Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome.

Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and informatic study, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in Drosophila melanogaster, offering significant improvements to the existing community reference assembly. Our work successfully recovers previously elusive segments, including complete reconstructions of the histone locus and the pericentric heterochromatin of the X chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative of crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.

Policy and laboratory practice: How quality control procedures for genetic testing perpetuate biological essentialism and discrimination against transgender, gender diverse, and intersex people.

Transgender, gender diverse, and intersex (TGDI) individuals face significant health disparities due to individual and systemic experiences of discrimination, impacting their access to healthcare. While clinical genetic testing has become increasingly accessible to the general population, the field of clinical genetics perpetuates a narrative of biological essentialism, which creates barriers for TGDI patients. Biological essentialism upholds that sex is a binary, fixed, and innate characteristic, a misconception that has been historically weaponized against the TGDI community in both individual experiences of discrimination and anti-trans legislation, among other systemic forms of oppression. Rejecting this discriminatory framework requires careful consideration of, and changes to, long-established practices that often go unquestioned, such as quality control metrics in genetic testing, in order to improve TGDI patients' outcomes and access to genetic services. The sex-check, comparing an individuals reported sex against their sex chromosomes, is an example of how laboratory genetics practices reinforce the narrative that sex is determined purely by chromosomal composition. Additionally, the sex-check "outs" TGDI people in clinical settings, creating a discriminatory and unsafe environment for these patients. Alternative quality control procedures and inclusive practices, such as clearer delineation of sex and gender on test requisition forms, are proposed to improve TGDI patient experiences. Genetic counselors and other clinical providers have a responsibility to address historical discrimination and advocate for changes to laboratory practice, so as to create affirming experiences for TGDI patients.

Comprehensive metabolomics of Philippine Stichopus cf. horrens reveals diverse classes of valuable small molecules for biomedical applications.

Stichopus cf. horrens is an economically important sea cucumber species in Southeast Asia due to their presumed nutritional and medicinal benefits. However, compared to other sea cucumbers such as Apostichopus japonicus, there are no biochemical studies on which compounds contribute to the purported bioactivities of S. cf. horrens. To address this, a high-throughput characterization of the global metabolite profile of the species was performed through LC-MS/MS experiments and utilizing open-access platforms such as GNPS, XCMS, and metaboAnalyst. Bioinformatics-based molecular networking and chemometrics revealed the abundance of phospholipids such as phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), phosphatidylinositols (PIs), and phosphatidylserines (PSs) in the crude samples. Body wall extracts were observed to have higher levels of structural, diacylated PCs, while the viscera have higher relative abundance of single-tail PCs and PEs that could be involved in digestion via nutrient absorption and transport for sea cucumbers. PEs and sphingolipids could also be implicated in the ecological response and morphological transformations of S. cf. horrens in the presence of predatory and other environmental stress. Interestingly, terpenoid glycosides and saponins with reported anti-cancer benefits were significantly localized in the body wall. The sulfated alkanes and sterols present in S. cf. horrens bear similarity to known kairomones and other signaling molecules. All in all, the results provide a baseline metabolomic profile of S. cf. horrens that may further be used for comparative and exploratory studies and suggest the untapped potential of S. cf. horrens as a source of bioactive molecules.

Which fatigue scale should I use? A Rasch analysis of two fatigue scales in inflammatory conditions.

OBJECTIVES: This study aimed to assess the psychometric properties of two widely used fatigue scales in a sample of patients with inflammatory conditions. METHODS: Rasch analysis was used to examine scale reliability, item bias, unidimensionality and overall fit to the Rasch model. Sub-test methodology was utilised to attempt to improve model fit for the CFQ and BRAF-MDQ. RESULTS: Initial analysis displayed strong reliability (PSI=0.89 0.96), alongside a lack of item bias in both scales. However, evidence for unidimensionality was not found for either scale. Overall fit to the Rasch model was marginal for the CFQ, and misfitting for the BRAF-MDQ. Local dependency was observed, as well as significant item misfit for both scales. Sub-test modifications resulted in the best model fit for the BRAF-MDQ (χ2(16)=15.77, p=0.469) and the CFQ (χ2(25)=15.49, p=0.929). Modifications resulted in improved fit, reductions in measurement error, and the production of ordinal-to-interval conversion tables for both scales. Conversion tables apply the benefits of enhanced measurement accuracy, valid comparison of BRAF-MDQ and CFQ scores to other interval-level data, appropriate use in parametric statistics, and enhanced precision in clinical cut-off scores-without the need to change administration format. CONCLUSION: The BRAF-MDQ and CFQ are valid, reliable tools for fatigue assessment. Psychometric indices and content factors suggest the CFQ is suited to measuring general fatigue, particularly when response burden is a concern, while the BRAF-MDQ should be used in clinical presentations where other symptoms are severe and the impact of fatigue on daily living, emotional, and social well-being is of interest.

Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies.

The acquisition of novel sexually dimorphic traits poses an evolutionary puzzle: How do new traits arise and become sex-limited? Recently acquired color vision, sexually dimorphic in animals like primates and butterflies, presents a compelling model for understanding how traits become sex-biased. For example, some Heliconius butterflies uniquely possess UV (ultraviolet) color vision, which correlates with the expression of two differentially tuned UV-sensitive rhodopsins, UVRh1 and UVRh2. To discover how such traits become sexually dimorphic, we studied Heliconius charithonia, which exhibits female-specific UVRh1 expression. We demonstrate that females, but not males, discriminate different UV wavelengths. Through whole-genome shotgun sequencing and assembly of the H. charithonia genome, we discovered that UVRh1 is present on the W chromosome, making it obligately female-specific. By knocking out UVRh1, we show that UVRh1 protein expression is absent in mutant female eye tissue, as in wild-type male eyes. A PCR survey of UVRh1 sex-linkage across the genus shows that species with female-specific UVRh1 expression lack UVRh1 gDNA in males. Thus, acquisition of sex linkage is sufficient to achieve female-specific expression of UVRh1, though this does not preclude other mechanisms, like cis-regulatory evolution from also contributing. Moreover, both this event, and mutations leading to differential UV opsin sensitivity, occurred early in the history of Heliconius. These results suggest a path for acquiring sexual dimorphism distinct from existing mechanistic models. We propose a model where gene traffic to heterosomes (the W or the Y) genetically partitions a trait by sex before a phenotype shifts (spectral tuning of UV sensitivity).

FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies.

The accurate determination of allele frequencies is crucially important across a wide range of problems in genetics, such as developing population genetic models, making inferences from genome-wide association studies, determining genetic risk for diseases, as well as other scientific and medical applications. Furthermore, understanding how allele frequencies change over time in populations is central to ascertaining their evolutionary dynamics. We present a precise, efficient, and economical method (FREQ-Seq2) for quantifying the relative frequencies of different alleles at loci of interest in mixed population samples. Through the creative use of paired barcode sequences, we exponentially increased the throughput of the original FREQ-Seq method from 48 to 2,304 samples. FREQ-Seq2 can be targeted to specific genomic regions of interest, which are amplified using universal barcoded adapters to generate Illumina sequencing libraries. Our enhanced method, available as a kit along with open-source software for analyzing sequenced libraries, enables the detection and removal of errors that are undetectable in the original FREQ-Seq method as well as other conventional methods for allele frequency quantification. Finally, we validated the performance of our sequencing-based approach with a highly multiplexed set of control samples as well as a competitive evolution experiment in Escherichia coli and compare the latter to estimates derived from manual colony counting. Our analyses demonstrate that FREQ-Seq2 is flexible, inexpensive, and produces large amounts of data with low error, low noise, and desirable statistical properties. In summary, FREQ-Seq2 is a powerful method for quantifying allele frequency that provides a versatile approach for profiling mixed populations.

Structural phases of classical 2D clusters with competing two-body and three-body interactions.

In modeling systems of interacting particles, many-body terms beyond pairwise interactions are often overlooked. Nevertheless, in certain scenarios, even small contributions from three-body or higher-order terms can disrupt significant changes in their collective behavior. Here we investigate the effects of three-body interactions on the structure and stability of 2D, harmonically confined clusters. We consider clusters with three distinct pairwise interactions:logr,1/r, ande-κr/r, thus covering a wide range of condensed and soft matter systems, such as vortices in mesoscopic superconductors, charged colloids, and dusty plasma. In each case, we evaluate the energetics and normal mode spectra of equilibrium and metastable configurations as the intensity of an attractive, Gaussian three-body potential is varied. We demonstrate that, above a threshold value of the three-body energy strength, the cluster shrinks and eventually becomes self-sustained, that is, it remains cohesive after the confinement potential is shut down. Depending on the strengths of the two-body and three-body interaction terms, this compaction can be continuous or abrupt. The latter case is characterized by a discontinuous jump in the particle density and coexsitence of the compact and non-compact phases as metastable states, as in a first-order phase transition. For some values of the particle number, the compaction is preceded by one or more structural changes, resulting in configurations not usually seen in purely pairwise-additive clusters.

The development, implementation, and evaluation of an optimal model for the case detection, referral, and case management of Neglected Tropical Diseases.

BACKGROUND: People affected by Neglected Tropical Diseases (NTDs), specifically leprosy, Buruli ulcer (BU), yaws, and lymphatic filariasis, experience significant delays in accessing health services, often leading to catastrophic physical, psychosocial, and economic consequences. Global health actors have recognized that Sustainable Development Goal 3:3 is only achievable through an integrated inter and intra-sectoral response. This study evaluated existing case detection and referral approaches in Liberia, utilizing the findings to develop and test an Optimal Model for integrated community-based case detection, referral, and confirmation. We evaluate the efficacy of implementing the Optimal Model in improving the early diagnosis of NTDs, thus minimizing access delays and reducing disease burden. METHODS: We used a participatory action research approach to develop, implement, and evaluate an Optimal Model for the case detection, referral, and management of case management NTDs in Liberia. We utilized qualitative and quantitative methods throughout the cycle and implemented the model for 12 months. RESULTS: During the implementation of our optimal model, the annual number of cases detected increased compared to the previous year. Cases were detected at an earlier stage of disease progression, however; gendered dynamics in communities shape the case identification process for some individuals. Qualitative data showed increased knowledge of the transmission, signs, symptoms, and management options among community health workers (CHW). CONCLUSION: The results provide evidence of the benefits of an integrated approach and the programmatic challenges to improve access to health services for persons affected by NTDs. The effectiveness of an integrated approach depends on a high level of collaboration, joint planning, and implementation embedded within existing health systems infrastructure.

Making It to Sustainability: Evaluating Billing Strategies for Collaborative Care.

The collaborative care model (CoCM) is an effective strategy to manage common mental disorders in primary care. Despite the growing adoption of newer CoCM billing codes to support these programs, few studies have investigated the use of these codes. This column evaluated the implementation of CoCM billing codes by comparing clinics using different billing strategies and assessed the impact of CoCM code implementation on revenue and on clinical and process-of-care outcomes. Qualitative data were obtained to understand provider perspectives. The results indicate that CoCM billing code implementation is operationally feasible, does not adversely affect the delivery of patient care or revenue, and is acceptable to providers.

Persistent disparities of cervical cancer among American Indians/Alaska natives: Are we maximizing prevention tools?

BACKGROUND: Cervical cancer incidence and mortality disparities experienced by American Indian/Alaska Native (AI/AN) women have persisted for decades. Pap smear screening and HPV vaccination are powerful tools to prevent cervical cancer. We evaluated the utilization of these tools among AI/ANs living in the Pacific Northwest (PNW). METHODS: The Indian Health Service (IHS) National Data Warehouse's Epi Data Mart was analyzed using all healthcare visits from 2010 to 2020 from IHS, Tribal, and Urban Indian clinics in the PNW. Women ages 21-64 were included and considered up-to-date on pap smears if they had either cytology within 3 years or cytology with HPV testing within 5 years of the most recent clinical encounter. HPV vaccination rates for both sexes were calculated for individuals ages 9-26. HPV vaccination was considered complete if: two vaccines were received prior to age 15 or after three vaccinations if initiated after age 15. FINDINGS: Cervical cancer screening rates are below the national average of 73.5% ranging between 57.1% - 65.0%. Sub-analysis of age groups shows substantially lower rates of up-to-date pap smear screening in the 50-64 age group. HPV vaccination rates have increased over time for both sexes across all age groups. However, the current vaccination rate of 58.6% is well below the Healthy People 2030 goal of 84.3%. INTERPRETATION: Cervical cancer screening and HPV vaccination are the cornerstones of cervical cancer prevention and early detection. These tools are underutilized and public health efforts can be strengthened to improve cervical cancer disparities in AI/AN women. FUNDING: Author ASB: Funding for this project has been provided through the Robert Wood Johnson Foundation Harold Amos Minority Faculty Development Grant and the National Cancer Institute K08 Mentored Clinical Scientist Development Award.

White patients' physical responses to healthcare treatments are influenced by provider race and gender.

The healthcare workforce in the United States is becoming increasingly diverse, gradually shifting society away from the historical overrepresentation of White men among physicians. However, given the long-standing underrepresentation of people of color and women in the medical field, patients may still associate the concept of doctors with White men and may be physiologically less responsive to treatment administered by providers from other backgrounds. To investigate this, we varied the race and gender of the provider from which White patients received identical treatment for allergic reactions and measured patients' improvement in response to this treatment, thus isolating how a provider's demographic characteristics shape physical responses to healthcare. A total of 187 White patients experiencing a laboratory-induced allergic reaction interacted with a healthcare provider who applied a treatment cream and told them it would relieve their allergic reaction. Unbeknownst to the patients, the cream was inert (an unscented lotion) and interactions were completely standardized except for the provider's race and gender. Patients were randomly assigned to interact with a provider who was a man or a woman and Asian, Black, or White. A fully blinded research assistant measured the change in the size of patients' allergic reaction after cream administration. Results indicated that White patients showed a weaker response to the standardized treatment over time when it was administered by women or Black providers. We explore several potential explanations for these varied physiological treatment responses and discuss the implications of problematic race and gender dynamics that can endure "under the skin," even for those who aim to be bias free.

The 3D architecture of the pepper genome and its relationship to function and evolution.

The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints.

Sustainable Hues: Exploring the Molecular Palette of Biowaste Dyes through LC-MS Metabolomics.

Underutilized biowaste materials are investigated for their potential as sustainable textile colorants through an approach based on mass spectrometry, bioinformatics, and chemometrics. In this study, colorful decoctions were prepared from the outer bark of Eucalyptus deglupta and fruit peels of Syzygium samarangense, Syzygium malaccense, Diospyros discolor, and Dillenia philippinensis. Textile dyeing was performed along with liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics to determine the small molecules responsible for the observed colors. Global Natural Products Social Molecular Networking (GNPS) guided the annotation of black-producing proanthocyanidins in D. philippinensis and E. deglupta through complexation with FeSO4 mordant. Flavonoids from the yellow-colored D. philippinensis extracts were found to be similar to those in Terminalia catappa, a known traditional dye source. A higher intensity of epicatechin in E. deglupta produced a red-brown color in the presence of Cu2+. Furthermore, Syzygium fruit peels have poor wash-fastness in cotton fibers, but bioactive chalcone unique to S. samarangense samples may be a potential nutritional food colorant. Unsupervised PCA and supervised OPLS-DA chemometrics distinguished chemical features that affect dyeing properties beyond the observed color. These findings, along with growing data on natural dyes, could guide future research on sustainable colorants.

Vaccination practices for Leptospira spp. on New Zealand dairy farms.

AIMS: To describe leptospiral vaccination practices in dairy herds in New Zealand and evaluate conformity with best practice guidelines issued by the New Zealand Veterinary Association using data from a questionnaire administered by participating veterinary practices. METHODS: A cross-sectional study of 200 randomly selected dairy farms stratified by herd size and region throughout New Zealand was conducted from January to April 2016 to investigate leptospiral vaccination practices in dairy herds in New Zealand. Using a pre-tested questionnaire administered during a face-to-face interview, vaccination practice details such as vaccine types, time, and age of vaccination and whether vaccines were administered by veterinary or farm staff, were collected. RESULTS: Leptospiral vaccination programmes had been implemented on 199/200 (99.5 (95% CI = 97.2-99.9)%) farms, and on 178 (89.4%) of those, programmes had been running for ≥5 years. Most farmers used bivalent vaccines containing antigens for leptospiral serovars Pomona and Hardjo (144/179 (80.4%) in calves, 112/167 (60.7%) in heifers, and 112/163 (68.7%) in cows), rather than trivalent vaccines which also include antigens for L. interrogans serovar Copenhageni. In total, 123/200 (61.5%) of farmers purchased only vaccinated animals but 51/199 (25.6%) were unsure of the vaccination status of purchased cattle. Sixty-one percent (105/172) of farmers had other livestock on their farms and of them, 78/186 (42%) vaccinated some or all for Leptospira spp. Leptospiral vaccines were administered always or sometimes with other animal remedies on 30/190 (15.8%) and 91/190 (47.9%) of farms, respectively. Most farmers had not made changes to their vaccination programme in the previous 5 years. Timing of first vaccination of calves ranged from 2 weeks to 10 months of age, with 112/189 (59.3%) vaccinating by 4 months of age. Approximately half of the farms followed the best practice guideline for the timing of vaccinations for calves (high-risk farms; 67/162; 41.4%) heifers (72/165, 43.6%), and cows (171/184; 92.9%). CONCLUSIONS: The results of this survey suggest that there is almost universal adoption of leptospiral vaccination for dairy cattle in New Zealand. However, there remain areas for improvement regarding the proportion of farmers following best practice guidelines and refinement of vaccination programmes, particularly with respect to timing of vaccination in calves.

Small in size, big on taste: Metabolomics analysis of flavor compounds from Philippine garlic.

Philippine garlic (Allium sativum L.) is arguably known to pack flavor and aroma in smaller bulbs compared to imported varieties saturating the local market. In this study, ethanolic extracts of Philippine garlic cultivars were profiled using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF). γ-Glu dipeptides, oligosaccharides and lipids were determined in Philippine garlic cultivars through bioinformatics analysis in GNPS Molecular Networking Platform and fragmentation analysis. Multivariate statistical analysis using XCMS Online showed the abundance of γ-Glu allyl cysteine in Batanes-sourced garlic while γ-Glu propenyl cysteine, γ-Glu methyl cysteine, and alliin are enriched in the Ilocos cultivar. Principal component analysis showed that the γ-Glu dipeptides found in local garlic influenced their distinct separation across PC1 from imported varieties. This presence of high levels of γ-Glu dipeptides and probiotic oligosaccharides may potentially contribute to the superior flavor and nutritional benefits of Philippine garlic.

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation.

Mechanisms controlling CO2 and CH4 production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO2 and CH4 dynamics.

Evolution of genome structure in the Drosophila simulans species complex.

The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila.

Topologically associating domains (TADs) were recently identified as fundamental units of three-dimensional eukaryotic genomic organization, although our knowledge of the influence of TADs on genome evolution remains preliminary. To study the molecular evolution of TADs in Drosophila species, we constructed a new reference-grade genome assembly and accompanying high-resolution TAD map for D. pseudoobscura Comparison of D. pseudoobscura and D. melanogaster, which are separated by ∼49 million years of divergence, showed that ∼30%-40% of their genomes retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower expression divergence than those located in nonconserved TADs. Furthermore, we found that a substantial proportion of long genes (>50 kbp) in D. melanogaster (42%) and D. pseudoobscura (26%) constitute their own TADs, implying transcript structure may be one of the deterministic factors for TAD formation. By using structural variants (SVs) identified from 14 D. melanogaster strains, its three closest sibling species from the D. simulans species complex, and two obscura clade species, we uncovered evidence of selection acting on SVs at TAD boundaries, but with the nature of selection differing between SV types. Deletions are depleted at TAD boundaries in both divergent and polymorphic SVs, suggesting purifying selection, whereas divergent tandem duplications are enriched at TAD boundaries relative to polymorphism, suggesting they are adaptive. Our findings highlight how important TADs are in shaping the acquisition and retention of structural mutations that fundamentally alter genome organization.