Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia.

Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.

Predictors of Human Papillomavirus Seropositivity in Appalachian Women Aged 18 to 26 Years.

BACKGROUND: Key informants of the Appalachian community questioned whether their unique environmental stressors would alter their immune response to human papillomavirus (HPV) infections. The primary aim of this study is to determine predictors of HPV seroprevalence to at least 1 of the 4 vaccine-related HPV types before vaccination using a psychoneuroimmunologic model in Appalachian women. METHOD: Women aged 18 to 26 years (n = 185) who had not received HPV vaccination provided cervical HPV DNA and blood samples. Human papillomavirus DNA was identified through Hybrid Capture 2 assay and then genotyped for HPV types 6, 11, 16, and 18 by Roche Linear Array. Competitive Luminex Immunoassay measured the type-specific antibodies to HPV types 6, 11, 16, and 18 in milli-Merck units per milliliter. Nine psychoneuroimmunology scales measuring attributes of stress were self-completed. RESULTS: Human papillomavirus DNA was detected in 50% (92/183) of participants, with only 14% (26/183) positive for HPV-6/11/16/18 DNA. Seropositivity for at least one anti-HPV-6/11/16 or 18, on the other hand, was present in 35% (64/183) of women, with only 10% (19/183) concomitantly infected and seropositive for the vaccine-related types. The Perceived Stress Scale was not a strong predictor of HPV seropositivity. CONCLUSIONS: Both HPV infection and vaccine-related HPV type seropositivity is common among Appalachian women aged 18 to 26 years. The anticipated effect of environmental stressors on HPV seropositivity was not seen when multiple predictors were considered.

A box on the river: The phylogenetics and phylogeography of Eucalyptus baueriana (Eucalyptus sect. Adnataria ser. Heterophloiae).

We present a phylogeographic study of the tree species Eucalyptus baueriana Schauer, which occurs in disjunct areas on the near coastal plains and ranges of the south-east Australian mainland. DArTseq data are used to build a phylogeny including E. baueriana and closely related taxa to test its monophyly, test the genetic distinctness of the three subspecies of E. baueriana, and investigate relationships between its disjunct populations. Additionally, we use population structure analysis to investigate the genetic distinctness of populations, and MaxEnt to investigate the environmental factors potentially influencing the species' distribution. We show E. baueriana is monophyletic and most closely related to three other Blue Box eucalypt species: E. conica H.Deane & Maiden, E. dalveenica T.L.Collins, R.L.Andrew & J.J.Bruhl and E. magnificata L.A.S.Johnson & K.D.Hill, with some evidence for genetic introgression between these taxa. Within E. baueriana, the deepest genetic breaks do not correspond with the subspecies classification as the two geographically restricted subspecies, together with samples of the more widespread E. baueriana subsp. baueriana from west of the Gippsland lowlands, form a south-western clade with that is sister to other populations of subsp. baueriana. The oldest genetic break in the species occurs in far eastern Gippsland (Victoria), corresponding to one of the shortest geographic disjunctions in the species' distribution. Genetic breaks in other species have been observed in this region which is broadly referred to as the southern transition zone. Both total annual rainfall and the seasonality of this rainfall are hypothesised to affect the species' distribution; gaps in its distribution are in areas of higher rainfall that support closed forest and in regions with more winter dominated rainfall.

Divergent lineages in a semi-arid mallee species, Eucalyptus behriana, correspond to a major geographic break in southeastern Australia.

AIM: To infer relationships between populations of the semi-arid, mallee eucalypt, Eucalyptus behriana, to build hypotheses regarding evolution of major disjunctions in the species' distribution and to expand understanding of the biogeographical history of southeastern Australia. LOCATION: Southeastern Australia. TAXON: Eucalyptus behriana (Myrtaceae, Angiospermae). METHODS: We developed a large dataset of anonymous genomic loci for 97 samples from 11 populations of E. behriana using double digest restriction site-associated DNA sequencing (ddRAD-seq), to determine genetic relationships between the populations. These relationships, along with species distribution models, were used to construct hypotheses regarding environmental processes that have driven fragmentation of the species' distribution. RESULTS: Greatest genetic divergence was between populations on either side of the Lower Murray Basin. Populations west of the Basin showed greater genetic divergence between one another than the eastern populations. The most genetically distinct population in the east (Long Forest) was separated from others by the Great Dividing Range. A close relationship was found between the outlying northernmost population (near West Wyalong) and those in the Victorian Goldfields despite a large disjunction between them. CONCLUSIONS: Patterns of genetic variation are consistent with a history of vicariant differentiation of disjunct populations. We infer that an early disjunction to develop in the species distribution was that across the Lower Murray Basin, an important biogeographical barrier separating many dry sclerophyll plant taxa in southeastern Australia. Additionally, our results suggest that the western populations fragmented earlier than the eastern ones. Fragmentation, both west and east of the Murray Basin, is likely tied to climatic changes associated with glacial-interglacial cycles although it remains possible that major geological events including uplift of the Mount Lofty Ranges and basalt flows in the Newer Volcanics Province also played a role.

The complete chloroplast genome sequence of the Australian Mirbelioid pea Platylobium obtusangulum Hook. (Leguminosae: subf. Papilionoideae, tribe Bossiaeeae).

We sequenced and assembled the whole chloroplast genome of the Australian-endemic shrub Platylobium obtusangulum. The total size of the genome is 150,090 base pairs (bp), including two inverted repeat regions of 25,511 bp each, one large single copy region of 80,567 bp and a small single copy region of 18,501 bp. The genome has a GC content of 36.7% and includes 127 annotated genes (83 protein coding, 36 tRNA genes and eight rRNA genes). Phylogenetic analysis of chloroplast genomes placed the Platylobium obtusangulum genome in the expected position of the Mirbelioid clade in the legume family (Leguminosae: Papilionoideae).

Analysis of downstream revenue to an academic medical center from a primary care network.

PURPOSE: Many academic medical centers (i.e., teaching hospitals) have established primary care networks for not only assuring a referral base but also for educating students in the primary care setting. Such networks generally are not profitable when analyzed on an individual facility basis. However, revenues generated at the medical center in terms of inpatient admissions, laboratory testing etc., usually are much larger than generated on site. In this study, the downstream revenue from 18 practice sites was evaluated at The Ohio State University Medical Center. METHOD: Revenues in fiscal year July 1, 2003, to June 30, 2004, were broken down into four streams, including inpatient and outpatient charges and collections for both network and specialist physicians. A fifth stream evaluated specialist professional fees. The authors developed a novel conservative weighting system to capture the concept that not all revenues generated from network patients were actually dependent on the use of the network. RESULTS: Findings included that the downstream direct contribution margin of US dollars 14 million just from the admissions and outpatient tests and procedures directly generated by network physicians alone was nearly twice the US dollars 8.3 million network operating loss. The total downstream net revenue of nearly US dollars 115 million was more than 6 times the US dollars 18.9 million net revenue to the network. The downstream direct contribution margin of US dollars 52 million was 6.3 times the network loss. Total downstream gross revenue (charges) to the medical center was over US dollars 250 million and over US dollars 300 million when the specialist gross revenues were included. CONCLUSIONS: This study demonstrates that a primary care network can generate significant financial support for an academic medical center.

Effect of lung volume reduction surgery on diaphragmatic neuromechanical coupling at 2 years.

STUDY OBJECTIVES: We previously reported that patients with emphysema show an increase in diaphragmatic neuromechanical coupling at 3 months after lung volume reduction surgery. Diaphragmatic neuromechanical coupling was quantified as the quotient of tidal volume (normalized to total lung capacity) to tidal change in transdiaphragmatic pressure (normalized to maximal transdiaphragmatic pressure). As such, neuromechanical coupling estimates the fraction of diaphragmatic capacity used to generate tidal breathing. The present investigation was conducted to determine whether benefit is maintained at 2 years. SUBJECTS: Fifteen patients with severe COPD, 8 of whom completed the 2-year study. METHODS: Lung volumes, exercise capacity (6-min walking distance), diaphragmatic function (maximal transdiaphragmatic pressure and twitch transdiaphragmatic pressure elicited by phrenic nerve stimulation), and diaphragmatic neuromechanical coupling were recorded before surgery, and at 3 months and 2 years after surgery. RESULTS: Two years after surgery, lung volumes deteriorated to preoperative values, but patients showed persistent improvements in 6-min walking distance (p < 0.05). Three months after surgery, maximal transdiaphragmatic pressure (p < 0.05), twitch transdiaphragmatic pressure (p < 0.01), and diaphragmatic neuromechanical coupling (p < 0.01) had increased over preoperative values. The improvements in neuromechanical coupling resulted from improvements in diaphragmatic strength and, to a lesser extent, from a decrease in transdiaphragmatic pressure required to maintain tidal breathing. The change in respiratory muscle function at 2 years varied among patients: diaphragmatic contractility was > 10% of preoperative value in half of the patients who concluded our study, and neuromechanical coupling was > 10% of preoperative value in three fourths of the patients who concluded our study. Patients who maintained their gains in neuromechanical coupling also maintained their gains in 6-min walking distance. CONCLUSION: Patients undergoing lung volume reduction surgery can maintain early gains in neuromechanical coupling and exercise capacity 2 years later.

Retinal bipolar cells: temporal filtering of signals from cone photoreceptors.

The temporal dynamics of the response of neurons in the outer retina were investigated by intracellular recording from cones, bipolar, and horizontal cells in the intact, light-adapted retina of the tiger salamander (Ambystoma tigrinum), with special emphasis on comparing the two major classes of bipolars cells, the ON depolarizing bipolars (Bd) and the OFF hyperpolarizing bipolars (Bh). Transfer functions were computed from impulse responses evoked by a brief light flash on a steady background of 20 cd/m(2). Phase delays ranged from about 89 ms for cones to 170 ms for Bd cells, yielding delays relative to that of cones of about 49 ms for Bh cells and 81 ms for Bd cells. The difference between Bd and Bh cells, which may be due to a delay introduced by the second messenger G-protein pathway unique to Bd cells, was further quantified by latency measurements and responses to white noise. The amplitude transfer functions of the outer retinal neurons varied with light adaptation in qualitative agreement with results for other vertebrates and human vision. The transfer functions at 20 cd/m(2) were predominantly low pass with 10-fold attenuation at about 13, 14, 9.1, and 7.7 Hz for cones, horizontal, Bh, and Bd cells, respectively. The transfer function from the cone voltage to the bipolar voltage response, as computed from the above measurements, was low pass and approximated by a cascade of three low pass RC filters ("leaky integrators"). These results for cone-->bipolar transmission are surprisingly similar to recent results for rod-->bipolar transmission in salamander slice preparations. These and other findings suggest that the rate of vesicle replenishment rather than the rate of release may be a common factor shaping synaptic signal transmission from rods and cones to bipolar cells.

Natural images and contrast encoding in bipolar cells in the retina of the land- and aquatic-phase tiger salamander.

Intracellular recordings were obtained from 57 cone-driven bipolar cells in the light-adapted retina of the land-phase (adult) tiger salamander (Ambystoma tigrinum). Responses to flashes of negative and positive contrast for centered spots of optimum spatial dimensions were analyzed as a function of contrast magnitude. On average, the contrast/response curves of depolarizing and hyperpolarizing bipolar cells in the land-phase animals were remarkably similar to those of aquatic-phase animals. Thus, the primary retinal mechanisms mediating contrast coding in the outer retina are conserved as the salamander evolves from the aquatic to the land phase. To evaluate contrast encoding in the context of natural environments, the distribution of contrasts in natural images was measured for 65 scenes. The results, in general agreement with other reports, show that the vast majority of contrasts in nature are very small. The efficient coding hypothesis of Laughlin was examined by comparing the average contrast/response curves of bipolar cells with the cumulative probability distribution of contrasts in natural images. Efficient coding was found at 20 cd/m2 but at lower levels of light adaptation, the contrast/response curves were much too shallow. Further experiments show that two fundamental physiological factors-light adaptation and the nonlinear transfer across the cone-bipolar synapse are essential for the emergence of efficient contrast coding. For both land- and aquatic-based animals, the extent and symmetry of the dynamic range of the contrast/response curves of both classes of bipolar cells varied greatly from cell to cell. This apparent substrate for distributed encoding is established at the bipolar cell level, since it is not found in cones. As a result, the dynamic range of the bipolar cell population brackets the distribution of contrasts found in natural images.

Center-surround organization in bipolar cells: symmetry for opposing contrasts.

Intracellular recordings were obtained from 73 cone-driven bipolar cells in the light-adapted retina of the tiger salamander (Ambystoma tigrinum). Responses to flashes of negative and positive contrast for centered spots and concentric annuli of optimum spatial dimensions were analyzed as a function of contrast magnitude. For both depolarizing and hyperpolarizing bipolar cells, it was found that remarkably similar responses were observed for the center and surround when comparisons were made between responses of the same response polarity and thus, responses to opposite contrast polarity. Thus, spatial information and contrast polarity appear to be rather strongly confounded in many bipolar cells. As a rule, the form of the contrast/response curves for center and surround approximated mirror images of each other. Contrast gain and C50 (the contrast required for half-maximal response) were quantitatively similar for center and surround when comparisons were made for responses of the same response polarity. The average contrast gain of the bipolar cell surround was 3-5 times higher than that measured for horizontal cells. Contrast/latency measurements and interactions between flashed spots and annuli showed that the surround response is delayed by 20-80 ms with respect to that of the receptive-field center. Cones showed no evidence for center-surround antagonism while for bipolar cells, the average strength of the surround ranged from about 50% to 155% of the center, depending on the test and response polarity. The results of experiments on the effects of APB (100 microM) on depolarizing bipolar cells suggest that the relative contribution of the feedback pathway (horizontal cell to cones) and the feedforward pathway (horizontal cell to bipolar cell) to the bipolar surround varies in a distributed manner across the bipolar cell population.

Retinal bipolar cells: contrast encoding for sinusoidal modulation and steps of luminance contrast.

Contrast encoding for sinusoidal modulations of luminance contrast was investigated by intracellular recording in the intact salamander retina. In what appears to be the first study of this kind for vertebrate bipolar cells, responses of the central receptive-field mechanism of cone-driven cells to modulation of 3 Hz were analyzed quantitatively via both signal averaging and a Fast Fourier Transform (FFT) while the retina was light adapted to 20 cd/m2. Depolarizing and hyperpolarizing bipolar cells showed very similar encoding. Both responded with sinusoidal waveforms whose amplitude varied linearly with modulation depths ranging up to 7-8%. The slope of the modulation/response curve was very steep in this range. Thus, the contrast gain was high, reaching values of 6-7, and the half-maximal response was achieved at modulations of 9% or less. At modulations above approximately 15%, the responses typically showed strong compressive nonlinearity and the waveform was increasingly distorted. At maximum modulation, the higher harmonics of the FFT constituted about 30% of the amplitude of the fundamental. Measurements were also made for cones and horizontal cells. Both cell types showed predominantly linear responses and low contrast gain, in marked contrast to bipolar cells. These results suggest that the high contrast gain and strong nonlinearity of bipolar cells largely arise postsynaptic to cone transmitter release. Further experiments were performed to compare responses to contrast steps versus those to sinusoidal modulation. In the linear range, we show that the contrast gains of cones and horizontal cells are low and virtually identical for both steps and sinusoidal modulations. In bipolar cells, on the other hand, the contrast gain is about two times greater for steps than that for the 3-Hz sine waves. These results suggest that mechanisms intrinsic to bipolar cells act like a high-pass filter with a short time constant to selectively emphasize contrast transients over slower changes in contrast.