Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish.

BACKGROUND: Cis-regulatory mutations often underlie phenotypic evolution. However, because identifying the locations of promoters and enhancers in non-coding regions is challenging, we have fewer examples of identified causative cis-regulatory mutations that underlie naturally occurring phenotypic variations than of causative amino acid-altering mutations. Because cis-regulatory elements have epigenetic marks of specific histone modifications, we can detect cis-regulatory elements by mapping and analyzing them. Here, we investigated histone modifications and chromatin accessibility with cleavage under targets and tagmentation (CUT&Tag) and assay for transposase-accessible chromatin-sequencing (ATAC-seq). RESULTS: Using the threespine stickleback (Gasterosteus aculeatus) as a model, we confirmed that the genes for which nearby regions showed active marks, such as H3K4me1, H3K4me3, and high chromatin accessibility, were highly expressed. In contrast, the expression levels of genes for which nearby regions showed repressive marks, such as H3K27me3, were reduced, suggesting that our chromatin analysis protocols overall worked well. Genomic regions with peaks of histone modifications showed higher nucleotide diversity within and between populations. By comparing gene expression in the gills of the marine and stream ecotypes, we identified several insertions and deletions (indels) with transposable element fragments in the candidate cis-regulatory regions. CONCLUSIONS: Thus, mapping and analyzing histone modifications can help identify cis-regulatory elements and accelerate the identification of causative mutations in the non-coding regions underlying naturally occurring phenotypic variations.

Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation.

Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.

Validation of the

The cluster structure of the neutron-rich isotope ^{10}Be has been probed via the (p,pα) reaction at 150 MeV/nucleon in inverse kinematics and in quasifree conditions. The populated states of ^{6}He residues were investigated through missing mass spectroscopy. The triple differential cross section for the ground-state transition was extracted for quasifree angle pairs (θ_{p},θ_{α}) and compared to distorted-wave impulse approximation reaction calculations performed in a microscopic framework using successively the Tohsaki-Horiuchi-Schuck-Röpke product wave function and the wave function deduced from antisymmetrized molecular dynamics calculations. The remarkable agreement between calculated and measured cross sections in both shape and magnitude validates the molecular structure description of the ^{10}Be ground-state, configured as an α-α core with two valence neutrons occupying π-type molecular orbitals.

Gudgeon fish with and without genetically determined countershading coexist in heterogeneous littoral environments of an ancient lake.

Countershading, characterized by a darker dorsal surface and lighter ventral surface, is common among many animals. This dorsoventral pigment polarity is often thought to be adaptive coloration for camouflage. By contrast, noncountershaded (melanistic) morphs often occur within a species due to genetic color polymorphism in terrestrial animals. However, the polymorphism with either countershaded or melanistic morphs is poorly known in wild aquatic animals. This study explored the genetic nature of diverged color morphs of a lineage of gudgeon fish (genus Sarcocheilichthys) in the ancient Lake Biwa and propose this system as a novel model for testing hypotheses of functional aspects of countershading and its loss in aquatic environments. This system harbors two color morphs that have been treated taxonomically as separate species; Sarcocheilichthys variegatus microoculus which occurs throughout the littoral zone and Sarcocheilichthys biwaensis which occurs in and around rocky areas. First, we confirmed that the divergence of dorsoventral color patterns between the two morphs is under strict genetic control at the levels of chromatophore distribution and melanin-related gene expression under common garden rearing. The former morph displayed sharp countershading coloration, whereas the latter morph exhibited a strong tendency toward its loss. The crossing results indicated that this divergence was likely controlled by a single locus in a two-allele Mendelian inheritance pattern. Furthermore, our population genomic and genome-wide association study analyses detected no genome-wide divergence between the two morphs, except for one region near a locus that may be associated with the color divergence. Thus, these morphs are either in a state of intraspecific color polymorphism or two incipient species. Evolutionary forces underlying this polymorphism appear to be associated with heterogeneous littoral environments in this lake. Future ecological genomic research will provide insight into adaptive functions of this widespread coloration, including the eco-evolutionary drivers of its loss, in the aquatic world.

Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates.

How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and has proceeded with gene flow, possibly driven by ecological selection. We identified 27 differentiation islands between the closely related H. discus and H. madaka characterized by high FST and dA, but not high dXY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high FST, dXY, and dA values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the Western Pacific abalones appear to occupy the early stages speciation continuum, and the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.

Multiple paths to the same destination: Influence of gene flow on convergent evolution.

Elucidation of the genetic mechanisms of convergent evolution, the evolution of similar or the same phenotypes in phylogenetically independent lineages, helps predict how populations will respond to the same selective pressures. Convergent evolution can be caused by either the fixation of identical-by-descent alleles, independent mutations at the same gene, or mutations in different genes controlling the same trait. To what extent does the fixation of identical-by-descent alleles lead to convergent evolution in isolated populations where inflow of adaptive alleles from other populations is limited? In a From the Cover article in this issue of Molecular Ecology, Kemppainen et al. (2021) compared the genetic basis for the reduction of pelvic structures in three isolated freshwater populations of nine-spined stickleback (Pungitius pungitius) from Northern Europe. The authors used quantitative trait loci (QTL) mapping to reveal that the pelvic reduction in these three populations was caused by mutations at different genetic loci. In contrast to studies in three-spined stickleback (Gasterosteus aculeatus), where independently derived Pitx1 mutations were shown to be responsible for plate reduction across multiple freshwater populations, Kemppainen et al. (2021) found Pitx1 to be the candidate causative gene for only one population of P. pungitius. This study highlights the importance of genetic studies of convergent evolution, not only in the presence of gene flow but also in its absence for a better understanding of the genetic architecture of convergent evolution.

Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks.

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis, whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Ecosystem size predicts the probability of speciation in migratory freshwater fish.

Predicting speciation is a fundamental goal of research in evolutionary ecology. The probability of speciation is often positively correlated with ecosystem size. Although the mechanisms driving this correlation are generally difficult to identify, a shared geographical and ecological context provides a suitable condition to study the mechanisms that promote speciation in large ecosystems by reducing the number of factors to be considered. Here, we determined the correlation between speciation and ecosystem size, and discuss the underlying mechanisms of this relationship, using a probable parallel ecotype formation for freshwater fish. Our population genetic analysis revealed that speciation of the landlocked goby, Rhinogobius sp. YB, of the Ryukyu Archipelago, Japan, from its migratory ancestor, R. brunneus, occurred in parallel across five islands. Logistic regression analysis showed that speciation probability could be predicted using island size. The results suggest that ecosystem size predicts the occurrence of adaptation and reproductive isolation, probably through its association with three possible factors: divergent selection strength, population persistence, and occurrence probability of habitat separation.

A key metabolic gene for recurrent freshwater colonization and radiation in fishes.

Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.

Evidence for prevalent Z = 6 magic number in neutron-rich carbon isotopes.

The nuclear shell structure, which originates in the nearly independent motion of nucleons in an average potential, provides an important guide for our understanding of nuclear structure and the underlying nuclear forces. Its most remarkable fingerprint is the existence of the so-called magic numbers of protons and neutrons associated with extra stability. Although the introduction of a phenomenological spin-orbit (SO) coupling force in 1949 helped in explaining the magic numbers, its origins are still open questions. Here, we present experimental evidence for the smallest SO-originated magic number (subshell closure) at the proton number six in 13-20C obtained from systematic analysis of point-proton distribution radii, electromagnetic transition rates and atomic masses of light nuclei. Performing ab initio calculations on 14,15C, we show that the observed proton distribution radii and subshell closure can be explained by the state-of-the-art nuclear theory with chiral nucleon-nucleon and three-nucleon forces, which are rooted in the quantum chromodynamics.

Time-Reversal Measurement of the p-Wave Cross Sections of the

The cross sections of the ^{7}Be(n,α)^{4}He reaction for p-wave neutrons were experimentally determined at E_{c.m.}=0.20-0.81 MeV slightly above the big bang nucleosynthesis (BBN) energy window for the first time on the basis of the detailed balance principle by measuring the time-reverse reaction. The obtained cross sections are much larger than the cross sections for s-wave neutrons inferred from the recent measurement at the n_TOF facility in CERN, but significantly smaller than the theoretical estimation widely used in the BBN calculations. The present results suggest the ^{7}Be(n,α)^{4}He reaction rate is not large enough to solve the cosmological lithium problem, and this conclusion agrees with the recent result from the direct measurement of the s-wave cross sections using a low-energy neutron beam and the evaluated nuclear data library ENDF/B-VII.1.

Phylogeny, hybridization, and life history evolution of Rhinogobius gobies in Japan, inferred from multiple nuclear gene sequences.

Rhinogobius fishes (Gobiidae) are distributed widely in East and Southeast Asia, and represent the most species-rich group of freshwater gobies with diversified life histories (i.e., amphidromous, fluvial, and lentic). To reveal their phylogenetic relationships and life history evolution patterns, we sequenced six nuclear and three mitochondrial DNA (mtDNA) loci from 18 species, mainly from the mainland of Japan and the Ryukyu Archipelago. Our phylogenetic tree based on nuclear genes resolved three major clades, including several distinct subclades. The mtDNA and nuclear DNA phylogenies showed large discordance, which strongly suggested mitochondrial introgression through large-scale interspecific hybridization in these regions. On the basis of the molecular dating using geological data as calibration points, the hybridization occurred in the early to middle Pleistocene. Reconstruction of the ancestral states of life history traits based on nuclear DNA phylogeny suggests that the evolutionary change from amphidromous to freshwater life, accompanied by egg size change, occurred independently in at least three lineages. One of these lineages showed two life history alterations, i.e., from amphidromous (small egg) to fluvial (large egg) to lentic (small egg). Although more inclusive analysis using species outside Japan should be further conducted, the present results suggest the importance of the life history evolution associated with high adaptability to freshwater environments in the remarkable species diversification in this group. Such life history divergences may have contributed to the development of reproductive isolation.

Joint space narrowing, body mass index, and knee pain: the ROAD study (OAC1839R1).

OBJECTIVE: The objective of the present study was to clarify the association of joint space narrowing with knee pain in Japanese men and women using a large-scale population-based cohort of the Research on Osteoarthritis/osteoporosis Against Disability (ROAD) study. METHODS: This study examined the association between minimum joint space width (mJSW) in the medial compartment and pain at the knee. mJSW was measured in the medial and lateral compartments of the knee using a knee osteoarthritis (OA) computer-aided diagnosis system. RESULTS: From the 3040 participants in the ROAD study, the present study analyzed 2733 participants who completed the radiographic examinations and questionnaires regarding knee pain (975 men and 1758 women; mean age, 69.9 ± 11.2 years). Subjects with lateral knee OA were excluded. After adjustment for age and Body mass index (BMI), medial mJSW, as well as medial mJSW/lateral mJSW, was significantly associated with knee pain. Sex and BMI affected the association of medial mJSW with knee pain. The threshold of medial mJSW was approximately 3 mm in men and 2 mm in women, while that of medial mJSW/lateral mJSW was approximately 60% in both men and women. BMI was found to have a distinct effect on the association of mJSW with pain. CONCLUSION: The present cross-sectional study using a large-scale population from the ROAD study showed that joint space narrowing had a significant association with knee pain. The thresholds of joint space narrowing for knee pain were also established.

Association of occupational activity with joint space narrowing and osteophytosis in the medial compartment of the knee: the ROAD study (OAC5914R2).

OBJECTIVE: We investigated the association of occupational activity with joint space narrowing and osteophytosis at the knee separately in Japanese subjects using a large-scale population-based cohort of the Research on Osteoarthritis Against Disability (ROAD). METHODS: From the baseline survey of the ROAD study, 1,402 participants (512 men and 890 women) living in mountainous and seacoast communities were analyzed. Information collected included a lifetime occupational history and details of specific workplace physical activities. To estimate the severity of joint space narrowing and osteophytosis at the knee, minimum joint space width (mJSW) and osteophyte area (OPA) in the medial compartment of the knee were measured using a knee osteoarthritis (OA) computer-aided diagnosis system. RESULTS: For women, agricultural, forestry, and fishery workers had significantly lower mJSW values compared with clerical workers or technical experts, whereas OPA did not differ significantly among job titles in men or women. For occupational activities, kneeling and squatting were associated with lower mJSW as well as higher OPA. Walking and heavy lifting were associated with lower mJSW, but not with OPA. CONCLUSION: This cross-sectional study using a population-based cohort suggests that an occupational activity that includes kneeling and squatting appears to have a greater effect on knee OA.

Association of radiographic and symptomatic knee osteoarthritis with health-related quality of life in a population-based cohort study in Japan: the ROAD study.

OBJECTIVE: Knee osteoarthritis (OA) is a major public health issue causing chronic pain and disability. However, there is little information on the impact of this disease on quality of life (QOL) in Japanese men and women. The objective of the present study was to clarify the impact of radiographic and symptomatic knee OA on QOL in Japan. METHODS: This study examined the association of radiographic and symptomatic knee OA with QOL parameters such as the Medical Outcomes Study Short Form-8 (SF-8), EuroQOL (EQ-5D) and Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). Radiographic knee OA was defined according to Kellgren/Lawrence (KL) grades, and symptomatic knee OA was defined as KL=3 or 4 with knee pain. We also examined the independent association of symptomatic knee OA and grip strength with QOL. RESULTS: From the 3040 participants in the Research on Osteoarthritis Against Disability (ROAD) study, the present study analyzed 2126 subjects older than 40 years who completed the questionnaires (767 men and 1359 women; mean age, 68.9+/-10.9 years). Subjects with KL=3 or 4 had significantly lower physical QOL as measured by the physical component summary (PCS) score of the SF-8 and pain domains of the WOMAC, whereas mental QOL, as measured by the mental component summary (MCS) score of the SF-8, was higher in subjects with KL=3 or 4 than KL=0 or 1. Symptomatic knee OA was significantly more likely than radiographic knee OA without pain to be associated with physical QOL loss as measured by the PCS score and physical domains of the WOMAC. Symptomatic knee OA and grip strength were independently associated with physical QOL. CONCLUSION: This cross-sectional study revealed that subjects with symptomatic knee OA had significantly lower physical QOL than subjects without it.

Intra-articular lentivirus-mediated delivery of galectin-3 shRNA and galectin-1 gene ameliorates collagen-induced arthritis.

Different members of the galectin family may have inhibitory or stimulatory roles in controlling immune responses and regulating inflammatory reactions in autoimmune diseases such as rheumatoid arthritis (RA). A hypothetical model of a cross talk between galectin-1 and galectin-3 has been established in the circumstance of rheumatoid joints. As galectin-3 is a positive regulator and galectin-1 is a negative regulator of inflammation and autoimmune responses, in this study we evaluated the effects of local knockdown of galectin-3 or overexpression of galectin-1 on ameliorating collagen-induced arthritis (CIA) in rats. Lentiviral vectors encoding galectin-3 small hairpin RNA (shRNA) and galectin-1, as well as two control vectors expressing luciferase shRNA and green fluorescent protein, were individually injected intra-articularly into the ankle joints of rats with CIA, and their treatment responses were monitored by measuring the clinical, radiological and histological changes. Our results show that both knockdown of galectin-3 and overexpression of galectin-1 induced higher percentages of antigen-induced T-cell death in the lymph node cells from arthritic rats. Furthermore, these treatments significantly reduced articular index scores, radiographic scores and histological scores, accompanied with decreased T-cell infiltrates and reduced microvessel density in the ankle joints. Our findings implicate galectin-3 and galectin-1 as potential therapeutic targets for the treatment of RA.

Prevalence of radiographic knee osteoarthritis and its association with knee pain in the elderly of Japanese population-based cohorts: the ROAD study.

OBJECTIVE: We investigated the prevalence of radiographic knee osteoarthritis (OA) and knee pain in the Japanese elderly using a large-scale population of a nationwide cohort study, Research on Osteoarthritis Against Disability (ROAD), and examined their association. METHODS: From the baseline survey of the ROAD study, 2,282 participants > or =60 years (817 men and 1,465 women) living in urban, mountainous and seacoast communities were analyzed. The radiographic severity at both knees was determined by the Kellgren/Lawrence (KL) grading system. KL> or =2 and KL> or =3 knee OA were examined separately to assess osteophytosis and joint space narrowing (JSN). RESULTS: The prevalence of KL> or =2 OA (47.0% and 70.2% in men and women, respectively) was much higher than that of previous studies in Caucasians, while that of KL> or =3 OA was not much different in men. Age, BMI, female sex and rural residency were risk factors for radiographic knee OA, knee pain and their combination. The prevalence of knee pain was age-dependent in women, but not in men. Knee pain was more strongly associated with KL> or =3 OA than with KL=2, and the association was higher in men than in women. Female sex was a strong risk factor even in the subgroup without radiographic knee OA (KL=0/1). CONCLUSION: The present cross-sectional study revealed a high prevalence of radiographic knee OA in the Japanese elderly. Knee pain was strongly associated with JSN especially in men, while women tended to have knee pain even without radiographic OA.

Prevalence of radiographic lumbar spondylosis and its association with low back pain in elderly subjects of population-based cohorts: the ROAD study.

OBJECTIVES: Although lumbar spondylosis is a major cause of low back pain and disability in elderly people, few epidemiological studies have been performed. The prevalence of radiographic lumbar spondylosis was investigated in a large-scale population study and the association with low back pain was examined. METHODS: From a nationwide cohort study (Research on Osteoarthritis Against Disability; ROAD), 2288 participants aged > or =60 years (818 men and 1470 women) living in urban, mountainous and coastal communities were analysed. The radiographic severity at lumbar intervertebral levels from L1/2 to L5/S was determined by Kellgren/Lawrence (KL) grading. RESULTS: In the overall population the prevalence of radiographic spondylosis with KL> or =2 and > or =3 at the severest intervertebral level was 75.8% and 50.4%, respectively, and that of low back pain was 28.8%. Although KL> or =2 spondylosis was more prevalent in men, KL> or =3 spondylosis and low back pain were more prevalent in women. Age and body mass index were risk factors for both KL > or =2 and KL> or =3 spondylosis. Although KL = 2 spondylosis was not significantly associated with low back pain compared with KL = 0 or 1, KL> or =3 spondylosis was related to the pain only in women. CONCLUSIONS: This cross-sectional study in a large population revealed a high prevalence of radiographic lumbar spondylosis in elderly subjects. Gender seems to be distinctly associated with KL> or =2 and KL> or =3 lumbar spondylosis, and disc space narrowing with or without osteophytosis in women may be a risk factor for low back pain.

Dynamic spin ice: Pr2Sn2O7.

In this Letter, we report a new spin ice--Pr2Sn2O7--which appears to have enhanced residual entropy due to the dynamic nature of the spins. Neutron scattering experiments show that at 200 mK, there is a significant amount of magnetic diffuse scattering which can be fit to the dipolar spin-ice model. However, these short-ranged ordered spins have a quasielastic response that is atypical of the canonical spin ices, and suggests that the ground state is dynamic (i.e., composed of locally ordered two-in-two-out spin configurations that can tunnel between energetically equivalent orientations). We report this as an example of a dynamic spin ice down to 200 mK.

Coexpression of Flt3 ligand and GM-CSF genes modulates immune responses induced by HER2/neu DNA vaccine.

DNA vaccine and dendritic cells (DCs)-based vaccine have emerged as promising strategies for cancer immunotherapy. Fms-like tyrosine kinase 3-ligand (Flt3L) and granulocyte-macrophage-colony-stimulating factor (GM-CSF) have been exploited for the expansion of DC. It was reported previously that combination of plasmid encoding GM-CSF with HER2/neu DNA vaccine induced predominantly CD4(+) T-cell-mediated antitumor immune response. In this study, we investigated the modulation of immune responses by murine Flt3L and GM-CSF, which acted as genetic adjuvants in the forms of bicistronic (pFLAG) and monocistronic (pFL and pGM) plasmids for HER2/neu DNA vaccine (pN-neu). Coexpression of Flt3L and GM-CSF significantly enhanced maturation and antigen-presentation abilities of splenic DC. Increased numbers of infiltrating DC at the immunization site, higher interferon-gamma production, and enhanced cytolytic activities by splenocytes were prominent in mice vaccinated with pN-neu in conjunction with pFLAG. Importantly, a potent CD8(+) T-cell-mediated antitumor immunity against bladder tumors naturally overexpressing HER2/neu was induced in the vaccinated mice. Collectively, our results indicate that murine Flt3L and GM-CSF genes coexpressed by a bicistronic plasmid modulate the class of immune responses and may be superior to those codelivered by two separate monocistronic plasmids as the genetic adjuvants for HER2/neu DNA vaccine.