Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenctic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny

Substance-Abusing Mothers and fathers\u27 Willingness to Allow Their Children to Receive Mental Health Treatment

The purpose of this study was to examine attitudes of substance-abusing mothers and fathers entering outpatient treatment toward allowing their children to participate in individual- or family-based interventions. Data were collected from a brief anonymous survey completed by adults at intake into a large substance abuse treatment program in western New York. Only one-third of parents reported that they would be willing to allow their children to participate in any form of mental health treatment. Results of chi-square analyses revealed that a significantly greater proportion of mothers reported that they would allow their children to participate in mental health treatment (41%) compared to fathers (28%). Results of logistic regression analyses revealed even after controlling for child age, mothers were more likely than fathers to indicate their willingness to allow their children to receive mental health treatment; however, type of substance abuse (alcohol versus drug abuse) was not associated with parents\u27 willingness to allow their children to receive treatment. Parental reluctance to allow their children to receive individual or family-based treatment is a significant barrier in efforts to intervene with these at-risk children

A photometricity and extinction monitor at the Apache Point Observatory

An unsupervised software ``robot'' that automatically and robustly reduces and analyzes CCD observations of photometric standard stars is described. The robot measures extinction coefficients and other photometric parameters in real time and, more carefully, on the next day. It also reduces and analyzes data from an all-sky $10 \mu m$ camera to detect clouds; photometric data taken during cloudy periods are automatically rejected. The robot reports its findings back to observers and data analysts via the World-Wide Web. It can be used to assess photometricity, and to build data on site conditions. The robot's automated and uniform site monitoring represents a minimum standard for any observing site with queue scheduling, a public data archive, or likely participation in any future National Virtual Observatory.Comment: accepted for publication in A

MeerKAT view of the dancing ghosts : peculiar galaxy pair PKS 2130-538 in Abell 3785

We present MeerKAT L-band (886–1682 MHz) observations of the extended radio structure of the peculiar galaxy pair PKS 2130−538 known as the ‘Dancing Ghosts’. The complex of bending and possibly interacting jets and lobes originate from two active galactic nuclei hosts in the Abell 3785 galaxy cluster, one of which is the brightest cluster galaxy. The radio properties of the PKS 2130−538 – flux density, spectral index, and polarization – are typical for large, bent-tail galaxies. We also investigate a number of thin extended low surface brightness filaments originating from the lobes. South-east from the Dancing Ghosts, we detect a region of low surface brightness emission that has no clear origin. While it could originate from the Abell 3785 radio halo, we investigate the possibility that it is associated with the two PKS 2130−538 hosts. We find no evidence of interaction between the two PKS 2130−538 hosts

Genomic evidence of contemporary hybridization between Schistosoma species

This work was supported by the Wellcome Trust (grant number 206194); the Biotechnology and Biological Sciences Research Council, the Department for International Development, the Economic & Social Research Council, the Medical Research Council, the Natural Environment Research Council and the Defence Science & Technology Laboratory, under the Zoonoses and Emerging Livestock Systems (ZELS) programme (grant number BB/L018985/1 to JPW and MS and grant number BB/S013822/1 to JPW, MS and NDD). FA, AE and MR received funding from the Wellcome Trust (grant number 104958/Z/14/Z).Hybridization between different species of parasites is increasingly being recognised as a major public and veterinary health concern at the interface of infectious diseases biology, evolution, epidemiology and ultimately control. Recent research has revealed that viable hybrids and introgressed lineages between Schistosoma spp. are prevalent across Africa and beyond, including those with zoonotic potential. However, it remains unclear whether these hybrid lineages represent recent hybridization events, suggesting hybridization is ongoing, and/or whether they represent introgressed lineages derived from ancient hybridization events. In human schistosomiasis, investigation is hampered by the inaccessibility of adult-stage worms due to their intravascular location, an issue which can be circumvented by post-mortem of livestock at abattoirs for Schistosoma spp. of known zoonotic potential. To characterise the composition of naturally-occurring schistosome hybrids, we performed whole-genome sequencing of 21 natural livestock infective schistosome isolates. To facilitate this, we also assembled a de novo chromosomal-scale draft assembly of Schistosoma curassoni. Genomic analyses identified isolates of S. bovis, S. curassoni and hybrids between the two species, all of which were early generation hybrids with multiple generations found within the same host. These results show that hybridization is an ongoing process within natural populations with the potential to further challenge elimination efforts against schistosomiasis.Publisher PDFPeer reviewe

The confounding effects of high genetic diversity on the determination and interpretation of differential gene expression analysis in the parasitic nematode Haemonchus contortus

Differential expression analysis between parasitic nematode strains is commonly used to implicate candidate genes in anthelmintic resistance or other biological functions. We have tested the hypothesis that the high genetic diversity of an organism such as Haemonchus contortus could complicate such analyses. First, we investigated the extent to which sequence polymorphism affects the reliability of differential expression analysis between the genetically divergent H. contortus strains MHco3(ISE), MHco4(WRS) and MHco10(CAVR). Using triplicates of 20 adult female worms from each population isolated under parallel experimental conditions, we found that high rates of sequence polymorphism in RNAseq reads were associated with lower efficiency read mapping to gene models under default TopHat2 parameters, leading to biased estimates of inter-strain differential expression. We then showed it is possible to largely compensate for this bias by optimising the read mapping single nucleotide polymorphism (SNP) allowance and filtering out genes with particularly high single nucleotide polymorphism rates. Once the sequence polymorphism biases were removed, we then assessed the genuine transcriptional diversity between the strains, finding ≥824 differentially expressed genes across all three pairwise strain comparisons. This high level of inter-strain transcriptional diversity not only suggests substantive inter-strain phenotypic variation but also highlights the difficulty in reliably associating differential expression of specific genes with phenotypic differences. To provide a practical example, we analysed two gene families of potential relevance to ivermectin drug resistance; the ABC transporters and the ligand-gated ion channels (LGICs). Over half of genes identified as differentially expressed using default TopHat2 parameters were shown to be an artifact of sequence polymorphism differences. This work illustrates the need to account for sequence polymorphism in differential expression analysis. It also demonstrates that a large number of genuine transcriptional differences can occur between H. contortus strains and these must be considered before associating the differential expression of specific genes with phenotypic differences between strains

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

A Multi-wavelength Study of the Sunyaev-Zel'dovich Effect in the Triple-Merger Cluster MACS J0717.5+3745 with MUSTANG and Bolocam

We present 90, 140, and 268GHz sub-arcminute resolution imaging of the Sunyaev-Zel'dovich effect (SZE) in MACSJ0717.5+3745. Our 90GHz SZE data result in a sensitive, 34uJy/bm map at 13" resolution using MUSTANG. Our 140 and 268GHz SZE imaging, with resolutions of 58" and 31" and sensitivities of 1.8 and 3.3mJy/beam respectively, was obtained using Bolocam. We compare these maps to a 2-dimensional pressure map derived from Chandra X-ray observations. Our MUSTANG data confirm previous indications from Chandra of a pressure enhancement due to shock-heated, >20keV gas immediately adjacent to extended radio emission seen in low-frequency radio maps. The MUSTANG data also detect pressure substructure that is not well-constrained by the X-ray data in the remnant core of a merging subcluster. We find that the small-scale pressure enhancements in the MUSTANG data amount to ~2% of the total pressure measured in the 140GHz Bolocam observations. The X-ray template also fails on larger scales to accurately describe the Bolocam data, particularly at the location of a subcluster known to have a high line of sight optical velocity (~3200km/s). Our Bolocam data are adequately described when we add an additional component - not described by a thermal SZE spectrum - coincident with this subcluster. Using flux densities extracted from our model fits, and marginalizing over the temperature constraints for the region, we fit a thermal+kinetic SZE spectrum to our data and find the subcluster has a best-fit line of sight proper velocity of 3600+3440/-2160km/s. This agrees with the optical velocity estimates for the subcluster. The probability of velocity<0 given our measurements is 2.1%. Repeating this analysis using flux densities measured non-parametrically results in a 3.4% probability of a velocity<=0. We note that this tantalizing result for the kinetic SZE is on resolved, subcluster scales.Comment: 10 Figures, 18 pages. this version corrects issues with the previous arXiv versio

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Lipoprotein(a), Lp(a), is a modified low-density lipoprotein particle that contains apolipoprotein(a), encoded by LPA, and is a highly heritable, causal risk factor for cardiovascular diseases that varies in concentrations across ancestries. Here, we use deep-coverage whole genome sequencing in 8392 individuals of European and African ancestry to discover and interpret both single-nucleotide variants and copy number (CN) variation associated with Lp(a). We observe that genetic determinants between Europeans and Africans have several unique determinants. The common variant rs12740374 associated with Lp(a) cholesterol is an eQTL for SORT1 and independent of LDL cholesterol. Observed associations of aggregates of rare non-coding variants are largely explained by LPA structural variation, namely the LPA kringle IV 2 (KIV2)-CN. Finally, we find that LPA risk genotypes confer greater relative risk for incident atherosclerotic cardiovascular diseases compared to directly measured Lp(a), and are significantly associated with measures of subclinical atherosclerosis in African Americans

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

The original version of this article contained an error in the name of the author Ramachandran S. Vasan, which was incorrectly given as Vasan S. Ramachandran. This has now been corrected in both the PDF and HTML versions of the article