of evolutionary bi-stability has impli- cations for human, animal and other plant diseases. An ill-judged change in a disease control programme could cause the pathogen to evolve a new, and possibly more damaging, combination of transmission modes. Similarly, environmental changes can shift the balance between transmission modes, with adverse effects on human, animal and plant health.

Managing threatened species – the ecological toolbox, evolutionary theory and the declining-population paradigm

1. The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining-population paradigm identified by Caughley. 2. There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour-based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application. 3. These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviourbased models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions. 4. Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past. 5. Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population-level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level. 6. Synthesis and applications. It is argued that evolutionary theory underpins Caughley’s declining-population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision-making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.

Genesis and expansion of metazoan transcription factor gene classes

We know little about the genomic events that led to the advent of a multicellular grade of organization in animals, one of the most dramatic transitions in evolution. Metazoan multicellularity is correlated with the evolution of embryogenesis, which presumably was underpinned by a gene regulatory network reliant on the differential activation of signaling pathways and transcription factors. Many transcription factor genes that play critical roles in bilaterian development largely appear to have evolved before the divergence of cnidarian and bilaterian lineages. In contrast, sponges seem to have a more limited suite of transcription factors, suggesting that the developmental regulatory gene repertoire changed markedly during early metazoan evolution. Using whole- genome information from the sponge Amphimedon queenslandica, a range of eumetazoans, and the choanoflagellate Monosiga brevicollis, we investigate the genesis and expansion of homeobox, Sox, T- box, and Fox transcription factor genes. Comparative analyses reveal that novel transcription factor domains ( such as Paired, POU, and T- box) arose very early in metazoan evolution, prior to the separation of extant metazoan phyla but after the divergence of choanoflagellate and metazoan lineages. Phylogenetic analyses indicate that transcription factor classes then gradually expanded at the base of Metazoa before the bilaterian radiation, with each class following a different evolutionary trajectory. Based on the limited number of transcription factors in the Amphimedon genome, we infer that the genome of the metazoan last common ancestor included fewer gene members in each class than are present in extant eumetazoans. Transcription factor orthologues present in sponge, cnidarian, and bilaterian genomes may represent part of the core metazoan regulatory network underlying the origin of animal development and multicellularity.

Evolutionary relationships of "candidatus riesia spp.," endosymbiotic enterobacteriaceae living within hematophagous primate lice

The primary endosymbiotic bacteria from three species of parasitic primate lice were characterized molecularly. We have confirmed the characterization of the primary endosymbiont (P-endosymbiont) of the human head/body louse Pediculus humanus and provide new characterizations of the P-endosymbionts from Pediculus schaeffi from chimpanzees and Pthirus pubis, the pubic louse of humans. The endosymbionts show an average percent sequence divergence of 11 to 15% from the most closely related known bacterium "Candidatus Arsenophonus insecticola." We propose that two additional species be added to the genus "Candidatus Riesia." The new species proposed within "Candidatus Riesia" have sequence divergences of 3.4% and 10 to 12% based on uncorrected pairwise differences. Our Bayesian analysis shows that the branching pattern for the primary endosymbionts was the same as that for their louse hosts, suggesting a long coevolutionary history between primate lice and their primary endosymbionts. We used a calibration of 5.6 million years to date the divergence between endosymbionts from human and chimpanzee lice and estimated an evolutionary rate of nucleotide substitution of 0.67% per million years, which is 15 to 30 times faster than previous estimates calculated for Buchnera, the primary endosymbiont in aphids. Given the evidence for cospeciation with primate lice and the evidence for fast evolutionary rates, this lineage of endosymbiotic bacteria can be evaluated as a fast-evolving marker of both louse and primate evolutionary histories.

The genome strikes back: The evolutionary importance of defence against mobile elements

Increasingly, we regard the genome as a site and source of genetic conflict. This fascinating 'bottom-up' view brings up appealing connections between genome biology and whole-organism ecology, in which populations of elements compete with one another in their genomic habitat. Unlike other habitats, though, a host genome has its own evolutionary interests and is often able to defend itself against molecular parasites. Most well-studied organisms employ strategies to protect their genomes against the harmful effects of genomic parasites, including methylation, various pathways of RNA interference, and more unusual tricks such as repeat induced point-mutation (RIP). These genome defence systems are not obscure biological curiosities, but fundamentally important to the integrity and cohesion of the genome, and exert a powerful influence on genome evolution.

Large punctuational contribution of speciation to evolutionary divergence at the molecular level

A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.

Molecular evidence from ascidians for the evolutionary origin of vertebrate cranial sensory placodes

Cranial sensory placodes are specialised areas of the head ectoderm of vertebrate embryos that contribute to the formation of the cranial sense organs and associated ganglia. Placodes are often considered a vertebrate innovation, and their evolution has been hypothesised as one key adaptation underlying the evolution of active predation by primitive vertebrates. Here, we review recent molecular evidence pertinent to understanding the evolutionary origin of placodes. The development of vertebrate placodes is regulated by numerous genes, including members of the Pax, Six, Eya, Fox, Phox, Neurogenin and Pou gene families. In the sea squirt Ciona intestinalis (a basal chordate and close relative of the vertebrates), orthologues of these genes are deployed in the development of the oral and atrial siphons, structures used for filter feeding by the sessile adult. Our interpretation of these findings is that vertebrate placodes and sea squirt siphon primordia have evolved from the same patches of specialised ectoderm present in the common ancestor of the chordates.

Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes

Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates. Despite their importance for understanding vertebrate origins, the evolutionary origin of placodes has remained obscure. Here, we use a panel of molecular markers from the Six, Eya, Pax, Dach, FoxI, COE and POUIV gene families to examine the tunicate Ciona intestinalis for evidence of structures homologous to vertebrate placodes. Our results identify two domains of Ciona ectoderm that are marked by the genetic cascade that regulates vertebrate placode formation. The first is just anterior to the brain, and we suggest this territory is equivalent to the olfactoty/adenohypophyseal placodes of vertebrates. The second is a bilateral domain adjacent to the posterior brain and includes cells fated to form the atrium and atrial siphon of adult Ciona. We show this bares most similarity to placodes fated to form the vertebrate acoustico-lateralis system. We interpret these data as support for the hypothesis that sensory placodes did not arise de novo in vertebrates, but evolved froth pre-existing specialised areas of ectoderm that contributed to sensory organs in the common ancestor of vertebrate and tunicates. Published by Elsevier Inc.

Managing threatened species: the ecological toolbox, evolutionary theory and declining-population paradigm

1. The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining-population paradigm identified by Caughley. 2. There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour-based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application. 3. These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviour-based models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions. 4. Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past. 5. Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population-level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level. 6. Synthesis and applications. It is argued that evolutionary theory underpins Caughley's declining-population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision-making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.

The life history legacy of evolutionary body size change in carnivores

We estimate the body sizes of direct ancestors of extant carnivores, and examine selected aspects of life history as a function not only of species' current size, but also of recent changes in size. Carnivore species that have undergone marked recent evolutionary size change show life history characteristics typically associated with species closer to the ancestral body size. Thus, phyletic giants tend to mature earlier and have larger litters of smaller offspring at shorter intervals than do species of the same body size that are not phyletic giants. Phyletic dwarfs, by contrast, have slower life histories than nondwarf species of the same body size. We discuss two possible mechanisms for the legacy of recent size change: lag (in which life history variables cannot evolve as quickly as body size, leading to species having the 'wrong' life history for their body size) and body size optimization (in which life history and hence body size evolve in response to changes in energy availability); at present, we cannot distinguish between these alternatives. Our finding that recent body size changes help explain residual variation around life history allometries shows that a more dynamic view of character change enables comparative studies to make more precise predictions about species traits in the context of their evolutionary background.