Mionectes oleagineus (Aves, Tyrannidae) is a small, sexually monomorphic, lek breeding bird. The behaviour and mating system of this species were studied on Costa Rica's Osa Peninsula over two years. In this thesis I ask three questions: 1) What kind of social organization does M. oleagineus exhibit? 2) Does habitat influence male display dispersion? and 3) What is the function of song in attracting mates and in male-male interactions? In Chapter 2, I describe M. oleagineus' social organization. There were three categories of males: territory owners, satellites and floaters. The latter 2 categories were non-territorial and represented half of the male population. I describe interactions between displaying males and visitors to their territories, including courtship display and aggressive interactions between males. Male display dispersion was highly variable in the study area, including classical leks, in which territories shared contiguous boundaries, an exploded lek, where the territories did not share boundaries, and solitary display territories. In Chapter 3, I test the hypothesis that the number of males that can settle in an area, and their subsequent display dispersion, is determined by the availability and dispersion of suitable habitat. Discriminant function analysis of measures of vegetation structure from both territories and non-territory sample plots showed that territory habitat could be distinguished from non-territory habitat. Eleven percent of the sample plots were described as suitable habitat in the analysis. Given that half the male population is non-territorial, the existence of unoccupied, suitable habitat makes it unlikely that habitat availability determines the number of males settling, or their display dispersion. The major occupation of males on their display territories is singing. In Chapter 4, I investigate the function of song for M. oleagineus using behavioural observation and an experiment involving temporary muting. Males which sang at higher rates received more visitors of both sexes. The territories of most muted territorial males were rapidly usurped by other males. Two of the muted males regained their territories upon regaining the ability to sing. This study is the first to directly demonstrate a key role for song in male-male interactions on leks. It also provides evidence that females use song in mate assessment. / Science, Faculty of / Zoology, Department of / Graduate

京都大学 / 新制・課程博士 / 博士(医学) / 甲第23421号 / 医博第4766号 / 新制||医||1053(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 小濱 和貴, 教授 妹尾 浩, 教授 川口 義弥 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

De nombreux espèces utilisent des signaux multicomposants/multimodales. Au cours de cette thèse, nous avons étudié les signaux acoustiques et visuels produits dans le cadre du choix du partenaire chez le Manchot royal. Concernant les composantes acoustiques, nous avons identifié des arrangements syllabiques spécifiques à chacun des sexes. La fréquence fondamentale et l'énergie des cris des manchots royaux, ainsi que certaines caractéristiques colorimétriques signalent des informations sur la classe d'âge de l'émetteur. Nous avons montré que l'appareil vocal des manchots royaux permet les individus de produire deux bandes de fréquences harmoniques puisqu'ils présentent un syrinx trachéo-bronchique et donc deux sources sonores. En résumé, ce travail de thèse a contribué à une meilleure compréhension des signaux utilisés dans le cadre du choix du partenaire chez une espèce monomorphique qui présente un comportement reproducteur très coûteux. / Communication signals used in sexual selection can be costly to produce and even reduce the emitter’s fitness. Many species use multicomponent signals communication systems in different signal modalities. Here, we study visual and acoustic signals produced in the context of mate choice on a sexually monomorphically ornamented seabird, the king penguin. We identified a sex-specific syllable pattern in the vocalisations of 1-year-old fledglings, juveniles and adult birds. We found that fundamental frequency and energy components of calls and beak spot and ear patch ornament parameters signal information about the age-class of the emitter. Investigating the vocal apparatus of adult king penguins, we showed that king penguins can produce “two voices” since they have a tracheobronchial syrinx, i.e. two sound sources. This thesis contributed to our understanding of signals used in mate choice in a sexually monomorphically ornamented species that exhibits a very costly breeding behaviour.

Depuis 157 ans et la publication originelle de la théorie de l’évolution par sélection naturelle de Charles Darwin, ce concept n’a cessé d’évoluer. Un principe fondamental suggère que des traits handicapants aient évolués dans la mesure où ils informent de manière honnête les congénères sur la qualité intrinsèque du porteur. Le manchot royal est un modèle exceptionnel permettant de tester la valeur sélective de ce signal dans un contexte sexuel et social (non-reproductif). Mes résultats suggèrent que l’apparition et le maintien de certains de ces traits au cours de l’évolution se sont opérés sous l’influence de la sélection sexuelle et d’un choix mutuel du partenaire, tandis que d’autre, non contraint par la condition fluctuante de l’individu, aurait évolué sous l’influence de la sélection sociale. Ce travail de recherche participe à la compréhension des mécanismes impliqués dans l’évolution de signaux coûteux, et à la nature des bénéfices ultimes que ces traits procurent. / Darwin’s seminal theory of evolution by means of natural selection, first published 157 years ago, has been in constant refinement ever since. The production and maintenance of extravagant ornaments is widely suggested to evolve by conspecific preference providing information on individual intrinsic quality in sexual contexts or on individual social quality in non-reproductive contexts. The king penguin is a monomorphic bird species and an outstanding model to study ornament evolution. My results show that those ornaments are partly condition-dependent, and reliable traits that may be used to assess the quality of a potential sexual partner, implying that their evolution and maintenance is partly determined by sexual selection. On the other hand, some traits remained condition-independent in their production, suggesting that the cost associated with their expression was deferred over time and the evolution of those ornaments likely shaped by non-sexual social selection.

Le cuivre, souvent utilisé pour gérer les bactérioses en agriculture, est largement utilisé dans la lutte contre Xanthomonas citri pv. citri (Xcc), agent responsable du chancre asiatique des agrumes. La récente détection d’un phénotype résistant au cuivre (CuR) chez Xcc dans deux territoires ultramarins français a motivé une étude génomique qui a révélé, dans les génomes de souches CuR, la présence d’un plasmide conjugatif portant un transposon adaptatif de type Tn3. Sa conservation chez plusieurs espèces de Xanthomonas phytopathogènes suggère le rôle des transferts horizontaux (HGT) dans l’adaptation de Xcc. Nous avons donc analysé, dans l’océan Indien, les relations phylogénétiques de souches sensibles et CuR en prenant en compte à la fois les SNP et les variations de contenu en gènes. La datation de la phylogénie a permis de formuler des scenarii d’introduction de la bactérie dans la région. La phylogénie a montré une structure géographique forte à l’échelle de l’océan Indien, qui s’estompe à l’échelle de la Réunion et disparaît à l’échelle du verger. Au sein des vergers, l’admixture est un élément favorable aux HGT entre souches génétiquement différentes. Ils sont pourtant peu caractérisés chez les bactéries du genre Xanthomonas. Nous avons ainsi analysé la dispersion de l’ensemble des gènes plasmidiques connus de la famille des Xanthomonadaceae dans l’ensemble des génomes bactériens de NCBI, mettant en évidence à la fois la forte prévalence des gènes plasmidiques au sein des Xanthomonadaceae mais aussi la limite taxonomique forte à leur échange par conjugaison. L’importance du mosaïsme plasmidique, en partie lié aux éléments mobiles a aussi été illustrée. L’ensemble de nos résultats souligne l’importance des HGT dans l’évolution des bactéries du genre Xanthomonas, et la nécessité de caractériser finement le contenu et le fonctionnement du génome environnemental des Xanthomonadaceae pour appréhender au mieux l’adaptation de ces bactéries phytopathogènes. / Copper, frequently used in agriculture to control bacterial diseases, is commonly used against Xanthomonas citri pv. citri (Xcc), the bacterial agent of Asiatic citrus canker. The recent detection of a copper-resistant phenotype in two French overseas regions motivated a genomic study which revealed, in copper-resistant (CuR) strains, a conjugative plasmid encoding an adaptive transposon of the Tn3 family. Its conservation in several Xanthomonas species suggested the role of horizontal gene transfer (HGT) in Xcc adaptation. We therefore analyzed the evolutionary history of susceptible and CuR Xcc strains in the Indian Ocean using both SNP and gene content variations. The dating of the obtained phylogeny allowed us to hypothesize the history of Xcc introduction into the region. The phylogeny showed a strong geographic structure among islands of the Indian Ocean region, which faded at the Réunion scale and disappeared at the grove scale. Among the groves, admixture is a factor favoring HGT between genetically distinct strains. This form of evolution is however largely uncharacterized in the Xanthomonas genus. To fill this gap, we searched genetic homology between the whole known plasmid gene content of the Xanthomonadaceae family and the complete set of genomes hosted in NCBI databases. We highlighted both the ubiquity of plasmid genes in the Xanthomonadaceae family and the taxonomical barrier of their sharing by conjugation. The small fraction of genes that were exchanged through the complete sharing of plasmids also revealed the importance of plasmid mosaicism, partly due to mobile genetic elements. Taken together, our results highlight the importance of bacterial communities in the evolution of phytopathogenic bacteria of the Xanthomonas genus, and the need for a precise characterization of the content and the functioning of the Xanthomonadaceae environmental genome in order to fully apprehend the adaptation of these phytopathogenic bacteria.

Unambiguous gender identification (ID) is needed to assess parameters in studies of population dynamics, behavior, and evolutionary biology of Caribbean Flamingo (Phoenicopterus ruber ruber) and other birds. Due to its importance for management and conservation, molecular (DNA-based) avian gender ID assays targeting intron-size differences of the Chromosome Helicase ATPase DNA Binding (CHD) gene of males (CHD-Z) and females (CHD-W) have been developed. Male (ZZ) and female (WZ) genotypes are usually scored as size polymorphisms through agarose or acrylamide gels. For certain species, W-specific restriction sites or multiplex polymerase chain-reaction (PCR) involving CHD-W specific primers are needed. These approaches involve a minimum of three steps following DNA isolation: PCR, gel electrophoresis, and photo-documentation, which limit high throughput scoring and automation potential. In here, a short amplicon (SA) High-resolution Melting Analysis (HRMA) assay for avian gender ID is developed. SA-HRMA of an 81-Base Pair (bp) segment differentiates heteroduplex female (WZ) from homoduplex male (ZZ) genotypes by targeting Single-nucleotide Polymorphisms (SNPs) instead of intron-size differences between CHD-Z and CHD-W genes. To demonstrate the utility of the approach, the gender of Caribbean Flamingo (P. ruber ruber) (17 captive from the Dallas Zoo and 359 wild from Ria Lagartos, Yucatan, Mexico) was determined. The assay was also tested on specimens of Lesser Flamingo (P. minor), Chilean Flamingo (P. chilensis), Saddle-billed Stork (Ephippiorhynchus senegalensis), Scarlet Ibis (Eudocimus ruber), White-bellied Stork (Ciconia abdimii), Roseate Spoonbill (Platalea ajaja), Marabou Stork (Leptoptilos crumeniferus), Greater Roadrunner (Geococcyx californianus), and Attwater's Prairie Chicken (Tympanuchus cupido attwateri). Although the orthologous 81 bp segments of Z and W are highly conserved, sequence alignments with 50 avian species across 15 families revealed mismatches affecting one or more nucleotides within the SA-HRMA forward or reverse primers. Most mismatches were located along the CHD-Z gene that may generate heteroduplex curves and thus gender ID errors. For such cases, taxon and species-specific primer sets were designed. The SA-HRMA gender ID assay can be used in studies of avian ecology and behavior, to assess sex-associated demographics and migratory patterns, and as a proxy to determine the health of the flock and the degree by which conservation and captive breeding programs are functioning.