Ever-young sex chromosomes in European tree frogs.

Non-recombining sex chromosomes are expected to undergo evolutionary decay, ending up genetically degenerated, as has happened in birds and mammals. Why are then sex chromosomes so often homomorphic in cold-blooded vertebrates? One possible explanation is a high rate of turnover events, replacing master sex-determining genes by new ones on other chromosomes. An alternative is that X-Y similarity is maintained by occasional recombination events, occurring in sex-reversed XY females. Based on mitochondrial and nuclear gene sequences, we estimated the divergence times between European tree frogs (Hyla arborea, H. intermedia, and H. molleri) to the upper Miocene, about 5.4-7.1 million years ago. Sibship analyses of microsatellite polymorphisms revealed that all three species have the same pair of sex chromosomes, with complete absence of X-Y recombination in males. Despite this, sequences of sex-linked loci show no divergence between the X and Y chromosomes. In the phylogeny, the X and Y alleles cluster according to species, not in groups of gametologs. We conclude that sex-chromosome homomorphy in these tree frogs does not result from a recent turnover but is maintained over evolutionary timescales by occasional X-Y recombination. Seemingly young sex chromosomes may thus carry old-established sex-determining genes, a result at odds with the view that sex chromosomes necessarily decay until they are replaced. This raises intriguing perspectives regarding the evolutionary dynamics of sexually antagonistic genes and the mechanisms that control X-Y recombination.

Efecte de la recurrència dels incendis sobre la vegetació i el sòl a les zones de matollar del Macizo Central Ourensano

El matollar sec europeu format per Erica australis, Erica arborea, Pterosparum tridentatum, Halimium lasianthum i Calluna vulgaris com a espècies predominants és cremat en les serralades del Massís Central de forma repetida durant el pas dels anys. Això ha sigut, tradicionalment, a causa de la necessitat de mantenir-lo transitable per al bestiar, encara que altres circumstàncies s’han afegit actualment a aquesta necessitat, que incrementen el risc d’incendi d’aquesta comunitat, disparant-se el número d’incendis en els últims 30 anys. Sabent això, vam decidir realitzar un estudi a les zones de matollar que trobem al Massís Central situat a la zona del Concello de Villariño de Conso, a Ourense, per conèixer com es comporten les espècies característiques d’aquest tipus d’ecosistema després dels incendis, mitjançant la realització de mostrejos i perfils del sòl. D’aquesta manera hem volgut veure com es desenvolupen les espècies vegetals de matollar al llarg del temps, després de ser cremats. Gràcies a l’estudi hem pogut veure com el matollar observat te unes característiques que li permet sobreviure als incendis i tindre una capacitat de regeneració elevada després de patir aquesta pertorbació. Això es degut a la capacitat per rebrotar d’aquestes espècies arbustives i a la seva competitivitat. També hem vist com a necessari, donar un valor econòmic a la bona conservació de l’hàbitat, per tal de que la població local abandoni pràctiques de gestió forestal nocives, com el foc.

Variació temporal de paràmetres de qualitat del sòl ocasionada per l’ús i abandó agrícola del Cap de Creus

Estudi i avaluació de les principals propietats del sòl i la dinàmica erosiva relacionades amb l’ús del sòl i l’abandó agrícola en diferents ambients de la península del Cap de Creus. Per dur a terme aquest estudi s’han seleccionat 7 ambients diferentsrepresentatius d’una seqüència d’usos fins l’abandó en diferents etapes desuccessió vegetal. Els ambients són diferenciats entre sòls cultivats (vinya iolivera), sòls forestals (sureda i pineda), pastures (prats) i matollars (Cistusmonspeliensis i d’Erica arborea) respectivament cremat reiteradament i nocremat durant 25 anys. En cada ambient s’han instal.lat parcel.les d’erosióque permeten avaluar la producció de sediments i la mobilització de nutrients (carboni i nitrogen) durant els episodis de precipitació que generen escolament superficial

The contribution of patch topology and demographic parameters to PVA predictions: the case of the European tree frog

Population viability analyses (PVA) are increasingly used in metapopulation conservation plans. Two major types of models are commonly used to assess vulnerability and to rank management options: population-based stochastic simulation models (PSM such as RAMAS or VORTEX) and stochastic patch occupancy models (SPOM). While the first set of models relies on explicit intrapatch dynamics and interpatch dispersal to predict population levels in space and time, the latter is based on spatially explicit metapopulation theory where the probability of patch occupation is predicted given the patch area and isolation (patch topology). We applied both approaches to a European tree frog (Hyla arborea) metapopulation in western Switzerland in order to evaluate the concordances of both models and their applications to conservation. Although some quantitative discrepancies appeared in terms of network occupancy and equilibrium population size, the two approaches were largely concordant regarding the ranking of patch values and sensitivities to parameters, which is encouraging given the differences in the underlying paradigms and input data.

Extreme heterochiasmy and nascent sex chromosomes in European tree frogs.

We investigated sex-specific recombination rates in Hyla arborea, a species with nascent sex chromosomes and male heterogamety. Twenty microsatellites were clustered into six linkage groups, all showing suppressed or very low recombination in males. Seven markers were sex linked, none of them showing any sign of recombination in males (r=0.00 versus 0.43 on average in females). This opposes classical models of sex chromosome evolution, which envision an initially small differential segment that progressively expands as structural changes accumulate on the Y chromosome. For autosomes, maps were more than 14 times longer in females than in males, which seems the highest ratio documented so far in vertebrates. These results support the pleiotropic model of Haldane and Huxley, according to which recombination is reduced in the heterogametic sex by general modifiers that affect recombination on the whole genome.

Evolution of Y chromosomes : lessons from mammals and amphibians

RÉSUMÉ : Le sexe des individus peut être déterminé par l'environnement ou la génétique. Lorsque la détermination du sexe est génétique, il y a dans le génome, la présence de chromosomes spécifiques qui détermineront le sexe. Dans cette thèse, j'ai étudié l'évolution des chromosomes sexuels et dans quel contexte des marqueurs sur ces chromosomes peuvent être utilisés. Pour explorer la formation du chromosome Y, nous avons étudié les caractéristiques des chromosomes sexuels chez la rainette verte, Hyla arborea. Dans un premier temps, nous avons utilisé un marqueur situé sur les chromosomes sexuels X et Y chez plusieurs espèces appartenant au groupe de la rainette verte. Cela nous a permis de révéler chez toutes ces espèces une hétérogamétie mâle. Dans un deuxième temps, nous avons tiré profit de deux autres marqueurs situés sur les chromosomes sexuels pour montrer que la recombinaison est supprimée chez les mâles mais pas chez les femelles. Pour expliquer la réduction de la variabilité sur le chromosome Y, il n'est pas nécessaire d'invoquer le balayage sélectif ou la sélection d'arrière-plan : le nombre de copies plus petit du chromosome Y dans le génome et l'absence de recombinaison suffisent à l'expliquer. Nous avons également analysé plus en détail la suppression de la recombinaison chez les mâles de H. arborea. Les modèles classiques de l'évolution des chromosomes sexuels supposent que la taille de la région non-recombinante augmente progressivement pendant l'évolution du chromosome Y, due à l'accumulation de changements structuraux. Dans cette étude, nous montrons un modèle différent, à savoir que la recombinaison est supprimée ou diminuée non seulement sur les chromosomes sexuels mais aussi sur les autosomes chez les mâles, dû à l'action de modificateurs généraux. En utilisant des marqueurs localisés sur le chromosome Y, ainsi que sur l'ADN mitochondrial et le chromosome X, nous avons étudié l'histoire évolutive de la musaraigne musette, Crocidura russula. Cette étude illustre que les analyses génétiques avec plusieurs types de marqueurs génétiques peuvent faciliter l'interprétation de l'histoire évolutive des espèces, mais que l'utilisation des marqueurs sur les chromosomes X et Y pour des études phylogéographiques est limitée par le peu de polymorphisme observé sur ces deux types de marqueurs. Le même jeu de données combiné avec des simulations a été employé pour comprendre les facteurs responsables de la faible variabilité sur le chromosome Y qui peut être expliqué, dans notre étude, par la démographie et les traits d'histoire de vie de C. russula. SUMMARY The sex of an individual is determined either by its environment or its genetics. Genetic sex determination relies on the presence of specific chromosomes that will determine the sex of their bearer. In this thesis, I studied the evolution of the sex chromosomes and the context in which markers on this type of chromosomes can be used. To explore the evolution of a Y chromosome, we studied the nascent sex chromosomes in the European tree frog Hyla arborea. First; we amplified a sex specific marker in several related species of European tree frog and found a homogeneous pattern of male heterogamety. Secondly, we used two additional sex-specific markers to show that recombination is suppressed in males but not in females. There is, therefore, no need to invoke background selection or selective sweeps to explain the reduced genetic variability on the Y chromosome, because the lower number of copies of the Y chromosomes per breeding pair and the absence of recombination are sufficient. To further analyze the suppression of recombination in male European. tree frogs, we constructed a microsatellite linkage map for this species. Classical models of sex-chromosome evolution assume that the non-recombining region expands progressively during the long-term evolution of the Y chromosome, owing to the accumulation of structural changes. Here we show a strikingly different pattern: recombination is suppressed or depressed both on sex chromosomes and autosomes in the heterogametic sex, presumably due to the action of general modifiers. We investigated the evolutionary history of the greater white-toothed shrew, Crocidura russula, using markers on both sex chromosomes and mtDNA. This study illustrates that multilocus genetic analyses facilitates the interpretation of a species' evolutionary history. It also demonstrates that phylogeographic inferences from X and Y chromosomal markers are restricted by the low levels of observed polymorphism. Combining this genetic study with simulations, we determined that the demography and the life-history traits of this species can alone be responsible for the low Y diversity. In conclusion, this thesis shows that sex chromosomes, in combination with autosomes or mtDNA, are necessary to understand the evolution of sex chromosomes and to precisely infer the population history of a species.

Efeitos do fracionamento da adubação mineral, da adubação orgânica e da calagem na produtividade e incidência de vassoura-de-bruxa em cacaueiros da Amazônia

A resposta do cacaueiro à aplicação de micronutrientes, matéria orgânica, calcário e fracionamento da adubação foi determinada em dois experimentos, instalados em solos das unidades Terra Roxa estruturada eutrófica (TR) e Latossolo Amarelo (LA), no Estado do Pará, no período de 1988 a 1993. As lavouras de cacau do híbrido Sca 6 x Be 10 foram implantadas pelo sistema de derrubada total e queima da floresta primária, utilizando-se sombreamento provisório de bananeira (Musa spp.) e permanente de Erythrina poeppigiana ou Gmelina arborea. Os tratamentos foram distribuídos em blocos casualizados, com três repetições, sendo a parcela constituída de 20 plantas úteis. Os resultados de produção de cacau demonstraram que não houve interação significativa entre tratamentos e solos ou ano de condução do experimento. O fracionamento da adubação NPK em três aplicações/ano e a adubação NPK + Zn foram os melhores tratamentos, provocando incrementos (P < 0,05) na produtividade do cacaueiro da ordem de 27,5% e 10,9%, respectivamente. A menor incidência (P < 0,05) de frutos atacados pela enfermidade vassoura-de-bruxa, causada pelo fungo Crinipellis perniciosa, foi observada nos tratamentos em que se aplicaram uma mistura de micronutrientes (B, Cu, Zn, Fe e Mo) ou esterco de gado na dosagem de 5 t ha-1; as porcentagens de frutos doentes dos demais tratamentos não diferiram da adubação NPK (testemunha). Para o aumento da produtividade, a estratégia de adubação mais eficiente foi o fracionamento da adubação NPK (60 kg ha-1 de N, P(2)0(5) e K(2)0) em três aplicações ao ano. O efeito de micronutrientes e do esterco de gado na infecção da vassoura-de-bruxa merece ser investigado com mais atenção.

Homologous sex chromosomes in three deeply divergent anuran species.

Comparative genomic studies are revealing that, in sharp contrast with the strong stability found in birds and mammals, sex determination mechanisms are surprisingly labile in cold-blooded vertebrates, with frequent transitions between different pairs of sex chromosomes. It was recently suggested that, in context of this high turnover, some chromosome pairs might be more likely than others to be co-opted as sex chromosomes. Empirical support, however, is still very limited. Here we show that sex-linked markers from three highly divergent groups of anurans map to Xenopus tropicalis scaffold 1, a large part of which is homologous to the avian sex chromosome. Accordingly, the bird sex determination gene DMRT1, known to play a key role in sex differentiation across many animal lineages, is sex linked in all three groups. Our data provide strong support for the idea that some chromosome pairs are more likely than others to be co-opted as sex chromosomes because they harbor key genes from the sex determination pathway.

Utilização de características microbiológicas na avaliação da degradação ou recuperação de uma área sob mineração de ferro

O estado de degradação e, ou, recuperação de diferentes sítios de uma área de mineração de ferro no município de Mariana (MG) foi avaliado pela atividade microbiana, número de esporos de fungos micorrízicos arbusculares (FMA) e população total de fungos e bactérias. Os substratos presentes em cada sítio, caracterizados como Rejeito de flotação (Rj), Solo superficial (SS), Subsolo (Ss), Subsolo com vegetação (SsV), Área em revegetação (AR) e Mata secundária (MS), foram amostrados na profundidade de 10-25 cm, retirando-se uma amostra composta, formada por oito amostras simples. A atividade microbiana foi avaliada pela evolução de CO2 em amostras ao natural e com adição de sacarose ou sacarose + uréia. Fez-se também a determinação de características químicas e teor de umidade. A colonização do substrato SsV por gramíneas e plantas de candeia (Vanillosmopsis erythropappa Schult. Bip.) foi acompanhada pelo número de esporos de FMA, teor de carbono orgânico e atividade microbiana. Os esporos de FMA só foram observados em áreas com vegetação. O armazenamento da camada superficial de solo (sítio SS) reduziu os teores de carbono orgânico, nitrogênio total, número de esporos de FMA e atividade microbiana. Nos substratos resultantes da atividade mineradora, houve necessidade do fornecimento conjunto de carbono e nitrogênio para estimular a atividade microbiana. As características microbiológicas avaliadas apresentaram valores maiores no sítio de mata secundária do que nos demais amostrados, indicando que aqueles em recuperação não possuíam o mesmo equilíbrio biológico. As avaliações microbiológicas do solo foram capazes de distinguir os estados de perturbação ou recuperação das diferentes áreas estudadas.

A sex-specific marker reveals male heterogamety in European tree frogs.

Most amphibians examined so far show undifferentiated sex chromosomes. The heterogametic sex's identity, usually revealed through indirect means, often varies among closely related species or even populations (as do sex-linkage groups), suggesting great evolutionary instability of the sex-determining genes. Here we take advantage of a sex-specific marker that amplifies in several related species of European tree frogs (Hyla arborea group) to disclose a homogeneous pattern of male heterogamety. Besides relevance for evolutionary studies of sex determination in amphibians, our results have potential for addressing practical issues in conservation biology because sex reversal by anthropogenic endocrine disruptors is considered one possible cause of amphibian decline.

Maintenance of ancestral sex chromosomes in Palearctic tree frogs: direct evidence from Hyla orientalis.

Contrasting with the situation found in birds and mammals, sex chromosomes are generally homomorphic in poikilothermic vertebrates. This homomorphy was recently shown to result from occasional X-Y recombinations (not from turnovers) in several European species of tree frogs (Hyla arborea, H. intermedia and H. molleri). Because of recombination, however, alleles at sex-linked loci were rarely diagnostic at the population level; support for sex linkage had to rely on multilocus associations, combined with occasional sex differences in allelic frequencies. Here, we use direct evidence, obtained from anatomical and histological analyses of offspring with known pedigrees, to show that the Eastern tree frog (H. orientalis) shares the same pair of sex chromosomes, with identical patterns of male heterogamety and complete absence of X-Y recombination in males. Conservation of an ancestral pair of sex chromosomes, regularly rejuvenated via occasional X-Y recombination, seems thus a widespread pattern among Hyla species. Sibship analyses also identified discrepancies between genotypic and phenotypic sex among offspring, associated with abnormal gonadal development, suggesting a role for sexually antagonistic genes on the sex chromosomes.

New vineyard cultivation practices create patchy ground vegetation, favouring Woodlarks

Intensive agriculture, in which detrimental farming practices lessen food abundance and/or reduce food accessibility for many animal species, has led to a widespread collapse of farmland biodiversity. Vineyards in central and southern Europe are intensively cultivated; though they may still harbour several rare plant and animal species, they remain little studied. Over the past decades, there has been a considerable reduction in the application of insecticides in wine production, with a progressive shift to biological control (integrated production) and, to a lesser extent, organic production. Spraying of herbicides has also diminished, which has led to more vegetation cover on the ground, although most vineyards remain bare, especially in southern Europe. The effects of these potentially positive environmental trends upon biodiversity remain mostly unknown as regards vertebrates. The Woodlark (Lullula arborea) is an endangered, short-distance migratory bird that forages and breeds on the ground. In southern Switzerland (Valais), it occurs mostly in vineyards. We used radiotracking and mixed effects logistic regression models to assess Woodlark response to modern vineyard farming practices, study factors driving foraging micro-habitat selection, and determine optimal habitat profile to inform management. The presence of ground vegetation cover was the main factor dictating the selection of foraging locations, with an optimum around 55% at the foraging patch scale. These conditions are met in integrated production vineyards, but only when grass is tolerated on part of the ground surface, which is the case on ca. 5% of the total Valais vineyard area. In contrast, conventionally managed vineyards covering a parts per thousand yen95% of the vineyard area are too bare because of systematic application of herbicides all over the ground, whilst the rare organic vineyards usually have a too-dense sward. The optimal mosaic with ca. 50% ground vegetation cover is currently achieved in integrated production vineyards where herbicide is applied every second row. In organic production, ca. 50% ground vegetation cover should be promoted, which requires regular mechanical removal of ground vegetation. These measures are likely to benefit general biodiversity in vineyards.

Cryptic recombination in the ever-young sex chromosomes of Hylid frogs.

Sex chromosomes are expected to evolve suppressed recombination, which leads to degeneration of the Y and heteromorphism between the X and Y. Some sex chromosomes remain homomorphic, however, and the factors that prevent degeneration of the Y in these cases are not well understood. The homomorphic sex chromosomes of the European tree frogs (Hyla spp.) present an interesting paradox. Recombination in males has never been observed in crossing experiments, but molecular data are suggestive of occasional recombination between the X and Y. The hypothesis that these sex chromosomes recombine has not been tested statistically, however, nor has the X-Y recombination rate been estimated. Here, we use approximate Bayesian computation coupled with coalescent simulations of sex chromosomes to quantify X-Y recombination rate from existent data. We find that microsatellite data from H. arborea, H. intermedia and H. molleri support a recombination rate between X and Y that is significantly different from zero. We estimate that rate to be approximately 10(5) times smaller than that between X chromosomes. Our findings support the notion that very low recombination rate may be sufficient to maintain homomorphism in sex chromosomes.

Density, climate and varying return points: an analysis of long-term population fluctuations in the threatened European tree frog.

Experimental research has identified many putative agents of amphibian decline, yet the population-level consequences of these agents remain unknown, owing to lack of information on compensatory density dependence in natural populations. Here, we investigate the relative importance of intrinsic (density-dependent) and extrinsic (climatic) factors impacting the dynamics of a tree frog (Hyla arborea) population over 22 years. A combination of log-linear density dependence and rainfall (with a 2-year time lag corresponding to development time) explain 75% of the variance in the rate of increase. Such fluctuations around a variable return point might be responsible for the seemingly erratic demography and disequilibrium dynamics of many amphibian populations.

Genetic bottlenecks driven by population disconnection.

Connectivity among populations plays a crucial role in maintaining genetic variation at a local scale, especially in small populations affected strongly by genetic drift. The negative consequences of population disconnection on allelic richness and gene diversity (heterozygosity) are well recognized and empirically established. It is not well recognized, however, that a sudden drop in local effective population size induced by such disconnection produces a temporary disequilibrium in allelic frequency distributions that is akin to the genetic signature of a demographic bottleneck. To document this effect, we used individual-based simulations and empirical data on allelic richness and gene diversity in six pairs of isolated versus well-connected (core) populations of European tree frogs. In our simulations, population disconnection depressed allelic richness more than heterozygosity and thus resulted in a temporary excess in gene diversity relative to mutation drift equilibrium (i.e., signature of a genetic bottleneck). We observed a similar excess in gene diversity in isolated populations of tree frogs. Our results show that population disconnection can create a genetic bottleneck in the absence of demographic collapse.