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PubMed2003

Mechanisms of autoantibody diversification to SLE-related autoantigens.

Systemic lupus erythematosus is a prototype of systemic autoimmunity with autoantibodies (autoAbs) to ribonucleoproteins such as Ro/La, snRNP, dsDNA, and other cellular constituents. A/J mice were used to explore the mechanism of autoAb diversification with recombinant proteins and synthetic peptides. Previous studies showed that Ro60(316-335) induced Abs to Ro60, La, and snRNP proteins. Specific Abs to determinants outside Ro60(316-335) were detected. Absorption experiments showed that Abs to La and snRNP proteins were due to the induction of anti-Ro60 Abs cross-reactive with these peptides. With snRNP proteins, SmD, SmB, and A-RNP as immunogens, specific patterns of intermolecular spreading were obtained in addition to Abs to the immunogens. With SmD-immunized mice, specific Abs to A-RNP and SmB were detected. With SmB as the immunogen, specific Abs to A-RNP were detected in the majority of the mice. Only in a rare incident, specific Abs to SmD were induced. In A-RNP-immunized mice, only Abs to the 70-kD U1-RNP were seen. In all cases, Abs capable of precipitating snRNP particles were detected. Thus, the intermolecular epitope spreading is immunogen-dependent. Evidence for the presence of cross-reactive T cells to more than one autoAg was obtained. The Ag-dependent unique patterns of Ab diversification will facilitate analyses of patients' sera. These results have implications regarding the nature of the Ag-driven autoimmune process.

Amino Acid Sequence↗
PubMed2025

Doubled Genomes, Divergent Fates: Genomic Insights Into Diversification in an Allotetraploid Cavefish.

Cave environments impose unique challenges that drive remarkable genetic and phenotypic changes in cave-dwelling organisms. In this study, we investigated the genomic basis of adaptation in the small eye golden-line fish (Sinocyclocheilus microphthalmus), an allotetraploid cavefish endemic to Guangxi, China. Using whole-genome resequencing data from 47 individuals across six cave locations, we examined how neutral and selective forces influence diversification. Our analyses uncovered significant population structure indicative of allopatric divergence, along with evidence of locus-specific selection contributing to genomic differentiation. We identified seven single outlier clusters (SOCs), each tied to the divergence of specific populations, underscoring the role of local processes in driving diversity. Genes associated with vision showed relaxed selection, likely reflecting adaptation to darkness, while positive selection on other loci revealed additional functional shifts. Notably, allopolyploidy was found to fuel divergence through subgenome-specific patterns and asymmetric evolution within SOCs and among homoeologs. Taken together, these findings provide valuable insights into mechanisms of cave evolution and illustrate how allotetraploid genomes can facilitate diversification, potentially contributing to speciation in extreme environments.

Animals↗
PubMed2025

Historical introgression as a driver of diversification of diploid Picris (Compositae) in the Mediterranean Basin.

The Mediterranean Basin is recognized as one of the world's most prominent biodiversity hotspots, where past climatic changes have driven range shifts, secondary contact between populations, and gene exchange. This study investigates the impact of historical introgression on the diversification of diploid members of the genus Picris (Compositae). Using nuclear and plastid genome data obtained through the Hyb-Seq approach, we assess whether introgression contributed to the evolution of the Mediterranean Picris, potentially giving rise to multiple regional endemics. We also test whether introgression was associated with the transfer of traits such as life strategy and fruit morphology, which are involved in habitat-specific adaptation. Phylogenetic network analysis revealed two major introgression events that shaped evolutionary trajectories within the genus. The earliest and most complex events involved the Turkish endemic P. campylocarpa, which hybridized with the most recent common ancestor (MRCA) of the P. cyprica-P. pauciflora lineage and with the MRCA of the B1 subclade, comprising the P. hieracioides group and the P. scaberrima-P. strigosa lineage. The latter introgression preceded shifts from iteroparity to semelparity and from heterocarpy to homocarpy, ruling out an adaptive introgression origin for these traits. Nevertheless, all detected historical introgression events contributed to the diversification of diploid Picris taxa.

Diploidy↗
PubMed2003

Genomic diversification among archival strains of Salmonella enterica serovar typhimurium LT7.

To document genomic changes during long periods of storage, we analyzed Salmonella enterica serovar Typhimurium LT7, a mutator strain that was previously reported to have higher rates of mutations compared to other serovar Typhimurium strains such as LT2. Upon plating directly from sealed agar stabs that had been stocked at room temperature for up to four decades, many auxotrophic mutants derived from LT7 gave rise to colonies of different sizes. Restreaking from single colonies consistently yielded colonies of diverse sizes even when we repeated single-colony isolation nine times. Colonies from the first plating had diverse genomic changes among and even within individual vials, including translocations, inversions, duplications, and point mutations, which were detected by rare-cutting endonuclease analysis with pulsed-field gel electrophoresis. Interestingly, even though the colony size kept diversifying, all descendents of the same single colonies from the first plating had the same sets of detected genomic changes. We did not detect any colony size or genome structure diversification in serovar Typhimurium LT7 stocked at -70 degrees C or in serovar Typhimurium LT2 stocked either at -70 degrees C or at room temperature. These results suggest that, although colony size diversification occurred during rapid growth, all detected genomic changes took place during the storage at room temperature and were carried over to their descendents without further changes during rapid growth in rich medium. We constructed a genomic cleavage map on the LT7 strain that had been stocked at -70 degrees C and located all of the detected genomic changes on the map. We speculated on the significance of mutators for survival and evolution under environmentally stressed conditions.

Biological Specimen Banks↗
PubMed2005

Diversification of DNA sequences in the symbiotic genome of Rhizobium etli.

Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification.

DNA, Bacterial↗
PubMed1998

Multigene tracking of hepatitis C virus quasispecies after liver transplantation: correlation of genetic diversification in the envelope region with asymptomatic or mild disease patterns.

To investigate the role of hepatitis C virus (HCV) quasispecies mutation in the pathogenesis of HCV infection, we analyzed changes in the genetic diversity of HCV genomes in 22 patients before and after liver transplantation by using heteroduplex mobility assay (HMA) technology. All patients were infected with HCV genotype 1 and developed high-titer posttransplant viremia. Each patient was classified according to the severity of posttransplant hepatitis, as assessed by standard biochemical and histological criteria. HCV quasispecies were characterized by HMA analysis of eight separate subgenomic regions of HCV, which collectively comprise 44% of the entire genome. The glycoprotein genes E1 and E2, as well as the nonstructural protein genes NS2 and NS3, had the greatest genetic divergence after liver transplantation (the change in the heteroduplex mobility ratio [HMR] ranged from 2.5 to 7.0%). In contrast, genes encoding the core, NS4, and NS5b proteins had the least amount of genetic divergence after liver transplantation (range, 0.3 to 1.2%). The E1/E2 region showed the greatest change in genetic diversity after liver transplantation, and the change in HMRs was 2.5- to 3.3-fold greater in patients with asymptomatic or moderate disease than in those with severe disease. The E1-5' region of HCV quasispecies isolated from patients in the asymptomatic group had a significantly greater degree of diversification after liver transplantation than the same regions of HCV quasispecies isolated from patients in the severe disease group (P = 0.05). While changes in the genetic diversity of some nonstructural genes were also greater in asymptomatic patients or in patients with mild disease than in patients with severe disease, the results were not significant. Data from this cohort demonstrate that greater rates of HCV quasispecies diversification are associated with mild or moderate liver disease activity in this immunosuppressed population.

Base Sequence↗
PubMed1998

Extensive diversification of human immunodeficiency virus type 1 subtype B strains during dual infection of a chimpanzee that progressed to AIDS.

A chimpanzee (C-499) infected for more than 9 years with two subtype B isolates of human immunodeficiency virus type 1 (HIV-1), one (HIV-1(SF2)) that replicates poorly and one (HIV-1(LAV-1b)) that replicates efficiently in chimpanzees, died of AIDS 11 years after initial infection (F. J. Novembre et al., J. Virol. 71:4086-4091, 1997). Nucleotide sequence and phylogenetic analyses of the C2 to V5 region of env (C2-V5env) in proviral DNA from peripheral blood lymphocytes obtained 22 months before death revealed two distinct virus populations. One of these populations appeared to be a recombinant in env, having the V3 loop from HIV-1(SF2) and the V4-V5 region from HIV-1(LAV-1b); the other population had evolved from HIV-1(LAV-1b). In addition to C2-V5env, the entire p17gag and nef genes were sequenced; however, based on nucleotide sequences and phylogeny, whether the progenitor of the p17gag and nef genes was SF2 or LAV-1b could not be determined. Compared to the two original viruses, the divergence of all clones of C2-V5env ranged from 9.37 to 20.2%, that of p17gag ranged from 3.11 to 9.29%, and that of nef ranged from 4.02 to 7.9%. In contrast, compared to the maximum variation of 20.2% in C2-V5env for C-499, the maximum diversities in C2-V5env in proviruses from two chimpanzees infected with HIV-1(LAV-1b) for 9 and 10 years were 9.65 and 2.48%, respectively. These results demonstrate that (i) two distinct HIV-1 populations can coexist and undergo extensive diversification in chimpanzees with progressive HIV-1-induced disease and (ii) recombination between two subtype B strains occurred even though the second strain was inoculated 15 months after the first one. Furthermore, evaluation of env genes from three chimpanzees infected with the same strain suggests that the magnitude of HIV-1 diversification could be related to higher viral burdens, manifestations of disease, and/or dual infection.

Acquired Immunodeficiency Syndrome↗
PubMed1999

Effect of retreatment with interferon alone or interferon plus ribavirin on hepatitis C virus quasispecies diversification in nonresponder patients with chronic hepatitis C.

Alpha interferon (IFN-alpha) treatment is effective on a long-term basis in only 15 to 25% of patients with chronic hepatitis C. The results of recent trials indicate that response rates can be significantly increased when IFN-alpha is given in combination with ribavirin. However, a large number of patients do not respond even to combination therapy. Nonresponsiveness to IFN is characterized by evolution of the hepatitis C virus (HCV) quasispecies. Little is known about the changes occurring within the HCV genomes when nonresponder patients are retreated with IFN or with IFN plus ribavirin. In the present study we have examined the genetic divergence of HCV quasispecies during unsuccessful retreatment with IFN or IFN plus ribavirin. Fifteen nonresponder patients with HCV-1 (4 patients with HCV-1a and 11 patients with HCV-1b) infection were studied while being retreated for 2 months (phase 1) with IFN-alpha (6 MU given three times a week), followed by IFN plus ribavirin or IFN alone for an additional 6 months (phase 2). HCV quasispecies diversification in the E2 hypervariable region-1 (HVR1) and in the putative NS5A IFN sensitivity determining region (ISDR) were analyzed for phase 1 and phase 2 by using the heteroduplex tracking assay and clonal frequency analysis techniques. A major finding of this study was the relatively rapid evolution of the HCV quasispecies observed in both treatment groups during the early phase 1 compared to the late phase 2 of treatment. The rate of quasispecies diversification in HVR1 was significantly higher during phase 1 versus phase 2 both in patients who received IFN plus ribavirin (P = 0.017) and in patients who received IFN alone (P = 0. 05). A trend toward higher rates of quasispecies evolution in the ISDR was also observed during phase 1 in both groups, although the results did not reach statistical significance. However, the NS5A quasispecies appeared to be rather homogeneous and stable in most nonresponder patients, suggesting the presence of a single well-fit major variant, resistant to antiviral treatment, in agreement with published data which have identified an IFN sensitivity determinant region within the NS5A. During the entire 8 months of retreatment, there was no difference in the rate of fixation of mutation between patients who received combination therapy and patients who were treated with IFN alone, suggesting that ribavirin had no major effects on the evolution of the HCV quasispecies after the initial 2 months of IFN therapy.

Adult↗
PubMed2005

Exploitation of convenience food in view of a diet diversification for better nutrition.

Social and economic changes as well as technological innovations in recent years, have caused dramatic changes regarding the kind of nutrition supply observed. The provoking question now is, if a recommendable nutrition and diet diversification is possible with the convenience products available on the market at present. Depending on the degree of cooking or preparation the following convenience steps can be differentiated: initial grade--ready-for-kitchen processing--ready-to-cook--ready-to-mix--ready-to-heat--ready-to-eat. Various preservation strategies can be applied to the food products of each step. In order to keep the nutritional and sensory quality of the food product, these necessary preservation methods should, of course, be as gentle as possible. On each convenience-step a large variety of products exists. By separation of preparation from consumption and the therefore necessary preservation methods, these products are available throughout the whole year. Seasonal limitations are less important, which enhances diet diversification. On the other hand, an impoverishment in raw materials occurs due to the existing concentration tendencies in food production and especially in food trade.

Cooking↗
PubMed2002

V(D)J recombinatorial repertoire diversification during intraclonal pro-B to B-cell differentiation.

The initial B-cell repertoire is generated by combinatorial immunoglobulin V(D)J gene segment rearrangements that occur in a preferential sequence. Because cellular proliferation occurs during the course of these rearrangement events, it has been proposed that intraclonal diversification occurs during this phase of B-cell development. An opportunity to examine this hypothesis directly was provided by the identification of a human acute lymphoblastic leukemic cell line that undergoes spontaneous differentiation from pro-B cell to the pre-B and B-cell stages with concomitant changes in the gene expression profile that normally occur during B-cell differentiation. After confirming the clonality of the progressively differentiating cells, an analysis of immunoglobulin genes and transcripts indicated that pro-B cell members marked by the same DJ rearrangement generated daughter B cells with multiple V(H) and V(L) gene segment rearrangements. These findings validate the principle of intraclonal V(D)J diversification during B-cell generation and define a manipulable model of human B-cell differentiation.

Antibody Diversity↗
PubMed2006

Polyphyly of the hawk genera Leucopternis and Buteogallus (Aves, Accipitridae): multiple habitat shifts during the Neotropical buteonine diversification.

BACKGROUND: The family Accipitridae (hawks, eagles and Old World vultures) represents a large radiation of predatory birds with an almost global distribution, although most species of this family occur in the Neotropics. Despite great morphological and ecological diversity, the evolutionary relationships in the family have been poorly explored at all taxonomic levels. Using sequences from four mitochondrial genes (12S, ATP8, ATP6, and ND6), we reconstructed the phylogeny of the Neotropical forest hawk genus Leucopternis and most of the allied genera of Neotropical buteonines. Our goals were to infer the evolutionary relationships among species of Leucopternis, estimate their relationships to other buteonine genera, evaluate the phylogenetic significance of the white and black plumage patterns common to most Leucopternis species, and assess general patterns of diversification of the group with respect to species' affiliations with Neotropical regions and habitats. RESULTS: Our molecular phylogeny for the genus Leucopternis and its allies disagrees sharply with traditional taxonomic arrangements for the group, and we present new hypotheses of relationships for a number of species. The mtDNA phylogenetic trees derived from analysis of the combined data posit a polyphyletic relationship among species of Leucopternis, Buteogallus and Buteo. Three highly supported clades containing Leucopternis species were recovered in our phylogenetic reconstructions. The first clade consisted of the sister pairs L. lacernulatus and Buteogallus meridionalis, and Buteogallus urubitinga and Harpyhaliaetus coronatus, in addition to L. schistaceus and L. plumbeus. The second clade included the sister pair Leucopternis albicollis and L. occidentalis as well as L. polionotus. The third lineage comprised the sister pair L. melanops and L. kuhli, in addition to L. semiplumbeus and Buteo buteo. According to our results, the white and black plumage patterns have evolved at least twice in the group. Furthermore, species found to the east and west of the Andes (cis-Andean and trans-Andean, respectively) are not reciprocally monophyletic, nor are forest and non-forest species. CONCLUSION: The polyphyly of Leucopternis, Buteogallus and Buteo establishes a lack of concordance of current Accipitridae taxonomy with the mtDNA phylogeny for the group, and points to the need for further phylogenetic analysis at all taxonomic levels in the family as also suggested by other recent analyses. Habitat shifts, as well as cis- and trans-Andean disjunctions, took place more than once during buteonine diversification in the Neotropical region. Overemphasis of the black and white plumage patterns has led to questionable conclusions regarding the relationships of Leucopternis species, and suggests more generally that plumage characters should be used with considerable caution in the taxonomic evaluation of the Accipitridae.

Animals↗
PubMed2006

Cardioblast-intrinsic Tinman activity controls proper diversification and differentiation of myocardial cells in Drosophila.

The NK homeobox gene tinman (tin) is required for the specification of the cardiac, visceral muscle and somatic muscle progenitors in the early dorsal mesoderm of Drosophila. Like its vertebrate counterpart Nkx2.5, the expression of tin is maintained in cardiac cells during cardiac maturation and differentiation; however, owing to the complete lack of a dorsal vessel in tin mutant embryos, the function of tin in these cells has not been defined. Here we show that myocardial cells and dorsal vessels can form even though they lack Tin, and that viable adults can develop, as long as Tin is provided in the embryonic precardiac mesoderm. However, embryos in which tin expression is specifically missing from cardial cells show severe disruptions in the normal diversification of the myocardial cells, and adults exhibit severe defects in cardiac remodeling and function. Our study reveals that the normal expression and activity of Tin in four of the six bilateral cardioblasts within each hemisegment of the heart allows these cells to adopt a cell fate as ;working' myocardium, as opposed to a fate as inflow tract (ostial) cells. This function of tin involves the repression of Dorsocross (Doc) T-box genes and, hence, the restriction of Doc to the Tin-negative cells that will form ostia. We conclude that tin has a crucial role within myocardial cells that is required for the proper diversification, differentiation, and post-embryonic maturation of cardiomyocytes, and we present a pathway involving regulatory interactions among seven-up, midline, tinman and Dorsocross that establishes these developmental events upon myocardial cell specification.

Animals↗
PubMed2025

Diversification, loss, and virulence gains of the major effector AvrStb6 during continental spread of the wheat pathogen Zymoseptoria tritici.

Interactions between plant pathogens and their hosts are highly dynamic and mainly driven by pathogen effectors and plant receptors. Host-pathogen co-evolution can cause rapid diversification or loss of pathogen genes encoding host-exposed proteins. The molecular mechanisms that underpin such sequence dynamics remains poorly investigated at the scale of entire pathogen species. Here, we focus on AvrStb6, a major effector of the global wheat pathogen Zymoseptoria tritici, evolving in response to the cognate receptor Stb6, a resistance widely deployed in wheat. We comprehensively captured effector gene evolution by analyzing a global thousand-genome panel using reference-free sequence analyses. We found that AvrStb6 has diversified into 59 protein isoforms with a strong association to the pathogen spreading to new continents. Across Europe, we found the strongest differentiation of the effector consistent with high rates of Stb6 deployment. The AvrStb6 locus showed also a remarkable diversification in transposable element content with specific expansion patterns across the globe. We detected AvrStb6 gene losses and evidence for transposable element-mediated disruptions. We used virulence datasets of genome-wide association mapping studies to predict virulence changes across the global panel. Genomic predictions suggested marked increases in virulence on Stb6 cultivars concomitant with the spread of the pathogen to Europe and the subsequent spread to further continents. Finally, we genotyped French bread wheat cultivars for Stb6 and monitored resistant cultivar deployment concomitant with AvrStb6 evolution. Taken together, our data provides a comprehensive view of how a rapidly diversifying effector locus can undergo large-scale sequence changes concomitant with gains in virulence on resistant cultivars. The analyses highlight also the need for large-scale pathogen sequencing panels to assess the durability of resistance genes and improve the sustainability of deployment strategies.

Ascomycota↗
PubMed2025

Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans.

Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.

Xanthomonas↗
PubMed2006

Antibody diversification: mutational mechanisms and oncogenesis.

Antibody diversification processes play a major role in protecting humans from pathogens. Somatic hypermutation and gene conversion increase the affinity of pathogen-specific antibodies by changing the sequence within antibody variable genes, while the class switch recombination (CSR) process changes the antibody's effector function by replacing the constant region of the antibody gene with a different constant region. Activation-induced cytidine deaminase (AID) initiates each of these three processes by deaminating cytidines within antibody genes, while a host of other DNA transacting factors are involved in either creating new mutations or repairing DNA lesions introduced during these processes. This review will discuss the main features of antibody diversification and their role in lymphomagenesis, highlight outstanding issues and questions that remain in the field, and discuss our contributions to this field.

Antibody Diversity↗
PubMed2006

Global variation in the diversification rate of passerine birds.

Net diversification rates were estimated for samples of primarily tribe-to-family-level clades of passerine birds, taking into account extinction as well as speciation. Two samples were used. The first consisted of 37 clades of primarily temperate North American and primarily tropical South American passerines; the second comprised a global set of 90 clades, each distributed within one or more zoogeographic regions. Circumscription and ages of clades were taken from Sibley and Ahlquist's phylogeny based on DNA hybridization, with updates from more recent sequence analysis. Under a homogeneous speciation (rate = lamda) and extinction (rate = mu) process, the expected number of species (N) after t units of time can be described by the expression, N(t)= [exp(lamda(1 - kappa) t - kappa]/(1 - kappa), where kappa = mu/lamda. A nonlinear least-squares regression for the temperate and tropical American clades with more than one species estimated kappa = 0.938 +/- 0.076 (mean +/- SE), suggesting a high rate of turnover of lineages within clades. Because of the broad confidence limits in kappa, I used values ranging from 0.80 to 0.98 to calculate speciation rates in subsequent analyses, assuming that kappa is uniform among clades and does not vary with latitude. Speciation rate among South American clades exceeded that among North American clades for all kappa, whether monophyletic lineages were included or not. The estimated speciation rate was negatively related to clade age, suggesting that proliferation within clades slows with time. In the global data set, rate of speciation decreased with clade age and increased with the area of the region or regions within which a clade is distributed, and for any given value of kappa the speciation rate was significantly higher in tropical than in temperate regions. Relaxing the assumption of latitude independence in kappa, larger clade size in the tropics could be achieved by various combinations of relative speciation and extinction rates that obscure the underlying causes of global biodiversity patterns. Nonetheless, the results of this analysis clearly indicate that a higher rate of diversification in the tropics contributes to the pervasive latitudinal gradient in diversity observed in passerine birds.

Animals↗
PubMed2006

Evolutionary diversification and the origin of the diversity-environment relationship.

Global patterns in species richness have resisted explanation since they first caught the attention of ecologists in the 1960s. The failure of ecology to fully integrate the diversity issue into its core of accepted wisdom derives from an inappropriate concept of community and the rejection of history and region as formative contexts for ecological systems. Traditionally, ecologists have held that the pervasive relationship between species richness and conditions of the physical environment reflects the influence of environment on the ability of populations to coexist locally. However, many ecologists now recognize that this relationship can also develop historically from the evolutionary diversification of lineages within and between ecological zones. To assess the relative roles of local ecological constraint vs. regional and historical unfolding of diversity-environment relationships, we must abandon localized concepts of the community and adopt historical (particularly phylogenetic) and geographic methods to evaluate the evolution of diversity within large regions and its influence on diversity at local scales. This integrated perspective opens new research directions for ecologists to explore the formation of species, adaptive diversification, and the adjustment of ecological distributions of species on regional scales.

Animals↗
PubMedDate not supplied

Diversification of the Ig variable region gene repertoire of synovial B lymphocytes by nucleotide insertion and deletion.

Although the changes that occur in Ig V region genes during a B lymphocyte's response to antigen usually result from point mutations, nucleotide insertion and deletion also alter gene sequence. We identified nucleotide insertions and deletions (3 to 12 bp) at a frequency of 1.34%, in Ig V gene cDNA from B lymphocytes residing in the synovial tissues of patients with rheumatoid arthritis. Because the added or lost nucleotides occurred in multiples of 3, they maintained the original reading frame and coded a potentially intact receptor. These V gene modifications were generated somatically, because they were identified in the original cDNA by HCDR3-specific polymerase chain reaction and were not found in other B cells using the same VH genes. Insertions and deletions were detected only in IgG+ and IgA+ transcripts, which exhibited 3 times more point mutations than IgM+ transcripts. In addition, they were usually found in the complementarity determining region, typical targets of somatic mutation. The occurrence of insertion/ deletion in isotype-switched cDNA with higher numbers of V gene mutations that localized to hot spots for V gene mutation suggests that these diversification events were related to the somatic hypermutation process. In support of this, an AGY hot spot motif and a short stretch of DNA similar in sequence to the inserted or deleted segments could be found next to the insertions/deletions, suggesting that these modifications arose from DNA duplication following DNA stand breaks. Thus, nucleotide insertion/deletion can lead to B-cell receptor diversification in B lymphocytes that clonally expand in synovial tissues of patients with rheumatoid arthritis.

B-Lymphocytes↗