Application and comparative performance of network modularity algorithms to ecological communities classification

Network modularity is a well-studied large-scale connectivity pattern in networks. The detection of modules in real networks constitutes a crucial step towards a description of the network building blocks and their evolutionary dynamics. The performance of modularity detection algorithms is commonly quantified using simulated networks data. However, a comparison of the modularity algorithms utility for real biological data is scarce. Here we investigate the utility of network modularity algorithms for the classification of ecological plant communities. Plant community classification by the traditional approaches requires prior knowledge about the characteristic and differential species, which are derived from a manual inspection of vegetation tables. Using the raw species abundance data we constructed six different networks that vary in their edge definitions. Four network modularity algorithms were examined for their ability to detect the traditionally recognized plant communities. The use of more restrictive edge definitions significantly increased the accuracy of community detection, that is, the correspondence between network-based and traditional community classification. Random-walk based modularity methods yielded slightly better results than approaches based on the modularity function. For the whole network, the average agreement between the manual classification and the network-based modules is 76% with varying congruence levels for different communities ranging between 11% and 100%. The network-based approach recovered the known ecological gradient from riverside – sand and gravel bank vegetation – to dryer habitats like semidry grassland on dykes. Our results show that networks modularity algorithms offer new avenues of pursuit for the computational analysis of species communities

A robust sequential hypothesis testing method for brake squeal localisation

This contribution deals with the in situ detection and localisation of brake squeal in an automobile. As brake squeal is emitted from regions known a priori, i.e., near the wheels, the localisation is treated as a hypothesis testing problem. Distributed microphone arrays, situated under the automobile, are used to capture the directional properties of the sound field generated by a squealing brake. The spatial characteristics of the sampled sound field is then used to formulate the hypothesis tests. However, in contrast to standard hypothesis testing approaches of this kind, the propagation environment is complex and time-varying. Coupled with inaccuracies in the knowledge of the sensor and source positions as well as sensor gain mismatches, modelling the sound field is difficult and standard approaches fail in this case. A previously proposed approach implicitly tried to account for such incomplete system knowledge and was based on ad hoc likelihood formulations. The current paper builds upon this approach and proposes a second approach, based on more solid theoretical foundations, that can systematically account for the model uncertainties. Results from tests in a real setting show that the proposed approach is more consistent than the prior state-of-the-art. In both approaches, the tasks of detection and localisation are decoupled for complexity reasons. The localisation (hypothesis testing) is subject to a prior detection of brake squeal and identification of the squeal frequencies. The approaches used for the detection and identification of squeal frequencies are also presented. The paper, further, briefly addresses some practical issues related to array design and placement. (C) 2019 Author(s)

An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin

To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the archaebacteria, euryarchaeote genomes most frequently harbored the sister to the eukaryotic nuclear gene, whereas among eubacteria, the α-proteobacteria were most frequently represented within the sister group. Only 3 genes out of 571 gave a 3-domain tree. Homologues from α-proteobacterial genomes that branched as the sister to nuclear genes were found more frequently in genomes of facultatively anaerobic members of the rhiozobiales and rhodospirilliales than in obligate intracellular ricketttsial parasites. Following α-proteobacteria, the most frequent eubacterial sister lineages were γ-proteobacteria, δ-proteobacteria, and firmicutes, which were also the prokaryote genomes least frequently found as monophyletic groups in our trees. Although all 22 higher prokaryotic taxa sampled (crenarchaeotes, γ-proteobacteria, spirochaetes, chlamydias, etc.) harbor genes that branch as the sister to homologues present in the eukaryotic common ancestor, that is not evidence of 22 different prokaryotic cells participating at eukaryote origins because prokaryotic “lineages” have laterally acquired genes for more than 1.5 billion years since eukaryote origins. The data underscore the archaebacterial (host) nature of the eukaryotic informational genes and the eubacterial (mitochondrial) nature of eukaryotic energy metabolism. The network linking genes of the eukaryote ancestor to contemporary homologues distributed across prokaryotic genomes elucidates eukaryote gene origins in a dialect cognizant of gene transfer in nature

Data from: Concatenated alignments and the case of the disappearing tree

BackgroundAnalyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in prokaryotes, where lateral gene transfer (LGT) is a natural mechanism of generating genetic diversity, there are open questions as to whether concatenation amplifies or averages phylogenetic signals residing in individual genes. Here we investigate concatenations of prokaryotic and eukaryotic datasets to investigate possible sources of incongruence in phylogenetic trees and to examine the level of overlap between individual and concatenated alignments.ResultsWe analyzed prokaryotic datasets comprising 248 invidual gene trees from 315 genomes at three taxonomic depths spanning gammaproteobacteria, proteobacteria, and prokaryotes (bacteria plus archaea), and eukaryotic datasets comprising 279 invidual gene trees from 85 genomes at two taxonomic depths: across plants-animals-fungi and within fungi. Consistent with previous findings, the branches in trees made from concatenated alignments are, in general, not supported by any of their underlying individual gene trees, even though the concatenation trees tend to possess high bootstrap proportions values. For the prokaryote data, this observation is independent of phylogenetic depth and sequence conservation. The eukaryotic data show much better agreement between concatenation and single gene trees. LGT frequencies in trees were estimated using established methods. Sequence length in individual alignments, but not sequence divergence, was found to correlate with the generation of branches that correspond to the concatenated tree.ConclusionsThe weak correspondence of concatenation trees with single gene trees gives rise to the question where the phylogenetic signal in concatenated trees is coming from. The eukaryote data reveals a better correspondence between individual and concatenation trees than the prokaryote data. The question of whether the lack of correspondence between individual genes and the concatenation tree in the prokaryotic data is due to LGT or phylogenetic artefacts is remains unanswered. If LGT is the cause of incongruence between concatenation and individual trees, we would have expected to see greater degrees of incongruence for more divergent prokaryotic data sets, which was not observed, although estimated rates of LGT suggest that LGT is responsible for at least some of the observed incongruence

Dual radius spherical cardioid microphone arrays for binaural auralization

The direction dependent analysis of impulse response measurements using spherical microphone arrays can deliver a universal basis for binaural auralization. A new method using dual radius open sphere arrays is proposed to overcome limitations in practical realizations of such arrays. Different methods to combine the two radii have been analyzed and will be presented. A plane wave decomposition in conjunction with a high resolution HRTF database is used to generate a binaural auralization, wherein the different designs are simulated under ideal and real conditions. The results have been evaluated in a quality grading experiment. It is shown that the dual radius cardioids design is an effective method to enhance the perceived quality in comparison to conventional spherical array designs

A spatial filtering approach for directional audio coding

In hands-free telephony, spatial filtering techniques are employed to enhance intelligibility of speech. More precisely, these techniques aim at reducing the reverberation of the desired speech signal and attenuating interferences. Additionally, it is well-known that the spatially separate reproduction of desired and interfering sources enhance intelligibility of speech. For the latter task, Directional Audio Coding (DirAC) has proven to be an efficient method to capture and reproduce spatial sound. In this contribution, we propose a spatial filtering processing block, which works in the parameter domain of DirAC. Simulation results show that compared to a standard beamformer the novel technique offers significantly higher interference attenuation, while introducing comparably low distortion of the desired signal. Additional subjective tests of speech intelligibility confirm the instrumentally obtained results