Sex-dependent selection on an autosomal melanic female ornament promotes the evolution of sex ratio bias.

Sex-dependent selection often leads to spectacularly different phenotypes in males and females. In species in which sexual dimorphism is not complete, it is unclear which benefits females and males derive from displaying a trait that is typical of the other sex. In barn owls (Tyto alba), females exhibit on average larger black eumelanic spots than males but members of the two sexes display this trait in the same range of possible values. In a 12-year study, we show that selection exerted on spot size directly or on genetically correlated traits strongly favoured females with large spots and weakly favoured males with small spots. Intense directional selection on females caused an increase in spot diameter in the population over the study period. This increase is due to a change in the autosomal genes underlying the expression of eumelanic spots but not of sex-linked genes. Female-like males produced more daughters than sons, while male-like females produced more sons than daughters when mated to a small-spotted male. These sex ratio biases appear adaptive because sons of male-like females and daughters of female-like males had above-average survival. This demonstrates that selection exerted against individuals displaying a trait that is typical of the other sex promoted the evolution of specific life history strategies that enhance their fitness. This may explain why in many organisms sexual dimorphism is often not complete.

Design and analysis of ChIP-Seq experiments for nuclear factor I DNA-binding proteins

SUMMARY : Eukaryotic DNA interacts with the nuclear proteins using non-covalent ionic interactions. Proteins can recognize specific nucleotide sequences based on the sterical interactions with the DNA and these specific protein-DNA interactions are the basis for many nuclear processes, e.g. gene transcription, chromosomal replication, and recombination. New technology termed ChIP-Seq has been recently developed for the analysis of protein-DNA interactions on a whole genome scale and it is based on immunoprecipitation of chromatin and high-throughput DNA sequencing procedure. ChIP-Seq is a novel technique with a great potential to replace older techniques for mapping of protein-DNA interactions. In this thesis, we bring some new insights into the ChIP-Seq data analysis. First, we point out to some common and so far unknown artifacts of the method. Sequence tag distribution in the genome does not follow uniform distribution and we have found extreme hot-spots of tag accumulation over specific loci in the human and mouse genomes. These artifactual sequence tags accumulations will create false peaks in every ChIP-Seq dataset and we propose different filtering methods to reduce the number of false positives. Next, we propose random sampling as a powerful analytical tool in the ChIP-Seq data analysis that could be used to infer biological knowledge from the massive ChIP-Seq datasets. We created unbiased random sampling algorithm and we used this methodology to reveal some of the important biological properties of Nuclear Factor I DNA binding proteins. Finally, by analyzing the ChIP-Seq data in detail, we revealed that Nuclear Factor I transcription factors mainly act as activators of transcription, and that they are associated with specific chromatin modifications that are markers of open chromatin. We speculate that NFI factors only interact with the DNA wrapped around the nucleosome. We also found multiple loci that indicate possible chromatin barrier activity of NFI proteins, which could suggest the use of NFI binding sequences as chromatin insulators in biotechnology applications. RESUME : L'ADN des eucaryotes interagit avec les protéines nucléaires par des interactions noncovalentes ioniques. Les protéines peuvent reconnaître les séquences nucléotidiques spécifiques basées sur l'interaction stérique avec l'ADN, et des interactions spécifiques contrôlent de nombreux processus nucléaire, p.ex. transcription du gène, la réplication chromosomique, et la recombinaison. Une nouvelle technologie appelée ChIP-Seq a été récemment développée pour l'analyse des interactions protéine-ADN à l'échelle du génome entier et cette approche est basée sur l'immuno-précipitation de la chromatine et sur la procédure de séquençage de l'ADN à haut débit. La nouvelle approche ChIP-Seq a donc un fort potentiel pour remplacer les anciennes techniques de cartographie des interactions protéine-ADN. Dans cette thèse, nous apportons de nouvelles perspectives dans l'analyse des données ChIP-Seq. Tout d'abord, nous avons identifié des artefacts très communs associés à cette méthode qui étaient jusqu'à présent insoupçonnés. La distribution des séquences dans le génome ne suit pas une distribution uniforme et nous avons constaté des positions extrêmes d'accumulation de séquence à des régions spécifiques, des génomes humains et de la souris. Ces accumulations des séquences artéfactuelles créera de faux pics dans toutes les données ChIP-Seq, et nous proposons différentes méthodes de filtrage pour réduire le nombre de faux positifs. Ensuite, nous proposons un nouvel échantillonnage aléatoire comme un outil puissant d'analyse des données ChIP-Seq, ce qui pourraient augmenter l'acquisition de connaissances biologiques à partir des données ChIP-Seq. Nous avons créé un algorithme d'échantillonnage aléatoire et nous avons utilisé cette méthode pour révéler certaines des propriétés biologiques importantes de protéines liant à l'ADN nommés Facteur Nucléaire I (NFI). Enfin, en analysant en détail les données de ChIP-Seq pour la famille de facteurs de transcription nommés Facteur Nucléaire I, nous avons révélé que ces protéines agissent principalement comme des activateurs de transcription, et qu'elles sont associées à des modifications de la chromatine spécifiques qui sont des marqueurs de la chromatine ouverte. Nous pensons que lés facteurs NFI interagir uniquement avec l'ADN enroulé autour du nucléosome. Nous avons également constaté plusieurs régions génomiques qui indiquent une éventuelle activité de barrière chromatinienne des protéines NFI, ce qui pourrait suggérer l'utilisation de séquences de liaison NFI comme séquences isolatrices dans des applications de la biotechnologie.

Classificació i importància dels elements paisatgístics del territori Tsimane' segons la percepció local

En aquesta tesis es presenten els resultats de la investigació duta a terme a les comunitats indígenes Tsimane’ de l’Amazònia boliviana. La investigació estudia la percepció dels indígenes sobre l’etnoclassificació del seu territori. S’estableix una clau de classificació i es determina la importància dels elements paisatgístics del territori Tsimane’ segons la percepció local. Aquesta informació permetrà integrar el coneixement local dins dels programes de desenvolupament integral i de planificació territorial en l’Amazònia Boliviana. L’estudi conclou que la població Tsimane’ classifica els elements paisatgístics del seu entorn en 89 taques conformades per una espècies arbòria dominant i que estan incloses en un o més dels nou paisatges identificats: Därsi Därä, Sajras, Sinues Ojñi’, Mayes, Múcúya, Tsäquis Därä, Cum, Tajñi’ i Jaman. A partir d’un anàlisi multicriteri s’ha determinat una importància total per cada paisatge segons els següents criteris d’importància: diversitat de taques, activitats econòmiques realitzables, presència espiritual, percepció individual i importància relativa segons els altres paisatges. Així doncs s’ha trobat que el paisatge més important és el Därsi Därä (bosc primari caracteritzat per un estrat arbori superior a 50 metres d’altura). També s’han analitzat les dades discernint segons el gènere de l’entrevistat i segons la proximitat de les comunitats estudiades a la ciutat més propera.

Melanin pigmentation negatively correlates with plumage preening effort in barn owls

1. According to the handicap principle of sexual selection, colourful ornaments honestly signal absolute quality only if they entail fitness costs. The degree of melanism often covaries positively with aspects of individual quality, and hence melanin-based coloration should be costly to produce or to maintain in a good shape. This is, however, unlikely because melanin-based coloration is often strongly heritable and in birds the rate of feather wear decreases with the amount of melanin pigments packed in feathers. 2. The hypothesis that melanin pigments reduce the cost of maintaining colourful ornaments in a good shape predicts a negative correlation between the degree of melanism and both the size of the uropygial gland that produces preening secretions and the intensity of preening behaviour. 3. Using a correlative approach, I evaluated these two predictions in the barn owl Tyto alba in which the body underside varies from immaculate to heavily marked with black spots, a eumelanin-based trait, and from white to reddish-brown, a phaeomelanin-based trait. I correlated plumage traits with preening behaviour in nestlings and with the size and mass of the uropygial gland in dead adults. I also weighed nonornamental wing and tail feathers to assess whether the quality of nonornamental feathers is positively correlated with the degree of melanism of an ornamental plumage trait. 4. The degree of phaeomelanism was neither associated with preening behaviour nor with the size and mass of the uropygial gland. In line with the two predictions, individuals with more and larger black spots had a lighter uropygial gland and preened less frequently. Because nonornamental wing and tail feathers of spottier individuals were heavier per unit of surface area, the entire plumage of eumelanic individuals may be more robust and in turn require less care than the plumage of nonmelanic conspecifics. 5. In conclusion, the degree of eumelanism can be associated with aspects of individual quality even if eumelanic ornaments are neither costly to produce nor to maintain in a good shape. Document Type: Article

Bacillus and Serratia species for Scarab control

Few microorganisms are commercially available for use against white grubs (larvae of Scarabaeidae). Entomopathogenic bacteria, particularly Bacillus popilliae, have been used the longest for white grub suppression. Other bacteria, namely B. thuringiensis and Serratia spp. offer promise for future control. This papes examines two genera of bacteria (Bacillus and Serratia) from the historical and current perspective. Bacillus popilliae, the firs microbial control agent registered in the United States, has a long history of use in suppressing populations of the Japanese beetle, Popillia japonica. However, lack of in vitro production and the slow and sporadic nature of its activity, severely limits its utilization. B. thuringiensis, the most widely used microbial pesticide, has not been used for scarab, control. However, strains with scarab activity have recently been discovered. Scarab larvae have been collected in the United States with signs and symptoms similar to those characteristic of amber disease (caused by Serratia entomophila) in the New Zealand grass grub, Costelytra zealandica. A total of 147 bacteria have been obtained from the digestive tracts of larvae of the Japanese beetle and masked chafers, Cyclocephala spp., as well as from larvae and soil collected in Japan and China. Seventy five of these have been identified as Serratia spp. Most (40) of the remaining bacteria are in the genus Enterobacter. A majority of the bacteria (73) and of the Serratia (38) came from P. japonica.

The identification of Anopheles (Nyssorhynchus) rondoni (Diptera: Culicidae) in Mato Grosso, Brazil: an analysis of key character variability

A morphological study was made of a population of Anopheles (Nyssorhynchus) rondoni (Neiva and Pinto) from northern Mato Grosso, Brazil. This population usually lacked the primary key character of a dark basal band on hindtarsomere 3, i.e., hindtarsomere 3 was all white as in most other members of the subgenus. It was determined that this species can be recognized instead by the presence of a dark spot on the thorax made up of a large dark prescutellar space that is contiguous with a concolorous central area on the scutellum. A secondary character of a dark area on the costa created by the fusion of the humeral dark, presector dark and sector dark proximal spots is also usually reliable. Regression analyses comparing the lengths and ratios of the dark bands on hindtarsomeres 2 to those on 3 describe a straight line relationship. This suggests that the "atypical" population is at one end of a character gradient. We propose that in the subgenus Nyssorhynchus individuals that have a long basal band on hindtarsomere 2 are more likely to also have a basal band on hindtarsomere 3. The pupal stage of this species has not been previously described. Reared-associated specimens from this study show that the pupa can be easily differentiated from all other Nyssorhynchus by the relatively stout, usually 2 or 3 branched (1-5), setae 1 and 5 on segments IV-VII.

Ecological interactions of visceral leishmaniasis in the state of Bahia, Brazil

The laboratory and field observations summarized in this paper on visceral leishmaniasis ecology in the State of Bahia, Brazil are based on the author's observations over the past 35 years in a number of state's foci, public health records and literature citations. The disease is endemic with epidemic outbreaks occurring every ten years and its geographical distribution is expanding rapidly in the last years. Leishmania chagasi is the main ethiologic agent of the visceral leishmaniasis but Le. amazonensis s. lato was the only leishmania isolated by other authors from some visceral leishmaniasis human cases in the state. Lutzomyia longipalpis (with one or two spots on tergites III and IV and two sized different populations) was epidemiologically incriminated as the main vector. It was found naturally infected with promastigotes, and it was infected with four species of leishmanias in the laboratory. Although the experimental transmission of Le. amazonensis by the bite of Lu. longipalpis to hamsters was performed, the author was not successful in transmitting Le. chagasi in the same way. The dog is the most important domestic source for infection of the vector, however it is not a primary reservoir. The opossum Didelphis albiventris was found naturally infected with Le. chagasi but its role as reservoir is unknown. Foxes and rodents were not found infected with leishmanias in Bahia.

Female- and male-specific signals of quality in the barn owl

Most bird studies of female signalling have been confined to species in which females display a male-ornament in a vestigial form. However, a great deal of benefit may be gained from considering phenotypic traits that are specific to females. This is because (1) sex-specific traits may signal sex-specific qualities and (2) females may develop a male-ornament not because they are selected to do so, but because fathers transmit to daughters the underlying genes for its expression (genetic correlation between the sexes). We investigated these two propositions in the barn owl Tyto alba, a species in which male plumage is lighter in colour and less marked with black spots than that of females. Firstly, we present published evidence that female plumage spottiness reflects parasite resistance ability. We also show that male plumage coloration is correlated with reproductive success, male feeding rate and heart mass. Secondly, cross-fostering experiments demonstrate that plumage coloration and spottiness are genetically correlated between the sexes. This implies that if a given trait value is selected in one sex, the other sex will indirectly evolve towards a similar value. This prediction is supported by the observation that female plumage coloration and spottiness resembled that of males, in comparisons at the level of Tyto alba alba populations, Tyto alba subspecies and Tyto species. Our results therefore support the hypothesis that sex-specific traits signal sex-specific qualities and that a gene for a sex-specific trait can be expressed in the other sex as the consequence of a genetic correlation between the sexes.

Evolution démographique d'une population de musaraignes aquatiques (Neomys fodiens) en Suisse romande

Studies on water shrews, Neomy fodiens, showed a significant decrease of capture rates throughout the winter period. Thereafter, during reproduction, animals dispersed along the stream as far as one kilometer from their original site. In this work, we assess the extension of their dispersion movements. We suppose that very small populations persist wintertime at localized spots and from their recolonize the empty habitats

Stable isotope geochemistry and formation mechanisms of quartz veins; Extreme paleoaltitudes of the Central Alps in the Neogene

Quartz veins ranging in size from less than 50 cm length and 5 cm width to greater than 10 m in length and 5 m in width are found throughout the Central Swiss Alps. In some cases, the veins are completely filled with milky quartz, while in others, sometimes spectacular void-filling quartz crystals are found. The style of vein filling and size is controlled by host rock composition and deformation history. Temperatures of vein formation, estimated using stable isotope thermometry and mineral equilibria, cover a range of 450 degrees C down to 150 degrees C. Vein formation started at 18 to 20 Ma and continued for over 10 My. The oxygen isotope values of quartz veins range from 10 to 20 permil, and in almost all cases are equal to those of the hosting lithology. The strongly rock-buffered veins imply a low fluid/rock ratio and minimal fluid flow. In order to explain massive, nearly morromineralic quartz formation without exceptionally large fluid fluxes, a mechanism of differential pressure and silica diffusion, combined with pressure solution, is proposed for early vein formation. Fluid inclusions and hydrous minerals in late-formed veins have extremely low delta D values, consistent with meteoric water infiltration. The change from rock-buffered, static fluid to infiltration from above can be explained in terms of changes in the large-scale deformation style occurring between 20 and 15 Ma. The rapid cooling of the Central Alps identified in previous studies may be explained in part, by infiltration of cold meteoric waters along fracture systems down to depths of 10 km or more. An average water flux of 0.15 cm 3 cm(-2)yr(-1) entering the rock and reemerging heated by 40 degrees C is sufficient to cool rock at 10 km depth by 100 degrees C in 5 million years. The very negative delta D values of < -130 permil for the late stage fluids are well below the annual average values measured in meteoric water in the region today. The low fossil delta D values indicate that the Central Alps were at a higher elevation in the Neogene. Such a conclusion is supported by an earlier work, where a paleoaltitude of 5000 meters was proposed on the basis of large erratic boulders found at low elevations far from their origin.

Proteomics fingerprinting of phagosome maturation and evidence for the role of a Galpha during uptake.

Phagocytosis, whether of food particles in protozoa or bacteria and cell remnants in the metazoan immune system, is a conserved process. The particles are taken up into phagosomes, which then undergo complex remodeling of their components, called maturation. By using two-dimensional gel electrophoresis and mass spectrometry combined with genomic data, we identified 179 phagosomal proteins in the amoeba Dictyostelium, including components of signal transduction, membrane traffic, and the cytoskeleton. By carrying out this proteomics analysis over the course of maturation, we obtained time profiles for 1,388 spots and thus generated a dynamic record of phagosomal protein composition. Clustering of the time profiles revealed five clusters and 24 functional groups that were mapped onto a flow chart of maturation. Two heterotrimeric G protein subunits, Galpha4 and Gbeta, appeared at the earliest times. We showed that mutations in the genes encoding these two proteins produce a phagocytic uptake defect in Dictyostelium. This analysis of phagosome protein dynamics provides a reference point for future genetic and functional investigations.

Studies on populations of Lutzomyia longipalpis (Lutz & Neiva, 1912) (Diptera: Psychodidae: Phlebotominae) in Brazil

Studies were performed on five Brazilian populations of Lutzomyia longipalpis: Salvaterra (PA), São José do Ribamar (MA), Canindé (CE), Natal (RN) and Gruta da Lapinha, Lagoa Santa (MG). No morphological differences were observed that could distinguish between these populations. Homogeneity tests showed that the allopatric populations display a certain heterogeneity and that the sympatric populations, with different patterns of spots, are homogeneous. The Student-Newman-Keuls test, represented by Euler-Venn diagrams, showed a disjunction between the populations from the north/northeast and the one from Gruta da Lapinha. Genetic distances between the four populations (excluding the Canindé population) were within the range of intrapopulational differences. The Gruta da Lapinha population displayed a heterozygotic deficiency that could be a consequence of high levels of inbreeding due to cryptic habits of living in a small cave. These results do not favor the hypothesis of a L. longipalpis species complex in Brazil, and the species should be considered high polymorphic.

Description of immature stages of Culex ocossa Dyar & Knab, Culex delpontei Duret and Culex pereyrai Duret of the Melanoconion subgenus (Diptera: Culicidae)

The larva and pupa of Culex (Melanoconion) ocossa Dyar & Knab are redescribed and those of Culex (Melanoconion) delpontei Duret and Culex (Melanoconion) pereyrai Duret are described from specimens collected in the states of São Paulo and Paraná, Brazil. The pupa of Cx. ocossa differs from those of the other two species in having seta 5-IV-VI dark with strongly aciculated branches, and caudolateral angle of segment VIII produced into sharp point, and seta 1-P present; Cx. delpontei can be distinguished from Cx. pereyrai in possessing paddle lightly tanned, trumpet flared, and wing and leg cases lightly tanned, without pattern of dark spots; Cx. pereyrai can be recognized by having wing case with pattern of dark, discontinuously pigmented, longitudinal lines, and trumpet cylindrical, not flared. The larvae of the three species share the presence of seta 2-C placed medially to seta 1-C.

Wing geometry as a tool for studying the Lutzomyia longipalpis (Diptera: Psychodidae) complex

Toro Toro (T) and Yungas (Y) have been described as genetically well differentiated populations of the Lutzomyia longipalpis (Lutz & Neiva, 1912) complex in Bolivia. Here we use geometric morphometrics to compare samples from these populations and new populations (Bolivia and Nicaragua), representing distant geographical origins, qualitative morphological variation ("one-spot" or "two-spots" phenotypes), ecologically distinct traits (peridomestic and silvatic populations), and possibly different epidemiological roles (transmitting or nor transmitting Leishmania chagasi). The Nicaragua (N) (Somotillo) sample was "one-spot" phenotype and a possible peridomestic vector. The Bolivian sample of the Y was also "one-spot" phenotype and a demonstrated peridomestic vector of visceral leishmaniasis (VL). The three remaining samples were silvatic, "two-spots" phenotypes. Two of them (Uyuni and T) were collected in the highlands of Bolivian where VL never has been reported. The last one (Robore, R) came from the lowlands of Bolivia, where human cases of VL are sporadically reported. The decomposition of metric variation into size and shape by geometric morphometric techniques suggests the existence of two groups (N/Y/R, and U/T). Several arguments indicate that such subdivision of Lu. longipalpis could correspond to different evolutionary units.

Design of a Control Slide for Cyanoacrylate Polymerization : Application to the CA-Bluestar Sequence

Casework expercience has shown that, in some cases, long exposures of surfaces subjected to cyanoacrylate (CA) fuming had detrimental effects on the subsequent application of Bluestar. This study aimed to develop a control mechanism to monitor the amount of CA deposited prior to the subsequent treatment. A control slide bearing spots of sodium hydroxide (NaOH) of known concentrations and volume was designed and validated against both scanning electron microscopy (SEM) observations and latent print examiners' assessments of the quality of the developed marks. The control slide allows one to define three levels of development that were used to monitor the Bluestar reaction on depleting footwear marks left in diluted blood. The appropriate conditions for a successful application of both CA and Bluestar were determined.