The effect on inferences of population size of the sampling scheme for intraspecific DNA sequences

Variation in samples of DNA sequences from within one species can be informative about the demographic processes that have affected that species, revealing signals of migration patterns and population size changes in the past. The demographic models that are fitted to the data might vary, as might the way the data are used, but one almost ubiquitous assumption is that the samples sequenced in the study are randomly chosen. Yet this is rarely plausible either because random sampling is practically impossible to perform or indeed because the samples for analysis are very consciously selected in some non-random way. This thesis explores the robustness of a particular flexible class of models used for inference of variable population size, the so-called skyline plot methods, to non-randomness of sampling by taking a simulation approach. The particular sampling scheme investigated takes sequences belonging to one subtree (or haplogroup) of the genealogy of a non-recombining locus. Pitfalls of analyses ignoring the sampling scheme are reported and a recommendation for the interpretation of such analyses is made. This work uses the Bayesian skyline plot model to infer population sizes and in simulation settings this model proves to be accurate in estimating population size as a function of time, from random samples. When a non-random sample defined by a haplogroup is analysed, the model can infer the shape of the population curve well but fails to capture the magnitude, when compared to the population curve inferred from a random sample or to the true population curve. Functional data analysis techniques were used to explore the relationship between the population curves inferred from random and non-random samples. After establishing that there is indeed a strong relationship between the two, the goal was to develop a straightforward post hoc correction to the inferred population curve from the non-random sample that is easy to apply and permits practitioners to allow for the violations of model assumptions caused by the non-random sample, so obtaining a more reliable estimate of population size. This is illustrated by applying the approach to samples of sequences taken from human mitochondrial DNA. The correction uses information on the prevalence of the mutation defining the non-random subtree

A Hidden Markov Movement Model for rapidly identifying behavioral states from animal tracks

Electronic telemetry is frequently used to document animal movement through time. Methods that can identify underlying behaviors driving specific movement patterns can help us understand how and why animals use available space, thereby aiding conservation and management efforts. For aquatic animal tracking data with significant measurement error, a Bayesian state‐space model called the first‐Difference Correlated Random Walk with Switching (DCRWS) has often been used for this purpose. However, for aquatic animals, highly accurate tracking data are now becoming more common. We developed a new hidden Markov model (HMM) for identifying behavioral states from animal tracks with negligible error, called the hidden Markov movement model (HMMM). We implemented as the basis for the HMMM the process equation of the DCRWS, but we used the method of maximum likelihood and the R package TMB for rapid model fitting. The HMMM was compared to a modified version of the DCRWS for highly accurate tracks, the DCRWS [Formula: see text] , and to a common HMM for animal tracks fitted with the R package moveHMM. We show that the HMMM is both accurate and suitable for multiple species by fitting it to real tracks from a grey seal, lake trout, and blue shark, as well as to simulated data. The HMMM is a fast and reliable tool for making meaningful inference from animal movement data that is ideally suited for ecologists who want to use the popular DCRWS implementation and have highly accurate tracking data. It additionally provides a groundwork for development of more complex modeling of animal movement with TMB. To facilitate its uptake, we make it available through the R package swim

Quality of life and deinstitutionalisation : an examination of the effects of relocating people with learning disabilities from hospital to life in the community

The quality of life for people with learning disabilities was examined for 50 people leaving hospital to live in a range of community residences and for 50 people remaining in hospital. Individuals were followed up for up to 30 months at six monthly intervals. The social validity of quality of life assessment was examined by comparing the importance of a number of service objectives to people with and without learning disabilities. This then informed the development of two measures used to assess aspects of quality of life. A range of measures were employed to address both objective and subjective dimensions of quality of life. Five main areas were identified and examined in two studies - competence and personal growth; health and well-being; quality of care; engagement in activity and staff resident interactions. The issues reflecting some of the difficulties in assessing subjective states of people with learning disabilities are discussed. Overall there was some relatively small changes in the areas of competence and personal growth, quality of care and staff interactions for people moving from hospital to live in the community. The changes tended to occur within six months of moving with little improvement thereafter. In general, there was no change for the people remaining in hospital. Implications for the detailed examination of the effects of deinstitutionalisation are discussed

Matamek annual report for 1978

This is a report describing activities associated with the Matamek program in 1978. Research was conducted on biological, chemical and physical factors related to salmonid production in Matamek River and Matamek Lake. Canadian universities, the Quebec government and Woods Hole Oceanographic Institution cooperated in this program .Supported by the Woods Hole Oceanographic Institution and the Department of Tourism, Fish and Game of the Province of Quebec

ETN Technical Standards Report

Development of technical standards for specific European lines and tagging projects in the form of a report

Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities

Establishment of adequate conservation areas represents a challenging but crucial task in the conservation of genetic diversity and biological variability. Anthropogenic pressures on marine ecosystems and organisms are steadily increasing. Whether and to what extent these pressures influence marine genetic biodiversity is only starting to be revealed. Using 16S rRNA gene amplicon sequencing, we analysed the microbial community structure of 33 individuals of the habitat-forming glass sponge Vazella pourtalesii, as well as reference seawater, sediment, and biofilm samples. We assessed how two anthropogenic impacts, i.e. habitat destruction by trawling and artificial substrate provision (moorings made of composite plastic), correspond with in situ V. pourtalesii microbiome variability. In addition, we evaluated the role of two bottom fishery closures in preserving sponge-associated microbial diversity on the Scotian Shelf, Canada. Our results illustrate that V. pourtalesii sponges collected from pristine sites within fishery closures contained distinct and taxonomically largely novel microbial communities. At the trawled site we recorded significant quantitative differences in distinct microbial phyla, such as a reduction in Nitrospinae in sponges and environmental references. Individuals of V. pourtalesii growing on the mooring were significantly enriched in Bacteroidetes, Verrucomicrobia and Cyanobacteria in comparison to sponge individuals growing on the natural seabed. Due to a concomitant enrichment of these taxa in the mooring biofilm, we propose that biofilms on artificial substrates may ‘prime’ sponge-associated microbial communities when small sponges settle on such substrates. These observations likely have relevant management implications when considering the increase of artificial substrates in the marine environment, e.g., marine litter, off-shore wind parks, and petroleum platforms

The breeding-season population structure of three sympatric, territorial sticklebacks (Pisces: Gasterosteidae)

Animals breeding only once late in life should spend most of the time during their one reproductive season attempting to reproduce. Contrary to this prediction, we found that the individuals of three species of sticklebacks (Pisces: Gasterosteidae) spent very short periods of time on their breeding ground. Tidal flooding of the site controlled patterns offish immigration and emigration. Inundations early in the breeding season brought in new immigrants which replaced most resident fish. However, towards the end of the breeding season there was less immigration and a higher percentage of the residents remained in their pools. We expected to see movements among pools by surplus males searching for sites to establish a territory; instead, few fish moved among pools, and most ofthose that did were females. A high energetic cost of breeding in this unstable habitat may best explain these residency patterns

Effects of recreational angling and air exposure on the physiological status and reflex impairment of European grayling (Thymallus thymallus)

European grayling (Thymallus thymallus) is a popular recreational fish that may be lifted out of the water to facilitate hook removal or for admiration. To evaluate the effects of air exposure and angling-induced exhaustive exercise on released grayling condition, we assessed blood physiology and reflexes of grayling after angling and air exposure in the subarctic River Lakselva (Norway) at midsummer temperatures (i.e., 17–18 °C). Blood samples were drawn 30 min after angling and analyzed for lactate anions, glucose, sodium ions, and pH. Reflex impairment was determined with orientation and tail grab reflex action assessments immediately after landing, after air exposure, and after 30 min holding. Blood physiology did not indicate an exacerbating effect of air exposure relative to just angling-induced exercise, but significant and prolonged reflex impairment was associated with the 120 s air exposure interval. Anglers must take care to minimize air exposure to adhere to best handling practices.publishedVersio