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  • 1
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    Lévy flight movements prevent extinctions and maximize population abundances in fragile Lotka–Volterra systems (2018)
    National Academy of Sciences
    Details
    Publication Date: 2018-03-26
    Description: Multiple-scale mobility is ubiquitous in nature and has become instrumental for understanding and modeling animal foraging behavior. However, the impact of individual movements on the long-term stability of populations remains largely unexplored. We analyze deterministic and stochastic Lotka–Volterra systems, where mobile predators consume scarce resources (prey) confined in patches. In fragile systems (that is, those unfavorable to species coexistence), the predator species has a maximized abundance and is resilient to degraded prey conditions when individual mobility is multiple scaled. Within the Lévy flight model, highly superdiffusive foragers rarely encounter prey patches and go extinct, whereas normally diffusing foragers tend to proliferate within patches, causing extinctions by overexploitation. Lévy flights of intermediate index allow a sustainable balance between patch exploitation and regeneration over wide ranges of demographic rates. Our analytical and simulated results can explain field observations and suggest that scale-free random movements are an important mechanism by which entire populations adapt to scarcity in fragmented ecosystems.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Long-Term Balancing Selection in LAD1 Maintains a Missense Trans-Species Polymorphism in Humans, Chimpanzees, and Bonobos (2015)
    Oxford University Press
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    Publication Date: 2015-04-25
    Description: Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo–Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees, and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 My of independent evolution. Although the majority of these trSNPs were found in three genes of the major histocompatibility locus cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1 . All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here, we focus on the trSNP in LAD1 , a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1 .
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Sustainability, Vol. 11, Pages 6160: The LED Paradox: How Light Pollution Challenges Experts to Reconsider Sustainable Lighting (2019)
    MDPI
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    Publication Date: 2019
    Description: In the 21st century, the notion of “sustainable lighting” is closely associated with LED technology. In the past ten years, municipalities and private light users worldwide have installed light-emitting diodes in urban spaces and public streets to save energy. Yet an increasing body of interdisciplinary research suggests that supposedly sustainable LED installations are in fact unsustainable, because they increase light pollution. Paradoxically, blue-rich cool-white LED lighting, which is the most energy-efficient, also appears to be the most ecologically unfriendly. Biologists, physicians and ecologists warn that blue-rich LED light disturbs the circadian day-and-night rhythm of living organisms, including humans, with potential negative health effects on individual species and whole ecosystems. Can the paradox be solved? This paper explores this question based on our transdisciplinary research project Light Pollution—A Global Discussion. It reveals how light pollution experts and lighting professionals see the challenges and potential of LED lighting from their different viewpoints. This expert feedback shows that “sustainable LED lighting” goes far beyond energy efficiency as it raises complex design issues that imply stakeholder negotiation. It also suggests that the LED paradox may be solved in context, but hardly in principle.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI
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  • 4
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    Sustainability, Vol. 11, Pages 1696: Lighting Professionals versus Light Pollution Experts? Investigating Views on an Emerging Environmental Concern (2019)
    MDPI
    Details
    Publication Date: 2019
    Description: Concerns about the potential negative effects of artificial light at night on humans, flora and fauna, were originally raised by astronomers and environmentalists. Yet, we observe a growing interest in what is called light pollution among the general public and in the lighting field. Although lighting professionals are often critical of calling light ‘pollution’, they increasingly acknowledge the problem and are beginning to act accordingly. Are those who illuminate joining forces with those who take a critical stance towards artificial light at night? We explore this question in more detail based on the results of a non-representative worldwide expert survey. In our analysis, we distinguish between “lighting professionals” with occupational backgrounds linked to lighting design and the lighting industry, and “light pollution experts” with mostly astronomy- and environment-related professional backgrounds, and explore their opposing and shared views vis-à-vis issues of light pollution. Our analysis reveals that despite seemingly conflicting interests, lighting professionals and light pollution experts largely agree on the problem definition and problem-solving approaches. However, we see diverging views regarding potential obstacles to light pollution mitigation and associated governance challenges.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI
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  • 5
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    Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne (2016)
    National Academy of Sciences
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    Publication Date: 2016-09-16
    Description: In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this “transitional” assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal–Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    The time geography of segregation during working hours (2018)
    Royal Society
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    Publication Date: 2018-10-04
    Description: While segregation is usually evaluated at the residential level, the recent influx of large streams of data describing urbanites’ movement across the city allows to generate detailed descriptions of spatio-temporal segregation patterns across the activity space of individuals. For instance, segregation across the activity space is usually thought to be lower compared with residential segregation given the importance of social complementarity, among other factors, shaping the economies of cities. However, these new dynamic approaches to segregation convey important methodological challenges. This paper proposes a methodological framework to investigate segregation during working hours. Our approach combines three well-known mathematical tools: community detection algorithms, segregation metrics and random walk analysis. Using Santiago (Chile) as our model system, we build a detailed home–work commuting network from a large dataset of mobile phone pings and spatially partition the city into several communities. We then evaluate the probability that two persons at their work location will come from the same community. Finally, a randomization analysis of commuting distances and angles corroborates the strong segregation description for Santiago provided by the sociological literature. While our findings highlights the benefit of developing new approaches to understand dynamic processes in the urban environment, unveiling counterintuitive patterns such as segregation at our workplace also shows a specific example in which the exposure dimension of segregation is successfully studied using the growingly available streams of highly detailed anonymized mobile phone registries.
    Keywords: complexity, computer modelling and simulation
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 7
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    Sensors, Vol. 19, Pages 92: Design and Testing of a Co-Rotating Vibration Excitation System (2018)
    MDPI
    In: Sensors
    Details
    Publication Date: 2018
    Description: A vibration excitation system (VES) in a form of an active coupling is proposed, designed and manufactured. The system is equipped with a set of piezoelectric stack actuators uniformly distributed around the rotor axis and positioned parallel to each other. The actuator arrangement allows an axial displacement of the coupling halves as well as their rotation about any transverse axis. Through the application of the VES an aimed vibration excitation is realised in a co-rotating coordinate system, which enables a non-invasive and precise modal analysis of rotating components. As an example, the VES is applied for the characterisation of the structural dynamic behaviour of a generic steel rotor at different rotational speeds. The first results are promising for both stationary and rotating conditions.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Published by MDPI
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  • 8
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    Genetic Evidence of Human Adaptation to a Cooked Diet (2016)
    Oxford University Press
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    Publication Date: 2016-04-15
    Description: Humans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. Here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. Liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not by caloric intake or consumer energy balance. Genes affected by cooking were highly correlated with genes known to be differentially expressed in liver between humans and other primates, and more genes in this overlap set show signals of positive selection in humans than would be expected by chance. Sequence changes in the genes under selection appear before the split between modern humans and two archaic human groups, Neandertals and Denisovans, supporting the idea that human adaptation to a cooked diet had begun by at least 275,000 years ago.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-03-19
    Description: Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vernot, Benjamin -- Tucci, Serena -- Kelso, Janet -- Schraiber, Joshua G -- Wolf, Aaron B -- Gittelman, Rachel M -- Dannemann, Michael -- Grote, Steffi -- McCoy, Rajiv C -- Norton, Heather -- Scheinfeldt, Laura B -- Merriwether, David A -- Koki, George -- Friedlaender, Jonathan S -- Wakefield, Jon -- Paabo, Svante -- Akey, Joshua M -- 5R01GM110068/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 Apr 8;352(6282):235-9. doi: 10.1126/science.aad9416. Epub 2016 Mar 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, Washington, USA. ; Department of Genome Sciences, University of Washington, Seattle, Washington, USA. Department of Life Sciences and Biotechnology, University of Ferrara, Italy. ; Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. ; Department of Anthropology, University of Cincinnati, Cincinnati, OH, USA. ; Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA. ; Department of Anthropology, Binghamton University, Binghamton, NY, USA. ; Institute for Medical Research, Goroka, Eastern Highlands Province, Papua New Guinea. ; Department of Anthropology, Temple University, Philadelphia PA, USA. ; Department of Statistics, University of Washington, Seattle, Washington, USA. ; Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. paabo@eva.mpg.de akeyj@uw.edu. ; Department of Genome Sciences, University of Washington, Seattle, Washington, USA. paabo@eva.mpg.de akeyj@uw.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26989198" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA/*genetics ; Genetic Variation ; Genome, Human/*genetics ; Humans ; Melanesia ; Neanderthals/*genetics ; Oceanic Ancestry Group/*genetics ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    A high-coverage Neandertal genome from Vindija Cave in Croatia (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-11-03
    Description: To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
    Keywords: Anthropology, Genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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