Échantillonnage et modélisation de l’habitat des communautés de poissons de rivière des basses Laurentides

Plusieurs études à grande échelle ont identifié la modification ou la perte d’habitats comme menace principale à la conservation des communautés de poissons d’eau douce. Au Canada, « aucune perte nette dans la capacité productive des habitats » (NNL) est le principe directeur de la politique de gestion des habitats du ministère des Pêches et Océans. Le respect du NNL implique l’avancement des connaissances au niveau des relations entre les poissons et leurs habitats, de même que des outils pour quantifier l’impact de la modification des habitats sur les poissons. Les modèles d’utilisation de l’habitat des poissons (FHUM) sont des outils qui permettent d’améliorer nos connaissances des relations poissons – habitat, de prédire la distribution des espèces, mais aussi leurs densités, biomasses ou abondances, sur la base des caractéristiques de l’environnement. L’objectif général de mon mémoire est d’améliorer la performance des FHUM pour les rivières des basses Laurentides, en suggérant des perfectionnements au niveau de 2 aspects cruciaux de l’élaboration de tels modèles : la description précise de la communauté de poissons et l’utilisation de modèles statistiques efficaces. Dans un premier chapitre, j’évalue la performance relative de la pêcheuse électrique et de l’échantillonnage en visuel (plongée de surface) pour estimer les abondances des combinaisons d’espèces et de classes de taille des poissons en rivière. J’évalue aussi l’effet des conditions environnementales sur les différences potentielles entre les communautés observées par ces 2 méthodes d’échantillonnage. Pour ce faire, 10 sections de rivière de 20 m de longueur ont été échantillonnées à l’aide de ces 2 méthodes alors qu’elles étaient fermées par des filets de blocage. 3 plongeurs performèrent l’échantillonnage en visuel en se déplaçant de l’aval vers l’amont des sections, tout en dénombrant les espèces et classes de taille. Par la suite, nous avons fait 3 passages de pêcheuse électrique et les abondances furent estimées grâce à un modèle restreint de maximum de vraisemblance, basé sur la diminution des abondances observées. De plus grandes abondances de poissons furent observées en visuel qu’avec la pêcheuse électrique à tous les sites. La richesse spécifique observée en visuel était plus élevée (6/10) ou égale (4/10) à celle observée avec la pêcheuse électrique. Les différences entre les communautés de poissons observées à l’aide de ces 2 méthodes ne purent être reliées aux conditions environnementales. Les résultats de cette expérience sont contraires à ceux de toutes les études comparant ces 2 méthodes d’échantillonnage, lesquels suggèrent une supériorité de la pêcheuse électrique. Les conditions environnementales de notre expérience étaient distinctes de celles observées dans les autres études (absence d’arbres tombés dans l’eau, très peu de substrats grossiers), mais la différence la plus marquante était en terme de communauté de poissons observée (dominance des cyprinidés et des centrarchidés plutôt que des salmonidés). Je termine ce chapitre en suggérant que les caractéristiques comportementales favorisant l’évitement de la capture (formation de bancs) et facilitant l’observation en visuel (curiosité) sont responsables de la supériorité de la plongée de surface pour échantillonner les communautés dans les rivières des basses Laurentides. Dans un deuxième chapitre, je développe des FHUM pour des communautés de poissons de rivière ayant plusieurs espèces. Dans le but de simplifier la modélisation de telles communautés et d’améliorer notre compréhension des relations poissons – habitat, j’utilise les concepts de guilde écologique et de filtre environnemental pour explorer les relations entre les guildes formées sur la bases de différents types de traits (reproducteurs, taxonomiques, éco-morphologiques et alimentaires) et les conditions environnementales locales à l’échelle du méso-habitat. Les modèles d’habitats basés sur les guildes reproductrices ont clairement surpassé les autres modèles, parce que l’habitat de fraie reflète l’habitat de préférence en dehors de la période de reproduction. J’ai également utilisé l’approche inverse, c’est à dire définir des guildes d’utilisation de l’habitat et les mettre en relation avec les traits des espèces. Les traits reliés à l’alimentation des poissons ont semblés être les meilleurs pour expliquer l’appartenance aux groupes d’utilisation de l’habitat, mais le modèle utilisé ne représentait pas bien la relation entre les groupes. La validation de notre modèle basé sur les guildes reproductrices avec un jeu de données indépendant pourrait confirmer notre découverte, laquelle représente une manière prometteuse de modéliser les relations poissons – environnement dans des communautés de poissons complexes. En conclusion, mon mémoire suggère d’importantes améliorations aux FHUM pour les communautés de poissons des basses Laurentides, en suggérant de prendre en compte les caractéristiques biologiques des cours d’eau dans le choix d’une méthode d’échantillonnage, et également en utilisant une méthode prometteuse pour simplifier les FHUM de communautés de poissons complexes : les guildes reproductrices.

The effects of habitat fragmentation on the demography and population genetic structure of Uromys Caudimaculatus

Habitat fragmentation can have an impact on a wide variety of biological processes including abundance, life history strategies, mating system, inbreeding and genetic diversity levels of individual species. Although fragmented populations have received much attention, ecological and genetic responses of species to fragmentation have still not been fully resolved. The current study investigated the ecological factors that may influence the demographic and genetic structure of the giant white-tailed rat (Uromys caudimaculatus) within fragmented tropical rainforests. It is the first study to examine relationships between food resources, vegetation attributes and Uromys demography in a quantitative manner. Giant white-tailed rat densities were strongly correlated with specific suites of food resources rather than forest structure or other factors linked to fragmentation (i.e. fragment size). Several demographic parameters including the density of resident adults and juvenile recruitment showed similar patterns. Although data were limited, high quality food resources appear to initiate breeding in female Uromys. Where data were sufficient, influx of juveniles was significantly related to the density of high quality food resources that had fallen in the previous three months. Thus, availability of high quality food resources appear to be more important than either vegetation structure or fragment size in influencing giant white-tailed rat demography. These results support the suggestion that a species’ response to fragmentation can be related to their specific habitat requirements and can vary in response to local ecological conditions. In contrast to demographic data, genetic data revealed a significant negative effect of habitat fragmentation on genetic diversity and effective population size in U. caudimaculatus. All three fragments showed lower levels of allelic richness, number of private alleles and expected heterozygosity compared with the unfragmented continuous rainforest site. Populations at all sites were significantly differentiated, suggesting restricted among population gene flow. The combined effects of reduced genetic diversity, lower effective population size and restricted gene flow suggest that long-term viability of small fragmented populations may be at risk, unless effective management is employed in the future. A diverse range of genetic reproductive behaviours and sex-biased dispersal patterns were evident within U. caudimaculatus populations. Genetic paternity analyses revealed that the major mating system in U. caudimaculatus appeared to be polygyny at sites P1, P3 and C1. Evidence of genetic monogamy, however, was also found in the three fragmented sites, and was the dominant mating system in the remaining low density, small fragment (P2). High variability in reproductive skew and reproductive success was also found but was less pronounced when only resident Uromys were considered. Male body condition predicted which males sired offspring, however, neither body condition nor heterozygosity levels were accurate predictors of the number of offspring assigned to individual males or females. Genetic spatial autocorrelation analyses provided evidence for increased philopatry among females at site P1, but increased philopatry among males at site P3. This suggests that male-biased dispersal occurs at site P1 and female-biased dispersal at site P3, implying that in addition to mating systems, Uromys may also be able to adjust their dispersal behaviour to suit local ecological conditions. This study highlights the importance of examining the mechanisms that underlie population-level responses to habitat fragmentation using a combined ecological and genetic approach. The ecological data suggested that habitat quality (i.e. high quality food resources) rather than habitat quantity (i.e. fragment size) was relatively more important in influencing giant white-tailed rat demographics, at least for the populations studied here . Conversely, genetic data showed strong evidence that Uromys populations were affected adversely by habitat fragmentation and that management of isolated populations may be required for long-term viability of populations within isolated rainforest fragments.

HABITAT : a longitudinal multilevel study of physical acitvity change in mid-aged adults

Purpose. To explore the role of the neighborhood environment in supporting walking Design. Cross sectional study of 10,286 residents of 200 neighborhoods. Participants were selected using a stratified two-stage cluster design. Data were collected by mail survey (68.5% response rate). Setting. The Brisbane City Local Government Area, Australia, 2007. Subjects. Brisbane residents aged 40 to 65 years. Measures. Environmental: street connectivity, residential density, hilliness, tree coverage, bikeways, and street lights within a one kilometer circular buffer from each resident’s home; and network distance to nearest river or coast, public transport, shop, and park. Walking: minutes in the previous week categorized as < 30 minutes, ≥ 30 < 90 minutes, ≥ 90 < 150 minutes, ≥ 150 < 300 minutes, and ≥ 300 minutes. Analysis. The association between each neighborhood characteristic and walking was examined using multilevel multinomial logistic regression and the model parameters were estimated using Markov chain Monte Carlo simulation. Results. After adjustment for individual factors, the likelihood of walking for more than 300 minutes (relative to <30 minutes) was highest in areas with the most connectivity (OR=1.93, 99% CI 1.32-2.80), the greatest residential density (OR=1.47, 99% CI 1.02-2.12), the least tree coverage (OR=1.69, 99% CI 1.13-2.51), the most bikeways (OR=1.60, 99% CI 1.16-2.21), and the most street lights (OR=1.50, 99% CI 1.07-2.11). The likelihood of walking for more than 300 minutes was also higher among those who lived closest to a river or the coast (OR=2.06, 99% CI 1.41-3.02). Conclusion. The likelihood of meeting (and exceeding) physical activity recommendations on the basis of walking was higher in neighborhoods with greater street connectivity and residential density, more street lights and bikeways, closer proximity to waterways, and less tree coverage. Interventions targeting these neighborhood characteristics may lead to improved environmental quality as well as lower rates of overweight and obesity and associated chromic disease.

Neighborhood disadvantage and physical activity : baseline results from the HABITAT multilevel longitudinal study

PURPOSE: To examine the association between neighborhood disadvantage and physical activity (PA). ---------- METHODS: We use data from the HABITAT multilevel longitudinal study of PA among mid-aged (40-65 years) men and women (n=11, 037, 68.5% response rate) living in 200 neighborhoods in Brisbane, Australia. PA was measured using three questions from the Active Australia Survey (general walking, moderate, and vigorous activity), one indicator of total activity, and two questions about walking and cycling for transport. The PA measures were operationalized using multiple categories based on time and estimated energy expenditure that were interpretable with reference to the latest PA recommendations. The association between neighborhood disadvantage and PA was examined using multilevel multinomial logistic regression and Markov Chain Monte Carlo simulation. The contribution of neighborhood disadvantage to between-neighborhood variation in PA was assessed using the 80% interval odds ratio. ---------- RESULTS: After adjustment for sex, age, living arrangement, education, occupation, and household income, reported participation in all measures and levels of PA varied significantly across Brisbane’s neighborhoods, and neighborhood disadvantage accounted for some of this variation. Residents of advantaged neighborhoods reported significantly higher levels of total activity, general walking, moderate, and vigorous activity; however, they were less likely to walk for transport. There was no statistically significant association between neighborhood disadvantage and cycling for transport. In terms of total PA, residents of advantaged neighborhoods were more likely to exceed PA recommendations. ---------- CONCLUSIONS: Neighborhoods may exert a contextual effect on residents’ likelihood of participating in PA. The greater propensity of residents in advantaged neighborhoods to do high levels of total PA may contribute to lower rates of cardiovascular disease and obesity in these areas

Off-world robotic excavation for Large-scale habitat construction and resource extraction

This paper describes technologies we have developed to perform autonomous large-scale off-world excavation. A scale dragline excavator of size similar to that required for lunar excavation was made capable of autonomous control. Systems have been put in place to allow remote operation of the machine from anywhere in the world. Algorithms have been developed for complete autonomous digging and dumping of material taking into account machine and terrain constraints and regolith variability. Experimental results are presented showing the ability to autonomously excavate and move large amounts of regolith and accurately place it at a specified location.

Predicting loss and fragmentation of habitat of the vulnerable subtropical rainforest tree Macadamia integrifolia with models developed from compiled ecological data

Habitat models are widely used in ecology, however there are relatively few studies of rare species, primarily because of a paucity of survey records and lack of robust means of assessing accuracy of modelled spatial predictions. We investigated the potential of compiled ecological data in developing habitat models for Macadamia integrifolia, a vulnerable mid-stratum tree endemic to lowland subtropical rainforests of southeast Queensland, Australia. We compared performance of two binomial models—Classification and Regression Trees (CART) and Generalised Additive Models (GAM)—with Maximum Entropy (MAXENT) models developed from (i) presence records and available absence data and (ii) developed using presence records and background data. The GAM model was the best performer across the range of evaluation measures employed, however all models were assessed as potentially useful for informing in situ conservation of M. integrifolia, A significant loss in the amount of M. integrifolia habitat has occurred (p < 0.05), with only 37% of former habitat (pre-clearing) remaining in 2003. Remnant patches are significantly smaller, have larger edge-to-area ratios and are more isolated from each other compared to pre-clearing configurations (p < 0.05). Whilst the network of suitable habitat patches is still largely intact, there are numerous smaller patches that are more isolated in the contemporary landscape compared with their connectedness before clearing. These results suggest that in situ conservation of M. integrifolia may be best achieved through a landscape approach that considers the relative contribution of small remnant habitat fragments to the species as a whole, as facilitating connectivity among the entire network of habitat patches.

The influence of habitat heterogeneity on patterns of connectivity among rabbit populations in southern Queensland

Patterns of connectivity among local populations influence the dynamics of regional systems, but most ecological models have concentrated on explaining the effect of connectivity on local population structure using dynamic processes covering short spatial and temporal scales. In this study, a model was developed in an extended spatial system to examine the hypothesis that long term connectivity levels among local populations are influenced by the spatial distribution of resources and other habitat factors. The habitat heterogeneity model was applied to local wild rabbit populations in the semi-arid Mitchell region of southern central Queensland (the Eastern system). Species' specific population parameters which were appropriate for the rabbit in this region were used. The model predicted a wide range of long term connectivity levels among sites, ranging from the extreme isolation of some sites to relatively high interaction probabilities for others. The validity of model assumptions was assessed by regressing model output against independent population genetic data, and explained over 80% of the variation in the highly structured genetic data set. Furthermore, the model was robust, explaining a significant proportion of the variation in the genetic data over a wide range of parameters. The performance of the habitat heterogeneity model was further assessed by simulating the widely reported recent range expansion of the wild rabbit into the Mitchell region from the adjacent, panmictic Western rabbit population system. The model explained well the independently determined genetic characteristics of the Eastern system at different hierarchic levels, from site specific differences (for example, fixation of a single allele in the population at one site), to differences between population systems (absence of an allele in the Eastern system which is present in all Western system sites). The model therefore explained the past and long term processes which have led to the formation and maintenance of the highly structured Eastern rabbit population system. Most animals exhibit sex biased dispersal which may influence long term connectivity levels among local populations, and thus the dynamics of regional systems. When appropriate sex specific dispersal characteristics were used, the habitat heterogeneity model predicted substantially different interaction patterns between female-only and combined male and female dispersal scenarios. In the latter case, model output was validated using data from a bi-parentally inherited genetic marker. Again, the model explained over 80% of the variation in the genetic data. The fact that such a large proportion of variability is explained in two genetic data sets provides very good evidence that habitat heterogeneity influences long term connectivity levels among local rabbit populations in the Mitchell region for both males and females. The habitat heterogeneity model thus provides a powerful approach for understanding the large scale processes that shape regional population systems in general. Therefore the model has the potential to be useful as a tool to aid in the management of those systems, whether it be for pest management or conservation purposes.

Molecular phylogeny, biogeography, and habitat preference evolution of marsupials

Marsupials exhibit great diversity in ecology and morphology. However, compared to their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene, and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

Temporal and spatial distribution and habitat associations of an urban population of New Zealand long-tailed bats (Chalinolobus tuberculatus)

Two ultrasound survey methods were used to determine the presence and activity patterns of New Zealand long-tailed bats (Chalinolobus tuberculatus) in the city of Hamilton. First, 13 monthly surveys conducted at 18 green spaces found C. tuberculatus in only one urban forest reserve, Hammond Bush, where they were found consistently throughout the year. Bat activity was strongly related to temperature. Second, twice-yearly citywide surveys conducted over 2 years determined the distribution and habitat associations of C. tuberculatus. Bats were found only in the southern part of the city and were strongly associated with the Waikato River. Bat activity was negatively correlated with housing and street light density and positively correlated with topographical complexity. In Hamilton, topographical complexity indicates the presence of gullies. Gullies probably provide foraging and roosting opportunities and connect the river to distant forest patches. These results suggest that urban habitats can be useful for bats if gullies can link these to distant habitat fragments.

Home range and habitat selection by a threatened bat in exotic plantation forest

Individuals' home ranges are constrained by resource distribution and density, population size, and energetic requirements. Consequently, home ranges and habitat selection may vary between individuals of different sex and reproductive conditions. Whilst home ranges of bats are well-studied in native habitats, they are often not well understood in modified landscapes, particularly exotic plantation forests. Although Chalinolobus tuberculatus (Vespertilionidae, Chiroptera) are present in plantation forests throughout New Zealand their home ranges have only been studied in native forest and forest-agricultural mosaic and no studies of habitat selection that included males had occurred in any habitat type. Therefore, we investigated C. tuberculatus home range and habitat selection within exotic plantation forest. Home range sizes did not differ between bats of different reproductive states. Bats selected home ranges with higher proportions of relatively old forest than was available. Males selected edges with open unplanted areas within their home ranges, which females avoided. We suggest males use these edges, highly profitable foraging areas with early evening peaks in invertebrate abundance, to maintain relatively low energetic demands. Females require longer periods of invertebrate activity to fulfil their needs so select older stands for foraging, where invertebrate activity is higher. These results highlight additional understanding gained when data are not pooled across sexes. Mitigation for harvest operations could include ensuring that areas suitable for foraging and roosting are located within a radius equal to the home range of this bat species.