Gene flow at a snail\u27s pace: phylogeography and conservation genetics of relict populations of the Iowa Pleistocene snail

The Iowa Pleistocene snail, Discus macclintocki, is a federally endangered land snail found only in northeast Iowa and northwestern Illinois. This species is believed to be a glacial relict with populations isolated for the last 16,000 years. In this study, I investigated the amount of genetic variation within, and the gene flow among, ten isolated populations of the Iowa Pleistocene snail, Discus macclintocki (Baker). I sequenced part of the 16s region of the mitochondrial DNA from 175 snails. Populations clustered clearly by watershed, suggesting that flooding events may have been the historical avenue of gene flow rather than overland dispersal. On a single small watershed, Buck Creek, individuals could not reliably be assigned to their population, suggesting that either gene flow is still occurring or the populations have not been separated as long as the others. Within populations, an extremely high amount of variation was observed. Polymorphism was very high, with up to seven haplotypes per population;The high level of genetic variation observed is not purely a population size effect, as polymorphism was not related to size estimates determined in a mark-recapture study I conducted. Population sizes were estimated at fourteen sites using standard mark-recapture analyses, as well as Bayesian estimates, which account for small sample sizes. Discus macclintocki has a very high mutation rate and seems to have a very healthy amount of genetic variation. When the number of variable sites in 16s rDNA was compared among species in a variety of taxonomic groups, snails showed an extremely high level of variability;Although I only investigated mitochondrial genetic variation in Discus macclintocki, many organisms have been examined for variation in the nuclear genome as well. These studies sometimes give conflicting results of how much variation is present within a population. One potential reason for differences in levels of nuclear variation and mitochondrial variation is due to differential dispersal rates and/or dispersal distances between the sexes. These ideas are explored through an analysis of data from the literature

Quantifying sample completeness and comparing diversities among assemblages.

We develop a novel class of measures to quantify sample completeness of a biological survey. The class of measures is parameterized by an order q ≥ 0 to control for sensitivity to species relative abundances. When q = 0, species abundances are disregarded and our measure reduces to the conventional measure of completeness, that is, the ratio of the observed species richness to the true richness (observed plus undetected). When q = 1, our measure reduces to the sample coverage (the proportion of the total number of individuals in the entire assemblage that belongs to detected species), a concept developed by Alan Turing in his cryptographic analysis. The sample completeness of a general order q ≥ 0 extends Turing's sample coverage and quantifies the proportion of the assemblage's individuals belonging to detected species, with each individual being proportionally weighted by the (q − 1)th power of its abundance. We propose the use of a continuous profile depicting our proposed measures with respect to q ≥ 0 to characterize the sample completeness of a survey. An analytic estimator of the diversity profile and its sampling uncertainty based on a bootstrap method are derived and tested by simulations. To compare diversity across multiple assemblages, we propose an integrated approach based on the framework of Hill numbers to assess (a) the sample completeness profile, (b) asymptotic diversity estimates to infer true diversities of entire assemblages, (c) non‐asymptotic standardization via rarefaction and extrapolation, and (d) an evenness profile. Our framework can be extended to incidence data. Empirical data sets from several research fields are used for illustration.publishedVersionPaid Open Acces

Utilisation des caméras de piégeage et des modèles de capture-recapture pour l'estimation des densités de chimpanzés d'Afrique occidentale (Pan troglodytes verus) en Côte d'Ivoire

Des estimations de densité exactes et précises sont indispensables pour évaluer les effets des menaces spécifiques sur une espèce, mesurer le succès de décisions de conservation, et pour comprendre l'écologie des populations animales. La méthode des caméras de piégeage, combinée aux modèles de capture-recapture (C-R), a récemment été mise au point pour surmonter les limitations des techniques conventionnelles d'inventaire des populations de grands singes. Cependant, aucune validation de la méthode n'a été réalisée à ce jour. Dans cette étude, je vise à valider l'utilisation de caméras de piégeage en combinaison avec les modèles de C-R pour estimer les densités de chimpanzés d'Afrique occidentale (Pan troglodytes verus). Plus précisément, je vise à identifier : 1) quelle est la meilleure méthode de C-R pour estimer les densités de chimpanzés par caméras de piégeage, 2) quel est l'effort de piégeage minimum requis pour des estimations de densités exactes et précises, et 3) si un placement aléatoire des caméras peut donner des mesures de densité fiables et robustes. Afin de répondre à ces trois objectifs, j'ai mené une étude de caméras de piégeage de 10 mois sur le territoire d'une communauté de chimpanzés habituée à la présence humaine, et donc où la densité totale de chimpanzés est déjà connue. Les caméras ont été placées selon deux placements différents : systématiquement, où les caméras ont été installées à chaque kilomètre, ou stratégiquement, à des endroits fréquemment visités par les chimpanzés. Les résultats montrent que tous les modèles de C-R ont donné des estimations de densité plus exactes et plus précises que les autres méthodes couramment utilisées pour le recensement des populations de grands singes. Les chimpanzés avaient deux fois plus de chances d'être filmés par les caméras placées de façon stratégique, mais les densités issues des caméras systématiques étaient aussi précises et robustes. Ainsi, cette étude met l'accent sur la pertinence des caméras de piégeage et des modèles de C-R comme outils de surveillance des populations des grands singes.\ud ______________________________________________________________________________ \ud MOTS-CLÉS DE L’AUTEUR : caméras de piégeage, chimpanzés, pan troglodytes verus, suivi, densité, capture-marquage-recapture, modèles spatiaux de capture-marquage-recapture, Côte d'Ivoire

Estimation de la taille de la population dans les expériences de capture-recapture

La thèse présentée ici traite du problème de l'estimation de la taille de la population dans les modèles de capture-recapture. Elle s'intéresse, en particulier, à la question de l'estimation de la taille de la population dans le cadre d'une expérience de capture-recapture à structure d'échantillonnage imbriquée, qui combine les méthodes de population fermée à l'intérieur des périodes primaires (PP) et de population ouverte d'une PP à une autre : le design robuste. Cette thèse propose une méthodologie d'estimation de la taille de la population et de l'incertitude associée aux estimateurs obtenus dans le contexte du design robuste. Dans un premier temps, on aborde le problème de l'estimation des paramètres du design robuste dans le cas d'un nombre suffisamment élevé d'occasions de capture. On généralise le papier fondamental de Jolly (1965) au design robuste en proposant une procédure séquentielle d'estimation des paramètres pour la classe des modèles de design robuste présentés dans Rivest and Daigle (2004) et un estimateur de la variance des paramètres par bootstrap paramétrique. Ces résultats théoriques ont été appliqués à des données d'activation d'applications sur les téléphones intelligents. Les données sont recueillies sur une période d'un an et demi et concernent des utilisateurs de téléphones intelligents qui ont visité un grand concessionnaire automobile basé aux États-Unis. Dans un deuxième temps, on s'intéresse à l'estimation de la taille de la population à partir de deux sources d'information du design robuste: les données à l'intérieur d'une PP (ou intra-période) et les données d'une PP à une autre (ou inter-période). On démontre que les estimateurs de la taille de la population obtenus avec les informations intra-période et inter-période sont asymptotiquement indépendants pour une large classe de modèles de population fermée à l'intérieur des PP. Ainsi, l'estimateur du maximum de vraisemblance pour la taille de la population dans le cas du design robuste est asymptotiquement équivalent à un estimateur pondéré pour le modèle de population ouverte et le modèle de population fermée. On montre que l'estimateur pondéré diffère de celui donné dans Kendall et al. (1995); on démontre que leur estimateur n'est pas efficace, puis on donne une formule explicite pour son efficacité comparativement à l'estimateur pondéré. La perte d'efficacité est ensuite évaluée dans une étude de simulation, puis à travers un exemple tiré de Santostasi et al. (2016) et qui traite de l'estimation de la taille de la population d'une espèce de dauphins vivant dans le Golfe de Corinthe (Grèce). Enfin, on se propose d'étendre les résultats du problème précédent aux modèles de design robuste présentés dans Kendall et al. (1995) et implémentés dans MARK (White and Burnham, 1999). Dans le contexte du design robuste, on dérive l'estimateur du maximum de vraisemblance pour la taille de la population; on propose également trois méthodes d'estimation de la variance de l'erreur associée à l'estimateur. On démontre ensuite que l'estimateur du maximum de vraisemblance pour la taille de la population est plus efficace que l'estimateur des moments proposé par Kendall et al. (1995); la perte d'efficacité de l'estimateur de Kendall ainsi que la performance des trois méthodes d'estimation de la variance de l'erreur associée à l'estimateur du maximum de vraisemblance sont évaluées via une étude de simulation.This thesis deals with the capture-recapture estimation of population sizes under a hierarchical study design where a capture-recapture experiment, involving secondary capture occasions, is carried out within each sampling period (SP) of an open population model: the robust design. This thesis proposes a methodology for the estimation of population sizes under the robust design and the uncertainty associated with the estimators. The first problem deals with the estimation of the parameters of a robust design with an arbitrary large number of capture occasions. To do so, we generalize the seminal paper of Jolly (1965) to the robust design and propose a sequential estimation procedure for the class of robust design models presented in Rivest and Daigle (2004). A simple parametric bootstrap variance estimator for the model parameters is also proposed. These results are used to analyze a data set about the mobile devices that visited the auto-dealerships of a major auto brand in a US metropolitan area over a period of one year and a half. The second problem deals with the estimation of population sizes using two sources of information for the robust design: the within and the between primary period data. We prove that the population size estimators derived from the two sources are asymptotically independent for a large class of closed population models. In this context, the robust design maximum likelihood estimator of population size is shown to be asymptotically equivalent to a weighted sum of the estimators for the open population Jolly-Seber model (Jolly 1965; Seber 1965) and for the closed population model. This article shows that the weighted estimator is more efficient than the moment estimator of Kendall et al.(1995). A closed form expression for the efficiency associated with this estimator is given and the loss of precision is evaluated in a MonteCarlo study and in a numerical example about the estimation of the size of dolphin populations living in the Gulf of Corinth (Greece) and discussed by Santostasi et al. (2016). The third problem deals with the estimation of population sizes under the robust design models presented in Kendall et al. (1995) and implemented in MARK (White and Burnham, 1999). We derive the maximum likelihood estimator for the population size and propose three methods of estimation for its uncertainty. We prove that the derived maximum likelihood estimator is more efficient than the moment estimator provided in Kendall et al. (1995). The loss of precision associated with the Kendall estimator and the performance of the three methods of estimation for the variance of the maximum likelihood estimator are evaluated in a MonteCarlo study

Habitat mosaic and understory bird communities in Mexican cloud forest

Cloud forest is one of the most threatened ecosystems in Mexico and is important for its high biological diversity and for the ecological services that it provides. The Mexican cloud forests (CF) have been fragmented as a result of anthropogenic activities and deforestation. The south of Mexico contains almost 30% of the country's cloud forest, only a small proportion of which is protected in nature reserves. Conservation effort needs to be focused on the ecological value of agroecosystems that surround nature reserves. The study areas are located in the south of Mexico. Two are in the El Triunfo biosphera reserve in la Sierra Madre de Chiapas, and one is located in the central Region Mountains of Veracruz. The coffee is cultivated in transitional areas between natural forest and adjoining land systems. Based on the type of management, the structure and vegetation, it is possible to distinguish five main coffee production systems: two traditional shaded agroforests (with native trees), one commercially oriented polyspecific shaded system (where several fruit trees are used as shade), and two "modern" systems shaded (Inga) and unshaded monocultures (sun coffee). This research attempts to explain the effects of cloud forest patches (natural forest and coffee plantations) on bird diversity.Bird communities have been surveyed in 4 habitat types by point counts and mist-net techniques. The surveys were taken across a gradient from extensive primary and relatively undisturbed forest to intensive agricultural land uses (coffee plantations). Patterns of bird populations (species richness, abundance, density and community composition) and patch characteristics (size, altitudinal range, and topographic complexity) were analysed over this gradient.Of a total of 4560 birds recorded in point counts, there were 294 species, 168 genera and 41 families. In the patches of CF, from a total of 256 bird species, 36 were migratory and 53 have some status of conservation. In the patches of coffee plantations from a total of 159 species, 49 were migratory and 52 were under some status of conservation. Forest habitats, including continuous and patch forests, and shade coffee plantations, are found to support the most species and individuals. Nearctic-Neotropical migratory species are most numerous in shade coffee. Bird communities in shade coffee (natural and Inga) are characterised by a higher proportion of frugivorous and nectarivorous species, than communities in native forests. Using mist-net techniques, a total of 105 species, 87 genera and 23 families of birds were captured in 1600 net/hours for all the habitats.The size of forest patch is the main characteristic affecting forest interior and generalist species. Decreasing forest patch sizes appears to have unfavourable effects on forest generalist birds and positive effects on forest border species. The bird species most sensitive to forest fragmentation are those species restricted to the forest interior. The species richness and abundance demonstrate that many human-altered habitats are potentially valuable for birds. Further conservation efforts in tropical areas need to give more attention to the significance of agricultural lands as wildlife habitats

The diversity of flower-visiting insects in the gardens of English country houses

Flower-visiting insects provide essential pollination services, ensuring both global food security and the continuity of wild plants. Recently documented declines in pollinators give cause for concern. Identifying previously unappreciated habitats that support diverse assemblages of these insects is an essential first step in mitigating further losses. This study evaluates, for the first time, the role that large English country-house gardens play in supporting flower visitors within expanses of intensively farmed agricultural land. Focussing on 17 properties in lowland Central England, the results show that these novel ecosystems are important sites for hoverflies, bees and butterflies. In 2010 almost 10,000 flower-visitors from 174 species were recorded Hoverflies were the only group to show a significant difference in species richness across the sites. An important characteristic of these rural gardens is the high diversity of flowering plants available. More than a fifth of the world's plant families were represented, of which approximately 68% were non-native. The results showed that flower visitors did not prefer native plants over aliens, and that the dominance by aliens was no barrier for extensive use by the insects present. Both the species richness and abundance of flower visitors increased as plant richness increased. The study revealed that half of all insect-plant interaction networks examined exhibited a nested structure, a common feature of natural environments that has not previously been assessed in rural gardens. In addition to flower resources influencing insect species richness, landscape-scale effects were also significant. Insect groups responded differently to components in the landscape according to the time of year and the spatial scale considered. Bumblebees exhibited the greatest response to landscape factors and did so at larger scales than other groups. The deployment of commercial trap-nests for solitary cavity-nesting red mason bees in walled gardens revealed new insights into the differential mortality suffered by male and female progeny. Female offspring were found to be disproportionately affected by a combination of development and parasitism losses. This finding suggests that effective mitigation strategies are needed before this species can be considered for use as a managed-pollinator. Further research assessing the benefits crops such as oilseed rape derive from the presence of insects in nearby rural gardens would be a useful addition to this work. Overall, the gardens of English country-houses emerge as sites of important natural as well as cultural heritage

An extension of Chao's estimator of population size based on the first three capture frequency counts

A new estimator for estimating the size of an elusive target population is presented using frequency counts from capture-recapture sampling. The proposed estimator is developed by extending the idea of Chao's estimator using monotonicity of ratios of neighbouring frequency counts under a specific Poisson mixture sampling framework, the Poisson-Gamma mixture or negative binomial. The new estimator is achieved using a simple linear model on the basis of the log-ratio of neighbouring frequency counts as dependent variable which is valid under the Poisson-Gamma mixture. A simulation study is provided to study the performance of the proposed estimator under a variety of heterogeneous Poisson capture probabilities. Confidence interval estimation is done by means of an approximating normal approach and a modified bootstrap method, and was found to perform well. A variety of real data sets were also examined in order to illustrate the use of the proposed method.Estimation of population size Capture-recapture methods Horvitz-Thompson estimator Chao's estimator Homogeneous and heterogeneous Poisson models Negative binomial

Doctor of Philosophy

dissertationIn Panama, a high level of spatial turnover in tree species is correlated with a rainfall gradient. Seasonal drought is known to exclude tree species typical of wetter forests from drier forests; however, the factors contributing to the converse are ambiguous. This dissertation research experimentally tested the hypothesis that pathogens attacking seedlings contribute to the exclusion of dry-forest tree species from wetter forests. We tested two related hypotheses: that the phytopathogens attacking seedlings are (i) geographically widespread and (ii) host generalists. To test if pathogens exclude dry-forest species from wetter forests, wet- and dry-forest tree species were planted in wetter and drier forests in Panama and monitored for pathogen-caused damage and mortality. Seedlings suffered more pathogen-caused damage and mortality in the wetter forest, while dry-forest tree species suffered a greater impact from pathogen attack than wet-forest species. Together, these results support our hypothesis. Next, fungi isolated from symptomatic seedlings were identified using molecular techniques and phylogenetic analyses. We observed 28 fungal species and found that, while diversity was greater in the wetter forest, one-third of the observed fungal species were found in both the wetter and drier forests. This suggests that some phytopathogens are geographically widespread and that the elevated impact from pathogens in wetter forests may not be the result of different pathogen communities. Finally, we surveyed the tree species in which potential phytopathogens occurred and used inoculation experiments to assess the pathogenicity and host ranges of the potential phytopathogens. Most of the potential phytopathogens were isolated from multiple, phylogenetically distant families of trees. Similarly, in the experiments, phytopathogens were able to attack phylogenetically distant tree species. Tree species were differentially vulnerable to attack, suggesting that these generalist phytopathogens can influence plant community composition. While specialist phytopathogens have received considerable attention for their role in the maintenance of local diversity, this work highlights the underappreciated effect of generalist pathogens on regional diversity, represents one of the few studies to experimentally assess the host ranges of seedling pathogens in the tropics, and provides the first estimate of the taxonomy, diversity, and spatial structure of tropical phytopathogens at the landscape scale

The implications of fynbos phytogeography for wetland photoassessment

The initial focus of the present study was intended to develop phyto-assessment tools for the evaluation of the environmental condition of lowland wetlands in the Fynbos biome of the South Western Cape of South Africa. A field survey and analysis of freshwater wetland vegetation across the Cape coastal lowlands (below 200m a.s.l.) was undertaken in the present study to explore the potential to identify aspects of the vegetation that could serve as indicators of the present environmental state within wetlands. The Braun Blanquet approach was employed for the vegetation sampling of 59 wetlands in three subregions of the coastal lowlands of the Fynbos biome