Bayesian Reconstruction Research Articles

Evidence of historical isolation and genetic structuring among broadnose sevengill sharks (Notorynchus cepedianus) from the world’s major oceanic regions

Cosmopolitan marine pelagic species display variable patterns of population connectivity among the world’s major oceans. While this information is crucial for informing management, information is lacking for many ecologically important species, including apex predators. In this study we examine patterns of genetic structure in the broadnose sevengill shark, Notorynchus cepedianus across its global distribution. We estimate patterns of connectivity among broadnose sevengill shark populations from three major oceanic regions (South Atlantic, Oceania and Eastern Pacific) by contrasting mitochondrial and nuclear DNA haplotype frequencies. We also produced time calibrated Bayesian Inference phylogenetic reconstructions to analyses global phylogeographic patterns and estimate divergence times among distinctive shark lineages. Our results demonstrate significant genetic differentiation among oceanic regions (ΦST = 0.9789, P < 0.0001) and a lack of genetic structuring within regions (ΦST = − 0.007; P = 0.479). Time calibrated Bayesian Inference phylogenetic reconstructions indicate that the observed patterns of genetic structure among oceanic regions are historical, with regional populations estimated to have diverged from a common ancestor during the early to mid-Pleistocene. Our results indicate significant genetic structuring and a lack of gene flow among broadnose sevengill shark populations from the South Atlantic, Oceania and Eastern Pacific regions. Evidence of deep lineage divergences coinciding with the early to mid-Pleistocene suggests historical glacial cycling has contributed to the vicariant divergence of broadnose sevengill shark populations from different ocean basins. These finding will help inform global management of broadnose sevengill shark populations, and provides new insights into historical and contemporary evolutionary processes shaping populations of this ecologically important apex predator.

Molecular phylogeny of Atractocarpus (Rubiaceae): taxonomic implications for several New Caledonian Gardenieae species

Background and aims – New Caledonia is a hotspot of biodiversity in the world. Among the most diverse New Caledonian plant families is Rubiaceae, which consist of 30 genera containing 220 species, with a level of endemism of 93%. The tribe Gardenieae is represented by four genera, Gardenia (8 species), Aidia (2 species), Randia (7 species), and Atractocarpus (10 species). As Randia has now been restricted to the Neotropics, the New Caledonian Randia species remain unplaced within the tribe. Atractocarpus is a Pacific genus, easily characterized by long imbricated stipules, a feature also present in the Randia species and in several Gardenia species in New Caledonia. The aims of the present study are to test the monophyly of Atractocarpus and to assess the phylogenetic placement of the Randia and Gardenia species with long imbricated stipules within Gardenieae and specifically their relationships with taxa of the Porterandia group to which Atractocarpus belongs. Material and methods – We investigated 63 species of Pacific Gardenieae, with a focus on the Porterandia group, in a Bayesian phylogenetic reconstruction (cpDNA: trnTF and rpl32, and nrDNA: ITS). Key results – Our study provides a mostly supported consensus tree topology of the Porterandia group. Five Gardenia and seven Randia species fall within a clade that comprises the New Caledonian Atractocarpus species, rendering both Atractocarpus and Gardenia polyphyletic. Conclusion – We enlarge the delimitation of Atractocarpus to include 12 New Caledonian Randia and Gardenia species. New Caledonia is consequently confirmed as the centre of diversity for Atractocarpus with 31 species. According to our study, three genera of Gardenieae occur in the archipelago: Aidia, Gardenia, and Atractocarpus.

On the model uncertainties in Bayesian source reconstruction using an ensemble of weather predictions, the emission inverse modelling system FREAR v1.0, and the Lagrangian transport and dispersion model Flexpart v9.0.2

Abstract. Bayesian source reconstruction is a powerful tool for determining atmospheric releases. It can be used, amongst other applications, to identify a point source releasing radioactive particles into the atmosphere. This is relevant for applications such as emergency response in case of a nuclear accident or Comprehensive Nuclear-Test-Ban treaty verification. The method involves solving an inverse problem using environmental radioactivity observations and atmospheric transport models. The Bayesian approach has the advantage of providing an uncertainty quantification on the inferred source parameters. However, it requires the specification of the inference input errors, such as the observation error and model error. The latter is particularly hard to provide as there is no straightforward way to determine the atmospheric transport and dispersion model error. Here, the importance of model error is illustrated for Bayesian source reconstruction using a recent and unique case where radionuclides were detected on several continents. A numerical weather prediction ensemble is used to create an ensemble of atmospheric transport and dispersion simulations, and a method is proposed to determine the model error.

The Bayesian reconstruction and the evolutionary history of Salivirus type 1 and type 2: the worldwide spreading.

Salivirus (SalV) represents an emerging problem in public health especially during the recent years. In this study, the Bayesian evolutionary history and the spread of the virus through the different countries have been reported. a database of 81 sequences of SalV structural VP1 fragment were downloaded from GenBank, aligned and manually edited by Bioedit Software. ModelTest v. 3.7 software was used to estimate the simplest evolutionary model fitting the sequence dataset. A Maximum-Likelihood tree has been generated using MEGA-X to test the "clockliness" signal using TempEst 1.5.1. The Bayesian phylogenetic tree was built by BEAST. Homology modelling was performed by SWISS-Model and protein variability evaluated by ConSurf server. the phylogenetic tree showed a clade of SalV A2 and three main clades of SalV A1, revealing several infections in humans in South Korea, India, Tunisia, China, Nigeria, Ethiopia and USA. The Bayesian maximum clade credibility tree and the time of the most common recent ancestor dated back the root of the tree to the year 1788 with the probable origin in USA. Selective pressure analysis revealed two positive selection sites, His at 100th and Leu at 116th positions that at the homology modelling resulted important to guarantee protein stability and variability. This could contribute to the development of new mutations modifying the clinical features of this evolving virus. Bayesian phylogenetic and phylodynamic represented a useful tool to follow the transmission dynamic of SalV and to prevent new epidemics worldwide.

Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographical structuring of nuclear gene pools.

The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers. We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes. Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South American landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions. Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers.

Is the endophytic fungus Neofusicoccum kwambonambiense another brick in the wall of the post-harvest pathogenic fruit fungi system?

Entophytic fungi are characterized as microorganisms that colonize plant tissues without causing infection symptoms. These organisms are sources of genetic and biochemical diversity for numerous applications, from the production of pharmaceutical compounds to foods. However, many of these fungi can become pathogenic to plants if they find suitable substrate for their infection and development. Neofusicoccum spp. has been considered a phytopathogenic fungus for many agricultural crops, being aggressive for some of them both in their woody parts or fruits, either while still in the orchards or after being harvested. The identification and pathogenicity of the isolates are two important aspects for their characterization. Thus, the objective of this work was to characterize the pathogenicity of two endophytic isolates of the fungus Neofusicoccum sp. in different fruits in the post-harvest process. Therefore, isolates identity confirmation was obtained using Bayesian reconstruction of the internal transcribed spacer region (ITS) and translation elongation factor 1-alpha (TEF 1-α). Subsequently, the isolates were inoculated in zucchini, banana, persimmon, green beans, guava, orange, apple, melon, papaya and tomato, followed by a 10-day evaluation in order to calculate the areas under the disease progress curve. Phylogenetic reconstruction allowed identification of two isolates of the endophytic fungus of Brazilian cherry leaves as Neofusicoccum kwambonambiense, which were confirmed as pathogenic for the following fruits: Brazilian cherry, papaya, tomato, banana and apple, with variations in aggressiveness. However, no infections were found in zucchini, melon and guava by any of the isolates. This is believed to be the first occurrence of N. kwambonambiense isolated from plants of Eugenia uniflora, with pathogenicity in different post-harvest fruits.

Métodos de reconstrucción filogenética II: inferencia bayesiana

Phylogenetic reconstruction through Bayesian inference is currently widely used. The main advantage of this method is the direct output of posterior probabilities for each clade on the final phylogeny. Thus, it does not require bootstrapping as a measure of uncertainty. Moreover, Bayesian inference is perfectly fit for dating phylogenies through molecular clocks. In this paper, the basics of Bayesian inference applied to phylogenetic reconstruction are described, starting with an explanation of Bayes’ theorem. Then, the use of the Metropolis-Hastings algorithm to sample topologies from the posterior distribution is characterized and illustrated through a simple example. At the end, there is a mention of the software used for Bayesian phylogeny reconstruction.&#x0D;

Higher order Hamiltonian Monte Carlo sampling for cosmological large-scale structure analysis

ABSTRACT We investigate higher order symplectic integration strategies within Bayesian cosmic density field reconstruction methods. In particular, we study the fourth-order discretization of Hamiltonian equations of motion (EoM). This is achieved by recursively applying the basic second-order leap-frog scheme (considering the single evaluation of the EoM) in a combination of even numbers of forward time integration steps with a single intermediate backward step. This largely reduces the number of evaluations and random gradient computations, as required in the usual second-order case for high-dimensional cases. We restrict this study to the lognormal-Poisson model, applied to a full volume halo catalogue in real space on a cubical mesh of 1250 h−1 Mpc side and 2563 cells. Hence, we neglect selection effects, redshift space distortions, and displacements. We note that those observational and cosmic evolution effects can be accounted for in subsequent Gibbs-sampling steps within the COSMIC BIRTH algorithm. We find that going from the usual second to fourth order in the leap-frog scheme shortens the burn-in phase by a factor of at least ∼30. This implies that 75–90 independent samples are obtained while the fastest second-order method converges. After convergence, the correlation lengths indicate an improvement factor of about 3.0 fewer gradient computations for meshes of 2563 cells. In the considered cosmological scenario, the traditional leap-frog scheme turns out to outperform higher order integration schemes only when considering lower dimensional problems, e.g. meshes with 643 cells. This gain in computational efficiency can help to go towards a full Bayesian analysis of the cosmological large-scale structure for upcoming galaxy surveys.

Bayesian reconstruction of fluorescent molecular tomography via iteration of measurements.

Fluorescent molecular tomography (FMT) is an important molecular imaging technique for medical diagnosis and treatment. In FMT, a typical forward model is the diffusion approximation. However, this approximation is not valid in biological tissues with low-scattering regions. To overcome this problem, a Bayesian method in combination with the model error is proposed. Further, an iteration method of boundary measurements is incorporated into the reconstruction process to improve the efficiency of reconstruction for FMT. Simulation results obtained demonstrate that the proposed approach can effectively improve the quality of the reconstructed results and speed up the reconstruction process.

Bayesian reconstruction of gravitational-wave signals from binary black holes with nonzero eccentricities

We present a comprehensive study on how well gravitational-wave signals of binary black holes (BBHs) with nonzero eccentricities can be recovered with state of the art model-independent waveform reconstruction and parameter estimation techniques. For this we use BayesWave, a Bayesian algorithm used by the LIGO–Virgo Collaboration for unmodeled reconstructions of signal waveforms and parameters. We used two different waveform models to produce simulated signals of BBHs with eccentric orbits and embed them in samples of simulated noise of design-sensitivity Advanced LIGO detectors. We studied the network overlaps and point estimates of central moments of signal waveforms recovered by BayesWave as a function of e, the eccentricity of the binary at 8 Hz orbital frequency. BayesWave recovers signals of near-circular (e ≲ 0.2) and highly eccentric (e ≳ 0.7) binaries with network overlaps similar to that of circular (e = 0) ones, however it produces lower network overlaps for binaries with e ∈ [0.2, 0.7]. Estimation errors on central frequencies and bandwidths (measured relative to bandwidths) are nearly independent from e, while estimation errors on central times and durations (measured relative to durations) increase and decrease with e above e ≳ 0.5, respectively. We also tested how BayesWave performs when reconstructions are carried out using generalized wavelets with linear frequency evolution (chirplets) instead of sine-Gaussian wavelets. We have found that network overlaps improve by ∼10–20 percent when chirplets are used, and the improvement is the highest at low (e < 0.5) eccentricities. There is however no significant change in the estimation errors of central moments when the chirplet base is used.

Molecular Characterization of Chelonid Alphaherpesvirus 5 in a Black Turtle (Chelonia mydas) Fibropapilloma from Baja California Sur, Mexico.

Simple SummaryFibropapillomatosis in sea turtles is a neoplastic disease associated with an infection by chelonid alphaherpesvirus 5, which can be fatal to turtles. The Baja California peninsula in the Mexican Pacific has been a relatively pristine environment for local aquatic wildlife; however, in the last decade, several turtles with this disease have been reported in the foraging areas of the region. Reasons for this are unknown but may be related to population growth, the surge of unchecked tourism, pollution, and fisheries, which have increased in the area over the past two decades. Finding a black turtle with fibropapillomatosis and chelonid alphaherpesvirus 5 in a natural protected area to host one of the most important foraging areas for sea turtles in the Mexican Pacific represents a potential risk for the population of black turtles and other species of sea turtles that visit the feeding grounds of the peninsula. This suggests a need to strengthen research lines on the west coast of Mexico and generate conservation strategies for organisms and the ecosystems that they inhabit.During routine monitoring in Ojo de Liebre Lagoon, Mexico, a juvenile black turtle (Chelonia mydas) was captured, physically examined, measured, weighed, sampled, and tagged. The turtle showed no clinical signs suggestive of disease. Eleven months later, this turtle was recaptured in the same area, during which one lesion suggestive of fibropapilloma on the neck was identified and sampled for histopathology and molecular analysis. Histopathology revealed hyperkeratosis, epidermal hyperplasia, acanthosis, papillary differentiation and ballooning degeneration of epidermal cells, increased fibroblasts in the dermis, and angiogenesis, among other things. Hematological values were similar to those reported for clinically healthy black turtles and did not show notable changes between the first capture and the recapture; likewise, clinicopathological evaluation did not show structural or functional damage in the turtle’s systems. The chelonid alphaherpesvirus 5 (ChHV5) UL30 gene was amplified and sequenced for phylogeny; Bayesian reconstruction showed a high alignment with the genus Scutavirus of the Eastern Pacific group. This is one of the first reports of ChHV5 in a cutaneous fibropapilloma of a black turtle in the Baja California peninsula.

Quantitative bone SPECT/CT reconstruction utilizing anatomical information

BackgroundBone SPECT/CT has been shown to offer superior sensitivity and specificity compared to conventional whole-body planar scanning. Furthermore, bone SPECT/CT allows quantitative imaging, which is challenging with planar methods. In order to gain better quantitative accuracy, Bayesian reconstruction algorithms, including both image derived and anatomically guided priors, have been utilized in reconstruction in PET/CT scanning, but they have not been widely used in SPECT/CT studies. Therefore, the aim of this work was to evaluate the performance of CT-guided reconstruction in quantitative bone SPECT.MethodsThree Bayesian reconstruction methods were evaluated against the conventional ordered subsets expectation maximization (OSEM) reconstruction method. One of the studied Bayesian methods was the relative difference prior (RDP), which has recently gained popularity in PET reconstruction. The other two methods, anatomically guided smoothing prior (AMAP-S) and anatomically guided relative difference prior (AMAP-R), utilized anatomical information from the CT scan. The reconstruction methods were evaluated in terms of quantitative accuracy with artificial lesions inserted in clinical patient studies and with 20 real clinical patients. Maximum and mean standardized uptake values (SUVs) of the lesions were defined.ResultsThe analyses showed that all studied Bayesian methods performed better than OSEM and the anatomical priors also outperformed RDP. The average relative error in mean SUV for the artificial lesion study for OSEM, RDP, AMAP-S, and AMAP-R was − 53%, − 35%, − 15%, and − 10%, when the CT study had matching lesions. In the patient study, the RDP method gave 16 ± 9% higher maximum SUV values than OSEM, while AMAP-S and AMAP-R offered increases of 36 ± 8% and 36 ± 9%, respectively. Mean SUV increased for RDP, AMAP-S, and AMAP-R by 18 ± 9%, 26 ± 5%, and 33 ± 5% when compared to OSEM.ConclusionsThe Bayesian methods with anatomical prior, especially the relative difference prior-based method (AMAP-R), outperformed OSEM and reconstruction without anatomical prior in terms of quantitative accuracy.

Molecular Placement of an Outbreak-Causing Gall Wasp,Zapatella davisae(Hymenoptera: Cynipidae), with Comments on Phylogenetic Arrangements in the Tribe Cynipini

AbstractGall wasps (Hymenoptera: Cynipidae) have fascinated researchers for centuries due to the elaborate diversity of charismatic galls they produce, the presence of unique reproductive systems (e.g., a form of cyclical parthenogenesis), the possible convergent evolution of semiparasitic gall wasp forms (i.e., “inquilines”), and their multitrophic interactions. While many classifications for gall wasps have been proposed, recent DNA sequence efforts combined with taxonomic revisions are beginning to clarify the evolutionary relationships of this group. To date, however, a well resolved phylogeny is lacking, complicating the study of outbreak-causing pest species. Outbreaks by one such species, the black oak gall wasp, Zapatella davisae Buffington &amp; Melika (Hymenoptera: Cynipidae: Cynipini), have led to extensive damage and mortality of black oaks, Quercus velutina L. (Fagales: Fagaceae), in the northeastern United States. Here we sequenced fragments of the nuclear ribosomal gene 28S, and the nuclear protein coding gene long-wavelength opsin from samples of Z. davisae collected on Cape Cod, MA, and Long Island, NY. Using these sequences and sequences previously published from the mitochondrial locus cytochrome b, we performed Bayesian and maximum likelihood multilocus phylogenetic reconstructions based on a concatenated alignment including species of gall wasps in the tribe Cynipini from which all three loci were present in the GenBank database. Confirming morphological work, we find that Z. davisae is most closely related to species in the genera Callirhytis and Neuroterus, and appears to be a basal member of the “Quercus” section of the tribe Cynipini. We find that recent generic reclassifications within the Cynipini have made great progress towards clarifying the taxonomic relationships of species of gall-inducing wasps in this tribe, and we comment on several classifications that require additional research.

Robust and Guided Bayesian Reconstruction of Single-Photon 3D Lidar Data: Application to Multispectral and Underwater Imaging

3D Lidar imaging can be a challenging modality when using multiple wavelengths, or when imaging in high noise environments (e.g., imaging through obscurants). This paper presents a hierarchical Bayesian algorithm for the robust reconstruction of multispectral single-photon Lidar data in such environments. The algorithm exploits multi-scale information to provide robust depth and reflectivity estimates together with their uncertainties to help with decision making. The proposed weight-based strategy allows the use of available guide information that can be obtained by using state-of-the-art learning based algorithms. The proposed Bayesian model and its estimation algorithm are validated on both synthetic and real images showing competitive results regarding the quality of the inferences and the computational complexity when compared to the state-of-the-art algorithms.

Cosmic birth: efficient Bayesian inference of the evolving cosmic web from galaxy surveys

ABSTRACT We present cosmic birth (COSMological Initial Conditions from Bayesian Inference Reconstructions with THeoretical models): an algorithm to reconstruct the primordial and evolved cosmic density fields from galaxy surveys on the light-cone. The displacement and peculiar velocity fields are obtained from forward modelling at different redshift snapshots given some initial cosmic density field within a Gibbs-sampling scheme. This allows us to map galaxies, observed in a light-cone, to a single high redshift and hereby provide tracers and the corresponding survey completeness in Lagrangian space including tetrahedral tessellation mapping. These Lagrangian tracers in turn permit us to efficiently obtain the primordial density field, making the cosmic birth code general to any structure formation model. Our tests are restricted for the time being to augmented Lagrangian perturbation theory. We show how to robustly compute the non-linear Lagrangian bias from clustering measurements in a numerical way, enabling us to get unbiased dark matter field reconstructions at initial cosmic times. We also show that we can accurately recover the information of the dark matter field from the galaxy distribution based on a detailed simulation. Novel key ingredients to this approach are a higher order Hamiltonian-sampling technique and a non-diagonal Hamiltonian mass matrix. This technique could be used to study the Eulerian galaxy bias from galaxy surveys and could become an ideal baryon acoustic reconstruction technique. In summary, this method represents a general reconstruction technique, including in a self-consistent way a survey mask, non-linear and non-local bias, and redshift-space distortions, with an efficiency about 10 times superior to previous comparable methods.

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

BackgroundAnnelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and families within the phylum Annelida are still represented by a single specimen of a single species. The genus of interstitial annelids Ophryotrocha (Dorvilleidae, Errantia, Annelida) is among these neglected groups, despite its extensive use as model organism in numerous studies on the evolution of life history, physiological and ecological traits. To compensate for the paucity of genomic information in this genus, we here obtained novel complete mitochondrial genomes of six Ophryotrocha species using next generation sequencing. In addition, we investigated the evolution of the reproductive mode in the Ophryotrocha genus using a phylogeny based on two mitochondrial markers (COXI and 16S rDNA) and one nuclear fragment (Histone H3).ResultsSurprisingly, gene order was not conserved among the six Ophryotrocha species investigated, and varied greatly as compared to those found in other annelid species within the class Errantia. The mitogenome phylogeny for the six Ophryotrocha species displayed a separation of gonochoric and hermaphroditic species. However, this separation was not observed in the phylogeny based on the COX1, 16S rDNA, and H3 genes. Parsimony and Bayesian ancestral trait reconstruction indicated that gonochorism was the most parsimonious ancestral reproductive mode in Ophryotrocha spp.ConclusionsOur results highlight the remarkably high level of gene order variation among congeneric species, even in annelids. This encourages the need for additional mitogenome sequencing of annelid taxa in order to properly understand its mtDNA evolution, high biodiversity and phylogenetic relationships.

Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China

H7N7 avian influenza virus (AIV) can divided into low-pathogenic AIV and high-pathogenic AIV groups. It has been shown to infect humans and animals. Its prevalence state in wild birds in China remains largely unclear. In this study, a new strain of H7N7 AIV, designated CM1216, isolated from wild birds in Shanghai, China, was characterized. Phylogenetic and nucleotide sequence analyses of CM1216 revealed that HA, NA, PB1, NP, and M genes shared the highest nucleotide identity with the Japan H7 subtype AIV circulated in 2019; the PB2 and PA genes shared the highest nucleotide identity with the Korea H7 subtype AIV circulated in wild birds in 2018, while NS gene of CM1216 was 98.93% identical to that of the duck AIV circulating in Bangladesh, and they all belong to the Eurasian lineage. A Bayesian phylogenetic reconstruction of the 2 surface genes of CM1216 showed that multiple reassortments might have occurred in 2015. Mutations were found in HA (A135 T, T136S, and T160 A [H3 numbering]), M1 (N30D and T215 A), NS1 (P42S and D97 E), PB2 (R389 K), and PA (N383D) proteins; these mutations have been shown to be related to mammalian adaptation and changes in virulence of AIVs. Infection studies demonstrated that CM1216 could infect mice and cause symptoms characteristic of influenza virus infection and proliferate in the lungs without prior adaption. This study demonstrates the need for routine surveillance of AIVs in wild birds and detection of their evolution to become a virus with high pathogenicity and ability to infect humans.

Three new species of Peniophorella (Basidiomycota) from East Asia

Three new Peniophorella species (Hymenochaetales) growing on dead wood, are described and illustrated. Peniophorella aspersa was collected in Taiwan and mainland China, and characterized by minutely warted hymenial surface, well-developed subiculum, rare stephanocysts and cylindrical-suballantoid spores. Peniophorella crystallifera collected in mainland China, Taiwan and Japan, is distinguished by sparsely grandinioid hymenial surface, immersed heavily encrusted cystidia, stephanocysts and ellipsoid-subcylindrical spores. The characteristic features of P. reticulata, found in Taiwan, are minutely porulose, odontioid basidiomata, provided with peg-like groups of hyphae, stellate crystalline incrustations on hyphal ends and oblong-ellipsoid spores. Maximum likelihood and Bayesian phylogenetic reconstructions based on ITS and 28S sequences demonstrated that P. aspersa and P. reticulata belong to the same group of species, and the all three species are most closely related to P. praetermissa and P. rude.

Bayesian Reconstruction of Fourier Pairs

In a number of data-driven applications such as detection of arrhythmia, interferometry or audio compression, observations are acquired indistinctly in the time or frequency domains: temporal observations allow us to study the spectral content of signals (e.g., audio), while frequency-domain observations are used to reconstruct temporal/spatial data (e.g., MRI). Classical approaches for spectral analysis rely either on i) a discretisation of the time and frequency domains, where the fast Fourier transform stands out as the de facto off-the-shelf resource, or ii) stringent parametric models with closed-form spectra. However, the general literature fails to cater for missing observations and noise-corrupted data. Our aim is to address the lack of a principled treatment of data acquired indistinctly in the temporal and frequency domains in a way that is robust to missing or noisy observations, and that at the same time models uncertainty effectively. To achieve this aim, we first define a joint probabilistic model for the temporal and spectral representations of signals, to then perform a Bayesian model update in the light of observations, thus jointly reconstructing the complete (latent) time and frequency representations. The proposed model is analysed from a classical spectral analysis perspective, and its implementation is illustrated through intuitive examples. Lastly, we show that the proposed model is able to perform joint time and frequency reconstruction of real-world audio, healthcare and astronomy signals, while successfully dealing with missing data and handling uncertainty (noise) naturally against both classical and modern approaches for spectral estimation.

Different and common brain signals of altered neurocognitive mechanisms for unfamiliar face processing in acquired and developmental prosopagnosia

Neuropsychological studies have shown that prosopagnosic individuals perceive face structure in an atypical way. This might preclude the formation of appropriate face representations and, consequently, hamper effective recognition. The present ERP study, in combination with Bayesian source reconstruction, investigates how information related to both external (E) and internal (I) features was processed by E.C. and I.P., suffering from acquired and developmental prosopagnosia, respectively. They carried out a face-feature matching task with new faces. E.C. showed poor performance and remarkable lack of early face-sensitive P1, N170 and P2 responses on right (damaged) posterior cortex. Although she presented the expected mismatch effect to target faces in the E-I sequence, it was of shorter duration than in Controls, and involved left parietal, right frontocentral and dorsofrontal regions, suggestive of reduced neural circuitry to process face configurations. In turn, I.P. performed efficiently but with a remarkable bias to give “match” responses. His face-sensitive potentials P1–N170 were comparable to those from Controls, however, he showed no subsequent P2 response and a mismatch effect only in the I-E sequence, reflecting activation confined to those regions that sustain typically the initial stages of face processing. Relevantly, neither of the prosopagnosics exhibited conspicuous P3 responses to features acting as primes, indicating that diagnostic information for constructing face representations could not be sufficiently attended nor deeply encoded. Our findings suggest a different locus for altered neurocognitive mechanisms in the face network in participants with different types of prosopagnosia, but common indicators of a deficient allocation of attentional resources for further recognition.