Genomics reveals a genetically isolated population of the Pacific white-sided dolphin (Lagenorhynchus obliquidens) distributed in the Sea of Japan.

The processes by which animals become genetically isolated in an open environment such as the ocean have not yet been fully elucidated. Morphologically different populations of Pacific white-sided dolphin Lagenorhynchus obliquidens are observed sympatrically in the Sea of Japan. However, genetic studies that exclusively used limited mitochondrial loci or microsatellite DNA have failed to demonstrate the existence of genetically distinct populations. Here, to reveal the population structure, we analysed genome-wide population genetic data using single nucleotide polymorphisms (SNPs) gathered in 2018-2021 from all domestic captive individuals in aquaria, the majority of which originated from the wild, as well as from some stranded individuals, together covering a wide area of coastal water around Japan (n = 123). Multiplexed intersimple sequence repeat genotyping-by-sequencing analysis was performed to obtain the SNP data. Principal coordinate analysis and the clustering method structure indicated that two genetically-distinct populations exist, with little interpopulation gene flow revealed. In addition, the genotypic segregation was reflected in differences in external morphotype. Furthermore, a population demographic analysis based on the whole-genome sequences of an individual from each population indicated that sea-level changes during the Last Glacial Period probably led to allopatric divergence of this species in a limited area of the Sea of Japan, with that group subsequently sharing a distribution area with the other population. These findings yield insights into the formation of genetically isolated sympatric populations in the ocean.

Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient.

Adaptive divergence occurs even between insufficiently isolated populations when there is a great difference in environments between their habitats. Individuals present in an intermediate zone of the two divergent populations are expected to have an admixed genetic structure due to gene flow. A selective pressure that acts on the genetically admixed individuals may limit the gene flow and maintain the adaptive divergence. Here, we addressed a question whether selection occurs in the genetically admixed individuals between two divergent populations. Arabidopsis halleri is a perennial montane plant, which has clear phenotypic dimorphisms between highland and lowland habitats in Mt. Ibuki, central Japan. We obtained the whole-genome sequences of Arabidopsis halleri plants along an altitudinal gradient of 359-1,317 m with a high spatial resolution (mean altitudinal interval of 20 m). We found a zone where the highland and lowland genes were mixing (intermediate subpopulation). In the intermediate subpopulation, we identified 5 and 13 genome regions, which included 3 and 8 genes, that had a high frequency of alleles that are accumulated in highland and lowland subpopulations, respectively. In addition, we also found that the frequency of highland alleles of these selected genome regions was smaller in the lowland subpopulation compared with that of the non-selected regions. These results suggest that the selection in the intermediate subpopulation might limit the gene flow and contribute to the adaptive divergence between altitudes. We also identified 7 genome regions that had low heterozygote frequencies in the intermediate subpopulation. We conclude that different types of selection in addition to gene flow occur at the intermediate altitude and shape the genetic structure across altitudes.

Temperature-related cline in the root mass fraction in East Asian wild radish along the Japanese archipelago.

Wild plants with a wide distribution, including those exposed to a wide variety of environmental conditions, may have variations in key functional traits relevant for agricultural applications. The East Asian wild radish (Raphanus sativus var. raphanistroides) is an appropriate model plant because it is widely distributed and has outstanding sink capacity as well as two cultivars within the species. Multiple common garden trials with 14 populations and three testing sites were conducted across the Japanese archipelago to quantify variations in yield and allocation. Significant inter-population variations and interaction effects with testing sites were detected for the root and shoot mass and the root mass fraction (RMF). While the rank order of the population changed drastically among sites and the variance components of genetic effects were small in yield traits (2.4%-4.7%), RMF displayed a large genetic variance (23.2%) and was consistently higher in the northern populations at all sites. Analyses revealed that the mean temperature of growing season of the seed origin was the most prominent factor explaining variation in RMF, irrespective of the sites. We concluded that the trait of resource allocation had a temperature-related cline and plants in cooler climates could invest more resources into their roots.

Plasticity of functional traits and optimality of biomass allocation in elevational ecotypes of Arabidopsis halleri grown at different soil nutrient availabilities.

In mountainous areas, plant distribution is constrained by various environmental stresses. Plasticity and constancy in plant functional traits may relate to optimal strategies at respective habitats and to ecotypic differentiation along elevation. Although plant biomass allocation has been extensively studied in relation to adaptation to soil nutrient availability along elevation, its optimality is still poorly understood. We examined soil nutrient availability in the field and conducted growth analysis for two elevational ecotypes of Arabidopsis halleri grown under different nutrient availabilities. We determined plasticity in morphological and physiological traits and evaluated optimal biomass allocation using an optimality model. Our field investigation indicated that soil nitrogen (N) availability increased rather than decreased with increasing elevation. Our growth analysis revealed that lowland ecotype was more plastic in morphological variables and N concentrations, whereas the highland ecotype was more plastic in other physiological variables such as the net assimilation rate (NAR). The leaf mass ratio (LMR) in the lowland ecotype was moderately plastic at the whole range of N availabilities, whereas LMR in the highland ecotype was very plastic at higher N availabilities only. The optimality model indicated that the LMR of the lowland ecotype was nearly optimal throughout the range of studied N availabilities, whereas that of the highland ecotype was suboptimal at low N availability. These results suggest that highland ecotype is adapted only to high N availability, whereas the lowland ecotype is adapted to a relatively wide range of N availabilities as a result of natural selection in their respective habitats. We conclude that an adaptive differentiation has occurred between the two ecotypes and plasticity in the biomass allocation is directly related to its optimization in changing environments.

Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis.

Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae. The duplication frequency of retained genes in the Arabidopsis lineage was ∼10 times higher than the duplication frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss (Physcomitrella patens). The difference of duplication frequencies can be explained by a rapid decay of anciently duplicated genes. To examine the degree of selection pressure on genes duplicated in either the A. halleri-lyrata or the A. halleri lineage, we examined positive and purifying selection in the A. halleri-lyrata and A. halleri lineages throughout the ratios of nonsynonymous to synonymous substitution rates (KA/KS). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. Interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication compared with immediately after gene duplication.

From the laboratory to the field: assaying histone methylation at FLOWERING LOCUS C in naturally growing Arabidopsis halleri.

Gene regulatory mechanisms are often defined in studies performed in the laboratory but are seldom validated for natural habitat conditions, i.e., in natura. Vernalization, the promotion of flowering by winter cold, is a prominent naturally occurring phenomenon, so far best characterized using artificial warm and cold treatments. The floral inhibitor FLOWERING LOCUS C (FLC) gene of Arabidopsis thaliana has been identified as the central regulator of vernalization. FLC shows an idiosyncratic pattern of histone modification at different stages of cold exposure, believed to regulate transcriptional responses of FLC. Chromatin modifications, including H3K4me3 and H3K27me3, are routinely quantified using chromatin immunoprecipitation (ChIP), standardized for laboratory samples. In this report, we modified a ChIP protocol to make it suitable for analysis of field samples. We first validated candidate normalization control genes at two stages of cold exposure in the laboratory and two seasons in the field, also taking into account nucleosome density. We further describe experimental conditions for performing sampling and sample preservation in the field and demonstrate that these conditions give robust results, comparable with those from laboratory samples. The ChIP protocol incorporating these modifications, "Field ChIP", was used to initiate in natura chromatin analysis of AhgFLC, an FLC orthologue in A. halleri, of which a natural population is already under investigation. Here, we report results on levels of H3K4me3 and H3K27me3 at three representative regions of AhgFLC in controlled cold and field samples, before and during cold exposure. We directly compared the results in the field with those from laboratory samples. These data revealed largely similar trends in histone modification dynamics between laboratory and field samples at AhgFLC, but also identified some possible differences. The Field ChIP method described here will facilitate comprehensive chromatin analysis of AhgFLC in the future to contribute to our understanding of gene regulation in fluctuating natural environments.

A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species.

Adaptive divergence at the microgeographic scale has been generally disregarded because high gene flow is expected to disrupt local adaptation. Yet, growing number of studies reporting adaptive divergence at a small spatial scale highlight the importance of this process in evolutionary biology. To investigate the genetic basis of microgeographic local adaptation, we conducted a genome-wide scan among sets of continuously distributed populations of Arabidopsis halleri subsp. gemmifera that show altitudinal phenotypic divergence despite gene flow. Genomic comparisons were independently conducted in two distinct mountains where similar highland ecotypes are observed, presumably as a result of convergent evolution. Here, we established a de novo reference genome and employed an individual-based resequencing for a total of 56 individuals. Among 527,225 reliable SNP loci, we focused on those showing a unidirectional allele frequency shift across altitudes. Statistical tests on the screened genes showed that our microgeographic population genomic approach successfully retrieve genes with functional annotations that are in line with the known phenotypic and environmental differences between altitudes. Furthermore, comparison between the two distinct mountains enabled us to screen out those genes that are neutral or adaptive only in either mountain, and identify the genes involved in the convergent evolution. Our study demonstrates that the genomic comparison among a set of genetically connected populations, instead of the commonly-performed comparison between two isolated populations, can also offer an effective screening for the genetic basis of local adaptation.

Poor correlation between the removal or deposition of pollen grains and frequency of pollinator contact with sex organs.

Pollinators deposit pollen grains on stigmas and remove pollen grains from anthers. The mechanics of these transfers can now be quantified with the use of high-speed video. We videoed hawkmoths, carpenter bees, and swallowtail butterflies pollinating Clerodendrum trichotomum. The number of grains deposited on stigmas did not vary significantly with the number of times pollinators contacted stigmas. In contrast, pollen removal from the anthers increased significantly with the number of contacts to anthers. Pollen removal varied among the three types of pollinators. Also, the three types carried pollen on different parts of their bodies. In hawkmoths and carpenter bees, a large number of contacted body part with anthers differed significantly from the body part that attached a large number of pollen grains. Our results indicate that a large number of contacts by pollinators does not increase either the male or female reproductive success of plants compared to a small number of contacts during a visit.

Successful engraftment after reduced-intensity umbilical cord blood transplantation for adult patients with advanced hematological diseases.

PURPOSE: The purpose of this research was to evaluate the feasibility of reduced-intensity unrelated cord-blood transplantation (RI-UCBT) in adult patients with advanced hematological diseases. EXPERIMENTAL DESIGN: Thirty patients (median age, 58.5 years; range, 20-70 years) with advanced hematological diseases underwent RI-UCBT at Toranomon Hospital between September 2002 and August 2003. Preparative regimen composed of fludarabine 25 mg/m(2) on days -7 to -3, melphalan 80 mg/m(2) on day -2, and 4 Gy total body irradiation on day -1. Graft-versus-host disease prophylaxis was composed of cyclosporin alone. RESULTS: Twenty-six patients achieved primary neutrophil engraftment after a median of 17.5 days. Median infused total cell dose was 3.1 x 10(7)/kg (range, 2.0-4.3 x 10(7)/kg). Two transplant-related mortalities occurred within 28 days of transplant, and another 2 patients displayed primary graft failure. Cumulative incidence of complete donor chimerism at day 60 was 93%. Grade II-IV acute graft-versus-host disease occurred in 27% of patients, with median onset 36 days. Primary disease recurred in 3 patients, and transplant-related mortality within 100 days was 27%. Estimated 1-year overall survival was 32.7%. Excluding 7 patients with documented infection, 19 patients displayed noninfectious fever before engraftment (median onset, day 9). Manifestations included high-grade fever, eruption, and diarrhea. The symptoms responded well to corticosteroid treatments in 7 of 13 treated patients. CONCLUSION: This study demonstrated the feasibility of RI-UCBT in adults.

Prostatic acid phosphatase: a possible diagnostic marker of intravascular large B-cell lymphoma.

BACKGROUND AND OBJECTIVE: Intravascular large B-cell lymphoma (IVL) has been treated as fever of unknown origin (FUO), and many patients have been treated inadequately based on incorrect diagnoses. We previously cares for a patient with IVL who tested positive for prostatic acid phosphatase (PAP), a marker of prostate cancer. Since then, we have regularly examined this mather when IVL was suspected to investigate the usefulness of PAP as a diagnostic marker for IVL. We retrospectively evaluated the usefulness of PAP as diagnostic marker of IVL. DESIGN AND METHODS: We reviewed the clinical courses of 5 patients with IVL (3 males, 2 females) in comparison with 23 controls with hematologic malignancies other than IVL. RESULTS: Serum levels of PAP were elevated in all 5 patients with IVL and 2 of the 23 controls. The difference was statistically significant using a chi-squared test (p=0.0002). The sensitivity and specificity of PAP were 100% and 91%, respectively, in the diagnosis of IVL. Its serum levels were closely associated with disease status. INTERPRETATION AND CONCLUSIONS: This study suggests that PAP might be a useful marker for the screening and assessment of disease activity and responses to the treatment of IVL.

Non-myeloablative hematopoietic stem cell transplantation for the treatment of adult T-cell lymphoma in a patient with advanced hepatic impairment.

A 59-year-old man with liver cirrhosis due to hepatitis B virus infection received non-myeloablative stem-cell transplantation (NST) for the treatment of adult T-cell lymphoma. The preparative regimen consisted of cyclophosphamide and fludarabine. While the pharmacokinetics of these drugs was altered in this patient, his clinical course was uneventful without the development of severe hepatic damage. Complete remission was achieved on day 56. Although he finally died of hemorrhage from esophageal varices on day 68, this case suggests that ATL may be a good candidate for allogeneic HSCT, and that NST may be feasible for patients with hepatic impairment.

Consequences of differences in flowering date on seed production in Heloniopsis orientalis (Liliaceae).

We examined the consequences of differences in flowering date on seed production in the self-compatible herb Heloniopsis orientalis. The number of selfed seeds per fruit, as determined by microsatellite markers, did not depend on when the plant flowered, whereas the number of outcrossed seeds per fruit increased with later flowering dates. Consequently, the selfing rate decreased with later flowering dates. The number of seeds (including both selfed and outcrossed ones) per fruit and the seed : ovule ratio increased with later flowering dates. We also examined the effects of pollinators and plant size on seed production. The visitation rate of Diptera did not depend on the flowering season, whereas that of Hymenoptera markedly increased as the flowering season progressed. Diptera stayed longer than Hymenoptera on each plant and flower. Seed production per fruit did not depend on plant size. Thus, the change in selfing rate associated with later flowering dates resulted from the seasonal change in pollinators rather than plant size.

Sustained molecular remission in a patient with CML in blastic crisis receiving dose-reduced hematopoietic stem-cell transplantation followed by early withdrawal of cyclosporine and prophylactic use of interferon-alpha.

A 54-year-old man with chronic myelocytic leukemia in blastic phase received reduced-intensity transplantation (RIST) from an HLA-identical unrelated donor. The preparative regimen consisted of busulfan, fludarabine, and anti-thymocyte globulin. Graft-versus-host disease (GVHD) prophylaxis was cyclosporine alone. Because he had a high risk of relapse, we discontinued cyclosporine on day 37, but he did not develop any signs of acute GVHD. To induce GVHD and augment a graft-versus-leukemia effect, we initiated interferon-alpha therapy on day 80 to a maximum dosage of three million units five times a week. He achieved molecular remission on day 94 followed by the development of extensive chronic GVHD the severity of which paralleled to the dose of interferon-alpha GVHD gradually subsided after discontinuation of interferon-alpha and the patient remains in molecular remission 18 months after transplantation. This case suggests that early withdrawal of cyclosporine and the prophylactic use of interferon-alpha are promising in RIST for high-risk leukemia.

Fatal airway obstruction caused by invasive aspergillosis of the thyroid gland.

Invasive aspergillosis is a common form of fungal infection in patients with hematological malignancies. Because Aspergillus species have angioinvasive properties, they frequently disseminate from the lung to a variety of organs via hematogenous spread. Extra-pulmonary involvement occurs at an advanced stage of invasive aspergillosis, and represents an ominous sign. However, few reports have been published on extra-pulmonary involvement in cases of aspergillosis. Its clinical features have not been fully clarified. We experienced a patient who developed thyrotoxicosis and fatal airway obstruction caused by invasive aspergillosis of the thyroid. A 26-year-old man was admitted to our hospital for the treatment of non-Hodgkin's lymphoma. During myelosuppression following the chemotherapy, he developed cervical swelling and hyperthyroidism. We suspected lymphoma infiltration to the thyroid, and irradiated it with a total of 26 Gy. However, the cervical lesion enlarged rapidly, and he complained of wheezing and dyspnea. We underwent immediate tracheostomy to secure the airway, but he died. Autopsy findings were striking. Extensive necrosis with diffuse infiltration of Aspergillus hyphae was observed in the thyroid gland. Necrotic tissues of the thyroid protruded into the tracheal lumen, causing airway obstruction. This case demonstrated that invasive aspergillosis of the thyroid can lead to medical emergency.