Effects of errors in range maps on estimates of historical species richness of mammals in Canadian national parks

Aim Tests for faunal relaxation in reserves, particularly for mammals, have relied on comparisons of current species richness with estimates of species richness derived from historical range maps. However, any range map reflects the extent of occurrence of species and not necessarily the area of occupancy. Thus, estimates of historical species richness might be prone to error introduced by ‘false positives’, that is, a species might be considered to have been present in locations where it actually was not. The effect of such ‘false positives’ could bias statistical tests of faunal relaxation to type I error, and result in estimates of the extent of faunal relaxation in reserves greater than was actually the case. We evaluated the potential for errors in historical range maps to generate inflated estimates of historical species richness of mammals at sites that are reserves today. Location Canadian national parks in the Canadian portion of the Alleghenian‐‐Illinoian mammal province in south‐eastern Canada (the maritime region and parts of southern Québec, Ontario and Manitoba). Methods The effect of varying levels of error in range maps on estimates of historical species richness was tested using geographical information systems (GIS)‐based statistical sampling of simulated historical ranges. Species’ areas of occupancy were simulated to be only 25%, 75% and 95% of published historical species ranges. For each reserve, estimates of historical species richness from these simulated species ranges were then compared with similar, previously published estimates of richness based on published historical species ranges. Results Previous estimates of historical species richness for reserves were inversely and linearly related to the degree of inaccuracy of species ranges. If species ranges were, on average, 5% smaller than the accepted ranges, then estimates of historical species richness agreed with previous estimates in c. 90% of cases. However, if historical ranges were, on average, 25% smaller than those used in previous analyses, then previous historical estimates of species richness may be overestimates in c. 40% of cases. Main conclusions Estimates of the extent of faunal relaxation in reserves that use historical range maps to quantify past species richness appear to be sensitive to even small errors in the degree to which range maps may overestimate ‘area of occupancy’.     

Evaluating Burkholderia pseudomallei Bip proteins as vaccines and Bip antibodies as detection agents

Burkholderia pseudomallei is a biothreat agent and an important natural pathogen, causing melioidosis in humans and animals. A type III secretion system (TTSS-3) has been shown to be critical for virulence. Because TTSS components from other pathogens have been used successfully as diagnostic agents and as experimental vaccines, it was investigated whether this was the case for BipB, BipC and BipD, components of B. pseudomallei's TTSS-3. The sequences of BipB, BipC and BipD were found to be highly conserved among B. pseudomallei and B. mallei isolates. A collection of monoclonal antibodies (mAbs) specific for each Bip protein was obtained. Most recognized both native and denatured Bip protein. Burkholderia pseudomallei or B. mallei did not express detectable BipB or BipD under the growth conditions used. However, anti-BipD mAbs did recognize the TTSS needle structures of a Shigella strain engineered to express BipD. The authors did not find that BipB, BipC or BipD are protective antigens because vaccination of mice with any single protein did not result in protection against experimental melioidosis. Enzyme-linked immunosorbent assay (ELISA) studies showed that human melioidosis patients had antibodies to BipB and BipD. However, these ELISAs had low diagnostic accuracy in endemic regions, possibly due to previous patient exposure to B. pseudomallei.     

Identification of <Emphasis Type="Italic">Pm58</Emphasis> from <Emphasis Type="Italic">Aegilops tauschii</Emphasis>

Key message

A novel powdery mildew-resistance gene, designated Pm58, was introgressed directly from Aegilops tauschii to hexaploid wheat, mapped to chromosome 2DS, and confirmed to be effective under field conditions. Selectable KASP? markers were developed for MAS.

Abstract

Powdery mildew caused by Blumeria graminis (DC.) f. sp. tritici (Bgt) remains a significant threat to wheat (Triticum aestivum L.) production. The rapid breakdown of race-specific resistance to Bgt reinforces the need to identify novel sources of resistance. The d-genome species, Aegilops tauschii, is an excellent source of disease resistance that is transferrable to T. aestivum. The powdery mildew-resistant Ae. tauschii accession TA1662 (2n?=?2x?=?DD) was crossed directly with the susceptible hard white wheat line KS05HW14 (2n?=?6x?=?AABBDD) followed by backcrossing to develop a population of 96 BC₂F₄ introgression lines (ILs). Genotyping-by-sequencing was used to develop a genome-wide genetic map that was anchored to the Ae. tauschii reference genome. A detached-leaf Bgt assay was used to screen BC₂F_4:6 ILs, and resistance was found to segregate as a single locus (χ?=?2.0, P value?=?0.157). The resistance gene, referred to as Pm58, mapped to chromosome 2DS. Pm58 was evaluated under field conditions in replicated trials in 2015 and 2016. In both years, a single QTL spanning the Pm58 locus was identified that reduced powdery mildew severity and explained 21% of field variation (P value?<?0.01). KASP? assays were developed from closely linked GBS-SNP markers, a refined genetic map was developed, and four markers that cosegregate with Pm58 were identified. This novel source of powdery mildew-resistance and closely linked genetic markers will support efforts to develop wheat varieties with powdery mildew resistance.

     

Preconceptional cystic fibrosis carrier screening: opinions of general practitioners, gynecologists, and pediatricians in the Netherlands

Knowledge of the opinions of physicians with regard to preconceptional cystic fibrosis (CF) carrier screening and the possible factors that are associated with their opinions is important for the implementation of such a screening program. Data were obtained from a study in which genetic knowledge, opinions with regard to genetic testing and related skills were investigated. A questionnaire, developed and used by American researchers, was adapted to the Dutch health care situation, and sent to randomly selected general practitioners (GPs) (n = 200), gynecologists (GYNs) (n = 300), and pediatricians (PEDs) (n = 265). In this part of the study, their opinions with regard to genetic preconceptional CF carrier screening in different situations were assessed. The response rate for the GPs, GYNs, and PEDs was 64%, 69%, and 72%, respectively. In total, 63% of the GPs, 69% of the GYNs and 72% of the PEDs supported preconceptional CF carrier testing if a couple requested a test. Sixteen percent, 19% and 25%, respectively, were in favor of actively offering a test with 95% test sensitivity to all couples who were planning a pregnancy. A positive opinion on preconceptional CF carrier screening was associated with the following variables: "considering the test sensitivity as less important" (GPs, GYNs), "high perceived risk of having a child with CF" (GYNs), "providing genetic counselling in their own practice" (PEDs) and "reassurance when both partners test negative" (PEDs). Physicians are sympathetic toward preconceptional CF carrier screening if the couples themselves request a test. Physicians had reservations about routinely offering a CF carrier test.     

Femtosecond dynamics of intracellular water probed with nonlinear optical Kerr effect microspectroscopy

A nonlinear optical Kerr effect (OKE) microscope was developed and used to elucidate the ultra-fast diffusive motions of intracellular water molecules. In the OKE microscope, a pump-induced birefringence is sensed by a delayed probe pulse within a spatially confined volume that measures 0.5 microm in the lateral direction and 4.0 microm along the axial coordinate. This microscope allows the recording of time-resolved Kerr signals, which reflect the ultra-fast structural relaxation of the liquid, exclusively from intracellular aqueous domains. Because relaxation occurs on a picosecond time scale, only local diffusive motions are probed. The microscopic OKE signal is therefore insensitive to long-time-scale hindered translational motions enforced by intracellular mechanical barriers but probes the intrinsic orientational mobility of water molecules in cells instead. The Kerr response as determined from single intact mammalian cells under physiological conditions shows a structural relaxation time of 1.35 ps, which is 1.7 times slower than the Kerr decay observed in pure water. The data indicate that the mobility of water molecules in cellular domains is moderately restricted due to the high intracellular content of proteins and solutes.     

Patterns and potential drivers of intraspecific variability in the body C,N, and P composition of a terrestrial consumer,the snowshoe hare (Lepus americanus)

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Invasive clonal plant species have a greater root-foraging plasticity than non-invasive ones

Clonality is frequently positively correlated with plant invasiveness, but which aspects of clonality make some clonal species more invasive than others is not known. Due to their spreading growth form, clonal plants are likely to experience spatial heterogeneity in nutrient availability. Plasticity in allocation of biomass to clonal growth organs and roots may allow these plants to forage for high-nutrient patches. We investigated whether this foraging response is stronger in species that have become invasive than in species that have not. We used six confamilial pairs of native European clonal plant species differing in invasion success in the USA. We grew all species in large pots under homogeneous or heterogeneous nutrient conditions in a greenhouse, and compared their nutrient-foraging response and performance. Neither invasive nor non-invasive species showed significant foraging responses to heterogeneity in clonal growth organ biomass or in aboveground biomass of clonal offspring. Invasive species had, however, a greater positive foraging response in terms of root and belowground biomass than non-invasive species. Invasive species also produced more total biomass. Our results suggest that the ability for strong root foraging is among the characteristics promoting invasiveness in clonal plants.     

Focus on Weed Control: Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia

Recent rapid evolution and spread of resistance to the most extensively used herbicide, glyphosate, is a major threat to global crop production. Genetic mechanisms by which weeds evolve resistance to herbicides largely determine the level of resistance and the rate of evolution of resistance. In a previous study, we determined that glyphosate resistance in Kochia scoparia is due to the amplification of the 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) gene, the enzyme target of glyphosate. Here, we investigated the genomic organization of the amplified EPSPS copies using fluorescence in situ hybridization (FISH) and extended DNA fiber (Fiber FISH) on K. scoparia chromosomes. In both glyphosate-resistant K. scoparia populations tested (GR1 and GR2), FISH results displayed a single and prominent hybridization site of the EPSPS gene localized on the distal end of one pair of homologous metaphase chromosomes compared with a faint hybridization site in glyphosate-susceptible samples (GS1 and GS2). Fiber FISH displayed 10 copies of the EPSPS gene (approximately 5 kb) arranged in tandem configuration approximately 40 to 70 kb apart, with one copy in an inverted orientation in GR2. In agreement with FISH results, segregation of EPSPS copies followed single-locus inheritance in GR1 population. This is the first report of tandem target gene amplification conferring field-evolved herbicide resistance in weed populations.Glyphosate [N-(phosphonomethyl) Gly] is the most widely used agricultural pesticide globally (Duke and Powles, 2008). Originally, being a nonselective herbicide, its use was limited to vegetation management in noncrop areas; however, introduction of glyphosate-resistant (GR) crops in the late 1990s, coupled with their exceptional adoption, led to accelerated use totaling approximately 128 million ha worldwide in 2012 (James, 2012). GR crop technology has made a significant contribution to global agriculture and the environment, as it not only increased farm income by $32.2 billion (Brookes and Barfoot, 2013), but also moderated the negative environmental impacts of mechanical weed management practices (Gardner and Nelson, 2008; Bonny, 2011). Glyphosate offers a simple, effective, and economic weed management option in GR crops. In addition, it provides immense value in no-till crop production systems by enabling soil and moisture conservation. However, due to intensive glyphosate selection pressure, several weed populations globally have evolved resistance through a variety of mechanisms. Globally, herbicide resistance, in particular the recent proliferation of glyphosate resistance in weed species, is a major crop protection threat; nearly two dozen GR weed species have been reported in the last 15 years (Heap, 2014).Glyphosate, an aminophosphonic analog of the natural amino acid Gly, nonselectively inhibits 5-Enolpyruvylshikimate-3-Phosphate synthase (EPSPS) in plants, preventing the biosynthesis of the aromatic amino acids Phe, Tyr, and Trp (Steinrücken and Amrhein, 1980), resulting in the death of glyphosate-sensitive individuals. In plants, EPSPS is one of the key enzymes in the shikimate pathway (Herrmann and Weaver, 1999), and glyphosate inhibits EPSPS by binding to EPSPS-shikimate-3-P binary complex forming an EPSPS-shikimate-3-P-glyphosate complex (Alibhai and Stallings, 2001). Bradshaw et al. (1997) hypothesized against the likelihood of weeds evolving resistance to glyphosate, primarily because of its complex biochemical interactions in the shikimate pathway and also due to the absence of known glyphosate metabolism in plants. Nonetheless, several cases of glyphosate resistance, as a result of difference in glyphosate translocation (Preston and Wakelin, 2008) or mutations in the EPSPS, were confirmed (Baerson et al., 2002). More importantly, duplication/amplification of the EPSPS appears to be the basis for glyphosate resistance in several weeds (Sammons and Gaines, 2014). Here, we use duplication to refer to the formation of first repetition of a chromosomal segment and amplification to refer to increase in number of the repetitions (more than two repetitions of a chromosomal segment) under positive selection. The first case of EPSPS amplification as a basis for glyphosate resistance was reported in an Amaranthus palmeri population from GA (Gaines et al., 2010). In this A. palmeri population, there is a massive increase (>100-fold relative to glyphosate-susceptible [GS] plants) in EPSPS copies, and these copies are dispersed throughout the genome (Gaines et al., 2010).Field-evolved GR Kochia scoparia populations were first reported in western Kansas in 2007 (Heap, 2014). We previously determined that evolution of GR populations of K. scoparia in the U.S. Great Plains is also due to amplification of the EPSPS (A. Wiersma and P. Westra, unpublished data). Unlike in GR A. palmeri, we found relative EPSPS:acetolactate synthase (ALS) copies ranging from three to nine in GR K. scoparia populations. While it quickly became widespread in the region, its presence was reported in another five Great Plains states by 2013 (Heap, 2014). GR K. scoparia populations we tested were 3- to 11-times resistant (population level) to glyphosate compared with a GS population (Godar, 2014), and EPSPS expression positively correlated with genomic EPSPS copy number (A. Wiersma and P. Westra, unpublished data). Here, we reveal the genomic organization of the amplified EPSPS copies in two GR K. scoparia populations, an alternative mechanism of gene amplification to that reported in GR A. palmeri.