Imaging the 44 au Kuiper Belt Analog Debris Ring around HD 141569A With GPI Polarimetry

We present the first polarimetric detection of the inner disk component around the pre-main-sequence B9.5 star HD 141569A. Gemini Planet Imager H-band (1.65 μm) polarimetric differential imaging reveals the highest signal-to-noise ratio detection of this ring yet attained and traces structure inward to 0.″25 (28 au at a distance of 111 pc). The radial polarized intensity image shows the east side of the disk, peaking in intensity at 0.″40 (44 au) and extending out to 0.″9 (100 au). There is a spiral arm-like enhancement to the south, reminiscent of the known spiral structures on the outer rings of the disk. The location of the spiral arm is coincident with 12CO J = 3-2 emission detected by ALMA and hints at a dynamically active inner circumstellar region. Our observations also show a portion of the middle dusty ring at ∼220 au known from previous observations of this system. We fit the polarized H-band emission with a continuum radiative transfer Mie model. Our best-fit model favors an optically thin disk with a minimum dust grain size close to the blowout size for this system, evidence of ongoing dust production in the inner reaches of the disk. The thermal emission from this model accounts for virtually all of the far-infrared and millimeter flux from the entire HD 141569A disk, in agreement with the lack of ALMA continuum and CO emission beyond ∼100 au. A remaining 8-30 μm thermal excess a factor of ∼2 above our model argues for an as-yet-unresolved warm innermost 5-15 au component of the disk

Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions

Mitochondrial genomes are becoming more available thanks to recent technological advances in molecular biology. Its popularity as the tool of choice for phylogenetic analyses in a variety of taxa is increasing, and has resulted in improvement of overall results, as compared to traditional use of single mitochondrial markers such as the control region and CYTB. These differences in phylogenetic robustness provide incongruent conclusions among studies based on single mitochondrial markers and complete mitogenomes. Through detailed analysis of phylogenetic estimates from different genes we detected the most informative regions and the minimum amount of data necessary to reproduce mitogenomic-type results. We made use of two recently published complete mitogenome datasets of delphinids (Family Delphinidae) and killer whales (Orcinus orca) to compare phylogenetic estimation among individual genes and the mitogenome. Statistical comparative phylogenetics were employed to address differences in topologies, divergence dates and clock-like behavior among genes for both taxonomic groups. In both cases informative regions were coding genes and corresponded to less than a quarter of the complete mitogenome, yet these were not the same across both taxonomic groups, suggesting gene information content can depend on divergence time and taxonomy of the group studied. Although our results indicate that complete mitogenomes provide the most robust results, a minimum amount of data can be used when the complete sequence is unavailable, and previous studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates closer to those obtained using the entire mitogenome.Magíster en Ciencias BiológicasMaestrí

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.

Homoplasic SNPs are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for clinically relevant traits such as antibiotic resistance and virulence. Here we present a new tool, SNPPar, for efficient detection and analysis of homoplasic SNPs from large whole genome sequencing datasets (>1000 isolates and/or >100 000 SNPs). SNPPar takes as input an SNP alignment, tree and annotated reference genome, and uses a combination of simple monophyly tests and ancestral state reconstruction (ASR, via TreeTime) to assign mutation events to branches and identify homoplasies. Mutations are annotated at the level of codon and gene, to facilitate analysis of convergent evolution. Testing on simulated data (120 Mycobacterium tuberculosis alignments representing local and global samples) showed SNPPar can detect homoplasic SNPs with very high specificity (zero false-positives in all tests) and high sensitivity (zero false-negatives in 89 % of tests). SNPPar analysis of three empirically sampled datasets (Elizabethkingia anophelis, Burkholderia dolosa and M. tuberculosis) produced results that were in concordance with previous studies, in terms of both individual homoplasies and evidence of convergence at the codon and gene levels. SNPPar analysis of a simulated alignment of ~64 000 genome-wide SNPs from 2000 M. tuberculosis genomes took ~23 min and ~2.6 GB of RAM to generate complete annotated results on a laptop. This analysis required ASR be conducted for only 1.25 % of SNPs, and the ASR step took ~23 s and 0.4 GB of RAM. SNPPar automates the detection and annotation of homoplasic SNPs efficiently and accurately from large SNP alignments. As demonstrated by the examples included here, this information can be readily used to explore the role of homoplasy in parallel and/or convergent evolution at the level of nucleotide, codon and/or gene

Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics

International audienceViral evolutionary analyses are confronted with increasingly large sequence data sets, both in terms of sequence length and number of sequences. This can result in considerable computational burden, not only to infer phylogenies but also to obtain associated estimates such as their time scales and phylogeographic patterns. Here, we illustrate two frequently-used approaches to obtain phylogenomic estimates of time-measured trees and spatial dispersal patterns for fast-evolving viruses. First, we discuss computationally efficient procedures that employ a fixed tree topology obtained through maximum likelihood inference to estimate molecular clock rates and phylogeographic spread for Dengue virus genomes. Using the same viral example, we also illustrate Bayesian phylodynamic inference that jointly infers time-measured trees and phylogeo-graphy, including covariates of spatial dispersal, from sequence and trait data. We highlight state-of-the-art efforts to perform such computations more efficiently. Finally, we compare the estimates obtained by both approaches and discuss their strengths and potential pitfalls

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

International audienceThe natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics

Selection pressures in five genes from bat- and dog-related RABVs.

<p>Selection pressures in five genes from bat- and dog-related RABVs.</p

Evolutionary rates of RABV genes in the dog-related group.

<p>(<b>A</b>) Rates of nucleotide substitution per site, per year were estimated for each RABV gene: nucleoprotein (N), phosphoprotein (P), matrix (M), glycoprotein (G) and polymerase (L), for the concatenated non-coding regions (NC) and for the five concatenated RABV genes (5 genes). Both the mean and the 95% highest posterior density (HPD) values on the rate are shown. (<b>B</b>) Substitution rates in the N and G genes of the dog-related group RABV, a sub-set of RABV circulating in mongooses (MG) in Africa-3 clade and in the Caribbean, in ferret-badgers (FB) in Asia, and in dogs in Asia and Africa. Note the different y-axes (rates) in both cases.</p

Maximum clade credibility phylogeny of 248 dog-related RABV utilizing five concatenated genes.

<p>Tip times represent the time (year) of sampling. Bayesian estimates of divergence time are also shown. Upper and lower limits of the 95% highest posterior density (HPD) estimates and the posterior probability values are shown for major nodes.</p

Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350000years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification