Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1

SYNOPSIS. Developmental Evolution (DE) contributes to various research programs in biology, such as the assessment of homology and the determination of the genetic architecture underlying species differences. The most distinctive contribution offered by DE to evolutionary biology, however, is the elucidation of the role of developmental mechanisms in the origin of evolutionary innovations. To date, explanations of evolutionary innovations have remained beyond the reach of classical evolutionary genetics, because such explanations require detailed information on the function of genes and the emergent developmental dynamics of their interactions with other genetic factors. We argue that this area has the potential to become the core of DE’s disciplinary identity. The main challenge in developing a research program for DE along these lines, however, is to provide a methodological framework that accounts for the fact that developmental mechanisms continue to evolve after a character has originated. Developmental mechanisms elucidated in a derived species may therefore not provide insights into the evolutionary origin of the character in question. To meet this challenge, we propose a set of questions that may guide us in our search for valid inferences on the role of developmental mechanisms in the explanation of evolutionary innovations.
Analysis of Hydrogen Peroxide–independent Expression of the High-light–inducible ELIP2 Gene with the Aid of the ELIP2 Promoter–Luciferase Fusion¶

Abstract Intense and excessive light triggers the evolution of reactive oxygen species in chloroplasts, and these have the potential to cause damage. However, plants are able to respond to light stress and protect the chloroplasts by various means, including transcriptional regulation at the nucleus. Activation of light stress–responsive genes is mediated via hydrogen peroxide–dependent and –independent pathways. In this study, we characterized the Early-Light–Inducible Protein 2 (ELIP2) promoter–luciferase gene fusion (ELIP2::LUC), which responds only to the hydrogen peroxide–independent pathway. Our results show that ELIP2::LUC is expressed under nonstressful conditions in green tissue containing juvenile and developing chloroplasts. Upon light stress, expression was activated in leaves with mature as well as developing chloroplasts. In contrast to another high-light–inducible gene, APX2, which responds to the hydrogen peroxide–dependent pathway, the activation of ELIP2::LUC was cell autonomous. The activation was suppressed by application of 3-(3,4)-dichlorophenyl-1,1-dimethylurea, an inhibitor of the reduction of plastoquinone, whereas 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, an inhibitor of the oxidation of plastoquinone, gave the contrasting effect, which may suggest that the redox state of the plastoquinone plays an important role in triggering the hydrogen peroxide–independent light stress signaling.
Distribuição e Variação na Pelagem de Callicebus coimbrai (Primates, Pitheciidae) nos Estados de Sergipe e Bahia, Brasil

São Bernardo, C. S. e Galetti M. 2004. Densidade e tamanho populacional de primatas em um fragmento florestal no sudeste do Brasil. Rev. Bras. Zool. 21(4): 827–832. Shaffer, M. L. 1981. Minimum population sizes for species conservation. BioScience 31(2): 131–134. Silva, J. M. C. e Casteleti, C. H. M. 2005. Estado da biodiversidade da Mata Atlântica brasileira. Em: Mata Atlântica – Biodiversidade, Ameaças e Perspectivas, C. Galindo-Leal e I. G. Câmara (eds.), pp.43-59. Fundação SOS Mata Atlântica e Conservação Internacional, Belo Horizonte. Stevenson, M. F. e Rylands, A. B. 1988. The marmosets, genus Callithrix. Em: Ecology and Behavior of Neotropical Primates, vol. 2, R. A. Mittermeier, A. B. Rylands, A. F. Coimbra-Filho e G. A. B. Fonseca (eds.), pp.131–211. World Wildlife Fund, Washington, D.C. Thomas, L. , Laake, J. L. , Strindberg, S. , Marques, F. F. C. , Buckland, S. T. , Borchers, D. L. , Anderson, D. R. , Burnham, K. P., Hedley, S. L. , Pollard, J. H. , Bishop, J. R. B. e Marques T. A. 2005. Distance 5.0. Release Beta 5. Research Unit for Wildlife Population Assessment, University of St. Andrews, UK. Sítio: . Acessada em 20 de abril de 2006. Vieira, M. V. , Faria, D. M. , Fernandez, F. A. S. , Ferrari, S. F. , Freitas, S. R. , Gaspar, D. A. , Moura, R. T. , Olifiers, N. , Oliveira, P. P., Pardini, R. , Pires, A. S. , Ravetta, A. , Mello, M. A. R. , Ruiz-Miranda, C. R. e Setz, E. Z. F. 2003. Mamíferos. Em: Fragmentação de Ecossistemas: Causas e Efeitos Sobre a Biodiversidade e Recomendações de Políticas Públicas, D. M. Rambaldi e D. A. S. Oliveira (eds.), pp.125–151. MMA/CNPq, Brasília.
Effects of Multiple Disturbances (Fire and Hurricane) on Epiphyte Community Dynamics in a Subtropical Forest, Florida, U.S.A.1

Abstract We addressed the interacting effects of a natural large-scale fire and a subsequent major hurricane on relative positions of epiphytes in a subtropical forest. In Everglades National Park, subtropical hammocks (hardwood tree “islands”; burned and unburned) during the Ingraham Fire (1989) were surveyed for trees and epiphytic bromeliads (Tillandsia spp.) one year before, as well as one and five years after, Hurricane Andrew (1992). We measured trees (species, diameter, and status [alive/dead]) and epiphytes (species, height, host tree characteristics, substrate life status, and density). The fire decreased the height of epiphytes during the hurricane because branches and bark of trees killed by the fire were unstable epiphyte substrates in the high winds. Proportions of epiphytes on Quercus virginiana were equally increased after the hurricane in both unburned and burned hammocks; the large size and bark characteristics resulted in greater proportional survival of epiphytes on this species. During the five years following the hurricane, changes in the distributions of epiphytes generally were toward pre-hurricane distributions, but recovery was faster in unburned than burned hammocks. We conclude that disturbances that kill trees are likely to amplify the vertical reduction of epiphytes during a subsequent hurricane and that effects of a single disturbance on plant populations can be influenced by the disturbance history of the system, including different types of disturbances.
THE EVOLUTION OF SPERM-ALLOCATION STRATEGIES AND THE DEGREE OF SPERM COMPETITION

Abstract The prevailing viewpoint in the study of sperm competition is that male sperm-allocation strategies evolve in response to the degree of sperm competition an ejaculate can expect to experience within a given mating. If males cannot assess the degree of sperm competition their ejaculate will face and/or they are unable to facultatively adjust sperm investment in response to perceived levels of competition, high sperm allocation (per mating) is predicted to evolve in the context of high sperm competition. An implicit assumption of the framework used to derive this result is that the degree of sperm competition is unaffected by changes in sperm-allocation strategies. We present theory based on an alternative perspective, in which the degree of sperm competition and the sperm-allocation strategy are coupled traits that coevolve together. Our rationale is that the pattern of sperm allocation in the population will, in part, determine the level of sperm competition by affecting the number of ejaculates per female in the population. In this setting, evolution in sperm-allocation strategies is driven by changes in underlying environmental parameters that influence both the degree of sperm competition and sperm allocation. This change in perspective leads to predictions that are qualitatively different from those of previous theory.
SAWAREF: Multi-component Toolkit for Arabic morphosytactic tagging

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THE CONTRIBUTION OF EDAPHIC HETEROGENEITY TO THE EVOLUTION AND DIVERSITY OF BURSERACEAE TREES IN THE WESTERN AMAZON

Environmental heterogeneity in the tropics is thought to lead to specialization in plants and thereby contribute to the diversity of the tropical flora. We examine this idea with data on the habitat specificity of 35 western Amazonian species from the genera Protium, Crepidospermum, and Tetragastris in the monophyletic tribe Protieae (Burseraceae) mapped on a molecular-based phylogeny. We surveyed three edaphic habitats that occur throughout terra firme Amazonia: white-sand, clay, and terrace soils in eight forests across more than 2000 km in the western Amazon. Twenty-six of the 35 species were found to be associated with only one of three soil types, and no species was associated with all three habitats; this pattern of edaphic specialization was consistent across the entire region. Habitat association mapped onto the phylogenetic tree shows association with terrace soils to be the probable ancestral state in the group, with subsequent speciation events onto clay and white-sand soils. The repeated gain of clay association within the clade likely coincides with the emergence of large areas of clay soils in the Miocene deposited during the Andean uplift. Character optimizations revealed that soil association was not phylogenetically clustered for white-sand and clay specialists, suggesting repeated independent evolution of soil specificity is common within the Protieae. This phylogenetic analysis also showed that multiple cases of putative sister taxa with parapatric distributions differ in their edaphic associations, suggesting that edaphic heterogeneity was an important driver of speciation in the Protieae in the Amazon basin.
Evidence for Yellow Light Suppression of Lettuce Growth¶

Abstract Researchers studying plant growth under different lamp types often attribute differences in growth to a blue light response. Lettuce plants were grown in six blue light treatments comprising five blue light fractions (0, 2, 6% from high-pressure sodium [HPS] lamps and 6, 12, 26% from metal halide [MH] lamps). Lettuce chlorophyll concentration, dry mass, leaf area and specific leaf area under the HPS and MH 6% blue were significantly different, suggesting wavelengths other than blue and red affected plant growth. Results were reproducible in two replicate studies at each of two photosynthetic photon fluxes, 200 and 500 μmol m−2 s−1. We graphed the data against absolute blue light, phytochrome photoequilibrium, phototropic blue, UV, red:far red, blue:red, blue:far red and ‘yellow’ light fraction. Only the ‘yellow’ wavelength range (580–600 nm) explained the differences between the two lamp types.
TRITURUS NEWTS DEFY THE RUNNING-SWIMMING DILEMMA

Abstract Conflicts between structural requirements for carrying out different ecologically relevant functions may result in a compromise phenotype that maximizes neither function. Identifying and evaluating functional trade-offs may therefore aid in understanding the evolution of organismal performance. We examined the possibility of an evolutionary trade-off between aquatic and terrestrial locomotion in females of European species of the newt genus Triturus. Biomechanical models suggest a conflict between the requirements for aquatic and terrestrial locomotion. For instance, having an elongate, slender body, a large tail, and reduced limbs should benefit undulatory swimming, but at the cost of reduced running capacity. To test the prediction of an evolutionary trade-off between swimming and running capacity, we investigated relationships between size-corrected morphology and maximum locomotor performance in females of ten species of newts. Phylogenetic comparative analyses revealed that an evolutionary trend of body elongation (increasing axilla-groin distance) is associated with a reduction in head width and forelimb length. Body elongation resulted in reduced maximum running speed, but, surprisingly, also led to a reduction in swimming speed. The evolution of longer tails was associated with an increase in maximal swimming speed. We found no evidence for an evolutionary trade-off between aquatic and terrestrial locomotor performance, probably because of the unexpected negative effect of body elongation on swimming speed. We conclude that the idea of a design conflict between aquatic and terrestrial locomotion, mediated through antagonistic effects of body elongation, does not apply to our model system.
Photooxidative Treatment of Sulfurous Water for Its Potabilization¶

Abstract The feasibility of potabilization of sulfurous water was investigated by photochemical oxidation processes using a batch photoreactor and a continuous-flow photoreactor, equipped with UV lamps of 1000 W and 1500 W, respectively. Additionally, two advanced processes of oxidation were applied i.e. with a use of a UV light/H2O2/air and UV light/H2O2/O3/air. These two processes were compared for their efficiency to the direct oxidation process where ozone is used in the absence of UV light. Results obtained for both advanced processes showed better oxidation than takes place by ozone in the absence of UV light. After the photooxidation processes, different processes for the absorption or precipitation of sulfates were investigated to comply with the World Health Organization (WHO) norm that demands a limit of ≤250 mgL−1 of SO42− in drinking water. Additionally, reverse osmosis was simulated using Osmonics Inc. software to predict the feasibility of lowering the salt concentration below WHO limits.
Variation in Species and Trophic Composition of Insect Communities in Puerto Rico1

Abstract Insects are important participants in many ecosystem processes, but the effects of anthropogenic and natural disturbances on insect communities have been poorly studied. To describe how disturbances affect insect communities, we addressed two questions: Do insect communities return to a pre-hurricane composition? And how do insect communities change during succession? To answer these questions, we studied insect communities in a chronosequence of two abandoned pastures (5 yr and 32 yr) and a mature forest (>80 yr) that were recently disturbed by two hurricanes (Hurricane Hugo, 1989; Hurricane Georges, 1998). Although insect abundance and richness fluctuated during the study, all sites returned to pre-hurricane (Hurricane Georges) abundance and richness in less than one year. All trophic categories present before Hurricane Georges were present after the hurricane, but richness within categories fluctuated greatly. Insect richness did not increase during succession; the 5 yr site had the highest richness, the >80 yr site had an intermediate richness, and the 32 yr site the lowest. Nevertheless, the species composition of the two forested sites was different in comparison to the 5 yr site. These results suggest that trophic structure varies little in time and space, but the species composition within each trophic category is highly variable.
Use of Fruiting Trees by Birds in Continuous Forest and Riparian Forest Remnants in Los Tuxtlas, Veracruz, Mexico1

Abstract The composition of plant species in fragmented landscapes may be influenced by the pattern of visitation by birds to fruiting trees and by the movement of seeds among and within fragments. We compared bird visitation patterns to two tree species (Dendropanax arboreus, Araliaceae; Bursera simaruba, Burseraceae) in continuous forest and remnants of riparian vegetation in a region dominated by pasture in Los Tuxtlas, Veracruz, Mexico. We quantified frequency of visitation, fruit consumption, consistency of visitation (percentage of total tree observation periods during which a given bird species was recorded), and species composition of birds at individuals of both tree species in continuous forest and riparian remnants. Bird visitation rate, species richness, and fruit consumption rates were similar within both tree species in the two habitats. Species assemblages at D. arboreus were different between continuous forest and remnants. Species assemblages at B. simaruba did not differ by habitat. Our results demonstrate that habitat disturbance may influence avian visitation patterns, which may in turn affect subsequent recruitment patterns in some tree species. Our results, however, were not consistent between the tree species, suggesting that it is difficult to generalize concerning the effects of forest disturbance on avian species assemblages in fruiting trees.
Blind channel estimation for OFDM systems

AbstmctA novel approach of blind channel estimation for OFDM systems is proposed. The information bearing blocks are preprocessed by a mimple linear preeading scheme, which does not introduce redundancy to the block, nor it changes the block length. The precoding imposes a correlation structure on the transmitted blocks, which Ebe exploited at the receiver to r e cover the channel via a computationally simpla cross-correlation procedure. For the Eof BPSK signal the channel estimation is possible based on a single black, while for high-order constellations a small lynount of averaging over successive blocks is required. The performance of the proposed approach b tested analytically, thmugh a mean-square error analysis, and also via simulations. Our resulta suggest that, at low SNR. our blind e_ timstion perform better that channel Bstimation based on training data.
Wildfire effects on β-diversity and species turnover in a forested landscape

Abstract Questions: What are the effects of fire on the relationships between community composition and environment? Does fire affect β-diversity and rates of species turnover along spatial and environmental gradients? Do these effects differ among functional groups? Location: Linville Gorge, in the southern Appalachians of western North Carolina, USA. Methods: We sampled all vascular plants in 20 plots (200 to 400 m2) before and after a wildfire. We used Non-metric Multidimensional Scaling to compare pre- and post-fire relationships between community composition and elevation, fire history, and topographic moisture. We compared Whittaker's βw and quantified rates of species turnover along geographic and environmental gradients for all plants, trees, shrubs, and herbs. Randomization tests were used to determine whether rates of species turnover changed after the fire. Results: Correlations between community composition and environmental variables generally increased after fire. The largest increase was for elevation, reflecting its potential to influence fire severity. βw decreased only slightly and the only statistically significant change in species turnover rates occurred for herbs over geographic distance. Conclusions: Large changes in community composition occurred after fire due to immigration of herbaceous species. Community-environment correlations increased but β-diversity did not change because fire effects and immigration were influenced by the same environmental gradients that structured vegetation pre-fire. Results differed for herbaceous species that responded to environmental but not spatial gradients post-fire. Dispersal limitation and community resilience through resprouting or regeneration from serotinous cones in dominant woody vegetation maintain β-diversity and species turnover after fire. Nomenclature: Kartesz (1994).
Sex in Space: Pollination among Spatially Isolated Plants1

ABSTRACT Plant distributions are changing at unprecedented rates, primarily due to habitat clearance and the spread of alien invasive species. Landscape pattern and local density can affect plant sexual processes, particularly those mediated by biotic vectors, by acting on the composition and behavior of pollinators and seed dispersers. Ecologists are now grappling with the likely effects of these altered processes on future forest composition as existing plant reproductive mutualisms break down or adjust to new spatial circumstances. Here, we introduce five papers that address pollinator responses and pollination outcomes in a variety of human-dominated landscapes and emphasize the need to better understand the dynamic nature of plant–pollinator interactions.
Why Do Some Tropical Forests Have So Many Species of Trees

Understanding why there are so many kinds of tropical trees requires learning, not only how tree species coexist, but what factors drive tree speciation and what governs a tree clade’s diversification rate. Many report that hybrid sterility evolves very slowly between separated tree populations. If so, tree species rarely originate by splitting of large populations. Instead, they begin with few trees. The few studies available suggest that reproductive isolation between plant populations usually results from selection driven by lowered fitness of hybrids: speciation is usually a response to a ‘‘niche opportunity. ’’ Using Hubbell’s neutral theory of forest dynamics as a null hypothesis, we show that if new tree species begin as small populations, species that are now common must have spread more quickly than chance allows. Therefore, most tree species have some setting in which they can increase when rare. Trees face trade-offs in suitability for different microhabitats, different-sized clearings, different soils and climates, and resistance to different pests. These trade-offs underlie the mechanisms maintaining a-diversity and species turnover. Disturbance and microhabitat specialization appear insufficient to maintain a-diversity of tropical trees, although they may maintain tree diversity north of Mexico or in northern Europe. Many studies show that where trees grow readily, tree diversity is higher and temperature and rainfall are less seasonal. The few data available suggest that pest pressure is higher, maintaining higher tree diversity, where winter is absent. Tree a-diversity is also higher in regions with more tree species, which tend to be larger, free for a longer time from major shifts of climate, or in the tropics, where there are more opportunities for local coexistence.
A Comparison of Four Series of CISCO Network Processors

Network processors have created new opportunities by performing more complex calculations. Routers perform the most useful and difficult processing operations. In this paper the routers of VXR 7200, ISR 4451-X, SBC 7600, 7606 have been investigated which their main positive points include scalability, flexibility, providing integrated services, high security, supporting and updating with the lowest cost, and supporting standard protocols of network. In addition, in the current study these routers have been explored from hardware and processor capacity viewpoints separately.
Lexical anaphors in Danish and French

The article treats lexically varied noun-phrase anaphors, so-called ‘unfaithful anaphors’, which are found more frequently in French than in Danish texts. The difference is related to more fundamental differences between the two languages, and types of language, at different linguistic levels. Thus, French lexicalises more semantic content in nouns than in verbs, and vice versa in Danish, the former language preferring exocentric ordering at the syntactic level compared to Danish endocentric ordering. Much of the information of unfaithful anaphors being new, French can be said to communicate presupposed information, where Danish ‘poses’, i.e. states new information. And finally, in French the semantic content of an unfaithful anaphor often entertains a rhetorical relation with its host predicate, where Danish sets the relation explicitly.