Diversification with gene flow and niche divergence in a lizard species along the South American “diagonal of open formations”
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Emanuel M. Fonseca↗
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Results for “divergence”
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On the divergence of first-order resonance widths at low eccentricities
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Renu Malhotra↗
Timing the diversification of the Amazonian biota: butterfly divergences are consistent with Pleistocene refugia
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Ivonne J. Garzón‐Orduña↗
Divergent stutter bisimulation abstraction for controller synthesis with linear temporal logic specifications
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Sahar Mohajerani↗
Co-Variability between the Surface Wind Divergence and Vorticity over the Ocean
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Robert Jacobs↗
Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution
When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that generate the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Both cis- and trans-acting regulatory divergence can be hastened by directional selection through adaptation, sexual selection, and inter-sexual conflict, in addition to cryptic evolution under stabilizing selection. Dysfunctional sex-biased gene expression, in particular, may provide an important source of sexually-dimorphic genetic incompatibilities. Here, we characterize and compare male and female/hermaphrodite transcriptome profiles for sibling nematode species Caenorhabditis briggsae and C. nigoni, along with allele-specific expression in their F 1 hybrids, to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, misexpression of sex-biased genes pervades F 1 hybrids of both sexes. This finding implicates greater fragility of male genetic networks to produce dysfunctional organismal phenotypes. Spermatogenesis genes are especially prone to high divergence in both expression and coding sequences, consistent with a “faster male” model for Haldane’s rule and elevated sterility of hybrid males. Moreover, underdominant expression pervades male-biased genes compared to female-biased and sex-neutral genes and an excess of cis-trans compensatory regulatory divergence for X-linked genes underscores a “large-X effect” for hybrid male expression dysfunction. Extensive regulatory divergence in sex determination pathway genes likely contributes to demasculinization of XX hybrids. The evolution of genetic incompatibilities due to regulatory versus coding sequence divergence, however, are expected to arise in an uncorrelated fashion. This study identifies important differences between the sexes in how regulatory networks diverge to contribute to sex-biases in how genetic incompatibilities manifest during the speciation process.
59 BASIC BIOLOGICAL SCIENCES↗
A counter example in linear feature selection theory
The linear feature selection problem in multi-class pattern recognition is described as that of linearly transforming statistical information from n-dimensional (real Euclidean) space into k-dimensional space, while requiring that average interclass divergence in the transformed space decrease as little as possible. Divergence is the expected interclass divergence derived from Hajek two-class divergence; it is known that there always exists a k x n matrix B such that the transformation determined by B maximizes the divergence in k-dimensional space. It is known that, if Q is any k x k invertible matrix, and B is as defined above, then QB again maximizes the divergence in k-space. It is shown that the converse of this result is false: two matrices exist, B sub 1 and B sub 2, each of which maximizes transformed divergence, which are not related in the fashion B sub 2 = QB sub 1 for any k x k matrix Q.
Brown, D. R.↗
Low-frequency variations in the atmospheric branch of the global hydrological cycle
The annual variation of the hydrological cycle is illustrated in terms of hemispheric-mean hydrological variables for the Northern and Southern Hemispheres, while the intraseasonal variations of the global hydrological cycle are illustrated with mean values over two hemispheres that form an east-west partition of the globe. This partition is defined by the 60 deg E-120 deg W great circle and was chosen so that the mean precipitation difference and the divergent water vapor transport between the two hemispheres was maximized. Two years (1979-80) of daily precipitation estimates from the Goddard Laboratory for Atmospheres an 14 years (1979-92) of upper-air data generated by the Global Data Assimilation System at the National Meteorological Center are used in making quantitative estimates of the annual and intraseasonal variations in the global hydrological cycle. The annual variations in hemispheric-mean precipitation (P-circumflex) and water vapor flux divergence (del(vector differential operator) dot Q-circumflex) for the Northern and Southern Hemispheres are comparable with amplitudes of about 0.5 approximately 0.7 mm/day. Both (P-circumflex) and (del(vector differential operator) dot Q-circumflex) vary annually in a coherent way in each hemisphere so that water vapor diverges from the winter hemisphere, where (P-circumflex) reaches its minimum, to the summer hemisphere, where (P-circumflex) attains its maximum. In fact, the hemispheric-mean divergence of water vapor flux changes sign during the annual cycle. Intraseasonal variations of hemispheric-mean precipitation mean P-tilde, evaporation mean E-tilde, and water vapor flux divergence mean del (vector differential operator) dot Q-tilde in the two hemisphres in the east-west direction are comparable with amplitudes of about 0.1 approximately 0.2 mm/day, although amplitudes in some cases exceed 0.3 mm/day. Hemispheric-mean precipitation mean P-tilde varies coherently in opposite phase for the two hemispheres, while mean del (vector differential operator) dot Q-tilde varies so that water vapor diverges from the hemisphere of maximum mean P-tilde to the hemisphere to the hemisphere of minimum mean P-tilde. Intraseasonal variations of mean P-tilde, mean E-tilde, and mean del (vector differential oprator) dot Q-tilde are in accord with the eastward propagation of the intraseasonal global divergent circulation.
Chen, Tsing-Chang↗
Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes
Introduction: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results: We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion: Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.
59 BASIC BIOLOGICAL SCIENCES↗
Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization
Abstract A signaling complex comprising members of the LORELEI (LRE)-LIKE GPI-anchored protein (LLG) and Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) families perceive RAPID ALKALINIZATION FACTOR (RALF) peptides and regulate growth, reproduction, immunity, and stress responses in Arabidopsis (Arabidopsis thaliana). Genes encoding these proteins are members of multigene families in most angiosperms and could generate thousands of signaling complex variants. However, the links between expansion of these gene families and the functional diversification of this critical signaling complex as well as the evolutionary factors underlying the maintenance of gene duplicates remain unknown. Here, we investigated LLG gene family evolution by sampling land plant genomes and explored the function and expression of angiosperm LLGs. We found that LLG diversity within major land plant lineages is primarily due to lineage-specific duplication events, and that these duplications occurred both early in the history of these lineages and more recently. Our complementation and expression analyses showed that expression divergence (i.e. regulatory subfunctionalization), rather than functional divergence, explains the retention of LLG paralogs. Interestingly, all but one monocot and all eudicot species examined had an LLG copy with preferential expression in male reproductive tissues, while the other duplicate copies showed highest levels of expression in female or vegetative tissues. The single LLG copy in Amborella trichopoda is expressed vastly higher in male compared to in female reproductive or vegetative tissues. We propose that expression divergence plays an important role in retention of LLG duplicates in angiosperms.
Plant Sciences↗
Comment on "Table-Top Laser-Based Source of Femtosecond, Collimated, Ultrarelativistic Positron Beams"
Sarri et al. have reported the generation of low divergence (~3 mrad), high-density (10 14 cm –3 ) positron beams using millimeter-scale converter targets and a 50 pC, 200 MeV laser-wakefield accelerated (LWFA) electron source. It was argued that the positron divergence was dominated by the pair-production birth cone angle $θ_{e+} ≈ 1/γ_{e–}$. The small, energy-independent divergence value was used to infer a positron beam density of 2 × 10 14 cm –3 from a 4.2 mm Ta converter target where the divergence and yield measurements agreed with their Monte Carlo (MC) simulations. We have repeated these simulations using experimental conditions and disagree with the reported density, divergence, and yield values by up to factors > 50. In our work, we find that a divergence on the order of milliradian is not physical and can only be achieved if inelastic particle scattering is omitted in the calculations.
47 OTHER INSTRUMENTATION↗
Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone
We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (~0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.
54 ENVIRONMENTAL SCIENCES↗
Meso-beta scale perturbations of the wind field by thunderstorm cells
Data from the high density storm-scale rawinsonde network of the Severe Environmental Storms and Mesoscale Experiment revealed temporal and spatial changes in the divergence fields of the troposphere in response to severe storm evolution on May 2, 1979; these changes were detectable on the meso-beta scale. This unique set of data was subsequently used to study the evolution of the wind, divergence and vertical motion fields in the presence of intense convection. Mid- and upper-tropospheric divergence was superimposed over low-level convergence. The divergence, which has a maximum value of .0004/s, occurred 75 to 100 km upwind as well as over the tornadic cells. To the south of the storm cells, the kinematic pattern was in reverse, upper level convergence was superimposed over low-level divergence. A vertical motion doublet was found to ascend over the squall line and descend about 70 km south of the squall line. It is suggested that the following effects are accountable for the nature of the kinematic fields: (1) blocking of tropospheric environmental flow by the storm cells, (2) anvil outflows, particularly from the tornadic cells, and (3) divergence from the exit region of the jet stream.
Ulanski, S. L.↗
Supersonic aeroelastic instability results for a NASP-like wing model
An experimental study and an analytical study have been conducted to examine static divergence for hypersonic-vehicle wing models at supersonic conditions. A supersonic test in the Langley Unitary Plan Wind Tunnel facility was conducted for two wind-tunnel models. These models were nearly identical with the exception of airfoil shape. One model had a four-percent maximum thickness airfoil and the other model had an eight-percent maximum thickness airfoil. The wing models had low-aspect ratios and highly swept leading edges. The all-movable wing models were supported by a single-pivot mechanism along the wing root. For both of the wind-tunnel models, configuration changes could be made in the wing-pivot location along the wing root and in the wing-pivot pitch stiffness. Three divergence conditions were measured for the four-percent thick airfoil model in the Mach number range of 2.6 to 3.6 and one divergence condition was measured for the eight-percent thick airfoil model at a Mach number of 2.9. Analytical divergence calculations were made for comparison with experimental results and to evaluate the parametric effects of wing-pivot stiffness, wing-pivot location, and airfoil thickness variations. These analyses showed that decreasing airfoil thickness, moving the wing-pivot location upstream, or increasing the pitch-pivot stiffness have the beneficial effect of increasing the divergence dynamic pressures. The calculations predicted the trend of experimental divergence dynamic pressure with Mach number accurately; however, the calculations were approximately 25 percent conservative with respect to dynamic pressure.
Cole, Stanley R.↗
An integrated view of the 1987 Australian monsoon and its mesoscale convective systems. II - Vertical structure
The vertical structure of monsoon thermal forcing by precipitating convection is diagnosed in terms of horizontal divergence. Airborne Doppler-radar divergence profiles from nine diverse mesoscale convective systems (MCSs) are presented. The MCSs consisted of multicellular convective elements which in time gave rise to areas of stratiform precipitation. Each of the three basic building blocks of the MCSs - convective, intermediary, and stratiform precipitation areas - has a consistent, characteristic divergence profile. Convective areas have low-level convergence, with its peak at 2-4 km altitude, and divergence above 6 km. Intermediary areas have convergence aloft, peaked near 10 km, feeding into mean ascent high in the upper troposphere. Stratiform areas have mid-level convergence, indicating a mesoscale downdraught below the melting level, and a mesoscale updraught aloft. Rawinsonde composite divergence profiles agree with the Doppler data in at least one important respect: the lower-tropospheric convergence into the MCSs peaks 2-4-km above the surface. Rawinsonde vorticity profiles show that monsoonal tropical cyclones spin-up at these elevated levels first, then later descend to the surface. Rawinsonde observations on a larger, continental scale demonstrate that at large horizontal scales only the 'gravest vertical mode' of MCS heating is felt, while the effects of shallower components of the heating (or divergence) profiles are trapped near the heating, as predicted by geostrophic adjustment theory.
Mapes, Brian↗
Influence of ocean surface conditions on atmospheric vertical thermodynamic structure and deep convection
The authors analyze the influence of Sea Surface Temperature (SST) and surface wind divergence on atmospheric thermodynamic structure and the resulting effects on the occurrence of deep convection using National Meteorological Center radiosonde data and International Satellite Cloud Climatology Program data for July 1983-July 1985. The onset of deep convection requires not only the existence of positive convective available potential energy (CAPE), but also an unstable planetary boundary layer (PBL). A stable PBL is observed to suppress deep convection even when CAPE is positive. Variations of SST have a major effect on CAPE, but surface wind divergence can also affect deep convection by changing the lapse rate in the lower troposphere and humidity in the PBL. Specifically, when SST is greater than or equal to 28 C, CAPE is always positive, and surface wind divergence does not qualitatively change the buoyancy profile above the PBL. Strong surface wind divergence, however, stabilizes the PBL so as to suppress the initiation of deep convection. In warm SST regions, CAPE is greater than 0 regardless of assumptions about condensate loading, although the pseudoadiabatic limit is more consistent with the observed deep convection than the reversible moist-adiabatic limit under these circumstances. When SST is less than 27 C, CAPE is usually negative and inhibits convection, but strong surface wind convergence can destabilize the inversion layer and moisten the PBL enough to make the atmosphere neutrally stable in the mean. As a result, deep convection is generally enhanced either when SST is greater than or equal to 28 C in the absence of strong surface wind divergence or when strong surface wind convergence occurs even if SST is less than 27 C. The anomalous suppression of deep convection in the warm area of the equatorial west Pacific lying between the intertropical convergence zone (ITCZ) and south Pacific convergence zone (SPCZ) is probably caused by dryness in the PBL and an inversion in that area. The seasonal cycles of deep convection and surface wind divergence are in phase with the maximum solar radiation and lead SST for one to three months in the central Pacific. The change of PBL relative humidity plays a critical role in the changeover to convective instability in this case. The seasonal change of deep convection and associated clouds seems not to have important effects on the seasonal change of local SST in the central Pacific.
Fu, Rong↗
Convergence Rates for Empirical Estimation of Binary Classification Bounds
Bounding the best achievable error probability for binary classification problems is relevant to many applications including machine learning, signal processing, and information theory. Many bounds on the Bayes binary classification error rate depend on information divergences between the pair of class distributions. Recently, the Henze–Penrose (HP) divergence has been proposed for bounding classification error probability. We consider the problem of empirically estimating the HP-divergence from random samples. We derive a bound on the convergence rate for the Friedman–Rafsky (FR) estimator of the HP-divergence, which is related to a multivariate runs statistic for testing between two distributions. The FR estimator is derived from a multicolored Euclidean minimal spanning tree (MST) that spans the merged samples. We obtain a concentration inequality for the Friedman–Rafsky estimator of the Henze–Penrose divergence. We validate our results experimentally and illustrate their application to real datasets.
97 MATHEMATICS AND COMPUTING↗
A conservative, consistent, and scalable meshfree mimetic method
Mimetic methods discretize divergence by restricting the Gauss theorem to mesh cells. Because point clouds lack such geometric entities, construction of a compatible meshfree divergence remains a challenge. In this work, we define an abstract Meshfree Mimetic Divergence (MMD) operator on point clouds by contraction of field and virtual face moments. This MMD satisfies a discrete divergence theorem, provides a discrete local conservation principle, and is first-order accurate. We consider two MMD instantiations. The first one assumes a background mesh and uses generalized moving least squares (GMLS) to obtain the necessary field and face moments. This MMD instance is appropriate for settings where a mesh is available but its quality is insufficient for a robust and accurate mesh-based discretization. The second MMD operator retains the GMLS field moments but defines virtual face moments using computationally efficient weighted graph-Laplacian equations. This MMD instance does not require a background grid and is appropriate for applications where mesh generation creates a computational bottleneck. It allows one to trade an expensive mesh generation problem for a scalable algebraic one, without sacrificing compatibility with the divergence operator. We demonstrate the approach by using the MMD operator to obtain a virtual finite-volume discretization of conservation laws on point clouds. Finally, numerical results in the paper confirm the mimetic properties of the method and show that it behaves similarly to standard finite volume methods.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗