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Teleost fish scales form distinct growth rings deposited in proportion to somatic growth in length, and are routinely used in fish ageing and growth analyses. Extraction of incremental growth data from scales is labour intensive. We present a fully automated method to retrieve this data from fish scale images using Convolutional Neural Networks (CNNs). Our pipeline of two CNNs automatically detects the centre of the scale and individual growth rings (circuli) along multiple radial transect emanating from the centre. The focus detector was trained on 725 scale images and achieved an average precision of 99%; the circuli detector was trained on 40 678 circuli annotations and achieved an average precision of 95.1%. Circuli detections were made with less confidence in the freshwater zone of the scale image where the growth bands are most narrowly spaced. However, the performance of the circuli detector was similar to that of another human labeller, highlighting the inherent ambiguity of the labelling process. The system predicts the location of scale growth rings rapidly and with high accuracy, enabling the calculation of spacings and thereby growth inferences from salmon scales. The success of our method suggests its potential for expansion to other species.

Identifying and characterizing top predators’ use of trophic resources provides important information about animal ecology and their response to changing conditions. Information from sources such as stable isotopes can be used to infer changes in resource use as direct observations in the wild are difficult to obtain, particularly in the marine environment. Stable carbon and nitrogen isotope values were recovered from the canine teeth of grey seals collected from haul outs in the central North Sea in the 1970/1980s (n = 44) and 2000s (n = 25), spanning a period of marked ecosystem changes in the region. Extracting material deposited during juvenile and adult life-stages, we reconstructed a multi-decadal record of δ15N and δ13C variation. Using established correlations between stable isotope ratios and sea bottom temperature we created a proxy for baseline isotopic variability to account for this source of temporal change. We found 1) a significant long-term decline in juvenile grey seal δ15N values, suggesting trophic position has decreased over time; 2) a decline in adult δ15N values and contraction in stable isotopic niche space after the North Sea regime shift, signifying both a decline in trophic position and change in foraging habits over the 20th century; and 3) evidence for dietary segregation between juvenile and adult animals, showing juvenile individuals feeding at a lower trophic position and in more nearshore areas than adults. Our results demonstrate the efficacy of mining archived biological samples to address ecological questions and imply important ontogenetic and long-term shifts in the feeding ecology of a top predator. Long-term changes in grey seal trophic dynamics may be partly in response to well documented ecosystem changes in the North Sea. Such indirect monitoring of marine predators may have utility when set in the context of ecosystem assessments where paucity of long-term monitoring data is prevalent.

Despite technical advances in archival tag attachment and functional longevity, long-term tracking of individuals of some fish species remains prohibitively difficult. Here we combined high resolution stable isotope sampling of otoliths, genetic assignment, growth increment analyses and a simple movement model to inform a hidden Markov model of the location of individual wild Atlantic salmon ( Salmo salar L.) at sea. The model provided a reconstruction of North Atlantic migration for a species which is extremely difficult to track throughout its marine life-stage. We show that plausible emigration and return migration patterns can be achieved from wild fish. Simulations of simplified northward and westward movement patterns in the North Atlantic were used to quantify precision and accuracy of the model which differed between these two directional scenarios. Because otolith-derived migratory information does not rely on capture, release and subsequent recapture of the individual, this can be retrieved from any fish. Thus these techniques offer a powerful tool for improving our understanding of the processes that govern movement and survival of individual fish during a protracted and largely unobservable life-stage in the oceanic environment.

The harbour seal population in Orkney, off the north coast of Scotland, has reduced by 65% between 2001 and 2010. The cause(s) of this decline are unknown but must affect the demographic parameters of the population. Here, satellite telemetry data were used to test the hypothesis that increased pup mortality could be a primary driver of the decline in Orkney. Pup mortality and tag failure parameters were estimated from the duration of operation of satellite tags deployed on harbour seal pups from the Orkney population (n = 24) and from another population on the west coast of Scotland (n = 24) where abundance was stable. Survival probabilities from both populations were best represented by a common gamma distribution and were not different from one another, suggesting that increased pup mortality is unlikely to be the primary agent in the Orkney population decline. The estimated probability of surviving to 6 months was 0.390 (95% CI 0.297 - 0.648) and tag failure was represented by a Gaussian distribution, with estimated mean 270 (95% CI = 198 - 288) and s.d. 21 (95% CI = 1 - 66) days. These results suggest that adult survival is the most likely proximate cause of the decline. They also demonstrate a novel technique for attaining age-specific mortality rates from telemetry data.

The harbour seal population in Orkney, off the north coast of Scotland, has reduced by 65% between 2001 and 2010. The cause(s) of this decline are unknown but must affect the demographic parameters of the population. Here, satellite telemetry data were used to test the hypothesis that increased pup mortality could be a primary driver of the decline in Orkney. Pup mortality and tag failure parameters were estimated from the duration of operation of satellite tags deployed on harbour seal pups from the Orkney population (n = 24) and from another population on the west coast of Scotland (n = 24) where abundance was stable. Survival probabilities from both populations were best represented by a common gamma distribution and were not different from one another, suggesting that increased pup mortality is unlikely to be the primary agent in the Orkney population decline. The estimated probability of surviving to 6 months was 0.390 (95% CI 0.297 - 0.648) and tag failure was represented by a Gaussian distribution, with estimated mean 270 (95% CI = 198 - 288) and s.d. 21 (95% CI = 1 - 66) days. These results suggest that adult survival is the most likely proximate cause of the decline. They also demonstrate a novel technique for attaining age-specific mortality rates from telemetry data.

Monitoring the response of upper trophic level animals to ecological change is important to understanding the state and stability of ecosystems. Marine predators integrate information over large geographical scales and are relatively long-lived; furthermore, many of these organisms are restricted to terrestrial or freshwater habitats at certain times during their life history and are accessible to researchers. This thesis investigated the response of marine predators to ecological change at a variety of spatial and temporal scales using stable isotope ratio methods with the aims of developing meaningful proxies, or indices, of variability in marine ecosystems. The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental) factors important to modulating variation in the stable isotope ratios of C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the Southern Ocean. In the second study, long-term records of variation in δ15N δ13C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus) tooth dentin provided evidence for large-scale climate forcing across the eastern North Atlantic. In the following study, a more detailed examination of intra- and inter-individual stable isotope variation in Atlantic salmon within a single year was undertaken in an attempt to better understand recent declines in somatic condition of these fish. The last two studies were concerned with the development of high resolution sampling of fish otoliths using secondary mass spectrometry (SIMS) and the application of this technique to reconstructing the thermal and metabolic histories of individual Atlantic salmon from intra-otolith δ13C and δ18O values. Stable isotope proxies can be used to document shifts in trophic dynamics and animal movement that may be associated with ecological change. Using multiple tissues, elements and species, such studies provide unique monitoring tools at a range of spatial and temporal scales.

Two non-covalently linked copies of the retrovirus genome are specifically recruited to the site of virus particle assembly and packaged into released particles. Retroviral RNA packaging requires RNA export of the unspliced genomic RNA from the nucleus, translocation of the genome to virus assembly sites, and specific interaction with Gag, the main viral structural protein. While some aspects of the RNA packaging process are understood, many others remain poorly understood. In this review, we provide an update on recent advancements in understanding the mechanism of RNA packaging for retroviruses that cause disease in humans, i.e., HIV-1, HIV-2, and HTLV-1, as well as advances in the understanding of the details of genomic RNA nuclear export, genome translocation to virus assembly sites, and genomic RNA dimerization.

Contemporary dictators routinely co-opt institutions crucial for democratic governance. Although an extensive literature examines why and how aspiring autocrats bring elections and parties under their control, constitutions—and the judicial or quasi-judicial bodies charged with interpreting constitutions—are often assumed to reflect the existing balance of power. But following regime change, constitutional courts’ power of review makes them integral for establishing political supremacy. We detail how President Nursultan Nazarbayev of Kazakhstan captured the Constitutional Court via its transformation into the Constitutional Council. The uncertainty and upheaval of the post-Soviet collapse created opportunities for formal institutional changes that made the court susceptible to executive capture. Nazarbayev subsequently used the council rulings to lay claim to democratic and constitutional legitimacy in a clear example of authoritarian constitutionalism. To trace the process of capture and legitimation, we examine key court rulings throughout the president’s tenure using a database of Constitutional Council decisions.