Vitellogenin Underwent Subfunctionalization to Acquire Caste and Behavioral Specific Expression in the Harvester Ant Pogonomyrmex barbatus.

The reproductive ground plan hypothesis (RGPH) proposes that the physiological pathways regulating reproduction were co-opted to regulate worker division of labor. Support for this hypothesis in honeybees is provided by studies demonstrating that the reproductive potential of workers, assessed by the levels of vitellogenin (Vg), is linked to task performance. Interestingly, contrary to honeybees that have a single Vg ortholog and potentially fertile nurses, the genome of the harvester ant Pogonomyrmex barbatus harbors two Vg genes (Pb_Vg1 and Pb_Vg2) and nurses produce infertile trophic eggs. P. barbatus, thus, provides a unique model to investigate whether Vg duplication in ants was followed by subfunctionalization to acquire reproductive and non-reproductive functions and whether Vg reproductive function was co-opted to regulate behavior in sterile workers. To investigate these questions, we compared the expression patterns of P. barbatus Vg genes and analyzed the phylogenetic relationships and molecular evolution of Vg genes in ants. qRT-PCRs revealed that Pb_Vg1 is more highly expressed in queens compared to workers and in nurses compared to foragers. By contrast, the level of expression of Pb_Vg2 was higher in foragers than in nurses and queens. Phylogenetic analyses show that a first duplication of the ancestral Vg gene occurred after the divergence between the poneroid and formicoid clades and subsequent duplications occurred in the lineages leading to Solenopsis invicta, Linepithema humile and Acromyrmex echinatior. The initial duplication resulted in two Vg gene subfamilies preferentially expressed in queens and nurses (subfamily A) or in foraging workers (subfamily B). Finally, molecular evolution analyses show that the subfamily A experienced positive selection, while the subfamily B showed overall relaxation of purifying selection. Our results suggest that in P. barbatus the Vg gene underwent subfunctionalization after duplication to acquire caste- and behavior- specific expression associated with reproductive and non-reproductive functions, supporting the validity of the RGPH in ants.

Perturbation expansions of multilocus fixation probabilities for frequency-dependent selection with applications to the Hill-Robertson effect and to the joint evolution of helping and punishment.

Natural populations are of finite size and organisms carry multilocus genotypes. There are, nevertheless, few results on multilocus models when both random genetic drift and natural selection affect the evolutionary dynamics. In this paper we describe a formalism to calculate systematic perturbation expansions of moments of allelic states around neutrality in populations of constant size. This allows us to evaluate multilocus fixation probabilities (long-term limits of the moments) under arbitrary strength of selection and gene action. We show that such fixation probabilities can be expressed in terms of selection coefficients weighted by mean first passages times of ancestral gene lineages within a single ancestor. These passage times extend the coalescence times that weight selection coefficients in one-locus perturbation formulas for fixation probabilities. We then apply these results to investigate the Hill-Robertson effect and the coevolution of helping and punishment. Finally, we discuss limitations and strengths of the perturbation approach. In particular, it provides accurate approximations for fixation probabilities for weak selection regimes only (Ns < or = 1), but it provides generally good prediction for the direction of selection under frequency-dependent selection.

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In so-called unisexual teleost fishes, a broad spectrum of evolutionaty stages with varying amounts of sexual elements has evolved. These range from pure sperm-dependent parthenogenesis (gynogenesis) without or with different amounts of paternal leakage to hybridogenesis with hemiclonal diploid gametogenesis or genome elimination folowed by meiosis (meiotic hybridogenesis). All of these phenomena are hybrid origin. Many of these fish form complexes which involve the coexistence of one or more sexually reproducing species with derived all-female forms that have various ploidy levels and reproductive modes, including gynogenesis, (meiotic) hybridogenesis nnd sexual reproduction. In teleosts, parthenogenetic reproduction is strictly dependent on sperm to initate embryonic development. As opposed to true parthenogenesis, sperm-dependent parthenogenetic teleost lineages must primarily coexist with their "sperm donor", usually males from a parental sexual lineage or from a related sexual species. In some systems, gynogens were able to escape from their initial sperm donors ("host switch") and therefore, to enlarge their ranges and ecological niches. Sperm donors normally do not contribue genetically to the next generation. However, paternal leakage is observed in many systems contributing differing amounts of genetic material (from microchromosomes to entire chromosome sets) allowing interaction between genomes of different origin. Hybridogenesis is similar to gynogenesis in depending upon coexisence with sexual species but incorporates recombined genetic material by true fertilizazion. While hybridogens usually form clonal gametes, some triploids are capable of genome elimination followed by a normal diploid meiosis. Sperm-dependent parthenogenesis and hybridogenesis combine disadvantages and advantages from both sexuality and asexuality. Here, we give an overview of sperm-dependent breeding complexes in fishes, discuss the evolutionary consequences of paternal leakage, and speculate about the evolutionary significance of intergenomic (re)combination.

DL4-mediated Notch signaling is required for the development of fetal αβ and γδ T cells.

T-cell development depends upon interactions between thymocytes and thymic epithelial cells (TECs). The engagement of delta-like 4 (DL4) on TECs by Notch1 expressed by blood-borne BM-derived precursors is essential for T-cell commitment in the adult thymus. In contrast to the adult, the earliest T-cell progenitors in the embryo originate in the fetal liver and migrate to the nonvascularized fetal thymus via chemokine signals. Within the fetal thymus, some T-cell precursors undergo programmed TCRγ and TCRδ rearrangement and selection, giving rise to unique γδ T cells. Despite these fundamental differences between fetal and adult T-cell lymphopoiesis, we show here that DL4-mediated Notch signaling is essential for the development of both αβ and γδ T-cell lineages in the embryo. Deletion of the DL4 gene in fetal TECs results in an early block in αβ T-cell development and a dramatic reduction of all γδ T-cell subsets in the fetal thymus. In contrast to the adult, no dramatic deviation of T-cell precursors to alternative fates was observed in the fetal thymus in the absence of Notch signaling. Taken together, our data reveal a common requirement for DL4-mediated Notch signaling in fetal and adult thymopoiesis.

Stimulation of hematopoiesis in vivo by recombinant bacterial murine interleukin 3.

Mouse interleukin 3 (IL-3) cDNA was cloned into a plasmid construction, allowing the synthesis of very high quantities of IL-3 in Escherichia coli. The recombinant (r) IL-3, purified to homogeneity, was active in vitro on the proliferation and differentiation of various hematopoietic progenitor cells at 1 pM. To maintain detectable blood levels of IL-3, osmotic pumps containing rIL-3 or control solutions were placed under the skin of normal and irradiated C3H/HeJ and (BALB X B10) F1 mice. The effect of IL-3 on hematopoietic progenitor cell numbers in spleen and bone marrow was evaluated 3 and 7 days later by using an in vitro clonal assay. The results demonstrated the following: (i) Doses of IL-3 infused at the rate of 2.5-5 ng per g of body weight per hr were sufficient to increase the numbers of hematopoietic progenitors in normal mice by at least 2-fold within 3 days. (ii) In mice with progenitor cell levels depressed by sublethal irradiation, 7-day treatment with IL-3 resulted in a 10-fold increase to near normal levels. (iii) The erythroid and myeloid lineages appeared to be enhanced to the same extent. (iv) Enhancement of hematopoiesis occurred primarily in spleen, but hematopoietic foci were also evident in the liver; in contrast, total cell and progenitor cell numbers were decreased in the bone marrow.

Behavioural Flexibility: evolutionary past and its role in a changing world

A través de la historia de la vida, gran parte de los organismos han desarrollado estrategias para responder a un mundo en constante cambio. Hoy en día, las actividades humanas producen cambios ambientales a una velocidad sin precedentes, lo cual se traduce en grandes desafíos para la persistencia de biodiversidad. Esta investigación evalúa las respuesta de los animales a los cambios ambientales enfocándose en la flexibilidad del comportamiento como estrategia adaptativa. En una primera aproximación a una escala evolutiva, se otorgan evidencias del vínculo hasta ahora tenue entre la cognición e historias de vida, entregando un claro apoyo a la relación entre longevidad, vida reproductiva y el tamaño del cerebro en mamíferos. La longevidad es el centro de muchas hipótesis respecto a las ventajas de desarrollar un cerebro grande, como por ejemplo en la hipótesis del buffer cognitivo y las respuestas flexibles frente a nuevos ambientes. En un segundo nivel, se abordan factores extrínsecos e intrínsecos que podrían explicar las diferencias individuales en innovación, un componente clave en la flexibilidad del comportamiento. Por medio de una aproximación experimental, se evalúan potenciales escenarios que podrían conducir a consistentes diferencias individuales en uno de los principales factores subyacentes a la innovación (i.e. la motivación), y el potencial control endocrino sobre estos escenarios. Posteriormente, con el objetivo de evaluar la respuesta de los animales frente a los cambios ambientales actuales, se explora la respuesta de los animales frente a una de las actividades humanas mas disruptivas sobre los ecosistemas, la urbanización. Por medio de un analisis filogenetico comparativo a nivel global en aves se abordan los mecanismos implicados en la perdida de biodiversidad observada en ambientes urbanos. Los resultados entregan evidencias sobre la importancia de procesos de dispersión local junto con el papel clave de los rasgos de historia de vida, pero en un sentido diferente al clasicamente pensado. Finalmente por medio de una revisión bibliográfica se entregan evidencias teóricas y empíricas que respaldan el rol clave de la flexibilidad del comportamiento en confrontar los desafíos de una vida urbana. La integración de estos resultados muestra cómo el pasado evolutivo contribuye a hacer frente a los retos ambientales actuales, y pone de relieve posibles consecuencias ante un planeta más cambiante que nunca.

Strong reproductive barriers in a narrow hybrid zone of West-Mediterranean green toads (Bufo viridis subgroup) with Plio-Pleistocene divergence

Background One key question in evolutionary biology deals with the mode and rate at which reproductive isolation accumulates during allopatric speciation. Little is known about secondary contacts of recently diverged anuran species. Here we conduct a multi-locus field study to investigate a contact zone between two lineages of green toads with an estimated divergence time of 2.7 My, and report results from preliminary experimental crosses. Results The Sicilian endemic Bufo siculus and the Italian mainland-origin B. balearicus form a narrow hybrid zone east of Mt. Etna. Despite bidirectional mtDNA introgression over a ca. 40 km North-South cline, no F1 hybrids could be found, and nuclear genomes display almost no admixture. Populations from each side of the contact zone showed depressed genetic diversity and very strong differentiation (FST = 0.52). Preliminary experimental crosses point to a slightly reduced fitness in F1 hybrids, a strong hybrid breakdown in backcrossed offspring (F1 x parental, with very few reaching metamorphosis) and a complete and early mortality in F2 (F1 x F1). Conclusion Genetic patterns at the contact zone are molded by drift and selection. Local effective sizes are reduced by the geography and history of the contact zone, B. balearicus populations being at the front wave of a recent expansion (late Pleistocene). Selection against hybrids likely results from intrinsic genomic causes (disruption of coadapted sets of genes in backcrosses and F2-hybrids), possibly reinforced by local adaptation (the ranges of the two taxa roughly coincide with the borders of semiarid and arid climates). The absence of F1 in the field might be due to premating isolation mechanisms. Our results, show that these lineages have evolved almost complete reproductive isolation after some 2.7 My of divergence, contrasting sharply with evidence from laboratory experiments that some anuran species may still produce viable F1 offspring after > 20 My of divergence.

Specific duplication and dorsoventrally asymmetric expression patterns of Cycloidea-like genes in zygomorphic species of Ranunculaceae.

Floral bilateral symmetry (zygomorphy) has evolved several times independently in angiosperms from radially symmetrical (actinomorphic) ancestral states. Homologs of the Antirrhinum majus Cycloidea gene (Cyc) have been shown to control floral symmetry in diverse groups in core eudicots. In the basal eudicot family Ranunculaceae, there is a single evolutionary transition from actinomorphy to zygomorphy in the stem lineage of the tribe Delphinieae. We characterized Cyc homologs in 18 genera of Ranunculaceae, including the four genera of Delphinieae, in a sampling that represents the floral morphological diversity of this tribe, and reconstructed the evolutionary history of this gene family in Ranunculaceae. Within each of the two RanaCyL (Ranunculaceae Cycloidea-like) lineages previously identified, an additional duplication possibly predating the emergence of the Delphinieae was found, resulting in up to four gene copies in zygomorphic species. Expression analyses indicate that the RanaCyL paralogs are expressed early in floral buds and that the duration of their expression varies between species and paralog class. At most one RanaCyL paralog was expressed during the late stages of floral development in the actinomorphic species studied whereas all paralogs from the zygomorphic species were expressed, composing a species-specific identity code for perianth organs. The contrasted asymmetric patterns of expression observed in the two zygomorphic species is discussed in relation to their distinct perianth architecture.

Disease in the dark: molecular characterization of Polychromophilus murinus in temperate zone bats revealed a worldwide distribution of this malaria-like disease.

For a better understanding of the complex coevolutionary processes between hosts and parasites, accurate identification of the actors involved in the interaction is of fundamental importance. Blood parasites of the Order Haemosporidia, responsible for malaria, have become the focus of a broad range of studies in evolutionary biology. Interestingly, molecular-based studies on avian malaria have revealed much higher species diversity than previously inferred with morphology. Meanwhile, studies on bat haemosporidian have been largely neglected. In Europe, only one genus (Polychromophilus) and two species have been morphologically described. To evaluate the presence of potential cryptic species and parasite prevalence, we undertook a molecular characterization of Polychromophilus in temperate zone bats. We used a nested-PCR approach on the cytochrome b mitochondrial gene to detect the presence of parasites in 237 bats belonging to four different species and in the dipteran bat fly Nycteribia kolenatii, previously described as being the vector of Polychromophilus. Polychromophilus murinus was found in the four bat species and in the insect vector with prevalence ranging from 4% for Myotis myotis to 51% for M. daubentoni. By sequencing 682 bp, we then investigated the phylogenetic relationships of Polychromophilus to other published malarial lineages. Seven haplotypes were found, all very closely related, suggesting the presence of a single species in our samples. These haplotypes formed a well-defined clade together with Haemosporidia of tropical bats, revealing a worldwide distribution of this parasite mostly neglected by malarial studies since the 1980s.

T cell fate specification and alphabeta/gammadelta lineage commitment.

The development of T cells from pluripotent stem cells involves a coordinated series of lineage-commitment steps. Common lymphoid precursors in the fetal liver or adult bone marrow must first choose between a T, B or NK cell fate. Committed T cell precursors in the thymus then differentiate into cells committed to the alphabeta or gammadelta lineages. Recent advances have been made in our understanding of the mechanisms underlying T cell fate specification and alphabeta/gammadelta lineage divergence.

Evolutionary and Functional Analyses of the Interaction between the Myeloid Restriction Factor SAMHD1 and the Lentiviral Vpx Protein.

SAMHD1 has recently been identified as an HIV-1 restriction factor operating in myeloid cells. As a countermeasure, the Vpx accessory protein from HIV-2 and certain lineages of SIV have evolved to antagonize SAMHD1 by inducing its ubiquitin-proteasome-dependent degradation. Here, we show that SAMHD1 experienced strong positive selection episodes during primate evolution that occurred in the Catarrhini ancestral branch prior to the separation between hominoids (gibbons and great apes) and Old World monkeys. The identification of SAMHD1 residues under positive selection led to mapping the Vpx-interaction domain of SAMHD1 to its C-terminal region. Importantly, we found that while SAMHD1 restriction activity toward HIV-1 is evolutionarily maintained, antagonism of SAMHD1 by Vpx is species-specific. The distinct evolutionary signature of SAMHD1 sheds light on the development of its antiviral specificity.

A critical lineage-nonspecific role for pTalpha in mediating allelic and isotypic exclusion in TCRbeta-transgenic mice.

Although it is well established that early expression of TCRbeta transgenes in the thymus leads to efficient inhibition of both endogenous TCRbeta and TCRgamma rearrangement (also known as allelic and "isotypic" exclusion, respectively) the role of pTalpha in these processes remains controversial. Here, we have systematically re-evaluated this issue using three independent strains of TCRbeta-transgenic mice that differ widely in transgene expression levels, and a sensitive intracellular staining assay that detects endogenous TCRVbeta expression in individual immature thymocytes. In the absence of pTalpha, both allelic and isotypic exclusion were reversed in all three TCRbeta-transgenic strains, clearly demonstrating a general requirement for pre-TCR signaling in the inhibition of endogenous TCRbeta and TCRgamma rearrangement. Both allelic and isotypic exclusion were pTalpha dose dependent when transgenic TCRbeta levels were subphysiological. Moreover, pTalpha-dependent allelic and isotypic exclusion occurred in both alphabeta and gammadelta T cell lineages, indicating that pre-TCR signaling can potentially be functional in gammadelta precursors. Finally, levels of endogenous RAG1 and RAG2 were not down-regulated in TCRbeta-transgenic immature thymocytes undergoing allelic or isotypic exclusion. Collectively, our data reveal a critical but lineage-nonspecific role for pTalpha in mediating both allelic and isotypic exclusion in TCRbeta-transgenic mice.

Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub.

Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species.

Molecular evolutionary patterns in the Glomeromycota;

Abstract Arbuscular mycorrhizal fungi (AMF) form symbiosis with roots of approximately 80% of known land plants. These fungi play a key role in the ecology and adaptation of plants to various ecosystems.by increasing the plant resources for various nutrients. Despite their important ecological role, we still have poor understanding of their genetic structure and their molecular evolution. The work presented in this thesis aims to isolate and analyse AMF genes with various molecular techniques, in order to obtain new insights about their genetics, phylogeny and molecular evolution. Some AMF genes were shown through phylogenetic analyses to be more related with plants or mycoparasites than with other fungal organisms. These results led to the prediction that lateral gene transfers (LGT) occurred between AMF and plants during their long-term co-évolution. By phylogenetic and molecular analyses, in the chapter 2 I demonstrate that the hypothesis of LGT is most likely a consequence of analyses carried out on contaminant non AMF-DNA. In addition, various features characteristic of AMF genes have been determined, allowing researchers to scan their own sequence databases for potential non-AMF contaminants. Phylogenetic relationships of AMF with other fungi has been mostly analysed using molecular markers of ribosomal origin. In chapter 2 I successfully isolated gene encoding α- and ß-tubulins from several AMF genera. Consequently, phylogenetic analyses showed that AMF possess an unexpected relationship with ancestral aquatic fungi (chytrids). These results are consistent with the prediction stating that AMF may have played an important role in the colonisation of land by green plants through the establishment of a symbiosis and after the divergence of AMF from aquatic ancestors. In Chapter 4 I tried to isolate the entire AMF gene family encoding P-Type II ATPases, in order to determine their molecular evolution with the fungal kingdom. These genes were further analysed to detect the level of sequence polymorphism that is present within an AMF population. The results obtained show that mutational events previously thought as occurring only among divergent evolutionary lineages (gene duplications, indel mutations in coding regions) can occur within a single population of AMF. These results have far reaching consequences for our understanding of the genetics and ecology of AMF. Résumé Les champignons endomycorrhiziens arbusculaires (CEA) forment une symbiose racinaire avec environ 80% des plantes vasculaires connues. Ces champignons possèdent un rôle important dans l'écologie et l'adaptation des plantes au sein de différents écosystèmes en .augmentant leurs ressources en nutriments. Le travail présenté dans cette thèse se propose d'isoler et d'analyser certains gènes de CEA avec différentes techniques moléculaires à fin d'obtenir de pÌus amples informations concernant l'évolution moléculaire, la phylogénie et leur diversité génétique à diverses échelles taxonomiques. Certaines analyses phylogénétiques des CEA ont conduit à l'hypothèse que des transferts horizontaux de gènes (THG) ont pu avoir lieu durant leur longue co-évolution avec les plantes vasculaires. Dans le chapitre 2 de cette thèse nous démontrons par analyses moléculaire et phylogénétique que l'hypothèse de THG est une conséquence de contaminations à partir d'ADN de plante ou d'autres micro-organismes. De plus, de nombreuses caractéristiques moléculaires de CEA ont pu être déterminées, permettant la mise en place d'un plan à suivre lors de l'analyse de gènes de CEA dans les études futures. Les relations évolutives des. CEA avec d'autres champignons ont été analysées majoritairement à l'aide de marqueurs moléculaires d'origine ribosomiale. Dans les chapitres 2 et 3 j'ai isolé des gènes codant pour l'a- et la ß-tubuline chez différents genres, de CEA. Les analyses phylogénétiques ont démontré une parenté entre les CEA et des champignons aquatiques ancestraux (chytrides). Ces résultats sont en accord avec l'hypothèse selon laquelle les CEA ont probablement joué un rôle primordial dans l'établissement des plantes sur terre à travers une symbiose et suite à leur évolution à partir d'ancêtres vivant dans des milieux aquatiques: Dans le chapitre 4 j'ai isolé une entière famille de gènes chez les CEA codant des ATPases de la membrane plasmique, et étudié leur évolution moléculaire dans le règne des champignons. Ces mêmes gènes ont été analysés ultérieurement à fin de déterminer le degré de polymorphisme de séquence qui peut être présent au sein d'une population de CEA. Les résultats obtenus montrent que des évènements mutationnels considérés comme apparaissant exclusivement dans des lignées évolutives très divergentes (duplication de gènes, insertions/délétions dans des régions transcrites du génome) ont lieu sein d'une même population de CEA. Cette découverte a un impact important sur nos connaissances concernant la génétique des populations des CEA et leur écologie.

Multiple origins of invasive and "native" water frogs (Pelophylax spp.) in Switzerland

The marsh frog (Pelophylax ridibundus) has been introduced in many places of Central and Western Europe due to commercial trades with Eastern Europe, and is rapidly replacing the native pool frog (P. lessonae). A large number of Pelophylax species are distributed in Eastern Europe and the strong phenotypic similarity between these species is rendering their identification hazardous. Consequently, alien populations of Pelophylax might not strictly be composed of P. ridibundus as previously suspected. In the present study, we analyzed the cytochrome b and NADH dehydrogenase subunit 3 genes of introduced and native Pelophylax from Switzerland (299 individuals), in order to properly identify the source populations of the invaders and the genetic status of the native species. Our study highlighted the occurrence of several genetic lineages of invasive frogs in western Switzerland. Unexpectedly, we also showed that several populations of the native pool frog (P. lessonae) cluster with the Italian pool frog P. bergeri from central Italy (considered by some authors as a subspecies of P. lessonae) Hence, these populations are probably also the result of introductions, meaning that the number of native P. lessonae populations is less important than expected in Switzerland. These findings have important implications concerning the conservation of the endemic pool frog populations, as the presence of multiple alien species could strongly affect their long-term subsistence.