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Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long‐snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine‐lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome‐level genome assembly and described genome‐wide patterns of diversity and divergence through the analysis of 112 whole‐genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked‐read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo‐overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation. [ABSTRACT FROM AUTHOR]

In their most extreme form, sex chromosomes exhibit a complete lack of genetic recombination along much of their length in the heterogametic sex. Some recent models explain the evolution of such suppressed recombination by the "sheltering" of deleterious mutations by chromosomal inversions that prevent recombination around a polymorphic locus controlling sex. This sheltering hypothesis is based on the following reasoning. An inversion that is associated with the male-determining allele (with male heterogamety) is present only in the heterozygous state. If such an inversion carries a lower-than-average number of deleterious mutations, it will accrue a selective advantage and will be sheltered from homozygosity for any mutations that it carries due to the enforced heterozygosity for the inversion itself. It can, therefore, become fixed among all carriers of the male-determining allele. Recent population genetics models of this process are discussed. It is shown that, except under the unlikely scenario of a high degree of recessivity of most deleterious mutations, inversions of this type that lack any other fitness effects will have, at best, a modest selective advantage; they will usually accumulate on proto-Y chromosomes at a rate close to, or less than, the neutral expectation. While the existence of deleterious mutations does not necessarily prevent the spread of Y-linked inversions, it is unlikely to provide a significant selective advantage to them. [ABSTRACT FROM AUTHOR]

Let A (n , k) represent the collection of all n × n zero-and-one matrices, with the sum of all rows and columns equalling k . This set can be ordered by an extension of the classical Bruhat order for permutations, seen as permutation matrices. The Bruhat order on A (n , k) differs from the Bruhat order on permutations matrices not being, in general, graded, which results in some intriguing issues. In this paper, we focus on the maximum length of antichains in A (n , k) with the Bruhat order. The crucial fact that allows us to obtain our main results is that two distinct matrices in A (n , k) with an identical number of inversions cannot be compared using the Bruhat order. We construct sets of matrices in A (n , k) so that each set consists of matrices with the same number of inversions. These sets are hence antichains in A (n , k) . We use these sets to deduce lower bounds for the maximum length of antichains in these partially ordered sets. [ABSTRACT FROM AUTHOR]

Large structural variants in the genome, such as inversions, may play an important role in producing population structure and local adaptation to the environment through suppression of recombination. However, relatively few studies have linked inversions to phenotypic traits that are sexually selected and may play a role in reproductive isolation. Here, we found that geographic differences in the sexually selected plumage of a warbler, the common yellowthroat (Geothlypis trichas), are largely due to differences in the Z (sex) chromosome (males are ZZ), which contains at least one putative inversion spanning 40% (31/77 Mb) of its length. The inversions on the Z chromosome vary dramatically east and west of the Appalachian Mountains, which provides evidence of cryptic population structure within the range of the most widespread eastern subspecies (G. t. trichas). In an eastern (New York) and western (Wisconsin) population of this subspecies, female prefer different male ornaments; larger black facial masks are preferred in Wisconsin and larger yellow breasts are preferred in New York. The putative inversion also contains genes related to vision, which could influence mating preferences. Thus, structural variants on the Z chromosome are associated with geographic differences in male ornaments and female choice, which may provide a mechanism for maintaining different patterns of sexual selection in spite of gene flow between populations of the same subspecies. [ABSTRACT FROM AUTHOR]

In 1974, Carlitz and Scoville introduced the Stirling–Eulerian polynomial A n (x , y | α , β) as the enumerator of permutations by descents, ascents, left-to-right maxima and right-to-left maxima. Recently, Ji considered a refinement of A n (x , y | α , β) , denoted P n (u 1 , u 2 , u 3 , u 4 | α , β) , which is the enumerator of permutations by valleys, peaks, double ascents, double descents, left-to-right maxima and right-to-left maxima. Using Chen's context-free grammar calculus, Ji proved a formula for the generating function of P n (u 1 , u 2 , u 3 , u 4 | α , β) , generalizing the work of Carlitz and Scoville. Ji's formula has many nice consequences, one of which is an intriguing γ -positivity expansion for A n (x , y | α , β) . In this paper, we prove a q-analog of Ji's formula by using Gessel's q-compositional formula and provide a combinatorial approach to her γ -positivity expansion of A n (x , y | α , β) . [ABSTRACT FROM AUTHOR]

The purpose of the article is to summarize theoretical and methodological approaches to the study of such a phenomenon as inversions and inversion processes in socio-economic sciences and to identify the features of the application of these approaches in research in the field of spatial economics, as well as their use in assessing the development of the border North Arctic territories of the Far East both at the national and international levels. The analysis of existing research approaches to understanding the essence, characteristics and tools for studying inversion processes in scientific areas in the socio-economic field allows us to interpret them in relation to spatial-economic research and identify specific methods of their application that are related to spatial economics. The identified research methods are used to study the Far Eastern North Arctic territories, which are currently undergoing deep qualitative transformations in their production specialization, auxiliary cycles and chains, as well as in the infrastructure that provided these processes. On the basis of both previous and current author’s studies, it is stated that in the regulation of inversion processes both in the spatial economy as a whole and in the conduct of specific studies on the development of the North Arctic territories, the leading role is played by the balance of opposing endogenous and exogenous elements of the infrastructure of spatial- economic formations at all their hierarchical levels. In conclusion, the article presents the generalizing results of the research in all its directions

The Turkana jet is an equatorial low-level jet (LLJ) in East Africa. The jet influences both flooding and droughts, and powers Africa's largest wind farm. Much of what we know about the jet, including the characteristics of its diurnal cycle, derives from reanalysis simulations that are not constrained by radiosonde observations in the region. Here, we report the characteristics of the Turkana jet with data from a field campaign during March–April 2021: The Radiosonde Investigation for the Turkana Jet (RIFTJet). The southeasterly jet forms on average at 380 m above the surface, with mean speeds of 15.0 m s−1. The strongest low-level winds are during the night and early morning from 0300 to 0600 LT (>16 m s−1). The average wind profile retains a characteristic low-level jet structure throughout the day, with the low-level wind maximum weakening to a minimum of 10.9 m s−1 at 1500 LT. There is significant shear, of up to 1.5 m s−1 (100 m)−1 maintained through the 1000 m above the wind maximum. The diurnal cycle of the jet is associated with the nocturnal strengthening and lowering of elevated subsidence inversions, which form above the jet. Reanalysis simulations (ERA5 and MERRA-2) do not capture the daytime persistence of the jet and underestimate the speed of the jet throughout the diurnal cycle. The largest absolute errors of over 4.5 m s−1 (−35%) occur at 0900 LT. The reanalyses also fail to simulate the elevated subsidence inversions above the jet and associated dry layer in the lower troposphere. [ABSTRACT FROM AUTHOR]

The world has seen an increase in the frequency and severity of elevated outdoor pollution events exacerbated by the rise in distant polluting events (i.e., wildfires). We examined the intersection between indoor and outdoor air quality in an urban area using research-grade sensors to explore PM2.5 infiltration across a variety of pollution events by testing two separate indoor environments within the same building. We confirmed prior work suggesting that indoor environments in buildings are most protective during wintertime inversion events and less so during fireworks and wildfire events. The building indoor environment protectiveness varies notably during different pollution episodes, especially those that have traveled longer distances (e.g., wildfires), and we found evidence of varied infiltration rates across PM2.5 types. Inversion events have the lowest infiltration rates (13–22%), followed by fireworks (53–58%), and wildfires have the highest infiltration rates (62–70%), with distant wildfire events persisting longer and, therefore, infiltrating for greater durations than local-wildfire-related particle matter. The differences in PM infiltration rates were likely due to the combined effects of several factors, including varying particle size, concentration, and chemistry. Subsequently, the local wildfires had different temporal air quality impacts than distant wildfire pollution in this case. Based on these findings, indoor air quality appears more conducive to protective action and policies than outdoor air quality because the built environment may serve to shield individuals from outdoor air. [ABSTRACT FROM AUTHOR]

Persistent cold air pools (PCAP), also referred to colloquially as inversions, are responsible for some of the greatest enhancements in air pollution in Utah’s Wasatch Front. PCAPs, which can last for a period of days or weeks, trap warm air beneath a layer of colder air, which results in the accumulation of particulates during the inversion. Fine particulate matter (PM2.5) sampling occurred in seven field sites across Salt Lake County (SLCo) during Wintertime (November–April). Concentrations of the organic mass of PM2.5 increased during inversion events (μinv = 4.0 μg/m3) when compared to the wintertime baseline (μbaseline = 3.5 μg/m3). However, organic mass enhancements during PCAPs were most pronounced at lowest-altitude field sites situated near potential PM2.5 sources. Four sources of organic carbon were identified, comprised of industrial, abrasive, wood burning, and onroad sources. During PCAP events, PM2.5 species profiles exhibited greater spatial heterogeneity, due to lower wind speeds and caps on vertical mixing (Coefficient of Determinationinv = 0.51, Coefficient of Determinationbaseline = 0.43). These results indicate both elevation and local source emissions may be of increased importance in understanding PM2.5 concentrations during PCAP events.

Inversions have been proposed to facilitate local adaptation, by linking together locally coadapted alleles at different loci. Prior work addressing this question theoretically has considered the spread of inversions in "continent-island" scenarios in which there is a unidirectional flow of maladapted migrants into the island population. In this setting, inversions capturing locally adaptive haplotypes are most likely to invade when selection is weak, because stronger local selection (i) more effectively purges maladaptive alleles and (ii) generates linkage disequilibrium between adaptive alleles, thus lessening the advantage of inversions. We show this finding only holds under limited conditions by studying the establishment of inversions in a more general two-deme model, which explicitly considers the dynamics of allele frequencies in both populations linked by bidirectional migration. In this model, the level of symmetry between demes can be varied from complete asymmetry (continent-island) to complete symmetry. For symmetric selection and migration, strong selection increases the allele frequency divergence between demes thereby increasing the frequency of maladaptive alleles in migrants, favoring inversions—the opposite of the pattern seen in the asymmetric continent-island scenario. We also account for the likelihood that a new inversion captures an adaptive haplotype in the first instance. When considering the combined process of capture and invasion in "continent island" and symmetric scenarios, relatively strong selection increases inversion establishment probability. Migration must also be low enough that the inversion is likely to capture an adaptive allele combination, but not so low as to eliminate the inversion's advantage. Overall, our analysis suggests that inversions are likely to harbor larger effect alleles that experience relatively strong selection. [ABSTRACT FROM AUTHOR]

Satellite retrievals of carbon monoxide (CO) are routinely assimilated in atmospheric chemistry models to improve air quality forecasts, produce reanalyzes and to estimate emissions. This study applies the quantile‐conserving ensemble filter framework, a novel assimilation algorithm that can deal with non‐Gaussian and modestly nonlinear distributions. Instead of assuming normal distributions like the Ensemble Adjustments Kalman Filter (EAKF), we now apply a bounded normal rank histogram (BNRH) distribution for the prior. The goal is to efficiently estimate bounded quantities such as CO atmospheric mixing ratios and emission fluxes while maintaining the good performance achieved by the EAKF. We contrast assimilating meteorological and MOPITT (Measurement of Pollution in the Troposphere) observations for May 2018. We evaluate the results with the fourth deployment of the NASA Atmospheric Tomography Mission (ATom‐4) airborne field campaign. We also compare simulations with CO tropospheric columns from the network for the detection of atmospheric composition change and surface in‐situ observations from NOAA carbon cycle greenhouse gases. While the differences remain small, the BNRH approach clearly works better than the EAKF in comparison to all observation data sets. Plain Language Summary: The MOPITT instrument on the NASA/Terra satellite can detect carbon monoxide (CO) pollution in the lower and mid‐tropospheric atmosphere but cannot accurately differentiate small changes in the altitude of pollution plumes. Such satellite observations are assimilated in numerical model predictions to improve the spatial and temporal distribution of CO in the atmosphere and to estimate emission fluxes. We present a novel method that does not require assumptions about the model and the observations, leading to a more efficient and accurate assimilation of the satellite observations. Key Points: A novel non Gaussian and nonlinear ensemble data assimilation (DA) framework is applied to MOPITT joint state/flux optimizationThe new method performs better than the Ensemble Adjustment Kalman Filter in comparison to independent observationsMOPITT observations indicate that CAMS‐GLOB‐ANT_v5.3 emission fluxes are underestimated across the mid‐latitudes in May 2018 [ABSTRACT FROM AUTHOR]

Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature of life on Earth. One evolutionary outcome of such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, adaptive tracking can lead to the long-term maintenance of functional polymorphism despite allele frequency change due to selection. Although adaptive tracking is likely a common process, we still have a limited understanding of aspects of its genetic architecture and its strength relative to other evolutionary forces such as drift. Drosophila melanogaster living in temperate regions evolve to track seasonal fluctuations and are an excellent system to tackle these gaps in knowledge. By sequencing orchard populations collected across multiple years, we characterized the genomic signal of seasonal demography and identified that the cosmopolitan inversion In(2L)t facilitates seasonal adaptive tracking and shows molecular footprints of selection. A meta-analysis of phenotypic studies shows that seasonal loci within In(2L)t are associated with behavior, life history, physiology, and morphological traits. We identify candidate loci and experimentally link them to phenotype. Our work contributes to our general understanding of fluctuating selection and highlights the evolutionary outcome and dynamics of contemporary selection on inversions. [ABSTRACT FROM AUTHOR]

Genome skimming (shallow whole‐genome sequencing) offers time‐ and cost‐efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter‐plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnSGGA – rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade. [ABSTRACT FROM AUTHOR]

High-quality genome assemblies across a range of nontraditional model organisms can accelerate the discovery of novel aspects of genome evolution. The Drosophila virilis group has several attributes that distinguish it from more highly studied species in the Drosophila genus, such as an unusual abundance of repetitive elements and extensive karyotype evolution, in addition to being an attractive model for speciation genetics. Here, we used long-read sequencing to assemble five genomes of three virilis group species and characterized sequence and structural divergence and repetitive DNA evolution. We find that our contiguous genome assemblies allow characterization of chromosomal arrangements with ease and can facilitate analysis of inversion breakpoints. We also leverage a small panel of resequenced strains to explore the genomic pattern of divergence and polymorphism in this species and show that known demographic histories largely predicts the extent of genome-wide segregating polymorphism. We further find that a neo-X chromosome in Drosophila americana displays X-like levels of nucleotide diversity. We also found that unusual repetitive elements were responsible for much of the divergence in genome composition among species. Helitron-derived tandem repeats tripled in abundance on the Y chromosome in D. americana compared to Drosophila novamexicana , accounting for most of the difference in repeat content between these sister species. Repeats with characteristics of both transposable elements and satellite DNAs expanded by 3-fold, mostly in euchromatin, in both D. americana and D. novamexicana compared to D. virilis. Our results represent a major advance in our understanding of genome biology in this emerging model clade. [ABSTRACT FROM AUTHOR]

This study quantifies the overturning circulation in the Arctic Ocean and associated heat transport (HT) and freshwater transport (FWT) from October 2004 to May 2010 based on hydrographic and current observations. Our main data source consists of 1165 moored instrument records in the four Arctic main gateways: Davis Strait, Fram Strait, Bering Strait, and the Barents Sea Opening. We employ a box inverse model to obtain mass and salt balanced velocity fields, which are then used to quantify the overturning circulation as well as HT and FWT. Atlantic Water is transformed into two different water masses in the Arctic Ocean at a rate of 4.3 Sv (1 Sv ≡ 106 m3 s−1). Combined with 0.7 Sv of Bering Strait inflow and 0.15 Sv of surface freshwater flux, 2.2 Sv flows back to the south through Davis Strait and western Fram Strait as the upper limb of the overturning circulation, and 2.9 Sv returns southward through Fram Strait as the lower limb of the overturning. The Arctic Ocean imports heat of 180 ± 57 TW (long-term mean ± standard deviation of monthly means) with a methodological uncertainty of 20 TW and exports FW of 156 ± 91 mSv with an uncertainty of 61 mSv over the 6 years with a potential offset of ∼30 mSv. The HT and FWT have large seasonalities ranging between 110 and 260 TW (maximum in winter) and between 40 and 260 mSv (maximum in winter), respectively. The obtained overturning circulation and associated HT and FWT presented here are vital information to better understand the northern extent of the Atlantic meridional overturning circulation. [ABSTRACT FROM AUTHOR]

Background: Compounding in German is a frequent and highly productive word formation strategy. Monolingual children begin to form compound words in regular language acquisition at around the age of two. There is individual evidence in the literature of early phases of non-target language production in the form of inversions, i.e., exchange of compound components. For bilingual language acquisition, pilot study results show that such inversions still occur at the age of seven to eight or after three to four years of exposure to German (Scherger & Kliemke, 2021). Method In the present study, inversions in the comprehension and production of neologistic compound nouns were investigated in 19 bilingual school-age children (n = 11 with German as L2 and n = 8 with 2L1 acquisition) in a quasi-experimental design using picture naming and word-picture matching tasks. These children were compared with two control groups of monolingual children: an age-matched group (n = 9, mean age = 7;2) and a group that was compared with the groups of bilingual children in terms of contact time with German (n = 7, mean age = 3;11). Results: There are differences between children with German as L2 and the age-matched control group of monolingual children and between children with L2 and monolingual children matched according to their length of exposure in the comprehension task. In addition, children with 2L1 show better comprehension performance than children with L2. Conclusion! Since composition is one of the most important word formation strategies in German, especially in the context of academic language, its comprehension and production should be monitored particularly in children with German as an L2 and - if necessary - promoted. Doing so, the resources for cross-linguistic comparisons and multilingual learning based on knowledge of the structures in the respective heritage language may be integrated positively. [ABSTRACT FROM AUTHOR]

Chromosome aberrations are an example of the mutation process that happens at the chromosome level of DNA packaging. The occurrence of inversions and complex translocations has not been studied well enough due to the complexity of their detection using the conventional methods of differential staining. It is well-known that ionizing radiation is one of the factors that increases the frequency of chromosomal rearrangements. The objective of this pilot research was to study the frequency of inversions involving telomere regions of the chromosomes and complex translocations in T-cells of 25 chronically exposed residents of the Southern Urals. Inversions were studied in the group of 12 exposed individuals (one man, 11 women, exposure doses ranging from 0.001 to 2.9 Gy) using the Q-FISH method. Complex translocations were analyzed in the group of 13 people (nine women, four men, exposure dose ranging from 0.5 to 3.1 Gy) with the help of M-FISH method. The groups did not overlap. As a result of this analysis, it has been revealed that complex translocations occur six times less frequently than simple ones (р < 0.001). Chromatid variants of inversions predominated as compared to chromosomal ones (9 : 0.17 per 100 cells, p < 0.001). No dependence of the studied parameters on the exposure dose to red bone marrow was noted. [ABSTRACT FROM AUTHOR]

On 13 April 2022, the Russian warship Moskva was hit by two Ukrainian Neptune anti-ship missiles in the Black Sea, leading to its demise. Before launching an anti-ship missile, a target must first be detected and positioned, for example, by an accompanying radar system. However, when the missiles hit the Moskva she was well beyond the normal radar horizon of any ground-based radar system, making the ship undetectable under normal circumstances. Using meteorological reanalysis data, we show that at the time of the missile launch the prevailing weather conditions allowed a ground-based radar to detect targets far beyond the normal radar horizon through anomalous propagation conditions. During such conditions, the atmospheric index of refraction decreases rapidly with height, making electromagnetic radiation bend downward to, partly or fully, compensate the curvature of the Earth. The results show that atmospheric conditions must be considered carefully, even during warfare, as their impact on radar wave propagation can be considerable. [ABSTRACT FROM AUTHOR]

Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach. [ABSTRACT FROM AUTHOR]

In this paper, we propose a q-analogue of the number of permutations i(n, k) of length n having k inversions known by Mahonian numbers. We investigate useful properties and some combinatorial interpretations by lattice paths/partitions and tilings. Furthermore, we give two constructive proofs of the strong q-log-concavity of the q-Mahonian numbers in k and n, respectively. In particular for q = 1 , we obtain two constructive proofs of the log-concavity of the Mahonian numbers in k and n, respectively. [ABSTRACT FROM AUTHOR]

The paper presents the results of studies of the content of particulate matter PM1–PM10 in the atmosphere of the western coast of Southern Baikal with high temporal resolution. It has been established that PM are emitted into the atmosphere of Southern Baikal from both anthropogenic and natural sources. In winter, the influence of thermal power facilities increases, as evidenced by synchronous increases in the concentrations of submicron aerosol PM1 and sulfur dioxide. In summer, remote forest fires make a significant contribution to atmospheric pollution with particulate matter. The relationship between the increase in the concentration of PM1 in the atmosphere in the region under study and mesometeorological features (temperature inversions and mesoscale transfer of plumes from large thermal power plants) has been revealed. Increases in PM1 concentrations in most cases occur during the night and morning hours, which is associated with a decrease in the thickness of the atmospheric boundary layer. [ABSTRACT FROM AUTHOR]

The impact of segmental duplications on human evolution and disease is only just starting to unfold, thanks to advancements in sequencing technologies that allow for their discovery and precise genotyping. The 15q11-q13 locus is a hotspot of recurrent copy number variation associated with Prader–Willi/Angelman syndromes, developmental delay, autism, and epilepsy and is mediated by complex segmental duplications, many of which arose recently during evolution. To gain insight into the instability of this region, we characterized its architecture in human and nonhuman primates, reconstructing the evolutionary history of five different inversions that rearranged the region in different species primarily by accumulation of segmental duplications. Comparative analysis of human and nonhuman primate duplication structures suggests a human-specific gain of directly oriented duplications in the regions flanking the GOLGA cores and HERC segmental duplications, representing potential genomic drivers for the human-specific expansions. The increasing complexity of segmental duplication organization over the course of evolution underlies its association with human susceptibility to recurrent disease-associated rearrangements. [ABSTRACT FROM AUTHOR]

Abstract Range expansions can lead to increased contact of divergent populations, thus increasing the potential of hybridization events. Whether viable hybrids are produced will most likely depend on the level of genomic divergence and associated genomic incompatibilities between the different entities as well as environmental conditions. By taking advantage of historical Baltic cod (Gadus morhua) otolith samples combined with genotyping and whole genome sequencing, we here investigate the genetic impact of the increased spawning stock biomass of the eastern Baltic cod stock in the mid 1980s. The eastern Baltic cod is genetically highly differentiated from the adjacent western Baltic cod and locally adapted to the brackish environmental conditions in the deeper Eastern basins of the Baltic Sea unsuitable for its marine counterparts. Our genotyping results show an increased proportion of eastern Baltic cod in western Baltic areas (Mecklenburg Bay and Arkona Basin)—indicative of a range expansion westwards—during the peak population abundance in the 1980s. Additionally, we detect high frequencies of potential hybrids (including F1, F2 and backcrosses), verified by whole genome sequencing data for a subset of individuals. Analysis of mitochondrial genomes further indicates directional gene flow from eastern Baltic cod males to western Baltic cod females. Our findings unravel that increased overlap in distribution can promote hybridization between highly divergent populations and that the hybrids can be viable and survive under specific and favourable environmental conditions. However, the observed hybridization had seemingly no long‐lasting impact on the continuous separation and genetic differentiation between the unique Baltic cod stocks.

Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating inversions suppress recombination and facilitate the maintenance of LD between locally adapted loci, they are also commonly found to be associated with adaptive divergence. However, it is unclear what fraction of an adaptive response can be attributed to inversions and alleles of large effect, and whether the loci within an inversion could still drive adaptation in the absence of its recombination-suppressing effect. Here, we use genome-wide association studies to explore patterns of local adaptation in three species of sunflower: Helianthus annuus, Helianthus argophyllus, and Helianthus petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome harbouring an inversion in one species. This shows that while inversions may facilitate local adaptation, at least some of the loci can still harbour mutations that make substantial contributions without the benefit of recombination suppression in species lacking a segregating inversion. While a large number of genomic regions show evidence of repeated adaptation, most of the strongest signatures of association still tend to be species-specific, indicating substantial genotypic redundancy for local adaptation in these species.

Mitochondrial gene order has contributed to the elucidation of evolutionary relationships in several animal groups. It generally has found its application as a phylogenetic marker for deep nodes. Yet, in Orthoptera limited research has been performed on the gene order, although the group represents one of the oldest insect orders. We performed a comprehensive study on mitochondrial genome rearrangements (MTRs) within Orthoptera in the context of mitogenomic sequence‐based phylogeny. We used 280 published mitogenome sequences from 256 species, including three outgroup species, to reconstruct a molecular phylogeny. Using a heuristic approach, we assigned MTR scenarios to the edges of the phylogenetic tree and reconstructed ancestral gene orders to identify possible synapomorphies in Orthoptera. We found all types of MTRs in our dataset: inversions, transpositions, inverse transpositions, and tandem‐duplication/random loss events (TDRL). Most of the suggested MTRs were in single and unrelated species. Out of five MTRs which were unique in subgroups of Orthoptera, we suggest four of them to be synapomorphies; those were in the infraorder Acrididea, in the tribe Holochlorini, in the subfamily Pseudophyllinae, and in the two families Phalangopsidae and Gryllidae or their common ancestor (leading to the relationship ((Phalangopsidae + Gryllidae) + Trigonidiidae)). However, similar MTRs have been found in distant insect lineages. Our findings suggest convergent evolution of specific mitochondrial gene orders in several species, deviant from the evolution of the mitogenome DNA sequence. As most MTRs were detected at terminal nodes, a phylogenetic inference of deeper nodes based on MTRs is not supported. Hence, the marker does not seem to aid resolving the phylogeny of Orthoptera, but adds further evidence for the complex evolution of the whole group, especially at the genetic and genomic levels. The results indicate a high demand for more research on patterns and underlying mechanisms of MTR events in Orthoptera. [ABSTRACT FROM AUTHOR]

Abstract Background The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti. Results In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms. Conclusion These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.

Range expansions can lead to increased contact of divergent populations, thus increasing the potential of hybridization events. Whether viable hybrids are produced will most likely depend on the level of genomic divergence and associated genomic incompatibilities between the different entities as well as environmental conditions. By taking advantage of historical Baltic cod (Gadus morhua) otolith samples combined with genotyping and whole genome sequencing, we here investigate the genetic impact of the increased spawning stock biomass of the eastern Baltic cod stock in the mid 1980s. The eastern Baltic cod is genetically highly differentiated from the adjacent western Baltic cod and locally adapted to the brackish environmental conditions in the deeper Eastern basins of the Baltic Sea unsuitable for its marine counterparts. Our genotyping results show an increased proportion of eastern Baltic cod in western Baltic areas (Mecklenburg Bay and Arkona Basin)—indicative of a range expansion westwards—during the peak population abundance in the 1980s. Additionally, we detect high frequencies of potential hybrids (including F1, F2 and backcrosses), verified by whole genome sequencing data for a subset of individuals. Analysis of mitochondrial genomes further indicates directional gene flow from eastern Baltic cod males to western Baltic cod females. Our findings unravel that increased overlap in distribution can promote hybridization between highly divergent populations and that the hybrids can be viable and survive under specific and favourable environmental conditions. However, the observed hybridization had seemingly no long‐lasting impact on the continuous separation and genetic differentiation between the unique Baltic cod stocks. [ABSTRACT FROM AUTHOR]

Background: Information on common markers of metabolic resistance in malaria vectors from countries sharing similar eco-climatic characteristics can facilitate coordination of malaria control. Here, we characterized populations of the major malaria vector Anopheles coluzzii from Sahel region, spanning four sub-Saharan African countries: Nigeria, Niger, Chad and Cameroon. Results: Genome-wide transcriptional analysis identified major genes previously implicated in pyrethroid and/or cross-resistance to other insecticides, overexpressed across the Sahel, including CYP450s, glutathione S-transferases, carboxylesterases and cuticular proteins. Several, well-known markers of insecticide resistance were found in high frequencies—including in the voltage-gated sodium channel (V402L, I940T, L995F, I1527T and N1570Y), the acetylcholinesterase-1 gene (G280S) and the CYP4J5-L43F (which is fixed). High frequencies of the epidemiologically important chromosomal inversion polymorphisms, 2La, 2Rb and 2Rc, were observed (~80% for 2Rb and 2Rc). The 2La alternative arrangement is fixed across the Sahel. Low frequencies of these inversions (<10%) were observed in the fully insecticide susceptible laboratory colony of An. coluzzii (Ngoussou). Several of the most commonly overexpressed metabolic resistance genes sit in these three inversions. Two commonly overexpressed genes, GSTe2 and CYP6Z2, were functionally validated. Transgenic Drosophila melanogaster flies expressing GSTe2 exhibited extremely high DDT and permethrin resistance (mortalities <10% in 24h). Serial deletion of the 5′ intergenic region, to identify putative nucleotide(s) associated with GSTe2 overexpression, revealed that simultaneous insertion of adenine nucleotide and a transition (T->C), between Forkhead box L1 and c-EST putative binding sites, were responsible for the high overexpression of GSTe2 in the resistant mosquitoes. Transgenic flies expressing CYP6Z2 exhibited marginal resistance towards 3-phenoxybenzylalcohol (a primary product of pyrethroid hydrolysis by carboxylesterases) and a type II pyrethroid, α-cypermethrin. However, significantly higher mortalities were observed in CYP6Z2 transgenic flies compared with controls, on exposure to the neonicotinoid, clothianidin. This suggests a possible bioactivation of clothianidin into a toxic intermediate, which may make it an ideal insecticide against populations of An. coluzzii overexpressing this P450. Conclusions: These findings will facilitate regional collaborations within the Sahel region and refine implementation strategies through re-focusing interventions, improving evidence-based, cross-border policies towards local and regional malaria pre-elimination. [ABSTRACT FROM AUTHOR]

Reconstructing the history of polar temperature from ice core water isotope (δ18O) calibration has remained a challenge in paleoclimate research, because of our incomplete understanding of various temperature--δ18O relationships. This paper resolves this classical problem in a new framework called the unified slope equations (USE), which illustrates the general relations among spatial and temporal δ18O--surface temperature slopes. The USE is applied to the Antarctica temperature change during the last deglaciation in model simulations and observations. It is shown that the comparable Antarcticamean spatial slope with deglacial temporal slope in δ18O--surface temperature reconstruction is caused, accidentally, by the compensation responses between the δ18O--inversion layer temperature relation and the inversion layer temperature itself. Furthermore, in light of the USE, we propose that the present seasonal slope of δ18O--inversion layer temperature is an optimal paleothermometer that is more accurate and robust than the spatial slope. This optimal slope suggests the possibility of reconstructing past Antarctic temperature changes using present and future instrumental observations. [ABSTRACT FROM AUTHOR]

This paper was inspired by Donald Knuth’s celebrated explanation of the remarkable connection between q-binomial coefficients and integer partitions. In the spirit of Knuth’s proof, we offer a new proof of the well-known result that a certain q-analogue of multinomial coefficients furnishes a q-counting of the set of permutations of an associated multiset of positive integers, according to the number of inversions in such arrangements. Our proof uses the fact that such q-multinomial coefficients enumerate certain classes of chains of subspaces of a finite dimensional vector space over a finite field of cardinality q. Additionally, we investigate the function that counts the number of permutations of a multiset having a fixed number of inversions. [ABSTRACT FROM AUTHOR]

Plasticity of Pseudomonas aeruginosa chromosomes is mainly driven by an extended accessory genome that is shaped by insertion and deletion events. Further modification of the genome composition can be induced by chromosomal inversion events which lead to relocation of genes in the affected genomic DNA segments, modify the otherwise highly conserved core genome synteny and could even alter the location of the replication terminus. Although the genome of the first sequenced strain, PAO1, displayed such a large genomic inversion, knowledge on such recombination events in the P. aeruginosa population is limited. Several large inversions had been discovered in the late 1990s in cystic fibrosis isolates of the major clonal lineage C by physical genome mapping, and subsequent work on these examples led to the characterization of the DNA at the recombination breakpoints and a presumed recombination mechanism. Since then, the topic was barely addressed in spite of the compilation of thousands of P. aeruginosa genome sequences that are deposited in databases. Due to the use of second-generation sequencing, genome contig assembly had usually followed synteny blueprints provided by the existing reference genome sequences. Inversion detection was not feasible by these approaches, as the respective read lengths did not allow reliable resolution of sequence repeats that are typically found at the borders of inverted segments. In this study, we applied PacBio and MinION long-read sequencing to isolates of the mentioned clone C collection. Confirmation of inversions predicted from the physical mapping data demonstrated that unbiased sequence assembly of such read datasets allows the detection of genomic inversions and the resolution of the recombination breakpoint regions. Additional long-read sequencing of representatives of the other major clonal lineage, PA14, revealed large inversions in several isolates, from cystic fibrosis origin as well as from other sources. These findings indicated that inversion events are not restricted to strains from chronic infection background, but could be widespread in the P. aeruginosa population and contribute to genome plasticity. Moreover, the monitored examples emphasized the role of small mobile DNA units, such as IS elements or transposons, and accessory DNA elements in the inversion-related recombination processes. [ABSTRACT FROM AUTHOR]

Background: The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti. Results: In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms. Conclusion: These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily. [ABSTRACT FROM AUTHOR]

Supergenes are clusters of linked loci that control complex phenotypes, such as alternative forms of social organization in ants. Explaining the long‐term maintenance of supergenes is challenging, particularly when the derived haplotype lacks homozygous lethality and causes gene drive. In the Alpine silver ant, Formica selysi, a large and ancient social supergene with two haplotypes, M and P, controls colony social organization. Single‐queen colonies only contain MM females, while multiqueen colonies contain MP and PP females. The derived P haplotype, found only in multiqueen colonies, selfishly enhances its transmission through maternal effect killing, which could have led to its fixation. A population genetic model showed that a stable social polymorphism can only be maintained under a narrow set of conditions, which includes partial assortative mating by social form (which is known to occur in the wild), and low fitness of PP queens. With a combination of field and laboratory experiments, we show that the P haplotype has deleterious effects on female fitness. The survival rate of PP queens and workers was around half that of other genotypes. Moreover, P‐carrying queens had lower fertility and fecundity compared to other queens. We discuss how cryptic lethal effects of the P haplotype help stabilize this ancient polymorphism. [ABSTRACT FROM AUTHOR]

The level of genetic variability in the population of malaria mosquito Anopheles messeae Fall. from the settlement of Kolarovo (Tomsk oblast) in 1974 through 2020 was assessed based on cytogenetic analysis of polytene chromosomes. Analysis of the inversion polymorphism dynamics in the malaria mosquito Anopheles messeae Fall. between 1974 and 2020 with respect to the frequencies of inversion variants of chromosomes and gametes in the population from the settlement of Kolarovo showed the replacement of "northern" variants with "southern" variants during 1990s and stabilization of these changes until 2020. A correlation between the chromosomale inversion frequency distributions in 1972 through 2020 with annual temperature, which includes semiannual average temperature in April–September and that in October–March was found. The results obtained made it possible to shed light on the nature of long-term dynamic processes associated with climate warming. Spatiotemporal stationarity (dynamic stability) of adaptive inversion polymorphism is evidence of the absence of tendencies to speciation. [ABSTRACT FROM AUTHOR]

Plasticity of Pseudomonas aeruginosa chromosomes is mainly driven by an extended accessory genome that is shaped by insertion and deletion events. Further modification of the genome composition can be induced by chromosomal inversion events which lead to relocation of genes in the affected genomic DNA segments, modify the otherwise highly conserved core genome synteny and could even alter the location of the replication terminus. Although the genome of the first sequenced strain, PAO1, displayed such a large genomic inversion, knowledge on such recombination events in the P. aeruginosa population is limited. Several large inversions had been discovered in the late 1990s in cystic fibrosis isolates of the major clonal lineage C by physical genome mapping, and subsequent work on these examples led to the characterization of the DNA at the recombination breakpoints and a presumed recombination mechanism. Since then, the topic was barely addressed in spite of the compilation of thousands of P. aeruginosa genome sequences that are deposited in databases. Due to the use of second-generation sequencing, genome contig assembly had usually followed synteny blueprints provided by the existing reference genome sequences. Inversion detection was not feasible by these approaches, as the respective read lengths did not allow reliable resolution of sequence repeats that are typically found at the borders of inverted segments. In this study, we applied PacBio and MinION long-read sequencing to isolates of the mentioned clone C collection. Confirmation of inversions predicted from the physical mapping data demonstrated that unbiased sequence assembly of such read datasets allows the detection of genomic inversions and the resolution of the recombination breakpoint regions. Additional long-read sequencing of representatives of the other major clonal lineage, PA14, revealed large inversions in several isolates, from cystic fibrosis origin as well as from other sources. These findings indicated that inversion events are not restricted to strains from chronic infection background, but could be widespread in the P. aeruginosa population and contribute to genome plasticity. Moreover, the monitored examples emphasized the role of small mobile DNA units, such as IS elements or transposons, and accessory DNA elements in the inversion-related recombination processes.

The genomic processes enabling speciation and species coexistence in sympatry are still largely unknown. Here we describe the whole-genome sequencing and assembly of 3 closely related species from the butterfly genus Morpho : Morpho achilles (Linnaeus, 1758), Morpho helenor (Cramer, 1776), and Morpho deidamia (Höbner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest. They live in sympatry in a wide range of their geographical distribution and display parallel diversification of dorsal wing color pattern, suggesting local mimicry. By sequencing, assembling, and annotating their genomes, we aim at uncovering prezygotic barriers preventing gene flow between these sympatric species. We found a genome size of  480 Mb for the 3 species and a chromosomal number ranging from 2 n = 54 for M. deidamia to 2 n = 56 for M. achilles and M. helenor. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover in each species at least 12,000 protein-coding genes and to discover duplications of genes potentially involved in prezygotic isolation like genes controlling color discrimination (L-opsin). Altogether, the assembly and the annotation of these 3 new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishing Morpho butterflies as a new eco-evolutionary model. [ABSTRACT FROM AUTHOR]

Background: Wildfire smoke may dampen fire severity through effects on weather and the persistence of atmospheric inversions, but empirical work on the link between smoke and fire severity is scarce. Aims: To assess the influence of daily smoke characteristics on wildfire severity in complex terrain. Methods: A customised smoke detection algorithm based on MODIS imagery was integrated into statistical models of fire severity across 106 wildfires between 2002 and 2018 in the Klamath Mountains, USA. Key results: Smoke characteristics improved predictions of fire severity in non-reburn areas but not in reburns. Maximum daily smoke cover interacted with elevation, showing a strong dampening effect of high smoke cover on fire severity at low elevations consistent with prior work and a weaker amplifying effect on fire severity at middle elevations with low smoke cover. Conclusions: Feedbacks between smoke and atmospheric inversions dampen fire severity in valleys but may amplify fire severity at middle elevations above inversion layers. Implications: The influence of smoke on fire severity may strengthen in the future as large fires and extreme fire weather become more common, yet may also weaken as reburns become more prevalent. Smoke cover over valleys may reduce wildfire severity by affecting weather. We quantified the effect of smoke cover on fire severity for 106 fires in the Klamath Mountains, USA. Smoke reduced fire severity at low elevations as expected, yet side slopes just above smoke plumes experienced more severe fire effects. [ABSTRACT FROM AUTHOR]

Every machine needs a suitable mechanism to impart motion and transmit power. Hence, it becomes necessary to study the various aspects of a mechanism in terms of synthesis and structural analysis of kinematic chain. In past few decades, a lot of researchers had put their efforts in identifying distinct kinematic chain with a given degree of freedom, tested them for isomorphism and identified the distinct number of mechanisms (inversions) that can be obtained by fixing a link in a particular kinematic chain. All those methods are solely dependent on the study and analysis of two basic factors of any kinematic chain i.e links and joints. However, the presence of loops and its effect in driving a mechanism is somehow neglected. The complete analysis of the structure of a kinematic chain depends on the study of all the three factors i.e. links, joints and loops. This paper approaches with a new method based on matrix composition to identify the accurate number of distinct mechanisms which can be obtained in a particular kinematic chain. The method adopted is quite simple and reliable as it considers the presence of loop among the kinematic chain along with the links and the joints hence uses link-joint-loop adjacency. [ABSTRACT FROM AUTHOR]

Polymorphic inversions are ubiquitous in humans and they have been linked to both adaptation and disease. Following their discovery in Drosophila more than a century ago, inversions have proved to be more elusive than other structural variants. A wide variety of methods for the detection and genotyping of inversions have recently been developed: multiple techniques based on selective amplification by PCR, short‐ and long‐read sequencing approaches, principal component analysis of small variant haplotypes, template strand sequencing, optical mapping, and various genome assembly methods. Many methods apply complex wet lab protocols or increasingly refined bioinformatic analyses. This review is an attempt to provide a practical summary and comparison of the methods that are in current use, with a focus on metrics such as the maximum size of segmental duplications at inversion breakpoints that each method can tolerate, the size range of inversions that they recover, their throughput, and whether the locations of putative inversions must be known beforehand. [ABSTRACT FROM AUTHOR]

В работе используется маломодовая модель αΩ-динамо для моделирования режимов генерации магнитного поля при незначительных изменениях поля скорости вязкой жидкости. В рамках этой модели интенсивность α-эффекта регулируется процессом с памятью, который вводится в магнитогидродинамическую систему (МГД-система) как аддитивная поправка в виде функционала Z(t) от энергии поля. В качестве ядра J(t) функционала Z(t) выбрана функция, определяющая затухающие колебания с варьируемым коэффициентом затухания и постоянной частотой затухания, принятой равной единице. Исследование поведения магнитного поля проводится на больших временных масштабах, поэтому для численных расчётов используется перемасштабированная и обезразмеренная МГД-система, где в качестве единицы времени принято время диссипации магнитного поля (104 лет). Управляющими параметрами системы выступают число Рейнольдса и амплитуда α-эффекта, в которых заложена информация о крупномасштабном и турбулентном генераторах. Результаты численного моделирования режимов генерации магнитного поля при различных значениях коэффициента затухания и постоянной частоте затухания отражены на фазовой плоскости управляющих параметров. В работе исследуется вопрос о динамике изменения картины на фазовой плоскости в зависимости от значения коэффициента затухания. Проводится сравнение с результатами, полученными ранее при постоянной интенсивности α-эффекта и при изменении интенсивности α — эффекта, которое определялось функционалом Z(t) с показательным ядром и аналогичными значениями коэффициента затухания.

When a party or candidate loses the popular vote but still wins the election, do voters view the winner as legitimate? This scenario, known as an electoral inversion, describes the winners of two of the last six presidential elections in the United States. We report results from two experiments testing the effect of inversions on democratic legitimacy in the US context. Our results indicate that inversions significantly decrease the perceived legitimacy of winning candidates. Strikingly, this effect does not vary with the margin by which the winner loses the popular vote, nor by whether the candidate benefiting from the inversion is a co-partisan. The effect is driven by Democrats, who punish inversions regardless of candidate partisanship; few effects are observed among Republicans. These results suggest that the experience of inversions increases sensitivity to such outcomes among supporters of the losing party. [ABSTRACT FROM AUTHOR]

Inversions, i.e. a change in orientation of a segment of DNA, are a recognized cause of human diseases which remain overlooked due to their balanced nature. Inversions can have severe or more subtle impacts on gene expression. We describe two families that exemplify these aspects and underline the need for inversion detection in routine diagnosis. The first family (F1) displayed a sibship with two constitutional mismatch repair deficiency patients and a family history of colon cancer in the paternal branch. The second family (F2) displayed a severe history of Lynch syndrome. These families were analyzed using a whole gene panel (WGP) strategy i.e. including colon cancer genes with their intronic and flanking genomic regions. In F1, a PMS2 inversion encompassing the promoter region to intron 1 and a PMS2 splice variant were found in the maternal and paternal branch, respectively. In F2, we described the first MSH6 inversion, involving the 5′ part of MSH6 and the 3′ part of the nearby gene ANXA4. Inversion detection mandates genomic sequencing, but makes a valuable contribution to the diagnostic rate. WGP is an attractive strategy as it maximizes the detection power on validated genes and keeps sufficient depth to detect de novo events. [ABSTRACT FROM AUTHOR]

Due to translocation heterozygosity for all chromosomes in the cell complement, the oyster plant (Tradescantia spathacea) forms a complete meiotic ring. It also shows Rabl-arrangement at interphase, featured by polar centromere clustering. We demonstrate that the pericentromeric regions of the oyster plant are homogenized in concert by three subtelomeric sequences: 45S rDNA, (TTTAGGG)n motif, and TSrepI repeat. The Rabl-based clustering of pericentromeric regions may have been an excellent device to combine the subtelomere-pericentromere sequence migration (via inversions) with the pericentromere-pericentromere DNA movement (via whole arm translocations) that altogether led to the concerted homogenization of all the pericentromeric domains by the subtelomeric sequences. We also show that the repetitive sequence landscape of interstitial chromosome regions contains many loci consisting of Arabidopsis-type telomeric sequence or of TSrepI repeat, and it is extensively heterozygous. However, the sequence arrangement on some chromosomal arms suggest segmental inversions that are fully or partially homozygous, a fact that could be explained if the inversions started to create linkages already in a bivalent-forming ancestor. Remarkably, the subterminal TSrepI loci reside exclusively on the longer arms that could be due to sharing sequences between similarly-sized chromosomal arms in the interphase nucleus. Altogether, our study spotlights the supergene system of the oyster plant as an excellent model to link complex chromosome rearrangements, evolution of repetitive sequences, and nuclear architecture. [ABSTRACT FROM AUTHOR]