Pearce E.,South Parks Road |
Pearce E.,University of Oxford |
Stringer C.,Natural History Museum in London |
Dunbar R.I.M.,South Parks Road
Proceedings of the Royal Society B: Biological Sciences | Year: 2013
Previous research has identified morphological differences between the brains of Neanderthals and anatomically modern humans (AMHs). However, studies using endocasts or the cranium itself are limited to investigating external surface features and the overall size and shape of the brain. A complementary approach uses comparative primate data to estimate the size of internal brain areas. Previous attempts to do this have generally assumed that identical total brain volumes imply identical internal organization. Here, we argue that, in the case of Neanderthals and AMHs, differences in the size of the body and visual system imply differences in organization between the same-sized brains of these two taxa. We show that Neanderthals had significantly larger visual systems than contemporary AMHs (indexed by orbital volume) and that when this, along with their greater body mass, is taken into account, Neanderthals have significantly smaller adjusted endocranial capacities than contemporary AMHs. We discuss possible implications of differing brain organization in terms of social cognition, and consider these in the context of differing abilities to cope with fluctuating resources and cultural maintenance. © 2013 The Author(s) Published by the Royal Society. All rights reserved.
Rao V.,Duke University |
Teh Y.W.,South Parks Road
Journal of Machine Learning Research | Year: 2013
Markov jump processes (or continuous-time Markov chains) are a simple and important class of continuous-time dynamical systems. In this paper, we tackle the problem of simulating from the posterior distribution over paths in these models, given partial and noisy observations. Our approach is an auxiliary variable Gibbs sampler, and is based on the idea of uniformization. This sets up a Markov chain over paths by alternately sampling a finite set of virtual jump times given the current path, and then sampling a new path given the set of extant and virtual jump times. The first step involves simulating a piecewise-constant inhomogeneous Poisson process, while for the second, we use a standard hidden Markov model forward filtering-backward sampling algorithm. Our method is exact and does not involve approximations like time-discretization. We demonstrate how our sampler extends naturally toMJP-based models likeMarkov-modulated Poisson processes and continuous-time Bayesian networks, and show significant computational benefits over state-ofthe- art MCMC samplers for these models. © 2013 Vinayak Rao and Yee Whye Teh.
Iqbal Z.,Oxford Genetics |
Turner I.,South Parks Road |
McVean G.,Oxford Genetics
Bioinformatics | Year: 2013
We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide polymorphisms, indels and larger events in a single framework. We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction of a graph of known sequence and variation in a species, against which new samples can be compared rapidly. We demonstrate the ease-of-use and power by reproducing the results of studies using both long and short reads. © 2012 The Author. Published by Oxford University Press. All rights reserved.
Pearce E.,South Parks Road
Proceedings. Biological sciences / The Royal Society | Year: 2013
Previous research has identified morphological differences between the brains of Neanderthals and anatomically modern humans (AMHs). However, studies using endocasts or the cranium itself are limited to investigating external surface features and the overall size and shape of the brain. A complementary approach uses comparative primate data to estimate the size of internal brain areas. Previous attempts to do this have generally assumed that identical total brain volumes imply identical internal organization. Here, we argue that, in the case of Neanderthals and AMHs, differences in the size of the body and visual system imply differences in organization between the same-sized brains of these two taxa. We show that Neanderthals had significantly larger visual systems than contemporary AMHs (indexed by orbital volume) and that when this, along with their greater body mass, is taken into account, Neanderthals have significantly smaller adjusted endocranial capacities than contemporary AMHs. We discuss possible implications of differing brain organization in terms of social cognition, and consider these in the context of differing abilities to cope with fluctuating resources and cultural maintenance.
Kirby K.J.,South Parks Road
Hacquetia | Year: 2015
Wood-pastures are important for their open-ground biodiversity and for the old trees they contain. However, younger trees to replace the current generation of old trees are often scarce, a potential threat to the future of the habitat mosaic and of species dependent on the trees. A simple model was used to illustrate how many younger trees might be expected under different assumptions of desired final density of old trees and rates of loss as trees age for an oak-dominated wood-pasture. From these the overall canopy cover of the landscape was estimated under an active pollarding regime and where the trees grow to full crown size. Canopy cover was often five times as great under full crown as under a pollarding regime; much of the canopy cover was in the younger (often missing) cohorts. The openness of current wood-pastures is in part a consequence of the absence of a sustainable tree population structure. Some protected sites may be too small to allow space for the missing generation of trees and at the same time retain current levels of openness. Analogies between current wood-pasture structures and 'natural wood-pastures' of the pre-Neolithic era must take account of the missing generations of trees. © by Keith J. Kirby 2015.
Platt B.,South Parks Road |
Kadosh K.C.,South Parks Road |
Lau J.Y.F.,South Parks Road
Depression and Anxiety | Year: 2013
Adolescence is a period of major risk for depression, which is associated with negative personal, social, and educational outcomes. Yet, in comparison to adult models of depression, very little is known about the specific psychosocial stressors that contribute to adolescent depression, and whether these can be targeted by interventions. In this review, we consider the role of peer rejection. First, we present a comprehensive review of studies using innovative experimental paradigms to understand the role of peer rejection in adolescent depression. We show how reciprocal relationships between peer rejection and depressive symptoms across adolescence powerfully shape and maintain maladaptive trajectories. Second, we consider how cognitive biases and their neurobiological substrates may explain why some adolescents are more vulnerable to the effects of, and perhaps exposure to, peer rejection compared to others. Finally, we draw attention to emerging cognitive and functional magnetic resonance imaging-based neurofeedback training, which by modifying aspects of information processing may promote more adaptive responses to peer rejection. A better understanding of the mechanisms underlying adolescent depression may not only alleviate symptoms during a period of substantial developmental challenges, but may also reduce the burden of the disorder across the lifespan. © 2013 Wiley Periodicals, Inc.
Ali W.,South Parks Road |
Deane C.M.,South Parks Road
Molecular BioSystems | Year: 2010
Local alignments of protein interaction networks have found little conservation among several species. While this could be a consequence of the incompleteness of interaction data-sets and presence of error, an intriguing prospect is that the process of network evolution is sufficient to erase any evidence of conservation. Here, we aim to test this hypothesis using models of network evolution and also investigate the role of error in the results of network alignment. We devised a distance metric based on summary statistics to assess the fit between experimental and simulated network alignments. Our results indicate that network evolution alone is unlikely to account for the poor quality alignments given by real data. Alignments of simulated networks undergoing evolution are considerably (4 to 5 times) larger than real alignments. We compare several error models in their ability to explain this discrepancy. Our estimates of false negative rates vary from 20 to 60% dependent on whether incomplete proteome sampling is taken into account or not. We also find that false positives appear to affect network alignments little compared to false negatives indicating that incompleteness, not spurious links, is the major challenge for interactome-level comparisons. © 2010 The Royal Society of Chemistry.
Wade J.,South Parks Road |
Wood B.J.,South Parks Road |
Norris C.A.,South Parks Road
Chemical Geology | Year: 2013
Although at 1atm pressure the oxidation state of W in silicate melts is 6+at oxygen fugacities from air down to several logfO2 units below Fe-FeO (IW) equilibrium, Cottrell et al. (2009) suggested that, at pressures above 6GPa, W becomes predominantly 4+in this oxygen fugacity range. Wade and Wood (2005), using a similar, but expanded metal-silicate partitioning dataset found, however, no evidence for an oxidation state change. In order to resolve the issue we collected tungsten L3 edge XANES spectra of a series of synthetic tungsten- bearing glass standards and of silicates from a range of high-pressure (1.5 to 25GPa) metal/silicate partitioning experiments. Glass standards were made at 1atm pressure and equilibrated at oxygen fugacities spanning a range from approximately 5.5 log units below the Fe-FeO buffer (IW-5.5) to Air. Metal-silicate partitioning experiments were performed at oxygen fugacities between IW-6.2 and IW-1 and at pressures between 1.5 and 25GPa. At low pressures and oxygen fugacities above IW-3.5, W exists in the silicate melt almost exclusively as W6+ (identical L3-edge energy to WO3) with the progressive reduction to W4+ completed by about IW-6. The XANES spectra of W from experiments at 6, 7 and 25GPa are completely consistent with those from 1atm and 1.5GPa experiments and with that of WO3. We conclude that there is no change of oxidation state with increasing pressure to 25GPa and that modelling of the oxygen-fugacity dependence of core formation requires use of a+6 oxidation state of W. © 2012 Elsevier B.V.
Li N.,South Parks Road |
Dickinson H.G.,South Parks Road
Proceedings of the Royal Society B: Biological Sciences | Year: 2010
Key aspects of seed development in flowering plants are held to be under epigenetic control and to have evolved as a result of conflict between the interests of the male and female gametes (kinship theory). Attempts to identify the genes involved have focused on imprinted sequences, although imprinting is only one mechanism by which male or female parental alleles may be exclusively expressed immediately post-fertilization. We have studied the expression of a subset of endosperm gene classes immediately following interploidy crosses in maize and show that departure from the normal 2 : 1 ratio between female and male genomes exerts a dramatic effect on the timing of expression of some, but not all, genes investigated. Paternal genomic excess prolongs the expression of early genes and delays accumulation of reserves, while maternal genomic excess foreshortens the expression period of early genes and dramatically brings forward endosperm maturation. Our data point to a striking interdependence between the phases of endosperm development, and are consonant with previous work from maize showing progression from cell proliferation to endoreduplication is regulated by the balance between maternal and paternal genomes, and from Arabidopsis suggesting that this 'phasing' is regulated by maternally expressed imprinted genes. Our findings are discussed in context of the kinship theory. © 2009 The Royal Society.
Lamb S.,South Parks Road
Tectonophysics | Year: 2011
New Zealand straddles the obliquely convergent boundary between the Pacific and Australian plates, with subduction of Pacific plate along the Hikurangi margin. Finite plate reconstructions predict ~. 800. km of relative plate motion since ~. 43. Ma, with 80-90° clockwise rotation of the Hikurangi margin since ~. 20. Ma, at an average rate of 4-4.5°/Myr, and the short-term deformation (<10. kyr) shows that rotation is still active. Paleomagnetic measurements in Cretaceous and Cenozoic sedimentary and volcanic rocks record rotation about vertical axes of crustal blocks along the Hikurangi margin, conforming closely with that indicated by the plate reconstructions. Since ~. 20. Ma, this was accommodated relative to the Australian plate by along strike gradients of extension and shortening, together with dextral shear on arcuate strike-slip faults. The ends of the rotating part of the Hikurangi margin define hinges. In the south, this is accommodated by dextral shear in the Marlborough Fault Zone, and crustal blocks, 1-50. km across, have rotated 50-130°clockwise, creating the eastern part of the New Zealand Orocline. In the north, the hinge is an onshore arcuate zone of dextral shear, 10-50. km wide, with normal faulting. The Paleogene rotational history is poorly constrained, but the few paleomagnetic observations are consistent with distributed shear of basement terranes in a zone of dextral simple shear, < 200 km wide, running up the western part of the New Zealand, and linking with subduction farther north, creating the western half of the New Zealand Orocline. The overall pattern of rotation shows that the continental lithosphere in the Australian Plate is weak, so that deformation is controlled mainly by boundary forces along the plate interface, and passively follows the change in trend of the subduction zone through time. © 2011 Elsevier B.V.