This work analysed phylogenetic utility of several characters associated with basic coloration, moulting and whorls in Cervidae via comparison of these traits with relatively robust phylogeny of this group based on several morphological, ethological and molecular data. I was able to detect probable evolutionary history of some selected traits, their ancestral state and synapomorphies of recognized clades.

abstract: Animals have evolved a diversity of signaling traits, and in some species, they co-occur and are used simultaneously to communicate. Although much work has been done to understand why animals possess multiple signals, studies do not typically address the role of inter-signal interactions, which may vary intra- and inter-specifically and help drive the evolutionary diversity in signals. For my dissertation, I tested how angle-dependent structural coloration, courtship displays, and the display environment interact and co-evolved in hummingbird species from the “bee” tribe (Mellisugini). Most “bee” hummingbird species possess an angle-dependent structurally colored throat patch and stereotyped courtship (shuttle) display. For 6 U.S. “bee” hummingbird species, I filmed male shuttle displays and mapped out the orientation- and-position-specific movements during the displays. With such display paths, I was able to then recreate each shuttle display in the field by moving plucked feathers from each male in space and time, as if they were naturally displaying, in order to measure each male’s color appearance during their display (i.e. the interactions between male hummingbird plumage, shuttle displays, and environment) from full-spectrum photographs. I tested how these interactions varied intra- and inter-specifically, and which of these originating traits might explain that variation. I first found that the solar-positional environment played a significant role in explaining variation in male color appearance within two species (Selasphorus platycercus and Calypte costae), and that different combinations of color-behavior-environment interactions made some males (in both species) appear bright, colorful, and flashy (i.e. their color appearance changes throughout a display), while other males maintained a consistent (non-flashing) color display. Among species, I found that plumage flashiness positively co-varied with male display behaviors, while another measure of male color appearance (average brightness/colorfulness) co-varied with the feather reflectance characteristics themselves. Additionally, species that had more exaggerated plumage features had less exaggerated shuttle displays. Altogether, my dissertation work illustrates the complexity of multiple signal evolution and how color-behavior-environment interactions are vital to understanding the evolution of colorful and behavioral display traits in animals. / Dissertation/Thesis / Doctoral Dissertation Biology 2018

abstract: The origin and function of color in animals has been a subject of great interest for taxonomists and ecologists in recent years. Coloration in animals is useful for many important functions like species identification, camouflage and understanding evolutionary relationships. Quantitative measurements of color signal and patch size in mammals, birds and reptiles, to name a few are strong indicators of sexual selection cues and individual health. These measurements provide valuable insights into the impact of environmental conditions on habitat and breeding of mammals, birds and reptiles. Recent advances in the area of digital cameras and sensors have led to a significant increase in the use of digital photography as a means of color quantification in animals. Although a significant amount of research has been conducted on ways to standardize image acquisition conditions and calibrate cameras for use in animal color quantification, almost no work has been done on designing automated methods for animal color quantification. This thesis presents a novel perceptual"–"based framework for the automated extraction and quantification of animal coloration from digital images with slowly varying (almost homogenous) background colors. This implemented framework uses a combination of several techniques including color space quantization using a few dominant colors, foreground"–"background identification, Bayesian classification and mixture Gaussian modelling of conditional densities, edge"–"enhanced model"–"based classification and Saturation"–"Brightness quantization to extract the colored patch. This approach assumes no prior information about the color of either the subject or the background and also the position of the subject in the image. The performance of the proposed method is evaluated for the plumage color of the wild house finches. Segmentation results obtained using the implemented framework are compared with manually scored results to illustrate the performance of this system. The segmentation results show a high correlation with manually scored images. This novel framework also eliminates common problems in manual scoring of digital images such as low repeatability and inter"–"observer error. / Dissertation/Thesis / M.S. Electrical Engineering 2013

Orientador: Jose Roberto Trigo / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-10T19:03:33Z (GMT). No. of bitstreams: 1 Massuda_KamilaFerreira_M.pdf: 3824014 bytes, checksum: d4db5cb4afb22e7d40b4afc3d0677236 (MD5) Previous issue date: 2008 / Resumo: As defesas químicas em lepidópteros compreendem mecanismos que vão desde o seqüestro de compostos do metabolismo secundário de plantas até a biossíntese de novo de compostos que podem torná-los tóxicos ou impalatáveis. As larvas da borboleta Methona themisto (Nymphalidae: Ithomiinae), que apresentam coloração conspícua e se alimentam apenas da solanácea Brunfelsia uniflora, rica em compostos do metabolismo secundário, foram analisadas sob vários aspectos, para verificar se são quimicamente defendidas. O acompanhamento da sobrevivência das larvas indicou que a predação afeta significativamente a sobrevivência em seu ambiente natural. As defesas químicas dessas larvas são aparentemente ineficazes contra predadores invertebrados, como a aranha Lycosa erythrognatha e a formiga Camponotus crassus (100% dos indivíduos testados predaram as larvas), mas parecem ser eficazes contra os mantídeos Oxyopsis saussuurei (redução no tempo de manipulação da presa e predação em um segundo contato). Para predadores vertebrados como o lagarto Tropidurus itambere e a ave Gallus gallus, a defesa parece atuar em relação à palatabilidade e à coloração conspícua. Gallus gallus apresentou maior predação de larvas de 1o ínstar, sugerindo que há um incremento na impalatabilidade da larva no decorrer de seu desenvolvimento. Os testes de aprendizagem dos pintinhos demonstraram que com poucos contatos com a presa impalatável já se obtém uma resposta de rejeição visual. O emprego de uma larva de coloração semelhante a da Methona themisto indica que os pintinhos são capazes de relacionar a cor com o gosto desagradável, rejeitando assim uma presa palatável. Apenas extratos diclorometânicos das larvas testados com Gallus gallus foram significativamente rejeitados em relação a seus controles. Dessa forma, esses dados comprovam que as defesas químicas das larvas de Methona themisto atuam principalmente contra predadores vertebrados visualmente orientados / Abstract: Chemical defense in Lepidoptera involves several mechanisms such as sequestration of secondary metabolismcompounds of host plants and de novo synthesis of compounds that can provide some unpalatability or toxicity. The larvae of the butterfly Methona themisto (Nymphalidae: Ithomiinae) have a conspicuous coloration and feed exclusively on Brunfelsia uniflora (Solanaceae), that is rich in compounds of the secondary metabolismo These larvae were analyzed under several aspects to confirm if they are chemically defended. Survivorship data showed predation significantly affecting larval survival in natural habitat. Larvae chemical defenses are inefficient against invertebrate predators, such as the spider Lycosa erythr-ognatha and the ant Campónotus crassus (100% of predation), but it seems to be efficient against the mantid Oxyopsis saussuurei (reduction of prey manipulation time and predation in a second contact). To vertebrate predators, like the lizard Tropidurus itambere and the chick Gallus gallus, defense acts through conspicuous coloration and palatability. Predation by Gallus gallus was highest upon 1st ínstar larvae, suggesting an increase of unpalatability throughout development. Learning avoidance tests with Gallus gallus demonstrated that few contacts with distasteful and warning colored prey could make the predator reject visually Methona themisto larvae. Chicks visually rejected palatable larvae painted in the same color pattem of Methona themisto larvae confirming their ability to associate taste and color. Only dichloromethanic extracts tested with chicks showed significant rejection in relation to controls. These results confirm that Methona themisto larvae are chemical defended against visually oriented vertebrate predators / Mestrado / Mestre em Ecologia

Vidros comerciais de base silicato do tipo sodo-cálcico, apresentam coloração pela presença de óxidos de metais de transição, tais como ferro e cobalto, ou pela presença de elementos não-metálicos, tais como o selênio. Geralmente, a presença de selênio metálico (Se°) num vidro silicato confere-lhe a cor rosa (depende de seu estado de oxidação). Desse modo, industrialmente, adiciona-se selênio à composição de vidros quando se deseja produzir vidros róseos ou, mais freqüentemente, quando se deseja mascarar a cor esverdeada conferida pela presença de ferro, o principal contaminante das matérias-primas naturais. Entretanto, o selênio é encontrado em pequenas quantidades na natureza, daí seu alto custo. Além disso, da quantidade inicial de selênio colocada na composição de vidros industriais sodo-cálcicos, quase 80% são vaporizados durante a etapa de fusão do vidro. Este trabalho é dedicado ao estudo do efeito da adição de diferentes compostos portadores de selênio como matéria-prima em substituição ao selênio metálico, visando a redução da volatilização de selênio durante a fusão. Além do selênio metálico, foram utilizados selenitos de sódio, de bário, de zinco e de ferro. Os vidros foram obtidos por fusões em escala de laboratório, em cadinhos de alta alumina, a 1500°C, em forno elétrico. A seguir determinou-se a composição química de cada vidro obtido, por fluorescência de raios X e sua cor, através da determinação de suas coordenadas cromáticas no sistema CIEL*a*b*. A análise dos resultados teve como principal conclusão que a concentração final de selênio no vidro é função apenas de sua quantidade no banho, independentemente do composto químico que lhe forneceu. / Commercial silicate glasses of the soda-lime system attain color by the presence of transition metal oxides, such as iron and cobalt, or by the presence of non-metallic elements, like selenium. Usually, the presence of metallic selenium (Se°) in a silicate glass results in a light pink coloration (depends on its oxidation state). Therefore, industrially, selenium is added to a glass composition when the objective is to obtain a pink color glass, or, more often, when the objective is to mask the greenish coloration resultant from the presence of iron, the most usual contaminant in the natural raw-materials. However, selenium occurs in the nature only in small quantities. Besides, from the initial selenium added to industrial soda-lime batch compositions, almost 80% volatilize during melting. This work is dedicated to the study of the effect of adding selenium from different raw-materials, substituting for the metallic selenium, with the principal objective of reducing the loss of this element during glass melting. Along with metallic selenium, sodium, barium, zinc, and iron selenites were employed. The glasses were obtained in laboratory scale meltings in alumina crucibles, at 1500°C, in an electrical furnace. After that, the chemical composition of each glass was obtained by X-ray fluorescence, and its color was measured according to the chromatic coordinates in the CIEL*a*b* method. The main conclusion that can be drawn from the analysis of the results is that the selenium concentration in the final glass is a function only of the quantity of selenium present in the melt, independently of the chemical compound which supplied such selenium.

Un graphe mixte est un graphe simple tel que un sous-ensemble des arêtes a une orientation. Pour entiers non négatifs j et k, un graphe mixte-(j,k) est un graphe mixte avec j types des arcs and k types des arêtes. La famille de graphes mixte-(j,k) contient graphes simple, (graphes mixte−(0,1)), graphes orienté (graphes mixte−(1,0)) and graphe coloré arête −k (graphes mixte−(0,k)).Un homomorphisme est un application sommet entre graphes mixte−(j,k) que tel les types des arêtes sont conservés et les types des arcs et leurs directions sont conservés. Le nombre chromatique−(j,k) d’un graphe mixte−(j,k) est le moins entier m tel qu’il existe un homomorphisme à une cible avec m sommets. Quand on observe le cas de (j,k) = (0,1), on peut déterminer ces définitions correspondent à les définitions usuel pour les graphes.Dans ce mémoire on etude le nombre chromatique−(j,k) et des paramètres similaires pour diverses familles des graphes. Aussi on etude les coloration incidence pour graphes and digraphs. On utilise systèmes de représentants distincts et donne une nouvelle caractérisation du nombre chromatique incidence. On define le nombre chromatique incidence orienté et trouves un connexion entre le nombre chromatique incidence orienté et le nombre chromatic du graphe sous-jacent. / A mixed graph is a simple graph in which a subset of the edges have been assigned directions to form arcs. For non-negative integers j and k, a (j,k)−mixed graph is a mixed graph with j types of arcs and k types of edges. The collection of (j,k)−mixed graphs contains simple graphs ((0,1)−mixed graphs), oriented graphs ((1,0)−mixed graphs) and k−edge- coloured graphs ((0,k)−mixed graphs).A homomorphism is a vertex mapping from one (j,k)−mixed graph to another in which edge type is preserved, and arc type and direction are preserved. The (j,k)−chromatic number of a (j,k)−mixed graph is the least m such that an m−colouring exists. When (j,k)=(0,1), we see that these definitions are consistent with the usual definitions of graph homomorphism and graph colouring.In this thesis we study the (j,k)−chromatic number and related parameters for different families of graphs, focussing particularly on the (1,0)−chromatic number, more commonly called the oriented chromatic number, and the (0,k)−chromatic number.In addition to considering vertex colourings, we also consider incidence colourings of both graphs and digraphs. Using systems of distinct representatives, we provide a new characterisation of the incidence chromatic number. We define the oriented incidence chromatic number and find, by way of digraph homomorphism, a connection between the oriented incidence chromatic number and the chromatic number of the underlying graph. This connection motivates our study of the oriented incidence chromatic number of symmetric complete digraphs.

Les métaux traces comme le plomb, le zinc sont essentiellement émis par les activités anthropiques et se retrouvent de ce fait à des concentrations beaucoup plus élevées en milieux urbains qu’en milieux ruraux. Durant ma thèse, j’ai tout d’abord testé les effets écotoxicologiques d’une exposition chronique au plomb et/ou au zinc, deux métaux particulièrement abondants en milieu urbain, chez le pigeon biset (Columba livia). J’ai ainsi pu montrer des effets nocifs du plomb, et bénéfiques du zinc sur l’immunité, le maintien de la corpulence et plusieurs paramètres de la reproduction. Du fait de la variabilité des réponses écophysiologiques des individus, les métaux traces sont susceptibles d’exercer de nouvelles pressions de sélection sur les populations urbaines et favoriser les individus capables de se détoxifier ou de tolérer de fortes concentrations en métaux. Au cours de ma thèse, j’ai mis en évidence le rôle de la mélanine dans la fixation du zinc et du plomb au niveau des plumes. Par ailleurs la coloration mélanique du plumage semblent moduler les effets du plomb et du zinc sur certains paramètres physiologiques, et les juvéniles au plumage davantage mélanique survivent mieux dans un environnement pollué en plomb. Quels que soient les mécanismes sous-jacents (i.e. rôle détoxifiant de la mélanine ou effets pléiotropes associés à sa synthèse), mes résultats soulignent l’avantage sélectif potentiel de la mélanisation du plumage dans un environnement pollué en métaux traces, dont notamment le milieu urbain. Cette étude apporte des réponses essentielles sur l’impact écologique de l’urbanisation et les mécanismes permettant le maintien du polymorphisme de coloration mélanique du plumage, et plus largement des phanères. / Trace metals, such as lead and zinc are mainly emitted by human activities, explaining their high concentrations in urban areas in comparison with rural environments. During my PhD, I first investigated the ecotoxicological effects of a chronic exposure to lead and/or zinc, two abundant metals in urban areas, in feral pigeons (Columba livia). I stressed deleterious effects of lead, while beneficial effects of zinc on immunity, body mass index maintenance and several parameters of reproduction. Because sensitivity to trace metals differs between individuals, trace metals may exert new selective pressures on urban populations and favour individuals with higher detoxification capacities and that are more tolerant to elevated environmental trace metals concentrations. My work puts ahead the role of melanin in the storage of zinc and lead in the feathers. Moreover, melanin-based plumage colouration seems to modulate the effects of lead and zinc on some of the physiological parameters measured and darker juveniles were more prone to survive than paler ones when exposed to lead. Whatever the underlying mechanism (i.e. the detoxification role of melanin or the pleiotropic effects associated with its synthesis), my results suggest a selective advantage of plumage melanism in environments polluted with trace metals, such as urban areas. This study brings key answers on the ecological impact of urbanization and on the mechanisms explaining melanin-based plumage colouration polymorphism maintenance.

Cette thèse a pour thème la coloration de diverses classes de graphes épars. Shearer montra en 1983 [She83] que le ratio d'indépendance des graphes sans triangle de degré maximal d est au moins (1-o(1))ln d/d, et 13 ans plus tard Johansson [Joh96] démontra que le nombre chromatique de ces graphes est au plus O(d/ln d) quand d tend vers l'infini. Ce dernier résultat fut récemment amélioré par Molloy [Mol19], qui montra que la borne (1+o(1))d/ln d est valide quand d tend vers l'infini.Tandis que le résultat de Molloy s'exprime à l'aide d'un paramètre global, le degré maximal du graphe, nous montrons qu'il est possible de l'étendre à la coloration locale. Il s'agit de la coloration par liste, où la taille de la liste associée à chaque sommet ne dépend que de son degré. Avec une méthode différente se basant sur les propriétés de la distribution hard-core sur les ensembles indépendants d'un graphe, nous obtenons un résultat similaire pour la coloration fractionnaire locale, avec des hypothèses plus faibles. Nous démontrons également un résultat concernant la coloration fractionnaire locale des graphes où chaque sommet est contenu dans un nombre borné de triangles, et une borne principalement optimale sur le taux d'occupation — la taille moyenne des ensembles indépendants — de ces graphes. Nous considérons également les graphes de maille 7, et prouvons des résultats similaires qui améliorent les bornes précédemment connues quand le degré maximal du graphe est au plus 10^7. Finalement, pour les graphes d-réguliers où d vaut 3, 4, ou 5, de maille g variant entre 6 et 12, nous démontrons de nouvelles bornes inférieures sur le ratio d'indépendance.Le Chapitre 2 est dédié à la coloration à distance t d'un graphe, qui généralise la notion de coloration forte des arêtes. Nous cherchons à étendre le théorème de Johansson à la coloration à distance t, par l'exclusion de certains cycles. Le résultat de Johansson s'obtient par exclusion des triangles, ou des cycles de taille k pour n'importe quelle valeur de k. Nous montrons que l'exclusion des cycles de taille 2k, pour n'importe quel k>t, a un effet similaire sur le nombre chromatique à distance t, et sur l'indice chromatique à distance t+1. En outre, quand t est impair, une conclusion similaire peut se faire pour le nombre chromatique à distance t par l'exclusion des cycles de d'une taille impaire fixée valant au moins 3t. Nous étudions l'optimalité de ces résultats à l'aide de constructions de nature combinatoire, algébrique, et probabiliste.Dans le Chapitre 3, nous nous intéressons à la densité bipartie induite des graphes sans triangle, un paramètre relaxant celui de la coloration fractionnaire. Motivés par une conjecture de Esperet, Kang, et Thomassé [EKT19], qui prétend que la densité bipartie induite de graphes sans triangle de degré moyen d est au moins de l'ordre de ln d, nous démontrons cette conjecture quand d est suffisamment grand en termes du nombre de sommets n, à savoir d est au moins de l'ordre de (n ln n)^(1/2). Ce résultat ne pourrait être amélioré que par une valeur de l'ordre de ln n, ce que nous montrons à l'aide d'une construction reposant sur le processus sans triangle. Nos travaux se ramènent à un problème intéressant, celui de déterminer le nombre chromatique fractionnaire maximal d'un graphe épars à n sommets. Nous prouvons des bornes supérieures non triviales pour les graphes sans triangle, et pour les graphes dont chaque sommet appartient à un nombre borné de triangles.Cette thèse est reliée aux nombres de Ramsey. À ce jour, le meilleur encadrement connu sur R(3,t) nous est donné par le résultat de Shearer, et par une analyse récente du processus sans triangle [BoKe13+,FGM13+], ce qui donne(1-o(1)) t²/(4 ln t) < R(3,t) < (1+o(1)) t²/ln t. (1)Beaucoup de nos résultats ne pourraient être améliorés à moins d'améliorer par la même occasion (1), ce qui constituerait une révolution dans la théorie de Ramsey quantitative. / This thesis focuses on generalisations of the colouring problem in various classes of sparse graphs.Triangle-free graphs of maximum degree d are known to have independence ratio at least (1-o(1))ln d/d by a result of Shearer [She83], and chromatic number at most O(d/ln d) by a result of Johansson [Joh96], as d grows to infinity. This was recently improved by Molloy, who showed that the chromatic number of triangle-free graphs of maximum degree d is at most (1+o(1))d/ln d as d grows to infinity.While Molloy's result is expressed with a global parameter, the maximum degree of the graph, we first show that it is possible to extend it to local colourings. Those are list colourings where the size of the list associated to a given vertex depends only on the degree of that vertex. With a different method relying on the properties of the hard-core distribution on the independent sets of a graph, we obtain a similar result for local fractional colourings, with weaker assumptions. We also provide an analogous result concerning local fractional colourings of graphs where each vertex is contained in a bounded number of triangles, and a sharp bound for the occupancy fraction — the average size of an independent set — of those graphs. In another direction, we also consider graphs of girth 7, and prove related results which improve on the previously known bounds when the maximum degree does not exceed 10^7. Finally, for d-regular graphs with d in the set {3,4,5}, of girth g varying between 6 and 12, we provide new lower bounds on the independence ratio.The second chapter is dedicated to distance colourings of graphs, a generalisation of strong edge-colourings. Extending the theme of the first chapter, we investigate minimal sparsity conditions in order to obtain Johansson-like results for distance colourings. While Johansson's result follows from the exclusion of triangles — or actually of cycles of any fixed length — we show that excluding cycles of length 2k, provided that k>t, has a similar effect for the distance-t chromatic number and the distance-(t+1) chromatic index. When t is odd, the same holds for the distance-t chromatic number by excluding cycles of fixed odd length at least 3t. We investigate the asymptotic sharpness of our results with constructions of combinatorial, algebraic, and probabilistic natures.In the third chapter, we are interested in the bipartite induced density of triangle-free graphs, a parameter which conceptually lies between the independence ratio and the fractional chromatic number. Motivated by a conjecture of Esperet, Kang, and Thomassé [EKT19], which states that the bipartite induced density of a triangle-free graph of average degree d should be at least of the order of ln d, we prove that the conjecture holds for when d is large enough in terms of the number of vertices n, namely d is at least of the order of (n ln n)^(1/2). Our result is shown to be sharp up to term of the order of ln n, with a construction relying on the triangle-free process. Our work on the bipartite induced density raises an interesting related problem, which aims at determining the maximum possible fractional chromatic number of sparse graph where the only known parameter is the number of vertices. We prove non trivial upper bounds for triangle-free graphs, and graphs where each vertex belongs to a bounded number of triangles.All the content of this thesis is a collection of specialisations of the off-diagonal Ramsey theory. To this date, the best-known bounds on the off-diagonal Ramsey number R(3,t) come from the aforementioned result of Shearer for the upper-bound, and a recent analysis of the triangle-free process [BoKe13+,FGM13+] for the lower bound, giving(1-o(1)) t²/(4 ln t) < R(3,t) < (1+o(1)) t²/ln t. (1)Many of our results are best possible barring an improvement of (1), which would be a breakthrough in off-diagonal Ramsey theory.

Sexual selection theory tries to explain evolution of apparently useless traits which mainly developed in males of numerous species. One such trait is also rich and vibrant coloration, typical for many of the bird species. These traits are difficult to be falsified, and therefore they honestly signal quality of the individual. Carotenoid coloration reflects the health condition and melanin coloration the social status, even though this traditional division might not be as strict according to the latest studies. Apart from these ways of maintaining honesty, recent studies are focusing more also on the effect of hormones, mainly two steroids: male sexual hormone - testosterone -, and the "stress" hormone - corticosterone. Both hormones could positively influence male's sexual traits such as ornamental coloration. On the other hand, elevated levels of these hormones possess risk to the organism (higher energetic expenditure, chronic stress), therefore also might potentially become costly. Using photographs of birds in standardized conditions as well as spectrophotometry I analyzed the plumage coloration of males of the Yellowhammer (Emberiza citrinella). Concentrations of testosterone and corticosterone deposited in feathers were analyzed using the LC-MS/MS. Also, for males in breeding season 2015,...

Multicomponent signals are complex stimuli directed to receptors of only single modality. Colourful ornaments of animals are multicomponent signals. In this thesis I present results of studies on the origin of coloration in turtles and squamate reptiles together with notes on relativistic view of the functionality of animal coloration. The results show that turtle coloration, which have been studied only marginally until now, is shaped by sexual selection. It is shown that turtles share mechanisms of coloration by vertical organization of different pigment cell types together with squamate reptiles. Turtles also produce colour by organization of collagen fibres which share trait with birds and mammals. Mechanisms of body coloration differ dramatically between closely related turtle species studied even though the individual constituting components are shared among these species. On the example of polymorphic lizards, it is shown that qualitative categorical difference between groups of individuals of the same population are maintained based on quantitative changes in pigment contents regulated by ancient loci shared by different species. The turtles and reptiles are valuable source of our knowledge on the evolution of multicomponent visual signalling due to their intriguing composition of skin....