Estimation des corrélations phylogénétiques entre paramètres d'évolution moléculaire et Traits d'histoire de vie

Depuis quelques années, l'évolution moléculaire cherche à caractériser les variations et l'intensité de la sélection grâce au rapport entre taux de substitution synonyme et taux de substitution non-synonyme (dN/dS). Cette mesure, dN/dS, a permis d'étudier l'histoire de la variation de l'intensité de la sélection au cours du temps ou de détecter des épisodes de la sélection positive. Les liens entre sélection et variation de taille efficace interfèrent cependant dans ces mesures. Les méthodes comparatives, quant a elle, permettent de mesurer les corrélations entre caractères quantitatifs le long d'une phylogénie. Elles sont également utilisées pour tester des hypothèses sur l'évolution corrélée des traits d'histoire de vie, mais pour être employées pour étudier les corrélations entre traits d'histoire de vie, masse, taux de substitution ou dN/dS. Nous proposons ici une approche combinant une méthode comparative basée sur le principe des contrastes indépendants et un modèle d'évolution moléculaire, dans un cadre probabiliste Bayésien. Intégrant, le long d'une phylogénie, sur les reconstructions ancestrales des traits et et de dN/dS nous estimons les covariances entre traits ainsi qu'entre traits et paramètres du modèle d'évolution moléculaire. Un modèle hiérarchique, a été implémenté dans le cadre du logiciel coevol, publié au cours de cette maitrise. Ce modèle permet l'analyse simultané de plusieurs gènes sans perdre la puissance donnée par l'ensemble de séquences. Un travail deparallélisation des calculs donne la liberté d'augmenter la taille du modèle jusqu'à l'échelle du génome. Nous étudions ici les placentaires, pour lesquels beaucoup de génomes complets et de mesures phénotypiques sont disponibles. À la lumière des théories sur les traits d'histoire de vie, notre méthode devrait permettre de caractériser l'implication de groupes de gènes dans les processus biologique liés aux phénotypes étudiés.

Mammal reproductive strategies driven by offspring mortality-size relationships

Trade-offs have long been a major theme in life-history theory, but they have been hard to document. We introduce a new method that reveals patterns of divergent trade-offs after adjusting for the pervasive variation in rate of resource allocation to offspring as a function of body size and lifestyle. Results suggest that preweaning vulnerability to predation has been the major factor determining how female placental mammals allocate production between a few large and many small offspring within a litter and between a few large litters and many small ones within a reproductive season. Artiodactyls, perissodactyls, cetaceans, and pinnipeds, which give birth in the open on land or in the sea, produce a few large offspring, at infrequent intervals, because this increases their chances of escaping predation. Insectivores, fissiped carnivores, lagomorphs, and rodents, whose offspring are protected in burrows or nests, produce large litters of small newborns. Primates, bats, sloths, and anteaters, which carry their young from birth until weaning, produce litters of one or a few offspring because of the need to transport and care for them.

The Evolution of Modularity in the Mammalian Skull I: Morphological Integration Patterns and Magnitudes

Morphological integration refers to the modular structuring of inter-trait relationships in an organism, which could bias the direction and rate of morphological change, either constraining or facilitating evolution along certain dimensions of the morphospace. Therefore, the description of patterns and magnitudes of morphological integration and the analysis of their evolutionary consequences are central to understand the evolution of complex traits. Here we analyze morphological integration in the skull of several mammalian orders, addressing the following questions: are there common patterns of inter-trait relationships? Are these patterns compatible with hypotheses based on shared development and function? Do morphological integration patterns and magnitudes vary in the same way across groups? We digitized more than 3,500 specimens spanning 15 mammalian orders, estimated the correspondent pooled within-group correlation and variance/covariance matrices for 35 skull traits and compared those matrices among the orders. We also compared observed patterns of integration to theoretical expectations based on common development and function. Our results point to a largely shared pattern of inter-trait correlations, implying that mammalian skull diversity has been produced upon a common covariance structure that remained similar for at least 65 million years. Comparisons with a rodent genetic variance/covariance matrix suggest that this broad similarity extends also to the genetic factors underlying phenotypic variation. In contrast to the relative constancy of inter-trait correlation/covariance patterns, magnitudes varied markedly across groups. Several morphological modules hypothesized from shared development and function were detected in the mammalian taxa studied. Our data provide evidence that mammalian skull evolution can be viewed as a history of inter-module parcellation, with the modules themselves being more clearly marked in those lineages with lower overall magnitude of integration. The implication of these findings is that the main evolutionary trend in the mammalian skull was one of decreasing the constraints to evolution by promoting a more modular architecture.

Detecção de predadores por dicromatas e tricromatas humanos e a sua implicação na evolução da visão de cores em primatas

Among placental mammals, primates are the only ones to present trichromatic color vision. However, the distribution of trichromacy among primates is not homogeneous: Old World primates shows an uniform trichromacy (with all individuals being trichromats) and New World primates exhibit a color vision polymorphism (with dichromatic males and dichromatic or trichromatic females). Visual ecology studies have investigated which selective pressures may have been responsible for the evolution of trichromacy in primates, diverging from the dichromat standard found in other mammals. Cues associated with foraging and the socio-reproductive status were analyzed, indicating a trichromatic advantage for the rapid detection of visually conspicuous objects against a green background. However, dichromats are characterized by an efficient capture of cryptic and camouflaged stimuli. These advantages regarding phenotype may be responsible for the maintenance of the visual polymorphism in New World primates and for the high incidence of color blindness in humans (standing around 8% in Caucasian men). An important factor that has not yet been experimentally taken into account is the predation risk and its effect on the evolution of trichromacy in primates. To answer this question, we prepared and edited pictures of animals with different coats: oncillas (Leopardus spp.), puma (Puma concolor) and ferret (Galictis cuja). The specimens were taxidermized and the photographs were taken in three different vegetation scenarios (dense forest, cerrado and grassland). The images of the predators were manipulated so that they fit into two categories of stimulus size (small or large). After color calibration and photo editing, these were presented to 40 humans (20 dichromats and 20 trichromats) by a computer program, which presented a set of four photos at a time (one picture containing the taxidermized animal amid the background vegetation and three depicting only the background vegetation) and recorded the response latency and success rate of the subjects. The results show a trichromatic advantage in detecting potential predators. The predator detection was influenced by the background, the predator species, the dimension of the stimulus and the observer s visual phenotype. As humans have a high rate of dyschromatopsias, when compared to wild Catarrhini or human tribal populations, it is possible that the increased rate of dichromats is a result of reduced pressure for rapid predator detection. Since our species came to live in more cohesive groups and resistant to attack by predators, with the advent of agriculture and the formation of villages, it is possible that the lower risk of predation has reduced the selection in favor of trichromats

Metabolic, ventilatory, and hygric physiology of a South American marsupial, the long-furred woolly mouse opossum

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Metabolic, ventilatory, and hygric physiology of the gracile mouse opossum (Gracilinanus agilis)

We present the first complete study of basic laboratory-measured physiological variables (metabolism, thermoregulation, evaporative water loss, and ventilation) for a South American marsupial, the gracile mouse opossum (Gracilinanus agilis). Body temperature (Tb) was thermolabile below thermoneutrality (Tb = 33.5°C), but a substantial gradient between Tb and ambient temperature (Ta) was sustained even at Ta = 12°C (Tb = 30.6°C). Basal metabolic rate of 1.00 mL O2 g-1 h-1 at Ta = 30°C conformed to the general allometric relationship for marsupials, as did wet thermal conductance (5.7 mL O2 g-1 h-1 °C-1). Respiratory rate, tidal volume, and minute volume at thermoneutrality matched metabolic demand such that O2 extraction was 12.4%, and ventilation increased in proportion to metabolic rate at low T a. Ventilatory accommodation of increased metabolic rate at low Ta was by an increase in respiratory rate rather than by tidal volume or O2 extraction. Evaporative water loss at the lower limit of thermoneutrality conformed to that of other marsupials. Relative water economy was negative at thermoneutrality but positive below Ta = 12°C. Interestingly, the Neotropical gracile mouse opossums have a more positive water economy at low Ta than an Australian arid-zone marsupial, perhaps reflecting seasonal variation in water availability for the mouse opossum. Torpor occurred at low Ta, with spontaneous arousal when . T b > 20°C. Torpor resulted in absolute energy and water savings but lower relative water economy. We found no evidence that gracile mouse opossums differ physiologically from other marsupials, despite their Neotropical distribution, sympatry with placental mammals, and long period of separation from Australian marsupials. © 2009 by The University of Chicago. All rights reserved.

Análise morfométrica do sistema auditivo periférico da preguiça (Bradypus variegatus)

A superordem Xenarthra é composta de 31 espécies viventes de tatus, tamanduás e preguiças. As arborícolas preguiças pertencem a dois gêneros, Choloepus e Bradypus, cuja divergência se deu a aproximadamente 40 milhões de anos atrás. As similaridades entre os dois taxa, tais como a presença de algas verdes nos pêlos e habilidade locomotora suspensória, são notáveis exemplos de evolução convergente. A exata posição da linhagem Xenarthra entre os mamíferos na árvore filogenética ainda não é completamente compreendida, com alguns rearranjos na árvore da família dos mamíferos placentários, considerando os Xenarthras mais relacionados entre Afrotheria (que inclui musaranhos, porcos-da-terra, peixes-boi e elefantes) ou a Boreoeutheria (que inclui primatas, roedores, carnívoros e ungulados). O objetivo deste trabalho é descrever pela primeira vez características morfológicas dos ouvidos médio e interno de Bradypus variegatus e compará-las a outros mamíferos placentários que possuam dados publicados na literatura. Nós usamos 13 espécimes adultas post-mortem (machos e fêmeas) e 15 crânios da coleção do Museu Paraense Emílio Goeldi. Além das medições, foram usadas técnicas de microscopia óptica, microscopia eletrônica de varredura e tomografia computadorizada. Através da árvore filogenética das preguiças, o gênero Bradypus é posicionado como táxon-irmão de todas as outras preguiças. Nossos resultados mostram que a morfologia do ouvido médio e interno de Bradypus variegatus é similar a de outros mamíferos com dados publicados na literatura e que apresentam escalonamento alométrico.

Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra

Background: Xenarthra (sloths, armadillos and anteaters) represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results: Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome). B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4). The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. Conclusions: Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly.

Guanylyl cyclase C is a selective marker for metastatic colorectal tumors in human extraintestinal tissues

Guanylyl cyclase C (GCC) has been detected only in intestinal mucosa and colon carcinoma cells of placental mammals. However, this receptor has been identified in several tissues in marsupials, and its expression has been suggested in tissues other than intestine in placental mammals. Selective expression of GCC by colorectal tumor cells in extraintestinal tissues would permit this receptor to be employed as a selective marker for metastatic disease. Thus, expression of GCC was examined in human tissues and tumors, correlating receptor function with detection by PCR. GCC was detected by ligand binding and catalytic activation in normal intestine and primary and metastatic colorectal tumors, but not in extraintestinal tissues or tumors. Similarly, PCR yielded GCC-specific amplification products with specimens from normal intestine and primary and metastatic colorectal tumors, but not from extraintestinal tissues or tumors. Northern blot analysis employing GCC-specific probes revealed an ≈4-kb transcript, corresponding to recombinant GCC, in normal intestine and primary and metastatic colorectal tumors, but not in extraintestinal tissues. Thus, GCC is selectively expressed in intestine and colorectal tumors in humans and appears to be a relatively specific marker for metastatic cancer cells in normal tissues. Indeed, PCR of GCC detected tumor cells in blood from some patients with Dukes B colorectal cancer and all patients examined with Dukes C and D colorectal cancer, but not in that from normal subjects or patients with Dukes A colon carcinoma or other nonmalignant intestinal pathologies.

Development of a bovine X chromosome linkage group and painting probes to assess cattle, sheep, and goat X chromosome segment homologies.

The X chromosome linkage group is conserved in placental mammals. However, X chromosome morphological differences, due to internal chromosome rearrangements, exist among mammalian species. We have developed bovine chromosome painting probes for Xp and Xq to assess segment homologies between the submetacentric bovine X chromosome and the acrocentric sheep and goat X chromosomes. These painting probes and their corresponding DNA libraries were developed by chromosome micromanipulation, DNA micropurification, microcloning, and PCR amplification. The bovine Xp painting probe identified an interstitially located homologous segment in the sheep and goat Xq region, most probably resulting from chromosome inversion. Ten type II (microsatellite) markers obtained from the bovine Xq library and five other X chromosome assigned, but unlinked, markers were used to generate a linkage map for Xq spanning 89.4 centimorgans. The chromosome painting probes and molecular markers generated in this study would be useful for comparative mapping and tracing of internal X chromosome rearrangements in all ruminant species and would contribute to the understanding of mammalian sex chromosome evolution.

Recombinant human uteroglobin suppresses cellular invasiveness via a novel class of high-affinity cell surface binding site.

The mechanism(s) that regulates invasion of trophoblasts through the uterine epithelium during embryo implantation and nidation in hemochorial placental mammals is poorly understood. While limited trophoblast invasion is essential for the establishment of normal pregnancy, dysregulation of this process may contribute to the pathogenesis of choriocarcinoma, a highly invasive and lethal form of cancer arising from the trophoblasts. We have previously demonstrated that rabbit uteroglobin (UG), a cytokine-like, antiinflammatory protein, produced by the endometrial epithelium during pregnancy, has a potent antichemotactic effect on neutrophils and monocytes in vitro. Here, we report that recombinant human UG (hUG) dramatically suppresses invasion of human trophoblasts and NIH 3T3 cells through an artificial basement membrane (Matrigel) in vitro but has no effect on that of human choriocarcinoma cells. We identified a previously unreported high-affinity, high molecular weight (approximately 190 kDa), nonglycosylated hUG-binding protein, readily detectable on human trophoblasts and NIH 3T3 cells but totally lacking on choriocarcinoma cells. Taken together, these results raise the possibility that (i) hUG plays a critical role in regulating cellular invasiveness, at least in part, via its previously unrecognized cell surface binding site, and (ii) some of the numerous biological activities of proteins of the UG family, reported so far, may be mediated via this binding site.

Contrasting histories of avian and mammalian Mhc genes revealed by class II B sequences from songbirds.

To explore the evolutionary dynamics of genes in the major histocompatibility complex (Mhc) in nonmammalian vertebrates, we have amplified complete sequences of the polymorphic second (beta1) and third (beta2) exons of class II beta chain genes of songbirds. The pattern of nucleotide substitution in the antigen-binding site of sequences cloned from three behaviorally and phylogenetically divergent songbirds [scrub jays Aphelocoma coerulescens), red-winged blackbirds (Agelaius phoeniceus), and house finches (Carpodacus mexicanus) reveals that class II B genes of songbirds are subject to the same types of diversifying forces as those observed at mammalian class II loci. By contrast, the tree of avian class II B genes reveals that orthologous relationships have not been retained as in placental mammals and that, unlike class II genes in mammals, genes in songbirds and chickens have had very recent common ancestors within their respective groups. Thus, whereas the selective forces diversifying class II B genes of birds are likely similar to those in mammals, their long-term evolutionary dynamics appear to be characterized by much higher rates of concerted evolution.

Human white blood cells contain cyclobutyl pyrimidine dimer photolyase.

Although enzymatic photoreactivation of cyclobutyl pyrimidine dimers in DNA is present in almost all organisms, its presence in placental mammals is controversial. We tested human white blood cells for photolyase by using three defined DNAs (supercoiled pET-2, nonsupercoiled bacteriophage lambda, and a defined-sequence 287-bp oligonucleotide), two dimer-specific endonucleases (T4 endonuclease V and UV endonuclease from Micrococcus luteus), and three assay methods. We show that human white blood cells contain photolyase that can photorepair pyrimidine dimers in defined supercoiled and linear DNAs and in a 287-bp oligonucleotide and that human photolyase is active on genomic DNA in intact human cells.

Ecology and evolution of primate colour vision

More than one hundred years ago, Grant Allen suggested that colour vision in primates, birds and insects evolved as an adaptation for foraging on colourful advertisements of plants-fruits and flowers. Recent studies have shown that well developed colour vision appeared long before fruits and flowers evolved. Thus, colour vision is generally beneficial for many animals, not only for those eating colourful food. Primates are the only placental mammals that have trichromatic colour vision. This may indicate either that trichromacy is particularly useful for primates or that primates are unique among placental mammals in their ability to utilise the signals of three spectrally distinct types of cones or both. Because fruits are an important component of the primate diet, primate trichromacy could have evolved as a specific adaptation for foraging on fruits. Alternatively, primate trichromacy could have evolved as an adaptation for many visual tasks. Comparative studies of mammalian eyes indicate that primates are the only placental mammals that have in their retina a pre-existing neural machinery capable of utilising the signals of an additional spectral type of cone. Thus, the failure of non-primate placental mammals to evolve trichromacy can be explained by constraints imposed on the wiring of retinal neurones.

The current molecular phylogeny of Eutherian mammals challenges previous interpretations of placental evolution.

Based on histology, the placentae of eutherians are currently grouped in epitheliochorial, endotheliochorial and haemochorial placentae. In a haeckelian sense, the epitheliochorial contact with marked histiotrophic feeding by uterine milk is generally considered as primitive, especially since similar contacts exist in Marsupials. In contrast, the more intimate endotheliochorial and haemochorial contact, facilitating haemotrophic nutrition, is interpreted as a derived state. A cladistic analysis based on the phylogenetic relationships established by molecular analyses reveals that the basic clades are all characterized by an endotheliochorial or haemochorial placenta, and that the epitheliochorial placenta evolved at least three times in a convergent manner. This evolution may be explained by the fact that the epitheliochorial placenta in eutherians is more efficient in nutritional transfer (flow rate by exchange surface). Moreover, this arrangement may confer an advantage to the mother who can probably reduce the degree of manipulation by a genetically imprinted embryo.