Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling.

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].

Detection of Class II caries on the iPad with Retina Display.

With the increasing use of digital radiography, the display parameters of the devices used to view radiographs have become important factors in caries detection. Interest in the use of tablet devices for this application has increased due to their availability, portability, and ease of use. However, to be effective in clinical situations, these portable devices must have displays that perform well under multiple lighting conditions and at different angles. The purpose of this study was to assess the utility of the iPad with Retina Display for the detection of Class II caries under common overhead lighting conditions. The device was used in both standing and angled positions by 5 reviewers, and their diagnoses of caries were compared to the diagnoses the same reviewers made using a thin-film transistor flat-panel display (TFT-FPD) in dim lighting conditions. Histological analysis was used as the gold standard to confirm the presence or absence of caries. In a standing position, the tablet device performed as well as the TFT-FPD. When used in the angled position, the tablet performed slightly worse than the TFT-FPD. The findings suggest that if the user can compensate for overhead glare, the tablet device may perform as well as a calibrated, upright display in a dimly lit room.

Evaluation of an ameloblastic fibro-odontoma with cone beam computed tomography.

BACKGROUND: The clinical presentation, radiographic features, and histopathological findings of a case of ameloblastic fibro-odontoma are described. The clinical and radiographic presentations of this case are typical of this benign odontogenic tumor. The patient was young and asymptomatic with the exception of the clinical absence of the permanent mandibular left first molar. Treatment consisted of simple enucleation with removal of the primary mandibular left second molar. METHODS: A panoramic image and cone beam computed tomography (CBCT) scan were acquired in order to determine the reason for clinical absence of the permanent mandibular left first molar. The CBCT image proved to be a valuable supplement to the conventional radiographic examination as it provided information not apparent on the 2-dimensional panoramic image. Both the extent of the lesion and its effects on adjacent structures were better delineated with CBCT. Additionally, the presence of calcifications, an important radiographic characteristic of this particular lesion, were visible on CBCT versus the panoramic image. CONCLUSIONS: This case report demonstrates that the CBCT scan provided important management and treatment planning information that was not apparent in the panoramic image.

Homoplastic microinversions and the avian tree of life.

BACKGROUND: Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. RESULTS: We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. CONCLUSIONS: Microinversions can provide valuable phylogenetic information, although power analysis indicates that large amounts of sequence data will be necessary to identify enough inversions (and similar RGCs) to resolve short branches in the tree of life. Moreover, microinversions are not perfect characters and should be interpreted with caution, just as with any other character type. Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences. Despite their low rate of accumulation, they have clearly contributed to genome evolution, suggesting that active identification of microinversions will prove useful in future phylogenomic studies.

Mitochondrial DNA based phylogeny of the woodpecker genera Colaptes and Piculus, and implications for the history of woodpecker diversification in South America.

The woodpecker genus Colaptes (flickers) has its highest diversity in South America and the closely related genus Piculus is restricted to South and Central America. Two species of flickers occur in North America, and one species is endemic to Cuba. We conducted a Bayesian phylogenetic analysis of three mitochondrial encoded genes (cyt b, COI, 12S rRNA) and confirmed that the two genera are paraphyletic. Three species historically classified as Piculus are actually flickers. We found that the Cuban endemic C. fernandinae is the most basal species within the flickers and that the Northern Flicker is the next most basal species within the Colaptes lineage. The South American clade is most derived. The age of the South American diversification is estimated to be 3.6MY, which is synchronous with the emergence of the Isthmus of Panama. The pattern of diversification of South American flickers is common among South American woodpeckers. Although woodpeckers have their greatest diversity in South America, we hypothesize that woodpeckers (Family Picidae) originated in Eurasia, dispersed to North America via the Bering land bridge, and multiple lineages entered South America as the Isthmus approached its final closing.

Phylogenomic evidence for multiple losses of flight in ratite birds.

Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.

Assessment of the efficiency of a pre- versus post-acquisition metal artifact reduction algorithm in the presence of 3 different dental implant materials using multiple CBCT settings: An in vitro study.

PURPOSE: The aim of this study was to assess artifacts generated in cone-beam computed tomography (CBCT) of 3 types of dental implants using 3 metal artifact reduction (MAR) algorithm conditions (pre-acquisition MAR, postacquisition MAR, and no MAR), and 2 peak kilovoltage (kVp) settings. MATERIALS AND METHODS: Titanium-zirconium, titanium, and zirconium alloy implants were placed in a dry mandible. CBCT images were acquired using 84 and 90 kVp and at normal resolution for all 3 MAR conditions. The images were analyzed using ImageJ software (National Institutes of Health, Bethesda, MD) to calculate the intensity of artifacts for each combination of material and settings. A 3-factor analysis of variance model with up to 3-way interactions was used to determine whether there was a statistically significant difference in the mean intensity of artifacts associated with each factor. RESULTS: The analysis of all 3 MAR conditions showed that using no MAR resulted in substantially more severe artifacts than either of the 2 MAR algorithms for the 3 implant materials; however, there were no significant differences between pre- and post-acquisition MAR. The 90 kVp setting generated less intense artifacts on average than the 84 kVp setting. The titanium-zirconium alloy generated significantly less intense artifacts than zirconium. Titanium generated artifacts at an intermediate level relative to the other 2 implant materials, but was not statistically significantly different from either. CONCLUSION: This in vitro study suggests that artifacts can be minimized by using a titanium-zirconium alloy at the 90 kVp setting, with either MAR setting.

Roundup negatively impacts the behavior and nerve function of the Madagascar hissing cockroach (Gromphadorhina portentosa).

Glyphosate is the active ingredient in Roundup formulations. Glyphosate-based herbicides are used globally in agriculture, forestry, horticulture, and in urban settings. Glyphosate can persist for years in our soil, potentially impacting the soil-dwelling arthropods that are primary drivers of a suite of ecosystem services. Furthermore, although glyphosate is not generally classified as neurotoxic to insects, evidence suggests that it may cause nerve damage in other organisms. In a series of experiments, we used food to deliver environmentally realistic amounts of Roundup ready-to-use III, a common 2% glyphosate-based herbicide formulation that lists isopropylamine salt as its active ingredient, to Madagascar hissing cockroaches. We then assessed the impact of contamination on body mass, nerve health, and behavior. Contaminated food contained both 30.6 mg glyphosate and so-called inert ingredients. Food was refreshed weekly for 26-60 days, depending on the experiment. We found that consumption of contaminated food did not impact adult and juvenile survivorship or body weight. However, consumption of contaminated food decreased ventral nerve cord action-potential velocity by 32%, caused a 29% increase in respiration rate, and caused a 74.4% decrease in time spent on a motorized exercise wheel. Such changes in behavior may make cockroaches less capable of fulfilling their ecological service, such as pollinating or decomposing litter. Furthermore, their lack of coordination may make them more susceptible to predation, putting their population at risk. Given the decline of terrestrial insect abundance, understanding common risks to terrestrial insect populations has never been more critical. Results from our experiments add to the growing body of literature suggesting that this popular herbicide can act as a neurotoxin.

A clinical comparison of extraoral panoramic and intraoral radiographic modalities for detecting proximal caries and visualizing open posterior interproximal contacts.

OBJECTIVES: The purpose of this study was to compare extraoral panoramic bitewings (BWs) to intraoral photostimulable phosphor (PSP) plate BWs for the detection of proximal surface caries and to establish if there was any difference between extraoral BWs, intraoral BWs and panoramic radiographs in visualizing open posterior interproximal contacts. METHODS: Extraoral panoramic and intraoral BW images were acquired on each of 20 patients, resulting in 489 total non-restored, readable surfaces that were evaluated by 4 observers. The ANOVA analysis to determine diagnostic variability between and within each subject was utilized. The surfaces included in the study extended from the distal of each canine to the last posterior contact in each arch with non-readable proximal surfaces excluded (i.e.surfaces where over half the enamel layer was overlapped or where those surfaces were not visible in one or both modalities). RESULTS: The statistical analysis indicated that the overall mean area under the receiver operating characteristic curves across all observers for the intraoral BWs and extraoral panoramic BWs were 0.832 and 0.827, respectively, and the difference of 0.005 was not significant at p = 0.7781. The percentage of non-readable proximal surfaces across the three modalities was 4.1% for intraoral BWs, 18.3% for extraoral panoramic BWs and 51.5% for the standard panoramic images. CONCLUSIONS: The investigators concluded there was no significant difference in posterior proximal surface caries detection between the modalities. Extraoral panoramic BWs were much better than panoramic radiographs in visualizing open posterior interproximal contacts, 81.7% vs 48.5%, but below the 95.9% value for intraoral BWs.

Dental digital radiography.

Digital images offer tremendous advantages to dentistry in terms of the potential for lower exposure to patients, absence of darkroom or processing problems, convenience of image enhancement techniques and capacity for remote teledentistry. Digital systems are now able to acquire all types of images including panoramic and cephalometric. As technology continues to improve they may ultimately replace film as the medium of choice for dental imaging.

Buccal bone formation after flapless extraction: a randomized, controlled clinical trial comparing recombinant human bone morphogenetic protein 2/absorbable collagen carrier and collagen sponge alone.

BACKGROUND: Flapless extraction of teeth allows for undisturbed preservation of the nearby periosteum and a source of osteoprogenitor cells. Recombinant human bone morphogenetic protein 2 (rhBMP-2) has been used for different bone augmentation purposes with great osteoinductive capacity. The aim of this study is to compare the bone regenerative ability of rhBMP-2 on an absorbable collagen sponge (ACS) carrier to a collagen sponge (CS) alone in extraction sites with ≥50% buccal dehiscence. METHODS: Thirty-nine patients requiring extraction of a hopeless tooth with ≥50% buccal dehiscence were enrolled. After flapless extraction and randomization, either rhBMP-2/ACS carrier or CS alone was placed in the extraction site. After extraction, a baseline cone beam computed tomography (CBCT) scan was obtained of the site, and a similar scan was obtained 5 months postoperatively. Medical imaging and viewing software were used to compare the baseline and 5-month postoperative images of the study site and assess ridge width measurements, vertical height changes, and buccal plate regeneration. RESULTS: Radiographically, CBCT analysis showed that with ≥50% of buccal bone destruction, rhBMP-2/ACS was able to regenerate a portion of the lost buccal plate, maintain theoretical ridge dimensions, and allow for implant placement 5 months after extraction. The test group performed significantly (P <0.05) better in regard to clinical buccal plate regeneration (4.75 versus 1.85 mm), clinical ridge width at 5 months (6.0 versus 4.62 mm), and radiographic ridge width at 3 mm from the alveolar crest (6.17 versus 4.48 mm) after molar exclusion. There was also significantly (P <0.05) less remaining buccal dehiscence, both clinically (6.81 versus 10.0 mm) and radiographically (3.42 versus 5.16 mm), at 5 months in the test group. Significantly (P <0.05) more implants were placed in the test group without the need for additional augmentation. The mean loss in vertical ridge height (lingual/palatal) was less in the test sites but was not significantly (P = 0.514) different between the test and control groups (0.39 versus 0.64 mm). CONCLUSIONS: rhBMP-2/ACS compared to CS alone used in flapless extraction sites with a buccal dehiscence is able to regenerate lost buccal plate, maintain theoretical ridge dimensions, and allow for implant placement 5 months later.

Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals.

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

Contrast-to-noise ratio with different large volumes in a cone-beam computerized tomography machine: an in vitro study.

OBJECTIVES: The objectives were to determine whether the images obtained from different cone-beam computerized tomography (CBCT) field of view (FOV) sizes with varying scan time and kilovolt peak using the Picasso Master 3D machine (Vatech, Hwasung, South Korea) differ in contrast-to-noise ratio (CNR). STUDY DESIGN: A phantom was used. Scans were acquired using the same voxel size, 2 scan times (15 and 24 seconds) for 3 different FOV sizes and 5 different kilovolt peaks. The contrast and CNR were calculated for each FOV. RESULTS: The CNRs were similar for the 2 scan times for all 3 FOV sizes. The CNR was lower in the 20 × 19 cm FOV compared with the other 2 FOVs for both scan times. CONCLUSIONS: The CNR does not vary significantly with increasing scan times for all FOV sizes. Smaller FOVs result in enhanced CNR and contrast.

Contrast-to-noise ratio difference in small field of view cone beam computed tomography machines.

Each of three cone beam computed tomography (CBCT) machines offer a small field of view (FOV); Promax, Accuitomo 3D, and Kodak 9000. The objectives were to determine, when using a small FOV, the difference in contrast-to-noise ratios (CNR) of images obtained from different machines and different scan settings within each machine. A phantom made of a dry mandible with an epoxy resin based substitute (ERBS) block was used. The ERBS block was fixed to the lingual cortex in the posterior left mandible. Water was used to simulate soft tissue. Twenty scans were acquired. CNR was calculated as the difference in density of the ERBS block and a control area divided by the standard deviation of the difference. The CNR obtained from images acquired with the Promax machine (voxel size of 0.2 mm) was higher than the other machines (voxel sizes 0.076, 0.08, or 0.125 mm) when using a small FOV. The Accuitomo 360° scan had higher CNR than the Accuitomo 180° scan due to the doubling of the number of basis images acquired. Smaller voxel size does not necessarily lead to enhanced CNR. Increasing the number of basis images did increase the CNR.