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Function and diversification of MADS-box genes in rice.

MADS-box genes play critical roles in a number of developmental processes in flowering plants, such as specification of floral organ identity, control of flowering time, and regulation of fruit development. Because of their crucial functions in flower development, diversification of the MADS-box gene family has been suggested to be a major factor responsible for floral diversity during radiation of the flowering plants. Inflorescences and flowers in the grass species have unique structures that are distinct from those in eudicots. Thus, it is plausible that the diversification of the function of MADS-box genes may have been a key driving force in the morphological divergence of the flowers and inflorescences in the grasses. Indeed, recent progress in genetic studies has shown that MADS-box genes function in flower development in Oryza sativa (rice), in support of the idea that functional diversification of the MADS-box genes was involved in evolution of the angiosperms. In this review, we summarize the functions of the major subfamilies of the MADS-box genes in rice and discuss their role in the development and evolution of rice flowers and inflorescences.

Flowers↗

Molecular evidence for Pleistocene glacial cycles driving diversification of a North American desert spider, Agelenopsis aperta.

The influence of historical climatic vs. geological changes on species diversification patterns was investigated in a widely distributed North American desert spider, Agelenopsis aperta (Araneae: Agelenidae), with particular reference to Pleistocene glacial cycles and earlier patterns of mountain building. Levels of sequence divergence obtained from the mitochondrial gene, cytochrome oxidase I, dated to the Pleistocene, eliminating Rocky Mountain orogeny as a cause of diversification, as orogeny ended 4 million years ago. The results of phylogenetic and network analyses showed the presence of three geographically defined clades, which were consistent with the presence of at least three glacial refugia: (i) east of the Rocky Mountains; (ii) between the Rocky Mountains and Sierra Nevadas; and (iii) west of the Sierra Nevadas. In addition, populations within the Rocky Mountains exhibited significantly lower genetic diversity than populations east of the Rocky Mountains and the haplotypes found within the Rockies were a subset of eastern haplotypes. These patterns suggest that a post-Pleistocene range expansion occurred out of an eastern glacial refugium into the Rocky Mountains. Examination of phylogeographical studies of other North American desert taxa indicated that mountain building explained diversification patterns more effectively for some taxa but Pleistocene climate change was more important for others, including A. aperta.

Animals↗

Patterns of diversification of Afrotropical Otiteselline fig wasps: phylogenetic study reveals a double radiation across host figs and conservatism of host association.

We studied the phylogenetic relationships of Otiteselline fig waSPS associated with Ficus in the Afrotropical region using rDNA sequences. African fig species usually host two species of Otiteselline fig waSPS. Phylogenetic analyses reveal that this pattern of association results from the radiation of two clades of waSPS superimposed on the fig system. Within each clade, wasp species generally cluster according to their host classification. The phylogenies of the two clades are also generally more congruent than expected by chance. Together these results suggest that Otiteselline wasp speciation is largely constrained by the diversification of their hosts. Finally, we show a difference in ovipositor length between the two Otiteselline species coexisting in the same Ficus species, which probably corresponds to ecological differences. The diversification of ecological niches within the fig is probably, with cospeciation, one of the key factors explaining the diversification and maintenance of species of parasites of the fig/pollinator system.

Animals↗

Somatic diversification of IgH genes in rabbit.

Rabbits have helped elucidate one of the major immunologic puzzles, namely the genetic control of antibody diversity. The primary IgH antibody repertoire in rabbits is dominated by B cells that use the same germline VH-gene segment in VDJ gene rearrangements. The VDJ genes of essentially all B lymphocytes undergo somatic diversification within the first few weeks of the rabbit's life. Such diversification occurs both by a somatic gene conversion-like mechanism as well as by somatic hyperpointmutation. The diversification that occurs early in ontogeny takes place in gut-associated lymphoid tissues and potentially depends on external factors such as microbial antigens. Few, if any, new B lymphocytes develop in adult rabbits and we discuss how the antibody repertoire is maintained throughout life. Finally, we discuss the molecular mechanism of somatic gene conversion of Ig genes, including the possibility that this involves the use of RAD51, an enzyme required for gene conversion-mediated mating type switch in yeast.

Animals↗

Comparative genomics reveals lineage-associated structural variation and diversification in a barley fungal pathogen.

Leaf rust, caused by Puccinia hordei, is a major barley disease worldwide. Despite repeated shifts in virulence, contrasting reproductive histories, and emerging fungicide insensitivity, the genomic basis of its diversification and adaptation remains poorly understood. In this study, we generated haplotype-resolved, chromosome-level genome assemblies for two isolates with contrasting virulence and analyzed 41 Australian isolates collected over 54 yr (1966-2020), integrating comparative and population genomics, mating-type gene phylogenies, chromosome-specific k-mer profiling, genome-wide copy-number variation (CNV) analysis, and gene-expression analysis. We identified a structurally dynamic chromosome characterized by repeat-associated rearrangements, structural variation, and lineage-associated CNV, representing the first evidence in a rust fungus of chromosome-scale structural diversification of this extent. Population analyses distinguished clonally expanded lineages from recombination-associated lineages, with mating-type gene phylogenies providing further support for lineage differentiation. More recently collected isolates showed increased duplication-associated variation, and CNV boundaries were associated with structural-variant breakpoints. We also identified lineage-associated amplification of Cyp51, with increased copy number associated with higher transcript abundance, supporting a potential role in fungicide adaptation. Overall, our findings highlight structural variation, contrasting reproductive histories, and lineage-associated CNV as important contributors to diversification in P. hordei, providing insights for future rust pathogen surveillance and management strategies.

Cyp51 gene↗

Ongoing diversification of the rearranged immunoglobulin light-chain gene in a bursal lymphoma cell line.

The chicken immunoglobulin light-chain gene (IgL) encodes only a single variable gene segment capable of recombination. To generate an immune repertoire, chickens diversify this unique rearranged VL gene segment during B-cell development in the bursa of Fabricius. Sequence analysis of IgL cDNAs suggests that both gene conversion events derived from VL segment pseudogene templates (psi VL) and non-template-derived single-base-pair substitutions contribute to this diversity. To facilitate the study of postrecombinational mechanisms of immunoglobulin gene diversification, avian B-cell lines were examined for the ability to diversify their rearranged IgL gene during in vitro passage. One line that retains this ability, the avian leukosis virus-induced bursal lymphoma cell line DT40, has been identified. After passage for 1 year in culture, 39 of 51 randomly sequenced rearranged V-J segments from a DT40 population defined novel subclones of the parental tumor. All cloned V-J segments displayed the same V-J joint, confirming that the observed diversity arose after V-J rearrangement. Most sequence variations that we observed (203 of 220 base pairs) appeared to result from psi VL-derived gene conversion events; 16 of the 17 novel single nucleotide substitutions were transitions. Based on these data, it appears that immunoglobulin diversification during in vitro passage of DT40 cells is representative of the diversification that occurs during normal B-cell development in the bursa of Fabricius.

Alleles↗

Late diversification in the clonal composition of human cytomegalovirus-specific CD8+ T cells following allogeneic hemopoietic stem cell transplantation.

To investigate the mechanisms of human T-cell reconstitution following allogeneic hemopoietic stem cell transplantation (alloSCT), we analyzed the clonal composition of human cytomegalovirus (HCMV)-specific or Epstein-Barr virus (EBV)-specific CD8+ T cells in 10 alloSC transplant recipients and their donors. All virus-specific CD8+ T-cell clones isolated from recipients after alloSCT contained DNA of donor origin. In all 6 D+/R+ sibling alloSCTs from seropositive donors into seropositive recipients, donor virus-specific clones transferred in the allograft underwent early expansion and were maintained long term in the recipient. In contrast, in 2 of 3 HCMV D+/R- alloSC transplant recipients in whom there was no detectable HCMV infection, donor HCMV-specific clones were undetectable, whereas donor EBV-specific clones were maintained in the same EBV-seropositive recipients, suggesting that transferred clones require antigen for their maintenance. Following D-/R+ transplantation from 3 seronegative donors into seropositive recipients, a delayed primary virus-specific CD8+ T-cell response was observed, in which the T cells contained donor DNA, suggesting that new antigen-specific T cells arose in the recipient from donor-derived progenitors. In 2 of 4 HCMV D+/R+ sibling allograft recipients the clonal composition underwent diversification as compared with their donors, with delayed persistent expansion of HCMV-specific clones that were undetectable in the donor or in the recipient during the early months after transplantation; this diversification may represent expansion of new clones generated from donor-derived progenitors. We conclude that, following alloSCT, late diversification of the HCMV-specific CD8+ T-cell clonal repertoire can occur in response to persistent viral antigen.

Adult↗

Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans.

BACKGROUND: Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have shaped the evolutionary history of diverse terrestrial organisms. Living xenarthrans (armadillos, anteaters and sloths) constitute an ideal model for studying the influence of past environmental changes on species diversification. Indeed, extant xenarthran species are relicts from an evolutionary radiation enhanced by their isolation in South America during the Tertiary era, a period for which major climate variations and tectonic events are relatively well documented. RESULTS: We applied a Bayesian approach to three nuclear genes in order to relax the molecular clock assumption while accounting for differences in evolutionary dynamics among genes and incorporating paleontological uncertainties. We obtained a molecular time scale for the evolution of extant xenarthrans and other placental mammals. Divergence time estimates provide substantial evidence for contemporaneous diversification events among independent xenarthran lineages. This correlated pattern of diversification might possibly relate to major environmental changes that occurred in South America during the Cenozoic. CONCLUSIONS: The observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans. Our findings open ways to test this hypothesis further in other South American mammalian endemics like hystricognath rodents, platyrrhine primates, and didelphid marsupials.

Animals↗

Distinct clonal Ig diversification patterns in young appendix compared to antigen-specific splenic clones.

The young rabbit appendix is a dynamic site for primary B cell repertoire development. To study diversification patterns during clonal expansion, we collected single appendix B cells from 3- to 9-wk-old rabbits and sequenced rearranged H and L chain genes. Single cells obtained by hydraulic micromanipulation or laser capture microdissection were lysed, PCR amplified, and products directly sequenced. Gene conversion-like changes occurred in rearranged H and L chain sequences by 3-4 wk of age. Somatic mutations were found in the D regions that lack known conversion donors and probably also occurred in the V genes. A few small sets of clonally related appendix B cells were found at 3-5 wk; by 5.5 wk, some larger clones were recovered. The diversification patterns in the clones from appendix were strikingly different from those found previously in splenic germinal centers where an immunizing Ag was driving the expansion and selection process toward high affinity. Clonally related appendix B cells developed different amino acid sequences in each complementarity-determining region (CDR) including CDR3, whereas dominant clones from spleen underwent few changes in CDR3. The variety of combining sites generated by diversification within individual clones suggests that at least some clonal expansion and selection, known to require normal gut flora, may be driven through indirect effects of microbial components rather than solely by their recognition as specific foreign Ags. This diversity of combining sites within B cell clones supports the proposed role of appendix in generating the preimmune repertoire.

Amino Acid Sequence↗

Diversification behavior of multihospital systems: patterns of change, 1983-1985.

Studies of diversification in the health care sector have typically focused on hospital-level activity. Little attention has been given to the broader organizational context in which many hospitals operate (multihospital systems, parent holding companies). This article empirically examines diversification behavior of 100 multihospital systems between 1983 and 1985 in order to assess how systems respond to resource constraints, uncertainty, and competitive pressures on inpatient care. Patterns of diversification are identified, and their implications for systems strategic behavior are discussed.

Commerce↗

Financial and organizational determinants of hospital diversification into subacute care.

OBJECTIVE: To examine the financial, market, and organizational determinants of hospital diversification into subacute inpatient care by acute care hospitals in order to guide hospital managers in undertaking such diversification efforts. STUDY SETTING: All nongovernment, general, acute care, community hospitals that were operating during the years 1985 through 1991 (3,986 hospitals in total). DATA SOURCES: Cross-sectional, time-series data were drawn from the American Hospital Association's (AHA) Annual Survey of Hospitals, the Health Care Financing Administration's (HCFA) Medicare Cost Reports, a latitude and longitude listing for all community hospital addresses, and the Area Resource File (ARF) published in 1992, which provides county level environmental variables. STUDY DESIGN: The study is longitudinal, enabling the specification of temporal patterns in conversion, causal inferences, and the treatment of right-censoring problems. The unit of analysis is the individual hospital. KEY FINDINGS: Significant differences were found in the average level of subacute care offered by investor-owned versus tax-exempt hospitals. After controlling for selection bias, financial performance, risk, size, occupancy, and other variables, IO hospitals offered 31.3 percent less subacute care than did NFP hospitals. Financial performance and risk are predictors of IO hospitals' diversification into subacute care, but not of NFP hospitals' activities in this market. Resource availability appears to expedite expansion into subacute care for both types of hospitals. CONCLUSIONS: Investment criteria and strategy differ between investor-owned and tax-exempt hospitals.

Cross-Sectional Studies↗

The origin and diversification of Galapagos mockingbirds.

Evolutionary radiations of colonists on archipelagos provide valuable insight into mechanisms and modes of speciation. The apparent diversification of Galapagos mockingbirds (Nesomimus) provoked Darwin's initial conception of adaptive radiation, but the monophyly of this historically important exemplar has not been evaluated with molecular data. Additionally, as with most Galapagos organisms, we have a poor understanding of the temporal pattern of diversification of the mockingbirds following colonization(s) from source populations. Here we present a molecular phylogeny of Galapagos and other mockingbird populations based on mitochondrial sequence data. Monophyly of Galapagos mockingbirds was supported, suggesting a single colonization of the archipelago followed by diversification. Our analyses also indicate that Nesomimus is nested within the traditional genus Mimus, making the latter paraphyletic, and that the closest living relatives of Galapagos mockingbirds appear to be those currently found in North America, northern South America, and the Caribbean, rather than the geographically nearest species in continental Ecuador. Thus, propensity for over-water dispersal may have played a more important role than geographic proximity in the colonization of Galapagos by mockingbirds. Within Galapagos, four distinct mitochondrial DNA clades were identified. These four clades differ from current taxonomy in several important respects. In particular, mockingbirds in the eastern islands of the archipelago (Española, San Cristóbal, and Genovesa) have very similar mitochondrial DNA sequences, despite belonging to three different nominal species, and mockingbirds from Isabela, in the west of the archipelago, are more phylogenetically divergent than previously recognized. Consistent with current taxonomy is the phylogenetic distinctiveness of the Floreana mockingbird (N. trifasciatus) and close relationships among most mockingbirds from the central and northern region of the archipelago (currently considered conspecific populations of N. parvulus). Overall, phylogeographic patterns are consistent with a model of wind-based dispersal within Galapagos, with colonization of more northerly islands by birds from more southern populations, but not the reverse. Further radiation in Galapagos would require coexistence of multiple species on individual islands, but this may be prevented by relatively limited morphological divergence among mockingbirds and by lack of sufficient habitat diversity in the archipelago to support more than one omnivorous mimid.

Animals↗

Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp.

An important question in evolutionary biology is how polyploidization generates raw material for phenotypic diversification. Transposable elements (TEs) represent an underestimated source of genetic variation in eukaryotic genomes. By integrating 516 whole-genome resequencing datasets and 236 transcriptomes from common carp (Cyprinus carpio), a representative allotetraploid fish, we constructed the first population-scale landscape of TE insertions in teleosts. TE insertions are widespread in the carp genome and preferentially associated with stress-responsive genes, with DNA transposons as major contributors. Relaxed purifying selection and TE burst events coexist, generating abundant variation for subsequent subspecies differentiation. Compared with a closely related diploid species, carp exhibits more exonic TE insertions and shorter TE-gene distances, and multiple TE superfamilies expanded during tetraploidization. Genome-wide association analyses uncovered intragenic TE variants underlying domesticated traits missed by SNPs, including DNA transposon deletions associated with scale reduction and altered body shape. Notably, lighter-colored individuals harbor homozygous deletions of LTR and DNA transposons within mdfic2, whose knockout in zebrafish reduces pigmentation. Most trait-associated variants reflect lineage-specific loss of ancient TE insertions rather than recent transposition. Overall, these findings highlight the distinct role of TEs in polyploid genome evolution and phenotypic diversification, providing new insights into TE dynamics in vertebrates.

allotetraploidization↗

Gene expression, cellular diversification and tumor progression to the metastatic phenotype.

Alterations in the expression of certain genes or in their products can render benign tumor cells metastatic. Experimentally this has been quickly performed by transferring dominantly acting oncogenes such as c-H-rasEJ into susceptible cells, but in vivo such a rapid qualitative change in a dominantly acting oncogene occurs only rarely, and progression to highly metastatic phenotypes is thought to occur through a slow stepwise process. Such slow changes can be reversible and need not involve known dominantly acting oncogenes, consistent with clinical observations. An important element of the natural progression of tumors to malignancy may be their ability to circumvent microenvironmental controls that regulate growth and cellular diversity and to evolve into heterogeneous phenotypes, a process that appears to involve mainly quantitative changes in gene expression but which can be rapidly stimulated in cell culture by the introduction of a dominantly acting oncogene. It is proposed that the highly malignant cells that have slowly evolved in vivo with only a few qualitative gene changes have undergone extensive cycles of diversification and accumulation of quantitative changes in the expression of genes that encode products that are related to malignancy and metastasis. Thus, highly malignant cellular phenotypes can arise quickly through specific qualitative changes in critical controlling genes or more slowly by less critical qualitative genetic changes, coupled with cellular diversification and accumulation of quantitative changes in gene expression.

Animals↗

Functional differentiation and repertoire diversification of T cells derived from single progenitor cells.

Functions of T cells derived from single progenitor cells were investigated. B10. Thy-1.1 recipient mice were either whole body-irradiated and marrow reconstituted or thymus-shielded, irradiated and marrow reconstituted, and limited numbers (3 x 10(3) or 6 x 10(3] of a 1:1 mixture of bone marrow cells from C57BL/6 and B6.Lyt-2.1 mice were transferred intrathymically (i.t.). Donor-type (Thy-1.2+) cells of the thymus of a small portion of recipients which expressed the phenotype of either Ly-2.2 or Ly-2.1 but not both were regarded to be a clone of T cells derived from a single progenitor cell, and such clones were assayed for polyclonal helper (Th) and polyclonal cytolytic (CTL) activities as well as alloantigen-specific proliferative (mixed lymphocyte reaction; MLR) and CTL activities. Clones taken 4 weeks after transfer (4-week-old clones) which were generated in the thymus of whole body-irradiated recipients showed polyclonal CTL but not polyclonal Th activity, whereas 4-week-old clones generated in the thymus of thymus-shielded recipients showed both polyclonal CTL and Th activities. Similarly, 4-week-old clones generated in whole body-irradiated recipients responded with CTL to alloantigens when induced in the presence of T cell growth factors but not with MLR, whereas 4-week-old clones generated in thymus-shielded recipients showed both MLR and CTL to alloantigens. Repertoire diversification of 4-week-old clones, however, was incomplete, since clones generated in whole body-irradiated recipient did not necessarily respond with CTL to all alloantigens examined, and those generated in thymus-shielded recipients did not necessarily respond with MLR to all the antigens. On the other hand, T cell clones were shown to fully mature by 7 weeks after transfer in terms of cell function as well as repertoire diversification.

Animals↗

Immunoglobulin diversification in embryonic chicken bursae and in individual bursal follicles.

Previous studies have shown that the same immunoglobulin (Ig) V lambda gene (V lambda 1) is rearranged in all chicken B cells, and that extensive sequence diversification of this gene occurs during B cell development in the bursa of Fabricius. We used two-dimensional gel electrophoresis to compare the heterogeneity of Ig lambda light chains produced by B cells at different stages of bursal development. Somatically diversified light chains were observed in Ig molecules produced by bursal cells as early as 15 days of embryonic incubation. The two principal species of light chain observed probably represent glycosylated and nonglycosylated forms of lambda chain encoded by alleles of a single lambda gene. Extensive diversification was observed during late embryogenesis. We also studied lambda light chain diversity in cyclophosphamide-treated birds repopulated with normal bursal cells. In these birds, individual bursal follicles are repopulated by single B cell precursors. Follicular cells derived from single B cell precursors were able to produce a spectrum of light chains almost as diverse as that of the total bursal cell population. We used two monoclonal anti-idiotype antibodies to study idiotype expression in individual normal or reconstituted follicles. About 30% of follicles contained 0.1% to 5% of lymphocytes which reacted with one or both of the antibodies. The results indicate that within individual bursal follicles bursa stem cells undergo Ig hyperdiversification.

Animals↗

Diversification of hypervariable region 1 of hepatitis C virus after liver transplantation.

Liver transplantation represents a unique model for studying hepatitis C virus (HCV) evolution. In the current study, we estimated the dynamics of HCV quasispecies evolution over a period of 2.5 years both in sera and in tissues, including three different anatomic sites of the liver in a patient undergoing liver transplantation. The patient displayed an extremely homologous virus population in either serum or liver at each time point after liver transplantation. However, there was a successive diversification of hypervariable region 1 (HVR1) of HCV under such an im-munocompromised status and the preexistence of matching HVR1 antibodies. This distinct evolutionary pattern of HVR1 suggests that immunosuppressed status does contribute to diminished genetic diversity of HVR1 at a given time point after liver transplantation. However, the dramatic diversification of HVR1 sequence over time is mainly due to the adaptation of new replicative site, the donor liver, indicating that HCV may obtain the higher replication fitness by mutating HVR1 domain.

Amino Acid Sequence↗

Isologous diversification for robust development of cell society.

Isologous diversification, proposed for cell differentiation, is shown to be stable against molecular and other external fluctuations, where amplification of noise-induced slight difference between cells leads to a noise-tolerant society with differentiated cell types. It is a general consequence of interacting cells with biochemical networks and cell divisions, as is confirmed by several model simulations. According to the theory, differentiation proceeds first by loss of synchrony of intracellular oscillations as the number of cells increases. Then the chemical composition of the cells is differentiated. The differentiated compositions become inherited by the next generation, and lead to determined cell types. As a result of successive occurrence of the cell differentiation, the cell society will be composed of different cell types. The whole developmental process is robust not only against molecular fluctuations but also against the removal of a cluster of cells. This robustness is a remarkable feature of isologous diversification, in contrast to the conventional threshold-type mechanism for development. As a testable consequence of the theory, we also discuss interaction-dependent tumor formation and negative correlation between growth speed and chemical diversity.

Animals↗