Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting.

Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135 Ma) divergence of living cichlids demanded by the vicariance model now represents a key calibration for teleost molecular clocks, this putative split pre-dates the oldest cichlid fossils by nearly 90 Myr. Here, we provide independent palaeontological and relaxed-molecular-clock estimates for the time of cichlid origin that collectively reject the antiquity of the group required by the Gondwanan vicariance scenario. The distribution of cichlid fossil horizons, the age of stratigraphically consistent outgroup lineages to cichlids and relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear genes all deliver overlapping estimates for crown cichlid origin centred on the Palaeocene (ca 65-57 Ma), substantially post-dating the tectonic fragmentation of Gondwana. Our results provide a revised macroevolutionary time scale for cichlids, imply a role for dispersal in generating the observed geographical distribution of this important model clade and add to a growing debate that questions the dominance of the vicariance paradigm of historical biogeography

Genetic Structure of Midwestern \u3ci\u3eAscaris suum\u3c/i\u3e Populations: A Comparison of Isoenzyme and RAPD Markers

Isoenzyme and random amplified polymorphic DNA (RAPD) markers were used to characterize the genetics of geographic variation among population samples of Ascaris suum from midwestern localities. Independent estimates of fixation indices (FST) based on isoenzyme and RAPD markers showed the same general patterns of differentiation and substantial statistical correlation (r=0.70). Of the total estimated gene diversity, 9.4% (isoenzyme) and 9.2% (RAPD) was distributed among infrapopulations. Geographic localities accounted for 7.8% (isoenzyme) and 6.2% (RAPD) of the total gene diversity. Only infrapopulations and localities, which indicates significant population subdivision among A. suum from farms within geographic regions. Departures from random mating were revealed by deficiencies of heterozygotes within infrapopulations and by high positive values of FIS among and between infrapopulations. The average inbreeding (FIS) coefficient among all infrapopulations was 0.22. Thus, the genetic composition of these A. suum infrapopulations, whether from a general geographic region or a single farm, was not consistent with a model of random recruitment from a larger panmictic pool of parasite life cycle stages

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

BACKGROUND: Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. RESULTS: We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. CONCLUSIONS: Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation

Testing Conditional Independence of Discrete Distributions

We study the problem of testing \emph{conditional independence} for discrete distributions. Specifically, given samples from a discrete random variable $(X, Y, Z)$ on domain $[\ell_1]\times[\ell_2] \times [n]$, we want to distinguish, with probability at least $2/3$, between the case that $X$ and $Y$ are conditionally independent given $Z$ from the case that $(X, Y, Z)$ is $\epsilon$-far, in $\ell_1$-distance, from every distribution that has this property. Conditional independence is a concept of central importance in probability and statistics with a range of applications in various scientific domains. As such, the statistical task of testing conditional independence has been extensively studied in various forms within the statistics and econometrics communities for nearly a century. Perhaps surprisingly, this problem has not been previously considered in the framework of distribution property testing and in particular no tester with sublinear sample complexity is known, even for the important special case that the domains of $X$ and $Y$ are binary. The main algorithmic result of this work is the first conditional independence tester with {\em sublinear} sample complexity for discrete distributions over $[\ell_1]\times[\ell_2] \times [n]$. To complement our upper bounds, we prove information-theoretic lower bounds establishing that the sample complexity of our algorithm is optimal, up to constant factors, for a number of settings. Specifically, for the prototypical setting when $\ell_1, \ell_2 = O(1)$, we show that the sample complexity of testing conditional independence (upper bound and matching lower bound) is \[ \Theta\left({\max\left(n^{1/2}/\epsilon^2,\min\left(n^{7/8}/\epsilon,n^{6/7}/\epsilon^{8/7}\right)\right)}\right)\,. \

Occipital GABA correlates with cognitive failures in daily life.

The brain has limited capacity, and so selective attention enhances relevant incoming information while suppressing irrelevant information. This process is not always successful, and the frequency of such cognitive failures varies to a large extent between individuals. Here we hypothesised that individual differences in cognitive failures might be reflected in inhibitory processing in the sensory cortex. To test this hypothesis, we measured GABA in human visual cortex using MR spectroscopy and found a negative correlation between occipital GABA (GABA+/Cr ratio) and cognitive failures as measured by an established cognitive failures questionnaire (CFQ). For a second site in parietal cortex, no correlation between CFQ score and GABA+/Cr ratio was found, thus establishing the regional specificity of the link between occipital GABA and cognitive failures. We further found that grey matter volume in the left superior parietal lobule (SPL) correlated with cognitive failures independently from the impact of occipital GABA and together, occipital GABA and SPL grey matter volume statistically explained around 50% of the individual variability in daily cognitive failures. We speculate that the amount of GABA in sensory areas may reflect the potential capacity to selectively suppress irrelevant information already at the sensory level, or alternatively that GABA influences the specificity of neural representations in visual cortex thus improving the effectiveness of successful attentional modulation

Mirror formation control in the vicinity of an asteroid

Two strategies are presented for the positioning and control of a spacecraft formation designed to focus sunlight onto a point on the surface of asteroid, thereby sublimating the material and ejecting debris creating thrust. In the first approach, the formation is located at artficial equilibrium points around the asteroid and controlled using the force from the solar radiation pressure. The second approach determines the optimal periodic formation orbits, subject to the gravitational perturbations from the asteroid, the solar radiation pressure and the control acceleration derived from a control law

Reproductive traits and age of barbeled plunderfishes from the Weddell Sea

AbstractThe genus Pogonophryne is the most species-rich genus of barbeled plunderfishes (Artedidraconidae) and includes more than 25 poorly known species endemic to the Southern Ocean. In this study, we provide new data on the age and reproductive traits of some species of Pogonophryne from the southern Weddell Sea, inferred through otolith reading and histological analyses of gonads. Individual age estimates ranged between 16 and 18 years for Pogonophryne barsukovi and Pogonophryne immaculata and between 10 and 22 years for Pogonophryne scotti. As is commonly found in notothenioids, P. barsukovi followed a group-synchronous type of ovarian development, with pre-vitellogenic and vitellogenic oocytes forming two well-separated egg-size groups. A single spawning female in the sample produced ~1097 eggs and 7.9 eggs g-1. The sample of P. immaculata consisted exclusively of developing males, with testes composed of cysts of spermatogonia, spermatocytes and spermatids. Pogonophryne scotti was the most abundant species, including relatively small males at immature or developing stages of gonad development. Larger females were regressing, being characterized by ovaries with postovulatory follicles and atretic oocytes. Based on the macroscopic and histological analyses of gonads, the spawning season would take place in autumn for P. barsukovi and P. immaculata and in spring–early summer for P. scotti

Changes in functional connectivity and GABA levels with long-term motor learning

Learning novel motor skills alters local inhibitory circuits within primary motor cortex (M1) (Floyer-Lea et al., 2006) and changes long-range functional connectivity (Albert et al., 2009). Whether such effects occur with long-term training is less well established. In addition, the relationship between learning-related changes in functional connectivity and local inhibition, and their modulation by practice, has not previously been tested. Here, we used resting-state functional magnetic resonance imaging (rs-fMRI) to assess functional connectivity and MR spectroscopy to quantify GABA in primary motor cortex (M1) before and after a 6 week regime of juggling practice. Participants practiced for either 30 min (high intensity group) or 15 min (low intensity group) per day. We hypothesized that different training regimes would be reflected in distinct changes in brain connectivity and local inhibition, and that correlations would be found between learning-induced changes in GABA and functional connectivity. Performance improved significantly with practice in both groups and we found no evidence for differences in performance outcomes between the low intensity and high intensity groups. Despite the absence of behavioral differences, we found distinct patterns of brain change in the two groups: the low intensity group showed increases in functional connectivity in the motor network and decreases in GABA, whereas the high intensity group showed decreases in functional connectivity and no significant change in GABA. Changes in functional connectivity correlated with performance outcome. Learning-related changes in functional connectivity correlated with changes in GABA. The results suggest that different training regimes are associated with distinct patterns of brain change, even when performance outcomes are comparable between practice schedules. Our results further indicate that learning-related changes in resting-state network strength in part reflect GABAergic plastic processes

Vortex annihilation in the ordering kinetics of the O(2) model

The vortex-vortex and vortex-antivortex correlation functions are determined for the two-dimensional O(2) model undergoing phase ordering. We find reasonably good agreement with simulation results for the vortex-vortex correlation function where there is a short-scaled distance depletion zone due to the repulsion of like-signed vortices. The vortex-antivortex correlation function agrees well with simulation results for intermediate and long-scaled distances. At short-scaled distances the simulations show a depletion zone not seen in the theory.Comment: 28 pages, REVTeX, submitted to Phys. Rev.

Fluctuations and defect-defect correlations in the ordering kinetics of the O(2) model

The theory of phase ordering kinetics for the O(2) model using the gaussian auxiliary field approach is reexamined from two points of view. The effects of fluctuations about the ordering field are included and we organize the theory such that the auxiliary field correlation function is analytic in the short-scaled distance (x) expansion. These two points are connected and we find in the refined theory that the divergence at the origin in the defect-defect correlation function $\tilde{g}(x)$ obtained in the original theory is removed. Modifications to the order-parameter autocorrelation exponent $\lambda$ are computed.Comment: 29 pages, REVTeX, to be published in Phys. Rev. E. Minor grammatical/syntax changes from the origina