What do we mean by diversity? : the path towards quantification

The concept of biological diversity has evolved from a simple count of species to more sophisticated measures that are sensitive to relative abundances and even to evolutionary divergence times between species. In the course of this evolution, diversity measures have often been borrowed from other disciplines. Biological reasoning about diversity often implicitly assumed that measures of diversity had certain mathematical properties, but most of biology?s traditional diversity measures did not actually possess these properties, a situation which often led to mathematically and biologically invalid inferences. Biologists now usually transform the traditional measures to the «effective number of species», whose mathematics does support most of the rules of inference that biologists apply to them. The effective number of species, then, seems to capture most (though not all) of what biologists mean by diversity

Euclidean versus hyperbolic congestion in idealized versus experimental networks

This paper proposes a mathematical justification of the phenomenon of extreme congestion at a very limited number of nodes in very large networks. It is argued that this phenomenon occurs as a combination of the negative curvature property of the network together with minimum length routing. More specifically, it is shown that, in a large n-dimensional hyperbolic ball B of radius R viewed as a roughly similar model of a Gromov hyperbolic network, the proportion of traffic paths transiting through a small ball near the center is independent of the radius R whereas, in a Euclidean ball, the same proportion scales as 1/R^{n-1}. This discrepancy persists for the traffic load, which at the center of the hyperbolic ball scales as the square of the volume, whereas the same traffic load scales as the volume to the power (n+1)/n in the Euclidean ball. This provides a theoretical justification of the experimental exponent discrepancy observed by Narayan and Saniee between traffic loads in Gromov-hyperbolic networks from the Rocketfuel data base and synthetic Euclidean lattice networks. It is further conjectured that for networks that do not enjoy the obvious symmetry of hyperbolic and Euclidean balls, the point of maximum traffic is near the center of mass of the network.Comment: 23 pages, 4 figure

Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model

<div><p>Shannon entropy <i>H</i> and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information (“Shannon differentiation”) between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (<i>Sturnus vulgaris</i>) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.</p></div

Diversity from genes to ecosystems : a unifying framework to study variation across biological metrics and scales

This work was assisted through participation in “Next Generation Genetic Monitoring” Investigative Workshop at the National Institute for Mathematical and Biological Synthesis, sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Hawaiian fish community data were provided by the NOAA Pacific Islands Fisheries Science Center's Coral Reef Ecosystem Division (CRED) with funding from NOAA Coral Reef Conservation Program. O.E.G. was supported by the Marine Alliance for Science and Technology for Scotland (MASTS). A. C. and C. H. C. were supported by the Ministry of Science and Technology, Taiwan. P.P.-N. was supported by a Canada Research Chair in Spatial Modelling and Biodiversity. K.A.S. was supported by National Science Foundation (BioOCE Award Number 1260169) and the National Center for Ecological Analysis and Synthesis. All data used in this manuscript are available in DRYAD (https://doi.org/dx.doi.org/10.5061/dryad.qm288) and BCO-DMO (http://www.bco-dmo.org/project/552879).Biological diversity is a key concept in the life sciences and plays a fundamental role in many ecological and evolutionary processes. Although biodiversity is inherently a hierarchical concept covering different levels of organisation (genes, population, species, ecological communities and ecosystems), a diversity index that behaves consistently across these different levels has so far been lacking, hindering the development of truly integrative biodiversity studies. To fill this important knowledge gap we present a unifying framework for the measurement of biodiversity across hierarchical levels of organisation. Our weighted, information-based decomposition framework is based on a Hill number of order q = 1, which weights all elements in proportion to their frequency and leads to diversity measures based on Shannon’s entropy. We investigated the numerical behaviour of our approach with simulations and showed that it can accurately describe complex spatial hierarchical structures. To demonstrate the intuitive and straightforward interpretation of our diversity measures in terms of effective number of components (alleles, species, etc.) we applied the framework to a real dataset on coral reef biodiversity. We expect our framework will have multiple applications covering the fields of conservation biology, community genetics, and eco-evolutionary dynamics.Publisher PDFPeer reviewe

Phylogenetic analysis of Andinia (Pleurothallidinae; Orchidaceae) and a systematic re-circumscription of the genus

Most of the species studied in this paper have previously been placed in either Pleurothallis or Lepanthes. However, at one time or another, members of the group have also been placed in the genera Andinia, Brachycladium, Lueranthos, Masdevalliantha, Neooreophilus, Oreophilus, Penducella, Salpistele and Xenosia. Phylogenetic analyses of nuclear ITS and plastid matK sequences indicate that these species form a strongly supported clade that is only distantly related to Lepanthes and is distinct from Pleurothallis and Salpistele. Since this clade includes the type species of Andinia, A. dielsii, and it has taxonomic precedence over all other generic names belonging to this group, Andinia is re-circumscribed and expanded to include 72 species segregated into five subgenera: Aenigma, Andinia, Brachycladium, Masdevalliantha and Minuscula. The required taxonomic transfers are made herein. We hypothesize that convergent evolution towards a similar pollinator syndrome involving deceit pollination via pseudocopulation by Diptera resulted in a similar floral morphology between species of subgenus Brachycladium and species of Lepanthes; hence the prior placement of the species of subgenus Brachycladium in Lepanthes. Species of the re-circumscribed Andinia are confined exclusively to the Andes, ranging from about 1,200 to 3,800 m, from Colombia south to Bolivia, making the generic name very apt. Elevational distributions of the individual clades are discussed in relation to the possible evolutionary diversification of the most species-rich clade, subgenus Brachycladium.La mayoría de las especies aquí estudiadas han sido previamente incluidas ya sea en el género Pleurothallis o en Lepanthes. Sin embargo, en un momento u otro, miembros del grupo también han sido colocados en los géneros Andinia, Brachycladium, Lueranthos, Masdevalliantha, Neooreophilus, Oreophilus, Penducella, Salpistele y Xenosia. Análisis filogenéticos de secuencias de las regiones ITS y matK indican que estas especies forman un clado fuertemente soportado que está solo distantemente relacionado con Lepanthes y que es diferente de las especies de Pleurothallis y Salpistele. Ya que este clado incluye la especie tipo de Andinia, A. dielsii y que tiene precedencia taxonómica sobre los demás nombres genéricos que pertenecen al grupo, se re-circunscribe y expande el género Andinia para incluir 72 especies segregadas en cinco subgéneros: Aenigma, Andinia, Brachycladium, Masdevalliantha y Minuscula y se hacen las transferencias taxonómicas requeridas. Hipotetizamos que la evolución convergente hacia un síndrome de polinización similar que involucra la polinización por engaño por medio de la pseudocópula por Diptera, resultó en una morfología floral similar entre las especies del subgénero Brachycladium y las especies de Lepanthes; de ahí la ubicación previa de las especies del subgénero Brachycladium en Lepanthes. Las especies de Andinia están confinadas exclusivamente a los Andes, distribuidas aproximadamente desde 1200 m a 3800 m desde Colombia hasta Bolivia, haciendo del nombre genérico uno muy adequado. Se discuten las distribuciones altitudinales de los clados individuales en relación a la posible diversificacion evolutiva del clado con más especies, el cual corresponde al subgénero Brachycladium.Universidad de Costa Rica/[814-B1-239]/UCR/Costa RicaUniversidad de Costa Rica/[814-B3-075]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL

New SOA Treatments Within the Energy Exascale Earth System Model (E3SM): Strong Production and Sinks Govern Atmospheric SOA Distributions and Radiative Forcing

Secondary organic aerosols (SOA) are large contributors to fine particle mass loading and number concentration and interact with clouds and radiation. Several processes affect the formation, chemical transformation, and removal of SOA in the atmosphere. For computational efficiency, global models use simplified SOA treatments, which often do not capture the dynamics of SOA formation. Here we test more complex SOA treatments within the global Energy Exascale Earth System Model (E3SM) to investigate how simulated SOA spatial distributions respond to some of the important but uncertain processes affecting SOA formation, removal, and lifetime. We evaluate model predictions with a suite of surface, aircraft, and satellite observations that span the globe and the full troposphere. Simulations indicate that both a strong production (achieved here by multigenerational aging of SOA precursors that includes moderate functionalization) and a strong sink of SOA (especially in the middle upper troposphere, achieved here by adding particle-phase photolysis) are needed to reproduce the vertical distribution of organic aerosol (OA) measured during several aircraft field campaigns; without this sink, the simulated middle upper tropospheric OA is too large. Our results show that variations in SOA chemistry formulations change SOA wet removal lifetime by a factor of 3 due to changes in horizontal and vertical distributions of SOA. In all the SOA chemistry formulations tested here, an efficient chemical sink, that is, particle-phase photolysis, was needed to reproduce the aircraft measurements of OA at high altitudes. Globally, SOA removal rates by photolysis are equal to the wet removal sink, and photolysis decreases SOA lifetimes from 10 to ~3 days. A recent review of multiple field studies found no increase in net OA formation over and downwind biomass burning regions, so we also tested an alternative, empirical SOA treatment that increases primary organic aerosol (POA) emissions near source region and converts POA to SOA with an aging time scale of 1 day. Although this empirical treatment performs surprisingly well in simulating OA loadings near the surface, it overestimates OA loadings in the middle and upper troposphere compared to aircraft measurements, likely due to strong convective transport to high altitudes where wet removal is weak. The default improved model formulation (multigenerational aging with moderate fragmentation and photolysis) performs much better than the empirical treatment in these regions. Differences in SOA treatments greatly affect the SOA direct radiative effect, which ranges from -0.65 (moderate fragmentation and photolysis) to -2 W m-2 (moderate fragmentation without photolysis). Notably, most SOA formulations predict similar global indirect forcing of SOA calculated as the difference in cloud forcing between present-day and preindustrial simulations. © 2020. The Authors

All inkjet-printed graphene-based conductive patterns for wearable e-textile applications

© 2017 The Royal Society of Chemistry. Inkjet printing of graphene inks is considered to be very promising for wearable e-textile applications as benefits of both inkjet printing and extra-ordinary electronic, optical and mechanical properties of graphene can be exploited. However, the common problem associated with inkjet printing of conductive inks on textiles is the difficulty to print a continuous conductive path on a rough and porous textile surface. Here we report inkjet printing of an organic nanoparticle based surface pre-treatment onto textiles to enable all inkjet-printed graphene e-textiles for the first time. The functionalized organic nanoparticles present a hydrophobic breathable coating on textiles. Subsequent inkjet printing of a continuous conductive electrical path onto the pre-treated coating reduced the sheet resistance of graphene-based printed e-textiles by three orders of magnitude from 1.09 × 106 Ω sq-1 to 2.14 × 103 Ω sq-1 compared with untreated textiles. We present several examples of how this finding opens up opportunities for real world applications of printed, low cost and environmentally friendly graphene wearable e-textiles

Environmental and Climatic Determinants of Molecular Diversity and Genetic Population Structure in a Coenagrionid Damselfly

Identifying environmental factors that structure intraspecific genetic diversity is of interest for both habitat preservation and biodiversity conservation. Recent advances in statistical and geographical genetics make it possible to investigate how environmental factors affect geographic organisation and population structure of molecular genetic diversity within species. Here we present a study on a common and wide ranging insect, the blue tailed damselfly Ischnuraelegans, which has been the target of many ecological and evolutionary studies. We addressed the following questions: (i) Is the population structure affected by longitudinal or latitudinal gradients?; (ii) Do geographic boundaries limit gene flow?; (iii) Does geographic distance affect connectivity and is there a signature of past bottlenecks?; (iv) Is there evidence of a recent range expansion and (vi) what is the effect of geography and climatic factors on population structure? We found low to moderate genetic sub-structuring between populations (mean FST = 0.06, Dest = 0.12), and an effect of longitude, but not latitude, on genetic diversity. No significant effects of geographic boundaries (e.g. water bodies) were found. FST-and Dest-values increased with geographic distance; however, there was no evidence for recent bottlenecks. Finally, we did not detect any molecular signatures of range expansions or an effect of geographic suitability, although local precipitation had a strong effect on genetic differentiation. The population structure of this small insect has probably been shaped by ecological factors that are correlated with longitudinal gradients, geographic distances, and local precipitation. The relatively weak global population structure and high degree of genetic variation within populations suggest that I. elegans has high dispersal ability, which is consistent with this species being an effective and early coloniser of new habitats

Evidence for rangewide panmixia despite multiple barriers to dispersal in a marine mussel

Oceanographic features shape the distributional and genetic patterns of marine species by interrupting or promoting connections among populations. Although general patterns commonly arise, distributional ranges and genetic structure are species-specific and do not always comply with the expected trends. By applying a multimarker genetic approach combined with Lagrangian particle simulations (LPS) we tested the hypothesis that oceanographic features along northeastern Atlantic and Mediterranean shores influence dispersal potential and genetic structure of the intertidal mussel Perna perna. Additionally, by performing environmental niche modelling we assessed the potential and realized niche of P. perna along its entire native distributional range and the environmental factors that best explain its realized distribution. Perna perna showed evidence of panmixia across > 4,000 km despite several oceanographic breaking points detected by LPS. This is probably the result of a combination of life history traits, continuous habitat availability and stepping-stone dynamics. Moreover, the niche modelling framework depicted minimum sea surface temperatures (SST) as the major factor shaping P. perna distributional range limits along its native areas. Forthcoming warming SST is expected to further change these limits and allow the species to expand its range polewards though this may be accompanied by retreat from warmer areas.Fundacao para a Ciencia e Tecnologia (FCT-MEC, Portugal) [UID/Multi/04326/2013, IF/01413/2014/CP1217/CT0004]; South African Research Chairs Initiative (SARChI) of the Department of Science and Technology; National Research Foundation; South African National Research Foundation (NRF); Portuguese Fundacao para a Ciencia e Tecnologia (FCT) [SFRH/BPD/85040/2012, SFRH/BPD/111003/2015]info:eu-repo/semantics/publishedVersio

Lessons Learned from Multi-scale Modeling of the Failing Heart

[EN] Heart failure constitutes a major public health problem worldwide. Affected patients experience a number of changes in the electrical function of the heart that predispose to potentially lethal cardiac arrhythmias. Due to the multitude of electrophysiological changes that may occur during heart failure, the scientific literature is complex and sometimes ambiguous, perhaps because these findings are highly dependent on the etiology, the stage of heart failure, and the experimental model used to study these changes. Nevertheless, a number of common features of failing hearts have been documented. Prolongation of the action potential (AP) involving ion channel remodeling and alterations in calcium handling have been established as the hallmark characteristics of myocytes isolated from failing hearts. Intercellular uncoupling and fibrosis are identified as major arrhythmogenic factors. Multi-scale computational simulations are a powerful tool that complements experimental and clinical research. The development of biophysically detailed computer models of single myocytes and cardiac tissues has contributed greatly to our understanding of processes underlying excitation and repolarization in the heart. The electrical, structural, and metabolic remodeling that arises in cardiac tissues during heart failure has been addressed from different computational perspectives to further understand the arrhythmogenic substrate. This review summarizes the contributions from computational modeling and simulation to predict the underlying mechanisms of heart failure phenotypes and their implications for arrhythmogenesis, ranging from the cellular level to whole-heart simulations. The main aspects of heart failure are presented in several related sections. An overview of the main electrophysiological and structural changes that have been observed experimentally in failing hearts is followed by the description and discussion of the simulation work in this field at the cellular level, and then in 2D and 3D cardiac structures. The implications for arrhythmogenesis in heart failure are also discussed including therapeutic measures, such as drug effects and cardiac resynchronization therapy. Finally, the future challenges in heart failure modeling and simulation will be discussed.This work was partially supported by (i) the "VI Plan Nacional de Investigacion Cientifica, Desarrollo e Innovacion Tecnologica" from the Ministerio de Economia y Competitividad of Spain and the European Commission (European Regional Development Funds ERDF-FEDER) (grant number TIN2012-37546-C03-01), and by (ii) Programa Prometeo de la Conselleria d'Educacio Formacio I Ocupacio, Generalitat Valenciana (grant number PROMETEO/2012/030).Gómez García, JF.; Cardona-Urrego, KE.; Trénor Gomis, BA. (2015). Lessons Learned from Multi-scale Modeling of the Failing Heart. Journal of Molecular and Cellular Cardiology. 89:146-159. https://doi.org/10.1016/j.yjmcc.2015.10.016S1461598