The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring ...beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.
Capsids of papilloma and polyoma viruses (papovavirus family) are composed of 72 pentameric capsomeres arranged on a skewed icosahedral lattice (triangulation number of seven, T=7). Cottontail rabbit ...papillo mavirus (CRPV) was reported previously to be a T=7
laevo(left-handed) structure, whereas human wart virus, simian virus 40, and murine polyomavirus were shown to be T=7
dextro(right-handed). The CRPV structure determined by cryoelectron microscopy and image reconstruction was similar to previously determined structures of bovine papillomavirus type 1 (BPV-1) and human papillomavirus type 1 (HPV-1). CRPV capsids were observed in closed (compact) and open (swollen) forms. Both forms have star-shaped capsomeres, as do BPV-1 and HPV-1, but the open CRPV capsids are ≈2 nm larger in radius. The lattice hands of all papillomaviruses examined in this study were found to be T=7
dextro. In the region of maximum contact, papillomavirus capsomeres interact in a manner similar to that found in polyomaviruses. Although papilloma and polyoma viruses have differences in capsid size (≈60
versus≈50 nm), capsomere morphology (11 to 12 nm star-shaped
versus8 nm barrel-shaped), and intercapsomere interactions (slightly different contacts between capsomeres), papovavirus capsids have a conserved, 72-pentamer, T=7
dextrostructure. These features are conserved despite significant differences in amino acid sequences of the major capsid proteins. The conserved features may be a consequence of stable contacts that occur within capsomeres and flexible links that form among capsomeres.
We present time-of-arrival (TOA) measurements and timing models of 47 millisecond pulsars observed from 2004 to 2017 at the Arecibo Observatory and the Green Bank Telescope by the North American ...Nanohertz Observatory for Gravitational Waves (NANOGrav). The observing cadence was three to four weeks for most pulsars over most of this time span, with weekly observations of six sources. These data were collected for use in low-frequency gravitational wave searches and for other astrophysical purposes. We detail our observational methods and present a set of TOA measurements, based on "narrowband" analysis, in which many TOAs are calculated within narrow radio-frequency bands for data collected simultaneously across a wide bandwidth. A separate set of "wideband" TOAs will be presented in a companion paper. We detail a number of methodological changes, compared to our previous work, which yield a cleaner and more uniformly processed data set. Our timing models include several new astrometric and binary pulsar measurements, including previously unpublished values for the parallaxes of PSRs J1832−0836 and J2322+2057, the secular derivatives of the projected semimajor orbital axes of PSRs J0613−0200 and J2229+2643, and the first detection of the Shapiro delay in PSR J2145−0750. We report detectable levels of red noise in the time series for 14 pulsars. As a check on timing model reliability, we investigate the stability of astrometric parameters across data sets of different lengths. We also report flux density measurements for all pulsars observed. Searches for stochastic and continuous gravitational waves using these data will be subjects of forthcoming publications.
We present a new analysis of the profile data from the 47 millisecond pulsars comprising the 12.5 yr data set of the North American Nanohertz Observatory for Gravitational Waves, which is presented ...in a parallel paper (Alam et al., hereafter NG12.5). Our reprocessing is performed using "wideband" timing methods, which use frequency-dependent template profiles, simultaneous time-of-arrival (TOA) and dispersion measure (DM) measurements from broadband observations, and novel analysis techniques. In particular, the wideband DM measurements are used to constrain the DM portion of the timing model. We compare the ensemble timing results to those in NG12.5 by examining the timing residuals, timing models, and noise-model components. There is a remarkable level of agreement across all metrics considered. Our best-timed pulsars produce encouragingly similar results to those from NG12.5. In certain cases, such as high-DM pulsars with profile broadening or sources that are weak and scintillating, wideband timing techniques prove to be beneficial, leading to more precise timing model parameters by 10%-15%. The high-precision, multiband measurements of several pulsars indicate frequency-dependent DMs. Compared to the narrowband analysis in NG12.5, the TOA volume is reduced by a factor of 33, which may ultimately facilitate computational speed-ups for complex pulsar timing array analyses. This first wideband pulsar timing data set is a stepping stone, and its consistent results with NG12.5 assure us that such data sets are appropriate for gravitational wave analyses.
Speciation with gene flow on Lord Howe Island Papadopulos, Alexander S.T; Baker, William J; Crayn, Darren ...
Proceedings of the National Academy of Sciences,
08/2011, Volume:
108, Issue:
32
Journal Article
Peer reviewed
Open access
Understanding the processes underlying the origin of species is a fundamental goal of biology. It is widely accepted that speciation requires an interruption of gene flow between populations: ongoing ...gene exchange is considered a major hindrance to population divergence and, ultimately, to the evolution of new species. Where a geographic barrier to reproductive isolation is lacking, a biological mechanism for speciation is required to counterbalance the homogenizing effect of gene flow. Speciation with initially strong gene flow is thought to be extremely rare, and few convincing empirical examples have been published. However, using phylogenetic, karyological, and ecological data for the flora of a minute oceanic island (Lord Howe Island, LHI), we demonstrate that speciation with gene flow may, in fact, be frequent in some instances and could account for one in five of the endemic plant species of LHI. We present 11 potential instances of species divergence with gene flow, including an in situ radiation of five species of Coprosma (Rubiaceae, the coffee family). These results, together with the speciation of Howea palms on LHI, challenge current views on the origin of species diversity.
NASA’s Global Ecosystem Dynamics Investigation (GEDI) is collecting spaceborne full waveform lidar data with a primary science goal of producing accurate estimates of forest aboveground biomass ...density (AGBD). This paper presents the development of the models used to create GEDI’s footprint-level (~25 m) AGBD (GEDI04_A) product, including a description of the datasets used and the procedure for final model selection. The data used to fit our models are from a compilation of globally distributed spatially and temporally coincident field and airborne lidar datasets, whereby we simulated GEDI-like waveforms from airborne lidar to build a calibration database. We used this database to expand the geographic extent of past waveform lidar studies, and divided the globe into four broad strata by Plant Functional Type (PFT) and six geographic regions. GEDI’s waveform-to-biomass models take the form of parametric Ordinary Least Squares (OLS) models with simulated Relative Height (RH) metrics as predictor variables. From an exhaustive set of candidate models, we selected the best input predictor variables, and data transformations for each geographic stratum in the GEDI domain to produce a set of comprehensive predictive footprint-level models. We found that model selection frequently favored combinations of RH metrics at the 98th, 90th, 50th, and 10th height above ground-level percentiles (RH98, RH90, RH50, and RH10, respectively), but that inclusion of lower RH metrics (e.g. RH10) did not markedly improve model performance. Second, forced inclusion of RH98 in all models was important and did not degrade model performance, and the best performing models were parsimonious, typically having only 1-3 predictors. Third, stratification by geographic domain (PFT, geographic region) improved model performance in comparison to global models without stratification. Fourth, for the vast majority of strata, the best performing models were fit using square root transformation of field AGBD and/or height metrics. There was considerable variability in model performance across geographic strata, and areas with sparse training data and/or high AGBD values had the poorest performance. These models are used to produce global predictions of AGBD, but will be improved in the future as more and better training data become available.
•NASA’s GEDI collects spaceborne lidar data used for mapping aboveground biomass.•A global database of field and airborne lidar was compiled.•Models stratified by Plant Functional Type and geographic region outperform a global model.•GEDI04_A models are OLS models predicting biomass as a function of RH metrics.•Maximum forest height is an important predictor of biomass across geographic domains.
We search for an isotropic stochastic gravitational-wave background (GWB) in the newly released 11 year data set from the North American Nanohertz Observatory for Gravitational Waves (NANOGrav). ...While we find no evidence for a GWB, we place constraints on a population of inspiraling supermassive black hole (SMBH) binaries, a network of decaying cosmic strings, and a primordial GWB. For the first time, we find that the GWB constraints are sensitive to the solar system ephemeris (SSE) model used and that SSE errors can mimic a GWB signal. We developed an approach that bridges systematic SSE differences, producing the first pulsar-timing array (PTA) constraints that are robust against SSE errors. We thus place a 95% upper limit on the GW-strain amplitude of AGWB < 1.45 × 10−15 at a frequency of f = 1 yr−1 for a fiducial f−2/3 power-law spectrum and with interpulsar correlations modeled. This is a factor of ∼2 improvement over the NANOGrav nine-year limit calculated using the same procedure. Previous PTA upper limits on the GWB (as well as their astrophysical and cosmological interpretations) will need revision in light of SSE systematic errors. We use our constraints to characterize the combined influence on the GWB of the stellar mass density in galactic cores, the eccentricity of SMBH binaries, and SMBH-galactic-bulge scaling relationships. We constrain the cosmic-string tension using recent simulations, yielding an SSE-marginalized 95% upper limit of G < 5.3 × 10−11-a factor of ∼2 better than the published NANOGrav nine-year constraints. Our SSE-marginalized 95% upper limit on the energy density of a primordial GWB (for a radiation-dominated post-inflation universe) is GWB(f) h2 < 3.4 × 10−10.
Background & Aims There is controversy regarding the role of the type 2 immune response in the pathogenesis of ulcerative colitis (UC)—few data are available from treatment-naive patients. We ...investigated whether genes associated with a type 2 immune response in the intestinal mucosa are up-regulated in treatment-naive pediatric patients with UC compared with patients with Crohn’s disease (CD)-associated colitis or without inflammatory bowel disease (IBD), and whether expression levels are associated with clinical outcomes. Methods We used a real-time reverse-transcription quantitative polymerase chain reaction array to analyze messenger RNA (mRNA) expression patterns in rectal mucosal samples from 138 treatment-naive pediatric patients with IBD and macroscopic rectal disease, as well as those from 49 children without IBD (controls), enrolled in a multicenter prospective observational study from 2008 and 2012. Results were validated in real-time reverse-transcription quantitative polymerase chain reaction analyses of rectal RNA from an independent cohort of 34 pediatric patients with IBD and macroscopic rectal disease and 17 controls from Cincinnati Children’s Hospital Medical Center. Results We measured significant increases in mRNAs associated with a type 2 immune response (interleukin IL5 gene, IL13 , and IL13RA2 ) and a type 17 immune response ( IL17A and IL23 ) in mucosal samples from patients with UC compared with patients with colon-only CD. In a regression model, increased expression of IL5 and IL17A mRNAs distinguished patients with UC from patients with colon-only CD ( P = .001; area under the receiver operating characteristic curve, 0.72). We identified a gene expression pattern in rectal tissues of patients with UC, characterized by detection of IL13 mRNA, that predicted clinical response to therapy after 6 months (odds ratio OR, 6.469; 95% confidence interval CI, 1.553–26.94), clinical response after 12 months (OR, 6.125; 95% CI, 1.330–28.22), and remission after 12 months (OR, 5.333; 95% CI, 1.132–25.12). Conclusions In an analysis of rectal tissues from treatment-naive pediatric patients with IBD, we observed activation of a type 2 immune response during the early course of UC. We were able to distinguish patients with UC from those with colon-only CD based on increased mucosal expression of genes that mediate type 2 and type 17 immune responses. Increased expression at diagnosis of genes that mediate a type 2 immune response is associated with response to therapy and remission in pediatric patients with UC.
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