Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships

The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods

Contribution of Transcription Factor Binding Site Motif Variants to Condition-Specific Gene Expression Patterns in Budding Yeast

It is now experimentally well known that variant sequences of a cis transcription factor binding site motif can contribute to differential regulation of genes. We characterize the relationship between motif variants and gene expression by analyzing expression microarray data and binding site predictions. To accomplish this, we statistically detect motif variants with effects that differ among environments. Such environmental specificity may be due to either affinity differences between variants or, more likely, differential interactions of TFs bound to these variants with cofactors, and with differential presence of cofactors across environments. We examine conservation of functional variants across four Saccharomyces species, and find that about a third of transcription factors have target genes that are differentially expressed in a condition-specific manner that is correlated with the nucleotide at variant motif positions. We find good correspondence between our results and some cases in the experimental literature (Reb1, Sum1, Mcm1, and Rap1). These results and growing consensus in the literature indicates that motif variants may often be functionally distinct, that this may be observed in genomic data, and that variants play an important role in condition-specific gene regulation.</p

Multi-color Optical and NIR Light Curves of 64 Stripped-Envelope Core-Collapse Supernovae

We present a densely-sampled, homogeneous set of light curves of 64 low redshift (z < 0.05) stripped-envelope supernovae (SN of type IIb, Ib, Ic and Ic-bl). These data were obtained between 2001 and 2009 at the Fred L. Whipple Observatory (FLWO) on Mt. Hopkins in Arizona, with the optical FLWO 1.2-m and the near-infrared PAIRITEL 1.3-m telescopes. Our dataset consists of 4543 optical photometric measurements on 61 SN, including a combination of UBVRI, UBVr'i', and u'BVr'i', and 2142 JHKs near-infrared measurements on 25 SN. This sample constitutes the most extensive multi-color data set of stripped-envelope SN to date. Our photometry is based on template-subtracted images to eliminate any potential host galaxy light contamination. This work presents these photometric data, compares them with data in the literature, and estimates basic statistical quantities: date of maximum, color, and photometric properties. We identify promising color trends that may permit the identification of stripped-envelope SN subtypes from their photometry alone. Many of these SN were observed spectroscopically by the CfA SN group, and the spectra are presented in a companion paper (Modjaz et al. 2014). A thorough exploration that combines the CfA photometry and spectroscopy of stripped-envelope core-collapse SN will be presented in a follow-up paper.Comment: 26 pages, 17 figures, 8 tables. Revised version resubmitted to ApJ Supplements after referee report. Additional online material is available through http://cosmo.nyu.edu/SNYU

Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade

Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms.Organismic and Evolutionary Biolog

Horizontal transfer of expressed genes in a parasitic flowering plant

Background: Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association between the parasite and its host. HGT in these systems has been invoked when a DNA sequence obtained from a parasite is placed phylogenetically very near to its host rather than with its closest relatives. Studies of HGT in parasitic plants have relied largely on the fortuitous discovery of gene phylogenies that indicate HGT, and no broad systematic search for HGT has been undertaken in parasitic systems where it is most expected to occur. Results: We analyzed the transcriptomes of the holoparasite Rafflesia cantleyi Solms-Laubach and its obligate host Tetrastigma rafflesiae Miq. using phylogenomic approaches. Our analyses show that several dozen actively transcribed genes, most of which appear to be encoded in the nuclear genome, are likely of host origin. We also find that hundreds of vertically inherited genes (VGT) in this parasitic plant exhibit codon usage properties that are more similar to its host than to its closest relatives. Conclusions: Our results establish for the first time a substantive number of HGTs in a plant host-parasite system. The elevated rate of unidirectional host-to- parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesia for maintaining these genes. Finally, a similar convergence in codon usage of VGTs has been shown in microbes with high HGT rates, which may help to explain the increase of HGTs in these parasitic plants.Organismic and Evolutionary Biolog

CfAIR2: Near Infrared Light Curves of 94 Type Ia Supernovae

CfAIR2 is a large homogeneously reduced set of near-infrared (NIR) light curves for Type Ia supernovae (SN Ia) obtained with the 1.3m Peters Automated InfraRed Imaging TELescope (PAIRITEL). This data set includes 4607 measurements of 94 SN Ia and 4 additional SN Iax observed from 2005-2011 at the Fred Lawrence Whipple Observatory on Mount Hopkins, Arizona. CfAIR2 includes JHKs photometric measurements for 88 normal and 6 spectroscopically peculiar SN Ia in the nearby universe, with a median redshift of z~0.021 for the normal SN Ia. CfAIR2 data span the range from -13 days to +127 days from B-band maximum. More than half of the light curves begin before the time of maximum and the coverage typically contains ~13-18 epochs of observation, depending on the filter. We present extensive tests that verify the fidelity of the CfAIR2 data pipeline, including comparison to the excellent data of the Carnegie Supernova Project. CfAIR2 contributes to a firm local anchor for supernova cosmology studies in the NIR. Because SN Ia are more nearly standard candles in the NIR and are less vulnerable to the vexing problems of extinction by dust, CfAIR2 will help the supernova cosmology community develop more precise and accurate extragalactic distance probes to improve our knowledge of cosmological parameters, including dark energy and its potential time variation.Comment: 31 pages, 15 figures, 10 tables. Accepted to ApJS. v2 modified to more closely match journal versio

Distribution of DHPS Mutations Among ITS Subtypes of P. carinii f. sp. hominis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/92387/1/j.1550-7408.2001.tb00481.x.pd

Type Ia Supernovae are Good Standard Candles in the Near Infrared: Evidence from PAIRITEL

We have obtained 1087 NIR (JHKs) measurements of 21 SNe Ia using PAIRITEL, nearly doubling the number of well-sampled NIR SN Ia light curves. These data strengthen the evidence that SNe Ia are excellent standard candles in the NIR, even without correction for optical light-curve shape. We construct fiducial NIR templates for normal SNe Ia from our sample, excluding only the three known peculiar SNe Ia: SN 2005bl, SN 2005hk, and SN 2005ke. The H-band absolute magnitudes in this sample of 18 SNe Ia have an intrinsic rms of only 0.15 mag with no correction for light-curve shape. We found a relationship between the H-band extinction and optical color excess of AH=0.2E(B-V). This variation is as small as the scatter in distance modulus measurements currently used for cosmology based on optical light curves after corrections for light-curve shape. Combining the homogeneous PAIRITEL measurements with 23 SNe Ia from the literature, these 41 SNe Ia have standard H-band magnitudes with an rms scatter of 0.16 mag. The good match of our sample with the literature sample suggests there are few systematic problems with the photometry. We present a nearby NIR Hubble diagram that shows no correlation of the residuals from the Hubble line with light-curve properties. Future samples that account for optical and NIR light-curve shapes, absorption, spectroscopic variation, or host-galaxy properties may reveal effective ways to improve the use of SNe Ia as distance indicators. Since systematic errors due to dust absorption in optical bands remain the leading difficulty in the cosmological use of supernovae, the good behavior of SN Ia NIR light curves and their relative insensitivity to reddening make these objects attractive candidates for future cosmological work.Comment: 37 pages. 8 Figures. 3 Tables. Revised to ApJ-accepted versio

Multi-Messenger Astronomy with Extremely Large Telescopes

The field of time-domain astrophysics has entered the era of Multi-messenger Astronomy (MMA). One key science goal for the next decade (and beyond) will be to characterize gravitational wave (GW) and neutrino sources using the next generation of Extremely Large Telescopes (ELTs). These studies will have a broad impact across astrophysics, informing our knowledge of the production and enrichment history of the heaviest chemical elements, constrain the dense matter equation of state, provide independent constraints on cosmology, increase our understanding of particle acceleration in shocks and jets, and study the lives of black holes in the universe. Future GW detectors will greatly improve their sensitivity during the coming decade, as will near-infrared telescopes capable of independently finding kilonovae from neutron star mergers. However, the electromagnetic counterparts to high-frequency (LIGO/Virgo band) GW sources will be distant and faint and thus demand ELT capabilities for characterization. ELTs will be important and necessary contributors to an advanced and complete multi-messenger network.Comment: White paper submitted to the Astro2020 Decadal Surve