'Bureaucratic' set systems, and their role in phylogenetics

We say that a collection \Cc of subsets of $X$ is {\em bureaucratic} if every maximal hierarchy on $X$ contained in \Cc is also maximum. We characterise bureaucratic set systems and show how they arise in phylogenetics. This framework has several useful algorithmic consequences: we generalize some earlier results and derive a polynomial-time algorithm for a parsimony problem arising in phylogenetic networks.Comment: 6 pages, 1 figur

On Patchworks and Hierarchies

Motivated by questions in biological classification, we discuss some elementary combinatorial and computational properties of certain set systems that generalize hierarchies, namely, 'patchworks', 'weak patchworks', 'ample patchworks' and 'saturated patchworks' and also outline how these concepts relate to an apparently new 'duality theory' for cluster systems that is based on the fundamental concept of 'compatibility' of clusters.Comment: 17 pages, 2 figure

Molecular phylogenetics, evolution of sexual systems and historical biogeography of Darwin's favourite orchids (Catasetinae) and Swan orchids (Cycnoches Lindl.)

The Orchidaceae are one of the most species rich and widespread lineages among angiosperms. They have evolved numerous remarkable vegetative and reproductive traits that have allowed them to successfully adapt and diversify into a wide array of environments. More importantly, they have developed several intricate symbiotic relationships with different kinds of organisms (e.g. animals, fungi) that for centuries have attracted the attention of botanists, biologists, amateurs and naturalists. Nevertheless, despite the extensive research done so far on orchid biology and phylogenetics, very little is known about the biotic and environmental variables as well as the evolution of several key traits that seem to be linked with the successful diversification of this lineage. This dissertation is focused on three puzzling aspects of plant evolutionary biology, specifically the phylogenetic incongruence between nuclear and plastid genomes, the evolution of sexual systems, and lineage migration and isolation through time. To address these topics, I chose as a group of study the sub tribe Catasetinae, an orchid lineage including ca. 350 species restricted to the Neotropical region. They show a remarkable set of sexual systems, namely protandry and Environmental Sex Determination (ESD), that were never studied before in a phylogenetic context. My dissertation includes as well a minor part on taxonomic and floristic work devoted to other representative orchid lineages of the Neotropical flora (i.e. Epidendrum and Lepanthes). Based on vegetal material collected during field trips, my taxonomic research resulted in the description of several new species and new chorological reports contributing to the Colombian and Costa Rican Floras. Using a set of nuclear and chloroplast loci obtained from material cultivated at the Botanic Garden Munich and collected during field work in several Latin American countries, I produced a well-supported and insofar the most representatively sampled phylogeny of Catasetinae. While gathering vegetal material, I encountered several complications such as extreme scarcity of individuals and worrisome, extensive bureaucratic administrative processes to obtain collection and research permits that finally undermined my taxon sampling. By studying in detail the Catasetinae internal phylogenetic relationships independently derived from nuclear and plastid loci, I came across several well supported conflicting phylogenetic positions. Most of the traditional phylogenetic methods developed to address these conflicts aim at the inference of a species tree only. In chapter 5, I explored the utility of co-phylogenetic tools (i.e. PACo and ParaFit) to quantify the conflicts between nuclear and plastid genomes. These tools have been largely employed in host-parasite/endosymbiont studies, hence they have the power to assess the contribution of single Operational Terminal Units (OTUs) to the phylogenetic pattern observed. As a result, using the Catasetinae chloroplast and nuclear datasets and extensive simulation approaches, I demonstrate that PACo successfully detects conflicting OTUs and its performance is overall better than ParaFit. In addition, my research provided strong evidence towards the bias of input data type (i.e. phylograms and cladograms) on distance-based co-phylogenetic methods. A pipeline to execute PACo and ParaFit tools in the software R to detect conflicting sequences in either small or big datasets was designed After inferring a strongly supported phylogeny, and by carrying in-situ and ex-situ observations plus searches of specialized literature on reproductive biology, I investigated the evolution of sexual systems of Catasetinae. I relied on Ancestral State Reconstruction (ASR) approaches and Bayesian statistical frameworks (chapter 6). As a result, ASR revealed three independent gains of ESD, once in the Last Common Ancestor (LCA) of Catasetum, Cycnoches and part of Mormodes, respectively, always derived from a protandrous ancestors. In contrast, protandry appears to have evolved only once, at the LCA of Catasetum, Clowesia, Cycnoches, Dressleria and Mormodes. The last chapter of this dissertation deals with the impact of the Andean uplift, the most important orographic event in South America, on evolution of epiphytic lowland Neotropical lineages. I used as a group of study Cycnoches (a member of the Catasetinae), which includes ca. 34 species and is distributed in Neotropical lowland wet forests. To address this goal, I produced the most completely sampled phylogeny of Cycnoches, and relied on Bayesian dating and Ancestral Area Estimation (AAE) approaches. The LCA of Cycnoches lived ca. 6 million years ago (MYA) in the Amazonian region. From this area, it expanded towards Central America and Choco in multiple migrations well after main Andean mountain building episodes. In addition, stochastic character mapping showed that within-region speciation (i.e. speciation in sympatric lineages) was a key process linked to diversification and range distribution evolution in Cycnoches

Biodiversity and Biocollections: Problem of Correspondence

This text is an English translation of those several sections of the original paper in Russian, where collection-related issues are considered. The full citation of the original paper is as following: Pavlinov I.Ya. 2016. [Bioraznoobrazie i biokollektsii: problema sootvetstvia]. In: Pavlinov I.Ya. (comp.). Aspects of Biodiversity. Archives of Zoological Museum of Lomonosov Moscow State University, Vol. 54, Pр. 733–786. Orientation of biology, as a natural science, on the study and explanation of the similarities and differences between organisms led in the second half of the 20th century to the recognition of a specifi c subject area of biological explorations, viz. biodiversity (BD). One of the important general scientifi c prerequisites for this shift was understanding that (at the level of ontology) the structured diversity of the living nature is its fundamental property equivocal to subjecting of some of its manifestations to certain laws. At the level of epistemology, this led to acknowledging that the “diversifi cationary” approach to description of the living beings is as justifi able as the before dominated “unifi cationary” one. This general trend has led to a signifi cant increase in the attention to BD. From a pragmatic perspective, its leitmotif was conservation of BD as a renewable resource, while from a scientifi c perspective the leitmotif was studying it was studying BD as a specifi c natural phenomenon. These two points of view are united by recognition of the need for scientific substantiation of BD conservation strategy, which implies the need for a detailed study of BD itself. At the level of ontology, one of the key problems in the study of BD (leaving aside the question of its genesis) is determination of its structure, which is interpreted as a manifestation of the structure of the Earth’s biota itself. With this, it is acknowledged that the subject area of empirical explorations is not the BD as a whole ( “Umgebung”) but its particular manifestations (“Umwelts”). It is proposed herewith to recognized, within the latter: fragments of BD (especially taxa and ecosystems), hierarchical levels of BD (primarily within- and interorganismal ones), and aspects of BD (before all taxonomic and meronomic ones). Attention is drawn to a new interpretation of bioinformatics as a discipline that studies the information support of BD explorations. An important fraction of this support are biocollections. The scientifi c value of collections means that they make it possible both empirical inferring and testing (verification) of the knowledge about BD. This makes biocollections, in their epistemological status, equivalent to experiments, and so makes studies of BD quite scientific. It is emphasized that the natural objects (naturalia), which are permanently kept in collections, contain primary (objective) information about BD, while information retrieved somehow from them is a secondary (subjective) one. Collection, as an information resource, serves as a research sample in the studies of BD. Collection pool, as the totality of all collection materials kept in repositories according to certain standards, can be treated as a general sample, and every single collection as a local sample. The main characteristic of collection-as-sample is its representativeness; so the basic strategy of development of the collection pool is to maximize its representativeness as a means to ensure correspondence of structure of biocollection pool to that of BD itself. The most fundamental characteristic of collection, as an information resource, is its scientific signifi cance. The following three main groups of more particular characteristics are distinguished: — the “proper” characteristics of every collection are its meaningfulness, informativeness, reliability, adequacy, documenting, systematicity, volume, structure, uniqueness, stability, lability; — the “external” characteristics of collection are resolution, usability, ethic constituent; — the “service” characteristics of collection are its museofication, storage system security, inclusion in metastructure, cost. In the contemporary world, development of the biocollection pool, as a specific resource for BD research, requires considerable organizational efforts, including work on their “information support” aimed at demonstrating the necessity of existence of the biocollections

Genomics and Population History of Black-headed Bulbul (Brachypodius atriceps) Color Morphs

Intraspecific polymorphism in birds, especially color polymorphism, is an area of active research in evolutionary biology. In this dissertation, I applied WGS to uncover the potential genetic underpinnings of color polymorphism in the Black-headed Bulbul (Brachypodius atriceps) of Southeast Asia. This species was selected because of the heterogeneous dispersion of two morphs across its range: a yellow form predominating on mainland Asia and the Greater Sunda Islands and a gray morph on two islands—Bawean and Maratua. I approached this project from three angles. First, I reconstructed the phylogeny of the bulbul family, Pycnonotidae, to examine patterns of coloration among all species and infer the commonality of color changes relevant to B. atriceps. To build the phylogenetic tree, I used a super-matrix approach, which allowed the inclusion of 121 of the 130 known species of bulbuls. Using the tree, I determined the most appropriate outgroups for comparison with B. atriceps in subsequent genomic study. Next, I generated a high-quality reference genome of a yellow individual of B. atriceps and, subsequently, sequenced low-coverage genomes of multiple gray and yellow individuals, and three outgroup taxa. I compared Fst values between genomes of gray and yellow individuals to locate peaks of divergence and identify potential candidate loci for the color polymorphism. I also tested the protein-coding genes between yellow and gray birds for signs of selection. Among genes potentially responsible for the color polymorphism, several involved in lipid uptake, transport, and deposition—processes fundamental to carotenoid expression. In the final chapter, I assessed characteristics among B. atriceps populations across the species range in Sundaland with an emphasis on Bawean and Maratua islands. The Bawean population was barely discernable genetically from that on mainland Borneo. The Maratua population, however, was notably divergent from the mainland Bornean and other populations. Therefore, I modelled its demographic parameters and used the information to gain a better idea of the historical processes that have led to its unique, singular coloration. The Maratua population was originally isolated from other Sundaic populations c. 1.9 Ma, but c. 1000 years ago began to experience a small amount of gene flow

The history of science and medicine in the context of COVID-19

This spotlight issue encourages reflection on the current COVID-19 pandemic, not simply through comparisons with previous epidemics, but also by illustrating that epidemics deserve study within their broader cultural, political, scientific, and geographic contexts. Epidemics are not solely a function of pathogens; they are also a function of how society is structured, how political power is wielded in the name of public health, how quantitative data is collected, how diseases are categorised and modelled, and how histories of disease are narrated. Each of these activities has its own history. As historians of science and medicine have long pointed out, even the most basic methodologies that underpin scientific research—observation, trust in numbers, the use of models, even the experimental method itself—have a history. They should not be taken as a given, but understood as processes, or even strategies, that were negotiated, argued for and against, and developed within particular historical contexts and explanatory schemes. Knowing the history of something—whether of numbers, narratives, or disease—enables us to see a broader range of trajectories available to us. These varied histories also remind us that we are currently in the midst of a chaotic drama of uncertainty, within our own unstable and unfolding narrative

Genetic Applications in Avian Conservation

A fundamental need in conserving species and their habitats is defining distinct entities that range from individuals to species to ecosystems and beyond (Table 1; Ryder 1986, Moritz 1994, Mayden and Wood 1995, Haig and Avise 1996, Hazevoet 1996, Palumbi and Cipriano 1998, Hebert et al. 2004, Mace 2004, Wheeler et al. 2004, Armstrong and Ball 2005, Baker 2008, Ellis et al. 2010, Winker and Haig 2010). Rapid progression in this interdisciplinary field continues at an exponential rate; thus, periodic updates on theory, techniques, and applications are important for informing practitioners and consumers of genetic information. Here, we outline conservation topics for which genetic information can be helpful, provide examples of where genetic techniques have been used best in avian conservation, and point to current technical bottlenecks that prevent better use of genomics to resolve conservation issues related to birds. We hope this review will provide geneticists and avian ecologists with a mutually beneficial dialogue on how this integrated field can solve current and future problems

From trees to networks and back

The evolutionary history of a set of species is commonly represented by a phylogenetic tree. Often, however, the data contain conflicting signals, which can be better represented by a more general structure, namely a phylogenetic network. Such networks allow the display of several alternative evolutionary scenarios simultaneously but this can come at the price of complex visual representations. Using so-called circular split networks reduces this complexity, because this type of network can always be visualized in the plane without any crossing edges. These circular split networks form the core of this thesis. We construct them, use them as a search space for minimum evolution trees and explore their properties. More specifically, we present a new method, called SuperQ, to construct a circular split network summarising a collection of phylogenetic trees that have overlapping leaf sets. Then, we explore the set of phylogenetic trees associated with a �fixed circular split network, in particular using it as a search space for optimal trees. This set represents just a tiny fraction of the space of all phylogenetic trees, but we still �find trees within it that compare quite favourably with those obtained by a leading heuristic, which uses tree edit operations for searching the whole tree space. In the last part, we advance our understanding of the set of phylogenetic trees associated with a circular split network. Specifically, we investigate the size of the so-called circular tree neighbourhood for the three tree edit operations, tree bisection and reconnection (tbr), subtree prune and regraft (spr) and nearest neighbour interchange (nni)

Improvisation of Science Education in Indian Universities: A Call for the Inclusion of Elements of National Importance in the Curriculum

India is steadily losing its early dominance in scientific research and development- that attained apogee during classic through middle-ages, and since independence it produced not a single Nobel Laureate in Science. This article examines some of the root causes of the problems that Indian science is facing, including extrinsic factors of bureaucracy and skewed funding. Correlation of research and development expenditures and H-index as revealed in the present study, combined with India’s poor 'average citations per paper' benchmark, suggests that a vast majority of scholarly literature that the country produces have little significant research impact. At the same time, the country also delivers a small number of high-quality papers. Almost entire gamut of intrinsic issues can be attributed to the state of science education in the Indian universities, especially much overlooked component, the syllabus. Two new core courses for graduate science curricula across disciplines are proposed: (i) History of Science and (ii) Scientific Ethics. Areas of science syllabi of Indian university curriculum that require urgent revision with respect to the inclusion of elements of national importance are identified and augmentation of curricular resources to subsume modern and effective didactic strategies including podcasts and Massive Open Online Courses (MOOC) are suggested, before concluding with related pedagogical recommendations that include well-developed lesson plans, implementation of Information and Communication Technologies through personal websites, summer/winter internships, and collaborative and interdisciplinary research