The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates.

Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds to the early conservation model or the hourglass model, respectively. Conflicting results have been reported, but in recent studies of animal transcriptomes the hourglass model has been favored. Studies usually report descriptive statistics calculated for all genes over all developmental time points. This introduces dependencies between the sets of compared genes and may lead to biased results. Here we overcome this problem using an alternative modular analysis. We used the Iterative Signature Algorithm to identify distinct modules of genes co-expressed specifically in consecutive stages of zebrafish development. We then performed a detailed comparison of several gene properties between modules, allowing for a less biased and more powerful analysis. Notably, our analysis corroborated the hourglass pattern at the regulatory level, with sequences of regulatory regions being most conserved for genes expressed in mid-development but not at the level of gene sequence, age, or expression, in contrast to some previous studies. The early conservation model was supported with gene duplication and birth that were the most rare for genes expressed in early development. Finally, for all gene properties, we observed the least conservation for genes expressed in late development or adult, consistent with both models. Overall, with the modular approach, we showed that different levels of molecular evolution follow different patterns of developmental constraints. Thus both models are valid, but with respect to different genomic features.

A probabilistic approach to niche-based community models for spatial forecasts of assemblage properties and their uncertainties

Aim Conservation strategies are in need of predictions that capture spatial community composition and structure. Currently, the methods used to generate these predictions generally focus on deterministic processes and omit important stochastic processes and other unexplained variation in model outputs. Here we test a novel approach of community models that accounts for this variation and determine how well it reproduces observed properties of alpine butterfly communities. Location The western Swiss Alps. Methods We propose a new approach to process probabilistic predictions derived from stacked species distribution models (S-SDMs) in order to predict and assess the uncertainty in the predictions of community properties. We test the utility of our novel approach against a traditional threshold-based approach. We used mountain butterfly communities spanning a large elevation gradient as a case study and evaluated the ability of our approach to model species richness and phylogenetic diversity of communities. Results S-SDMs reproduced the observed decrease in phylogenetic diversity and species richness with elevation, syndromes of environmental filtering. The prediction accuracy of community properties vary along environmental gradient: variability in predictions of species richness was higher at low elevation, while it was lower for phylogenetic diversity. Our approach allowed mapping the variability in species richness and phylogenetic diversity projections. Main conclusion Using our probabilistic approach to process species distribution models outputs to reconstruct communities furnishes an improved picture of the range of possible assemblage realisations under similar environmental conditions given stochastic processes and help inform manager of the uncertainty in the modelling results

Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology

The pace of on-going climate change calls for reliable plant biodiversity scenarios. Traditional dynamic vegetation models use plant functional types that are summarized to such an extent that they become meaningless for biodiversity scenarios. Hybrid dynamic vegetation models of intermediate complexity (hybrid-DVMs) have recently been developed to address this issue. These models, at the crossroads between phenomenological and process-based models, are able to involve an intermediate number of well-chosen plant functional groups (PFGs). The challenge is to build meaningful PFGs that are representative of plant biodiversity, and consistent with the parameters and processes of hybrid-DVMs. Here, we propose and test a framework based on few selected traits to define a limited number of PFGs, which are both representative of the diversity (functional and taxonomic) of the flora in the Ecrins National Park, and adapted to hybrid-DVMs. This new classification scheme, together with recent advances in vegetation modeling, constitutes a step forward for mechanistic biodiversity modeling.

Detection, analysis and monitoring of slope movements by high-resolution digital elevation models

Summary Detection, analysis and monitoring of slope movements by high-resolution digital elevation modelsSlope movements, such as rockfalls, rockslides, shallow landslides or debris flows, are frequent in many mountainous areas. These natural hazards endanger the inhabitants and infrastructures making it necessary to assess the hazard and risk caused by these phenomena. This PhD thesis explores various approaches using digital elevation models (DEMs) - and particularly high-resolution DEMs created by aerial or terrestrial laser scanning (TLS) - that contribute to the assessment of slope movement hazard at regional and local scales.The regional detection of areas prone to rockfalls and large rockslides uses different morphologic criteria or geometric instability factors derived from DEMs, i.e. the steepness of the slope, the presence of discontinuities, which enable a sliding mechanism, and the denudation potential. The combination of these factors leads to a map of susceptibility to rockfall initiation that is in good agreement with field studies as shown with the example of the Little Mill Campground area (Utah, USA). Another case study in the Illgraben catchment in the Swiss Alps highlighted the link between areas with a high denudation potential and actual rockfall areas.Techniques for a detailed analysis and characterization of slope movements based on high-resolution DEMs have been developed for specific, localized sites, i.e. ancient slide scars, present active instabilities or potential slope instabilities. The analysis of the site's characteristics mainly focuses on rock slopes and includes structural analyses (orientation of discontinuities); estimation of spacing, persistence and roughness of discontinuities; failure mechanisms based on the structural setting; and volume calculations. For the volume estimation a new 3D approach was tested to reconstruct the topography before a landslide or to construct the basal failure surface of an active or potential instability. The rockslides at Åknes, Tafjord and Rundefjellet in western Norway were principally used as study sites to develop and test the different techniques.The monitoring of slope instabilities investigated in this PhD thesis is essentially based on multitemporal (or sequential) high-resolution DEMs, in particular sequential point clouds acquired by TLS. The changes in the topography due to slope movements can be detected and quantified by sequential TLS datasets, notably by shortest distance comparisons revealing the 3D slope movements over the entire region of interest. A detailed analysis of rock slope movements is based on the affine transformation between an initial and a final state of the rock mass and its decomposition into translational and rotational movements. Monitoring using TLS was very successful on the fast-moving Eiger rockslide in the Swiss Alps, but also on the active rockslides of Åknes and Nordnesfjellet (northern Norway). One of the main achievements on the Eiger and Aknes rockslides is to combine the site's morphology and structural setting with the measured slope movements to produce coherent instability models. Both case studies also highlighted a strong control of the structures in the rock mass on the sliding directions. TLS was also used to monitor slope movements in soils, such as landslides in sensitive clays in Québec (Canada), shallow landslides on river banks (Sorge River, Switzerland) and a debris flow channel (Illgraben).The PhD thesis underlines the broad uses of high-resolution DEMs and especially of TLS in the detection, analysis and monitoring of slope movements. Future studies should explore in more depth the different techniques and approaches developed and used in this PhD, improve them and better integrate the findings in current hazard assessment practices and in slope stability models.Résumé Détection, analyse et surveillance de mouvements de versant à l'aide de modèles numériques de terrain de haute résolutionDes mouvements de versant, tels que des chutes de blocs, glissements de terrain ou laves torrentielles, sont fréquents dans des régions montagneuses et mettent en danger les habitants et les infrastructures ce qui rend nécessaire d'évaluer le danger et le risque causé par ces phénomènes naturels. Ce travail de thèse explore diverses approches qui utilisent des modèles numériques de terrain (MNT) et surtout des MNT de haute résolution créés par scanner laser terrestre (SLT) ou aérien - et qui contribuent à l'évaluation du danger de mouvements de versant à l'échelle régionale et locale.La détection régionale de zones propices aux chutes de blocs ou aux éboulements utilise plusieurs critères morphologiques dérivés d'un MNT, tels que la pente, la présence de discontinuités qui permettent un mécanisme de glissement ou le potentiel de dénudation. La combinaison de ces facteurs d'instabilité mène vers une carte de susceptibilité aux chutes de blocs qui est en accord avec des travaux de terrain comme démontré avec l'exemple du Little Mill Campground (Utah, États-Unis). Un autre cas d'étude - l'Illgraben dans les Alpes valaisannes - a mis en évidence le lien entre les zones à fort potentiel de dénudation et les sources effectives de chutes de blocs et d'éboulements.Des techniques pour l'analyse et la caractérisation détaillée de mouvements de versant basées sur des MNT de haute résolution ont été développées pour des sites spécifiques et localisés, comme par exemple des cicatrices d'anciens éboulements et des instabilités actives ou potentielles. Cette analyse se focalise principalement sur des pentes rocheuses et comprend l'analyse structurale (orientation des discontinuités); l'estimation de l'espacement, la persistance et la rugosité des discontinuités; l'établissement des mécanismes de rupture; et le calcul de volumes. Pour cela une nouvelle approche a été testée en rétablissant la topographie antérieure au glissement ou en construisant la surface de rupture d'instabilités actuelles ou potentielles. Les glissements rocheux d'Åknes, Tafjord et Rundefjellet en Norvège ont été surtout utilisés comme cas d'étude pour développer et tester les diverses approches. La surveillance d'instabilités de versant effectuée dans cette thèse de doctorat est essentiellement basée sur des MNT de haute résolution multi-temporels (ou séquentiels), en particulier des nuages de points séquentiels acquis par SLT. Les changements topographiques dus aux mouvements de versant peuvent être détectés et quantifiés sur l'ensemble d'un glissement, notamment par comparaisons des distances les plus courtes entre deux nuages de points. L'analyse détaillée des mouvements est basée sur la transformation affine entre la position initiale et finale d'un bloc et sa décomposition en mouvements translationnels et rotationnels. La surveillance par SLT a démontré son potentiel avec l'effondrement d'un pan de l'Eiger dans les Alpes suisses, mais aussi aux glissements rocheux d'Aknes et Nordnesfjellet en Norvège. Une des principales avancées à l'Eiger et à Aknes est la création de modèles d'instabilité cohérents en combinant la morphologie et l'agencement structural des sites avec les mesures de déplacements. Ces deux cas d'étude ont aussi démontré le fort contrôle des structures existantes dans le massif rocheux sur les directions de glissement. Le SLT a également été utilisé pour surveiller des glissements dans des terrains meubles comme dans les argiles sensibles au Québec (Canada), sur les berges de la rivière Sorge en Suisse et dans le chenal à laves torrentielles de l'Illgraben.Cette thèse de doctorat souligne le vaste champ d'applications des MNT de haute résolution et particulièrement du SLT dans la détection, l'analyse et la surveillance des mouvements de versant. Des études futures devraient explorer plus en profondeur les différentes techniques et approches développées, les améliorer et mieux les intégrer dans des pratiques actuelles d'analyse de danger et surtout dans la modélisation de stabilité des versants.

Sex-linked genetic markers in the shrews of the Sorex araneus group : from free gene flow to speciation

SUMMARY: The shrews of the Sorex araneus group are morphologically .very similar, but have undergone a spectacular chromosomal evolution. Altogether, the shrews of this group present a complete array of every possible level of chromosomal and genetic differentiation. In South-Western Europe, four species are recognised: S. antiriorii, S. araneus, S. coronatus and S. granarius, which differ essentially by the amount and the composition of Robertsonian metacentric chromosomés. Additionally, several chromosome races of S. araneus are also present in the same region (i.e. Bretolet, Carlit, Cordon, Jura and Vaud). The objective of this thesis was to examine the genetic relationships between populations, races and /or species of the Sorex araneus group with a special emphasis onsex-specific markers (mtDNA and Y chromosome). We first investigate the evolutionary history of the shrews of the Sorex araneus group distributed in the South-Western Europe. The results of. these analyses confirmed the difficulty to draw a single dichotomic tree within this group. Incongruent mtDNA and Y chromosome phylogenies suggest further that genetic and chromosomal evolution are in this group partially independent processes and that the evolutionary history of the south-western European populations of the S. araneus group can only be understood if we consider secondary contacts between taxa, after their divergence (with genetic exchanges by means of hybridization and / or introgression). Using one male-inherited, one female inherited and eight biparentally inherited markers, we investigate the population genetic structure of the Valais shrew (Sorex antinorii). Overall there results suggest that two already well-differentiated genetic lineages colonized the Swiss Alps after the last glacial period and came into contact in the Rhône Valley. After the Valais shrew (Sorex antinorii) reached the Swiss Alps, it came into contact with the common shrew (Sorex araneus). When two species come into contact and hybridize, endogenous counter-selection of hybrids is usually first expressed as a reduced fertility or viability in hybrids of the heterogametic sex, a mechanism know as Haldane's rule (Haldane 1922). We first evaluated the extent of introgression for Y chromosome, mtDNA and autosomal markers in a hybrid zone between S. antinoriii and S. araneus. The overall level of genetic and karyotypic differentiation between the two species must be strong .enough to allow the detection asymmetric introgression. Secondly, we compared the levels of gene flow between chromosome common to both species and chromosome differently rearranged in each of them. We detected a significantly stronger genetic structure in rearranged chromosomes. Over a 10-year period, we even observed a decrease of genetic structure for common chromosomes. These results strongly support the role of chromosomal rearrangements in the reproductive barrier between S. araneus and S. anfinorii. Overall, this thesis underlines the need to use different inherited (paternally, maternally and / or biparentally) and chromosomally located (on common vs. on rearranged chromosomes) markers to obtain more accurate pictures of genetic relationships between populations or species. RÉSUMÉ: Les musaraignes du groupe Sorex araneus sont morphologiquement très proches, mais ont connu une spectaculaire évolution chromosomique. Prises dans leur ensemble, les musaraignes de ce groupe présentent tous les nivaux possibles de différenciation génétique et chromosomique. Dans le sud-ouest de l'Europe, quatre espèces appartenant à ce groupe sont présentes : S. antinorii, S. araneus, S. coronatus et S. granarius. Celles-ci diffèrent essentiellement par leur caryotype dont la variabilité est principalement due à des fusions Robertsoniennes. De plus, plusieurs races chromosomiques appartenant à S. araneus sont aussi présentes dans la même région (i.e. les races Bretolet, Carlit, Cordon, Jura et Vaud). L'objectif de cette thèse était d'examiner les relations génétiques entre populations, races et/ou espèces du groupe S. araneus, en utilisant particulièrement des marqueurs liés aux sexes (ADN mitochondrial et Chromosome Y). Nous avons dans un premier temps retracé l'histoire évolutive des musaraignes de ce groupe dans le sud-ouest de l'Europe. Les résultats dé ces analyses confirment qu'il est difficile de tracer un simple arbre dichotomique au sein de ce groupe. Les arbres phylogénétiques obtenus sur l'ADN mitochondrial et le chromosome Y sont incongruents et suggèrent de plus que l'évolution génétique et chromosomique sont des processus indépendants. L'histoire évolutive -des populations de ce groupe ne peut. être comprise qu'en considérant des contacts secondaires entre taxa postérieure à leur divergence et induisant des échanges génétiques par hybridation et/ou introgression. Par la suite, nous avons examiné la structure génétique des populations de la musaraigne du Valais, S. antinorii, en utilisant un marqueur transmis par les mâles, un marqueur transmis par les femelles et huit marqueurs transmis par les 2 sexes. Nos résultats suggèrent que deux lignées génétiquement bien différenciées aient colonisé les Alpes Suisses, après les dernières glaciations et entrent en contact dans là Vallée du Rhône. Après avoir franchi les Alpes Suisses, la musaraigne du Valais est entrée en contact avec là musaraigne commune (S. araneus). Lorsque deux espèces entrent en contact et s'hybrident, la sélection contre les hybrides implique habituellement une baisse de fertilité ou de viabilité des hybrides du sexe hétérogamétique (i.e. les mâles XY chez les mammifères). Ce mécanisme est connu sous le nom de règle de Haldane (Haldane 1922) et implique une plus forte structuration génétique de marqueurs males - spécifiques que des marqueurs femelles spécifiques. Nous avons donc évalué le degré d'introgression des marqueurs situés sur le chromosome Y, sur l'ADN mitochondrial et sur des autosomes dans une zone hybride entre S. araneus et S. antinorii. Le niveau de différenciation chromosomique et génétique entre les 2 espèces doit être suffisamment fort pour ne pas permettre la détection d'une introgression asymétrique entre les sexes. Dans un second temps, nous avons comparé les niveaux de flux de gênes mesurés à l'échelle du chromosome, pour des chromosomes communs aux deux espèces et pour des chromosomes différemment arrangées dans chacune des deux espèces. Nous avons détecté une structure génétique significativement plus forte sur les chromosomes réarrangés et comme la zone hybride a été étudiée à dix années d'intervalle, nous observons même une diminution de la structure génétique pour les chromosomes communs au cours du temps.. Ces résultats soutiennent fortement l'hypothèse d'un rôle des réarrangements chromosomiques dans l'établissement d'une barrière reproductive entre S. araneus et S. antinorii. Ainsi cette thèse souligne l'utilité d'utiliser des marqueurs génétiques avec différents modes de transmission. (par les mâles, par les femelles et/ou par les 2 sexes) ou localisés au niveau du chromosome (chromosomes communs vs chromosomes réarrangés) afin d'obtenir une image plus juste ou du moins plus complète des relations génétiques entre populations ou espèces.

Accuracy of plant assemblage predictions from species distribution models varies along environmental gradients

Aim: Climatic niche modelling of species and community distributions implicitly assumes strong and constant climatic determinism across geographic space. This assumption had however never been tested so far. We tested it by assessing how stacked-species distribution models (S-SDMs) perform for predicting plant species assemblages along elevation. Location: Western Swiss Alps. Methods: Using robust presence-absence data, we first assessed the ability of topo-climatic S-SDMs to predict plant assemblages in a study area encompassing a 2800 m wide elevation gradient. We then assessed the relationships among several evaluation metrics and trait-based tests of community assembly rules. Results: The standard errors of individual SDMs decreased significantly towards higher elevations. Overall, the S-SDM overpredicted far more than they underpredicted richness and could not reproduce the humpback curve along elevation. Overprediction was greater at low and mid-range elevations in absolute values but greater at high elevations when standardised by the actual richness. Looking at species composition, the evaluation metrics accounting for both the presence and absence of species (overall prediction success and kappa) or focusing on correctly predicted absences (specificity) increased with increasing elevation, while the metrics focusing on correctly predicted presences (Jaccard index and sensitivity) decreased. The best overall evaluation - as driven by specificity - occurred at high elevation where species assemblages were shown to be under significant environmental filtering of small plants. In contrast, the decreased overall accuracy in the lowlands was associated with functional patterns representing any type of assembly rule (environmental filtering, limiting similarity or null assembly). Main Conclusions: Our study reveals interesting patterns of change in S-SDM errors with changes in assembly rules along elevation. Yet, significant levels of assemblage prediction errors occurred throughout the gradient, calling for further improvement of SDMs, e.g., by adding key environmental filters that act at fine scales and developing approaches to account for variations in the influence of predictors along environmental gradients.

Restricted gene flow at specific parts of the shrew genome in chromosomal hybrid zones.

The species and races of the shrews of the Sorex araneus group exhibit a broad range of chromosomal polymorphisms. European taxa of this group are parapatric and form contact or hybrid zones that span an extraordinary variety of situations, ranging from absolute genetic isolation to almost free gene flow. This variety seems to depend for a large part on the chromosome composition of populations, which are primarily differentiated by various Robertsonian fusions of a subset of acrocentric chromosomes. Previous studies suggested that chromosomal rearrangements play a causative role in the speciation process. In such models, gene flow should be more restricted for markers on chromosomes involved in rearrangements than on chromosomes common in both parent species. In the present study, we address the possibility of such differential gene flow in the context of two genetically very similar but karyotypically different hybrid zones between species of the S. araneus group using microsatellite loci mapped to the chromosome arm level. Interspecific genetic structure across rearranged chromosomes was in general larger than across common chromosomes. However, the difference between the two classes of chromosomes was only significant in the hybrid zone where the complexity of hybrids is expected to be larger. These differences did not distinguish populations within species. Therefore, the rearranged chromosomes appear to affect the reproductive barrier between karyotypic species, although the strength of this effect depends on the complexity of the hybrids produced.

Advanced geostatistical and machine-learning models for spatial data analysis of radioactively contaminated regions

Radioactive soil-contamination mapping and risk assessment is a vital issue for decision makers. Traditional approaches for mapping the spatial concentration of radionuclides employ various regression-based models, which usually provide a single-value prediction realization accompanied (in some cases) by estimation error. Such approaches do not provide the capability for rigorous uncertainty quantification or probabilistic mapping. Machine learning is a recent and fast-developing approach based on learning patterns and information from data. Artificial neural networks for prediction mapping have been especially powerful in combination with spatial statistics. A data-driven approach provides the opportunity to integrate additional relevant information about spatial phenomena into a prediction model for more accurate spatial estimates and associated uncertainty. Machine-learning algorithms can also be used for a wider spectrum of problems than before: classification, probability density estimation, and so forth. Stochastic simulations are used to model spatial variability and uncertainty. Unlike regression models, they provide multiple realizations of a particular spatial pattern that allow uncertainty and risk quantification. This paper reviews the most recent methods of spatial data analysis, prediction, and risk mapping, based on machine learning and stochastic simulations in comparison with more traditional regression models. The radioactive fallout from the Chernobyl Nuclear Power Plant accident is used to illustrate the application of the models for prediction and classification problems. This fallout is a unique case study that provides the challenging task of analyzing huge amounts of data ('hard' direct measurements, as well as supplementary information and expert estimates) and solving particular decision-oriented problems.

Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae).

BackgroundGenetic, phenotypic and ecological divergence within a lineage is the result of past and ongoing evolutionary processes, which lead ultimately to diversification and speciation. Integrative analyses allow linking diversification to geological, climatic, and ecological events, and thus disentangling the relative importance of different evolutionary drivers in generating and maintaining current species richness.ResultsHere, we use phylogenetic, phenotypic, geographic, and environmental data to investigate diversification in the Spanish sand racer (Psammodromus hispanicus). Phylogenetic, molecular clock dating, and phenotypic analyses show that P. hispanicus consists of three lineages. One lineage from Western Spain diverged 8.3 (2.9-14.7) Mya from the ancestor of Psammodromus hispanicus edwardsianus and P. hispanicus hispanicus Central lineage. The latter diverged 4.8 (1.5-8.7) Mya. Molecular clock dating, together with population genetic analyses, indicate that the three lineages experienced northward range expansions from southern Iberian refugia during Pleistocene glacial periods. Ecological niche modelling shows that suitable habitat of the Western lineage and P. h. edwardsianus overlap over vast areas, but that a barrier may hinder dispersal and genetic mixing of populations of both lineages. P. h. hispanicus Central lineage inhabits an ecological niche that overlaps marginally with the other two lineages.ConclusionsOur results provide evidence for divergence in allopatry and niche conservatism between the Western lineage and the ancestor of P. h. edwardsianus and P. h. hispanicus Central lineage, whereas they suggest that niche divergence is involved in the origin of the latter two lineages. Both processes were temporally separated and may be responsible for the here documented genetic and phenotypic diversity of P. hispanicus. The temporal pattern is in line with those proposed for other animal lineages. It suggests that geographic isolation and vicariance played an important role in the early diversification of the group, and that lineage diversification was further amplified through ecological divergence.