When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine.

The Seychelles magpie-robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation-for-recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re-sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss-of-function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3-fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.

A practical introduction to holo-omics.

Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main differences to generate and analyze the various types of omics, with a special focus on optimizing data generation and integration. We advocate for careful generation and distillation of data, followed by independent exploration and analyses of the single omic layers to obtain a better understanding of the study system, before the integration of multiple omic layers in a final model is attempted. We highlight critical decision points to achieve this aim and flag the main challenges to address complex biological questions regarding the integrative study of host-microbiota relationships.

Temporal dynamics of woolly mammoth genome erosion prior to extinction.

A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.

Framework for valorizing waste- and by-products through insects and their microbiomes for food and feed.

One third of the food produced for human consumption is currently lost or wasted. Insects have a high potential for converting organic waste- and by-products into food and feed for a growing human population due to symbiosis with microorganisms. These symbioses provide an untapped reservoir of functional microbiomes that can be used to improve industrial insect production but are poorly studied in most insect species. Here we review the most current understanding and challenges of valorizing organic waste- and by-products through insects and their microbiomes for food and feed, and emerging novel food technologies that can be used to investigate and manipulate host(insects)-microbiome interactions. We further construct a holistic framework, by integration of novel food technologies including holo-omics, genome editing, breeding, phage therapy, and administration of prebiotics and probiotics to investigate and manipulate host(insects)-microbiome interactions, and solutions for achieving stakeholder acceptance of novel food technologies for a sustainable food production.

Probing the interfacial structure of aqueous surfactants through helium atom evaporation.

Dissolved helium atoms evaporate from liquids in super-Maxwellian speed distributions because their interactions are too weak to enforce full thermal equilibration at the surface as they are "squeezed" out of solution. The excess speeds of these He atoms reflect their final interactions with solvent and solute molecules at the surfaces of water and other liquids. We extend this observation by monitoring He atom evaporation from salty water solutions coated with surfactants. These surface-active molecules span neutral, anionic, and cationic amphiphiles: butanol, 3-methyl-1-butanol, pentanol, pentanoic acid, pentanoate, tetrabutylammonium, benzyltrimethylammonium, hexyltrimethylammonium, and dodecyltrimethylammonium, each characterized by surface tension measurements. The helium energy distributions, recorded in vacuum using a salty water microjet, reveal a sharp distinction between neutral and ionic surfactant films. Helium atoms evaporate through neutral surfactant monolayers in speed distributions that are similar to a pure hydrocarbon, reflecting the common alkyl chains of both. In contrast, He atoms appear to evaporate through ionic surfactant layers in distributions that are closer to pure salty water. We speculate that the ionic surfactants distribute themselves more loosely and deeply through the top layers of the aqueous solution than do neutral surfactants, with gaps between the surfactants that may be filled with salty water. This difference is supported by prior molecular dynamics simulations and ion scattering measurements of surfactant solutions.

High variation in the response of calves to a low-dose lipopolysaccharide challenge is associated with early-life measurements.

Lipopolysaccharide (LPS) challenges are commonly used in animal studies as a model for infection with gram-negative bacteria and innate immune activation. We used a low-dose LPS challenge for evaluating interindividual variation in innate immune responses in calves. This was part of a larger study aimed at predicting interindividual variation in feed efficiency in veal calves by variation in feeding motivation, digestion, metabolism, immunology, and behavioral traits. However, due to unexpected high mortality, this LPS challenge was performed in 32 calves rather than in 130 calves, which was initially intended in that larger study, and the 32 calves subjected to the LPS challenge were removed from that larger study. The objective of this short communication is to report the effects of a low-dose LPS challenge in those 32 calves and to examine whether the high variation in calves' responses to LPS could be explained by parameters related to feeding motivation, digestion, behavior, and immunology measured in early life. Thirty-two male Holstein-Friesian calves of Dutch origin were intravenously injected with LPS (0.05 µg/kg of body weight) at an age of 72 ± 0.6 d. Rectal temperature and respiratory frequency were recorded before injection and every hour after injection up to 6 h. In the 8 wk before the LPS challenge, measurements were performed related to general health, feeding motivation, digestion, behavior, and immunity. Following LPS administration, 3 calves died of shock, a fourth calf was euthanized because of severe symptoms of shock and 3 other calves were treated with corticosteroids to counteract observed symptoms of shock. Within the group of 25 relatively mild-responding calves, large interindividual variation in clinical responses to LPS was observed. The maximum increase in rectal temperature varied from 0.6 to 1.9°C and averaged 1.2 ± 0.39°C (coefficient of variation was 32%). The maximum increase in respiratory frequency varied from 16 to 132 bouts/min and averaged 60 ± 28 bouts/min (coefficient of variation was 48%). Little differences were found in early-life measurements between the 7 heavy and 25 mild responders, although heavy responders tended to have a better umbilical hernia score, and had a lower score in a human approach test (i.e., were less reactive) and lower presence of fecal pathogens. The maximum increase in rectal temperature correlated negatively with blood hemoglobin concentration at arrival of the calves at the facilities (r = -0.59) and in wk 4 (r = -0.53). The maximum increase in respiratory frequency correlated negatively with fecal color score (r = -0.43) and positively with fur score in wk 5 (r = 0.50). Overall, mortality (12.5%) and variation in clinical response was high after a low-dose LPS challenge in clinically healthy calves and some hematological and health measurements in early life were related to the clinical response of calves to LPS.

Complexity of avian evolution revealed by family-level genomes.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Providing Hemodialysis in Unstable Areas: An Assessment and Framework for Effective Care.

Introduction: Providing hemodialysis to patients with kidney failure (KF) in conflict-affected areas poses a significant challenge. Achieving and sustaining reasonable quality hemodialysis operations in such regions necessitates a comprehensive approach. Methods: In the conflict area of Northwest (NW) Syria, a 3-phase project was initiated to address the quality of hemodialysis operations. The assessment phase involved the examination of infection prevention and control (IPC) protocols, staff training, medical protocols, individualized hemodialysis prescriptions, and laboratory testing capabilities. The second phase involved activities toward capacity building and implementing an action plan based on feasibility and sustainability. Results: The assessment phase revealed that only 7 of 14 centers had IPC protocols, and 8 centers provided IPC training for their staff. Furthermore, only 7 centers had medical protocols, and 5 used individualized hemodialysis prescriptions. Difficulties in testing for potassium was reported in 7 centers and the inability to perform hepatitis B and C serologies was reported in 3 centers. Only 2 centers adhered to machine and water treatment system maintenance guidelines, and 4 conducted daily water quality checks. Recommendations were formulated, and an action plan was developed for implementation in the second phase. The plan encompassed enhancements in IPC practices, medical protocols, record-keeping, laboratory testing, and equipment maintenance. Conclusion: This project underscores that hemodialysis services in conflict-affected areas do not meet the standards for quality care. It emphasizes the necessity of implementing a comprehensive framework that engages relevant stakeholders in defining and upholding quality care, a model that should be extended to other protracted conflict-affected regions.

Three-Dimensional Osseointegration Patterns of Cementless Femoral Stems: An ex Vivo Study with High-Resolution Imaging and Histological Evaluation.

BACKGROUND: Osseointegration is essential for the long-term survival of cementless femoral stems and is dependent on periprosthetic bone quality and correct implantation technique. The aim of this study was to evaluate the 3-dimensional long-term fixation patterns of, and bone microarchitecture around, cementless hip stems. METHODS: Four specimens with varying degrees of bone quality and fixation characteristics from body donors who had received Alloclassic Zweymüller hip stems during their lifetime (mean time in situ at the time of death: 12.73 years) were evaluated with use of radiographs, high-resolution computed tomography (CT) scans, and hard-tissue histology. The CT voxel size was 85 µm, and the following parameters were calculated: total bone volume, total bone volume fraction, trabecular bone volume, trabecular bone volume fraction, cortical bone volume, cortical bone volume fraction, and cortical thickness. Bone-implant contact and canal fill index values for each Gruen zone of the specimens were calculated with use of histological samples. RESULTS: Femoral stems with apparently good cortical contact on clinical radiographs showed higher values for cortical bone volume, trabecular bone volume, and cortical thickness in the high-resolution CT analysis than femoral stems with apparently weak cortical contact on clinical radiographs. Based on the histological evaluation, the mean bone-implant contact ranged from 22.94% to 57.24% and the mean canal fill index ranged from 52.33% to 69.67% among the specimens. CONCLUSIONS: This study demonstrated different osseointegration patterns of cementless femoral stems on the basis of radiographs, high-resolution CT scans, and histological evaluation. Femora with high cortical bone volume and cortical thickness were associated with higher canal fill indices, whereas femora with low cortical bone volume and cortical thickness had lower canal fill indices and showed a characteristic corner-anchorage pattern. CLINICAL RELEVANCE: Osseointegration patterns and thus the long-term survival of cementless femoral stems are dependent on cortical bone volume and cortical thickness.

Molecular Insights into Chemical Reactions at Aqueous Aerosol Interfaces.

Atmospheric aerosols facilitate reactions between ambient gases and dissolved species. Here, we review our efforts to interrogate the uptake of these gases and the mechanisms of their reactions both theoretically and experimentally. We highlight the fascinating behavior of N2O5 in solutions ranging from pure water to complex mixtures, chosen because its aerosol-mediated reactions significantly impact global ozone, hydroxyl, and methane concentrations. As a hydrophobic, weakly soluble, and highly reactive species, N2O5 is a sensitive probe of the chemical and physical properties of aerosol interfaces. We employ contemporary theory to disentangle the fate of N2O5 as it approaches pure and salty water, starting with adsorption and ending with hydrolysis to HNO3, chlorination to ClNO2, or evaporation. Flow reactor and gas-liquid scattering experiments probe even greater complexity as added ions, organic molecules, and surfactants alter the interfacial composition and reaction rates. Together, we reveal a new perspective on multiphase chemistry in the atmosphere.

Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation.

Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.

Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon.

Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.

Fully automated assessment of the knee alignment on long leg radiographs following corrective knee osteotomies in patients with valgus or varus deformities.

INTRODUCTION: The assessment of the knee alignment on long leg radiographs (LLR) postoperative to corrective knee osteotomies (CKOs) is highly dependent on the reader's expertise. Artificial Intelligence (AI) algorithms may help automate and standardise this process. The study aimed to analyse the reliability of an AI-algorithm for the evaluation of LLRs following CKOs. MATERIALS AND METHODS: In this study, we analysed a validation cohort of 110 postoperative LLRs from 102 patients. All patients underwent CKO, including distal femoral (DFO), high tibial (HTO) and bilevel osteotomies. The agreement between manual measurements and the AI-algorithm was assessed for the mechanical axis deviation (MAD), hip knee ankle angle (HKA), anatomical-mechanical-axis-angle (AMA), joint line convergence angle (JLCA), mechanical lateral proximal femur angle (mLPFA), mechanical lateral distal femoral angle (mLDFA), mechanical medial proximal tibia angle (mMPTA) and mechanical lateral distal tibia angle (mLDTA), using the intra-class-correlation (ICC) coefficient between the readers, each reader and the AI and the mean of the manual reads and the AI-algorithm and Bland-Altman Plots between the manual reads and the AI software for the MAD, HKA, mLDFA and mMPTA. RESULTS: In the validation cohort, the AI software showed excellent agreement with the manual reads (ICC: 0.81-0.99). The agreement between the readers (Inter-rater) showed excellent correlations (ICC: 0.95-0. The mean difference in the DFO group for the MAD, HKA, mLDFA and mMPTA were 0.50 mm, - 0.12°, 0.55° and 0.15°. In the HTO group the mean difference for the MAD, HKA, mLDFA and mMPTA were 0.36 mm, - 0.17°, 0.57° and 0.08°, respectively. Reliable outputs were generated in 95.4% of the validation cohort. CONCLUSION:  he application of AI-algorithms for the assessment of lower limb alignment on LLRs following CKOs shows reliable and accurate results. LEVEL OF EVIDENCE: Diagnostic Level III.

Effects of nondigestible oligosaccharides on inflammation, lung health, and performance of calves.

Our objective was to determine the effects of nondigestible oligosaccharides (NDO) on lung health and performance. Three hundred male Holstein-Friesian calves aged 18.0 ± 3.6 d received 1 of 6 treatments for 8.5 wk (period 1). Treatments included a negative control (CON), galacto-oligosaccharides (GOS) administered as a spray via the nose once daily (SPR), GOS administered via the milk replacer (MR) at 1% (GOS-L) and 2% (GOS-H), fructo-oligosaccharides administered via the MR at 0.25% (FOS) and a combination of GOS and fructo-oligosaccharides administered via the MR at 1% and 0.25%, respectively (GOS-FOS). Milk replacer was fed twice daily. Feeding levels were equal between calves and increased progressively in time. Body weight was measured every 4 wk and clinical health was scored weekly. Blood and broncho-alveolar lavage fluid (BALF) samples were collected bi-weekly from a subset of calves (n = 120). After period 1, all calves received the same control MR for 18 wk until slaughter (period 2), during which general performance and clinical health were measured. Generally, infection pressure was high, with clinical scores and BALF proinflammatory TNFα concentrations increasing with time in period 1, which resulted in a high number of required group antimicrobial treatments (6 group antimicrobial treatments in 13 wk, supplied to all calves). Average daily gain adjusted to equal solid feed intake was increased for GOS-L (+61 g/d) compared with CON calves from experimental wk 1 to 5. Plasma white blood cell concentration tended to be lowered by GOS-L, plasma IL-8 concentration was reduced by all orally supplemented NDO, plasma IL-6 was reduced by all NDO treatments except GOS-FOS and plasma IL-1ß was reduced by all NDO treatments compared with CON, although this differed per time point for SPR. The neutrophil percentage in BALF was reduced by GOS-L in wk 6, which was associated with a relative increase in macrophages. The BALF concentration of TNFα and IL-8 was reduced or tended to be reduced by GOS-L and GOS-H, while IL-6 was or tended to be reduced by SPR, GOS-L, GOS-H, and GOS-FOS, and IL-1ß was reduced by SPR, GOS-L, GOS-H, and FOS. Generally, feeding the combination of GOS and FOS was not more effective than feeding GOS or FOS alone, because feeding GOS-FOS resulted in higher concentrations of plasma and BALF cytokine and chemokine concentrations compared with feeding GOS-L alone, and resulted in higher plasma cytokine concentrations compared with feeding FOS alone. None of the BALF and plasma cytokine or chemokine concentrations differed between the GOS-L and GOS-H treatment. Performance and clinical scores in period 2 did not differ among treatments. Altogether, all tested NDO reduced systemic and lung inflammation in calves under high natural infection pressure and for GOS-fed calves, this increased performance during the first 4 wk. Combining GOS and FOS did not have a synergistic effect. The intranasal administration of GOS also lowered systemic and lung inflammation, but tended to negatively affect performance. Overall, this study demonstrates the potential of NDO to alleviate systemic and respiratory inflammation in calves.

"In the End You Keep Silent": Help-Seeking Behavior Upon Sexual Victimization in Older Adults.

Sexual violence is considered a prominent mental health problem. Exposure to sexual victimization during lifetime has been linked to mental health problems in old age. Research in adult victims has shown that they experience many barriers for disclosure and seeking professional help upon sexual victimization. However, information on help-seeking behavior in older victims of sexual violence is non-existent. With this study we aim for a better understanding of help-seeking behavior upon sexual violence in older adults. We used a mixed methods approach with an explanatory sequential design. Data were collected through structured face-to-face interviews with a random sample of 227 sexual violence victims of 70 years and older living in Belgium. Quantitative data were triangulated with qualitative data from 15 in-depth interviews with older victims. We found that up to 60% of older sexual violence victims never disclosed their experiences and 94% never sought professional help. Help-seeking is a complex process comprising several phases, which are affected by strong feelings of shame and self-blame, ageist premises and taboos about sexuality. In the end, most victims choose to cope on their own. Occasional disclosure only happens decades after the sexual violence took place. Older victims do not spontaneously disclose to healthcare workers but expect professionals to initiate the conversation. In conclusion, few older victims disclose or seek professional help upon sexual victimization. Healthcare professionals working with older adults need capacity building through training, screening tools, and care procedures to initiate conversation on sexual violence, and to detect signs, prevent, mitigate and respond to sexual victimization in older adults.

Exploring the microbial diversity of novel misos with metagenomics.

Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and koji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates. All misos were made with the same recipe and fermented for 3 months at 28 °C. Samples were collected at the end of fermentation for subsequent shotgun metagenomic sequencing and a genome-resolved metagenomic analysis. The taxonomic profile of the samples revealed the presence of koji mould (A. oryzae) and Bacillus amyloliquefaciens in all misos. Various species of the genera Latilactobacillus, Lactiplantibacillus, Pediococcus and Staphylococcus were also detected. The Metagenome-Assembled Genomes (MAGs) revealed genomic sequences belonging to 12 different species and functional analyses of these MAGs were performed. Notably, we detected the presence of Exiguobacterium-the first reported instance of the genus in miso-and Average Nucleotide Identity (ANI) analyses suggest a potentially new species. We hope these results will improve the scientific literature on misos and contribute to developing novel fermented plant-based foods.

The Evolution of Sinus Tarsi Syndrome-What Is the Underlying Pathology?-A Critical Review.

Background and Objectives: Sinus tarsi syndrome (STS) is defined as pain located at the lateral opening of the tarsal sinus. The exact etiology of sinus tarsi syndrome is not completely understood. Some do not believe it to be a true pathology. This review aims to clarify the definition of sinus tarsi syndrome to better understand the underlying pathologies. We further propose an algorithm to evaluate sinus tarsi pain and provide advice for consecutive treatment options. Design: This is a narrative review. By searching PubMed, the available current literature was reviewed. Articles were critically analyzed to determine the pathoanatomy, biomechanics, and etiology of sinus tarsi pain. Algorithms for clinical evaluation, diagnosis, and treatment were also recorded. Finally, the authors approach to evaluating and treating sinus tarsi pain was included in this review. Results: Reviewing the available literature, STS seems to be a catch-all phrase used to describe any pain in this anatomic region. Many causes of sinus tarsi pain were listed, including impingement, subtalar instability, and many other pathologies around the ankle. Conclusions: A thorough evaluation of patients presenting with pain in the sinus tarsi or instability of the hindfoot is essential to determining the underlying cause. When the cause of pain is still not clear after clinical exam and radiologic assessment, subtalar arthroscopy can be helpful as both a diagnostic and treatment tool. We propose that the term of STS should be avoided and that a more accurate diagnosis be used when possible. Once a diagnosis is made, appropriate treatment can be initiated.

Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences.

The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.

BACKGROUND: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. METHODS: We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. RESULTS: We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. CONCLUSIONS: We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.