Pollination biology of a disjunct population of the endangered sandhills endemic <Emphasis Type="Italic">Penstemon haydenii</Emphasis> S. Wats. (Scrophulariaceae) in Wyoming,USA

We studied the breeding system and flower visitors of the endangered plant, Penstemon haydenii, at several south-central Wyoming, USA occurrences. In agreement with earlier studies of the species 300 km to the east in Nebraska, we found Wyoming plants to be self-incompatible and pollinator-dependent for sexual reproduction. Flower visitors were several species of native bees in the families Apidae (particularly bumblebees), Halictidae (small sweat bees), and Megachilidae (especially in the genus Osmia); and the masarid wasp Pseudomasaris vespoides. Especially important was Osmia brevis, an abundant megachilid bee, and one of only two species (the sweat bee Lasioglossum (Dialictus) pruinosum was the other) present at all five sites. As in Nebraska, fruit set did not differ between our experimental cross-pollination treatment and an open-pollinated control. However, unlike Nebraska, open-pollinated treatments in Wyoming produced significantly fewer seeds per fruit than the experimental out-crossing treatment. We discuss several possible explanations for seed limitation: (1) a scarcity of pollinators early in the flowering season; (2) resource competition for developing ovules on open-pollinated inflorescences but not on experimental inflorescences; (3) the deposition of self pollen through intra-inflorescence and intra-genet pollinator movements; (4) few S-alleles and mating types in the Wyoming metapopulation compared to the Nebraska metapopulation, from which it likely derives.     

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

Background

RNA viruses have high mutation rates and exist within their hosts as large, complex and heterogeneous populations, comprising a spectrum of related but non-identical genome sequences. Next generation sequencing is revolutionising the study of viral populations by enabling the ultra deep sequencing of their genomes, and the subsequent identification of the full spectrum of variants within the population. Identification of low frequency variants is important for our understanding of mutational dynamics, disease progression, immune pressure, and for the detection of drug resistant or pathogenic mutations. However, the current challenge is to accurately model the errors in the sequence data and distinguish real viral variants, particularly those that exist at low frequency, from errors introduced during sequencing and sample processing, which can both be substantial.

Results

We have created a novel set of laboratory control samples that are derived from a plasmid containing a full-length viral genome with extremely limited diversity in the starting population. One sample was sequenced without PCR amplification whilst the other samples were subjected to increasing amounts of RT and PCR amplification prior to ultra-deep sequencing. This enabled the level of error introduced by the RT and PCR processes to be assessed and minimum frequency thresholds to be set for true viral variant identification. We developed a genome-scale computational model of the sample processing and NGS calling process to gain a detailed understanding of the errors at each step, which predicted that RT and PCR errors are more likely to occur at some genomic sites than others. The model can also be used to investigate whether the number of observed mutations at a given site of interest is greater than would be expected from processing errors alone in any NGS data set. After providing basic sample processing information and the site’s coverage and quality scores, the model utilises the fitted RT-PCR error distributions to simulate the number of mutations that would be observed from processing errors alone.

Conclusions

These data sets and models provide an effective means of separating true viral mutations from those erroneously introduced during sample processing and sequencing.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1456-x) contains supplementary material, which is available to authorized users.     

Fire and dynamics of granivory on a California grassland forb

This study examines the effects of burning and granivory on the reproductive success of the rare plant Amsinckia grandiflora (Boraginaceae). Fire is often used in California grasslands as a means of exotic species control, but the indirect effects these controls have on the reproductive ecology of native plants are rarely assessed. The interaction of fire with granivory of A. grandiflora seeds was examined in California grasslands over five years (1998–2002). In 1998 and 1999, both burned and unburned plots had bird-exclusion (netted) and no-exclusion (open) treatments. Predation rates were high (51–99%) and final predation rates did not differ among treatments. In 2000, granivory rates in the unburned, open plots were lower than in previous years (14%), and rodent trapping yielded only a single animal. Low granivory rates were observed in 2001 for unburned, open plots (47%). In 2001, burned/open plots experienced significantly more granivory (87%) than either burned/netted plots (37%) or unburned/open plots (47%). In 2002, every seed was taken from burned, open plots. Granivory was highly variable, ranging from 4 to 100% per plot over a 3-week period. Nearly all plots were discovered (>10% predation) by granivores in all trials in all years. When data from all treatments were combined, significant differences in granivory rates occurred among years, indicating stronger inter-year effects than within-year effects due to burning or bird exclusion. Fire affects granivory when overall predation rates are low, but when predation levels are high (as they were in 1998 and 1999), fire may not affect granivory occurring within the same year. Models extending seed survivorship through the dry summer indicate that most seeds are eaten, even when granivory rates are low.     

Diatomaceous earths as alternatives to chemical insecticides in stored grain

Diatomaceous earth （DE） is a natural inert dust used to control insect pests in stored grain as an alternative to synthetic residual insecticides. Various DE formulations are now registered as a grain protectant or for structural treatment in many different countries throughout the world. The mode of action of DE is through the absorption of cuticular waxes in the insect cuticle, and insect death occurs from desiccation. The main advantages of using DE are its low mammalian toxicity and its stability. The main limitations to widespread commercial use of DE are reduction of the bulk density and flowability of grain, irritant hazards during application and reduction in efficacy at high moisture contents. This paper is an updated review of published results of researches related to the use of DEs and discusses their potential use in large-scale, commercial storage and in small scale applications.     

Contrasting demographies and persistence of rare annual plants in highly variable environments

Spatial and temporal variation in critical life history traits differ markedly between two co-occurring, rare and endangered annual plants, Gilia tenuiflora arenaria and Chorizanthe pungens pungens, that have restricted, but overlapping geographic distributions in coastal habitats of central California, USA. Environmental variation was extreme during the 6-year study (1997–2002), with the greatest differences between an intense wet, warm El Niño year (1998), followed by a very dry, cool La Niña (1999). Both species have similar increases in adult survival and seed set with wetter, warmer weather in spring, but they differed in other traits: more Gilia germinated in years with high rainfall and temperature, while more Chorizanthe germinated in dry, cooler years; Gilia abundance increased with the number of years since the previous large El Niño event, while Chorizanthe abundance declined; and Gilia abundance was independent of the previous year’s seed set, while Chorizanthe density was directly related to the previous year’s seed set. The strong negative associations of Chorizanthe abundance with warm, wet weather and with time since the previous El Niño probably reflect the particular sequence of annual weather patterns from 1997 through 2002, especially the extremes in 1998 and 1999. Since it germinates readily in most years under a wide range of winter conditions and does not develop a long-lived seed bank, Chorizanthe seedling abundance reflects recent additions and depletions of its seed bank, rather than prevailing weather, per se. In contrast, Gilia seeds may remain in the seed bank for many years, until relatively rare winter conditions trigger significant germination. These species-specific demographies enhance persistence and coexistence of these species, but the mechanisms differ from each other and from those described for annuals in other highly variable environments.     

The extent of clonality and genetic diversity in the rare Caldesia grandis (Alismataceae): Comparative results for RAPD and ISSR markers

Genetic variation and clonal diversity of three natural populations of the rare, highly clonal marsh herb Caldesia grandis Samuelsson were investigated using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Both of the markers worked effectively in clone identification of C. grandis. RAPD markers detected more diversity than ISSR markers in the three populations examined. Of the 60 RAPD primers screened, seven produced highly reproducible bands. Using these primers, a total of 61 DNA fragments were generated with 52 (85.25%) being polymorphic indicating considerable genetic variation at the species level. Analysis of molecular variance (AMOVA) showed that a large proportion of genetic variation (81.5%) resided within populations, while only a small proportion (18.5%) resided among populations. With the use of 52 polymorphic RAPD markers, we were able to identify 127 genets among 342 samples from three populations. The proportion of distinguishable genets (PD: mean 0.37), Simpson's diversity index (D: mean 0.91), and evenness (E: mean 0.78) exhibited high levels of clonal diversity compared to other clonal plants. These results imply that sexual reproduction has played an important role at some time during the history of these populations. Nevertheless, the high level of diversity could have been also partially generated from somatic mutations, although this is unlikely to account for the high diversity generally found among C. grandis genets.     

Genetic variation of isolated and peripheral populations of Pinus sylvestris (L.) from glacial refugia

Analysis of variation at 10 polymorphic isoenzyme loci in 51 European populations of Pinus sylvestris both from its main continuous range and from isolated, marginal populations out of the continuous range, revealed differences in genetic structure. The highest genetic richness, measured as mean number of alleles per locus, was recorded for populations from the Iberian Peninsula, followed by those from Scotland and the Balkans. Marginal, isolated populations were characterized by much greater interpopulation variation than populations from the continuous range of the species. The highest mean observed heterozygosity was recorded for the Iberian populations. The highest gene flow was observed among populations in the continuous range of the species. The populations could be classified into five groups based on genetic similarities. Populations from the continuous range formed one group, those from Spain two groups, pines from Scotland one group and those from the Balkans one group. One population from Scotland was found to be most distinct from the other Scottish pines and was found to be grouped with the Balkan populations. The occurrence and frequencies of rare alleles in the populations showed a characteristic pattern, suggesting that populations from the Iberian Peninsula probably did not participate in the colonization of Europe by Pinus sylvestris after the last glaciation. In contrast, the migration of populations from the Balkan refugium into Central and Western Europe had a significant effect on the contemporary gene pools of populations of Pinus sylvestris in its continuous range.     

Logistic Bayesian LASSO for identifying association with rare haplotypes and application to age-related macular degeneration

Rare variants have been heralded as key to uncovering "missing heritability" in complex diseases. These variants can now be genotyped using next-generation sequencing technologies; nonetheless, rare haplotypes may also result from combination of common single nucleotide polymorphisms available from genome-wide association studies (GWAS). The National Eye Institute's data on age-related macular degeneration (AMD) is such an example. Studies on AMD had identified potential rare variants; however, due to lack of appropriate statistical tools, effects of individual rare haplotypes were never studied. Here we develop a method for identifying association with rare haplotypes for case-control design. A logistic regression based retrospective likelihood is formulated and is regularized using logistic Bayesian LASSO (LBL). In particular, we penalize the regression coefficients using appropriate priors to weed out unassociated haplotypes, making it possible for the rare associated ones to stand out. We applied LBL to the AMD data and identified common and rare haplotypes in the complement factor H gene, gaining insights into rare variants' contributions to AMD beyond the current literature. This analysis also demonstrates the richness of GWAS data for mapping rare haplotypes-a potential largely unexplored. Additionally, we conducted simulations to investigate the performance of LBL and compare it with Hapassoc. Our results show that LBL is much more powerful in identifying rare associated haplotypes when the false positive rates for both approaches are kept the same.     

广州市蕨类植物物种多样性研究

依据文献、标本与野外调查,简要回顾了历史上记录的广州蕨类植物,阐明了广州目前分布的蕨类植物的种类、区系特点、生态与地理分布、以及珍稀蕨类植物的种类与保护现状.广州地区有蕨类植物37科82属176种,其中乔芒萁(Dicranopteris gigantea)、刺边膜蕨(Hymenophyllm spinosum)和裸果鳞毛蕨(Dryopteris gymnosora)为广东分布新记录.广州蕨类植物区系以金星蕨科(Thelypteridaceae)、鳞毛蕨科(Dryopteridaceae)、水龙骨科(Polypo-diaceae)、蹄盖蕨科(Athyriaceae)和风尾蕨科(Pteridaceae)的植物最为丰富,没有本地特有种,亚洲热带亚热带分布成分和东亚分布成分占绝对优势.这176种蕨类植物中,约80%的种类生活在密林阴湿生境,约20%生活在疏林或灌草丛干旱生境,只有2种水生蕨类植物.在水平分布上,广州蕨类植物呈北多南少的分布格局,约90%的种类汇集在广州东北部的从化山区,74种在广州仅见于该山区.从物种多度上看,个体数量多(Cop2)的有33种,尚多(Cop1)的有48种,稀少(Sp)的有53种,很少(So1)的有41种.华南马尾杉(Phlegmariurus austrosbzicus)、福建观音座莲(Angiopteris fokiensis)、刺边膜蕨(Hymenophy llum spmosum)、粗齿桫椤(Alsophila denticulata)、小黑桫椤(A.m etteniana)、黑桫椤(A.podophylla)、桫椤(A.spinulosa)、水蕨(Ceratopteris thdictroides)、羽裂叶双盖蕨(Diplazium tomitaroanum)、闽浙圣蕨(Dictyocline mingchegensts)、微毛凸轴蕨(Metathelypteris adscendens)、峨眉茯蕨(Leptogramma scdlanll)、苏铁蕨(Brainea insignis)、珠芽狗脊(Woodwardia prolifera)和黑鳞复叶耳蕨(Arachniodes nigrospinosa)等15种被评估为广州的珍稀植物,它们亟待有效的保护.