Evolutionary sequence analysis of complete eukaryote genomes

BACKGROUND: Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation. RESULTS: Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies. CONCLUSION: Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes

Tres especies nuevas de Pristimantis (Lissamphibia: Anura) en los bosques montanos de la Cordillera Yanachaga en el centro del Perú

We describe three additional new species of Pristimantis from the Cordillera Yanachaga, a part of the Andes in central Peru. Analyses of DNA sequences of the mitochondrial rRNA genes show that one species is a close relative of P. bipunctatus (P. conspicillatus Group), another is a close relative of P. stictogaster (P. peruvianus Group), and the third is related to several species in the P. unistrigatus Group. The first two species are morphologically similar to their closest relatives but occur at lower elevations. Twenty-nine species of Pristimantis and Phrynopus are known from the vicinity of the Cordillera Yanachaga. The number of species, especially of Pristimantis, is high in the humid montane forest in comparison with other sites in humid montane forests in Peru, but the number is lower than on the western slopes of the Andes in Ecuador.Describimos tres especies nuevas de Pristimantis provenientes de la Cordillera Yanachaga, en los Andes del centro del Perú. Los análisis de las secuencias de ADN mitocondrial de genes ribosomales muestran que una de las especies está cercanamente relacionada con P. bipunctatus (Grupo P. conspicillatus), la segunda especie con P. stictogaster (Grupo P. peruvianus) y la tercera con varias especies del Grupo P. unistrigatus. Las primeras dos especies son morfológicamente similares a sus respectivas especies hermanas, pero sin embargo habitan en elevaciones más bajas. Se conocen 29 especies de ranas del g´nero Phrynopus y Pristimantis en las inmediaciones de la Cordillera Yanachaga. Esta diversidad de especies, particularmente de Pristimantis, es elevada en comparación con otras localidades de características similares en el Perú; sin embargo, es menor a la reportada en la vertiente occidental de los Andes del Ecuador

The evolutionary position of nematodes

BACKGROUND: The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes. RESULTS: We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes. CONCLUSION: We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms

On transversally elliptic operators and the quantization of manifolds with ff-structure

An $f$-structure on a manifold $M$ is an endomorphism field \phi\in\Gamma(M,\End(TM)) such that $\phi^3+\phi=0$. Any $f$-structure $\phi$ determines an almost CR structure E_{1,0}\subset T_\C M given by the $+i$-eigenbundle of $\phi$. Using a compatible metric $g$ and connection $\nabla$ on $M$, we construct an odd first-order differential operator $D$, acting on sections of $\S=\Lambda E_{0,1}^*$, whose principal symbol is of the type considered in arXiv:0810.0338. In the special case of a CR-integrable almost $\S$-structure, we show that when $\nabla$ is the generalized Tanaka-Webster connection of Lotta and Pastore, the operator $D$ is given by D = \sqrt{2}(\dbbar+\dbbar^*), where \dbbar is the tangential Cauchy-Riemann operator. We then describe two "quantizations" of manifolds with $f$-structure that reduce to familiar methods in symplectic geometry in the case that $\phi$ is a compatible almost complex structure, and to the contact quantization defined in \cite{F4} when $\phi$ comes from a contact metric structure. The first is an index-theoretic approach involving the operator $D$; for certain group actions $D$ will be transversally elliptic, and using the results in arXiv:0810.0338, we can give a Riemann-Roch type formula for its index. The second approach uses an analogue of the polarized sections of a prequantum line bundle, with a CR structure playing the role of a complex polarization.Comment: 31 page

A molecular timescale of eukaryote evolution and the rise of complex multicellular life

BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20–188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to ~10 types at 1500 Ma and 50 cell types at ~1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2–3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity

National registry for sudden unexpected deaths of infants and children in England: why do we need one and do families want one?

The sudden and unexpected death of an infant or child is devastating. An inability to explain why an infant or child died is difficult to accept for both families and professionals. No reliable national dataset exists to estimate precisely how many infants and children die unexpectedly each year in England. This lack of accurate epidemiological data belies the scale of this public health problem. Detailed controlled observational studies of infant deaths identifying risk factors and providing evidence-based advice for parents has seen a dramatic reduction in incidence over the last 30 years by almost 80% but greater knowledge is needed if future deaths of infants and older children are to be prevented and families optimally supported. We propose that a national registry of sudden unexpected deaths in infancy and childhood would accurately determine incidence, identify unknown risk factors and highlight good care practices, ensuring these can be standardised nationally. For such a project to be successful, however, parents must be at the heart of it. We held a consultation day between families, professionals and supporting charities (The Lullaby Trust, Child Bereavement UK, SUDC UK and CRY) to seek opinion on the desire for a registry and how best to ensure families are engaged. Here, we summarise our rationale for a registry and the feedback we received from attendees regarding their views of the proposal and the practical aspects of administering it

Isotopic composition of Murchison organic compounds: Intramolecular carbon isotope fractionation of acetic acid. Simulation studies of cosmochemical organic syntheses

Recently, in our laboratories, samples of Murchison acetic acid were decarboxylated successfully and the carbon isotopic composition was measured for the methane released by this procedure. These analyses showed significant differences in C-13/C-12 ratios for the methyl and carboxyl carbons of the acetic acid molecule, strongly suggesting that more than one carbon source may be involved in the synthesis of the Murchison organic compounds. On the basis of this finding, laboratory model systems simulating cosmochemical synthesis are being studied, especially those processes capable of involving two or more starting carbon sources

Validity and practical utility of accelerometry for the measurement of in-hand physical activity in horses

Background: Accelerometers are valid, practical and reliable tools for the measurement of habitual physical activity (PA). Quantification of PA in horses is desirable for use in research and clinical settings. The objective of this study was to evaluate a triaxial accelerometer for objective measurement of PA in the horse by assessment of their practical utility and validity. Horses were recruited to establish both the optimal site of accelerometer attachment and questionnaire designed to explore owner acceptance. Validity and cut-off values were obtained by assessing PA at various gaits. Validation study- 20 horses wore the accelerometer while being filmed for 10 min each of rest, walking and trotting and 5 mins of canter work. Practical utility study- five horses wore accelerometers on polls and withers for 18 h; compliance and relative data losses were quantified. Results: Accelerometry output differed significantly between the four PA levels (P <0•001) for both wither and poll placement. For withers placement, ROC analyses found optimal sensitivity and specificity at a cut-off of <47 counts per minute (cpm) for rest (sensitivity 99.5 %, specificity 100 %), 967–2424 cpm for trotting (sensitivity 96.7 %, specificity 100 %) and ≥2425 cpm for cantering (sensitivity 96.0 %, specificity 97.0 %). Attachment at the poll resulted in optimal sensitivity and specificity at a cut-off of <707 counts per minute (cpm) for rest (sensitivity 97.5 %, specificity 99.6 %), 1546–2609 cpm for trotting (sensitivity 90.33 %, specificity 79.25 %) and ≥2610 cpm for cantering (sensitivity 100 %, specificity 100 %) In terms of practical utility, accelerometry was well tolerated and owner acceptance high. Conclusion: Accelerometry data correlated well with varying levels of in-hand equine activity. The use of accelerometers is a valid method for objective measurement of controlled PA in the horse

Role of branched-chain fatty acids in pH stress tolerance in Listeria monocytogenes

In alkaline conditions, Listeria monocytogenes cells develop higher proportions of branched-chain fatty acids (FAs), including more anteiso forms. In acid conditions, the opposite occurs. Reduced growth of pH-sensitive mutants at adverse pH (5.0/9.0) was alleviated by the addition of 2-methylbutyrate (an anteiso-FA precursor), suggesting that anteiso-FAs are important in adaptation to adverse pH. The balance between anteiso- and iso-FAs may be more important than changes in the amounts and/or degrees of saturation of FAs in pH adaptation