Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic variation and divergence in populations of ayu Plecoglossus altivelis, including endangered subspecies, inferred from PCR‐RFLP analysis of the mitochondrial DNA D‐loop region

: The ayu Plecoglossus altivelis altivelis, including two ecological forms (amphidoromous and landlocked), is a common and commercially important freshwater fish in Japan, whereas the endangered subspecies P. a. ryukyuensis (Ryukyu-ayu) inhabits a limited area of the Ryukyu Islands in southern Japan. The efficiency of polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis containing the entire D-loop region was examined to evaluate genetic variability and divergence in ayu populations, including the endemic two populations of the Ryukyu-ayu on the same island, and was compared with genetic data obtained from nuclear markers presented previously. The haplotype diversities (h) of the two populations of Ryukyu-ayu (0.251 and 0) were far smaller than those of the two common forms (0.766–0.928), suggesting that strong founder and/or bottleneck effects occurred in the subspecies populations. A common haplotype was not observed between the two populations of Ryukyu-ayu, suggesting little or no gene flow between them. The net nucleotide sequence divergence value (dA) between the two populations of Ryukyu-ayu (0.276%) was almost same as that between the two forms of the former subspecies (0.265%). These results almost coincided with the results derived from nuclear markers and suggest that PCR-RFLP analysis of the mitochondrial DNA D-loop region is useful for evaluating genetic variability and divergence among ayu populations.
The Utility of Molecular Hypotheses for Uncovering Morphological Diversity in the Notropis rubellus Species Complex (Cypriniformes: Cyprinidae)

Abstract When molecular phylogeography results in the discovery of hidden diversity, this diversity is often labeled as cryptic. Few studies have gone back to the morphology to determine whether or not this molecular diversity is in fact detectable at the morphological level. The Notropis rubellus species complex has a widespread distribution in freshwater streams of eastern North America. Recent molecular studies have identified up to seven allopatric clades, suggesting that there may be morphologically cryptic diversity within the group. This study uses traditional meristics and geometric morphometric methods to test molecular hypotheses of cryptic diversity within the species complex. Meristic data and a principal component analysis of geometric morphometric data supported the cryptic hypothesis. Canonical variates analyses (CVA), however, were able to detect statistically significant, clade-specific morphological variation, suggesting that in this case, cryptic diversity was an artifact of the detection method. CVA thus provided a useful tool for identifying subtle or complex shape variation. However, morphological variation within the N. rubellus species complex was undetectable without a pre-existing molecular hypothesis.
Population Density and Habitat Preferences of Forest Duikers in Moukalaba-Doudou National Park, Gabon

We conducted a line-transect survey via direct observation to estimate the densities of forest duikers in Moukalaba-Doudou National Park, Gabon. Five 2-km line transects were established in different vegetation types, and each transect was walked at 1.0 km/h. We also conducted a ‘quick survey' by walking at c. 2.5 km/h along all transects. A detection function was estimated separately for each species by pooling all the data from the five transects. For Cephalophus silvicultor, all sighting records of the two surveys were used because there was no significant difference in the encounter rates. In total, Philantomba monticola, red duikers (Cephalophus spp.), and C. silvicultor were observed 100, 80, 33 times, respectively. Their individual densities were estimated at 16.43/km2 (95% CI: 11.4–23.6), 7.1/km2 (5.5–9.2), and 1.63 km2 (1.0–2.8), respectively. The encounter rate for P. monticola and C. silvicultor did not vary significantly between the transects, while that of red duikers was higher in the primary forest than in the young secondary or gallery forest. The duiker densities in our study area are among the highest in the African rainforest. Our results indicate that quick surveys may be an effective approach to estimate the densities of rare species.
Beech bark disease in northern hardwood forests: the importance of nitrogen dynamics and forest history for disease severity

Beech bark disease has been a major cause of mortality of American beech (Fagus grandifolia Ehrh.) in North America during the past century. Previous studies have suggested a positive relationship between disease severity and both bark nitrogen content and tree size, presumably due to higher rates of infestation by beech scale insects, which allow more extensive infection of the tree by Nectria fungi. Recent concerns about nitrogen saturation in north- eastern forests, particularly in old-growth forests, led us to examine patterns of disease severity as a function of bark tissue nitrogen content in old-growth and second-growth forests in the Adirondack region of New York and northern Maine. Trees growing in old-growth stands possessed significantly higher levels of bark nitrogen than similarly sized trees in second-growth forests. The severity of disease symptoms was more acute in the old-growth forests and was positively correlated with the percent nitrogen of the bark in both forest types. Comparisons of the coefficients of vari- ation between beech bark sampled from disease-free forests in the upper peninsula of Michigan and that sampled from diseased forests indicated that elevated bark nitrogen concentrations in diseased trees were a cause and not an effect of disease presence. While there was no difference in disease severity between control and nitrogen-fertilized forests in Maine, these forests had both been exposed to the disease for longer time periods than the other studied forests and they are likely approaching nitrogen saturation. Resume : En Amerique du Nord, la maladie corticale du hetre a ete une cause importante de mortalite du hetre d'Amerique (Fagus grandifolia Ehrh.) au cours du dernier siecle. Des etudes anterieures ont laisse entrevoir qu'il y avait une relation positive entre d'une part la severite de la maladie et d'autre part le contenu en azote de l'ecorce et la dimension des arbres, probablement a cause du taux eleve d'infestation par la cochenille du hetre qui favorise une plus forte infection des arbres par les champignons du genre Nectria. Des preoccupations recentes au sujet de la saturation en azote dans les forets du nord-est, particulierement dans les vieilles forets, nous ont amene a examiner le comporte-
Effects of altitude on tracheid differentiation and lignification of Norway spruce

The effect of altitude on lignification is important in developing an understanding of what drives natural variation in wood properties. Cambia of two Norway spruce trees, growing at altitudes of 580 and 1260 m a.s. l. , were periodically sampled to measure tracheid dimensions and cellular lignin content. The low-elevation tree showed a higher rate of cell division with thicker cell walls and wider growth rings. The maturation phase of tracheids at high elevation was completed by the end of October while low elevation latewood tracheids were still lignifying. As re- vealed by ultraviolet microscopy, lignin content in single cells, as well as in complete tree-rings, was higher at high elevation. Rank correlation analysis indicated high negative correlation between lignin content of tracheid cell walls and corresponding wall thickness. It is hypothesized that trees growing at higher altitudes compensate for the thinner cell walls with an increased lignin content which helps to maintain mechanical integrity of the xylem.
Geographical variation of harp seal underwater vocalizations

Underwater vocalizations of harp seals (Phoca groenlandica) were recorded during the breeding season in the Gulf of St. Lawrence and north of Jan Mayen Island. Each herd had one unique call type and shared (often in different proportions) an additional 17 call types. Of these 17, 13 common call types had sample sizes large enough to permit statistical analysis of five duration, repetition, and pitch features. Only one of these call types exhibited no interherd differences; the others exhibited 1 – 5 different features. The average and maximum numbers of elements per call were higher in the Gulf than the Jan Mayen herd. Within each herd there were no differences in the call types and numbers of call elements over a 19-year period. An implication of these findings and other separate tagging studies is that the two herds are reproductively isolated.
Developmental patterns of the crocodilian and avian columella auris: reappraisal of interpretations of the derivation of the dorsal hyoid arch in archosaurian tetrapods

The morphogenesis of the crocodilian and avian columella auris is analysed, using Alligator and Struthio as models that are studied in detail, and Crocodylus, Gallus, and Coturnix as models for comparative purposes. This investigation was undertaken to address controversies emanating from previous studies concerning the identity of archosaurian hyal elements, and to clarify confounding nomenclature that has been used for both topographic and phylogenetic purposes. We found that confusion in the identification of the reptilian and avian hyoid arch derivatives is attributable to: (1) redundant and/or inconsistently applied topographical terminology; (2) mixing of topographical and phylogenetic terminology; (3) interpretation in a recapitulatory framework; and (4) failure to consider that developmental pathways of recent archosaurians (reptilians and birds) might be divergently modified. Our analysis identifies errors in previous interpretations, misinterpretations of prior work, and histological observations that have been idealized. The most controversial issues are addressed – the derivation of the supracolumellar process; the concept of the laterohyal component; and segmentation of the distal part of the reptilian and avian columella auris. Based on new data, we suggest that the osteichthyan infrapharyngohyal, suprapharyngohyal, epihyal, and ceratohyal are not applicable terms for reptilian and avian columellar components from a phylogenetic perspective, and should not be used as topographical terms either. We further propose that the original morphogenetic program of the hyoid arch has been overwritten in newly derived evolutionary pathways of crocodilians and birds, in which a new functional and morphological patterning of the hyoid arch, as a specific sound-transmitting apparatus, have evolved. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156, 384–410.
Energy Storage and Reproduction in Mussels, Mytilus galloprovincialis: The Influence of Diet Quality

ABSTRACT The effect of diet quality on reproduction and energy storage in bivalves has not been widely investigated. Food quality and quantity influences reproductive success in many bivalve species, and the timing and rate of reproductive maturation is a dominant influence on natural population dynamics, whereas understanding and controlling reproduction is vital for the reliable production of juvenile mussels for aquaculture. In this study, adult mussels were fed for six weeks on 1 of 4 diets: (1) raw seawater; and raw seawater plus equivalent dry weights of (2) Chaetoceros calcitrans, (3) Pavlova lutheri, and (4) a 1:1 combination of the 2 species. Chaetoceros calcitrans has a higher proportion of simple sugars and sterols compared with P. lutheri, whereas P. lutheri has greater proportions of DHA. Diet composition had a significant effect on the glycogen concentration and reproductive indicators at the end of six weeks. The combined C. calcitrans and P. lutheri supplement showed no change in glycogen stores after 6 wk, however a greater percentage of animals spawned, and a greater proportion of vitellogenic and atretic mussels were produced. Mussels supplemented with C. calcitrans increased glycogen stores and produced greater proportions of mussels with vitellogenic oocytes. Those supplemented with P. lutheri produced a greater proportion of mussels with atretic oocytes, and a lower proportion of D-veliger larvae produced from the eggs. Mussels fed with raw seawater produced a greater proportion of resting mussels, and a lower percentage of mussels spawned at the end of the conditioning period. Oocyte diameter and fecundity showed no significant difference among diets. These results show that diet quality directly influences the allocation of energy to glycogen storage and gametogenesis, however, the mechanism by which this occurs is unclear. Investigation into the allocation of individual biochemical components to each of these processes would further illuminate the process by which diet quality influences the allocation of energy to glycogen storage versus gametogenesis.
Analysis of Dough Kneaders Using Numerical Flow Simulations

ABSTRACT The objective of this work is to characterize the various deformations to which dough is subjected during kneading, and to investigate the influence of mixer configurations and operating conditions. Several kneader geometries are modeled as representative of the mixing mechanisms taking place in various mixers. Based on the time-dependent velocity fields obtained, the type of deformation taking place in the mixers is characterized using relevant kinematic flow classification parameters. These parameters are then related to the mechanical action of the kneader. The results for the practical design of dough kneaders can be applied, and a complementary experimental program should fit within the design cycle.
The future of IPM: Whither or wither?

The acronym IPM (integrated pest management) has been around for over 50 years and now not only supposedly guides research and extension in pest management but also markets pesticides, is claimed to be undertaken by many growers, and even resonates with public perceptions and politicians. Whether or not IPM programs are sustainable in the longer term under the conflicting stresses and strains of the modern agricultural environment is debatable. We analyse three case studies of IPM development in Australia: citrus IPM in central Queensland, Brassica IPM in southeast Queensland and Helicoverpa management in cotton in eastern Australia. Many management practices for these pests have changed over time. In the more stable citrus system classical biological control along with changed practices (reduced pesticide use) have effectively controlled imported scale insect pests. In Brassicas and cotton, IPM is predominantly of the sample and spray variety where, increasingly, less broad-spectrum insecticides are used and, in cotton, Helicoverpa management includes the deployment of transgenic plants. We question whether or not IPM principles are always consistent with market forces and whether or not the approach is universally applicable for all pest insects when implemented at the small (field or farm) scale. Farmers will adopt cost-effective approaches that minimise their financial risks. For Australia as a whole over the last 30 years insecticide input costs per hectare have increased faster than the price index, reflecting more costly insecticides, changes to the combinations of crops grown and an increase in the overall area of crops cultivated together with possible concomitant changes in pest abundance. Any pest crisis will ensure rapid changes in practice and adoption of technologies, in order to mitigate the short-term financial stresses caused. However, regression to former practices tends to follow (e.g. in Brassica crops). In most cases, we cannot objectively test if changed management practices are responsible for changes in pest abundance, as is often claimed, or if the latter is simply a consequence of the weather and/or related large-scale landscape features (e.g. area of host plants). We argue that for many systems the future of pest management practice will require a change to landscape or area-wide approaches. We suspect, given how entrenched the acronym has become, whatever the nature of the approach it will be called IPM.
A Phylogenetic Analysis of Sexual Size Dimorphism in Turtles

Abstract Sexual size dimorphism (SSD) is widespread in a variety of vertebrate taxa, and its presence has been associated with a range of evolutionary and ecological factors. Turtles, as a lineage, have been shown to include species that exhibit both forms of SSD—male-biased (male larger) and female-biased (female larger)—as well as species that do not exhibit SSD (male size ≅ female size). Previous work has suggested that factors affecting the direction and magnitude of SSD in turtles may include habitat preference and fecundity; these correlations, however, have not been tested in a phylogenetic context. To provide a framework for evaluating potential correlates with the magnitude and direction of SSD in turtles, we examined the phylogenetic distribution of SSD in this clade. Published sources were surveyed for data on the direction and magnitude of SSD, carapace length, clutch size, egg size, and preferred habitat (terrestrial vs. nonterrestrial). Phylogenies were compiled from multiple published sources to develop a phylogeny for all taxa (n = 82) for which SSD data were assembled. The phylogenetic distribution of SSD was then evaluated using parsimony-based methods. These analyses indicated that the ancestral condition for extant turtles was female-biased SSD. Phylogenetic analyses conducted on subsets of the data (concentrated-changes tests, independent contrasts) indicated that changes in SSD state were not correlated with changes in habitat preference. Both male and female carapace length were found to be correlated with traits related to fecundity (egg size, clutch size), but the degree of dimorphism was not found to be correlated with these traits. A significant negative correlation between egg size and clutch size was also evident in turtles, as predicted by life-history theory.
The structural organization of the celiac ganglia

The ganglia incorporated in the celiac plexus are anatomically and functionally related to the splanchnic nerves. Components of the vagus nerves traverse this plexus but, according to current teaching, vagus nerve fibers do not effect synaptic connections with celiac ganglion cells. The latter, like the ganglion cells in the sympathetic trunk ganglia, have been regarded as constituting the distal links in visceral efferent conduction pathways and, consequently, exclusively efferent in function. This hypothesis, based mainly on the results of early physiological experimentation, has not been controverted by anatomical data. The results of certain recent physiological experiments, however, support the assumption that some of the celiac ganglion cells are involved in reflex mechanisms through which certain gastro-intestinal reflexes may be carried out in the absence of intact conduction pathways between the celiac plexus and the central nervous system.
In vitro culture of Telfairia occidentalis under different cytokinins and auxin combination

Telfairia occidentalis is a tropical vine and has been a good source of iron rich vegetable to man. It is normally propagated through seeds but the seeds are recalcitrant in nature. The vegetative propagation of T. occidentalis has been difficult hence there is a need to develop an in vitro method. Nodal cuttings of T. occidentalis was cultured on Murashige and Skoog (MS; 1962) basal media supplemented with IBA, IAA, NAA, BAP, and kinetin at different concentrations. Among all the growth hormones used, IBA and BAP combination gave the best result for both rooting and shooting while BAP in combination with NAA showed the highest number of nodes. The result showed that in vitro growth of T. occidentalis is hormone specific.
Biological Activities of Synthetic Oligosaccharides and Glycolipids from Mycobacteria

Glycolipids are essential components of mycobacterial cell envelopes. They are highly bioactive and involved in many aspects of virulence and persistence of mycobacteria. Many glycolipids have been isolated from mycobacterial surfaces. Some mycobacterial glycans and glycolipids, as well as their analogs, have been chemically synthesized. This report focuses on recent contributions in the synthesis of mycobacterial glycans and glycolipids to the study of their biological mechanisms and to the optimization of their activities, with highlights on the lipid and saccharide mimetics.
Geographical variation in echolocation vocalizations of the Himalayan leaf‐nosed bat: contribution of morphological variation and cultural drift

Ecologists and evolutionary biologists have a long-standing interest in the patterns and causes of geographical variation in animals’ acoustic signals. Nonetheless, the processes driving acoustic divergence are still poorly understood. Here, we studied the geographical variation in echolocation vocalizations (commonly referred to as echolocation ‘pulses’ given their short duration and relatively stereotypic nature, and to contrast them from the communicative vocalizations or ‘calls’) of a widespread bat species Hipposideros armiger in south China, and assessed whether the acoustic divergence was driven by either ecological selection, or cultural or genetic drift. Our results revealed that the peak frequency of echolocation pulses varied significantly across populations sampled, with the maximum variation of about 6 kHz. The peak frequency clustered into three groups: eastern and western China, Hainan and southern Yunnan. The population differences in echolocation pulses were not significantly related to the variation in climatic (mean annual temperature, mean annual relative humidity, and mean annual precipitable water) or genetic (genetic distance) factors, but significantly related to morphological (forearm length) variation which was correlated with mean annual temperature. Moreover, the acoustic differences were significantly correlated with geographical and latitudinal distance after controlling for ‘morphological distance’. Thus, neither direct ecological selection nor genetic drift contributed to the acoustic divergence observed in H. armiger. Instead, we propose that the action of both indirect ecological selection (i.e. selection on body size) as well as cultural drift promote, in part, divergence in echolocation vocalizations of individuals within geographically distributed populations.