60 results found
Neutral models of evolution assume the absence of natural selection. Formerly confined to ecology and evolutionary biology, neutral models are spreading. In recent years they’ve been applied to explaining the diversity of baby names, scientific citations, cryptocurrencies, pot decorations, literary lexica, tumour variants and much more besides. Here, we survey important neutral models and highlight their similarities. We investigate the most widely used tests of neutrality, show that they are weak and suggest more powerful methods. We conclude by discussing the role of neutral models in the explanation of diversity. We suggest that the ability of neutral models to fit low-information distributions should not be taken as evidence for the absence of selection. Nevertheless, many studies, in increasingly diverse fields, make just such claims. We call this tendency ‘neutral syndrome’.
Hintzen RE, Papadopoulou M, Mounce R, et al., 2020, Relationship between conservation biology and ecology shown through machine reading of 32,000 articles, Conservation Biology, Vol: 34, Pages: 721-732, ISSN: 0888-8892
Conservation biology was founded on the idea that efforts to save nature depend on a scientific understanding of how it works. It sought to apply ecological principles to conservation problems. We investigated whether the relationship between these fields has changed over time through machine reading the full texts of 32,000 research articles published in 16 ecology and conservation biology journals. We examined changes in research topics in both fields and how the fields have evolved from 2000 to 2014. As conservation biology matured, its focus shifted from ecology to social and political aspects of conservation. The 2 fields diverged and now occupy distinct niches in modern science. We hypothesize this pattern resulted from increasing recognition that social, economic, and political factors are critical for successful conservation and possibly from rising skepticism about the relevance of contemporary ecological theory to practical conservation. Article Impact statement: Quantitative literature evaluation reveals that the research topics of ecology and conservation biology are drawing apart. This article is protected by copyright. All rights reserved.
Here we investigate the evolutionary dynamics of several kinds of modern cultural artefacts-pop music, novels, the clinical literature and cars-as well as a collection of organic populations. In contrast to the general belief that modern culture evolves very quickly, we show that rates of modern cultural evolution are comparable to those of many animal populations. Using time-series methods, we show that much of modern culture is shaped by either stabilizing or directional forces or both and that these forces partly regulate the rates at which different traits evolve. We suggest that these forces are probably cultural selection and that the evolution of many artefact traits can be explained by a shifting-optimum model of cultural selection that, in turn, rests on known psychological biases in aesthetic appreciation. In sum, our results demonstrate the deep unity of the processes and patterns of cultural and organic evolution.
Leroi A, Lambert B, Mauch M, et al., On revolutions, Palgrave Communications, ISSN: 2055-1045
Sometimes the normal course of events is disrupted by a particularly swift and profoundchange. Historians have often referred to such changes as “revolutions” and, though theyhave identified many of them, they have rarely supported their claims with statisticalevidence. Here we present a method to identify revolutions based on a measure of themultivariate rate of change called Foote Novelty. We define revolutions as those periodsof time when the value of this measure, F, can, by a non-parametric test, be shown to besignificantly greater than the background rate. Our method also identifies conservativeperiods when the rate of change is unusually low. We apply it to several quantitativedata sets that capture long-term political, social and cultural changes and, in some ofthem, identify revolutions, both well known and not. Our method is a general one thatcan be applied to any phenomenon captured by multivariate time series data of sufficientquality.
Geier F, Leroi A, Bundy J, 2019, 13C labelling of nematode worms to improve metabolome coverage by heteronuclear nuclear magnetic resonance experiments, Frontiers in Molecular Biosciences, Vol: 6, ISSN: 2296-889X
Nuclear magnetic resonance (NMR) spectroscopy is widely used as a metabolomics tool, and 1D spectroscopy is overwhelmingly the commonest approach. The use of 2D spectroscopy could offer significant advantages in terms of increased spectral dispersion of peaks, but has a number of disadvantages—in particular, heteronuclear 2D spectroscopy is often much less sensitive than 1D NMR. One factor contributing to this low sensitivity in 13C/1H heteronuclear NMR is the low natural abundance of the 13C stable isotope; as a consequence, where it is possible to label biological material with 13C, there is a potential enhancement of sensitivity of up to around 90fold. However, there are some problems that can reduce the advantages otherwise gained—in particular, the fine structure arising from 13C/13C coupling, which is essentially non-existent at natural abundance, can reduce the possible sensitivity gain and increase the chances of peak overlap. Here, we examined the use of two different heteronuclear single quantum coherence (HSQC) pulse sequences for the analysis of fully 13C-labeled tissue extracts from Caenorhabditis elegans nematodes. The constant time ct-HSQC had improved peak shape, and consequent better peak detection of metabolites from a labeled extract; matching this against reference spectra from the HMDB gave a match to about 300 records (although fewer actual metabolites, as some of these represent false positive matches). This approach gives a rapid and automated initial metabolome assignment, forming an ideal basis for further manual curation.
Davies SK, Leroi A, Burt A, et al., 2016, The mutational structure of metabolism in Caenorhabditis elegans., Evolution, Vol: 70, Pages: 2239-2246, ISSN: 0014-3820
A properly functioning organism must maintain metabolic homeostasis. Deleterious mutations degrade organismal function, presumably at least in part via effects on metabolic function. Here we present an initial investigation into the mutational structure of the Caenorhabditis elegans metabolome by means of a mutation accumulation experiment. We find that pool sizes of 29 metabolites vary greatly in their vulnerability to mutation, both in terms of the rate of accumulation of genetic variance (the mutational variance, VM) and the rate of change of the trait mean (the mutational bias, ΔM). Strikingly, some metabolites are much more vulnerable to mutation than any other trait previously studied in the same way. Although we cannot statistically assess the strength of mutational correlations between individual metabolites, principal component analysis provides strong evidence that some metabolite pools are genetically correlated, but also that there is substantial scope for independent evolution of different groups of metabolites. Averaged over MA lines, PC3 is positively correlated with relative fitness, but a model in which metabolites are uncorrelated with fitness is nearly as good by Akaike's Information Criterion (AIC). This article is protected by copyright. All rights reserved.
Helmstetter AJ, Papadopulos AST, Igea J, et al., 2016, Viviparity Stimulates Diversification in an Order of Fish, Nature Communications, Vol: 7, ISSN: 2041-1723
Species richness is distributed unevenly across the tree of life, and this may be influenced by the evolution of novel phenotypes that promote diversification. Viviparity has originated approximately 150 times in vertebrates and is considered to be an adaptation to highly variable environments. Likewise, possessing an annual life cycle is common in plants and insects, where it enables the colonisation of seasonal environments, but rare in vertebrates. The extent to which these reproductive life-history traits have enhanced diversification, and their relative importance in the process remains unknown. We show that convergent evolution of viviparity causes large bursts of diversification in fish. We built a phylogenetic tree for Cyprinodontiformes, an order in which both annualism and viviparity have arisen, and reveal that while both traits have evolved multiple times, only viviparity played a major role in shaping patterns of diversity. These results demonstrate that changes in reproductive life-history strategy can stimulate diversification.
Davies SK, Bundy JG, Leroi AM, 2015, Metabolic Youth in Middle Age: Predicting Aging in Caenorhabditis elegans Using Metabolomics, Journal of Proteome Research, Vol: 14, Pages: 4603-4609, ISSN: 1535-3907
Many mutations and allelic variants are known that influence the rate at which animals age. But when in life do such variants diverge from normal patterns of ageing? And is this divergence visible in their physiologies? To investigate these questions we have used 1H NMR spectroscopy to study how the metabolome of the nematode Caenorhabditis elegans changes as it grows older. We identify a series of metabolic changes that, collectively, predict the age of wild-type worms. We then show that long-lived mutant daf-2(m41) worms are metabolically youthful compared to wild-type worms - but that this relative youth only appears in middle age. Finally, we show that metabolic age predicts the timing and magnitude of differences in age-specific mortality between these strains. Thus the future mortality of these two genotypes can be predicted long before most of the worms die.
Leroi AM, 2014, The Lagoon How Aristotle Invented Science, Publisher: Bloomsbury Publishing, ISBN: 9781408836217
And then, in another dozen books, he explained it all. In The Lagoon, acclaimed biologist Armand Marie Leroi recovers Aristotle's science.
Aging is a complex process, which involves changes in different cellular functions that all can be integrated on the metabolite level. This means that different gene regulation pathways that affect aging might lead to similar changes in metabolism and result in a metabolic signature of senescence. In this chapter, we describe how to establish a metabolic signature of senescence by analyzing the metabolome of various longevity mutants of the model organism Caenorhabditis elegans using gas chromatography-mass spectrometry (GC-MS). Since longevity-associated genes exist for other model organisms and humans, this analysis could be universally applied to body fluids or whole tissue samples for studing the relationship between senescence and metabolism. © Springer Science+Business Media New York 2013.
Aging is a complex process, which involves changes in different cellular functions that all can be integrated on the metabolite level. This means that different gene regulation pathways that affect aging might lead to similar changes in metabolism and result in a metabolic signature of senescence. In this chapter, we describe how to establish a metabolic signature of senescence by analyzing the metabolome of various longevity mutants of the model organism Caenorhabditis elegans using gas chromatography-mass spectrometry (GC-MS). Since longevity-associated genes exist for other model organisms and humans, this analysis could be universally applied to body fluids or whole tissue samples for studing the relationship between senescence and metabolism.
Leroi AM, MacCallum RM, Mauch M, et al., 2012, Reply to Claidiere et al.: Role of psychological bias in evolution depends on the kind of culture, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: E3527-E3527, ISSN: 0027-8424
MacCallum RM, Mauch M, Burt A, et al., 2012, Evolution of music by public choice, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: 12081-12086, ISSN: 0027-8424
Davies SK, Leroi AM, Bundy JG, 2012, Fluorodeoxyuridine affects the identification of metabolic responses to daf-2 status in Caenorhabditis elegans, MECHANISMS OF AGEING AND DEVELOPMENT, Vol: 133, Pages: 46-49, ISSN: 0047-6374
Casadevall i Solvas X, Geier FM, Leroi AM, et al., 2011, High-throughput age synchronisation of Caenorhabditis elegans, Chemical Communications, Vol: 47, Pages: 9801-9803
We present a passive microfluidic strategy for sorting adult C. elegans nematodes on the basis of age and size. The separation mechanism takes advantage of phenotypic differences between ‘adult’ and ‘juvenile’ organisms and their behaviour in microfluidic architectures. In brief, the microfluidic device allows worms to sort themselves in a passive manner.
Geier FM, Want EJ, Leroi AM, et al., 2011, Cross-Platform Comparison of Caenorhabditis elegans Tissue Extraction Strategies for Comprehensive Metabolome Coverage, ANALYTICAL CHEMISTRY, Vol: 83, Pages: 3730-3736, ISSN: 0003-2700
Rebbeck CA, Leroi AM, Burt A, 2011, Mitochondrial Capture by a Transmissible Cancer, SCIENCE, Vol: 331, Pages: 303-303, ISSN: 0036-8075
Fuchs S, Bundy JG, Davies SK, et al., 2010, A metabolic signature of long life in Caenorhabditis elegans, BMC BIOLOGY, Vol: 8
Thomas R, Rebbeck C, Leroi AM, et al., 2009, Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis, CHROMOSOME RESEARCH, Vol: 17, Pages: 927-934, ISSN: 0967-3849
Swire J, Fuchs S, Bundy JG, et al., 2009, The cellular geometry of growth drives the amino acid economy of Caenorhabditis elegans, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 276, Pages: 2747-2754, ISSN: 0962-8452
Leroi AM, 2008, Creationism and its critics in antiquity, NATURE, Vol: 452, Pages: 153-153, ISSN: 0028-0836
Tain LS, Lozano E, Saez AG, et al., 2008, Dietary regulation of hypodermal polyploidization in C-elegans, BMC DEVELOPMENTAL BIOLOGY, Vol: 8, ISSN: 1471-213X
Leroi AM, 2007, Armand Leroi - Q&A, Current Biology, Vol: 17, Pages: R619-R620, ISSN: 0960-9822
Leroi AM, 2006, The future of neo-eugenics., EMBO Reports, Vol: 7, Pages: 1184-1187, ISSN: 1469-221X
Lozano E, Sáez AG, Flemming AJ, et al., 2006, Regulation of growth by ploidy in Caenorhabditis elegans., Current Biology, Vol: 16, Pages: 493-498, ISSN: 0960-9822
Some animals, such as the larvae of Drosophila melanogaster, the larvae of the Appendicularian chordate Oikopleura, and the adults of the nematode Caenorhabditis elegans, are unusual in that they grow largely by increases in cell size. The giant cells of such species are highly polyploid, having undergone repeated rounds of endoreduplication. Since germline polyploid strains tend to have large cells, it is often assumed that endoreduplication drives cell growth, but this remains controversial. We have previously shown that adult growth in C. elegans is associated with the endoreduplication of nuclei in the epidermal syncitium, hyp 7. We show here that this relationship is causal. Manipulation of somatic ploidy both upwards and downwards increases and decreases, respectively, adult body size. We also establish a quantitative relationship between ploidy and body size. Finally, we find that TGF-beta (DBL-1) and cyclin E (CYE-1) regulate body size via endoreduplication. To our knowledge, this is the first experimental evidence establishing a cause-and-effect relationship between somatic polyploidization and body size in a metazoan.
Leroi AM, Swire J, 2006, The recovery of the past, WORLD OF MUSIC, Vol: 48, Pages: 43-54, ISSN: 0043-8774
Leroi AM, 2005, On human diversity, The Scientist, Vol: 19, Pages: 16-17, ISSN: 0890-3670
The past 50 years have seen the scientific community shun any discussion of the causes of normal physical variety in humans. This is primarily because scientists have attempted to remove the concept of race from scientific study. Despite the mass of knowledge regarding the diversity of blood types, allozymes, mitochondrial DNA, the Y chromosome and single nucleotide polymorphisms (SNPs),we know little about what causes of normal physical variety. We know very little about why the Dinka of the Sudan are so tall and African pygmies so small,why the Yakut of Siberia have such high basal metabolic rates, why the Sea Gypsies of Indonesia can see so well underwater, why the Yoruba of Nigeria have so many dizygotic twins, or even why the colors of our skin, eyes, and hair vary across the globe.
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