Miracle-dz/UniFAR-FTUs huggingface dataset:
EARLY MAMMALIAN RADIATIONS

The seventy-fifth anniversary of the Journal of Paleontology presents a felicitous opportunity to review major changes in interpretation of mammalian phylogeny. Founding of the journal coincides with the nascence of the career of the most influential paleomammalogist of the past century, George Gaylord Simpson (1902-1984). It occurred at a time when now-archaic models for mammalian systematics and evolution, such as the aristogenesis of H. F. Osborn (1857-1935) and the typological concept of taxa, were prevalent (e.g., Simpson, 1945). These models were soon to give way to “new ways of going at things” (Laporte, 2000, p. 87); most significantly, the incorporation of quantitative methods and the evolutionary synthesis (Simpson, 1944). Subsequent decades witnessed the rise and/or sophistication of other applications and perspectives in fossil-based interpretation of mammalian systematics, including form-function analysis (e.g., Szalay, 1994) and, particularly, cladistic approaches (e.g., McKenna, 1975). Within these broad ideological frameworks, major paradigm shifts have resulted from new discoveries, conceptual changes, or (most commonly) a combination of both. Finally, mammalian systematics currently lie at the verge of a monumental paradigm shift, providing important direction for the future.
Stable isotopes reveal age-dependent trophic level and spatial segregation during adult marine feeding in populations of salmon

Locating and differentiating the marine feeding areas used by adult salmon (Salmo salar) is essential to stock-based management and conservation, but traditional tagging studies are limited and influenced by the uneven distribution of the fisheries or research vessel surveys. Here, a novel approach is used, based on the observation that the isotopic composition of animal tissues is intrinsically linked to the environmental conditions during tissue growth, which allows for the distinction of pelagic fish feeding in different locations. This isotopic approach is applied using archived collections of salmon scales and shows that (i) salmon act as size-structured pelagic predators, (ii) adult salmon from different natal origins within the UK (and hence components of the southern European stock complex) feed in different oceanic regions before their return, (iii) one-sea-winter (1SW) and multi-sea-winter salmon returning to some rivers in the UK are separated in their marine feeding areas, whereas those from others are not, and (iv) salmon from the rivers sampled are not feeding in regions of the Northwest Atlantic used by 1SW salmon returning to rivers in Newfoundland. Therefore, the stable isotope approach allows for retrospective investigations of marine diet, location, and migration at stock- and cohort-specific levels.
Active DNA demethylation regulates tracheary element differentiation in Arabidopsis

A novel role of active DNA demethylation in plant development. DNA demethylation is important for the erasure of DNA methylation. The role of DNA demethylation in plant development remains poorly understood. Here, we found extensive DNA demethylation in the CHH context around pericentromeric regions and DNA demethylation in the CG, CHG, and CHH contexts at discrete genomic regions during ectopic xylem tracheary element (TE) differentiation. While loss of pericentromeric methylation occurs passively, DNA demethylation at a subset of regions relies on active DNA demethylation initiated by DNA glycosylases ROS1, DML2, and DML3. The ros1 and rdd mutations impair ectopic TE differentiation and xylem development in the young roots of Arabidopsis seedlings. Active DNA demethylation targets and regulates many genes for TE differentiation. The defect of xylem development in rdd is proposed to be caused by dysregulation of multiple genes. Our study identifies a role of active DNA demethylation in vascular development and reveals an epigenetic mechanism for TE differentiation.
Genetic mapping of ecotropic murine leukemia virus-inducing loci in six inbred strains

Mendelian segregation analysis was used to map chromosomal genes for the induction of endogenous N- and B-tropic ecotropic retroviruses (V loci) in high and low leukemic mouse strains. Patterns of virus expression were determined for mice of various inbred strains, congenic lines carrying single V loci, and the linkage testing stocks used in mapping studies. Segregation analysis resulted in the genetic mapping of V loci from six inbred strains to five mouse chromosomes. The V locus of A/J was mapped to chromosome 5 and shown to be allelic with that of BALB/cJ and C3H/HeJ (Cv); this suggests that Cv-represents a stable ancestral V locus present in Bagg albino stocks before the separation of inbred lines. The single, poorly inducible V locus of C57BL/10J and one of the four high virus loci of C58/Lw were mapped to the same region of chromosome 8 and may represent an allelic pair with different patterns of expression. An N-tropic V locus of the SEA/GnJ mouse was mapped to chromosome 9, and one of the three V loci of C3H/FgLw was mapped to chromosome 7. The endogenous B-tropic virus of B10.BR/SgLi was mapped to chromosome 11. These studies provide further evidence that endogenous ecotropic V loci are present at different chromosomal sites in unrelated mouse strains and emphasize the role of germ line reinfections in the generation of this diversity.
The effect of colony isolation of the predacious ant, Oecophylla smaragdina (F.) (Hymenoptera: Formicidae), on protection of cashew plantations from insect pests

Fierce boundary fights between Oecophylla smaragdina colonies were previously identified as the major factor limiting ant populations and the efficiency of ants as biological control agents. In order to determine the feasibility and effect ofpreventing boundary fights between colonies, experiments with full-, semi- and no-isolation of existing antcolonies in cashew plantations were done in 1996 and 1997. In a related experiment, ant colonies were transplanted from native vegetation to a cashew orchard. Trees with ant colonies which were fully isolated from other colonies were significantly less damaged by the main insect pests and produced significantly higher yield than those with ant colonies which were partly isolated or were not isolated. That was because fighting events between fully isolated ant colonies were eliminated, and the populations of these colonies were high throughout the cashew flowering and fruiting period. Trees in which O. smaragdina colonies were transplanted suffered little damage b.
Antimicrobial Effects of Sodium Benzoate on the Growth, Survival and Aflatoxin Production Potential of Some Species of Aspergillus in Garri During Storage

The antimicrobial effect of different concentrations (0.6, 0.4 and 0.2%) of sodium benzoate (SB) on the growth, survival and aflatoxin production potentials of Aspergillus niger, Aspergillus flavus and Aspergillus fumigatus in packaged garri (2kg/pack) during storage at ambient temperature (30±2 C) wa s o investigated. A decrease of 4.5, 2.5, 1.9; 4.5, 2.4, 1.8 and 4.6, 2.6 and 2.0 folds were recorded in the viable count of A. niger, A. flavus and A. fumigatus, for 0.6, 0.4 and 0.2% SB treated samples respectively. The effectiveness of SB against the various species of Aspergillius was in the order 0.6% > 0.4% > 0.2% . However 1.2 and 1.7 folds increase in the viable count of A. niger, A. flavus and A. fumigatus were recorded in the non treated samples (controls). No aflatoxin was detected in all the samples treated with different concentration of SB. However, aflatoxin was detected in the samples inoculated with Aspergillus flavus although unspecified and irregular florescence was noticed in other samples (controls).
Determination of Coscinodiscus cf. granii biovolume by confocal microscopy: comparison of calculation models

Biovolume is commonly used as a size descriptor in the study of phytoplankton ecology. Usually, biovolume is not measured directly but is obtained from a standardized set of geometric models based on linear dimensions measured by light microscopy. This commonly used method allows visualization and measurement in two dimensions (2D) yielding no information at all on the third dimension of phytoplankton cells. Inaccurate biovolume assessment resulting from geometric approximation leads to erroneous interpretation of eco-physiological processes and morpho-functional traits. Here, we use confocal microscopy coupled with an image analysis system (NIS Elements AR software, Nikon) to determine directly shape and biovolume by means a 3D reconstruction of Coscinodiscus cf. granii specimens. We evaluate the accuracy of current methods by comparing the results obtained using geometric models with direct biovolume and shape. We find that calculation of biovolume by approximation to geometric models (cylindrical and complex shapes) leads to a significant overestimation with respect to direct volume. We also propose a data-driven formula for calculating the biovolume of Coscinodiscus cf. granii specimens based on diameter or other linear measurements.
Social organization and movements of desert rodents during population “booms” and “busts” in central Australia

Abstract We monitored populations of 2 species of desert rodents, the sandy inland mouse (Pseudomys hermannsburgensis) and spinifex hopping-mouse (Notomys alexis), over 18 years in the Simpson Desert, central Australia. Populations fluctuated synchronously from very low numbers, or “busts,” during prolonged dry periods to high numbers, or “booms,” after heavy rainfall 3 times over the study period. On the basis of observations that food resources expand after rainfall, we predicted that rodents would show increased rates of recapture, fidelity to burrows, and burrow sharing during population increase (boom) phases compared with decline or bust phases, and also reduce their movements and foraging activity in open habitats during population booms. The behavior of both species was similar but not as we had anticipated. Burrow fidelity and numbers of animals per burrow were roughly 2-fold higher during both the population increase and decrease phases as compared with the population-low phase, whereas rates of movement were reduced by about half. As revealed by giving-up density trials, animals foraged less at experimental food patches during population increase and decrease phases than during busts, and also foraged less in open than in covered habitats. Recaptures of N. alexis were similar across all population phases, whereas P. hermannsburgensis was recaptured more often when populations were decreasing than at other times. The results suggest that both species are dispersed and highly mobile during bust periods but sedentary and more social during population increases and collapses. These changes in movements and social organization appear to be unusual in desert rodents, and we propose that future studies seek to identify the roles of food and other factors in driving them.
Erythrocyte Enzyme Variation in Brahmin and Rajput Populations of Himachal Pradesh, I. Shimla District

Abstract As part of a larger study plan among people inhabiting southern districts of Himachal Pradesh in northwest India, data are presented on the distribution of various erythrocyte enzyme polymorphisms in the Brahmin and Rajput populations of Shimla district, in the first instance. The present biochemical data revealed that the genetic make up of these two castes was very similar. Comparison with such other regional data indicated almost homogeneous distribution of the studied enzyme systems in subpopulations of the respective caste populations of this hill state.
Morphological, Physicochemical and Textural Properties of Starch Separated from Chinese Water Chestnut

Chinese water chestnut starch (CWCS) was isolated and its composition, morphological, physicochemical and textural properties investigated. Chinese water chestnut starch granules were round, oval and polyangular in shape, with volumetric mean diameter (D 50 ) 8.46 μm. CWCS had an A-type crystal pattern and an apparent amylose content of 32. 1%. Compared with tapioca and maize starch, CWCS exhibited moderate swelling power and turbidity and high stability against freeze-thaw treatment. Chinese water chestnut starch showed the highest peak (7957 mPa s), breakdown (4169 mPa s) and final viscosity (4816 mPa s), intermediate setback viscosity (1028 mPa s) and pasting temperature (68.7°C), and lowest enthalpy (10.8 J/g) of gelatinization of the three starches studied. The effect of food additives (NaCI, sucrose and glycerol monostearate) and heating processes (direct heating, steam heating, microwave heating and autoclaving) on the CWCS gel was determined by a texture analyzer. The CWCS gel hardness and gumminess proportionally increased with the concentration of starch gels, ranging from 6% to 16%, but gel springiness and cohesiveness changed indistinctively. CWCS gels with added NaCl gave inconsistent results, but for the most part, they showed similar or increased gel hardness and gumminess as compared with the control. CWCS gels with added glycerol monostearate had lower gel hardness and gumminess than the control. The addition of sucrose (< 15%, w/v) resulted in increased gel hardness and gumminess, but 20% sucrose decreased these features. Both microwave and steam heating on the one hand and autoclaving and directly heating on the other gave rise to similar gel hardness and gumminess, the values of the two groups being significantly different from each other.
Mycobiota in symptomless needles of Pinus mugo ssp. uncinata

Healthy-looking needles were randomly collected from Pinus mugo ssp. uncinata at two sites in the montane zone with different edaphic and microclimatic conditions and examined for the diversity of endophytic fungi. One site is on a mountain ridge, the other in a peat bog. On average, about 35–40% of the needles were colonized at both sites. Eleven species of fungi were isolated. Cenangium ferruginosum and Cyclaneusma minus dominated the endophytic mycobiota of the tree stand along the mountain ridge. C. ferruginosum and Lophodermium pinastri were the dominant species in the needles of the trees in the peat bog. C. ferruginosum and L. pinastri occurred mainly in the needle tip; C. minus occurred most frequently in the middle segment of the needles. The needle base was rarely colonized by these fungi. Endophyte colonization of trees along the mountain ridge increased significantly from the uppermost trees to the ones further down the ridge. No clear pattern of colonization was observed for trees in the peat bog except for the colonisation by L. pinastri , which showed a tendency to form infection centres. Species composition was constant within sites, but the frequency of colonization by C. minus and L. pinastri varied greatly among trees.
Effect of ammonium/nitrate ratio on growth and development of avocado plants under hydroponic conditions

An experiment was carried out to study the effects of the proportion of ammonium (NH4+) and nitrate (NO3−) in the nutrient solution on avocado plants in a hydroponic system. Five treatments were applied, consisting of the following proportions of ammonium to nitrate ions in the solution: T0 = 0:4, T1 = 1:3, T2 = 2:2, T3 = 3:1 and T4 = 4:0 at a constant nitrogen concentration of 4 mM. After 4 months, the plants were harvested and fresh and dry matter accumulation, leaf area, and leaf nitrogen and carbon content were measured. An architectural description of the shoot (length, number of nodes and branching) was made. Dry matter of shoots and leaves all decreased with increasing NH4+ concentrations. In contrast, water content in aerial organs increased with NH4+ concentration. Nitrogen and carbon content and the relationship between dry matter production and leaf nitrogen were not significantly affected by the treatments. The architectural analysis showed that the shoots developed over time in one or two dis.
Effect of Aloe vera and Curcuma longa (Turmeric) on Carcass Characteristics and Biochemical Parameters of Broilers

An experiment was conducted to study the inclusion of Aloe vera and Curcuma longa and its combinations on production performance, viz., weight gain, feed intake and feed conversion ratio, carcass characteristics and biochemical parameters for a period of six weeks with two hundred and eighty commercial, straight run day-old Vencobb broiler chicks. These chicks were randomly grouped into seven treatments with four replicates of ten chicks each. The treatment groups consisted of control (T ), 0.1 percent 1 Aloe vera powder (T ), 0.2 percent Aloe vera powder (T ), 0.1 percent Curcuma longa powder (T ), 0.2 2 3 4 percent Curcuma longa powder (T ) and 0.1 percent of Aloe vera and 0.1 percent of Curcuma longa powder 5 (T ) and 0.2 percent of Aloe vera and 0.2 percent of Curcuma longa powder (T ) included in the broiler diet. 6 7 The abdominal fat percentage, breast and thigh muscle cholesterol showed no significant difference between treatment groups. The serum glucose, total cholesterol, HDL cholesterol, LDL cholesterol and triglycerides level did not differ significantly between treatment groups. Haemagglutination inhibition titre against Newcastle disease revealed significant difference (P < 0.01) between treatment groups. T and T 2 3 showed higher titre value when compared with control.
Isoform-Specific Responses of Superoxide Dismutase to Oxidative Stresses and Hormones in Paraquat-Tolerant Rehmannia glutinosa

All accessions of Rehmannia glutinosa show the unique characteristic of intrinsic tolerance to paraquat. The higher level of endogenous superoxide dismutase (SOD) activity and its increase upon paraquat treatment indicated the involvement of SOD in the tolerance mechanism to paraquat in R. glutinosa. In this study, we examined the isoform-specific response of SOD to oxidative stresses and hormones. Six SOD isoforms were found in the leaf, and they were identified as two MnSODs (named MnSOD I and MnSOD II, in order of increasing mobility), one FeSOD and three Cu/ZnSODs (named Cu/ZnSOD I, Cu/ZnSOD II, and Cu/ZnSOD III, in order of increasing mobility). MnSOD I, MnSOD II, FeSOD, Cu/ZnSOD I, Cu/ZnSOD II, and Cu/ZnSOD III, contributed to 4, 11, 7, 15, 30, and 32% of the total SOD activity, respectively. Total SOD activity levels in the leaf were increased by 4, 24, and 21% by paraquat, salicylic acid (SA), and yeast extract (YE), respectively, but little by ethephon. Six SOD isoforms responded differentially to these stresses and hormones. The activities of all the isoforms were increased by YE and SA except that of MnSOD I which was decreased by SA. The activities of MnSOD I, FeSOD, and CuZnSOD I were increased by paraquat. These results suggest that amelioration of oxidative stresses by SOD is fine-tuned by the differential expression of isoforms in R. glutinosa.
Alternariol monomethyl ether and α, β-dehydrocurvularin from endophytic fungi Alternaria spp. Inhibit appressorium formation of Magnaporthe grisea

Appressorium formation pathway of Magnaporthe grisea (M. grisea) is a new target for developing rice blast controlling agent. Inhibitory activity of endophytic fungi against the appressorium formation of M. grisea was screened. Two compounds displaying the activity were isolated from Alternaria tenuissima and Alternaria sp. isolated from the leaves of Acacia mangium and were identified as alternariol monomethyl ether and (4S)-α, β-dehydrocurvularin with IC50s of 51.0 and 10.6 μg/mL, respectively. These compounds were of no practical implication due to its low activity. However, they would serve as biochemical tool to study appressorium development.
The effects of hatchery domestication on competitive dominance of juvenile spring Chinook salmon (Oncorhynchus tshawytscha)

We tested the null hypotheses that competitive dominance among juvenile Chinook salmon (Oncorhynchus tshawytscha) in contest and scramble experiments would not be affected by domestication selection after one generation of state-of-the-art hatchery culture. Dyadic challenges of size-matched juvenile fish were conducted after a 6-day accli- mation in 113.4 L aquaria. Differences in dominance and frequency of different types of agonistic interactions used were not significantly different in contest (n = 505) or scramble (n = 363) competition experiments (P > 0.05). How- ever, wild origin fish were more aggressive than hatchery origin fish in both types of experiments (P ≤ 0.05). Further- more, wild origin fish gained more weight than hatchery origin fish during contest experiments, and hatchery origin fish lost less weight than wild origin fish in scramble experiments (P ≤ 0.05). Dominant fish, regardless of origin, grew more than subordinate fish in both contest and scramble experiments (P ≤ 0.05). Our results indicate that aggression, and growth mediated by competition, can be affected by domestication after only one generation of state-of-the-art hatchery culture; however, impacts to competitive dominance appear to be small.
Mind the gaps: a state-space model for analysing the dynamics of North Sea herring spawning components

Payne, M. R. 2010. Mind the gaps: a state-space model for analysing the dynamics of North Sea herring spawning components. – ICES Journal of Marine Science, 67: 000– 000. The North Sea autumn-spawning herring (Clupea harengus) stock consists of a set of different spawning components. The dynamics of the entire stock have been well characterized, but although time-series of larval abundance indices are available for the individual components, study of the dynamics at the component level has historically been hampered by missing observations and high sampling noise. A simple state-space statistical model is developed that is robust to these problems, gives a good fit to the data, and proves capable of both handling and predicting missing observations well. Furthermore, the sum of the fitted abundance indices across all components proves an excellent proxy for the biomass of the total stock, even though the model utilizes information at the individual-component level. The Orkney–Shetland component appears to have recovered faster from historic depletion events than the other components, whereas the Downs component has been the slowest. These differences give rise to changes in stock composition, which are shown to vary widely within a relatively short time. The modelling framework provides a valuable tool for studying and monitoring the dynamics of the individual components of the North Sea herring stock.
Small rodents as significant dispersers of tree seeds in a Neotropical forest

Through seed dispersal and predation, terrestrial mammals should be an important component of the mecha- nisms that determine patterns of tree recruitment in tropical forests. Despite their great abundance and ubiquity in Neo- tropical forests, small rodents as seed predators and dispersers remain largely forgotten. To investigate the fates of seeds in a hunted primary forest in Belize, we tagged seeds ofAstrocaryum mexicanum (Palmae), Ampelocera hottlei (Ulmaceae), and Pouteria sapota (Sapotaceae) and placed them into open plots, exclosures accessible only to small mammals, and exclosures accessible to medium-sized and small mammals. The exclosure experiments and fates of the seeds show that the spiny pocket mouse, Heteromys desmarestianus (Heteromyidae), was the dominant handler of seeds of the first two species and also removed a significant proportion of the very large-seeded Pouteria. Most of the seeds were killed immediately upon removal, but many of the seeds (3 - 18 %) of the first two species were scatterhoarded (dispersed and buried in the soil) by Heteromys. Some of the scatterhoarded seeds (29 %) remain buried and therefore protected from predation by other animals. Agoutis (Dasyprocta punctata), a caviomorph rodent, buried 13 % of the seeds of Pouteria, and Heteromys consumed and dispersed but did not bury Pouteria seeds. Results of this study support predictions by some researchers that small rodents are dominant terrestrial granivores in Neotropical forests. The role of small rodents as seed dispersers, however, has never been fully appreciated.