Overlapping landscapes: A persistent,but misdirected concern when collecting and analyzing ecological data

A primary focus of wildlife ecology is studying how the arrangement, quality, and distribution of habitat influence wildlife populations at multiple spatial scales. A practical limitation of conducting wildlife–habitat investigations in the field, however, is that sampling points tend to be close to one another, resulting in spatial clustering. Consequently, when ecologists seek to quantify the effects of environmental predictors surrounding their sampling points, they encounter the issue of using landscapes that are partially or completely overlapping. A presumed problem of overlapping landscapes is that data generated from these landscapes, when used as predictors in statistical modeling, might violate the assumption of independence. However, the independence of error is the critical assumption, not the independence of predictor variables. Nonetheless, many researchers strive to avoid such overlaps through sampling design or alternative analytical procedures and specialized software programs have been created to assist with this. We present theoretical arguments and empirical evidence showing that changing the amount of overlap does not alter the degree of spatial autocorrelation. Using data derived from 2 broad-scaled avian monitoring programs, we quantified the relationship between forest cover and bird abundance and occurrence at multiple landscapes ranging from 100 m to 24 km across. We found no clear evidence that increasing overlap of landscapes increased spatial autocorrelation in model residuals. Our results demonstrate that the concern of overlapping landscapes as a potential cause of violation of spatial independency among sampling units is misdirected and represents an oversimplification of the statistical and ecological issues surrounding spatial autocorrelation. Overlapping landscapes and spatial autocorrelation are separate issues in the modeling of wildlife populations and their habitats; non-overlapping landscapes do not ensure spatial independency and overlapping landscapes do not necessarily lead to greater spatial autocorrelation in model errors. © 2011 The Wildlife Society.     

High-throughput genotyping of advanced congenic lines by high resolution melting analysis for identification of Bbaa2, a QTL controlling Lyme arthritis

Congenic mapping is a powerful strategy to identify genomic loci regulating quantitative traits. Generating congenic lines is an iterative process of refinement that is both time and resource intensive. Here we report an alternative to traditional microsatellite marker analysis or costly high-density oligonucleotide single nucleotide polymorphism (SNP) arrays for congenic genotyping. The identification of inherited SNP variability in congenic lines using high resolution melting analysis (HRMA) represents a novel application of the method. The blocked probe HRMA approach offers a scalable, low cost, closed-tube system that benefits from rapid turnaround times, and unequivocal interpretation. The markedly higher prevalence of SNPs relative to microsatellites in the genome allows much greater flexibility for the identification of new genotyping landmarks as congenic intervals are refined. We have adopted this approach in our development of B6.C3-Bbaa2 congenic lines for the identification of loci regulating murine Lyme arthritis severity. As a result, we have been able to fully genotype individuals prior to weaning age, and expand our number of breeding cages without increasing our colony budget. Thus far, 26 SNP markers have been successfully mapped to the Bbaa2 locus. This has facilitated the identification of 20 novel B6.C3-Bbaa2 congenic lines spanning the original interval.     

Gene expression profiling reveals unique pathways associated with differential severity of lyme arthritis

The murine model of Lyme disease provides a unique opportunity to study the localized host response to similar stimulus, Borrelia burgdorferi, in the joints of mice destined to develop severe arthritis (C3H) or mild disease (C57BL/6). Pathways associated with the response to infection and the development of Lyme arthritis were identified by global gene expression patterns using oligonucleotide microarrays. A robust induction of IFN-responsive genes was observed in severely arthritic C3H mice at 1 wk of infection, which was absent from mildly arthritic C57BL/6 mice. In contrast, infected C57BL/6 mice displayed a novel expression profile characterized by genes involved in epidermal differentiation and wound repair, which were decreased in the joints of C3H mice. These expression patterns were associated with disease state rather than inherent differences between C3H and C57BL/6 mice, because C57BL/6-IL-10(-/-) mice infected with B. burgdorferi develop more severe arthritis than C57BL/6 mice and displayed an early gene expression profile similar to C3H mice. Gene expression profiles at 2 and 4 wk postinfection revealed a common response of all strains that was likely to be important for the host defense to B. burgdorferi and mediated by NF-kappaB-dependent signaling. The gene expression profiles identified in this study add to the current understanding of the host response to B. burgdorferi and identify two novel pathways that may be involved in regulating the severity of Lyme arthritis.     

Serologic testing for symptomatic coccidioidomycosis in immunocompetent and immunosuppressed hosts

Serologic studies are an important diagnostic tool in the clinical evaluation and follow-up of persons with coccidioidomycosis. Numerous types of serologic tests are available, including immunodiffusion, enzyme immunoassay, and complement fixation. We conducted a retrospective review of the results of 1,797 serologic tests spanning 12 months from the onset of coccidioidomycosis in 298 immunocompetent and 62 immunosuppressed persons with symptomatic infection. Using the onset of symptoms as a reference point, we plotted the positive or negative serologic results over time for both groups. Compared with the immunocompetent group, immunosuppressed persons had lower rates of seropositivity for every type of test during the first year after onset of symptoms for coccidioidomycosis, although many results did not achieve statistical significance. Combining the results of these tests increased the sensitivity of the serologic evaluation in immunocompromised patients. Immunosuppressed persons have the ability to mount a serologic response to coccidioidomycosis, but in some circumstances, multiple methods may be required to improve detection.     

Signals of quality and age: the information content of multiple plumage ornaments in male western bluebirds Sialia mexicana

Male structural plumage coloration and UV signals in particular can provide information on individual quality and influence female choice, while melanin-pigmented plumage is largely considered to be important in intrasexual competition. Many avian species demonstrate both types of plumage ornamentation that may convey different information about the signaller's quality or condition in addition to age. We examine rufous and blue plumage ornamentation across multiple body regions in relation to age, condition and reproductive performance in male western bluebirds Sialia mexicana. We demonstrate a strong positive relationship between head plumage brightness and both male age and the mass of the offspring. Older males are in better condition and display a reduced plumage patch on the back while the size of the rufous breast patch increases with increasing condition but not with age. Spectral characters from the wings and rump were not associated with any of the reproductive parameters measured. In conjunction with published evidence showing that females preferentially accept extrapair copulations from older males, these data suggest a need for experimental manipulation of plumage colour in known-aged birds to understand mate choice in this species.     

Parasite–grass–forb interactions and rock–paper– scissor dynamics: predicting the effects of the parasitic plant Rhinanthus minor on host plant communities

1.  Parasitic plants affect the growth, reproduction and metabolism of their hosts and may also influence the outcome of competitive interactions between host species and, consequently, the structure of entire host communities.
2.  We investigate the effect of the root hemiparasitic plant Rhinanthus minor on plant community dynamics using a spatial theoretical model. The model is parameterized with data from pairwise interaction experiments under two nutrient levels between the hemiparasite and three grass species ( Cynosurus cristatus , Festuca rubra and Phleum bertolonii ) and three forb species ( Leucanthemum vulgare , Plantago lanceolata and Ranunculus acris ).
3.  Relative interaction coefficients were intransitive, with the dynamics of the system conforming to a rock–paper–scissors game. Stable deterministic dynamics emerge from parameters obtained under low-nutrient conditions. Under high-nutrient conditions, the dynamics are unstable, but are stabilized in spatially explicit models. The outcomes are sensitive to initial spatial pattern and frequency.
4.   Synthesis . This study supports the idea that hemiparasite populations may form 'shifting clouds' in natural populations and explains seemingly unpredictable shifts in host community structure following introduction of hemiparasites. Management of plant communities using hemiparasites needs to take these complex dynamics into account.     

Prevalence of radiographic detectable intervertebral disc calcifications in Dachshunds surgically treated for disc extrusion

Background  

An association between the occurrence of calcified discs, visible on radiographic examination (CDVR), and disc extrusions has been suggested in published literature over the past 10-20 years, mainly from Nordic countries. It has also been postulated that dogs without CDVR would not develop disc extrusions. Furthermore, inheritance of CDVR has been calculated and it has been postulated that, by selecting dogs for breeding with few, or no CDVR, the prevalence of disc extrusions in the Dachshund population may be reduced.     

Surgical Induction of Endolymphatic Hydrops by Obliteration of the Endolymphatic Duct

Surgical induction of endolymphatic hydrops (ELH) in the guinea pig by obliteration and obstruction of the endolymphatic duct is a well-accepted animal model of the condition and an important correlate for human Meniere''s disease. In 1965, Robert Kimura and Harold Schuknecht first described an intradural approach for obstruction of the endolymphatic duct (Kimura 1965). Although effective, this technique, which requires penetration of the brain''s protective covering, incurred an undesirable level of morbidity and mortality in the animal subjects. Consequently, Andrews and Bohmer developed an extradural approach, which predictably produces fewer of the complications associated with central nervous system (CNS) penetration.(Andrews and Bohmer 1989) The extradural approach described here first requires a midline incision in the region of the occiput to expose the underlying muscular layer. We operate only on the right side. After appropriate retraction of the overlying tissue, a horizontal incision is made into the musculature of the right occiput to expose the right temporo-occipital suture line. The bone immediately inferio-lateral the suture line (Fig 1) is then drilled with an otologic drill until the sigmoid sinus becomes visible. Medial retraction of the sigmoid sinus reveals the operculum of the endolymphatic duct, which houses the endolymphatic sac. Drilling medial to the operculum into the area of the endolymphatic sac reveals the endolymphatic duct, which is then packed with bone wax to produce obstruction and ultimately ELH. In the following weeks, the animal will demonstrate the progressive, fluctuating hearing loss and histologic evidence of ELH.Open in a separate windowClick here to view.^{(41M, flv)}     

Spiny Norman in the Garden of Eden? Dispersal and early biogeography of Placentalia

The persistent finding of clades endemic to the southern continents (Afrotheria and Xenarthra) near the base of the placental mammal tree has led molecular phylogeneticists to suggest an origin of Placentalia, the crown group of Eutheria, somewhere in the southern continents. Basal splits within the Placentalia have then been associated with vicariance due to the breakup of Gondwana. Southern-origin scenarios suffer from several problems. First, the place of origin of Placentalia cannot be reconstructed using phylogenetic reasoning without reference to outgroups. When available outgroups are considered, a Laurasian origin is most parsimonious. Second, a model of pure vicariance would require that basal placental splits occurred not with the breakup of Gondwana, but of Pangea in the Late Triassic—Early Jurassic. This event long preceded even the oldest molecular divergence estimates for the Placentalia and was coeval only with the earliest mammals in the fossil record. Third, a problem with the number of dispersal events that would be required emerges under different southern-origin scenarios. In considering the geographic distribution of the major placental clades at their first appearance (mostly Early Cenozoic), it becomes clear that a Laurasian center of origin would require fewer dispersal events. Southern-origin models would require at least twice the number of dispersal events in comparison with a model of Laurasian origins. This number of required dispersal events increases if extinct groups of placental mammals are also considered. Results are similar assuming a morphology-based phylogeny. These facts, along with earlier findings speaking against a major placental radiation deep in the Cretaceous without leaving fossil evidence, suggest an origin of Placentalia somewhere in Laurasia with few supraordinal splits occurring before the last 5–10 million years of the Cretaceous.