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PubMed2002

Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals.

The fully sequenced chloroplast genomes of maize (subfamily Panicoideae), rice (subfamily Bambusoideae), and wheat (subfamily Pooideae) provide the unique opportunity to investigate the evolution of chloroplast genes and genomes in the grass family (Poaceae) by whole-genome comparison. Analyses of nucleotide sequence variations in 106 cereal chloroplast genes with tobacco sequences as the outgroup suggested that (1) most of the genic regions of the chloroplast genomes of maize, rice, and wheat have evolved at similar rates; (2) RNA genes have highly conservative evolutionary rates relative to the other genes; (3) photosynthetic genes have been under strong purifying selection; (4) between the three cereals, 14 genes which account for about 28% of the genic region have evolved with heterogeneous nucleotide substitution rates; and (5) rice genes tend to have evolved more slowly than the others at loci where rate heterogeneity exists. Although the mechanism that underlies chloroplast gene diversification is complex, our analyses identified variation in nonsynonymous substitution rates as a genetic force that generates heterogeneity, which is evidence of selection in chloroplast gene diversification at the intrafamilial level. Phylogenetic trees constructed with the variable nucleotide sites of the chloroplast genes place maize basal to the rice-wheat clade, revealing a close relationship between the Bambusoideae and Pooideae.

Chloroplasts↗
PubMed2001

Diversification of neurotoxins by C-tail 'wiggling': a scorpion recipe for survival.

The structure of bioactive surfaces of proteins is a subject of intensive research, yet the mechanisms by which such surfaces have evolved are largely unknown. Polypeptide toxins produced by venomous animals such as sea anemones, cone snails, scorpions, and snakes show multiple routes for active site diversification, each maintaining a typical conserved scaffold. Comparative analysis of an array of genetically related scorpion polypeptide toxins that modulate sodium channels in neuronal membranes suggests a unique route of toxic site diversification. This premise is based on recent identification of bioactive surfaces of toxin representative of three distinct pharmacological groups and a comparison of their 3-dimensional structures. Despite their similar scaffold, the bioactive surfaces of the various toxins vary considerably, but always coincide with the molecular exterior onto which the C-tail is anchored. Superposition of the toxin structures indicates that the C-tails diverge from a common structural start point, which suggests that the pharmacological versatility displayed by these toxins might have been achieved along evolution via structural reconfiguration of the C-tail, leading to reshaping of new bioactive surfaces.

Amino Acid Sequence↗
PubMed2001

Timing of the HIV-1 subtype C epidemic in Ethiopia based on early virus strains and subsequent virus diversification.

OBJECTIVE: To trace the introduction of HIV-1 subtype C into Ethiopia based on virus diversification during the epidemic. DESIGN: A set of 474 serum samples obtained in Ethiopia in 1982-1985 was tested for HIV-1. HIV-1 env gp120 V3 and gag or pol regions were sequenced and analysed together with sequences from later stages of the epidemic. RESULTS: None of 98 samples from 1982-1983, one of 193 samples from 1984, and one of 183 samples from 1985 were HIV-1 positive. Phylogenetic analysis of virus sequences from positive samples revealed that they belong to the Ethiopian C, and not the C', cluster. Analysis of 81 Ethiopian C V3 sequences from 1984-1997 revealed that the consensus sequence of the Ethiopian epidemic has been stable over time. Both the 1984 and 1985 V3 sequences, in contrast with three out of 27 (11%) of the 1988 and none out of 51 of the 1992-1997 sequences, had no synonymous substitutions compared to the reconstructed common ancestor of the Ethiopian C viruses. A highly significant correlation between sampling years of the V3 sequences and their synonymous distances to the common ancestor was demonstrated. CONCLUSIONS: The increasing genetic heterogeneity together with stable consensus sequence of the Ethiopian HIV-1 C population demonstrates that evolution of the virus population is characterized by an unbiased expansion around a stationary consensus. Based on the rate of synonymous diversification of HIV-1 strains within the Ethiopian population, we were able to estimate 1983 (95% confidence interval, 1980-1984) as the year of HIV-1 C introduction into Ethiopia.

Adult↗
PubMed1990

The case for hospital diversification into long-term care.

Since the market for long-term care (LTC) services is expected to grow rapidly in the years ahead, the case for hospital diversification into LTC is a strong one. This article discusses the major LTC diversification options, the cost of entry, potential profitability, potential problems, and recommendations for implementing them.

Alabama↗
PubMed1987

Does hospital diversification improve financial outcomes?

Service or product diversification is a popular recommendation made to hospitals to increase profitability and reduce financial risk as they face a more hostile environment. This paper presents results from an empirical study of these claims. Using data from all California nonprofit hospitals, the study finds that diversification, regardless of whether it is related or unrelated to preexisting services, is not associated with either increased profitability or reduced financial risk. However, other variables that do have these effects are identified in the research. Future research should evaluate the effect of both the size of and the length of time since the initial diversifying investment on financial variables.

Accounting↗
PubMed2006

Diversification of Neoaves: integration of molecular sequence data and fossils.

Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

Animals↗
PubMed2000

Tracking colonization and diversification of insect lineages on islands: mitochondrial DNA phylogeography of Tarphius canariensis (Coleoptera: Colydiidae) on the Canary Islands.

The genus Tarphius Erichson (Coleoptera: Colydiidae) is represented by 29 species on the Canary Islands. The majority are rare, single-island endemics intimately associated with the monteverde (laurel forest and fayal-brezal). The Tarphius canariensis complex is by far the most abundant and geographically wide-spread, occurring on Gran Canaria, Tenerife and La Palma. Eighty-seven individuals from the T. canariensis complex were sequenced for 444 bp of the mitochondrial DNA cytochrome oxidase I gene (COI), 597 bp of the COII gene and the intervening tRNA(leu) gene. A neighbour-joining analysis of maximum-likelihood distances put La Palma as a single monophyletic clade of haplotypes occurring within a larger clade comprising all Tenerife haplotypes. Gran Canarian haplotypes were also monophyletic occurring on a separate lineage. Using a combination of the phylogeographic pattern for T. canariensis, geological data, biogeography of the remaining species and estimated divergence times, we proposed a Tenerifean origin in the old Teno massif and independent colonizations from here to north-eastern Tenerife (Anaga), Gran Canaria and La Palma. New methods of estimating diversification rates using branching times were applied to each island fauna. All islands exhibited a gradually decreasing rate of genetic diversification similar to that seen for Brachyderes rugatus (Coleoptera: Curculionidae) from the Canary Islands.

Animals↗
PubMed2003

Global diversification rates of passerine birds.

The distribution of species richness in families of passerine birds suggests that the net rate of diversification was significantly higher than average in as many as 7 out of 47 families. However, the absence of excess species richness among the 106 tribes within these families indicates that these high rates were transient, perhaps associated in some cases with tectonic movements or dispersal events that extended geographical ranges. Thus, large clade size among passerine birds need not represent intrinsic key innovations that influence the rate of diversification. Approximately 17 families and 30 tribes have too few species relative to other passerine taxa. Many of these are ecologically or geographically marginal, being especially overrepresented in the Australasian region. Observed intervals between lineage splitting suggest that extinction has occurred ca. 90% as frequently as speciation (waiting times of 1.03 and 0.93 Myr) and that the 47 modern families comprising 5712 species descended from approximately 430 passerine lineages extant 24 Myr ago. Speciation and extinction rates among small, marginal families might be 1-2 orders of magnitude lower.

Animals↗
PubMed2005

Unparallel diversification in bacterial microcosms.

Adaptive speciation has gained popularity as a fundamental process underlying the generation of diversity. We tested whether populations respond to similar forms of disruptive selection by diversifying in similar or parallel ways by investigating diversified populations of Escherichia coli B evolved in glucose and glucose-acetate environments. In both environments, the populations have differentiated into two phenotypes, named for their characteristic colony morphologies: large (L) and small (S). Each type is heritable and this polymorphism (or 'diversified pair') appears to be maintained by negative frequency dependence. The L and S phenotypes from different environments are convergent in their colony morphology and growth characteristics. We tested whether diversification was parallel by conducting competition experiments between L and S types from different environments. Our results indicate that replicate diversified pairs from different environments have not diversified in parallel ways and suggest that subtle differences in evolutionary environment can crucially affect the outcome of adaptive diversification.

Acetates↗
PubMed1993

New observations on antigenic diversification of RNA viruses. Antigenic variation is not dependent on immune selection.

Recent results have revealed novel features in the process of antigenic diversification of FMDV. (i) Antigenic variation is not necessarily the result of immune selection. (ii) Single, critical amino acid replacements may either have a minor effect on antigenic specificity or cause a drastic antigenic change affecting many epitopes on an antigenic site. (iii) The effect of such a critical replacement may be suppressed by additional substitutions at neighbouring sites. (iv) Antigenic diversification does not necessarily involve net accumulation of amino acid substitutions over time. We review evidence that some of these features apply also to other riboviruses and retroviruses. A model is proposed to relate antigenic variation without immune selection to the quasispecies structure of RNA virus populations.

Antigenic Variation↗
PubMed2000

Patterns of intraspecific diversification in the Piriqueta caroliniana complex in southeastern North America and the Bahamas.

We use chloroplast DNA (cpDNA) variation and nested clade phylogeographic analyses to infer the historical processes that have contributed to the high level of morphological and ecological diversification present in a group of herbaceous perennials (the Piriqueta caroliniana complex) in North America and the Bahamas. The presence of morphologically distinct and intercompatible varieties (morphotypes) that can be distinguished based on suites of taxonomic characters (e.g., leaf shape, pubescence type, stature) and contrasting habitat affinities (from marshes to dry pinelands and sand scrub) makes this group particularly appropriate for studies of intraspecific diversification. To examine the distribution of haplotypes among populations, we sampled 467 individuals from 55 locations in Florida, Georgia, and the northern Bahamas (Grand Bahama and Abaco) and screened each individual for cpDNA variation using restriction fragment length polymorphism (RFLP) and heteroduplex analyses. We develop a one-step haplotype phylogeny for this group and use the geographic distributions of haplotypes and clades to test specific phylogeographic hypotheses using the methods developed by Templeton and his colleagues (Templeton 1998). In general, the distribution of haplotypes was strongly influenced by limited dispersal distances, with the more recently derived haplotypes having much lower levels of dispersion and lower frequencies in populations than the ancestral haplotypes. The patterns of clade and haplotype dispersion and displacement and the distribution of morphotypes imply at least three cases of long-distance dispersal and one case of historical fragmentation. The historical patterns inferred for populations of Piriqueta are consistent with known biogeographical events, historical vegetation change, and the concordant patterns of multiple Pleistocene refugia that have been observed for a number of other taxa in southeastern North America.

Bahamas↗
PubMed2000

Colonization and diversification of the species Brachyderes rugatus (Coleoptera) on the Canary Islands: evidence from mitochondrial DNA COII gene sequences.

The genus Brachyderes Schönherr (Coleoptera: Curculionidae) is represented by the species B. rugatus Wollaston on the Canary Islands, with one subspecies on each of the islands of Gran Canaria, Tenerife, La Palma, and El Hierro. These four subspecies are associated with the endemic pine tree Pinus canariensis, and their distributions are broadly coincident. Eighty-eight individual Canarian Brachyderes, sampled from across the distributions of each subspecies, have been sequenced for 570 bp of the mitochondrial DNA (mtDNA) cytochrome oxidase II gene (COII). No mitotypes are shared among islands. Both maximum-likelihood and distance-based phylogenetic analyses have shown that: Tenerife is composed of a single monophyletic clade of mitotypes, El Hierro is composed of a single monophyletic clade occurring within a larger clade comprising all the La Palma mitotypes, and the mitotypes of these three islands form a monophyletic group distinct from Gran Canaria. New methods for estimating divergence times without the assumption of rate constancy have been used to reconstruct the direction and approximate timing of colonizations among the islands. Colonization has occurred from older to progressionally younger islands, and these colonizations are estimated to have occurred less than 2.6 million years ago, although the timing of the initial colonization of the archipelago is not discernable. New methods for the estimation of diversification rates that use branching times as the analyzed variable have been applied to each island fauna. Hypothesized effects of different levels of recent volcanism among islands were not apparent. All islands exhibit a gradually decreasing rate of genetic diversification that is marked by periodic sudden changes in rate.

Animals↗
PubMed2003

Nonstochastic variation of species-level diversification rates within angiosperms.

Variations in the origination and extinction rates of species over geological time often are linked with a range of factors, including the evolution of key innovations, changes in ecosystem structure, and environmental factors such as shifts in climate and physical geography. Before hypothesizing causality of a single factor, it is critical to demonstrate that the observed variation in diversification is significantly greater than one would expect due to natural stochasticity in the evolutionary branching process. Here, we use a likelihood-ratio test to compare taxonomic rate heterogeneity to a neutral birth-death model, using data on well-supported sister pairs of taxa and their species richness. We test the likelihood that the distribution of extant species among angiosperm genera and families could be the result of constant diversification rates. Results strongly support the conclusion that there is significantly more heterogeneity in diversity at the species level within angiosperms than would be expected due to stochastic processes. This result is consistent in datasets of genus pairs and family pairs and is not affected significantly by degrading pairs to simulate inaccuracy in the assumption of simultaneous origin of sister taxa. When we parse taxon pairs among higher groups of angiosperms, results indicate that a constant rates model is not rejected by rosid and basal eudicot pairs but is rejected by asterid and eumagnoliid pairs. These results provide strong support for the hypothesis that species-level rates of origination and/or extinction have varied nonrandomly within angiosperms and that the magnitude of heterogeneity varies among major groups within angiosperms.

Biological Evolution↗
PubMed2005

Processes of diversification and dispersion of rice yellow mottle virus inferred from large-scale and high-resolution phylogeographical studies.

Phylogeography of Rice yellow mottle virus (RYMV) was reconstructed from the coat protein gene sequences of a selection of 173 isolates from the 14 countries of mainland Africa where the disease occurred and from the full sequences of 16 representative isolates. Genetic variation was linked to geographical distribution and not to host species as isolates from wild rice always clustered with isolates from cultivated rice of the same region. Genetic variation was not associated to agro-ecology, viral interference and insect vector species. Distinct RYMV lineages occurred in East, Central and West Africa, although the Central African lineage included isolates from Benin, Togo and Niger at the west, adjacent to countries of the West African lineage. Genetic subdivision at finer geographical scales was apparent within lineages of Central and West Africa, although less pronounced than in East Africa. Physical obstacles, but also habitat fragmentation, as exemplified by the small low-lying island of Pemba offshore Tanzania mainland, explained strain localization. Three new highly divergent strains were found in eastern Tanzania. By contrast, intensive surveys in Cote d'Ivoire and Guinea at the west of Africa did not reveal any new variant. Altogether, this supported the view that the Eastern Arc Mountains biodiversity hotspot was the centre of origin of RYMV and that the virus spread subsequently from east to west across Africa. In West Africa, specific strains occurred in the Inner Niger Delta and suggested it was a secondary centre of diversification. Processes for diversification and dispersion of RYMV are proposed.

Africa↗
PubMed2004

A phylogenomic approach to reconstructing the diversification of serine proteases in fungi.

Using a phylogenomic approach with 10 fungi of very different virulence and habitat, we determined that there was substantial diversification of subtilase-type proteases early in ascomycete history (with subsequent loss in many lineages) but with no comparable diversification of trypsins. Patterns of intron loss and the degree of divergence between paralogues demonstrated that the proliferation of proteinase K subtilases and subtilisin type subtilases seen in pathogenic ascomycetes (Metarhizium anisopliae, Magnaporthe grisea, Fusarium graminearum) occurred after the basidiomycete/ascomycete split but predated radiation of ascomycete lineages. This suggests that the early ascomycetes had a lifestyle that selected for multiple proteases, whereas the current disparity in gene numbers between ascomycete lineages results from retention of genes in at least some pathogens that have been lost in other lineages (yeasts, Aspergillus nidulans, Neurospora crassa). A similar prevailing trend towards lineage specific gene loss of trypsins in saprophytes and some pathogens suggests that their phylogenetic breadth will have been much wider in early fungi than currently.

Cluster Analysis↗
PubMed1998

Diversification of response to hsp65 during the course of autoimmune arthritis is regulatory rather than pathogenic.

Determinant spreading has been implicated in the pathogenesis of certain autoimmune diseases in animal models. We have observed that during the course of adjuvant arthritis (AA) in the Lewis rat, there is 'diversification' of response to the bacterial 65-kDa heat shock protein (Bhsp65) towards its carboxy-terminal determinants (BCTD). Strikingly, pretreatment of naive Lewis rats with BCTD affords significant protection from AA. Our preliminary studies indicate that the diversification of response to BCTD in the Lewis rat is probably triggered in vivo by the induction and enhanced processing of self(rat) hsp65. Thus, the self hsp65-directed T-cell responses appear to be involved in mediating natural remission from acute inflammatory arthritis induced by a foreign antigen, Mycobacterium tuberculosis. This the first report describing that the new T-cell specificities arising during the course of an autoimmune disease are regulatory/protective rather than pathogenic. Moreover, our results suggest that a final common mechanism involving BCTD might be recruited by other rat strains which either are resistant to AA (WKY rats) or whose susceptibility to AA is modulated significantly by microbial flora (Fisher rats). The results of this study would contribute significantly to understanding of the pathogenesis of human rheumatoid arthritis, and in devising new therapeutic strategies for this disease.

Animals↗
PubMed1998

Towards understanding the evolutionary origins and early diversification of rearranging antigen receptors.

The rearranging antigen binding receptors, immunoglobulin heavy (IgH) and light (IgL) chains and the four classes of T-cell antigen receptors (TCR) are found in all contemporary species of jawed vertebrates examined thus far. Ig genes have undergone marked changes in organization and mechanisms of diversification during vertebrate phylogeny; whereas TCR genes, which are found in species as phylogenetically removed as man and cartilaginous fishes (e.g. skate), are generally similar in terms of structure, diversification and, presumably, function. The patterns of Ig divergence in cartilaginous fish are informative as to both the potential for genetic variation and the mechanisms that bring about such change. No evidence has been found for homologs of either Ig, TCR, recombination activating gene (RAG)1 or RAG2 in jawless vertebrates or invertebrates. Thus, a phylogenetic demarcation exists in terms of the presence and absence of the rearranging antigen binding receptor genes. It is presumed that the rearranging antigen binding receptors arose from a non-rearranging predecessor. The recent discovery of non-rearranging homologs of antigen binding receptor genes in several species offers insight into alternative forms of recognition, relationships between adaptive and innate mechanisms of immunity, and the origins of antigen recognition.

Animals↗
PubMed1993

Horizontal and vertical integration-diversification in rural hospitals: a national study of strategic activity, 1983-1988.

This study examines both the magnitude of and factors influencing the adoption of 13 horizontal and vertical integration and diversification strategies in a national sample of 797 U.S. rural hospitals during the period 1983-1988. Using organization theory, hypotheses were posed relating environmental and market factors, geographic location, and hospital characteristics to the adoption of horizontal and vertical integration and diversification. Results indicate that only one of 13 strategies was adopted by more than 50 percent of all rural hospitals during the study period, and that most of the directional hypotheses were not confirmed using Cox's proportional hazards models. In particular, environmental and market factors were unrelated to the strategies studied. Issues of methodology and theory are discussed; however, during an historically turbulent period, both relatively low levels of rural hospital strategic activities and lack of predictive power of the theory suggest caution in relying heavily on a policy for rural hospital survival that is dependent on individual market-oriented strategic behavior.

Chi-Square Distribution↗