Miracle-dz/UniFAR-FTUs huggingface dataset:
EVOLUTION AND STABILITY OF THE G-MATRIX ON A LANDSCAPE WITH A MOVING OPTIMUM

Abstract In quantitative genetics, the genetic architecture of traits, described in terms of variances and covariances, plays a major role in determining the trajectory of evolutionary change. Hence, the genetic variance-covariance matrix (G-matrix) is a critical component of modern quantitative genetics theory. Considerable debate has surrounded the issue of G-matrix constancy because unstable G-matrices provide major difficulties for evolutionary inference. Empirical studies and analytical theory have not resolved the debate. Here we present the results of stochastic models of G-matrix evolution in a population responding to an adaptive landscape with an optimum that moves at a constant rate. This study builds on the previous results of stochastic simulations of G-matrix stability under stabilizing selection arising from a stationary optimum. The addition of a moving optimum leads to several important new insights. First, evolution along genetic lines of least resistance increases stability of the orientation of the G-matrix relative to stabilizing selection alone. Evolution across genetic lines of least resistance decreases G-matrix stability. Second, evolution in response to a continuously changing optimum can produce persistent maladaptation for a correlated trait, even if its optimum does not change. Third, the retrospective analysis of selection performs very well when the mean G-matrix (Ḡ) is known with certainty, indicating that covariance between G and the directional selection gradient β is usually small enough in magnitude that it introduces only a small bias in estimates of the net selection gradient. Our results also show, however, that the contemporary Ḡ-matrix only serves as a rough guide to Ḡ. The most promising approach for the estimation of Ḡ is probably through comparative phylogenetic analysis. Overall, our results show that directional selection actually can increase stability of the G-matrix and that retrospective analysis of selection is inherently feasible. One major remaining challenge is to gain a sufficient understanding of the G-matrix to allow the confident estimation of Ḡ.
Effects of the Binding of α/β-type Small, Acid-soluble Spore Proteins on the Photochemistry of DNA in Spores of Bacillus subtilis and In Vitro¶

Abstract The main lesion produced in DNA by UV-C irradiation of spores of Bacillus subtilis is 5-thyminyl-5,6-dihydrothymine (spore photoproduct [SP]). In contrast, cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) pyrimidone photoproducts (6-4PP) are the main photolesions in other cell types. The novel photochemistry of spore DNA is accounted for in part by its reduced hydration, but largely by the saturation of spore DNA with α/β-type small, acid-soluble spore proteins (SASP). Using high-performance liquid chromatography–mass spectrometry analysis of the photoproducts, we showed that in wild-type B. subtilis spores (1) UV-C irradiation generates almost exclusively SP with little if any CPD and 6-4PP; (2) the SP generated is ∼99% of the intrastrand derivative, but ∼1% is in the interstrand form; and (3) there is no detectable formation of the SP analog between adjacent C and T residues. UV-C irradiation of spores lacking the majority of their α/β-type SASP gave less SP than with wild-type spores and significant levels of CPD and 6-4PP. The binding of an α/β-type SASP to isolated DNA either in dry films or in aqueous solution led to a large decrease in the yield of CPD and 6-4PP, and a concomitant increase in the yield of SP, although levels of interstrand photoproducts were extremely low.
BREAKDOWN OF SELF-INCOMPATIBILITY IN THE PERENNIAL ARABIDOPSIS LYRATA (BRASSICACEAE) AND ITS GENETIC CONSEQUENCES

Mating systems in plants are known to be highly labile traits, with frequent transitions from outcrossing to selfing. The genetic basis for breakdown in self-incompatibility (SI) systems has been studied, but data on variation in selfing rates in species for which the molecular basis of SI is known are rare. This study surveyed such variation in Arabidopsis lyrata (Brassicaceae), which is often considered an obligately outcrossing species, to examine the causes and genetic consequences of changes in its breeding system. Based on controlled self-pollinations in the greenhouse, three populations from the Great Lakes region of North America included a minority of self-compatible (SC) individuals, while two showed larger proportions of SC individuals and all populations contained some individuals capable of setting selfed seeds. Loss of SI was not associated with particular haplotypes at the S-locus (as estimated by alleles amplified at the SRK locus, the gene controlling female specificity) and all populations contained similar numbers of SRK alleles, suggesting that some other genetic factor is responsible for modifying the SI reaction. The loss of SI has resulted in an effective shift in the mating system, as the two populations with a high frequency of SC individuals showed significantly lower microsatellite-based multilocus outcrossing rates and higher inbreeding coefficients than the other populations. Based on microsatellites, observed heterozygosities and genetic diversity were also significantly depressed in these populations. These findings provide the unique opportunity to examine in detail the consequences of mating system changes within a species with a well-characterized SI system.
THE POPULATION GENETICS OF SPOROPHYTIC SELF-INCOMPATIBILITY IN SENECIO SQUALIDUS L. (ASTERACEAE): THE NUMBER, FREQUENCY, AND DOMINANCE INTERACTIONS OF S ALLELES ACROSS ITS BRITISH RANGE

Sporophytic self-incompatibility (SSI) was studied in 11 British Senecio squalidus populations to quantify mating system variation and determine how its recent colonization of the United Kingdom has influenced its mating behavior. S allele number, frequency, and dominance interactions in populations were assessed using full diallels of controlled pollinations. A mean of 5.1 S alleles per population was observed, and no population contained more than six S alleles. Numbers of S alleles within populations of S. squalidus declined with increasing distance from the center of its introduction (Oxford). Cross-classification of S alleles allowed an estimate of approximately seven and no more than 11 S alleles for the entire British S. squalidus population. The low number of S alleles observed in British S. squalidus compared to other SI species is consistent with the population bottleneck associated with S. squalidus’ introduction to the Oxford Botanic Garden and subsequent colonization of Britain. Extensive S allele dominance interactions were observed to be a feature of the S. squalidus SSI system and may represent an adaptive response to improve limited mate availability imposed by the presence of so few S alleles. Multilocus allozyme genotypes were also identified for individuals in all populations and geographic patterns of S locus and allozyme loci variation investigated. Less interpopulation structure was observed for the S locus than for allozyme diversity—a finding indicative of the effects of negative frequency-dependent selection at the S locus maintaining equal S phenotypes within populations and enhancing effective migration between populations.
BLUE AND GREEN EGG-COLOR INTENSITY IS ASSOCIATED WITH PARENTAL EFFORT AND MATING SYSTEM IN PASSERINES: SUPPORT FOR THE SEXUAL SELECTION HYPOTHESIS

Abstract Among several adaptive explanations proposed to account for variation in avian egg color, that related to sexual selection is of particular interest because of its possible generality. Briefly, it proposes that because biliverdin (the pigment responsible for blue-green eggshell coloration) is an antioxidant, deposition in the eggshell by laying females may signal the capacity of females to control free radicals, despite the handicap of removing this antioxidant from their body. If males adjust parental effort in response to the intensity of the blue coloration of eggs, thereby investing more in the offspring of high-quality mates, blue eggs may represent a postmating sexually selected signal in females. Here, by image and spectrophotometric analyses of the eggs of European passerines, we tested two different predictions of the hypothesis. First, variables related to intraspecific variation in parental effort (i.e., the duration of the nestling period controlled for body mass) should be positively related to the intensity of blue-green color of the eggshell across species. Second, there should be a positive relationship between intensity of blue-green color of eggs and degree of polygyny. These predictions were supported: intensity of blue-green coloration (i.e., chroma) was significantly related to the duration of the nestling period and to degree of polygyny after controlling for possible confounding variables (i.e., body mass, incubation period, and nest type) and similarity due to common descent. Nest type (hole or nonhole) also explained a significant proportion of variation in egg chroma, perhaps reflecting different selection pressures (i.e., light conditions, risk of parasitism) affecting species with the two types of nests.
False data injection attack on consensus‐based distributed estimation

We consider security issues for consensus‐based distributed estimation problem. In a sensor network, an attacker with limited power injects random false data into the communication links so as to degrade the network performance. First, an optimal estimator is designed by minimizing the mean‐squared estimation error of each sensor under hostile attacks. Then, a sufficient condition is provided to guarantee the stability of the proposed estimator. Finally, a set of suboptimal attacking sequences is obtained for the attacker to maximize the network estimation error. Illustrative examples are provided to verify the effectiveness of the suboptimal attacking strategy. Copyright © 2016 John Wiley & Sons, Ltd.
Protein Kinase C Epsilon Signals Ultraviolet Light-induced Cutaneous Damage and Development of Squamous Cell Carcinoma Possibly Through Induction of Specific Cytokines in a Paracrine Mechanism¶

Abstract Protein kinase C (PKC), a family of phospholipid-dependent serine/threonine kinases, is not only the major intracellular receptor for the mouse skin tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) but also is activated by a variety of stress factors including ultraviolet radiation (UVR). PKCϵ is among six isoforms (α, δ, ϵ, &eegr;, μ and ζ) expressed in the mouse skin. To determine the in vivo functional specificity of PKCϵ in mouse skin carcinogenesis, we generated PKCϵ transgenic mouse (FVB/N) lines 224 and 215 that overexpress PKCϵ protein approximately 8- and 18-fold, respectively, over endogenous levels in the basal epidermal cells and cells of the hair follicle. PKCϵ transgenic mice were observed to be highly sensitive to the development of papilloma-independent metastatic squamous cell carcinoma (mSCC) elicited either by repeated exposure to UVR or by the 7,12-Dimethylbenzanthracene–TPA tumor promotion protocol. The development of squamous cell carcinoma (SCC) appears to be linked to the PKCϵ-mediated induction of cytokine tumor necrosis factor–α(TNFα). Immunohistochemical analysis for the expression of PKCϵ in the SCC of PKCϵ transgenic mice revealed that PKCϵ was not expressed in the tumor itself; however, the uninvolved tissue surrounding the SCC exhibited intense PKCϵ expression. Also, human SCC, similar to mouse SCC, did not express PKCϵ in the tumor, whereas the surrounding uninvolved epidermis revealed strong PKCϵ expression. These findings in both the PKCϵ mouse model and human SCC indicate that overexpression of PKCϵ in epidermis may lead to a microenvironment, which is suitable for enhancing the development of mSCC by a paracrine mechanism involving specific cytokines including TNFα.
The Development of the Sauropsid Integument: A Contribution to the Problem of the Origin and Evolution of Feathers1

Abstract Developmental anatomical data are insufficient to discuss plausible intermediates between an ancestral, scaled, reptilian skin and appendage-bearing, avian skin. We also review adult tissue replacement and ubiquitous mechanisms underlying skin morphogenesis. Combining developmental data sensu lato with consideration of necessary biological roles permits evaluation of major form/function trends in skin evolution. New data on feathers reveal retention of the sauropsid synapomorphy of vertical alteration of α- and β-keratogenesis. By identifying roles that were obligatorily maintained throughout evolution, we demonstrate constraints on hypothetical skin morphologies in preavian taxa. We analyze feather origins as a problem of emergence of complex form via modulations of morphogenesis. While existing data do not permit presentation of sequential, hypothetical, intermediates culminating in a plumage, the analysis: (1) implies that a protofeather and its follicle are most easily derived from isolated, flattened, elongate, reptilian scales; (2) explains diversification of feather morphs from a contour-like “basic” feather and the similarity between feather and hair follicles; and thus (3) reveals several developmental constraints on structures proposed as antecedent to avian feathers, whether hypothetical constructs or palaeontological interpretations. Although these conclusions do not depend on any previous scenario, they are consistent with Regal's (1975) model and the limited, fossil evidence, especially that of the “basal archosaur” Longisquama.
Deforestation in Costa Rica: A Quantitative Analysis Using Remote Sensing Imagery1

Abstract Accurate estimates of forest cover and forest fragmentation are critical for developing countries such as Costa Rica, which holds four to five percent of the world's plant and bird species. We estimated forest cover for Costa Rica using Landsat 5 Thematic Mapper satellite scenes acquired between 1986 and 1991. In 1991, 29 percent (ca 14,000 km2) of the land cover of Costa Rica was closed forest cover; of that forested area, ca 30 percent is protected by national conservation policies. Forest loss in a study area representing ca 50 percent of Costa Rica's territory during a five-year period (1986–1991) was 2250 km2, and the estimated deforestation rate was ca 450 km2/yr, or ca 4.2 percent/yr, of remaining forest cover. Forests are almost completely eliminated from the Tropical Moist Forest and Premontane Moist Forest life zones, and the level of fragmentation of remaining forests may be more advanced than previously thought.
CORRELATED EVOLUTION OF HOST AND PARASITE BODY SIZE: TESTS OF HARRISON'S RULE USING BIRDS AND LICE

Abstract Large-bodied species of hosts often harbor large-bodied parasites, a pattern known as Harrison's rule. Harrison's rule has been documented for a variety of animal parasites and herbivorous insects, yet the adaptive basis of the body-size correlation is poorly understood. We used phylogenetically independent methods to test for Harrison's rule across a large assemblage of bird lice (Insecta: Phthiraptera). The analysis revealed a significant relationship between louse and host size, despite considerable variation among taxa. We explored factors underlying this variation by testing Harrison's rule within two groups of feather-specialist lice that share hosts (pigeons and doves). The two groups, wing lice (Columbicola spp.) and body lice (Physconelloidinae spp.), have similar life histories, despite spending much of their time on different feather tracts. Wing lice showed strong support for Harrison's rule, whereas body lice showed no significant correlation with host size. Wing louse size was correlated with wing feather size, which was in turn correlated with overall host size. In contrast, body louse size showed no correlation with body feather size, which also was not correlated with overall host size. The reason why body lice did not fit Harrison's rule may be related to the fact that different species of body lice use different microhabitats within body feathers. More detailed measurements of body feathers may be needed to explore the precise relationship of body louse size to relevant components of feather size. Whatever the reason, Harrison's rule does not hold in body lice, possibly because selection on body size is mediated by community-level interactions between body lice.
QUANTITATIVE GENETICS OF BIOENERGETICS AND GROWTH-RELATED TRAITS IN THE WILD MAMMAL, PHYLLOTIS DARWINI

Abstract We studied the potential for response to selection in typical physiological-thermoregulatory traits of mammals such as maximum metabolic rate (MMR), nonshivering thermogenesis (NST) and basal metabolic rate (BMR) on cold-acclimated animals. We used an animal model approach to estimate both narrow-sense heritabilities (h2) and genetic correlations between physiological and growth-related traits. Univariate analyses showed that MMR presented high, significant heritability (h2 = 0.69 ± 0.35, asymptotic standard error), suggesting the potential for microevolution in this variable. However, NST and BMR presented low, nonsignificant h2, and NST showed large maternal/common environmental/nonadditive effects (c2 = 0.34 ± 0.17). Heritabilities were large and significant (h2 > 0.5) for all growth-related traits (birth mass, growth rate, weaning mass). The only significant genetic correlations we found between a physiological trait and a growth-related trait was between NST and birth mass (r = −0.74; P < 0.05). Overall, these results suggest that additive genetic variance is present in several bioenergetic traits, and that genetic correlations could be present between those different kinds of traits.
Influence of UVB, UVA and UVA1 Irradiation on Histamine Release from Human Basophils and Mast Cells In Vitro in the Presence and Absence of Antioxidants¶

Abstract UV irradiation is widely used for the treatment of atopic eczema. In recent years, UVA1 phototherapy has gained increasing attention. This study analyzed the influence of different UV wavelengths—especially UVA1—on histamine release from human basophils and mast cells. The modulation of this parameter might be responsible for some of the therapeutic effects of UV irradiation. Enriched human basophils and human mast cells (HMC1 cell line) were irradiated with increasing doses of UVB, UVA and UVA1 in vitro. After irradiation, different stimulants were added to induce histamine release. In additional experiments, basophils were preincubated with superoxide dismutase, ascorbate or trolox to study the role of antioxidants in the modulation of histamine release after UV irradiation. UVA and UVA1 significantly inhibited histamine release from basophils and mast cells. UVB only had an inhibitory effect on mast cells. Preincubation with superoxide dismutase and ascorbate did not influence the inhibitory effect of UVA1 on basophil histamine release, whereas trolox decreased significantly the histamine release from nonirradiated basophils.
Seed Size, Seed Germination, and Seedling Survival of Brazilian Tropical Tree Species Differing in Successional Status1

Abstract Seed germination and seedling establishment patterns have been used to classify species as shade tolerant or intolerant. The main objective of this research was to investigate, under controlled conditions, seed germination of species from different successional positions as well as to follow seed germination and seedling survival under natural shade in the field. The species studied were Solanum granuloso-leprosum, Trema micrantha, Cecropia pachystachya, Croton piptocalyx, Bauhinia forficata subsp. pruinosa, Senna macranthera, Schizolobium parahyba, Piptadenia gonoacantha, Chorisia speciosa, Pseudobombax grandiflorum, Ficus guaranitica,Esenbeckia leiocarpa, Pachystroma longifolium, Myroxylon peruiferum, and Hymenaea courbaril. Field trials were carried out at Santa Genebra Municipal Reserve, Campinas, SP, Brazil, at the forest edge and in the understory. No significant correlations were detected between successional status and seed size or seed water content. Light-regulated germination was present only in small-seeded species. In field experiments, most species, including the light-sensitive ones, were able to germinate under the canopy, where a low red/far-red ratio predominates. Most species, mainly those of early- and intermediate successional positions, presented low seedling survival rates under shade. Myroxylon peruiferum was the most shade tolerant species, while S. granuloso-leprosum,C. speciosa,P. gonoacantha, F. guaranitica, T. micrantha, and S. parahyba were the most shade intolerant. These latter species showed little or no survival under the shade conditions.
Rapid Turnover and Edge Effects in Dung Beetle Assemblages (Scarabaeidae) at a Bolivian Neotropical Forest–Savanna Ecotone1

Habitat fragmentation and the widespread creation of habitat edges have recently stimulated interest in assessing the effects of ecotones on biodiversity. Ecotones, natural or anthropogenic, can greatly affect faunal movement, population dynamics, species interactions, and community structure. Few data exist, however, on insect community response to forest–savanna ecotones, a natural analog to anthropogenically cleared areas adjacent to forest. In this study, the abundance, total biomass, average individual biomass, and distribution of scarabaeine dung beetles were examined at a sharp tropical evergreen forest–savanna ecotone in Santa Cruz, Bolivia. The abundance, total biomass, and average individual biomass of dung beetles varied significantly across the forest, edge, and savanna habitats. Species richness (Sobs) also varied significantly across the three habitats, but statistical estimations of true species richness (Sest) did not. Habitat specificity of the dung beetles in this study was extremely high. Of the 50 most common species collected during the study, only 2 species were collected in both the forest and savanna habitats, signaling nearly complete community turnover in just a few meters. Strong edge effects were evidenced by the decline in abundance, total biomass, and species richness at the forest–savanna boundary.
RAPID FITNESS RECOVERY IN MUTATIONALLY DEGRADED LINES OF

Deleterious mutation accumulation has been implicated in many biological phenomena and as a potentially significant threat to human health and the persistence of small populations. The vast majority of mutations with effects on fitness are known to be deleterious in a given environment, and their accumulation results in mean population fitness decline. However, whether populations are capable of recovering from negative effects of prolonged genetic bottlenecks via beneficial or compensatory mutation accumulation has not previously been tested. To address this question, long-term mutation-accumulation lines of the nematode Caenorhabditis elegans, previously propagated as single individuals each generation, were maintained in large population sizes under competitive conditions. Fitness assays of these lines and comparison to parallel mutation-accumulation lines and the ancestral control show that, while the process of fitness restoration was incomplete for some lines, full recovery of mean fitness was achieved in fewer than 80 generations. Several lines of evidence indicate that this fitness restoration was at least partially driven by compensatory mutation accumulation rather than a result of a generic form of laboratory adaptation. This surprising result has broad implications for the influence of the mutational process on many issues in evolutionary and conservation biology.