Testing demographic models of effective population size.

Due to practical difficulties in obtaining direct genetic estimates of effective sizes, conservation biologists have to rely on so-called 'demographic models' which combine life-history and mating-system parameters with F-statistics in order to produce indirect estimates of effective sizes. However, for the same practical reasons that prevent direct genetic estimates, the accuracy of demographic models is difficult to evaluate. Here we use individual-based, genetically explicit computer simulations in order to investigate the accuracy of two such demographic models aimed at investigating the hierarchical structure of populations. We show that, by and large, these models provide good estimates under a wide range of mating systems and dispersal patterns. However, one of the models should be avoided whenever the focal species' breeding system approaches monogamy with no sex bias in dispersal or when a substructure within social groups is suspected because effective sizes may then be strongly overestimated. The timing during the life cycle at which F-statistics are evaluated is also of crucial importance and attention should be paid to it when designing field sampling since different demographic models assume different timings. Our study shows that individual-based, genetically explicit models provide a promising way of evaluating the accuracy of demographic models of effective size and delineate their field of applicability.

Inbreeding in the greater white-toothed shrew, Crocidura russula.

We combined mark-and-recapture studies with genetic techniques of parentage assignment to evaluate the interactions between mating, dispersal, and inbreeding, in a free-ranging population of Crocidura russula. We found a pattern of limited and female-biased dispersal, followed by random mating within individual neighborhoods. This results in significant inbreeding at the population level: mating among relatives occurs more often than random, and F(IT) analyses reveal significant deficits in heterozygotes. However, related mating partners were not less fecund, and inbred offspring had no lower lifetime reproductive output. Power analyses show these negative results to be quite robust. Absence of phenotypic evidence of inbreeding depression might result from a history of purging: local populations are small and undergo disequilibrium gene dynamics. Dispersal is likely caused by local saturation and (re)colonization of empty breeding sites, rather than inbreeding avoidance.

Ecological niche models and patterns of richness and endemism of the southern Andean genus Eurymetopum (Coleoptera, Cleridae)

Eurymetopum is an Andean clerid genus with 22 species. We modeled the ecological niches of 19 species with Maxent and used them as potential distributional maps to identify patterns of richness and endemicity. All modeled species maps were overlapped in a single map in order to determine richness. We performed an optimality analysis with NDM/VNDM in a grid of 1º latitude-longitude in order to identify endemism. We found a highly rich area, located between 32º and 41º south latitude, where the richest pixels have 16 species. One area of endemism was identified, located in the Maule and Valdivian Forest biogeographic provinces, which extends also to the Santiago province of the Central Chilean subregion, and contains four endemic species (E. parallelum, E. prasinum, E. proteus, and E. viride), as well as 16 non-endemic species. The sympatry of these phylogenetically unrelated species might indicate ancient vicariance processes, followed by episodes of dispersal. Based on our results, we suggest a close relationship between these provinces, with the Maule representing a complex area.

Breeding system and genetic variance in the monogamous, semi-social shrew, Crocidura russula

The population-genetic consequences of monogamy and male philopatry (a rare breeding system in mammals) were investigated using microsatellite markers in the semisocial and anthropophilic shrew Crocidura russula. A hierarchical sampling design over a 16-km geographical transect revealed a large genetic diversity (h = 0.813) with significant differentiation among subpopulations (F-ST = 5-6%), which suggests an exchange of 4.4 migrants per generation. Demic effective-size estimates were very high, due both to this limited gene inflow and to the inner structure of subpopulations. These were made of 13-20 smaller units (breeding groups), comprising an estimate of four breeding pairs each. Members of the same breeding groups displayed significant coancestries (F-LS = 9-10%), which was essentially due to strong male kinship: syntopic males were on average related at the half-sib level. Female dispersal among breeding groups was not complete (similar to 39%), and insufficient to prevent inbreeding. From our results, the breeding strategy of C. russula seems less efficient than classical mammalian systems (polygyny and male dispersal) in disentangling coancestry from inbreeding, but more so in retaining genetic variance.

Flexible social organization and high incidence of drifting in the sweat bee, Halictus scabiosae.

The very diverse social systems of sweat bees make them interesting models to study social evolution. Here we focus on the dispersal behaviour and social organization of Halictus scabiosae, a common yet poorly known species of Europe. By combining field observations and genetic data, we show that females have multiple reproductive strategies, which generates a large diversity in the social structure of nests. A detailed microsatellite analysis of 60 nests revealed that 55% of the nests contained the offspring of a single female, whereas the rest had more complex social structures, with three clear cases of multiple females reproducing in the same nest and frequent occurrence of unrelated individuals. Drifting among nests was surprisingly common, as 16% of the 122 nests in the overall sample and 44% of the nests with complex social structure contained females that had genotypes consistent with being full-sisters of females sampled in other nests of the population. Drifters originated from nests with an above-average productivity and were unrelated to their nestmates, suggesting that drifting might be a strategy to avoid competition among related females. The sex-specific comparison of genetic differentiation indicated that dispersal was male-biased, which would reinforce local resource competition among females. The pattern of genetic differentiation among populations was consistent with a dynamic process of patch colonization and extinction, as expected from the unstable, anthropogenic habitat of this species. Overall, our data show that H. scabiosae varies greatly in dispersal behaviour and social organization. The surprisingly high frequency of drifters echoes recent findings in wasps and bees, calling for further investigation of the adaptive basis of drifting in the social insects.

Evolution in heterogeneous populations: from migration models to fixation probabilities.

Although dispersal is recognized as a key issue in several fields of population biology (such as behavioral ecology, population genetics, metapopulation dynamics or evolutionary modeling), these disciplines focus on different aspects of the concept and often make different implicit assumptions regarding migration models. Using simulations, we investigate how such assumptions translate into effective gene flow and fixation probability of selected alleles. Assumptions regarding migration type (e.g. source-sink, resident pre-emption, or balanced dispersal) and patterns (e.g. stepping-stone versus island dispersal) have large impacts when demes differ in sizes or selective pressures. The effects of fragmentation, as well as the spatial localization of newly arising mutations, also strongly depend on migration type and patterns. Migration rate also matters: depending on the migration type, fixation probabilities at an intermediate migration rate may lie outside the range defined by the low- and high-migration limits when demes differ in sizes. Given the extreme sensitivity of fixation probability to characteristics of dispersal, we underline the importance of making explicit (and documenting empirically) the crucial ecological/ behavioral assumptions underlying migration models.

Relationships of Scincid Lizards (Mabuya spp; Reptilia: Scincidae) from the Cape Verde Islands Based on Mitochondrial and Nuclear DNA Sequences

Partial DNA sequences from two mitochondrial (mt) and one nuclear gene (cytochrome b, 12S rRNA, and C-mos) were used to estimate the phylogenetic relationships among the six extant species of skinks endemic to the Cape Verde Archipelago. The species form a monophyletic unit, indicating a single colonization of the islands, probably from West Africa. Mabuya vaillanti and M. delalandii are sister taxa, as indicated by morphological characters. Mabuya fogoensis and M. stangeri are closely related, but the former is probably paraphyletic. Mabuya spinalis and M. salensis are also probably paraphyletic. Within species, samples from separate islands always form monophyletic groups. Some colonization events can be hypothesized, which are in line with the age of the islands. C-mos variation is concordant with the topology derived from mtDNA.

Phylogeography of Mabuya maculilabris (Reptilia) from São Tomé Island (Gulf of Guinea) inferred from mtDNA sequences

The pattern of genetic variation of the lizard Mabuya maculilabris from São Tomé Island (Gulf of Guinea) was investigated using a combination of three mitochondrial DNA gene fragments. Forty-eight haplotypes were recovered among 66 individuals covering the whole island. The genealogy inferred from the most parsimonious network of haplotypes allows us to detect two main and long branches departing from the putative group of oldest haplotypes. The tips of these branches exhibit star-like phylogenies, which may indicate of recently expanded populations, most probably from a small number of founders. A nested clade analysis suggests a complex pattern of past events that gave rise to the extant geographical pattern found in the haplotype distribution: past and allopatric fragmentation, range expansion, restricted gene Xow and long-distance dispersal. These results are consistent with the complex geological history of the island where important volcanic activity with extensive lava Xows has occurred during several periods. Mismatch- distribution analysis and AMOVA also support these conclusions. Substantial genetic structuring among these lizards was detected as well as high levels of diVerentiation between the southern edge populations (particularly those from the Rolas Islet) and the remaining ones. However, variation is low relative to the geological age of the island. Our results indicate that patterns of variation observed in reptiles in other oceanic islands are not indicative of those observed in the islands of the Gulf of Guinea.

The evolution of helping and harming on graphs: the return of the inclusive fitness effect.

Evolutionary graph theory has been proposed as providing new fundamental rules for the evolution of co-operation and altruism. But how do these results relate to those of inclusive fitness theory? Here, we carry out a retrospective analysis of the models for the evolution of helping on graphs of Ohtsuki et al. [Nature (2006) 441, 502] and Ohtsuki & Nowak [Proc. R. Soc. Lond. Ser. B Biol. Sci (2006) 273, 2249]. We show that it is possible to translate evolutionary graph theory models into classical kin selection models without disturbing at all the mathematics describing the net effect of selection on helping. Model analysis further demonstrates that costly helping evolves on graphs through limited dispersal and overlapping generations. These two factors are well known to promote relatedness between interacting individuals in spatially structured populations. By allowing more than one individual to live at each node of the graph and by allowing interactions to vary with the distance between nodes, our inclusive fitness model allows us to consider a wider range of biological scenarios leading to the evolution of both helping and harming behaviours on graphs.

Distinct genetic structure in populations of Chrysoperla externa (Hagen) (Neuroptera, Chrysopidae) shown by genetic markers ISSR and COI gene

Distinct genetic structure in populations of Chrysoperla externa (Hagen) (Neuroptera, Chrysopidae) shown by genetic markers ISSR and COI gene. Green lacewings are generalist predators, and the species Chrysoperla externa presents a great potential for use in biological control of agricultural pests due to its high predation and reproduction capacities, as well as its easy mass rearing in the laboratory. The adaptive success of a species is related to genetic variability, so that population genetic studies are extremely important in order to maximize success of the biological control. Thus, the present study used nuclear (Inter Simple Sequence Repeat - ISSR) and mitochondrial (Cytochrome Oxidase I - COI) molecular markers to estimate the genetic variability of 12 populations in the São Paulo State, Brazil, as well as the genetic relationships between populations. High levels of genetic diversity were observed for both markers, and the highest values of genetic diversity appear associated with municipalities that have the greatest areas of native vegetation. There was high haplotype sharing, and there was no correlation between the markers and the geographic distribution of the populations. The AMOVA indicated absence of genetic structure for the COI gene, suggesting that the sampled areas formed a single population unit. However, the great genetic differentiation among populations showed by ISSR demonstrates that these have been under differentiation after their expansion or may also reflect distinct dispersal behavior between males and females.

Habitat-quality effects on metapopulation dynamics in greater white-toothed shrews, Crocidura russula.

The effects of patch size and isolation on metapopulation dynamics have received wide empirical support and theoretical formalization. By contrast, the effects of patch quality seem largely underinvestigated, partly due to technical difficulties in properly assessing quality. Here we combine habitat-quality modeling with four years of demographic monitoring in a metapopulation of greater white-toothed shrews (Crocidura russula) to investigate the role of patch quality on metapopulation processes. Together, local patch quality and connectivity significantly enhanced local population sizes and occupancy rates (R2 = 14% and 19%, respectively). Accounting for the quality of patches connected to the focal one and acting as potential sources improved slightly the model explanatory power for local population sizes, pointing to significant source-sink dynamics. Local habitat quality, in interaction with connectivity, also increased colonization rate (R2 = 28%), suggesting the ability of immigrants to target high-quality patches. Overall, patterns were best explained when assuming a mean dispersal distance of 800 m, a realistic value for the species under study. Our results thus provide evidence that patch quality, in interaction with connectivity, may affect major demographic processes.

Effects of (p)ppGpp on the progression of the cell cycle of Caulobacter crescentus.

Bacteria must control the progression of their cell cycle in response to nutrient availability. This regulation can be mediated by guanosine tetra- or pentaphosphate [(p)ppGpp], which are synthesized by enzymes of the RelA/SpoT homologue (Rsh) family, particularly under starvation conditions. Here, we study the effects of (p)ppGpp on the cell cycle of Caulobacter crescentus, an oligotrophic bacterium with a dimorphic life cycle. C. crescentus divides asymmetrically, producing a motile swarmer cell that cannot replicate its chromosome and a sessile stalked cell that is replication competent. The swarmer cell rapidly differentiates into a stalked cell in appropriate conditions. An artificial increase in the levels of (p)ppGpp in nonstarved C. crescentus cells was achieved by expressing a truncated relA gene from Escherichia coli, encoding a constitutively active (p)ppGpp synthetase. By combining single-cell microscopy, flow cytometry approaches, and swarming assays, we show that an increase in the intracellular concentration of (p)ppGpp is sufficient to slow down the swarmer-to-stalked cell differentiation process and to delay the initiation of chromosome replication. We also present evidence that the intracellular levels of two master regulators of the cell cycle of C. crescentus, DnaA and CtrA, are modulated in response to (p)ppGpp accumulation, even in the absence of actual starvation. CtrA proteolysis and DnaA synthesis seem indirectly inhibited by (p)ppGpp accumulation. By extending the life span of the motile nonreproductive swarmer cell and thus promoting dispersal and foraging functions over multiplication under starvation conditions, (p)ppGpp may play a central role in the ecological adaptation of C. crescentus to nutritional stresses.

Predicting species distribution: offering more than simple habitat models

n the last two decades, interest in species distribution models (SDMs) of plants and animals has grown dramatically. Recent advances in SDMs allow us to potentially forecast anthropogenic effects on patterns of biodiversity at different spatial scales. However, some limitations still preclude the use of SDMs in many theoretical and practical applications. Here, we provide an overview of recent advances in this field, discuss the ecological principles and assumptions underpinning SDMs, and highlight critical limitations and decisions inherent in the construction and evaluation of SDMs. Particular emphasis is given to the use of SDMs for the assessment of climate change impacts and conservation management issues. We suggest new avenues for incorporating species migration, population dynamics, biotic interactions and community ecology into SDMs at multiple spatial scales. Addressing all these issues requires a better integration of SDMs with ecological theory.

Evolutionary branching in deme-structured populations.

Adaptive dynamics shows that a continuous trait under frequency dependent selection may first converge to a singular point followed by spontaneous transition from a unimodal trait distribution into a bimodal one, which is called "evolutionary branching". Here, we study evolutionary branching in a deme-structured population by constructing a quantitative genetic model for the trait variance dynamics, which allows us to obtain an analytic condition for evolutionary branching. This is first shown to agree with previous conditions for branching expressed in terms of relatedness between interacting individuals within demes and obtained from mutant-resident systems. We then show this branching condition can be markedly simplified when the evolving trait affect fecundity and/or survival, as opposed to affecting population structure, which would occur in the case of the evolution of dispersal. As an application of our model, we evaluate the threshold migration rate below which evolutionary branching cannot occur in a pairwise interaction game. This agrees very well with the individual-based simulation results.

Unfolding nature "in silico" : overcoming practical and metodological limitations of species distribution models

Abstract : The existence of a causal relationship between the spatial distribution of living organisms and their environment, in particular climate, has been long recognized and is the central principle of biogeography. In turn, this recognition has led scientists to the idea of using the climatic, topographic, edaphic and biotic characteristics of the environment to predict its potential suitability for a given species or biological community. In this thesis, my objective is to contribute to the development of methodological improvements in the field of species distribution modeling. More precisely, the objectives are to propose solutions to overcome limitations of species distribution models when applied to conservation biology issues, or when .used as an assessment tool of the potential impacts of global change. The first objective of my thesis is to contribute to evidence the potential of species distribution models for conservation-related applications. I present a methodology to generate pseudo-absences in order to overcome the frequent lack of reliable absence data. I also demonstrate, both theoretically (simulation-based) and practically (field-based), how species distribution models can be successfully used to model and sample rare species. Overall, the results of this first part of the thesis demonstrate the strong potential of species distribution models as a tool for practical applications in conservation biology. The second objective this thesis is to contribute to improve .projections of potential climate change impacts on species distributions, and in particular for mountain flora. I develop and a dynamic model, MIGCLIM, that allows the implementation of dispersal limitations into classic species distribution models and present an application of this model to two virtual species. Given that accounting for dispersal limitations requires information on seed dispersal, distances, a general methodology to classify species into broad dispersal types is also developed. Finally, the M~GCLIM model is applied to a large number of species in a study area of the western Swiss Alps. Overall, the results indicate that while dispersal limitations can have an important impact on the outcome of future projections of species distributions under climate change scenarios, estimating species threat levels (e.g. species extinction rates) for a mountainous areas of limited size (i.e. regional scale) can also be successfully achieved when considering dispersal as unlimited (i.e. ignoring dispersal limitations, which is easier from a practical point of view). Finally, I present the largest fine scale assessment of potential climate change impacts on mountain vegetation that has been carried-out to date. This assessment involves vegetation from 12 study areas distributed across all major western and central European mountain ranges. The results highlight that some mountain ranges (the Pyrenees and the Austrian Alps) are expected to be more affected by climate change than others (Norway and the Scottish Highlands). The results I obtain in this study also indicate that the threat levels projected by fine scale models are less severe than those derived from coarse scale models. This result suggests that some species could persist in small refugias that are not detected by coarse scale models. Résumé : L'existence d'une relation causale entre la répartition des espèces animales et végétales et leur environnement, en particulier le climat, a été mis en évidence depuis longtemps et est un des principes centraux en biogéographie. Ce lien a naturellement conduit à l'idée d'utiliser les caractéristiques climatiques, topographiques, édaphiques et biotiques de l'environnement afin d'en prédire la qualité pour une espèce ou une communauté. Dans ce travail de thèse, mon objectif est de contribuer au développement d'améliorations méthodologiques dans le domaine de la modélisation de la distribution d'espèces dans le paysage. Plus précisément, les objectifs sont de proposer des solutions afin de surmonter certaines limitations des modèles de distribution d'espèces dans des applications pratiques de biologie de la conservation ou dans leur utilisation pour évaluer l'impact potentiel des changements climatiques sur l'environnement. Le premier objectif majeur de mon travail est de contribuer à démontrer le potentiel des modèles de distribution d'espèces pour des applications pratiques en biologie de la conservation. Je propose une méthode pour générer des pseudo-absences qui permet de surmonter le problème récurent du manque de données d'absences fiables. Je démontre aussi, de manière théorique (par simulation) et pratique (par échantillonnage de terrain), comment les modèles de distribution d'espèces peuvent être utilisés pour modéliser et améliorer l'échantillonnage des espèces rares. Ces résultats démontrent le potentiel des modèles de distribution d'espèces comme outils pour des applications de biologie de la conservation. Le deuxième objectif majeur de ce travail est de contribuer à améliorer les projections d'impacts potentiels des changements climatiques sur la flore, en particulier dans les zones de montagnes. Je développe un modèle dynamique de distribution appelé MigClim qui permet de tenir compte des limitations de dispersion dans les projections futures de distribution potentielle d'espèces, et teste son application sur deux espèces virtuelles. Vu que le fait de prendre en compte les limitations dues à la dispersion demande des données supplémentaires importantes (p.ex. la distance de dispersion des graines), ce travail propose aussi une méthode de classification simplifiée des espèces végétales dans de grands "types de disperseurs", ce qui permet ainsi de d'obtenir de bonnes approximations de distances de dispersions pour un grand nombre d'espèces. Finalement, j'applique aussi le modèle MIGCLIM à un grand nombre d'espèces de plantes dans une zone d'études des pré-Alpes vaudoises. Les résultats montrent que les limitations de dispersion peuvent avoir un impact considérable sur la distribution potentielle d'espèces prédites sous des scénarios de changements climatiques. Cependant, quand les modèles sont utilisés pour évaluer les taux d'extinction d'espèces dans des zones de montages de taille limitée (évaluation régionale), il est aussi possible d'obtenir de bonnes approximations en considérant la dispersion des espèces comme illimitée, ce qui est nettement plus simple d'un point dé vue pratique. Pour terminer je présente la plus grande évaluation à fine échelle d'impact potentiel des changements climatiques sur la flore des montagnes conduite à ce jour. Cette évaluation englobe 12 zones d'études réparties sur toutes les chaines de montages principales d'Europe occidentale et centrale. Les résultats montrent que certaines chaines de montagnes (les Pyrénées et les Alpes Autrichiennes) sont projetées comme plus sensibles aux changements climatiques que d'autres (les Alpes Scandinaves et les Highlands d'Ecosse). Les résultats obtenus montrent aussi que les modèles à échelle fine projettent des impacts de changement climatiques (p. ex. taux d'extinction d'espèces) moins sévères que les modèles à échelle large. Cela laisse supposer que les modèles a échelle fine sont capables de modéliser des micro-niches climatiques non-détectées par les modèles à échelle large.