Phylogenomics with incomplete taxon coverage: the limits to inference

<p>Abstract</p> <p>Background</p> <p>Phylogenomic studies based on multi-locus sequence data sets are usually characterized by partial taxon coverage, in which sequences for some loci are missing for some taxa. The impact of missing data has been widely studied in phylogenetics, but it has proven difficult to distinguish effects due to error in tree reconstruction from effects due to missing data per se. We approach this problem using a explicitly phylogenomic criterion of success, <it>decisiveness</it>, which refers to whether the pattern of taxon coverage allows for uniquely defining a single tree for all taxa.</p> <p>Results</p> <p>We establish theoretical bounds on the impact of missing data on decisiveness. Results are derived for two contexts: a fixed taxon coverage pattern, such as that observed from an already assembled data set, and a randomly generated pattern derived from a process of sampling new data, such as might be observed in an ongoing comparative genomics sequencing project. Lower bounds on how many loci are needed for decisiveness are derived for the former case, and both lower and upper bounds for the latter. When data are not decisive for all trees, we estimate the probability of decisiveness and the chances that a given edge in the tree will be distinguishable. Theoretical results are illustrated using several empirical examples constructed by mining sequence databases, genomic libraries such as ESTs and BACs, and complete genome sequences.</p> <p>Conclusion</p> <p>Partial taxon coverage among loci can limit phylogenomic inference by making it impossible to distinguish among multiple alternative trees. However, even though lack of decisiveness is typical of many sparse phylogenomic data sets, it is often still possible to distinguish a large fraction of edges in the tree.</p

Measurement and shaping of biphoton spectral wavefunctions

In this work we present a simple method to reconstruct the complex spectral wavefunction of a biphoton, and hence gain complete information about the spectral and temporal properties of a photon pair. The technique, which relies on quantum interference, is applicable to biphoton states produced with a monochromatic pump when a shift of the pump frequency produces a shift in the relative frequencies contributing to the biphoton. We demonstrate an example of such a situation in type-II parametric down-conversion (SPDC) allowing arbitrary paraxial spatial pump and detection modes. Moreover, our test cases demonstrate the possibility to shape the spectral wavefunction. This is achieved by choosing the spatial mode of the pump and of the detection modes, and takes advantage of spatiotemporal correlations.Comment: Supplementary information also available. Comments and feedback appreciated. Compared to the previous version, here we have made the following changes: -corrected a typo in the text between Eq. (11) and (12) -corrected a typo in the references -added reference

Universal typological dependencies should be detectable in the history of language families

1. Introduction We claim that making sense of the typological diversity of languages demands a historical/evolutionary approach.We are pleased that the target paper (Dunn et al. 2011a) has served to bring discussion of this claim into prominence, and are grateful that leading typologists have taken the time to respond (commentaries denoted by boldface). It is unfortunate though that a number of the commentaries in this issue of LT show significant misunderstandings of our paper. Donohue thinks we were out to show the stability of typological features, but that was not our target at all (although related methods can be used to do that: see, e.g., Greenhill et al. 2010a, Dediu 2011a). Plank seems to think we were arguing against universals of any type, but our target was in fact just the implicational universals of word order that have been the bread and butter of typology. He also seems to think we ignore diachrony, whereas in fact the method introduces diachrony centrally into typological reasoning, thereby potentially revolutionising typology (see Cysouw’s commentary). Levy & Daumé think we were testing for lineage-specificity, whereas that was in fact an outcome (the main finding) of our testing for correlated evolution. Dryer thinks we must account for the distribution of language types around the world, but that was not our aim: our aim was to test the causal connection between linguistic variables by taking the perspective of language evolution (diversification and change). Longobardi & Roberts seem to think we set out to extract family trees from syntactic features, but our goal was in fact to use trees based on lexical cognates and hang reconstructed syntactic states on each node of these trees, thereby reconstructing the processes of language change

Assessing changes in vascular permeability in a hamster model of viral hemorrhagic fever

<p>Abstract</p> <p>Background</p> <p>A number of RNA viruses cause viral hemorrhagic fever (VHF), in which proinflammatory mediators released from infected cells induce increased permeability of the endothelial lining of blood vessels, leading to loss of plasma volume, hypotension, multi-organ failure, shock and death. The optimal treatment of VHF should therefore include both the use of antiviral drugs to inhibit viral replication and measures to prevent or correct changes in vascular function. Although rodent models have been used to evaluate treatments for increased vascular permeability (VP) in bacterial sepsis, such studies have not been performed for VHF.</p> <p>Results</p> <p>Here, we use an established model of Pichinde virus infection of hamsters to demonstrate how changes in VP can be detected by intravenous infusion of Evans blue dye (EBD), and compare those measurements to changes in hematocrit, serum albumin concentration and serum levels of proinflammatory mediators. We show that EBD injected into sick animals in the late stage of infection is rapidly sequestered in the viscera, while in healthy animals it remains within the plasma, causing the skin to turn a marked blue color. This test could be used in live animals to detect increased VP and to assess the ability of antiviral drugs and vasoactive compounds to prevent its onset. Finally, we describe a multiplexed assay to measure levels of serum factors during the course of Pichinde arenavirus infection and demonstrate that viremia and subsequent increase in white blood cell counts precede the elaboration of inflammatory mediators, which is followed by increased VP and death.</p> <p>Conclusions</p> <p>This level of model characterization is essential to the evaluation of novel interventions designed to control the effects of virus-induced hypercytokinemia on host vascular function in VHF, which could lead to improved survival.</p

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function

A review of the dodo and its ecosystem: insights from a vertebrate concentration Lagerstätte in Mauritius

The dodo Raphus cucullatus Linnaeus, an extinct and flightless, giant pigeon endemic to Mauritius, has fascinated people since its discovery, yet has remained surprisingly poorly known. Until the mid-19th century, almost all that was known about the dodo was based on illustrations and written accounts by 17th century mariners, often of questionable accuracy. Furthermore, only a few fragmentary remains of dodos collected prior to the bird's extinction exist. Our understanding of the dodo's anatomy was substantially enhanced by the discovery in 1865 of subfossil bones in a marsh called the Mare aux Songes, situated in southeastern Mauritius. However, no contextual information was recorded during early excavation efforts, and the majority of excavated material comprised larger dodo bones, almost all of which were unassociated. Here we present a modern interdisciplinary analysis of the Mare aux Songes, a 4200-year-old multitaxic vertebrate concentration Lagerstätte. Our analysis of the deposits at this site provides the first detailed overview of the ecosystem inhabited by the dodo. The interplay of climatic and geological conditions led to the exceptional preservation of the animal and associated plant remains at the Mare aux Songes and provides a window into the past ecosystem of Mauritius. This interdisciplinary research approach provides an ecological framework for the dodo, complementing insights on its anatomy derived from the only associated dodo skeletons known, both of which were collected by Etienne Thirioux and are the primary subject of this memoir.publishedVersio

Movement of the inner retina complex during the development of primary full-thickness macular holes: implications for hypotheses of pathogenesis

Background: The inner retinal complex is a well-defined layer in spectral-domain OCT scans of the retina. The central edge of this layer at the fovea provides anatomical landmarks that can be observed in serial OCT scans of developing full-thickness macular holes (FTMH). Measurement of the movement of these points may clarify the mechanism of FTMH formation. Method: This is a retrospective study of primary FTMH that had a sequence of two OCT scans showing progression of the hole. Measurements were made of the dimensions of the hole, including measurements using the central edge of the inner retinal complex (CEIRC) as markers. The inner retinal separation (distance between the CEIRC across the centre of the fovea) and the Height-IRS (average height of CEIRC above the retinal pigment epithelium) were measured. Results: Eighteen cases were identified in 17 patients. The average increase in the base diameter (368 microns) and the average increase in minimum linear dimension (187 microns) were much larger than the average increase in the inner retinal separation (73 microns). The average increase in Height-IRS was 103 microns. Conclusion: The tangential separation of the outer retina to produce the macular hole is much larger than the tangential separation of the inner retinal layers. A model based on the histology of the Muller cells at the fovea is proposed to explain the findings of this study

Colliding Worlds: Asteroid research and the legitimization of war in space

Accepted versio