Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux.

Falcons are diverse birds of cultural and economic importance. They have undergone major lineage-specific chromosomal rearrangements, resulting in greatly-reduced chromosome counts relative to other birds. Here, we use 10X Genomics linked reads to provide new high-contiguity genomes for two gyrfalcons, a saker falcon, a lanner falcon, three subspecies of peregrine falcons, and the common kestrel. Assisted by a transcriptome sequenced from 22 gyrfalcon tissues, we annotate these genomes for a variety of genomic features, estimate historical demography, and then investigate genomic equilibrium in the context of falcon-specific chromosomal rearrangements. We find that falcon genomes are not in AT-GC equilibrium with a bias in substitutions towards higher AT content; this bias is predominantly but not exclusively driven by hypermutability of CpG sites. Small indels and large structural variants were also biased towards insertions rather than deletions. Patterns of disequilibrium were linked to chromosomal rearrangements: falcons have lost GC content in regions that have fused to larger chromosomes from microchromosomes and gained GC content in regions of macrochromosomes that have translocated to microchromosomes. Inserted bases have accumulated on regions ancestrally belonging to microchromosomes, consistent with insertion-biased gene conversion. We also find an excess of interspersed repeats on regions of microchromosomes that have fused to macrochromosomes. Our results reveal that falcon genomes are in a state of flux. They further suggest that many of the key differences between microchromosomes and macrochromosomes are driven by differences in chromosome size, and indicate a clear role for recombination and biased-gene-conversion in determining genomic equilibrium.

Preoperative Intra-articular Steroid Injections as Predictors of Hip Arthroscopy: 2-Year Outcomes.

BACKGROUND: In patients with femoroacetabular impingement, preoperative diagnostic injections are commonly used to establish a diagnosis of intra-articular pathology. In some cases, intra-articular steroid injections are also used for therapeutic purposes. PURPOSE/HYPOTHESIS: The purpose of this study was to determine if a positive response to intra-articular steroid injection was predictive of superior outcomes after hip arthroscopy to determine if the response to intra-articular steroid injection was predictive of outcomes after hip arthroscopy. It was hypothesized that a positive response to a preoperative hip injection would be predictive of improved short- to midterm outcomes after hip arthroscopy. STUDY DESIGN: Cohort study; Level of evidence, 3. METHODS: This was a retrospective study of 208 patients who elected to have ultrasound-guided intra-articular steroid injection before they underwent hip arthroscopy between January 2016 and December 2016. Patients were divided into 2 groups: those who showed improvement in pain after the injection (steroid responder group) and those who showed no response (nonresponder group). The authors compared the preoperative and 2-year postoperative patient-reported outcomes (modified Harris Hip Score [mHHS] and Hip Outcome Score-Activities of Daily Living [HOS-ADL]) and radiographic findings between groups. Clinical endpoints, including rates of revision and conversion to total hip arthroplasty, were also reviewed. RESULTS: There were 88 patients in the nonresponder group and 120 patients in the responder group, with no significant between-group differences in preoperative descriptive variables. The responder group had significantly higher 2-year mHHS and HOS-ADL, pre- to postoperative change in mHHS and HOS-ADL, percentage of patients achieving the patient acceptable symptomatic state (PASS) on the mHHS, and percentage of patients reaching the minimum clinically important difference and the PASS on the HOS-ADL. There was no difference in Tönnis grade, acetabular labrum articular disruption grade, revision rate, or conversion to total hip arthroplasty between the 2 groups. CONCLUSION: The response to preoperative intra-articular injection did aid in predicting 2-year patient-reported outcomes of hip arthroscopy for femoroacetabular impingement. Overall, the result of a preoperative intra-articular injection can be a helpful clinical tool for surgical decision-making and counseling patients on expected outcomes after hip arthroscopy.

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes.

Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.

Historical contingency, geography and anthropogenic patterns of exposure drive the evolution of host switching in the Blastocystis species-complex.

Parasites have the power to impose significant regulatory pressures on host populations, making evolutionary patterns of host switching by parasites salient to a range of contemporary ecological issues. However, relatively little is known about the colonization of new hosts by parasitic, commensal and mutualistic eukaryotes of metazoans. As ubiquitous symbionts of coelomate animals, Blastocystis spp. represent excellent candidate organisms for the study of evolutionary patterns of host switching by protists. Here, we apply a big-data phylogenetic approach using archival sequence data to assess the relative roles of several host-associated traits in shaping the evolutionary history of the Blastocystis species-complex within an ecological framework. Patterns of host usage were principally determined by geographic location and shared environments of hosts, suggesting that weight of exposure (i.e. propagule pressure) represents the primary force for colonization of new hosts within the Blastocystis species-complex. While Blastocystis lineages showed a propensity to recolonize the same host taxa, these taxa were often evolutionarily unrelated, suggesting that historical contingency and retention of previous adaptions by the parasite were more important to host switching than host phylogeny. Ultimately, our findings highlight the ability of ecological theory (i.e. 'ecological fitting') to explain host switching and host specificity within the Blastocystis species-complex.

Treatment of the Wave Sign With Femoral Osteoplasty With and Without Chondrolabral Stabilization Using Suture Anchors.

PURPOSE: To discuss the surgical outcomes of patients identified to have the wave sign without an accompanying labral tear treated with and without stabilization of the chondrolabral junction in conjunction with femoral osteoplasty. METHODS: A retrospective study was performed in patients with cartilage delamination (wave sign) treated with femoral osteoplasty alone (FO group) or femoral osteoplasty with chondrolabral stabilization (CLS group). Patient-reported outcomes including the modified Harris Hip Score, Hip Outcome Score (HOS)-Activities of Daily Living, and HOS-Sports-Specific Subscale were obtained at a minimum of 2 years postoperatively. Other outcomes included rates of revision hip arthroscopy and conversion to hip arthroplasty. RESULTS: The study consisted of 47 patients in the FO group and 38 in the CLS group. Both groups showed significant increases in all patient-reported outcomes over the study period compared with preoperative values. The final modified Harris Hip Score was 72.8 ± 9.2 in the FO group and 79.9 ± 9.3 in the CLS group (P < .001). The HOS-Activities of Daily Living in the FO and CLS groups was 81.4 ± 10.3 and 87.2 ± 7.5, respectively (P < .001). There was no difference in the HOS-Sports-Specific Subscale between the FO group (74.4 ± 10.3) and the CLS group (78.0 ± 14.6) at final follow-up (P = .198). Revision hip arthroscopy was required in 5 patients in the FO group (13%) and 3 in the CLS group (6.3%). No patient in either group required conversion to hip arthroplasty throughout the study period. CONCLUSIONS: Chondrolabral stabilization in conjunction with femoral osteoplasty is an effective treatment in patients with the wave sign without labral tears. LEVEL OF EVIDENCE: Level III, retrospective cohort study.

Improvements in Cervical Spinal Canal Diameter and Neck Disability Following Correction of Cervical Lordosis and Cervical Spondylolistheses Using Chiropractic BioPhysics Technique: A Case Series.

Cervical spondylolisthesis indicates instability of the spine and can lead to pain, radiculopathy, myelopathy and vertebral artery stenosis. Currently degenerative cervical spondylolisthesis is a wait-and-watch condition with no treatment guidelines. A literature review and discussion will be provided. 8 females presented with neck pain, disability, and history of motor vehicle collision. Radiographs revealed abnormal cervical alignment, spinal canal narrowing, and spondylolistheses. After 30 sessions of Chiropractic BioPhysics® care over 12 weeks, patients reported improved symptoms and disabilities. Radiographs revealed improvements in cervical alignment, spondylolistheses, and spinal canal diameter. Motor vehicle collision may cause instability and abnormal alignment of the cervical spine leading to cervical spondylolisthesis. Improving spinal alignment may be an effective treatment to reduce vertebral subluxation and cervical spondylolistheses and improve neck disability as a result of improved spinal alignment.

Hip Arthroscopy in the High-Level Athlete: Does Capsular Closure Make a Difference?

BACKGROUND: Hip arthroscopy has been shown to be effective in athletes who have femoral acetabular impingement and labral tearing. The effect of complete capsular closure versus nonclosure on return to play is unknown. HYPOTHESIS: Complete capsular closure after hip arthroscopy would lead to a higher rate and faster return to sports in high-level athletes. STUDY DESIGN: Cohort study; Level of evidence, 3. METHODS: A nonrandomized retrospective review was performed of high school, collegiate, and professional athletes undergoing hip arthroscopy by a single high-volume hip arthroscopic surgeon. Athletes were divided into those undergoing complete capsular closure (CC group) and non-capsular closure (NC group) after hip arthroscopy. Rate and time to return to play were determined between the 2 groups. Patient-reported outcomes including modified Harris Hip Score (mHHS), Hip Outcome Score Activities of Daily Living (HOS-ADL), and Hip Outcome Score Sport-Specific Subscale (HOS-SSS) were obtained at a minimum of 2 years. RESULTS: A total of 111 athletes with a minimum 2-year follow-up were included in the study. There were 62 in the CC group and 49 in the NC group. A higher percentage of athletes in the CC group returned to play compared with that in the NC group (90.3% vs 75.5%, respectively; P = .03). The CC group returned to play at a mean ± SD of 4.7 ± 1.9 months compared with 5.8 ± 2.6 months in the NC group (P < .001). Patients in the CC group met the minimal clinically important difference for the mHHS, HOS-ADL, and HOS-SSS patient-reported outcomes at higher percentages: mHHS, 98.3% vs 87.7% for CC vs NC, respectively (P = .02); HOS-ADL, 98.3% vs 87.7% (P = .02); and HOS-SSS, 96.7% vs 89.7% (P = .13). The difference between groups was statistically significant for mHHS and HOS-ADL. CONCLUSION: Complete capsular closure after hip arthroscopy was associated with faster return to play and a higher rate of return compared with that of nonclosure of the capsule in this sample population of high-level athletes. At a minimum 2-year follow-up, complete capsular closure was associated with significantly higher patient-reported outcomes compared with those of nonclosure in athletes who underwent hip arthroscopy.

Calcific Tendonitis of the Shoulder: Protector or Predictor of Cuff Pathology? A Magnetic Resonance Imaging-Based Study.

PURPOSE: The purpose of this investigation is to assess the incidence of rotator cuff tears in cases of calcific tendonitis and evaluate for differences in the incidences of rotator cuff tears by magnetic resonance imaging (MRI) between calcific lesions of different morphology, size, or location. METHODS: This single-center study involved a retrospective chart review searching for patients from January 2010 to April 2017 with a diagnosis of calcific tendonitis of the shoulder based on review of all MRI reads done on patients with shoulder pain. Anteroposterior radiographic and MRI studies were reviewed by a musculoskeletal radiologist to assess calcific tendonitis morphology, size, distance from cuff insertion, and any rotator cuff tear. An additional radiologist evaluated calcific tendonitis size, morphology, and location to evaluate the reliability of these variables. RESULTS: In the final cohort of 318 shoulders with calcific tendonitis, the incidence of concomitant rotator cuff tears was 56%. Of all 177 tears, 164 (93%) were partial-thickness and 13 (7%) were complete. Type III calcification morphology (cloudy with soft contour) was most frequently associated with rotator cuff tears and demonstrated an increased odds of tear by a factor of 1.8 (CI95% 1.1-2.9).There was no statistical difference regarding calcification size or location prognosticating rotator cuff tears or tear thickness. Intraclass correlation coefficients for calcification size, morphology, and location were 0.78, 0.30, and 0.50, respectively. CONCLUSIONS: The incidence of rotator cuff tears in cases of calcific tendonitis in this cohort of patients who underwent MRI is higher than previously reported. Cloudy-appearing calcified lesions showed a significant association with rotator cuff tears with an odds ratio of 1.8. Specific locations or sizes of calcified lesions do not appear to be reliable factors to predict concomitant rotator cuff tears. Interobserver agreement for these radiographic variables ranged from fair to substantial and prompt a cautious interpretation of these results. LEVEL OF EVIDENCE: IV Retrospective Case Series.

Falcon genomics in the context of conservation, speciation, and human culture.

Here, we review the diversity, evolutionary history, and genomics of falcons in the context of their conservation and interactions with humans, and provide a perspective on how new genomic approaches may be applied to expand our knowledge of these topics. For millennia, humans and falcons (genus Falco) have developed unique relationships through falconry, religious rituals, conservation efforts, and human lifestyle transitions. From an evolutionary perspective, falcons remain an enigma. Having experienced several recent radiations, they have reached an unparalleled and almost global distribution, with an intrageneric species richness that is roughly an order of magnitude higher than typical within their family (Falconidae) and across other birds (Phylum: Aves). This diversity has evolved in the context of unusual genomic architecture that includes unique chromosomal rearrangements, relatively low chromosome counts, extremely low microdeletion rates, and high levels of nuclear mitochondrial DNA segments (NUMTs). These genomic peculiarities combine with high levels of ecological and organismal diversity and a legacy of human interactions to make falcons obvious candidates for evolutionary studies, providing unique research opportunities in common topics, including chromosomal evolution, the mechanics of speciation, local adaptation, domestication, and urban adaptation.

WITHDRAWN: Indel-informed bayesian analysis suggests cryptic divisions between Plasmodium knowlesi of humans and long-tailed macaques (Macaca fascicularis) in Malaysian Borneo.

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Unprecedented Symbiont Eukaryote Diversity Is Governed by Internal Trophic Webs in a Wild Non-Human Primate.

Research on host-associated microbiomes has highlighted major divisions between the role of eukaryotes in free-living and symbiont systems. These trends call into question the relevance of macroecological processes to host-associated systems and the relative importance of parasitism, commensalism, and mutualism as evolutionary patterns across the domains of life. However, it is unclear as to whether these apparent differences reflect biological realities or methodologies in community characterization: free-living eukaryotes tend to be characterized using metabarcoding whereas symbiont eukaryotes are typically characterized with microscopy. Here, we utilize an Illumina high-throughput metabarcoding approach to characterize the diversity and dynamics of eukaryotic symbiont communities in the feces of a wild non-human primate, Macaca fascicularis, revealing functionally and taxonomically diverse communities of eukaryotes hitherto unreported from any vertebrate. Importantly, community assembly was consistent with top-down and bottom-up trophic food web dynamics, highlighting the applicability of macroecological principles to these communities. Ultimately, our findings highlight vertebrate-associated symbiont communities of the gut that are much more similar to free-living systems than previously realized. Additionally, our results support a role for symbiosis as a major recurrent life strategy among eukaryotes and highlight the potential for vertebrates to host vast reservoirs of unexplored eukaryotic diversity.

Comparative community-level associations of helminth infections and microparasite shedding in wild long-tailed macaques in Bali, Indonesia.

Helminthes have the capacity to modulate host immunity, leading to positive interactions with coinfecting microparasites. This phenomenon has been primarily studied during coinfections with a narrow range of geo-helminthes and intracellular microparasites in human populations or under laboratory conditions. Far less is known regarding differences in coinfection dynamics between helminth types, the range of microparasites that might be affected or the overall community-level effects of helminth infections on microparasites in wild systems. Here, we analysed the presence/absence and abundance patterns of enteric parasites in long-tailed macaques (Macaca fascicularis) on the island of Bali, Indonesia, to assess whether naturally occurring helminth infections were associated with increased shedding of the most common intracellular (Cryptosporidium spp., Isospora spp.) and extracellular (Entamoeba spp., Giardia spp.) microparasites. We also comparatively assessed the statistical correlations of different helminth taxa with microparasite shedding to determine if there were consistent relationships between the specific helminth taxa and microparasites. Helminth infections were associated with increased shedding of both intracellular and extracellular microparasites. Platyhelminthes repeatedly displayed strong positive correlations with several microparasites; while nematodes did not. Our results indicate that helminthes can influence microparasite community shedding dynamics under wild conditions, but that trends may be driven by a narrow range of helminthes.