Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba

The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan.

The stationary distribution of a continuously varying strategy in a class-structured population under mutation-selection-drift balance.

Many traits and/or strategies expressed by organisms are quantitative phenotypes. Because populations are of finite size and genomes are subject to mutations, these continuously varying phenotypes are under the joint pressure of mutation, natural selection and random genetic drift. This article derives the stationary distribution for such a phenotype under a mutation-selection-drift balance in a class-structured population allowing for demographically varying class sizes and/or changing environmental conditions. The salient feature of the stationary distribution is that it can be entirely characterized in terms of the average size of the gene pool and Hamilton's inclusive fitness effect. The exploration of the phenotypic space varies exponentially with the cumulative inclusive fitness effect over state space, which determines an adaptive landscape. The peaks of the landscapes are those phenotypes that are candidate evolutionary stable strategies and can be determined by standard phenotypic selection gradient methods (e.g. evolutionary game theory, kin selection theory, adaptive dynamics). The curvature of the stationary distribution provides a measure of the stability by convergence of candidate evolutionary stable strategies, and it is evaluated explicitly for two biological scenarios: first, a coordination game, which illustrates that, for a multipeaked adaptive landscape, stochastically stable strategies can be singled out by letting the size of the gene pool grow large; second, a sex-allocation game for diploids and haplo-diploids, which suggests that the equilibrium sex ratio follows a Beta distribution with parameters depending on the features of the genetic system.

Idiosyncratic evolution of maternal effects in response to juvenile malnutrition in Drosophila.

Maternal effects often affect fitness traits, but there is little experimental evidence pertaining to their contribution to response to selection imposed by novel environments. We studied the evolution of maternal effects in Drosophila populations selected for tolerance to chronic larval malnutrition. To this end, we performed pairwise reciprocal F1 crosses between six selected (malnutrition tolerant) populations and six unselected control populations and assessed the effect of cross direction on larval growth and developmental rate, adult weight and egg-to-adult viability expressed under the malnutrition regime. Each pair of reciprocal crosses revealed large maternal effects (possibly including cytoplasmic genetic effects) on at least one trait, but the magnitude, sign and which traits were affected varied among populations. Thus, maternal effects contributed significantly to the response to selection imposed by the malnutrition regime, but these changes were idiosyncratic, suggesting a rugged adaptive landscape. Furthermore, although the selected populations evolved both faster growth and higher viability, the maternal effects on growth rate and viability were negatively correlated across populations. Thus, genes mediating maternal effects can evolve to partially counteract the response to selection mediated by the effects of alleles on their own carriers' phenotype, and maternal effects may contribute to evolutionary trade-offs between components of offspring fitness.

Experimental evidence for multivariate stabilizing sexual selection

Stabilizing selection is a fundamental concept in evolutionary biology. In the presence of a single intermediate optimum phenotype (fitness peak) on the fitness surface, stabilizing selection should cause the population to evolve toward such a peak. This prediction has seldom been tested, particularly for suites of correlated traits. The lack of tests for an evolutionary match between population means and adaptive peaks may be due, at least in part, to problems associated with empirically detecting multivariate stabilizing selection and with testing whether population means are at the peak of multivariate fitness surfaces. Here we show how canonical analysis of the fitness surface, combined with the estimation of confidence regions for stationary points on quadratic response surfaces, may be used to define multivariate stabilizing selection on a suite of traits and to establish whether natural populations reside on the multivariate peak. We manufactured artificial advertisement calls of the male cricket Teleogryllus commodus and played them back to females in laboratory phonotaxis trials to estimate the linear and nonlinear sexual selection that female phonotactic choice imposes on male call structure. Significant nonlinear selection on the major axes of the fitness surface was convex in nature and displayed an intermediate optimum, indicating multivariate stabilizing selection. The mean phenotypes of four independent samples of males, from the same population as the females used in phonotaxis trials, were within the 95% confidence region for the fitness peak. These experiments indicate that stabilizing sexual selection may play an important role in the evolution of male call properties in natural populations of T. commodus.

Studying phenotypic evolution using multivariate quantitative genetics

Quantitative genetics provides a powerful framework for studying phenotypic evolution and the evolution of adaptive genetic variation. Central to the approach is G, the matrix of additive genetic variances and covariances. G summarizes the genetic basis of the traits and can be used to predict the phenotypic response to multivariate selection or to drift. Recent analytical and computational advances have improved both the power and the accessibility of the necessary multivariate statistics. It is now possible to study the relationships between G and other evolutionary parameters, such as those describing the mutational input, the shape and orientation of the adaptive landscape, and the phenotypic divergence among populations. At the same time, we are moving towards a greater understanding of how the genetic variation summarized by G evolves. Computer simulations of the evolution of G, innovations in matrix comparison methods, and rapid development of powerful molecular genetic tools have all opened the way for dissecting the interaction between allelic variation and evolutionary process. Here I discuss some current uses of G, problems with the application of these approaches, and identify avenues for future research.

Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics

A workshop recently held at the Ecole Polytechnique Federale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and landscape genomics and bringing together knowledge accumulated in both research fields. Indeed, an important challenge in theoretical population genetics is to incorporate effects of demographic history and population structure. But important design problems (e.g. focus on populations as units, focus on hard selective sweeps, no hypothesis-based framework in the design of the statistical tests) reduce their capability of detecting adaptive genetic variation. In parallel, landscape genomics offers a solution to several of these problems and provides a number of advantages (e.g. fast computation, landscape heterogeneity integration). But the approach makes several implicit assumptions that should be carefully considered (e.g. selection has had enough time to create a functional relationship between the allele distribution and the environmental variable, or this functional relationship is assumed to be constant). To address the respective strengths and weaknesses mentioned above, the workshop brought together a panel of experts from both disciplines to present their work and discuss the relevance of combining these approaches, possibly resulting in a joint software solution in the future.

“ The Creation of an Urban Landscape” in Adaptive reuse,the modern movement toward the future, 14th international conference proceedings, Do_co.mo.mo international, Lisboa ( indexed by SCOPUS)

The headquarters and park of the Calouste Gulbenkian Foundation in Lisbon represent the first modern Portuguese environment with an outstanding relation between exterior and interior as a spatial continuum . As such, the project refused the more common conceptual attitude of interior plus exterior. This unitary view revealed a clear understanding of the proposed site for the project and what could have been Calouste Sarkis Gulbenkian (1869-1955) expectations, while concretizing Modern Movement ideals regarding landscape architecture and architecture. Through its design the park mediates the relation between the buildings’ super-structures, the urban context, and the human scale, while generating a unifying system established by the complicity between natural and synthetic materials. From the first moment of the project’s design process, this complicity resulted in a set of strategies that met programmatic

Landscape composition and climatic parameters significant in the spread of an invasive species (Pine wood Nematode)

Dissertação para obtenção do Grau de Mestre em Engenharia do Ambiente

Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

It is generally accepted that most plant populations are locally adapted. Yet, understanding how environmental forces give rise to adaptive genetic variation is a challenge in conservation genetics and crucial to the preservation of species under rapidly changing climatic conditions. Environmental variation, phylogeographic history, and population demographic processes all contribute to spatially structured genetic variation, however few current models attempt to separate these confounding effects. To illustrate the benefits of using a spatially-explicit model for identifying potentially adaptive loci, we compared outlier locus detection methods with a recently-developed landscape genetic approach. We analyzed 157 loci from samples of the alpine herb Gentiana nivalis collected across the European Alps. Principle coordinates of neighbor matrices (PCNM), eigenvectors that quantify multi-scale spatial variation present in a data set, were incorporated into a landscape genetic approach relating AFLP frequencies with 23 environmental variables. Four major findings emerged. 1) Fifteen loci were significantly correlated with at least one predictor variable (R (adj) (2) > 0.5). 2) Models including PCNM variables identified eight more potentially adaptive loci than models run without spatial variables. 3) When compared to outlier detection methods, the landscape genetic approach detected four of the same loci plus 11 additional loci. 4) Temperature, precipitation, and solar radiation were the three major environmental factors driving potentially adaptive genetic variation in G. nivalis. Techniques presented in this paper offer an efficient method for identifying potentially adaptive genetic variation and associated environmental forces of selection, providing an important step forward for the conservation of non-model species under global change.

Evidence for morphological and adaptive genetic divergence between lake and stream habitats in European minnows (Phoxinus phoxinus, Cyprinidae).

Natural selection drives local adaptation, potentially even at small temporal and spatial scales. As a result, adaptive genetic and phenotypic divergence can occur among populations living in different habitats. We investigated patterns of differentiation between contrasting lake and stream habitats in the cyprinid fish European minnow (Phoxinus phoxinus) at both the morphological and genomic levels using geometric morphometrics and AFLP markers, respectively. We also used a spatial correlative approach to identify AFLP loci associated with environmental variables representing potential selective forces responsible for adaptation to divergent habitats. Our results identified different morphologies between lakes and streams, with lake fish presenting a deeper body and caudal peduncle compared to stream fish. Body shape variation conformed to a priori predictions concerning biomechanics and swimming performance in lakes vs. streams. Moreover, morphological differentiation was found to be associated with several environmental variables, which could impose selection on body and caudal peduncle shape. We found adaptive genetic divergence between these contrasting habitats in the form of 'outlier' loci (2.9%) whose genetic divergence exceeded neutral expectations. We also detected additional loci (6.6%) not associated with habitat type (lake vs. stream), but contributing to genetic divergence between populations. Specific environmental variables related to trophic dynamics, landscape topography and geography were associated with several neutral and outlier loci. These results provide new insights into the morphological divergence and genetic basis of adaptation to differentiated habitats.

Conservation of the Eurasian Lynx (Lynx lynx) in a fragmented landscape - habitat models, dispersal and potential distribution

Abstract: The expansion of a recovering population - whether re-introduced or spontaneously returning - is shaped by (i) biological (intrinsic) factors such as the land tenure system or dispersal, (ii) the distribution and availability of resources (e.g. prey), (iii) habitat and landscape features, and (iv) human attitudes and activities. In order to develop efficient conservation and recovery strategies, we need to understand all these factors and to predict the potential distribution and explore ways to reach it. An increased number of lynx in the north-western Swiss Alps in the nineties lead to a new controversy about the return of this cat. When the large carnivores were given legal protection in many European countries, most organizations and individuals promoting their protection did not foresee the consequences. Management plans describing how to handle conflicts with large predators are needed to find a balance between "overabundance" and extinction. Wildlife and conservation biologists need to evaluate the various threats confronting populations so that adequate management decisions can be taken. I developed a GIS probability model for the lynx, based on habitat information and radio-telemetry data from the Swiss Jura Mountains, in order to predict the potential distribution of the lynx in this mountain range, which is presently only partly occupied by lynx. Three of the 18 variables tested for each square kilometre describing land use, vegetation, and topography, qualified to predict the probability of lynx presence. The resulting map was evaluated with data from dispersing subadult lynx. Young lynx that were not able to establish home ranges in what was identified as good lynx habitat did not survive their first year of independence, whereas the only one that died in good lynx habitat was illegally killed. Radio-telemetry fixes are often used as input data to calibrate habitat models. Radio-telemetry is the only way to gather accurate and unbiased data on habitat use of elusive larger terrestrial mammals. However, it is time consuming and expensive, and can therefore only be applied in limited areas. Habitat models extrapolated over large areas can in turn be problematic, as habitat characteristics and availability may change from one area to the other. I analysed the predictive power of Ecological Niche Factor Analysis (ENFA) in Switzerland with the lynx as focal species. According to my results, the optimal sampling strategy to predict species distribution in an Alpine area lacking available data would be to pool presence cells from contrasted regions (Jura Mountains, Alps), whereas in regions with a low ecological variance (Jura Mountains), only local presence cells should be used for the calibration of the model. Dispersal influences the dynamics and persistence of populations, the distribution and abundance of species, and gives the communities and ecosystems their characteristic texture in space and time. Between 1988 and 2001, the spatio-temporal behaviour of subadult Eurasian lynx in two re-introduced populations in Switzerland was studied, based on 39 juvenile lynx of which 24 were radio-tagged to understand the factors influencing dispersal. Subadults become independent from their mothers at the age of 8-11 months. No sex bias neither in the dispersal rate nor in the distance moved was detected. Lynx are conservative dispersers, compared to bear and wolf, and settled within or close to known lynx occurrences. Dispersal distances reached in the high lynx density population - shorter than those reported in other Eurasian lynx studies - are limited by habitat restriction hindering connections with neighbouring metapopulations. I postulated that high lynx density would lead to an expansion of the population and validated my predictions with data from the north-western Swiss Alps where about 1995 a strong increase in lynx abundance took place. The general hypothesis that high population density will foster the expansion of the population was not confirmed. This has consequences for the re-introduction and recovery of carnivores in a fragmented landscape. To establish a strong source population in one place might not be an optimal strategy. Rather, population nuclei should be founded in several neighbouring patches. Exchange between established neighbouring subpopulations will later on take place, as adult lynx show a higher propensity to cross barriers than subadults. To estimate the potential population size of the lynx in the Jura Mountains and to assess possible corridors between this population and adjacent areas, I adapted a habitat probability model for lynx distribution in the Jura Mountains with new environmental data and extrapolated it over the entire mountain range. The model predicts a breeding population ranging from 74-101 individuals and from 51-79 individuals when continuous habitat patches < 50 km2 are disregarded. The Jura Mountains could once be part of a metapopulation, as potential corridors exist to the adjoining areas (Alps, Vosges Mountains, and Black Forest). Monitoring of the population size, spatial expansion, and the genetic surveillance in the Jura Mountains must be continued, as the status of the population is still critical. ENFA was used to predict the potential distribution of lynx in the Alps. The resulting model divided the Alps into 37 suitable habitat patches ranging from 50 to 18,711 km2, covering a total area of about 93,600 km2. When using the range of lynx densities found in field studies in Switzerland, the Alps could host a population of 961 to 1,827 residents. The results of the cost-distance analysis revealed that all patches were within the reach of dispersing lynx, as the connection costs were in the range of dispersal cost of radio-tagged subadult lynx moving through unfavorable habitat. Thus, the whole Alps could once be considered as a metapopulation. But experience suggests that only few disperser will cross unsuitable areas and barriers. This low migration rate may seldom allow the spontaneous foundation of new populations in unsettled areas. As an alternative to natural dispersal, artificial transfer of individuals across the barriers should be considered. Wildlife biologists can play a crucial role in developing adaptive management experiments to help managers learning by trial. The case of the lynx in Switzerland is a good example of a fruitful cooperation between wildlife biologists, managers, decision makers and politician in an adaptive management process. This cooperation resulted in a Lynx Management Plan which was implemented in 2000 and updated in 2004 to give the cantons directives on how to handle lynx-related problems. This plan was put into practice e.g. in regard to translocation of lynx into unsettled areas. Résumé: L'expansion d'une population en phase de recolonisation, qu'elle soit issue de réintroductions ou d'un retour naturel dépend 1) de facteurs biologiques tels que le système social et le mode de dispersion, 2) de la distribution et la disponibilité des ressources (proies), 3) de l'habitat et des éléments du paysage, 4) de l'acceptation de l'espèce par la population locale et des activités humaines. Afin de pouvoir développer des stratégies efficaces de conservation et de favoriser la recolonisation, chacun de ces facteurs doit être pris en compte. En plus, la distribution potentielle de l'espèce doit pouvoir être déterminée et enfin, toutes les possibilités pour atteindre les objectifs, examinées. La phase de haute densité que la population de lynx a connue dans les années nonante dans le nord-ouest des Alpes suisses a donné lieu à une controverse assez vive. La protection du lynx dans de nombreux pays européens, promue par différentes organisations, a entraîné des conséquences inattendues; ces dernières montrent que tout plan de gestion doit impérativement indiquer des pistes quant à la manière de gérer les conflits, tout en trouvant un équilibre entre l'extinction et la surabondance de l'espèce. Les biologistes de la conservation et de la faune sauvage doivent pour cela évaluer les différents risques encourus par les populations de lynx, afin de pouvoir rapidement prendre les meilleuresmdécisions de gestion. Un modèle d'habitat pour le lynx, basé sur des caractéristiques de l'habitat et des données radio télémétriques collectées dans la chaîne du Jura, a été élaboré afin de prédire la distribution potentielle dans cette région, qui n'est que partiellement occupée par l'espèce. Trois des 18 variables testées, décrivant pour chaque kilomètre carré l'utilisation du sol, la végétation ainsi que la topographie, ont été retenues pour déterminer la probabilité de présence du lynx. La carte qui en résulte a été comparée aux données télémétriques de lynx subadultes en phase de dispersion. Les jeunes qui n'ont pas pu établir leur domaine vital dans l'habitat favorable prédit par le modèle n'ont pas survécu leur première année d'indépendance alors que le seul individu qui est mort dans l'habitat favorable a été braconné. Les données radio-télémétriques sont souvent utilisées pour l'étalonnage de modèles d'habitat. C'est un des seuls moyens à disposition qui permette de récolter des données non biaisées et précises sur l'occupation de l'habitat par des mammifères terrestres aux moeurs discrètes. Mais ces méthodes de- mandent un important investissement en moyens financiers et en temps et peuvent, de ce fait, n'être appliquées qu'à des zones limitées. Les modèles d'habitat sont ainsi souvent extrapolés à de grandes surfaces malgré le risque d'imprécision, qui résulte des variations des caractéristiques et de la disponibilité de l'habitat d'une zone à l'autre. Le pouvoir de prédiction de l'Analyse Ecologique de la Niche (AEN) dans les zones où les données de présence n'ont pas été prises en compte dans le calibrage du modèle a été analysée dans le cas du lynx en Suisse. D'après les résultats obtenus, la meilleure mé- thode pour prédire la distribution du lynx dans une zone alpine dépourvue d'indices de présence est de combiner des données provenant de régions contrastées (Alpes, Jura). Par contre, seules les données sur la présence locale de l'espèce doivent être utilisées pour les zones présentant une faible variance écologique tel que le Jura. La dispersion influence la dynamique et la stabilité des populations, la distribution et l'abondance des espèces et détermine les caractéristiques spatiales et temporelles des communautés vivantes et des écosystèmes. Entre 1988 et 2001, le comportement spatio-temporel de lynx eurasiens subadultes de deux populations réintroduites en Suisse a été étudié, basé sur le suivi de 39 individus juvéniles dont 24 étaient munis d'un collier émetteur, afin de déterminer les facteurs qui influencent la dispersion. Les subadultes se sont séparés de leur mère à l'âge de 8 à 11 mois. Le sexe n'a pas eu d'influence sur le nombre d'individus ayant dispersés et la distance parcourue au cours de la dispersion. Comparé à l'ours et au loup, le lynx reste très modéré dans ses mouvements de dispersion. Tous les individus ayant dispersés se sont établis à proximité ou dans des zones déjà occupées par des lynx. Les distances parcourues lors de la dispersion ont été plus courtes pour la population en phase de haute densité que celles relevées par les autres études de dispersion du lynx eurasien. Les zones d'habitat peu favorables et les barrières qui interrompent la connectivité entre les populations sont les principales entraves aux déplacements, lors de la dispersion. Dans un premier temps, nous avons fait l'hypothèse que les phases de haute densité favorisaient l'expansion des populations. Mais cette hypothèse a été infirmée par les résultats issus du suivi des lynx réalisé dans le nord-ouest des Alpes, où la population connaissait une phase de haute densité depuis 1995. Ce constat est important pour la conservation d'une population de carnivores dans un habitat fragmenté. Ainsi, instaurer une forte population source à un seul endroit n'est pas forcément la stratégie la plus judicieuse. Il est préférable d'établir des noyaux de populations dans des régions voisines où l'habitat est favorable. Des échanges entre des populations avoisinantes pourront avoir lieu par la suite car les lynx adultes sont plus enclins à franchir les barrières qui entravent leurs déplacements que les individus subadultes. Afin d'estimer la taille de la population de lynx dans le Jura et de déterminer les corridors potentiels entre cette région et les zones avoisinantes, un modèle d'habitat a été utilisé, basé sur un nouveau jeu de variables environnementales et extrapolé à l'ensemble du Jura. Le modèle prédit une population reproductrice de 74 à 101 individus et de 51 à 79 individus lorsque les surfaces d'habitat d'un seul tenant de moins de 50 km2 sont soustraites. Comme des corridors potentiels existent effectivement entre le Jura et les régions avoisinantes (Alpes, Vosges, et Forêt Noire), le Jura pourrait faire partie à l'avenir d'une métapopulation, lorsque les zones avoisinantes seront colonisées par l'espèce. La surveillance de la taille de la population, de son expansion spatiale et de sa structure génétique doit être maintenue car le statut de cette population est encore critique. L'AEN a également été utilisée pour prédire l'habitat favorable du lynx dans les Alpes. Le modèle qui en résulte divise les Alpes en 37 sous-unités d'habitat favorable dont la surface varie de 50 à 18'711 km2, pour une superficie totale de 93'600 km2. En utilisant le spectre des densités observées dans les études radio-télémétriques effectuées en Suisse, les Alpes pourraient accueillir une population de lynx résidents variant de 961 à 1'827 individus. Les résultats des analyses de connectivité montrent que les sous-unités d'habitat favorable se situent à des distances telles que le coût de la dispersion pour l'espèce est admissible. L'ensemble des Alpes pourrait donc un jour former une métapopulation. Mais l'expérience montre que très peu d'individus traverseront des habitats peu favorables et des barrières au cours de leur dispersion. Ce faible taux de migration rendra difficile toute nouvelle implantation de populations dans des zones inoccupées. Une solution alternative existe cependant : transférer artificiellement des individus d'une zone à l'autre. Les biologistes spécialistes de la faune sauvage peuvent jouer un rôle important et complémentaire pour les gestionnaires de la faune, en les aidant à mener des expériences de gestion par essai. Le cas du lynx en Suisse est un bel exemple d'une collaboration fructueuse entre biologistes de la faune sauvage, gestionnaires, organes décisionnaires et politiciens. Cette coopération a permis l'élaboration du Concept Lynx Suisse qui est entré en vigueur en 2000 et remis à jour en 2004. Ce plan donne des directives aux cantons pour appréhender la problématique du lynx. Il y a déjà eu des applications concrètes sur le terrain, notamment par des translocations d'individus dans des zones encore inoccupées.

Combining niche modelling and landscape genetics to study local adaptation: A novel approach illustrated using alpine plants

Understanding the factors that shape adaptive genetic variation across species niches has become of paramount importance in evolutionary ecology, especially to understand how adaptation to changing climate affects the geographic range of species. The distribution of adaptive alleles in the ecological niche is determined by the emergence of novel mutations, their fitness consequences and gene flow that connects populations across species niches. Striking demographical differences and source sink dynamics of populations between the centre and the margin of the niche can play a major role in the emergence and spread of adaptive alleles. Although some theoretical predictions have long been proposed, the origin and distribution of adaptive alleles within species niches remain untested. In this paper, we propose and discuss a novel empirical approach that combines landscape genetics with species niche modelling, to test whether alleles that confer local adaptation are more likely to occur in either marginal or central populations of species niches. We illustrate this new approach by using a published data set of 21 alpine plant species genotyped with a total of 2483 amplified fragment length polymorphisms (AFLP), distributed over more than 1733 sampling sites across the Alps. Based on the assumption that alleles that were statistically associated with environmental variables were adaptive, we found that adaptive alleles in the margin of a species niche were also present in the niche centre, which suggests that adaptation originates in the niche centre. These findings corroborate models of species range evolution, in which the centre of the niche contributes to the emergence of novel adaptive alleles, which diffuse towards niche margins and facilitate niche and range expansion through subsequent local adaptation. Although these results need to be confirmed via fitness measurements in natural populations and functionally characterised genetic sequences, this study provides a first step towards understanding how adaptive genetic variation emerges and shapes species niches and geographic ranges along environmental gradients.

Landscape and farm scale management to enhance biodiversity conservation in the cocoa producing region of southern Bahia, Brazil

In southern Bahia, Brazil, large land areas are used for the production of cocoa (Theobroma cacao), which is predominantly grown under the shade of native trees in an agroforestry system locally known as cabruca. As a dominant forest-like landscape element of the cocoa region, the cabrucas play an important role in the conservation of the region`s biodiversity. The purpose of this review is to provide the scientific basis for an action plan to reconcile cocoa production and biodiversity conservation in southern Bahia. The available research collectively highlights the diversity of responses of different species and biological groups to both the habitat quality of the cabrucas themselves and to the general characteristics of the landscape, such as the relative extent and spatial configuration of different vegetation types within the landscape mosaic. We identify factors that influence directly or indirectly the occurrence of native species in the cabrucas and the wider landscape of the cocoa region and develop recommendations for their conservation management. We show that the current scientific knowledge already provides a good basis for a biodiversity friendly management of the cocoa region of southern Bahia, although more work is needed to refine some management recommendations, especially on shade canopy composition and density, and verify their economic viability. The implementation of our recommendations should be accompanied by appropriate biological and socioeconomic monitoring and the findings should inform a broad program of adaptive management of the cabrucas and the wider cocoa landscape.

Genetic diversity, phenotypic variation and local adaptation in the alpine landscape: case studies with alpine plant species

Plant survival in alpine landscapes is constantly challenged by the harsh and often unpredictable environmental conditions. Steep environmental gradients and patchy distribution of habitats lead to small size and spatial isolation of populations and restrict gene flow. Agricultural land use has further increased the diversity of habitats below and above the treeline. We studied the consequences of the highly structured alpine landscape for evolutionary processes in four study plants: Epilobium fleischeri, Geum reptans, Campanula thyrsoides and Poa alpina. The main questions were: (1) How is genetic diversity distributed within and among populations and is it affected by altitude, population size or land use? (2) Do reproductive traits such as allocation to sexual or vegetative reproduction vary with altitude or land use? Furthermore, we studied if seed weight increases with altitude. Within-population genetic diversity of the four species was high and mostly not related to altitude and population size. Nevertheless, genetic differentiation among populations was pronounced and strongly increasing with distance. In Poa alpina genetic diversity was affected by land use. Results suggest considerable genetic drift among populations of alpine plants. Reproductive allocation was affected by altitude and land use in Poa alpina and by succession in Geum reptans. Seed weight was usually higher in alpine species than in related lowland species. We conclude that the evolutionary potential to respond to global change is mostly intact in alpine plants, even at high altitude. Phenotypic variability is shaped by adaptive as well as by random evolutionary processes; moreover plastic responses to growth conditions seem to be crucial for survival of plants in the alpine landscape.