Audio phylogenetic analysis using geometric transforms

Whenever a multimedia content is shared on the Internet, a mutation process is being operated by multiple users that download, alter and repost a modified version of the original data leading to the diffusion of multiple near-duplicate copies. This effect is also experienced by audio data (e.g., in audio sharing platforms) and requires the design of accurate phylogenetic analysis strategies that permit uncovering the processing history of each copy and identify the original one. This paper proposes a new phylogenetic reconstruction strategy that converts the analyzed audio tracks into spectrogram images and compare them using alignment strategies borrowed from computer vision. With respect to strategies currently-available in literature, the proposed solution proves to be more accurate, does not require any a-priori knowledge about the operated transformations, and requires a significantly-lower amount of computational time

Multimedia Forensics

This book is open access. Media forensics has never been more relevant to societal life. Not only media content represents an ever-increasing share of the data traveling on the net and the preferred communications means for most users, it has also become integral part of most innovative applications in the digital information ecosystem that serves various sectors of society, from the entertainment, to journalism, to politics. Undoubtedly, the advances in deep learning and computational imaging contributed significantly to this outcome. The underlying technologies that drive this trend, however, also pose a profound challenge in establishing trust in what we see, hear, and read, and make media content the preferred target of malicious attacks. In this new threat landscape powered by innovative imaging technologies and sophisticated tools, based on autoencoders and generative adversarial networks, this book fills an important gap. It presents a comprehensive review of state-of-the-art forensics capabilities that relate to media attribution, integrity and authenticity verification, and counter forensics. Its content is developed to provide practitioners, researchers, photo and video enthusiasts, and students a holistic view of the field

Multimedia Forensics

This book is open access. Media forensics has never been more relevant to societal life. Not only media content represents an ever-increasing share of the data traveling on the net and the preferred communications means for most users, it has also become integral part of most innovative applications in the digital information ecosystem that serves various sectors of society, from the entertainment, to journalism, to politics. Undoubtedly, the advances in deep learning and computational imaging contributed significantly to this outcome. The underlying technologies that drive this trend, however, also pose a profound challenge in establishing trust in what we see, hear, and read, and make media content the preferred target of malicious attacks. In this new threat landscape powered by innovative imaging technologies and sophisticated tools, based on autoencoders and generative adversarial networks, this book fills an important gap. It presents a comprehensive review of state-of-the-art forensics capabilities that relate to media attribution, integrity and authenticity verification, and counter forensics. Its content is developed to provide practitioners, researchers, photo and video enthusiasts, and students a holistic view of the field

Cell markers for air chamber development in Marchantia polymorpha

Marchantia polymorpha, thanks to its small genome and its simple cellular architecture, is an excellent model for the study of developmental processes. Marchantia can propagate asexually producing small flat disc-like propagules, called gemmae, that develop into adult plants. Gemmae have an open mode of development, which facilitates the live observation of developmental processes. The fundamental processes underlying morphogenesis in plants are poorly understood and epidermal patterning represents one of the key events during plant development. Marchantia produces characteristic epidermal structures called air chambers that represent an example of a self-organising, three-dimensional morphological unit that has a modular and repetitive arrangement, similar to the one observed in stomata meristemoid cells in vascular plants. To date, the cellular scale and the genetic description of air chamber development are poorly resolved. Therefore, in this dissertation I applied modern genetic and microscopy tools to better map the process of air chamber morphogenesis at a cellular scale and to generate genetic markers to understand the steps involved in this developmental process. Similar tools have been used in Arabidopsis thaliana, and they have shown that patterning and cell differentiation can be dissected into discrete steps that provide insights into the mechanisms controlling the process and can also represent valuable targets for engineering the entire process. In my thesis, I developed high resolution imaging techniques to produce a systematic description of air chamber development. I generated genetic resources to identify potential candidate genes involved in air chamber development by comparing the transcriptome of wild type plants and the nopperabo1 (nop1) mutants that are unable to produce air chambers. Candidate genes were used to build a collection of cellular markers to be screened for their potential involvement in air chamber patterning. The screening led to the identification of two potential transcription factors, MpbHLH24 and MpWRKY10

GETTING TO THE ROOT CAUSE: THE GENETIC UNDERPINNINGS OF ROOT SYSTEM ARCHITECTURE AND RHIZODEPOSITION IN SORGHUM

Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key functions via root system architecture and root exudation directly determines plant performance, and thus reproductive fitness. Despite the significance of roots, the genetic controls contributing to their variation have gone understudied due to the technical difficulties associated with below-ground phenotyping. Domesticated plants provide an excellent framework for studying the genomic underpinnings of phenotypic diversity due to the telescoped evolutionary time frame under which artificial selection took place. The rapid evolution of domesticates from their extant antecedent affords direct observations of derived traits and their underlying genetic controls. Sorghum, a globally important domesticated grass species with a small diploid genome, few genetic repeats, and a wide variety of adaptations, serves as a good model for studying selection during domestication. Domesticated S. bicolor is an annual accession with large seeds and flowering organs compared to its wild relative, S. propinquum. Comparatively, S. propinquum is perennial with dense rhizomes and small flowering panicles. Due to their distinctly opposing root systems, a recombinant inbred line (RIL) population formed from a cross between S. bicolor and S. propinquum was used to identify the specific root morphological and metabolic adaptations that derived from domestication. The RIL population was phenotyped using high-throughput image analysis to locate the underlying genomic factors controlling derived traits via high-density Quantitative Trait Loci (QTL) mapping. Nine novel QTL influencing root morphology were identified. No QTL were identified for metabolic exudation; however, crown root growing angle was found to be a statistically significant predictor of the percentage of carbon and nitrogen in the rhizosphere. The relationship between steep growing angles and increased rhizosphere carbon and nitrogen suggests that increased exudation was derived during domestication. Candidate genes and pathways were identified including those that encode meristem transcription factors, plant hormone receptors, and actin trafficking. These findings advance our understanding of the underlying genomic factors controlling root system architecture (RSA) and root exudation that were selected during the domestication of Sorghum. The results of this study can be integrated into breeding programs for the establishment of elite root lines used to mitigate the effects of current and future environmental challenges of croplands in a sustainable manner

Lepidópteros galhadores (Cecidosidae) da América do Sul : filogeografia de Eucecidoses minutanus Bréthes e descrição de dois gêneros e de três espécies novas

O continente Sul Americano apresenta uma grande diversidade biológica, que pode ser explicada pelos resultados das interações entre plantas e animais, e de eventos climáticos e geológicos passados. Diferentes hipóteses sugerem como a biodiversidade da América do Sul pode ter evoluído; 1) através de um longo período de isolamento que, forneceu estabilidade e condições climáticas e biológicas; 2) com o soerguimento do Andes, por meio da vicariância geográfica e isolamento genético, aumentando a heterogeneidade e complexidade de habitats; e 3) pelas transgressões marinhas, que modificaram a paisagem, flora e fauna do continente. Por apresentar uma alta heterogeneidade de ecossistemas, a região Neotropical conta uma das maiores riquezas de insetos galhadores do mundo. Dentre esses, Lepidoptera, a segunda maior ordem de Insecta, conta com diversas famílias que são reconhecidas como indutoras de galhas e que, no entanto, não são devidamente exploradas/descritas. Cecidosidae são microlepidópteros indutores de galhas pouco conhecidos que apresentam uma estreita associação com plantas hospedeiras de Anacardiaceae. Na América do Sul, apenas quatro gêneros representam a família: Cecidoses, Eucecidoses, Oliera e Dicranoses (Davis 1998, Moreira 2012), sendo os três primeiros monotípicos. Neste contexto, o presente estudo explora a história evolutiva de Eucecidoses na região Neotropical, através de uma abordagem filogeográfica a partir de sua distribuição geográfica, associação com a planta hospedeira, e estrutura genética de populações deste táxon; e também descreve dois novos gêneros e espécies de Cecidosidae encontrados para o sul do Brasil e região central do Chile; os dados relacionados à história de vida, plantas hospedeiras e distribuição das novas espécies são fornecidos, assim como as relações filogenéticas destas novas espécies com as já descritas na literatura. Os resultados mostraram que o padrão de distribuição encontrado para Eucecidoses minutanus Brèthes (1916), não está relacionado diretamente com a distribuição de sua planta hospedeira, mas por eventos de dispersão e vicariância, que coincide com o arco orogênico Peripampásico. As análises revelaram seis linhagens distintas, geneticamente estruturadas e isoladas por distância em diferentes regiões biogeográficas. Um novo gênero e espécie de Cecidosidae, Cecidonius pampeanus Moreira e Gonçalves (2017), é descrito para o bioma Pampa no sul do Brasil; a galha induzida por esta espécie é severamente atacada por parasitoides e inquilinos, estes últimos modificando-a e tornando-a vistosa. Devido a isso, a espécie indutora permaneceu desconhecida por VIII muito tempo, sendo erroneamente atribuida a um hymenoptero, de fato um inquilino desta. C. pampeanus foi reconhecida através de filogenia molecular como uma linhagem nova e relacionada aos cecidosídeos Neotropicais. O novo gênero e espécie descrita para o Chile, Andescecidium parrai Moreira e Vargas (2018), aparentado com Cecidonius, passou por uma história de negligência semelhante à de C. pampeanus, sua galha foi por muito tempo estabelecida como induzida por um coleóptero, supostamente um cleptoparasita da galha do real indutor. Além de A. parrai, uma nova espécie adicional, Oliera saizi Moreira e Vargas (2018), é também descrita.The South American continent presents a great biological diversity that can be explained as results from plant and animal interactions, and from climatic and geological past events. Different hypothesis suggest how the South American biodiversity may have evolved; 1) through a long period of isolation, which provided stability and climatic and biological conditions; 2) the uplift of the Andes, through geographical vicariance and genetic isolation, raising the heterogeneity and habitat complex; 3) through marine transgressions, which modified the landscape, flora and fauna of the continent. Because of the high ecosystem heterogeneity, the Neotropical region counts with one of the greatest richness of galling insects in the world. Among them, Lepidoptera is the second largest order of Insecta and abridges several families that are recognized as gall inducing insects, however, they are not properly explored/described. Cecidosidae is a little known family of gall inducing microlepidoptera that presents strict relationship with Anacardiaceae host plants. In South America, only four genera represent the family: Cecidoses, Eucecidoses, Oliera and Dicranoses (Davis 1998, Moreira 2012), the first three being monotypic. In this context, the present study explores the evolutionary history of the genus Eucecidoses in the Neotropical region, through a phylogeograpical approach, association with hostplant, and genetic structure of populations of this taxa; and also describes two new genera and species of Cecidosidae found for south of Brazil and central region of Chile; the data related to life history, host-plants and distribution of the new species are provided, as well as the phylogenetic relations of these new species with the ones described in the literature. The results showed that the distributional pattern found for Eucecidoses minutanus Brèthes (1916), is not directly related to the host-plant distribution, but with events of dispersion and vicariance, which coincides with the Peripampasic orogenic arc. The analyzes revealed six distinct lineages, genetically structured and isolated by distance in different biogeographical regions. A new Cecidosidae genus and species, Cecidonius pampeanus Moreira e Gonçalves (2017) is described for the Pampa biome, south Brazil; the gall induced by this species is severely attacked by parasitoids and inquilines, the latter modifies the gall, promptly calling attention. Because of this, the true inducer remained unknown for a long period, being mistakenly attributed to a hymenoptera, in fact, its inquiline. Cecidonius pampeanus, X was recognized through molecular phylogeny as a new lineage related to the Neotropical cecidosids. The new genus and species described for Chile, Andescecidium parrai, related to Cecidonius, went through negligent history similarly to C. pampeanus, its gall was long established as induced by a coleoptera, supposedly a kleptoparasite of the true inducer. Besides to A. parrai, a new additional species, Oliera saizi Moreira e Vargas (2018), is also described

Experimental and computation approaches reveal mechanisms of evolution of gene regulatory networks underlying echinoderm skeletogenesis

The evolutionary mechanisms in distantly related animals involved in shaping complex gene regulatory networks (GRN) that encode morphologically similar structures remain elusive. In this context, echinoderm larval skeletons found only in brittle stars and sea urchins out of the five classes provide an ideal system. Here, we characterise for the first time the development of the larval skeleton in the poorly described class of echinoderms, the ophiuroid Amphiura filiformis, and we compare it systematically with the well-established sea urchin. In the first part of this study, we show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of regulatory states using 24 sea urchin candidates highlights that gene duplication, protein function diversification and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms. Our data allows to comment on the independent or homologous evolution of the larval skeleton in light of the recently established phylogeny of echinoderm classes. In the second part of this study, we employ mRNA sequencing to establish a transcriptome and analyse its content quantitatively and qualitatively. We identify a core set of skeletogenic genes that is highly conserved using various comparative genomic analyses including other three classes of echinoderms. Additionally, from a differential screen on samples with inhibited skeleton we obtain a list of candidates specific for brittle star skeleton development and analyse their expression using experimental techniques. Finally, we provide access to all transcriptomic and expression data via a customised web interface. In conclusion, we establish the brittle star A. filiformis as new developmental model system and provide novel insights into evolution of GRNs

Unraveling the genetic secrets of ancient Baikal amphipods

Lake Baikal is the oldest, by volume, the largest, and the deepest freshwater lake on Earth. It is characterized by an outstanding diversity of endemic faunas with more than 350 amphipod species and subspecies (Amphipoda, Crustacea, Arthropoda). They are the dominant benthic organisms in the lake, contributing substantially to the overall biomass. Eulimnogammarus verrucosus, E. cyaneus, and E. vittatus, in particular, serve as emerging models in ecotoxicological studies. It was, then, necessary to investigate whether these endemic littoral amphipods species form genetically separate populations across Baikal, to scrutinize if the results obtained --~for example, about stress responses~-- with samples from one single location (Bolshie Koty, where the biological station is located), could be extrapolated to the complete lake or not. The genetic diversity within those three endemic littoral amphipod species was determined based on fragments of Cytochrome C Oxidase I (COI) and 18S rDNA (only for E. verrucosus). Gammarus lacustris, a Holarctic species living in water bodies near Baikal, was examined for comparison. The intra-specific genetic diversities within E. verrucosus and E. vittatus (13% and 10%, respectively) were similar to the inter-species differences, indicating the occurrence of cryptic, morphologically highly similar species. This was confirmed with 18S rDNA for E. verrucosus. The haplotypes of E. cyaneus and G. lacustris specimens were, with intra-specific genetic distances of 3% and 2%, respectively, more homogeneous, indicating no --or only recent disruption of-- gene flow of E. cyaneus across Baikal, and recent colonization of water bodies around Baikal by G. lacustris. The data provide the first clear evidence for the formation of cryptic (sub)species within endemic littoral amphipod species of Lake Baikal and mark the inflows/outflow of large rivers as dispersal barriers. Lake Baikal has provided a stable environment for millions of years, in stark contrast to small, transient water bodies in its immediate vicinity. A highly diverse endemic amphipod fauna is found in one but not the other habitat. To gain more insights and explain the immiscibility barrier between Lake Baikal and non-Baikal environments faunas, the differences in the stress response pathways were studied. To this end, exposure experiments to increasing temperature and a heavy metal (cadmium) as proteotoxic stressors were conducted in Russia. High-quality de novo transcriptome assemblies were obtained, covering multiple conditions, for three amphipod species: E. verrucosus and E. cyaneus -Baikal endemics-, and G. lacustris -Holarctic- as a potential invader. After comparing the transcriptomic stress responses, it was found that both Baikal species possess intact stress response systems and respond to elevated temperature with relatively similar changes in their expression profiles. G. lacustris reacts less strongly to the same stressors, possibly because its transcriptome is already perturbed by acclimation conditions (matching the Lake Baikal littoral). Comprehensive genomic resources are of utmost importance for ecotoxicological and ecophysiological studies in an evolutionary context, especially considering the exceptional value of Baikal as a UNESCO World Heritage Site. In that context, the results presented here, on the genome of Eulimnogammarus verrucosus, have been the first massive step to establish genomic sequence resources for a Baikalian amphipod (other than mitochondrial genomes and gene expression data in the form of de novo transcriptomes assemblies). Based on the data from a survey of its genome (a single lane of paired-end Illumina HiSeq 2000 reads, 3X) as well as a full dataset (two complete flow cells, 46X) the genome size was estimated as nearly 10 Gb based on the k-mer spectra and the coverage of highly conserved miRNA, hox genes, and other Sanger-sequenced genes. At least two-thirds of the genome are non-unique DNA, and no less than half of the genomic DNA is composed of just five families of repetitive elements, including low complexity sequences. Some of the repeats families found in high abundance in E. verrucosus seem to be species-specific, or Baikalian-specific. Attempts to use off-the-shelf assembly tools on the available low coverage data, both before and after the removal of highly repetitive components, as well as on the full dataset, resulted in extremely fragmented assemblies. Nevertheless, the analysis of coverage in Hox genes and their homeobox showed no clear evidence for paralogs, indicating that a genome duplication did not contribute to the large genome size. Several mate-pair libraries with bigger insert sizes than the 2kb used here and long reads sequencing technology combined with semi-automated methods for genome assembly seem to be necessary to obtain a reliable assembly for this species

Genotyping and phenotyping the common pea and its wild relatives

In 1868, three men, Gregor Mendel, Charles Darwin and Friedrich Miescher made significant contributions in genetic inheritance, plant domestication and DNA extraction respectively. 150 years later, this thesis aims to better understand pea domestication through genotyping and phenotyping the common pea and its wild relatives. Peas (Pisum sativum) are a cool season legume important to food security due to their ability to fix nitrogen and produce nutritious food and animal fodder. A core collection of 350 accessions of wild, landrace and cultivated material was developed from the John Innes Pisum Collection. To characterise these accessions, image analysis, a modern phenotyping method was used. Current tools require user expertise, are not cross platform, are not applicable to certain plants or phenotypes. Here, MktStall, a novel multi-organ image analysis is presented, which requires no computational expertise. Pea is a large (4.5Gb) and highly repetitive genome. Here, the first publicly accessible pea genome reference is announced. In combination with a genotyping by sequencing (GBS) approach of this core collection a genome-wide association study (GWAS) was performed using on seed weight, plant height, leaflet margin, seed shape and pod shape. The results in this thesis show statistically significant differences in plant height in cultivars and leaflet length, perimeter and area in landraces in addition to identifying statistically significant loci for leaflet teeth, seed perimeter and seed eccentricity. Furthermore, potential candidate genes have be identified with roles in carbohydrate metabolism known to cause seed wrinkledness and POWERDRESS known to increase leaf area. The combination of novel contributions results in new tools, genomic resources and additional knowledge of pea domestication which can be used in marker assisted selection and improved breeding practices for an important crop for food security