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Prayer animal release (PAR)—a traditional "compassion‐based" religious practice of releasing captive animals into the wild to improve the karma of the releaser—has been regarded as a major anthropogenic pathway facilitating species invasions worldwide. However, comprehensive, quantitative assessments of PAR‐related invasion risks, crucial for the development of mitigation strategies, are lacking. To address this knowledge gap, we conducted a literature review of the prevalence of PAR events and examined the overlap between PAR intensity across China and habitat suitability for non‐native vertebrates released in these events. Our results revealed that 63% of the areas with high PAR intensity in China were also suitable for non‐native vertebrate establishment, a degree of overlap that was greater than expected by chance. In addition, field surveys in China detected higher richness of non‐native fishes at PAR sites than at non‐PAR sites. These findings imply an overall high risk of biological invasions associated with PARs. We recommend interdisciplinary cooperation among scientists, religious groups, and government agencies to effectively manage PARs and reduce the associated bioinvasion risk. [ABSTRACT FROM AUTHOR]

Background: The common carp (Cyprinus carpio) might best represent the domesticated allopolyploid animals. Although subgenome divergence which is well-known to be a key to allopolyploid domestication has been comprehensively characterized in common carps, the link between genetic architecture underlying agronomic traits and subgenome divergence is unknown in the selective breeding of common carps globally. Results: We utilized a comprehensive SNP dataset in 13 representative common carp strains worldwide to detect genome-wide genetic variations associated with scale reduction, vibrant skin color, and high growth rate in common carp domestication. We identified numerous novel candidate genes underlie the three agronomically most desirable traits in domesticated common carps, providing potential molecular targets for future genetic improvement in the selective breeding of common carps. We found that independently selective breeding of the same agronomic trait (e.g., fast growing) in common carp domestication could result from completely different genetic variations, indicating the potential advantage of allopolyploid in domestication. We observed that candidate genes associated with scale reduction, vibrant skin color, and/or high growth rate are repeatedly enriched in the immune system, suggesting that domestication of common carps was often accompanied by the disease resistance improvement. Conclusions: In common carp domestication, asymmetric subgenome selection is prevalent, while parallel subgenome selection occurs in selective breeding of common carps. This observation is not due to asymmetric gene retention/loss between subgenomes but might be better explained by reduced pleiotropy through transposable element-mediated expression divergence between ohnologs. Our results demonstrate that domestication benefits from polyploidy not only in plants but also in animals. [ABSTRACT FROM AUTHOR]

In this article, an efficient multi-objective optimization strategy for the Halbach array permanent magnet synchronous machine (PMSM) is developed by taking into consideration the nonlinear B-H behavior of soft magnetic materials. Based on the harmonic modeling (HM) technology, the electromagnetic performances (EPs) of the Halbach array PMSM can be computed. To specifically model the local magnetic saturation, the stator teeth are separated into several annular layers, and each tooth is further divided into several regions along the tangential direction. Then, the parameters of the Halbach array PMSM are optimized utilizing combined nonlinear semi-analytical model (SAM) and non-dominated sorting genetic algorithm II (NSGA-II). To validate the effectiveness and accuracy of the developed optimization scheme, a Halbach array prototype is then manufactured in accordance with the optimization results. The multi-objective rapid optimization strategy developed in this article, which includes but is not limited to Halbach array permanent magnet (PM) machines, serves as a reference for the design and optimization of various PM machines. [ABSTRACT FROM AUTHOR]

The uplift of the Tibetan Plateau significantly altered the geomorphology and climate of the Euroasia by creating large mountains and rivers. Fishes are more likely to be affected relative to other organisms, as they are largely restricted to river systems. Faced with the rapidly flowing water in the Tibetan Plateau, a group of catfish has evolved greatly enlarged pectoral fins with more numbers of fin-rays to form an adhesive apparatus. However, the genetic basis of these adaptations in Tibetan catfishes remains elusive. In this study, we performed comparative genomic analyses based on the chromosome-level genome of Glyptosternum maculatum in family Sisoridae and detected some proteins with conspicuously high evolutionary rates in particular in genes involved in skeleton development, energy metabolism, and hypoxia response. We found that the hoxd12a gene evolved faster and a loss-of-function assay of hoxd12a supports a potential role for this gene in shaping the enlarged fins of these Tibetan catfishes. Other genes with amino acid replacements and signatures of positive selection included proteins involved in low temperature (TRMU) and hypoxia (VHL) responses. Functional assays reveal that the G. maculatumTRMU allele generates more mitochondrial ATP than the ancestral allele found in low-altitude fishes. Functional assays of VHL alleles suggest that the G. maculatum allele has lower transactivation activity than the low-altitude forms. These findings provide a window into the genomic underpinnings of physiological adaptations that permit G. maculatum to survive in the harsh environment of the Tibetan Himalayas that mirror those that are convergently found in other vertebrates such as humans. [ABSTRACT FROM AUTHOR]

New mutations and standing genetic variations contribute significantly to repeated phenotypic evolution in sticklebacks. However, less is known about the role of introgression in this process. We analyzed taxonomically and geographically comprehensive genomic data from Pungitius sticklebacks to decipher the extent of introgression and its consequences for the diversification of this genus. Our results demonstrate that introgression is more prevalent than suggested by earlier studies. Although gene flow was generally bidirectional, it was often asymmetric and left unequal genomic signatures in hybridizing species, which might, at least partly, be due to biased hybridization and/or population size differences. In several cases, introgression of variants from one species to another was accompanied by transitions of pelvic and/or lateral plate structures—important diagnostic traits in Pungitius systematics—and frequently left signatures of adaptation in the core gene regulatory networks of armor trait development. This finding suggests that introgression has been an important source of genetic variation and enabled phenotypic convergence among Pungitius sticklebacks. The results highlight the importance of introgression of genetic variation as a source of adaptive variation underlying key ecological and taxonomic traits. Taken together, our study indicates that introgression-driven convergence likely explains the long-standing challenges in resolving the taxonomy and systematics of this small but phenotypically highly diverse group of fish. [ABSTRACT FROM AUTHOR]

The extraordinarily high species richness makes global biodiversity hotspots the top priorities for conservation planning and management, and natural laboratories for biological studies. Given the current era of rapid biodiversity loss, there is an urgent need to understand the mechanisms driving the biodiversity dynamics in biodiversity hotspots because these results could guide make conservation actions to protect species under threat from rapid environmental changes and extensive human impacts. Without considering the effects of climate change, the potential distribution area for each species increases on average by 72.5% (SD = 8%) in the scenario of potential regeneration, while climate change decreases the area of the potential occurrence of 252 species, which may suffer a mean reduction of 74.4% (SD = 9.3%) in their current potential distribution areas. [Extracted from the article]

Aim: Intraspecific genetic variation is a key component of biodiversity, with higher diversity indicating greater resilience and population substructuring suggesting unique evolutionary histories. Comparative approaches, in which intraspecific genetic variation is assessed across multiple species, are powerful tools to identify evolutionary hotspots, but are still rarely applied at spatial scales relevant to conservation planning. Here, we use comparative phylogeography to understand patterns and potential drivers of genetic variation within a biodiversity and ocean warming hotspot. Location: The South African coastline, Indian/Atlantic Oceans. Methods: A literature search was conducted to obtain mitochondrial DNA cytochrome oxidase c subunit I and cytochrome b sequence data for 17 marine fish and invertebrate species. From these data, we compared averages of haplotype and nucleotide diversity, and within‐region ΦST between four biogeographic provinces in the region. Mixed linear models tested whether environmental variability, habitat preference, or geographic location significantly influence genetic variation. Results: Average diversity values differed between haplotype and nucleotide diversity, but both broadly displayed highest diversity levels within the South‐West bioregion, which is also a region of high levels of within‐region ΦST. Range in sea surface temperatures (SSTs) was the only significant fixed‐effect term in the haplotype diversity mixed linear models. Mean SST, stability in SSTs since the Mid‐Holocene and position within the species' geographic distribution all had no significant effect on genetic variation. Main conclusions: Along this coastline characterized by high environmental heterogeneity, we find that variation in temperature is a prominent source of intraspecific variation. Genetic diversity differs between bioregions, but does not display higher levels within the core of each species' range when assessed across multiple species. With elevated levels of genetic diversity, the South‐West region of the South African coast is highlighted as a conservation priority area, representing both high genetic diversity and differentiation across taxa. [ABSTRACT FROM AUTHOR]

Aim: To assess the pattern of biotic regions (BR) and their boundaries, to detect chorotypes and to relate these patterns to key environmental factors. Location: Eastern Atlantic Ocean. Time period: Recent. Taxon studied: Bivalvia. Methods: Distributions were scored for 595 species. Operational geographical units are classified hierarchically using Baroni‐Urbani & Buser similarity index, clusters were assessed for statistical significance with the 'RMacoqui 1.0' software using G tests of independence, and chorotypes were inferred likewise from similarity between species distributions. Results: Three strong biotic boundaries delimit four BR: (1) European Atlantic and Mediterranean; (2) West African, from western Sahara to southern Angola; (3) Baia dos Tigres/Namibia; and (4) Saint Helena/Ascension. The West African BR is subdivided by two weak boundaries into three subordinate BR: the tropical region proper, the north‐western African transition zone and the cluster (southern Angola/São Tomé/Cape Verde Islands). Of the 429 species present in West Africa, 261 (60.7%) are endemic, and 19 genera (7.2%) are endemic. Sixteen chorotypes were identified; the European BR is correlated with chorotypes C5 (149 species mostly European and Mediterranean) and C3 (38 species mostly in northern Europe), whereas the West African BR is mainly characterized by chorotype C6 (221 species). Some discontinuous distribution patterns of tropical West African species were identified as chorotypes, but subordinate to chorotype C6. The West African BR is mainly characterized by sea surface temperature and chlorophyll; characterization without the islands also involved the extensive sandy coast. The north‐western African transition region is characterized by an arid climate and few rivers and influenced by seasonal upwelling. The cluster of southern Angola, Sao Tomé and Cape Verdes contrasts with the remainder of West Africa in having a predominantly rocky shore. Main conclusions: The present analyses provide an objective regionalization based on species occurrences, which supports the traditional recognition of West Africa as a major biotic region with a high level of endemism. Attention is called on that the unique endemic component is insufficiently represented in current marine protected areas. [ABSTRACT FROM AUTHOR]

Aim: Understanding the phylogeography of a species complex can provide important insights into its evolutionary history. However, phylogeographic inference often faces the dilemma of regionally inadequate sampling. Pungitius sticklebacks are a case in point: although the highest species diversity is found in Northeast Asia, their phylogeography in this region is still poorly understood. Location: Northeast Asia. Methods: With the aid of whole‐genome resequencing data, we investigated the phylogeography of Northeast Asian Pungitius sticklebacks, with newly sampled 83 worldwide Pungitius individuals from 11 locations including eight Chinese locations reported to host only P. sinensis. Results: We discovered that three of the eight Chinese locations hosted populations of P. kaibarae and P. bussei, species new to the fauna of China. Phylogeographic analyses further clarified the sequence and timing of colonization of Northeast Asia by different Pungitius species, shedding new light on their origins and current distribution ranges. Colonization of inland Northeast Asia by Pungitius sticklebacks occurred in multiple waves, and the widespread P. sinensis expanded its range relatively late in the Pleistocene. Main conclusions: This study complements our understanding of the phylogeography of Pungitius sticklebacks by extending sampling to cover an area that comprises nearly half of the known distribution area of this genus in Northeast Asia. The discovery of three Pungitus species from China is of particular interest, as translocations to support locally declining populations have occurred under the assumption that all sticklebacks in China—except the endangered P. stenurus—are P. sinensis, raising conservation concerns associated with unintentional translocations and possible admixture. [ABSTRACT FROM AUTHOR]

In hydrogen recirculation side channel pumps, the motor rotor is exposed to a high-pressure mixture of steam and hydrogen, which makes hydrogen embrittlement occur in permanent magnets (PMs). A protective coating is necessary for the PMs in high-pressure hydrogen. However, in the process of sleeve interference installation, the protective coating of the PMs is easily damaged. This paper proposes two surface-mounted insert permanent magnet (SIPM) synchronous motor topologies, SIPM1 and SIPM2, in which the retaining sleeves can be eliminated and the PM protective coating is safe in the assembling process. A dovetail PM and rotor core structure is used to protect the PM with higher rotor strength without retaining the sleeve. The electromagnetic performance of the motors with different rotors, including airgap flux density, output torque, torque ripple, and energy efficiency is compared and optimized. It is concluded that the output torque of the SIPM motor can be promoted by 22.4% and torque ripple can be reduced by 2.9%, while the PM volume remains the same as that of the conventional SPM motor. At the same time, the SIPM motor can have lower harmonic contents of back electromotive force (EMF) and rotor loss compared to the SPM motor with a retaining sleeve. Furthermore, the stress of the PM is analyzed under conditions of PM glue action and failure. The proposed SIPM2 has the ability to operate safely at high-speed and high-temperature operating conditions when the PM glue fails. [ABSTRACT FROM AUTHOR]

In this article, we propose a novel nonlinear semianalytical model (AM) for the magnetic field calculation of electric machines. The nonlinear properties and local saturation effect of the iron part are taken into consideration in Cartesian coordinates, which is the main contribution of the proposed model. Thus, high accuracy of electromagnetic field results can be obtained with the low computational time cost. The model is developed based on the harmonic modeling technique by solving Maxwell's equations. The detailed theoretical derivations, which use the complex Fourier series and the Cauchy product, are presented. To verify the proposed model, an axial flux permanent-magnet (PM) machine is selected to be investigated. Both finite-element model and experimental results agree well with that of the proposed model. Moreover, the nonlinear AM has potential application for other types of PM electrical motor in Cartesian coordinates, such as flat PM linear machines. [ABSTRACT FROM AUTHOR]

In this article, a novel magnetic field calculation approach that considers the static inclined eccentricity of axial flux permanent magnet (AFPM) machine is presented. The equivalent remanence of permanent magnet (PM) is introduced and calculated, in which the air-gap length can be regarded as uniform. Then, the analytical model based on harmonic subdomain technology can be used directly. The magnetic field distribution (MFD) and electromagnetic performance under eccentric state are calculated and compared. The effectiveness of the proposed method is verified both by the finite element (FE) model and experimental results. The main contribution of this article is to provide a simple and accurate method for the calculation of the eccentric magnetic field of the PM motor, not limited to the AFPM. [ABSTRACT FROM AUTHOR]

The tubular linear oscillating machine can achieve reciprocating movement directly without auxiliary transmission mechanisms, which is widely used in the free-piston energy conversion system. To achieve a lower thrust ripple and eliminate the eddy current effect, a circumferential silicon steel stack is usually utilized in the stator, however, it results in assembling difficulties. In this article, a radially split lamination tubular linear permanent magnet oscillating machine with auxiliary configuration (RSL-TLPMOMA) is proposed to solve the problem. First, the laminated coefficient expression of split-laminated is deduced, the influence of laminated number and radius ratio on laminated coefficient is discussed, and the optimal combination of the laminated number under different radius ratios is given. Second, the subdomain (SD) method is used to analyze RSL-TLPMOMA, the auxiliary teeth, slot, and end effect are considered. Finally, a prototype is manufactured and tested. [ABSTRACT FROM AUTHOR]

In this paper, we propose an order reduction method which can be applied in the approximated analytical model for linear permanent magnet machines (LPMMs). The proposed model takes the periodic boundary condition into account the Poisson and Laplace equations, hence, the analytical solution requires low harmonic orders in each subdomain. The magnetic results show that the proposed model can maintain high accuracy while taking low computational time. 2D finite element computations, as well as measurements, validate the proposed model. The proposed model in this paper can also be further applied in permanent magnet machines with high pole and slot combination, to reduce the computational time. [ABSTRACT FROM AUTHOR]

To facilitate the active magnetic bearing (AMB) design and analysis, an accurate and fast model that considers both rotor eccentricity and the saturation effect is necessary. In this article, a novel hybrid analytical model (HAM) for effective calculation of the magnetic field of the AMB is proposed. Eccentricity and local saturation are considered in the proposed HAM. In the proposed HAM, the stator and rotor are modeled by elementary subdomains (ESDs) and the air-gap is modeled by magnetic equivalent circuit (MEC). Direct coupling between the solutions in the ESD regions with MEC completes the whole model matrices. Compared to the existing literature, the proposed model considers both the rotor eccentricity and material nonlinearity. The effectiveness and accuracy of the proposed HAM are validated by both the finite element model and experimental results. The results show that the proposed HAM can accurately predict the magnetic quantities of the AMB. [ABSTRACT FROM AUTHOR]

This article proposes a rotor design method suitable for double-layer interior permanent magnet synchronous motor (DIPMSM), which can reduce electromagnetic torque ripple and at the same time reduce the electromagnetic noise of the motor. In previous studies, the inverse cosine function (ICF) was used to modify the rotor shape for making the air-gap flux density distribution sinusoidal under no-load conditions, which can reduce the torque ripple. However, conventional ICF can only be used in a single-layer interior rotor structure. Consequently, this article proposes a piecewise inverse cosine function (PICF) based on ICF, which can be applied to DIPMSM. To verify the improvement of the proposed method in the electromagnetic and noise aspects of the motor, the electromagnetic model and a noise prediction model of the 36-slot/8-pole motor are established by the finite element method. The PICF model is compared with the prototype in the aspects of electromagnetic performance and noise. The torque ripple is reduced by 54.16%, from ±2.4 to ±1.1 N m, and the electromagnetic noise is reduced by about 4.9 dB. Finally, the accuracy of the noise prediction model is verified by the noise test of the prototype. [ABSTRACT FROM AUTHOR]

This study proposes a method to reduce the electromagnetic noise of a double‐layer interior permanent magnet synchronous motor (DIPMSM) by optimising the flux barrier. First, a noise prediction model of the 36‐slot/8‐pole DIPMSM is established by finite element (FE). According to the simulation results, the noise of the motor is the loudest at 5000 rpm, especially with a noise component of 3333.3 Hz. From the results of modal analysis, it can be concluded that the four‐order radial force with a frequency of 3333.3 Hz resonates with the stator, resulting in the loudest noise. Then, the source of the radial force that causes the loudest noise is analysed, and it can be found that the 9th and 11th harmonics of rotor magnetic motive force have the greatest contribution to the force. By optimising the rotor, the radial force contributed by the 9th and 11th harmonics is weakened, thereby reducing the noise caused by these harmonics. Finally, the electromagnetic performance and noise of the optimised motor are checked by FE. Compared with the initial rotor, the torque ripple is reduced by 26.79%, and noise is reduced by 5.542 dB. The noise test on the prototype verifies the accuracy of the noise prediction model. [ABSTRACT FROM AUTHOR]

Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine‐spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene Pitx1, known to control pelvic reduction also in the three‐spined stickleback. In the two other crosses, PR was polygenic and attributed to 10 novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the Pitx1 regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large‐effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterized on empirical data, we hypothesize that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by >2× stronger population structuring among freshwater populations and >10× stronger genetic isolation by distance in the sea in nine‐spined sticklebacks as compared to three‐spined sticklebacks. see also the Perspective by Yo Y. Yamasaki and Jun Kitano. [ABSTRACT FROM AUTHOR]

This paper proposes an analytical model for the prediction of air gap magnetic field distribution for axial flux permanent magnet (AFPM) machine with various types of misalignments. The AFPM machine geometry is first transformed to a polar representation. Consequently, the subdomain model based on current sheet technique is developed. Then the stator coordinate system is chosen as reference coordinate to consider both static/dynamic angular and axis misalignments. The back electromagnetic forces and cogging torque are obtained accordingly based on Maxwell's equations. The results show that the proposed approach agrees with the finite-element method. The model is further validated by experiments under healthy, dynamic angular and axis misalignment conditions, which can validate the proposed approach. It turns out that the proposed approach can predict the performance of AFPM machines with types of misalignment quickly and effectively, which is greatly significant for further fault detection. [ABSTRACT FROM AUTHOR]

The degree to which adaptation to similar selection pressures is underlain by parallel versus non‐parallel genetic changes is a topic of broad interest in contemporary evolutionary biology. Sticklebacks provide opportunities to characterize and compare the genetic underpinnings of repeated marine‐freshwater divergences at both intra‐ and interspecific levels. While the degree of genetic parallelism in repeated marine‐freshwater divergences has been frequently studied in the three‐spined stickleback (Gasterosteus aculeatus), much less is known about this in other stickleback species. Using a population transcriptomic approach, we identified both genetic and gene expression variations associated with marine‐freshwater divergence in the nine‐spined stickleback (Pungitius pungitius). Specifically, we used a genome‐wide association study approach, and found that ~1% of the total 173,491 identified SNPs showed marine‐freshwater ecotypic differentiation. A total of 861 genes were identified to have SNPs associated with marine‐freshwater divergence, but only 12 of these genes have also been reported as candidates associated with marine‐freshwater divergence in the three‐spined stickleback. Hence, our results indicate a low degree of interspecific genetic parallelism in marine‐freshwater divergence. Moreover, 1,578 genes in the brain and 1,050 genes in the liver were differentially expressed between marine and freshwater nine‐spined sticklebacks, ~5% of which have also been identified as candidates associated with marine‐freshwater divergence in the three‐spined stickleback. However, only few of these (e.g., CLDND1) appear to have been involved in repeated marine‐freshwater divergence in nine‐spined sticklebacks. Taken together, the results indicate a low degree of genetic parallelism in repeated marine‐freshwater divergence both at intra‐ and interspecific levels. [ABSTRACT FROM AUTHOR]

Fishes exhibit greater species diversity than any other group of vertebrates. They are found in most bodies of water, including those that pose extreme challenges, such as sulfide springs, rivers contaminated with heavy metals and organic pollutants, and caves without light. Adaptation to these extreme environments usually occurs rapidly, which has stimulated much interest in uncovering the genetic basis of such rapid adaptation. Since the sequencing of the zebrafish genome in 2001, rapid development of high-throughput sequencing technology has facilitated the additional sequencing of ~ 210 ray-finned fish genomes to date. As a result of this wealth of resources, much attention has been focused on the genetic basis of adaptation in fishes, particularly in extreme environments. The goal of this review is to summarize recent advances in fish genomics, with a specific focus on the use of genomic data to understand the genetic basis of adaptation to extreme environments in fishes. The results highlight that fishes often adapt to extreme environments through phenotypic and physiological changes that have a confirmed or inferred genetic basis. Moreover, such changes are usually rapid and repeated when parallel adaptation to similar extreme environments occurs. Specifically, parallel genetic changes are usually observed at both the intra- and interspecific level. The advances in fish genomics provide the opportunity to understand how evolutionary changes feed back into ecosystems that are facing extreme environmental changes, as well as to advance our understanding of the repeatability and predictability of evolutionary response (of fishes) to extreme environmental changes. [ABSTRACT FROM AUTHOR]

The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts. [ABSTRACT FROM AUTHOR]

Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome‐anchored single nucleotide polymorphisms and de novo assembled RAD‐tag loci were constructed with RAD‐seq data. Both data sets yielded topologically identical and well‐supported species trees. Incongruence between nuclear and mitochondrial DNA‐based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology‐based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius‐complex, including suggestion of several trans‐Arctic invasions of Europe from the Northern Pacific. The well‐resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies. [ABSTRACT FROM AUTHOR]

This paper proposes an analytical model for the prediction of airgap magnetic field distribution for axial flux permanent magnet (AFPM) machine with partial magnet demagnetization. The AFPM machine geometry is first converted to a polar representation. Consequently, the subdomain model based on current sheet technique is developed. Then current sheet representation of PM is derived to consider the partial demagnetization using superposition principle. The back electromagnetic forces and cogging torque are obtained accordingly based on Maxwell's equations. The results show that the results of proposed approach agrees with that of finite-element method. The model is further validated by experiments under both healthy and demagnetized conditions, which can validate the proposed approach. Main contribution of the work is to consider the partial irreversible demagnetization. Moreover, the proposed method is applicable for both AFPM and radial flux permanent magnet machine. [ABSTRACT FROM AUTHOR]

In this paper, a new hybrid model is proposed for the prediction of air gap magnetic field distribution (MFD) in interior permanent magnet machines with any rotor configuration. The slotless magnetic field is first predicted by finite-element method (FEM) with automatic scripting in MATLAB to consider saturation in the rotor iron. Afterward, the conformal mapping viz., Schwarz–Christoffel mapping is introduced to take the slotting effect into account. Consequently, the MFD could be calculated. The back electromagnetic forces, cogging torque, and output torque are obtained accordingly. Then a subdomain model is developed to consider the armature reaction. The results show that the proposed hybrid approach agrees well with the FEM. The model is further verified by experiments. The main contribution of this paper is to reduce the computation time remarkably while maintaining the calculation accuracy. [ABSTRACT FROM AUTHOR]

In this paper, a general analytical model is proposed to calculate the back electromotive forces of various manufacturing imperfections in the double-rotor axial flux permanent magnet machine. First, the axial and circumferential flux density in the air gap under healthy condition is developed by Maxwell’s equations and Schwarz–Christoffel mapping. Second, the equations of air gap length and radii are introduced to calculate the flux density with manufacturing imperfections. The back EMFs of each case are calculated. For each case, finite-element (FE) method models are developed to validate the analytical model, and the results show that the analytical model predictions match well with the FE results. Finally, the analytical model is verified by experimental results. [ABSTRACT FROM AUTHOR]

Gene duplication generates new genetic material which, if retained after duplication, may contribute to organismal evolution. A whole-genome duplication occurred in the ancestry of teleost fish and consequently there are many duplicated genes in teleost genomes. Indeed, it has been proposed that the evolutionary diversification of teleost fish may have been stimulated by the fish-specific genome duplication (FSGD). However, it is not clear which factors determine which genes are retained as duplicate copies and which return to a singleton state after duplication. In the present study, gene complexity, in terms of encoded protein length and functional domain number, is compared between duplicate and singleton genes for nine well-annotated teleost genomes. A total of 933 gene families with retained duplicates and 4590 singleton gene families are analysed. Genes with retained duplicates are found to be significantly longer (27.9-38.2%) and to have more functional domains (20.5-26.5%) than singleton genes in all the nine teleost genomes, suggesting that genes encoded longer proteins with and more functional domains were preferentially retained after whole-genome duplication in teleosts. This differential retention of duplicated genes will have increased the genomic complexity of teleost fish after FSGD which, together with differential duplicated gene retention as a lineage-splitting force, may have greatly contributed to the successful diversification of teleost fish. [ABSTRACT FROM AUTHOR]

Quantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small-effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine-spined sticklebacks ( Pungitius pungitius) with the aid of novel multilocus QTL-mapping approaches based on a de-biased LASSO method. Apart from having more statistical power to detect QTL and reduced rate of false positives than conventional QTL-mapping approaches, the developed methods can handle large marker panels and provide estimates of genomic heritability. Single-locus analyses of an F2 interpopulation cross with 239 individuals and 15 198, fully informative single nucleotide polymorphisms (SNPs) uncovered 79 QTL associated with variation in stickleback brain size traits. Many of these loci were in strong linkage disequilibrium (LD) with each other, and consequently, a multilocus mapping of individual SNPs, accounting for LD structure in the data, recovered only four significant QTL. However, a multilocus mapping of SNPs grouped by linkage group (LG) identified 14 LGs (1-6 depending on the trait) that influence variation in brain traits. For instance, 17.6% of the variation in relative brain size was explainable by cumulative effects of SNPs distributed over six LGs, whereas 42% of the variation was accounted for by all 21 LGs. Hence, the results suggest that variation in stickleback brain traits is influenced by many small-effect loci. Apart from suggesting moderately heritable ( h2 ≈ 0.15-0.42) multifactorial genetic architecture of brain traits, the results highlight the challenges in identifying the loci contributing to variation in quantitative traits. Nevertheless, the results demonstrate that the novel QTL-mapping approach developed here has distinctive advantages over the traditional QTL-mapping methods in analyses of dense marker panels. [ABSTRACT FROM AUTHOR]

Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide polymorphisms ( SNPs) obtained with restriction site-associated DNA sequencing of pooled samples from 11 populations of Andrew's toad ( Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an altitudinal gradient from 1690 to 2768 m.a.s.l. We discovered significant geographic differentiation among all sites, with an average FST = 0.023 across all SNPs. Apart from clear patterns of isolation by distance, we discovered numerous outlier SNPs showing strong associations with variation in altitude (1394 SNPs), average annual temperature (1859 SNPs) or both (1051 SNPs). Levels and patterns of genetic differentiation in these SNPs were consistent with the hypothesis that they have been subject to directional selection and reflect adaptation to altitudinal variation among the study sites. Genes with footprints of selection were significantly enriched in binding and metabolic processes. Several genes potentially related to high altitude adaptation were identified, although the identity and functional significance of most genomic targets of selection remain unknown. In general, the results provide genomic support for results of earlier common garden and low coverage genetic studies that have uncovered substantial adaptive differentiation along altitudinal and latitudinal gradients in amphibians. [ABSTRACT FROM AUTHOR]

Detecting and estimating the degree of genetic differentiation among populations of highly mobile marine fish having pelagic larval stages is challenging because their effective population sizes can be large, and thus, little genetic drift and differentiation is expected in neutral genomic sites. However, genomic sites subject to directional selection stemming from variation in local environmental conditions can still show substantial genetic differentiation, yet these signatures can be hard to detect with low-throughput approaches. Using a pooled RAD-seq approach, we investigated genomewide patterns of genetic variability and differentiation within and among 20 populations of Atlantic herring in the Baltic Sea (and adjacent Atlantic sites), where previous low-throughput studies and/or studies based on few populations have found limited evidence for genetic differentiation. Stringent quality control was applied in the filtering of 1 791 254 SNPs, resulting in a final data set of 68 182 polymorphic loci. Clear differentiation was identified between Atlantic and Baltic populations in many genomic sites, while differentiation within the Baltic Sea area was weaker and geographically less structured. However, outlier analyses - whether including all populations or only those within the Baltic Sea - uncovered hundreds of directionally selected loci in which variability was associated with either salinity, temperature or both. Hence, our results support the view that although the degree of genetic differentiation among Baltic Sea herring populations is low, there are many genomic regions showing elevated divergence, apparently as a response to temperature- and salinity-related natural selection. As such, the results add to the increasing evidence of local adaptation in highly mobile marine organisms, and those in the young Baltic Sea in particular. [ABSTRACT FROM AUTHOR]

This paper investigates the electromagnetic and thermal performances of the open-circuit air cooled high-speed permanent magnet motor (HSPMM) with Gramme ring windings. Take a 36 kr/min, 75 kW HSPMM as an example, the electromagnetic losses, in particular the rotor eddy current loss and the stator iron loss of the motor are calculated. The influences of switching frequency and air gap length on these losses are studied. Then, a computational fluid dynamics (CFD) model is composed to calculate its coolant flow parameters and the temperature distribution. Based on the CFD results, a lumped-parameter thermal network (LPTN) is created and verified. Then, a 24 kr/min, 140 kW prototype with the same structure and cooling configuration is designed using the LPTN. Experiments show that the calculated results are with reasonable accuracy. Finally, a sensitivity analysis is applied to the 140 kW prototype based on the LPTN to disclose the influences of different parameters on the rotor permanent magnet temperature rise. [ABSTRACT FROM AUTHOR]

Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in five fish (teleost) species with completely sequenced genomes. The ancestor of these species has been subject to a fish-specific genome duplication (FSGD) event that occurred approximately 350 Ma. We find that duplicate genes contain at least 25% more indels than single-copy genes. These indels accumulated preferentially in the first 40 my after the FSGD. A lack of widespread asymmetric indel accumulation indicates that both members of a duplicate gene pair typically experience relaxed selection. Strikingly, we observe a 30–80% excess of deletions over insertions that is consistent for indels of various lengths and across the five genomes. We also find that indels preferentially accumulate inside loop regions of protein secondary structure and in regions where amino acids are exposed to solvent. We show that duplicate genes with high indel density also show high DNA sequence divergence. Indel density, but not amino acid divergence, can explain a large proportion of the tertiary structure divergence between proteins encoded by duplicate genes. Our observations are consistent across all five fish species. Taken together, they suggest a general pattern of duplicate gene evolution in which indels are important driving forces of evolutionary change. [ABSTRACT FROM PUBLISHER]

In his influential book "Evolution by Gene Duplication", Ohno postulated that frameshift mutation could lead to a new function after duplication, but frameshift mutation is generally thought to be deleterious, and thus drew little attention in functional innovation in duplicate evolution. To this end, we here report an exhaustive survey of the genomes of human, mouse, zebrafish, and fruit fly. We identified 80 duplicate genes that involved frameshift mutations after duplication. The frameshift mutation preferentially located close to the C-terminus in most cases (55/88), which indicated that a frameshift mutation that changed the reading frame in a small part at the end of a duplicate may likely have contributed to adaptive evolution (e.g., human genes NOTCH2NL and ARHGAP11B) otherwise too deleterious to survive. A few cases (11/80) involved multiple frameshift mutations, exhibiting various patterns of modifications of the reading frame. Functionality of duplicate genes involving frameshift mutations was confirmed by sequence characteristics and expression profile, suggesting a potential role of frameshift mutation in creating functional novelty. We thus showed that genomes have non-negligible numbers of genes that have experienced frameshift mutations following gene duplication. Our results demonstrated the potential importance of frameshift mutations in molecular evolution, as Ohno verbally argued 50 years ago. [ABSTRACT FROM AUTHOR]

The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclochellus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed. [ABSTRACT FROM AUTHOR]

A PCR survey for Sox genes in a young tetraploid fish Tor douronensis (Teleostei: Cyprinidae) was performed to access the evolutionary fates of important functional genes after genome duplication caused by polyploidization event. Totally 13 Sox genes were obtained in Tor douronensis, which represent SoxB, SoxC and SoxE groups. Phylogenetic analysis of Sox genes in Tor douronensis provided evidence for fish-specific genome duplication, and suggested that Sox19 might be a teleost specific Sox gene member. Sequence analysis revealed most of the nucleotide substitutions between duplicated copies of Sox genes caused by tetraploidization event or their orthologues in other species are silent substitutions. It would appear that the sequences are under purifying selective pressure, strongly suggesting that they represent functional genes and supporting selection against all null allele at either of two duplicated loci of Sox4a, Sox9a and Sox9b. Surprising variations of the intron length and similarities of two duplicated copies of Sox9a and Sox9b, suggest that Tor douronensis might be an allotetraploidy. [ABSTRACT FROM AUTHOR]

Simple Summary: Diptychus maculates and Gymnodiptychus dybowskii are two rare aboriginal fishes in the Xinjiang Uygur Autonomous Region. In recent years, due to overfishing and habitat fragmentation caused by construction of water conservancy and hydropower projects, the fishery resources have decreased sharply. Understanding the genetic background is of great significance for resource protection. In this study, we revealed the similar trends of population genetic diversities in these two species collected from the Tarim River and the Yili River. In addition, outlier SNPs associated with temperature and altitude were detected in both of them, indicating that Schizothoracinae fishes represented by D. maculates and G. dybowskii were still under the selection pressure of plateau environments. Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai–Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude and temperature gradient, respectively. No intersection was revealed in G. dybowskii. The results indicated that D. maculates was subject to much greater divergent selection pressure. A strong signal of isolation-by-distance (IBD) was detected across D. maculates (Mantel test, rs = 0.65; p = 0.05), indicating an evident geographical isolation in the Tarim River. Isolation-by-environment (IBE) analysis implied that temperature and altitude selections were more intensive in D. maculates, with greater environmental variation resulting in weak gene flow. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the nine-spined sticklebackPungitius pungitiuswas obtained with Illumina sequencing of genomic DNA. The assembled mitogenome sequence was 16 582 bp long, and the gene number, order and contents were identical to those of other sequencedPungitiusmitogenomes. The complete mitogenome ofP. pungitiusfrom its European range can provide an important template for further phylogenetic and population genetic studies of thePungitiusspecies complex. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome sequences of three divergent lineages of the smooth tail nine-spined stickleback (Pungitius laevis) were obtained with massive parallel sequencing of their genomic DNA. The genome sequences were 16 574–16 580 bp long, and the gene order and contents were identical to those of other sequencedPungitiusmitogenomes. Although the mitogenome sequences of all threeP. laevislineages clustered within the genusPungitius, they were clearly distinct and showed divergence comparable to that seen between somePungitiusspecies. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome of the Sakhalin nine-spined sticklebackPungitius tymensiswas determined using Illumina paired-end sequencing of genomic DNA. The genome sequence was 16 481 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region. The content and arrangement of the genes were identical to those of other Gasterosteidae species.P. tymensiswas phylogenetically positioned with otherPungitiusspecies (P. kaibarae,P. pungitiusandP. sinensis) with a clear distinction from them. Nucleotide identity in the 37 genic regions ranged from 94.7% to 94.9% betweenP. tymensisand the otherPungitiusspecies. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome of the Ukrainian nine-spined sticklebackPungitius platygasterwas obtained using massive parallel sequencing of genomic DNA. The mitogenome sequence was 16 570 bp long, and the gene order and contents were identical to those of other sequencedPungitiusmitogenomes. In a phylogenetic analysis, the mitogenome ofP. platygasterclustered with otherPungitiusmitogenomes, yet being clearly distinct from those ofP. pungitius,P. sinensisandP. kaibarae. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome of the Greek nine-spined sticklebackPungitius hellenicuswas obtained using Illumina high-throughput sequencing of genomic DNA. The genome was 16 713 bp long, and contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. The arrangement of the genes was identical to that of other Gasterosteidae fishes. However, the control region ofP. hellenicuscontained three copies of imperfect repeated sequences (72–78 bp in single motifs), whileP. pungitiusandP. tymensishave one or two copies. Nucleotide identity betweenP. hellenicusand three otherPungitiusspecies across all the 37 genic regions was 93.0% to 95.5%. [ABSTRACT FROM PUBLISHER]