Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

Chapter Three – Host–Parasite Interactions and the Evolution of Immune Defense

Parasites and pathogens are ubiquitous and act as an important selection pressure on animals. Here, drawing primarily on our own research, mostly on insects, we illustrate how host-parasite interactions have played a role in the evolution of a range of phenomena, including animal coloration, social behavior, foraging ecology, sexual selection, and life-history tradeoffs, as well as how variation in host behavior and ecology can drive variation in parasitism risk and host allocation of resources to immunity and other antiparasite defenses. We conclude by identifying key areas for future study.

The heart of a dragon: 3D anatomical reconstruction of the 'scaly-foot gastropod' (Mollusca: Gastropoda: Neomphalina) reveals its extraordinary circulatory system

Introduction: The 'scaly-foot gastropod' (Chrysomallon squamiferum Chen et al., 2015) from deep-sea hydrothermal vent ecosystems of the Indian Ocean is an active mobile gastropod occurring in locally high densities, and it is distinctive for the dermal scales covering the exterior surface of its foot. These iron-sulfide coated sclerites, and its nutritional dependence on endosymbiotic bacteria, are both noted as adaptations to the extreme environment in the flow of hydrogen sulfide. We present evidence for other adaptations of the 'scaly-foot gastropod' to life in an extreme environment, investigated through dissection and 3D tomographic reconstruction of the internal anatomy.

Results: Our anatomical investigations of juvenile and adult specimens reveal a large unganglionated nervous system, a simple and reduced digestive system, and that the animal is a simultaneous hermaphrodite. We show that Chrysomallon squamiferum relies on endosymbiotic bacteria throughout post-larval life. Of particular interest is the circulatory system: Chrysomallon has a very large ctenidium supported by extensive blood sinuses filled with haemocoel. The ctenidium provides oxygen for the host but the circulatory system is enlarged beyond the scope of other similar vent gastropods. At the posterior of the ctenidium is a remarkably large and well-developed heart. Based on the volume of the auricle and ventricle, the heart complex represents approximately 4 % of the body volume. This proportionally giant heart primarily sucks blood through the ctenidium and supplies the highly vascularised oesophageal gland. Thus we infer the elaborate cardiovascular system most likely evolved to oxygenate the endosymbionts in an oxygen poor environment and/or to supply hydrogen sulfide to the endosymbionts.

Conclusions: This study exemplifies how understanding the autecology of an organism can be enhanced by detailed investigation of internal anatomy. This gastropod is a large and active species that is abundant in its hydrothermal vent field ecosystem. Yet all of its remarkable features-protective dermal sclerites, circulatory system, high fecundity-can be viewed as adaptations beneficial to its endosymbiont microbes. We interpret these results to show that, as a result of specialisation to resolve energetic needs in an extreme chemosynthetic environment, this dramatic dragon-like species has become a carrying vessel for its bacteria.

Young People’s Early Offending: The Context of Strained Leisure Careers

Criminology has witnessed a growth of interest in the later stages of criminal careers with less attention given to providing an understanding of the onset of offending which goes beyond identifying the precipitative or ‘risk’ factors. Drawing on findings from a study of young people’s offending careers in Ireland, this article provides a contextualized understanding of the onset of crime located in young people’s biographical experiences and transition through youth more specifically. It focuses on one particular dimension of this process, suggesting that early offending can be understood as emerging in the context of strained leisure careers. The findings also highlight the close interaction between the development of young people’s leisure careers and their experiences of the local neighbourhood and social networks. It argues that responses to the early stages of youth offending must widen their focus from the individual to incorporate an understanding of broader socio-economic and cultural contexts.

From Boys to Men Phase One Key Findings

The From Boys to Men Project was funded by the Economic and Social Research
Council to explore why some boys become domestic abuse perpetrators when
others do not. In so doing, it sought to establish what more could be done to
reduce the number of young men who become perpetrators. The study
involved three phases of data collection including: Phase 1 - a survey of school
children aged 13-14, Phase 2 - focus groups with 69 young people aged 13-19,
and Phase 3 - life history interviews with 30 young men, aged 16-21, who had experienced domestic violence as victims, perpetrators or witnesses.

From Boys to Men Phase Two Key Findings

The From Boys to Men Project was funded by the Economic and Social Research
Council to explore why some boys become domestic abuse perpetrators when
others do not. In so doing, it sought to establish what more could be done to
reduce the number of young men who become perpetrators. The study
involved three phases of data collection including: Phase 1 - a survey of school
children aged 13-14, Phase 2 - focus groups with 69 young people aged 13-19,
and Phase 3 - life history interviews with 30 young men, aged 16-21, who had experienced domestic violence as victims, perpetrators or witnesses.

From Boys to Men Phase Three Key Findings

The From Boys to Men Project was funded by the Economic and Social Research
Council to explore why some boys become domestic abuse perpetrators when
others do not. In so doing, it sought to establish what more could be done to
reduce the number of young men who become perpetrators. The study
involved three phases of data collection including: Phase 1 - a survey of school
children aged 13-14, Phase 2 - focus groups with 69 young people aged 13-19,
and Phase 3 - life history interviews with 30 young men, aged 16-21, who
had experienced domestic violence as victims, perpetrators or witnesses.

From Boys to Men Overview and Recommendations

The From Boys to Men Project was funded by the Economic and Social Research
Council to explore why some boys become domestic abuse perpetrators when
others do not. In so doing, it sought to establish what more could be done to
reduce the number of young men who become perpetrators. The study
involved three phases of data collection including: Phase 1 - a survey of 1203
school children aged 13-14; Phase 2 - focus groups with 69 young people aged
13-19; and Phase 3 - life history interviews with 30 young men, aged 16-21,
who had experienced domestic abuse as victims, perpetrators or witnesses.
Reports on all stages of the project are freely available on our website
www.boystomenproject.com.
This report provides a brief overview of what we found and what
recommendations follow from the project’s findings.

Emotions & social change in Ireland:Exploring habitus shift in liquid modernity

Drawing on insights from a range of disciplines, including philosophy, psychology, history, politics, but particularly sociology and sociological theory, this thesis explores the relationship between emotions and social change in late or 'liquid' modernity. It deploys the Republic of Ireland in the twentieth century as a case study. It argues that the Irish case in an ideal site for this research given the speed and scale of changes that have occurred there, particularly since the 1950's. The primary research question guiding the study is: What has been the effect of 'social change' in Ireland on the emotional lives of Irish people? The thesis is structured in three parts. Part one (chapters one to three) is primarily theoretical. It aims to develop a distinctive theoretical framework, process-relational realism, and argues that three concepts, properly treated, are central to answering the research question. These are emotion, power and (emotional) habitus. Part two is a bridging chapter, in which the empirical portion of the study, its design and method, are outlined. This study is based on a series of qualitative life-history interviews conducted using the Biographical Narrative Research Method. Part three is primarily empirical. The first chapter critically explores Bauman's concept of liquid modernity in relation to the Irish case and offers a short social history of the Irish twentieth century, which focuses on emotions and power. The second deploys two (ideal-type) interview cases to support the argument that Ireland experienced a habitus shift, from a relatively homogeneous to a heterogeneous habitus, and a corresponding shift from a relatively repressive emotional regime to a more expressive one, with significant effects on the emotional habitus. The final chapter takes a broader view of these changes, suggests that social change has been ambivalent, and outlines a new typology of emotional pathologies that the study suggests are characteristic of contemporary emotional life.

Experiencing Youth Justice: Process, Meaning and Legitimacy

Reform of the youth justice system, including the wide incorporation of restorative justice approaches, was a central component of the Criminal Justice Review (2000). Following the devolution of policing and justice powers to the Assembly, the Youth Justice Review (2011) made a series of recommendations for further reforms. These included proposals for the introduction of a statutory time limit in youth cases to tackle avoidable delay. Strengthening legitimacy and advancing rights-based approaches are key themes underpinning the recommendations of Youth Justice Review (2011). Young people’s views of justice within the system are critical to our understanding of how such aims can be achieved. This presentation is based on findings from a longitudinal qualitative study exploring young people’s experiences of transitions into and from custody in the Juvenile Justice Centre. Using a life-history approach young people’s experiences of justice at various stages of the criminal justice process and in the wider context of their lives is explored. Key issues such as social contexts, legitimacy and perceptions of fairness are highlighted and the implications of this for system reform are critically examined.

Estimating biomass, fishing mortality, and "total allowable discards" for surveyed non-target fish

Demersal fisheries targeting a few high-value species often catch and discard other "non-target" species. It is difficult to quantify the impact of this incidental mortality when population biomass of a non-target species is unknown. We calculate biomass for 14 demersal fish species in ICES Area VIIg (Celtic Sea) by applying species-and length-based catchability corrections to catch records from the Irish Groundfish Survey (IGFS). We then combine these biomass estimates with records of commercial discards (and landings for marketable non-target species) to calculate annual harvesting rates (HR) for each study species. Uncertainty is incorporated into estimates of both biomass andHR. Our survey-based HR estimates for cod and whiting compared well with HR-converted fishing mortality (F) estimates from analytical assessments for these two stocks. Of the non-target species tested, red gurnard (Chelidonichthys cuculus) recorded some annual HRs greater than those for cod or whiting; challenging "Pope's postulate" that F on non-target stocks in an assemblage will not exceed that on target stocks. We relate HR for each species to two corresponding maximum sustainable yield (MSY) reference levels; six non-target species (including three ray species) show annual HRs >= HRMSY. This result suggests that it may not be possible to conserve vulnerable non-target species when F is coupled to that of target species. Based on biomass, HR, and HRMSY, we estimate "total allowable catch" for each non-target species.

Novel microsatellite loci for a deep sea fish (Macrourus berglax) and their amplification in other grenadiers (Gadiformes: Macrouridae)

Over-exploitation of traditional coastal stocks and a rising demand for seafood have resulted in the shift of commercial fishing towards less-known, deep-sea species in many parts of the world. Yet, the lack of knowledge of the biology, ecology and life-history of these species represents a serious impediment for establishing sound stock management plans. With the aim of providing tools that will allow assessment of the population genetic structure of Macrourus berglax, we have isolated and characterised a suite of novel microsatellite loci for this deep sea grenadier. Eight of these markers showed between 4 and 11 alleles per locus in two distant North Atlantic populations, with observed and expected heterozygosities between 0.17-0.83 and 0.35-0.87, respectively. Importantly, eight of these loci also cross-amplify in other Macrourid species. 

Spatial variation in adult sex ratio across multiple scales in the invasive golden apple snail, Pomacea canaliculata

Adult sex ratio (ASR) has critical effects on behavior and life history and has implications for population demography, including the invasiveness of introduced species. ASR exhibits immense variation in nature, yet the scale dependence of this variation is rarely analyzed. In this study, using the generalized multilevel models, we investigated the variation in ASR across multiple nested spatial scales and analyzed the underlying causes for an invasive species, the golden apple snail Pomacea canaliculata. We partitioned the variance in ASR to describe the variations at different scales and then included the explanatory variables at the individual and group levels to analyze the potential causes driving the variation in ASR. We firstly determined there is a significant female-biased ASR for this species when accounting for the spatial and temporal autocorrelations of sampling. We found that, counter to nearly equal distributed variation at plot, habitat and region levels, ASR showed little variation at the town level. Temperature and precipitation at the region level were significantly positively associated with ASR, whereas the individual weight, the density characteristic, and sampling time were not significant factors influencing ASR. Our study suggests that offspring sex ratio of this species may shape the general pattern of ASR in the population level while the environmental variables at the region level translate the unbiased offspring sex ratio to the female-biased ASR. Future research should consider the implications of climate warming on the female-biased ASR of this invasive species and thus on invasion pattern.

Histórias de vida e formação de professores/as: diálogos entre Brasil e Portugal

A presente tese problematiza a formação de professores/as, buscando sentidos de uma racionalidade instituinte que incorpore a vida dos sujeitos, em toda sua complexidade existencial, como componente fundamental do processo formativo. Num contexto de investigação-formação, tomamos as biografias educativas de seis professoras do Primeiro Ciclo do Ensino Básico, em Portugal, e seis dos primeiros anos do Ensino Fundamental, no Brasil como uma alternativa teórico-metodológica na tematização da vida como espaço/tempo de formação. No desenvolvimento, encontramos vestígios de que o processo formador se torna inteligível numa perspectiva que entretece os diferentes episódios em tessitura, onde as intrigas são articuladas na experiência narrativa. Reafirmamos, também, o sentido da docência como "lugar de memória", a contribuição do registro da história de vida, transformando biografia em herança e a perspectiva dialógica da aprendizagem que se dá quando nos confrontamos com o outro de quem, dialecticamente, nos ligamos e nos distanciamos, mediados por desejos e desafios. ### Abstract - The present thesis discusses the formation of teachers, looking for senses of a founding rationality that incorporates the life of individuals in all its existential complexity as a fundamental component in the formation process. In an investigation-formation context, we took the educational biographies of six teachers from Portuguese Elementary Schools, and six teachers from Brazilian Elementary Schools, as a theoretical-methodological alternative on the theme of life as space/time of formation. In the development, we find indications that the formation process becomes comprehensible under a perspective that interlaces different episodes, where the intrigues are articulated in the experience narrative. We also reassert the teaching sense as being "the memory place", the registry contribution of life history, converting biography into legacy, and the learning dialogical perspective that happens when we confront ourselves with the other, from whom, dialectically speaking, we are close to and far-off, mediated by longings and challenges.

Population genetics of C. Maenas : oceanography and larval dispersal

Decifrar a complexa interacção entre os ciclos de vida de espécies marinhas e a oceanografia revela-se fundamental para a compreensão do fluxo genético e da conectividade no meio marinho. Nas espécies marinhas com desenvolvimento indirecto o fluxo de genes entre populações depende da distância que separa as populações, bem como da interacção entre a duração do desenvolvimento larvar, do comportamento das larvas e dos padrões de circulação oceânica. A conectividade larvar influencia uma variedade de processos como a dinâmica de stocks e de populações, a distribuição e limites geográficos das espécies, a estrutura genética das populações e a dispersão de espécies invasivas e reveste-se consequentemente de uma importância fundamental na identificação das unidades populacionais evolucionariamente relevantes e para a gestão e conservação marinhas. Os marcadores genéticos e os Modelos Individuais Acoplados a Modelos Físico-Biológicos (“ICPBMs”) são actualmente ferramentas fundamentais para o estudo dos padrões de dispersão larvar e para avaliar o nível de conectividade populacional. A presente tese respeita à avaliação das escalas espaciais de conectividade de populações de uma espécie costeira, o caranguejo Carcinus maenas, e utiliza conjuntamente informação de marcadores genéticos, análise de séries temporais de fornecimento de larvas e um modelo numérico de circulação oceânica. O primeiro capítulo introduz a temática da conectividade em espécies marinhas e inclui algumas referências aos métodos moleculares, analíticos e de modelação seguidos ao longo da tese. Através da utilização de múltiplas ferramentas – avaliação da estrutura genética geográfica de C. maenas na sua distribuição nativa com recurso a marcadores de DNA (microssatélites) (Capítulo 2), avaliação da estrutura genética temporal das larvas que formam os eventos de fornecimento larvar à Ria de Aveiro, NW Portugal (Capítulo 3), descrição da variabilidade inter-anual do fornecimento larvar à Ria de Aveiro, NW Portugal (Capítulo 4) e validação de um modelo ICPBM que descreve os padrões observados de fornecimento (Capítulo 5) – esta tese espera poder contribuir para uma melhor compreensão dos mecanismos que regulam o fluxo de genes e a conectividade entre populações de organismos marinhos. No Capítulo 6 são apresentadas as principais conclusões da investigação. A análise genética com recurso a microssatélites indicou que as populações de C. maenas são geneticamente homogéneas ao longo de várias centenas de km, dentro da distribuição nativa da espécie. Paralelamente, não foram encontrados indícios da existência de reprodução por “sweepstakes” em C. maenas de populações da costa oeste da Península Ibérica, visto que não se obtiveram diferenças genéticas significativas entre os eventos larvares. Também não se encontrou qualquer estrutura familiar entre as larvas que formam cada episódio de fornecimento, e não houve nenhuma redução significativa da variabilidade genética das larvas quando comparada com a de caranguejos adultos. A análise de séries temporais de suprimento de larvas na Ria de Aveiro em cinco anos estudados indica que este é um fenómeno episódico e variável, sendo os maiores episódios de fornecimento coincidentes com as marés vivas e acentuados por fortes ventos de sul. O modelo ICPBM foi validado com sucesso e parece fornecer uma estimativa realística das escalas espaciais e temporais de dispersão larvar, de acordo com as observações da estrutura genética e da ausência de reprodução por “sweepstake” em C. maenas da costa oeste da Península Ibérica