Primary hemiepiphytism and gametophyte morphology in <Emphasis Type="Italic">Elaphoglossum amygdalifolium</Emphasis> (Dryopteridaceae)

Elaphoglossum amygdalifolium holds a critical phylogenetic position as sister to the remaining ca. 600 extant species of Elaphoglossum and may provide important insight into the evolution of epiphytism in this clade of ferns. Here, we present the first examination of growth habit and gametophyte morphology for this species. We show that the cordate to elongate-cordate gametophytes occur up to 0.5 m above the ground on the base of tree trunks. Unlike the gametophytes of all other studied species of Elaphoglossum, rhizoids are absent along the thallus margin and the hairs present on the margin lack whitish waxy caps; both differences are pleisiomorphic for the genus. Sporelings of E. amygdalifolium produce a single long root that grows straight into the soil where it branches profusely. Mature sporophytes have long-creeping rhizomes that climb to heights of at least 3 m and produce two types of roots: “feeding roots” that reach the ground and “clasping roots” that anchor the sporophyte to its host plant. Our observations reveal that E. amygdalifolium is a primary hemiepiphyte, the first example of this growth habit to be documented in Elaphoglossum. Results of an ancestral state reconstruction of growth habit in bolbitidoid ferns show that both primary hemiepiphytism and holoepiphytism are equally likely to be the ancestral character state for Elaphoglossum.     

Pyrodiversity begets plant–pollinator community diversity

Fire has a major impact on the structure and function of many ecosystems globally. Pyrodiversity, the diversity of fires within a region (where diversity is based on fire characteristics such as extent, severity, and frequency), has been hypothesized to promote biodiversity, but changing climate and land management practices have eroded pyrodiversity. To assess whether changes in pyrodiversity will have impacts on ecological communities, we must first understand the mechanisms that might enable pyrodiversity to sustain biodiversity, and how such changes might interact with other disturbances such as drought. Focusing on plant–pollinator communities in mixed‐conifer forest with frequent fire in Yosemite National Park, California, we examine how pyrodiversity, combined with drought intensity, influences those communities. We find that pyrodiversity is positively related to the richness of the pollinators, flowering plants, and plant–pollinator interactions. On average, a 5% increase in pyrodiversity led to the gain of approximately one pollinator and one flowering plant species and nearly two interactions. We also find that a diversity of fire characteristics contributes to the spatial heterogeneity (β‐diversity) of plant and pollinator communities. Lastly, we find evidence that fire diversity buffers pollinator communities against the effects of drought‐induced floral resource scarcity. Fire diversity is thus important for the maintenance of flowering plant and pollinator diversity and predicted shifts in fire regimes to include less pyrodiversity compounded with increasing drought occurrence will negatively influence the richness of these communities in this and other forested ecosystems. In addition, lower heterogeneity of fire severity may act to reduce spatial turnover of plant–pollinator communities. The heterogeneity of community composition is a primary determinant of the total species diversity present in a landscape, and thus, lower pyrodiversity may negatively affect the richness of plant–pollinator communities across large spatial scales.     

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.     

Validation of a high-performance liquid chromatographic assay method for pharmacokinetic evaluation of busulfan

The development and validation of a high-performance liquid chromatographic (HPLC) assay for determination of busulfan concentrations in human plasma for pharmacokinetic studies is described. Plasma samples containing busulfan and 1,6-bis(methanesulfonyloxy)hexane, and internal standard, were prepared by derivatization with sodium diethyldithio-carbamate (DDTC) followed by addition of methanol and extraction with ethyl acetate. The extract was dried under nitrogen and the samples reconstituted with 100 μl of methanol prior to HPLC determination. Chromatography was accomplished using a Waters NovaPak octadecylsilyl (ODS) (150×3.9 mm I.D.) analytical column, NovaPak ODS guard column, and mobile phase of methanol-water (80:20, v/v) at a flow-rate of 0.8 ml/min with UV detection at 251 nm. The limit of detection was 0.0200 μg/ml (signal-to-noise ratio of 6) with a limit of quantitation (LOQ) of 0.0600 μg/ml for busulfan in plasma. Calibration curves were linear from 0.0600 to 3.00 μg/ml in plasma (500 μl) using a weighting scheme. Precision of the assay, as represented by C.V. of the observed peak area ration values, ranged from 4.41 to 13.5% (13.5% at LOQ). No day-to-day variability was observed in predicted concentration values and the bias was low for all concentrations evaluated (bias: 0 to 4.76%; LOQ: 2.91%). The mean derivatization and extraction yield observed for busulfan in plasma at 0.200, 1.20 and 2.00 μg/ml was 98.5% (range 93.4 to 107%). Plasma samples containing potential busulfan metabolites and co-administered drugs, which may be present in clinical samples, provided no response indicating this assay procedure is selective for busulfan. This method was used to analyze plasma concentrations following administration of a 1 mg/kg oral busulfan dose.     

Identification of Mendelian inconsistencies between SNP and pedigree information of sibs

Background

Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement.

Methods

Straightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP) genotypes between parent and offspring (PAR-OFF). Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT). The second test compares pedigree and SNP-based relationships (SIBREL). All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals.

Results

Both SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL) identified 18 (22) additional inconsistent animals.Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error), were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error), were considerably higher for SIBREL compared to SIBCOUNT.

Conclusions

Tests to remove Mendelian inconsistencies between sibs should be preceded by a test for parent-offspring inconsistencies. This parent-offspring test should not only consider parent-offspring pairs based on pedigree data, but also those based on SNP information. Both SIB tests could identify pairs of sibs with Mendelian inconsistencies. Based on type I and II error rates, counting opposing homozygotes between sibs (SIBCOUNT) appears slightly more precise than comparing genomic and pedigree relationships (SIBREL) to detect Mendelian inconsistencies between sibs.     

Blechnum obtusum (Blechnaceae), a new species from western Venezuela

Blechnum obtusum is described and illustrated as a new species. It grows in páramos of western Venezuela and most resemblesB. werffii of Costa Rica and Panama.     

Relationship between immune cell phenotypes and pig growth in a commercial farm

The objective of this study was to evaluate the relationship between the level and function of circulating immune cells with average daily gain, live and carcass measurements, feed intake, and feed conversion. Production performance was monitored throughout the pig's lifetime. Pigs were moved in weekly batches through the nursery and growing/finishing rooms at specific target weights. Animals were individually weighed at birth and at weaning, and then every two weeks while they were "on test" until they were "off test" and sent to the slaughterhouse. At six to seven weeks of age, the pigs were bled in the nursery. The percentage of immune cell subsets and lymphocyte proliferation was estimated using swine monoclonal antibodies and flow cytometric analysis. The predictive effect of the immune cell subset markers and lymphocyte proliferation on production traits was statistically analyzed. The results indicated that the proportion of several peripheral cell subsets, including CD16+, CD2+/CD16+, and CD8+ lymphocytes, appear to predict growth during the entire productive life of the pig. Larger percentages of lymphocytes expressing CD16+ CD2+/CD16+, and CD8+receptors in blood resulted in a reduction in average daily gain. In addition, high percentages of SLA-DQ+ cells were associated with better carcass weight and feed conversion. The CD16+, CD2+/CD16+, CD8+, and SLA-DQ+/- cell subsets appear to be important biomarkers involved with the inherent ability of the pig to efficiently grow and produce better carcass weight in representative commercial environments.     

Can tropical seaweeds reduce herbivory by growing at night? Diel patterns of growth,nitrogen content,herbivory, and chemical versus morphological defenses

Summary Tropical seaweeds in the genus Halimeda reduce losses to grazing by capitalizing on diel patterns of herbivore activity. These seaweeds produce new, more herbivoresusceptible growth at night when herbivorous reef fishes are inactive. Plant portions more than 48 h old are low in food value, well defended morphologically (calcified and high in ash content), and relatively resistant to herbivory. Younger plant portions represent 3–4.5 times the food value (nitrogen or organic content) of older portions but are only moderately more susceptible to herbivores due to their high concentrations of the terpenoid feeding deterrents halimedatrial and halimedatetraacetate. Halimedatrial significantly deters grazing by both parrotfishes (Scaridae) and surgeonfishes (Acanthuridae) and occurs in high concentrations (2–4.5% of plant ash-free dry mass) in plant portions that are 4–12 h old, intermediate concentrations (0.3–2.3%) in portions that are 16–26 h old, and low concentrations (0.3%) in older plant portions. The related compound halimedatetraacetate is absent from the youngest plant portions, shows a rapid increase in concentration (from 0 to 1%) in plant material that is approximately 16 h old, and then rapidly declines to low levels (0.1 to 0.2%) in older plant portions. Thus, newly produced tissues are nutritionally valuable but contain high concentrations of defensive chemicals. As these tissues age, morphological defenses increase, the tissue becomes less valuable as a food for herbivores, and chemical defenses decrease. Additionally, new growth of Halimeda remains unpigmented until just before sunrise. Thus, the valuable, nitrogen-containing molecules associated with photosynthesis are not placed in the new, and more herbivore susceptible, growth until lights is available and they can start producing income for the plant.Experiments in a coral-reef microcosm, where diel patterns of light and water chemistry could be altered, indicated that Halimeda's growth pattern is cued by the timing of light-dark cycles rather than by co-occurring diel changes in water chemistry. Although the growth patterns of Halimeda seem unusual, similar patterns appear to occur in numerous other seaweeds and in microalgae such as diatoms and dinoflagellates.