Application of Graph Theory to the elaboration of personal genomic data for genealogical research

In this communication a representation of the links between DNA-relatives based on Graph Theory is applied to the analysis of personal genomic data to obtain genealogical information. The method is tested on both simulated and real data and its applicability to the field of genealogical research is discussed. We envisage the proposed approach as a valid tool for a streamlined application to the publicly available data generated by many online personal genomic companies. In this way, anonymized matrices of pairwise genome sharing counts can help to improve the retrieval of genetic relationships between customers who provide explicit consent to the treatment of their data

Classification of sedimentary and igneous rocks by laser induced breakdown spectroscopy and nanoparticle-enhanced laser induced breakdown spectroscopy combined with principal component analysis and graph theory

In this work, results are presented on the application of standard LIBS and Nanoparticle-Enhanced LIBS (NELIBS) to the classification of rocks (igneous and sedimentary). The classification of the spectra obtained with the two methods was performed using Principal Component Analysis (PCA) and Graph Theory method. The results obtained confirmed the advantages of the LIBS technique in geological applications, showing that excellent classification of the rocks analyzed (more than 99% of the spectra correctly classified) can be obtained using standard LIBS coupled to Graph Theory analysis, while NELIBS spectra, analyzed with the same technique, provide acceptable results, but with 10% of the spectra not classified. These findings are particularly interesting given the application of the LIBS technique in investigating natural samples having porous and/or rough surfaces

Practice-oriented controversies and borrowed epistemic credibility in current evolutionary biology: phylogeography as a case study

Although there is increasing recognition that theory and practice in science are intimately intertwined, philosophy of science perspectives on scientific controversies have been historically focused on theory rather than practice. As a step in the construction of frameworks for understanding controversies linked to scientific practices, here we introduce the notion of borrowed epistemic credibility (BEC), to describe the situation in which scientists, in order to garner support for their own stances, exploit similarities between tenets in their own field and accepted statements or positions properly developed within other areas of expertise. We illustrate the scope of application of our proposal with the analysis of a heavily methods-grounded, recent controversy in phylogeography, a biological subdiscipline concerned with the study of the historical causes of biogeographical variation through population genetics- and phylogenetics-based computer analyses of diversity in DNA sequences, both within species and between closely related taxa. Toward this end, we briefly summarize the arguments proposed by selected authors representing each side of the controversy: the ‘nested clade analysis’ school versus the ‘statistical phylogeography’ orientation. We claim that whereas both phylogeographic ‘research styles’ borrow epistemic credibility from sources such as formal logic, the familiarity of results from other scientific areas, the authority of prominent scientists, or the presumed superiority of quantitative vs. verbal reasoning, ‘theory’ plays essentially no role as a foundation of the controversy. Besides underscoring the importance of strictly methodological and other non-theoretical aspects of controversies in current evolutionary biology, our analysis suggests a perspective with potential usefulness for the re-examination of more general philosophy of biology issues, such as the nature of historical inference, rationality, justification, and objectivity

Graph clustering and portable X-Ray Fluorescence: An application for in situ, fast and preliminary classification of transport amphoras

In the last decade, numerous papers have been delivered on the potential of portable X-Ray Fluorescence (XRF) in archaeological ceramics. Additionally, new chemometric methods have been proposed to manage chemical dataset and facilitate the use of geochemical discrimination for provenance classification of ancient ceramics. In this contribute, the potential of portable Energy Dispersive X-Ray Fluorescence (ED-XRF) analysis and chemical data processing by Graph Clustering is evaluated for provenance classification of archaeological potteries, discussing possible merits and limits of the employed routine. A ceramic assemblage represented by seventy-three transport amphorae classified by typological analysis have been used as testing materials; spectra have been collected on samples simulating in situ analysis conditions (e.g. on fresh cut surfaces without any preparation) and Graph Clustering method has been applied in chemical data processing; comparison with classical Cluster Analysis (CA) and Principal Component Analysis (PCA) is also evaluated. The obtained results favor the use of Graph Clustering for a preliminary classification of ceramics, which can be chemically analyzed in easy, fast and non-destructive way. With a 75.35% of correct attribution, the study shows the suitability of portable ED-XRF in rapid screening of a large number of ceramic samples usually recovered in the framework of archaeological excavation. Misclassifications have been mostly verified for samples exhibiting a coarse-grained clay paste, suggesting that the method is particularly suitable for fine-grained ceramic materials

Practice-oriented controversies and borrowed epistemic credibility in current evolutionary biology: phylogeography as a case study

Although there is increasing recognition that theory and practice in science are intimately intertwined, philosophy of science perspectives on scientific controversies have been historically focused on theory rather than practice. As a step in the construction of frameworks for understanding controversies linked to scientific practices, here we introduce the notion of borrowed epistemic credibility (BEC), to describe the situation in which scientists, in order to garner support for their own stances, exploit similarities between tenets in their own field and accepted statements or positions properly developed within other areas of expertise. We illustrate the scope of application of our proposal with the analysis of a heavily methods-grounded, recent controversy in phylogeography, a biological subdiscipline concerned with the study of the historical causes of biogeographical variation through population genetics- and phylogenetics-based computer analyses of diversity in DNA sequences, both within species and between closely related taxa. Toward this end, we briefly summarize the arguments proposed by selected authors representing each side of the controversy: the ‘nested clade analysis’ school versus the ‘statistical phylogeography’ orientation. We claim that whereas both phylogeographic ‘research styles’ borrow epistemic credibility from sources such as formal logic, the familiarity of results from other scientific areas, the authority of prominent scientists, or the presumed superiority of quantitative vs. verbal reasoning, ‘theory’ plays essentially no role as a foundation of the controversy. Besides underscoring the importance of strictly methodological and other non-theoretical aspects of controversies in current evolutionary biology, our analysis suggests a perspective with potential usefulness for the re-examination of more general philosophy of biology issues, such as the nature of historical inference, rationality, justification, and objectivity

concepts - methods - visualization

While Darwin’s grand view of evolution has undergone many changes and shown up in many facets, there remains one outstanding common feature in its 150-year history: since the very beginning, branching trees have been the dominant scheme for representing evolutionary processes. Only recently, network models have gained ground reflecting contact-induced mixing or hybridization in evolutionary scenarios. In biology, research on prokaryote evolution indicates that lateral gene transfer is a major feature in the evolution of bacteria. In the field of linguistics, the mutual lexical and morphosyntactic borrowing between languages seems to be much more central for language evolution than the family tree model is likely to concede. In the humanities, networks are employed as an alternative to established phylogenetic models, to express the hybridization of cultural phenomena, concepts or the social structure of science. However, an interdisciplinary display of network analyses for evolutionary processes remains lacking. Therefore, this volume includes approaches studying the evolutionary dynamics of science, languages and genomes, all of which were based on methods incorporating network approaches

Evolutionary dynamics of speciation and extinction

Presented here is an interdisciplinary study that draws connections between the fields of physics, mathematics, and evolutionary biology. Importantly, as we move through the Anthropocene Epoch, where human-driven climate change threatens biodiversity, understanding how an evolving population responds to extinction stress could be key to saving endangered ecosystems. With a neutral, agent-based model that incorporates the main principles of Darwinian evolution, such as heritability, variability, and competition, the dynamics of speciation and extinction is investigated. The simulated organisms evolve according to the reaction-diffusion rules of the 2D directed percolation universality class. Offspring are generated according to one of three reproduction schemes. Mate choice dictates offspring placement, and it defines a species based on reproductive isolation (known as the biological species concept), while a globally enforced death process ensues within each generation. This system is shown to exhibit nonequilibrium, continuous phase transitions as a function of the individual death probability. The dynamical rules that enable phase transition and clustering behavior to transpire behavior is discussed, and a connection is drawn to another type of phase transition that arises by mate choice alone. Coalescent theory is then used to explore common descent in evolved phylogenetic tree structures at both the individual and cluster level. Finally, an extinction scenario is implemented where, after reaching a steady-state, a large population percentage is killed. Historical contingency is shown to play a major role in recovery from mass extinction at criticality --Abstract, page iii

Evolutionary Dynamics of Speciation and Extinction

Presented here is an interdisciplinary study that draws connections between the fields of physics, mathematics, and evolutionary biology. Importantly, as we move through the Anthropocene Epoch, where human-driven climate change threatens biodiversity, understanding how an evolving population responds to extinction stress could be key to saving endangered ecosystems. With a neutral, agent-based model that incorporates the main principles of Darwinian evolution, such as heritability, variability, and competition, the dynamics of speciation and extinction is investigated. The simulated organisms evolve according to the reaction-diffusion rules of the 2D directed percolation universality class. Offspring are generated according to one of three reproduction schemes. Mate choice dictates offspring placement, and it defines a species based on reproductive isolation (known as the biological species concept), while a globally enforced death process ensues within each generation. This system is shown to exhibit nonequilibrium, continuous phase transitions as a function of the individual death probability. The dynamical rules that enable phase transition and clustering behavior to transpire behavior is discussed, and a connection is drawn to another type of phase transition that arises by mate choice alone. Coalescent theory is then used to explore common descent in evolved phylogenetic tree structures at both the individual and cluster level. Finally, an extinction scenario is implemented where, after reaching a steady-state, a large population percentage is killed. Historical contingency is shown to play a major role in recovery from mass extinction at criticality

Handbook of Stemmatology

Stemmatology studies aspects of textual criticism that use genealogical methods. This handbook is the first to cover the entire field, encompassing both theoretical and practical aspects, ranging from traditional to digital methods. Authors from all the disciplines involved examine topics such as the material aspects of text traditions, methods of traditional textual criticism and their genesis, and modern digital approaches used in the field

Macroevolution: Explanation, Interpretation and Evidence

info:eu-repo/semantics/publishedVersio