Reconstructing (super)trees from data sets with missing distances: Not all is lost

The wealth of phylogenetic information accumulated over many decades of biological research, coupled with recent technological advances in molecular sequence generation, present significant opportunities for researchers to investigate relationships across and within the kingdoms of life. However, to make best use of this data wealth, several problems must first be overcome. One key problem is finding effective strategies to deal with missing data. Here, we introduce Lasso, a novel heuristic approach for reconstructing rooted phylogenetic trees from distance matrices with missing values, for datasets where a molecular clock may be assumed. Contrary to other phylogenetic methods on partial datasets, Lasso possesses desirable properties such as its reconstructed trees being both unique and edge-weighted. These properties are achieved by Lasso restricting its leaf set to a large subset of all possible taxa, which in many practical situations is the entire taxa set. Furthermore, the Lasso approach is distance-based, rendering it very fast to run and suitable for datasets of all sizes, including large datasets such as those generated by modern Next Generation Sequencing technologies. To better understand the performance of Lasso, we assessed it by means of artificial and real biological datasets, showing its effectiveness in the presence of missing data. Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed Lasso's ability to reconstruct supertrees. We demonstrate that, although not specifically designed for such a purpose, Lasso performs better than or comparably with five leading supertree algorithms on a challenging biological data set. Finally, we make freely available a software implementation of Lasso so that researchers may, for the first time, perform both rooted tree and supertree reconstruction with branch lengths on their own partial datasets

A comparative study of herbage intake, ingestive behaviour and diet selection, and effects of condensed tannins upon body and wool growth in lambs grazing Yorkshire fog (Holcus lanatus) and annual ryegrass (Lolium multiflorum) dominant swards

An experiment was carried out from August to early November 1994 to examine differences in diet selection, herbage intake, grazing behaviour and animal performance between weaned lambs rotationally grazing swards of annual ryegrass (Lolium multiflorum)/white clover (Trifolium repens) and Yorkshire fog (Holcus lanatus)/T. repens with or without Lotus corniculatus. There were four replicate groups of six lambs per treatment. The effects of condensed tannins (CT) on lamb production were assessed by twice-daily oral administration of 10g polyethylene glycol (PEG; molecular weight 4000) to half the lambs on each sward. The Lotus content of all swards was very low, and results are presented here for main sward comparisons meaned over lotus treatments. Overall mean estimates of pre-grazing herbage mass and sward surface height for the annual ryegrass and Yorkshire fog swards respectively, were 5820 v. 4360 +/- 190 kg DM/ha (P , P < 0.01) and liveweight gain (141 v. 120 +/- 4.3 g per lamb per day, P < 0.01), although differences in carcass weight (17.9 v. 18.2 +/- 0.3 kg) and FEC transformed values (9.6 v. 11.0 +/- 06 eggs/g fresh faeces) were not significant. The effects of CT on animal performance were greater in Yorkshire fog swards. CT had no significant effects on diet selection, herbage intake and grazing behaviour patterns

Cognitive Information Processing

Contains reports on one research project.National Institutes of Health (Grant 5 P01 GM14940-07

The Morphologies of the Small Magellanic Cloud

We compare the distribution of stars of different spectral types, and hence mean age, within the central SMC and find that the asymmetric structures are almost exclusively composed of young main sequence stars. Because of the relative lack of older stars in these features, and the extremely regular distribution of red giant and clump stars in the SMC central body, we conclude that tides alone are not responsible for the irregular appearance of the central SMC. The dominant physical mechanism in determining the current-day appearance of the SMC must be star formation triggered by a hydrodynamic interaction between gaseous components. These results extend the results of population studies (cf. Gardiner and Hatzidimitriou) inward in radius and also confirm the suggestion of the spheroidal nature of the central SMC based on kinematic arguments (Dopita et al; Hardy, Suntzeff & Azzopardi). Finally, we find no evidence in the underlying older stellar population for a ``bar'' or ``outer arm'', again supporting our classification of the central SMC as a spheroidal body with highly irregular recent star formation.Comment: 8 pages, accepted for publication in ApJ Letters (higher quality figures available at http://ngala.as.arizona.edu/dennis/mcsurvey.html

Intrinsic and extrinsic geometries of a tidally deformed black hole

A description of the event horizon of a perturbed Schwarzschild black hole is provided in terms of the intrinsic and extrinsic geometries of the null hypersurface. This description relies on a Gauss-Codazzi theory of null hypersurfaces embedded in spacetime, which extends the standard theory of spacelike and timelike hypersurfaces involving the first and second fundamental forms. We show that the intrinsic geometry of the event horizon is invariant under a reparameterization of the null generators, and that the extrinsic geometry depends on the parameterization. Stated differently, we show that while the extrinsic geometry depends on the choice of gauge, the intrinsic geometry is gauge invariant. We apply the formalism to solutions to the vacuum field equations that describe a tidally deformed black hole. In a first instance we consider a slowly-varying, quadrupolar tidal field imposed on the black hole, and in a second instance we examine the tide raised during a close parabolic encounter between the black hole and a small orbiting body.Comment: 27 pages, 4 figure

Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica.

Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales

Normal, Abby Normal, Prefix Normal

A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present results about the number $pnw(n)$ of prefix normal words of length $n$, showing that $pnw(n) =\Omega\left(2^{n - c\sqrt{n\ln n}}\right)$ for some $c$ and $pnw(n) = O \left(\frac{2^n (\ln n)^2}{n}\right)$. We introduce efficient algorithms for testing the prefix normal property and a "mechanical algorithm" for computing prefix normal forms. We also include games which can be played with prefix normal words. In these games Alice wishes to stay normal but Bob wants to drive her "abnormal" -- we discuss which parameter settings allow Alice to succeed.Comment: Accepted at FUN '1

New Evidence of a Post-Laurentide Local Cirque Glacier on Mount Washington, New Hampshire

As global temperatures warmed and the last North American continental ice sheet receded there were several climate reversals during which time mean temperatures in New England were significantly reduced. Decreased temperatures in combination with increased precipitation may have supported the formation or reactivation of local mountain glaciers in pre-existing cirques on Mt. Washington, New Hampshire. Evidence supporting the existence of a local cirque glacier would provide important constraints on climatic conditions during the late-glacial Holocene transition. Preliminary mapping done in the area has identified a potential terminal moraine associated with a local valley glacier in the Great Gulf, the largest cirque-like feature on Mount Washington. The presence of this landform is significant because any pre-Wisconsin evidence of valley glaciers in the Great Gulf would likely have been expunged by the presence of continental ice. In order to determine the origins of the terminal moraine, representative samples of the till composing the moraine were collected by digging five test pits across the feature, sampling ~50 hand-sized stones from each pit, and determining the provenence of individual stones. Results indicate that the landform is composed of unsorted clasts with provenances of both local and regional origin. Clasts sourced within the Great Gulf support the interpretation that they were deposited by processes dependent on the presence of a local mountain glacier during a post-Wisconsin climate reversal. Stones of more distant origins may be attributed to residual till, associated with a continental ice mass that occupied the cirque at the time of local glacier reactivation. This data shows that the landform was deposited from processes taking place within the Great Gulf, and the pronounced topography and volume of the landform would support its interpretation as a terminal moraine. By reconstructing the glacier using the feature as terminus, a paleo-ELA was calculated and climate conditions necessary to promote the growth of an icemass were ascertained. Comparing this climate to the contemporary allows us to evaluate the magnitude of late-Pleistocene climate reversals in the White Mountains