Miracle-dz/UniFAR-FTUs huggingface dataset:
The founding mothers: the genetic structure of newly established Daphnia populations

Colonization dynamics may strongly influence within and among population genetic variation and evolutionary potential of populations. We here analyze the genetic structure during the first three years of 12 cyclical parthenogenetic Daphnia populations in newly created pond habitats. One to three genotypes were observed to colonize the populations, indicating a limited number of founders. Pronounced changes in genetic structure were associated with hatching of sexual dormant eggs after a period of absence of the newly founded populations from the active community. Despite rapid colonization, genetic differentiation among populations was fairly high with limited decay over time, suggesting long-lasting founder effects. After initial colonization, no new alleles were observed in any of the populations, and our analyses suggests that this reflects reduced establishment success of later arrivals. Rare alleles increased in frequency, which likely is the result of inbreeding depression in selfed offspring of initially abundant clones, providing a fitness advantage to the sexual offspring of initially rare clones.
A New Species of the Bokermannohyla circumdata Group (Anura: Hylidae) from the Coastal Forests of Bahia, Northeastern Brazil

Abstract We describe a new species of tree frog related to the Bokermannohyla circumdata group, the northernmost record from Atlantic Forest remnants in eastern Bahia, northeastern Brazil, within regions known as Vale do Jiquiriçá, Baixo Sul, and Litoral Sul. The new species is diagnosed by medium size (snout–vent length 46.8–64.1 mm), head longer than wide, small tympanum, posterior surfaces of thighs with dark brown transverse stripes without additional thin stripes between them, vocal slits in adult males, and distinct advertisement call with a single note composed of 30–110 pulses distributed within 2–9 pulse groups, similar to the bleating of a goat. The new species is morphologically similar to B. hylax and B. lucianae, but is readily distinguished by the presence of barred posterior surfaces on the thighs without thin stripes between them (immaculate in B. lucianae; thin stripes intercalated with wider stripes in B. hylax) and by its distinct vocalization.
Ammonia-oxidizing Archaea in Kamchatka Hot Springs

Mounting evidence suggests that ammonia-oxidizing archaea (AOA) may play important roles in nitrogen cycling in geothermal environments. In this study, the diversity, distribution and ecological significance of AOA in terrestrial hot springs in Kamchatka (Far East Russia) were explored using amoA genes complemented by analysis of glycerol dialkyl glycerol tetraethers (GDGTs) of archaea. PCR amplification of functional genes (amoA) from AOA and ammonia-oxidizing bacteria (AOB) was performed on microbial mats/streamers and sediments collected from three hot springs (42°C to 87°C and pH 5.5-7.0). No amoA genes of AOB were detected. The amoA genes of AOA formed three distinct phylogenetic clusters with Cluster 3 representing the majority (∼59%) of OTUs. Some of the sequences from Cluster 3 were closely related to those from acidic soil environments, which is consistent with the predominance of low pH (<7.0) in these hot springs. Species richness (estimated by Chao1) was more frequently higher at temperatures below 75°C than above it, indicating that AOA may be favored in the moderately high temperature environments. Quantitative PCR of 16S rRNA genes showed that crenarchaeota counted for up to 80% of total archaea. S-LIBSHUFF separated all samples into two phylogenetic groups. The profiles of GDGTs were well separated among the studied springs, suggesting a spatial patterning of archaeal lipid biomarkers. However, this patterning did not correlate significantly with variation in archaeal amoA, suggesting that AOA are not the predominant archaeal group in these springs producing the observed GDGTs.
Breeding time and sex-specific health status in the barn swallow (Hirundo rustica)

Health status has been hypothesized to be an important factor associated with individual reproductive performance in birds. Sex-specific health status of early- and late-breeding barn swallows (Hirundo rustica) was studied during the prelaying and brood-rearing periods to test the prediction that early-arriving birds are in better health status than late-arriving individuals. During prelaying, early breeders (of both sexes) had lower leukocyte counts than late breeders, and males had fewer lymphocytes, heterophils, and total white blood cells than females. Sex differences in health status at arrival disappeared during brood rearing, owing to an increase in leukocytes of early-breeding males and a decrease in leukocytes of late-breeding females. Late-breeding males had a higher plasma lutein concentration than early breeders during brood rearing, and the lutein concentration increased significantly for both sexes between prelaying and brood rearing. T-cell immune response of late-breeding females was stron.
The Evolution of Plant Mating Systems: Multilocus Simulations of Pollen Dispersal

We simulated pollination in a plant population and explored how pollen dispersal distance and allocation among recipient individuals evolved in response to direct selection on three loci coding for dispersal phenotype and in response to indirect selection on two unlinked "genetic congruence" loci. Fitnesses at congruence loci were chosen to model "genetic" and "ecological" mechanisms that have been proposed to explain the observation that an intermediate outcrossing distance maximizes fitness in some plants. Simulations show (1) that dispersal genotype evolves rapidly in response to direct selection, apparently mediated mainly through competition for access to ovules; (2) that selection for intermediate genetic congruence affects final dispersal genotype in largely predictable ways and does not appear to provoke runaway evolution; and (3) that evolution of dispersal type influences the genetic structure of the population, which in turn influences the evolution of dispersal.
Average daily metabolic rate of rodents: habitat and dietary comparisons

1. Average daily metabolic rate (ADMR) is the metabolizable energy intake required by a caged animal to maintain constant body energy content. Linear regression of standardized, phylogenetically independent contrasts was used to describe the allometric relationship between ADMR and body mass in rodents. It was predicted that desert species would have a lower ADMR than non-desert species and that granivores would have a lower ADMR than those of herbivores and omnivores. The efficiency of utilization of energy for maintenance was also determined in these species. Here, it was predicted that the efficiency in granivores would be higher than in both herbivores and omnivores and in desert species would be higher than in non-desert species. 2. The regression of the phylogenetic contrasts of ADMR on body mass (mb) for 53 independent data points based on 63 species of rodents was highly significant (P < 0·0001) with an allometric slope of 0·53. Independent comparisons of both basal metabolic rate (BMR) and ADMR showed significantly lower rates in desert than in non-desert species. There was a trend for granivores to have a lower ADMR per g0.53 than either omnivores or herbivores, but this trend is not significant in independent comparisons between the categories. Thus, the predictions in regard to desert and non-desert habitats were confirmed, and there is a non-significant trend in the predicted direction with respect to diet. Herbivores and omnivores showed no significant difference in either BMR or ADMR. 3. In independent comparisons between categories, there was no evidence for trends in the efficiency of utilization of energy for maintenance (BMR:ADMR ratio or km) with either habitat or diet categories. Thus, these results are not in agreement with our predictions. Taking simple means, km equals 0·47±0·21, 0·37±0·12 and 0·56±0·11 for granivores, omnivores and herbivores, respectively, and 0·37±0·12 and 0·55±0·16 for desert and non-desert mammals, respectively. 4. It is recommended that conditions for ADMR measurements be standardized, as is common for basal metabolic rate measurements. This would allow more reliable comparisons among species measured in different laboratories and also provide more accurate estimates of efficiency of utilization of energy.
Desenvolvimento da cultura de mandioca sob interferência de plantas daninhas

One of the factors affecting the development of the cassava plant is the inadequate control of weeds. Thus, this work aimed to evaluate the development of the cassava plant under weed interference during different coexistence periods. Two experiments were installed in adjacent areas, in Vicosa, Minas Gerais - Brazil. In the first experiment, the treatments consisted of different periods of coexistence between the cassava culture and the weeds (25, 50, 75, 100 and 125 days after planting). In the second experiment, the cassava plants remained weed-free for the same pre-established periods. For both experiments, the 1.0 x 0.5 m spacing was adopted, being the useful portion area constituted by the two central lines, with 1.0 m being left at each extremity as front borders, adding 8.0 m2 up. Plant height and stem diameter were evaluated twelve times after planting at: 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325 and 350 days. Plant number, root length and diameter evaluations were carried out 12 months after planting. Coexistence equal or superior to 50 day interval after planting caused drastic reduction in the stem diameter and height of the cassava plants. Weed control in cassava crop should be initiated around 25 days after planting.
Descriptions and Keys for Ammocoetes of Lampreys from British Columbia, Canada

Characters useful for the identification of ammocoetes of lampreys found in British Columbia were verified by rearing ammocoetes through metamorphosis to specifically identifiable adults. We developed a key that employs new as well as some previously published features. We showed that published descriptions previously thought to be characteristic of species are unreliable for taxonomy. Counts of trunk myomeres and body proportions were not useful for separating species.Key words: ammocoetes, taxonomy, identification criteria
Spatial pattern of the density of Armillaria epiphytic rhizomorphs on tree collar in an oak stand

Summary The density of Armillaria gallica epiphytic rhizomorphs on tree collar was mapped in a young stand of pedunculate oaks (Quercus robur). A quick method to estimate the rhizomorph density was developed, investigating 19 trees, and was used in the subsequent study. The method consists of measuring the frequency of rhizomorphs present on a grid applied to an exposed small area of the tree collar. The pattern in tree collar rhizomorph density was closely related to the pattern of stump colonization by Armillaria and stumps were therefore important as inoculum sources. Rhizomorph density on tree collar showed a strong aggregated spatial pattern which could not be explained by variability in the soil characteristics, in particular waterlogging, or by a spatial pattern in tree vigour. Moreover, rhizomorph density on tree collar did not depend on their dominance status. Resume Nous avons cartographies la densite des rhizomorphes epiphytes d'Armillaria gallica sur le collet des arbres dans un jeune peuplement de chenes pedoncules (Quercus robur). Une methode rapide pour estimer la densite de rhizomorphes a ete mise au point sur 19 arbres et a ete utilisee ulterieurement. Cette estimation a ete faite en comptant la frequence des rhizomorphes epiphytes sur une grille appliquee sur une petit zone du collet qui avait ete degagee. Le patron spatial de densite de rhizomorphs etait etroitement relie au patron spatial de colonisation des souches par l'Armillaire; celles ci ont donc representee une source d'inoculum importante. La densite de rhizomorphes epiphytes sur le collet des arbres presentait un patron spatial agrege qui ne pouvait pas etre explique par une heterogeneite dans les caracteristiques du sol, en particulier l'hydromorphie, ou par un patron spatial de la vigueur des arbres. La densite de rhizomorphes ne dependait pas non plus du statut social des arbres. Zusammenfassung In einem jungen Stieleichenbestand (Quercus robur) wurde die Dichte der epiphytischen Rhizomorphen von Armillaria gallica am Wurzelhals kartiert. Anhand von 19 Baumen wurde eine Schnellmethode zur Schatzung der Rhizomorphen entwickelt und in der vorliegenden Untersuchung eingesetzt. Hierbei wird das Vorkommen von Rhizomorphen in einem Probenraster auf einer kleinen freigelegten Flache des Wurzelhalses bonitiert. Die Besiedelungsdichte mit Rhizomorphen am Wurzelhals war eng mit dem Muster der Stumpfbesiedelung durch Armillaria korreliert und die Stumpfe waren somit wichtige Inokulumquellen. Die Rhizomorphendichte am Wurzelhals war raumlich stark aggregiert. Dieses raumliche Muster konnte jedoch nicht durch Unterschiede in den Bodeneigenschaften, insbesondere Staunasse oder raumliche Verteilung der Baumvitalitat, erklart werden. Auch war die Rhizomorphendichte am Wurzelhals nicht von der Baumklasse abhangig.
Karyotyping of the chromosomes and physical mapping of the 5S rRNA and 18S-26S rRNA gene families in five different species in Capsicum

Since clear identification of individual chromosomes in Capsicum species was not possible due to the gradient in sizes and similar morphology, in situ hybridization using 5S rDNA and 18S-26S rDNA probes was utilized to karyotype the chromosomes of the five species, Capsicum annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens. The 5S rDNA located on only one pair of chromosomes in all five species. The 5S rDNA carrying chromosome was designated as chromosome 1 by the synteny relationship with tomato. In two species, C. baccatum and C. pubescens, the 5S rDNA was physically linked with a 18S-26S rDNA locus. The number and chromosomal location of 18S-26S rDNA loci were highly variable among the species. The number of loci was as few as two in C. annuum and as many as 14 in C. baccatum. The chromosomal positions of the 18S-26S loci were in the telomere regions in the corresponding chromosomes and some chromosomes showed hybridization signals in this region of both long and short arms. A pair of acrocentric chromosomes carrying the 18S-26S rDNA locus in the satellite region was found in all five species. The in situ and Southern hybridization patterns of the rDNAs were similar between C. annuum and C. chinense. C. frutescens was similar to C. chinense. C. baccatum and C. pubescens were speculated to be less related to the former three Capsicum species. The variable nature of the 18S-26S rDNA loci in the Capsicum species might provide a good model for rDNA evolution.
Tendências genéticas para escores visuais de conformação, precocidade e musculatura à desmama de bovinos Nelore

The aims of this study were to estimate heritability coefficients and genetic trends for visual scores of conformation (C), finishing precocity (P) and musculature (M) in Nelore beef cattle. Variance components and heritability coefficients were estimated by restrict maximum likelihood and breeding values were predicted by an animal mixed model using data from 56,076 animals born between 1990 and 2002. Genetic trends for each trait were estimated by the regression of breeding values on animal birth year. Heritability estimates for direct effect of C, P and M were respectively 0.122±0.012, 0.153±0.012 and 0.124±0.012. In the same order of traits, maternal effect heritability estimates were respectively 0.043±0.010, 0.038±0.009 and 0.056±0.010. Direct genetic trend estimates were respectively 0.013, 0.022 and 0.018 score units per year for C, P and M, which represent 0.42, 0.67, and 0.60% of the phenotypic average. Maternal effect genetic trends were respectively -0.0020, -0.0010 and -0.0009 for C, P and M, which represent -0.07, -0.03, and -0.03% of the phenotypic average of the population.
Vertical Position Reflects Increased Feeding Motivation in Growth Hormone Transgenic Coho Salmon (Oncorhynchus kisutch)

Growth hormone (GH) gene transgenesis has allowed the production of salmon with an inherently increased growth potential, on average two to threefold higher compared with daily specific growth rates observed in normal, non-transgenic fish. This difference quickly results in animals of very different sizes at age, and is associated with specific morphological effects and enhanced appetites in transgenic animals. However, less is known of the feeding and antipredator behaviour of GH-transgenic fish, information that can help with predictions of potential ecological consequences of release or escape of transgenic fish into the wild. In a series of experiments, transgenic (T) and normal (N) coho salmon of varying age and size (from 0.5 to 40 g, 3.5-21 mo) were studied singly, in pairs, and in groups during feeding and simulated predation threat. Vertical position generally did not differ between T and N fry, but at larger size (> 4 g) T fish remained closer to the surface than N fish both during feeding and predatory attacks, probably as a consequence of inherent differences in feeding motivation and later reinforcement by associative learning. This difference in vertical position was not the result of competition as it remained even after either fish in the pair had been removed. In nature, where predators may attack from above (birds) or below (fish), this kind of behaviour may translate into higher risk of predation, which could increase mortality and lower the fitness of transgenic fish, unless their increased growth rate can compensate for the increased risk-taking.
Distribution and retention of cleistothecia of Uncinula necator on bark of grapevines.

Clesitothecia of Uncinula necator were dispersed by late summer and early autumn rain to the bark of grapevines. Rain-dispersed ascocarps accumulated rapidly on bark during a 10-wk period and were then retained on bark through subsequent rain events between leaf abscission and budbreak the following spring. The density of populations on bark was significantly correlated (r = 0.72-0.88) with catches of cleistothecia in filter-paper funnels attached to the trunk of grapevines. The density of populations on bark during winter was not correlated with several measures of disease incidence and severity from the previous growing season. We concluded that while incidence and severity may determine the potential population available for dispersal, rain events determine the actual efficiency of transfer from infected organs to the bark of the vine. The percentage of ascocarps that reacted positively with the fluorescent vital stain fluorescein diacetate ranged from 50 to 62% and did not change significantly during overwintering until cleistothecia began to dehisce in spring. Therefore, the density and viability of populations of cleistothecia on bark at the time of budbreak appear to have been determined at the time of leaf fall the previous autumn and were not modified by subsequent environmental conditions. The densest aggregations of cleistothecia occurred on the cordons of cordon-trained vines, with successively lower densities occurring on the bark of the upper and lower trunks. The pruning and training system of vines of Vitis labrusca cv. Concord did not affect the density of populations of cleistothecia on bark
Stratification of Temperature and Tropical Forests

Past studies of forest structure have suggested that both plant and animal communities may be organized into several distinct vertical strata, the number of strata increasing with decreasing latitude. Hypotheses are proposed to explain the development of such strata. It is suggested that stratification may (1) optimize light utilization, (2) increase CO2 concentrations within the forest canopy, (3) increase pollination and dispersal rates, (4) reduce predation on flowers, fruit, and leaves, and (5) increase structural integrity of the forest. Causal explanations for stratification are also proposed.
Mesoscale features and phytoplankton biomass at the GoodHope line in the Southern Ocean during austral summer

Two sets of high-resolution subsurface hydrographic and underway surface chlorophyll a (Chl a) measurements are used, in conjunction with satellite remotely sensed data, to investigate the upper layer oceanography (mesoscale features and mixed layer depth variability) and phytoplankton biomass at the GoodHope line south of Africa, during the 2010–2011 austral summer. The link between physical parameters of the upper ocean, specifically frontal activity, to the spatially varying in situ and satellite measurements of Chl a concentrations is investigated. The observations provide evidence to show that the fronts act to both enhance phytoplankton biomass as well as to delimit regions of similar chlorophyll concentrations, although the front–chlorophyll relationships become obscure towards the end of the growing season due to bloom advection and ‘patchy’ Chl a behaviour. Satellite ocean colour measurements are compared to in situ chlorophyll measurements to assess the disparity between the two sampling techniques. The scientific value of the time-series of oceanographic observations collected at the GoodHope line between 2004 to present is being realised. Continued efforts in this programme are essential to better understand both the physical and biogeochemical dynamics of the upper ocean in the Atlantic sector of the Southern Ocean.
Estimation of Canopy Photosynthesis in Rice by Means of Daily Increases in Leaf Carbohydrate Concentrations

Procedures for rapid measurement of canopy photosynthesis are needed because current methods are time consuming and labor intensive. Our objective was to demonstrate that daily increases in nonstructural carbohydrates of shoots provide a good estimate of daily canopy photosynthesis for rice (Oryza sativa L.). Four cultivars-'IR72', 'IR64', 'IR50', and 'YRL39'- were grown in the field on a vertic tropaquept day soil. Canopy photosynthesis was measured in the field every 2 h from sunrise (0600 h) to sunset (1800 h) and plotted over time to determine daily photosynthesis. Increases in shoot nonstructural carbohydrates per day were calculated by subtracting sunrise concentrations from those at sunset. Highly significant positive relationships between daily canopy photosynthesis and irradiance (r 2 = 0.999) and leaf soluble sugars and irradiance (r 2 = 0.981) were observed. Coefficients of determination for relationships between daily canopy photosynthesis and daily increases in leaf soluble sugars were high (r 2 = 0.987). Growth stage comparisons showed the highest coefficients of determination at panicle initiation because non-structural carbohydrates in the shoot were dependent on canopy light interception and photosynthesis. Relationships during flowering were intermediate because the spikelet was the main carbon sink. Removal of panicles at flowering increased coefficients of determination to r 2 = 0.8. Relationships among cultivars for daily irradiance versus daily canopy photosynthesis or daily increases in leaf soluble sugars had r 2 values of 0.7 to 1.0. We conclude that measuring daily increases in leaf carbohydrates can provide a simple, rapid screening procedure for evaluating canopy photosynthesis in rice.