Pool Evolution: A Parallel Pattern for Evolutionary and Symbolic Computing

We introduce a new parallel pattern derived from a specific application domain and show how it turns out to have application beyond its domain of origin. The pool evolution pattern models the parallel evolution of a population subject to mutations and evolving in such a way that a given fitness function is optimized. The pattern has been demonstrated to be suitable for capturing and modeling the parallel patterns underpinning various evolutionary algorithms, as well as other parallel patterns typical of symbolic computation. In this paper we introduce the pattern, we discuss its implementation on modern multi/many core architectures and finally present experimental results obtained with FastFlow and Erlang implementations to assess its feasibility and scalability.

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.

Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization?

Repeated recolonization of freshwater environments following Pleistocene glaciations has played a major role in the evolution and adaptation of anadromous taxa. Located at the western fringe of Europe, Ireland and Britain were likely recolonized rapidly by anadromous fishes from the North Atlantic following the last glacial maximum (LGM). While the presence of unique mitochondrial haplotypes in Ireland suggests that a cryptic northern refugium may have played a role in recolonization, no explicit test of this hypothesis has been conducted. The three-spined stickleback is native and ubiquitous to aquatic ecosystems throughout Ireland, making it an excellent model species with which to examine the biogeographical history of anadromous fishes in the region. We used mitochondrial and microsatellite markers to examine the presence of divergent evolutionary lineages and to assess broad-scale patterns of geographical clustering among postglacially isolated populations. Our results confirm that Ireland is a region of secondary contact for divergent mitochondrial lineages and that endemic haplotypes occur in populations in Central and Southern Ireland. To test whether a putative Irish lineage arose from a cryptic Irish refugium, we used approximate Bayesian computation (ABC). However, we found no support for this hypothesis. Instead, the Irish lineage likely diverged from the European lineage as a result of postglacial isolation of freshwater populations by rising sea levels. These findings emphasize the need to rigorously test biogeographical hypothesis and contribute further evidence that postglacial processes may have shaped genetic diversity in temperate fauna.

Human Adaptation in Asian Palaeolithic:Hominin Dispersal and Behaviour during the Late Quaternary

This book examines the first human colonization of Asia and particularly the tropical environments of Southeast Asia during the Upper Pleistocene. In studyexamining the unique character of the Asian archaeological record, it reassesses long-accepted propositions about the development of human ‘modernity.’ Ryan J. Rabett reveals an evolutionarily relationship between colonization, the challenges encountered during this process – especially in relation to climatic and environmental change – and the forms of behaviour that emerged. This book argues that human ‘modernity’ is not something achieved in the remote past in one part of the world, but rather is a diverse, flexible, responsive, and on-going process of adaptation, one that continues to this day.

The emergence of bone technologies at the end of the pleistocene in Southeast Asia:Regional and evolutionary implications

For many decades Palaeolithic research viewed the development of early modern human behaviour as largely one of progress down a path towards the modernity of the present. The European Palaeolithic sequence the most extensively studied was for a long time the yard-stick against which records from other regions were judged. Recent work undertaken in Africa and increasingly Asia, however, now suggests that the European evidence may tell a story that is more parochial and less universal than previously thought. While tracking developments at the large scale (the grand narrative) remains important, there is growing appreciation that to achieve a comprehensive understanding of human behavioural evolution requires an archaeologically regional perspective to balance this. One of the apparent markers of human modernity that has been sought in the global Palaeolithic record, prompted by finds in the European sequence, is innovation in bonebased technologies. As one step in the process of re-evaluating and contextualizing such innovations, in this article we explore the role of prehistoric bone technologies within the Southeast Asian sequence, where they have at least comparable antiquity to Europe and other parts of Asia. We observe a shift in the technological usage of bone from a minor component to a medium of choice during the second half of the Last Termination and into the Holocene. We suggest that this is consistent with it becoming a focus of the kinds of inventive behaviour demanded of foraging communities as they adapted to the far-reaching environmental and demographic changes that were reshaping this region at that time. This record represents one small element of a much wider, much longerterm adaptive process, which we would argue is not confined to the earliest instances of a particular technology or behaviour, but which forms part of an on-going story of our behavioural evolution. © 2012 The McDonald Institute for Archaeological Research.

The imprint of the geographical, evolutionary and ecological context on species-area relationships

Species-area relationships (SAR) are fundamental in the understanding of biodiversity patterns and of critical importance for predicting species extinction risk worldwide. Despite the enormous attention given to SAR in the form of many individual analyses, little attempt has been made to synthesize these studies. We conducted a quantitative meta-analysis of 794 SAR, comprising a wide span of organisms, habitats and locations. We identified factors reflecting both pattern-based and dynamic approaches to SAR and tested whether these factors leave significant imprints on the slope and strength of SAR. Our analysis revealed that SAR are significantly affected by variables characterizing the sampling scheme, the spatial scale, and the types of organisms or habitats involved. We found that steeper SAR are generated at lower latitudes and by larger organisms. SAR varied significantly between nested and independent sampling schemes and between major ecosystem types, but not generally between the terrestrial and the aquatic realm. Both the fit and the slope of the SAR were scale-dependent. We conclude that factors dynamically regulating species richness at different spatial scales strongly affect the shape of SAR. We highlight important consequences of this systematic variation in SAR for ecological theory, conservation management and extinction risk predictions.

Responsiveness of dark-adaptation threshold to vitamin A and beta-carotene supplementation in pregnant and lactating women in Nepal.

BACKGROUND: Impaired dark adaptation occurs commonly in vitamin A deficiency. OBJECTIVE: We sought to examine the responsiveness of dark-adaptation threshold to vitamin A and beta-carotene supplementation in Nepali women. DESIGN: The dark-adapted pupillary response was tested in 298 pregnant women aged 15-45 y in a placebo-controlled trial of vitamin A and beta-carotene; 131 of these women were also tested at 3 mo postpartum. Results were compared with those for 100 nonpregnant US women of similar age. The amount of light required for pupillary constriction was recorded after bleaching and dark adaptation. RESULTS: Pregnant women receiving vitamin A had better dark-adaptation thresholds (-1.24 log cd/m(2)) than did those receiving placebo (-1.11 log cd/m(2); P: = 0. 03) or beta-carotene (-1.13 log cd/m(2); P: = 0.05) (t tests with Bonferroni correction). Dark-adaptation threshold was associated with serum retinol concentration in pregnant women receiving placebo (P: = 0.001) and in those receiving beta-carotene (P: = 0.003) but not in those receiving vitamin A. Among women receiving placebo, mean dark-adaptation thresholds were better during the first trimester (-1.23 log cd/m(2)) than during the second and third trimesters (-1.03 log cd/m(2); P: = 0.02, t test). The mean threshold of nonpregnant US women (-1.35 log cd/m(2)) was better than that of all 3 Nepali groups (P: < 0.001, t test, for all 3 groups). CONCLUSIONS: During pregnancy, pupillary dark adaptation was strongly associated with serum retinol concentration and improved significantly in response to vitamin A supplementation. This noninvasive testing technique is a valid indicator of population vitamin A status in women of reproductive age.

Adaptation and Evaluation of the Neighborhood Environment Walkability Scale in India (NEWS-India)

Physical inactivity is the fourth leading risk factor for global mortality, with most of these deaths occurring in low and middle-income countries (LMICs) like India. Research from developed countries has consistently demonstrated associations between built environment features and physical activity levels of populations. The development of culturally sensitive and reliable measures of the built environment is a necessary first step for accurate analysis of environmental correlates of physical activity in LMICs. This study systematically adapted the Neighborhood Environment Walkability Scale (NEWS) for India and evaluated aspects of test-retest reliability of the adapted version among Indian adults. Cultural adaptation of the NEWS was conducted by Indian and international experts. Semi-structured interviews were conducted with local residents and key informants in the city of Chennai, India. At baseline, participants (N = 370; female = 47.2%) from Chennai completed the adapted NEWS-India surveys on perceived residential density, land use mix-diversity, land use mix-access, street connectivity, infrastructure and safety for walking and cycling, aesthetics, traffic safety, and safety from crime. NEWS-India was administered for a second time to consenting participants (N = 62; female = 53.2%) with a gap of 2–3 weeks between successive administrations. Qualitative findings demonstrated that built environment barriers and constraints to active commuting and physical activity behaviors intersected with social ecological systems. The adapted NEWS subscales had moderate to high test-retest reliability (ICC range 0.48–0.99). The NEWS-India demonstrated acceptable measurement properties among Indian adults and may be a useful tool for evaluation of built environment attributes in India. Further adaptation and evaluation in rural and suburban settings in India is essential to create a version that could be used throughout India.

The duration compression effect is mediated by adaptation of both retinotopic and spatiotopic mechanisms

The duration compression effect is a phenomenon in which prior adaptation to a spatially circumscribed dynamic stimulus results in the duration of subsequent subsecond stimuli presented in the adapted region being underestimated. There is disagreement over the frame of reference within which the duration compression phenomenon occurs. One view holds that the effect is driven by retinotopic-tuned mechanisms located at early stages of visual processing, and an alternate position is that the mechanisms are spatiotopic and occur at later stages of visual processing (MT+). We addressed the retinotopic-spatiotopic question by using adapting stimuli – drifting plaids - that are known to activate global-motion mechanisms in area MT. If spatiotopic mechanisms contribute to the duration compression effect, drifting plaid adaptors should be well suited to revealing them. Following adaptation participants were tasked with estimating the duration of a 600ms random dot stimulus, whose direction was identical to the pattern direction of the adapting plaid, presented at either the same retinotopic or the same spatiotopic location as the adaptor. Our results reveal significant duration compression in both conditions, pointing to the involvement of both retinotopic-tuned and spatiotopic-tuned mechanisms in the duration compression effect.

Adaptable housing design for climate change adaptation

It is predicted that climate change will result in rising sea levels, more frequent and extreme weather events, hotter and drier summers and warmer and wetter winters. This will have a significant impact on the design of buildings, how they are kept cool and how they are weathered against more extreme climatic conditions. The residential sector is already a significant environmental burden with high associated operational energy. Climate change, and a growing population requiring residence, has the potential to exacerbate this problem seriously. New paradigms for residential building design are required to enable low-carbon dioxide operation to mitigate climate change. They must also face the reality of inevitable climate change and adopt climate change adaptation strategies to cope with future scenarios. However, any climate adaptation strategy for dwellings must also be cognisant of adapting occupant needs, influenced by ageing populations and new technologies. This paper presents concepts and priorities for changing how society designs residential buildings by designing for adaptation. A case study home is analysed in the context of its stated aims of low energy and adaptability. A post-occupancy evaluation of the house is presented, and future-proofing strategies are evaluated using climate projection data for future climate change scenarios.