Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance

We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can have the same label. Unlike most previous phylogenetic methods using gene trees, this method does not assume that gene tree incongruence is caused by a single, specific biological process, such as gene duplication and loss, deep coalescence, or lateral gene transfer. We prove that it is NP-hard to compute the RF distance between two mul-trees, but it is easy to calculate the generalized RF distance between a mul-tree and a singly-labeled tree. Motivated by this observation, we formulate the RF supertree problem for mul-trees (MulRF), which takes a collection of mul-trees and constructs a species tree that minimizes the total RF distance from the input mul-trees. We present a fast heuristic algorithm for the MulRF supertree problem. Simulation experiments demonstrate that the MulRF method produces more accurate species trees than gene tree parsimony methods when incongruence is caused by gene tree error, duplications and losses, and/or lateral gene transfer. Furthermore, the MulRF heuristic runs quickly on data sets containing hundreds of trees with up to a hundred taxa.Comment: 16 pages, 11 figure

A search for hidden white dwarfs in the ROSAT EUV survey II: Discovery of a distant DA+F6/7V binary system in a direction of low density neutral hydrogen

We report the results of our final search for hot white dwarfs in unresolved, Sirius-type, binary systems with IUE. One new system, RE J0500-364 (DA+F6/7V), has been identified. This star appears to lie at a distance of between 500-1000pc, making it one of the most distant white dwarfs, if not the most distant, to be detected in the EUV surveys. The very low line-of-sight neutral hydrogen volume density to this object could place a lower limit on the length of the Beta CMa interstellar tunnel of diffuse gas, which stretches away from the Local Bubble in a similar direction to RE J0500-364.Comment: 1 LaTex file plus 15 figures; accepted for publication in Monthly Notices of the Royal Astronomical Societ

The Arizona Radio Observatory CO Mapping Survey of Galactic Molecular Clouds: III. The Serpens Cloud in CO J=2-1 and 13CO J=2-1 Emission

We mapped 12CO and 13CO J = 2-1 emission over 1.04 square deg of the Serpens molecular cloud with 38 arcsec spatial and 0.3 km/s spectral resolution using the Arizona Radio Observatory Heinrich Hertz Submillimeter telescope. Our maps resolve kinematic properties for the entire Serpens cloud. We also compare our velocity moment maps with known positions of Young Stellar Objects (YSOs) and 1.1 mm continuum emission. We find that 12CO is self-absorbed and 13CO is optically thick in the Serpens core. Outside of the Serpens core, gas appears in filamentary structures having LSR velocities which are blue-shifted by up to 2 km/s relative to the 8 km/s systemic velocity of the Serpens cloud. We show that the known Class I, Flat, and Class II YSOs in the Serpens core most likely formed at the same spatial location and have since drifted apart. The spatial and velocity structure of the 12CO line ratios implies that a detailed 3-dimensional radiative transfer model of the cloud will be necessary for full interpretation of our spectral data. The starless cores region of the cloud is likely to be the next site of star formation in Serpens.Comment: 41 pages, 15 figure

Assessing systematic error in the inference of seed plant phylogeny

We used parametric bootstrapping to assess the performance of maximum parsimony and maximum likelihood phylogenetic analyses of a 12-locus seed plant data set. Evidence of biases in maximum parsimony analyses of single-locus data sets may explain some of the locus-specific variation among DNA-based hypotheses of seed plant phylogeny. In particular, there is strong evidence of bias in maximum parsimony analyses, especially of plastid loci, that favors placing Gnetales sister to other seed plants. We concatenated simulated single-locus data sets to examine biases in analyses of a 12-locus data set in which each locus is simulated with different substitution parameters and branch lengths. Maximum parsimony analyses of the simulated 12-locus data set also show evidence of biases in favor of recovering trees with Gnetales sister to other seed plants and against recovering anthophyte, gnepine, and gnetifer trees. These biases are most evident in analyses that include the fastest-evolving characters. In the maximum likelihood analyses of the simulated 12-locus data sets, there is evidence of a bias against recovering the anthophyte hypothesis. Otherwise, there is little evidence that the heterogeneous branch lengths and substitution processes among loci influence the results from maximum likelihood phylogenetic analyses. © 2007 by The University of Chicago. All rights reserved

Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life

Effects of taxonomic sampling and conflicting signal on the inference of seed plant trees supported in previous molecular analyses were explored using 13 single-locus data sets. Changing the number of taxa in single-locus analyses had limited effects on log likelihood differences between the gnepine (Gnetales plus Pinaceae) and gnetifer (Gnetales plus conifers) trees. Distinguishing among these trees also was little affected by the use of different substitution parameters. The 13-locus combined data set was partitioned into nine classes based on substitution rates. Sites evolving at intermediate rates had the best likelihood and parsimony scores on gnepine trees, and those evolving at the fastest rates had the best parsimony scores on Gnetales-sister trees (Gnetales plus other seed plants). When the fastest evolving sites were excluded from parsimony analyses, well-supported gnepine trees were inferred from the combined data and from each genomic partition. When all sites were included, Gnetales-sister trees were inferred from the combined data, whereas a different tree was inferred from each genomic partition. Maximum likelihood trees from the combined data and from each genomic partition were well-supported gnepine trees. A preliminary stratigraphic test highlights the poor fit of Gnetales-sister trees to the fossil data

A Near-Infrared Spectroscopic Study of the Accreting Magnetic White Dwarf SDSS J121209.31+013627.7 and its Substellar Companion

The nature of the excess near-infrared emission associated with the magnetic white dwarf commonly known as SDSS 1212 is investigated primarily through spectroscopy, and also via photometry. The inferred low mass secondary in this system has been previously detected by the emission and variation of H$\alpha$, and the $1-2.5$ $\mu$m spectral data presented here are consistent with the presence of a late L or early T dwarf. The excess flux seen beyond 1.5 $\mu$m in the phase-averaged spectrum is adequately modeled with an L8 dwarf substellar companion and cyclotron emission in a 7 MG magnetic field. This interesting system manifests several observational properties typical of polars, and is most likely an old interacting binary with a magnetic white dwarf and a substellar donor in an extended low state.Comment: 28 pages, 5 figures, Accepted to Ap

Assessing among-locus variation in the inference of seed plant phylogeny

Large multilocus analyses can greatly reduce sampling error in phylogenetic estimates and help resolve difficult phylogenetic questions. Yet conventional multilocus analyses may be confounded by variation in the phylogenetic signal or processes of evolution among loci. We used nonparametric bootstrapping methods to examine locus-specific variation within a 12-locus seed plant data set and to examine the effects of this variation on estimates of seed plant phylogeny. The observed maximum likelihood and maximum parsimony bootstrap support from phylogenetic analyses of sites within single loci often notably differs from the bootstrap support obtained by sampling an equal number of sites from the concatenated 12-locus data set. This indicates heterogeneity among loci in the phylogenetic inference, and the differences among loci are not explained by the distribution of fast and slowly evolving sites. Bootstrap analyses that resample loci with replacement, rather than sampling individual sites with replacement, reveal extensive sampling variance among loci. The results suggest that seed plant phylogenetic analyses may not be robust to sampling error when only 12 loci are used and indicate a need for further investigation into the causes of the locus-specific variation. © 2007 by The University of Chicago. All rights reserved