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PubMed1999

Evolutionary diversification of the mammalian defensins.

Defensins are cysteine-rich cationic peptides that function in antimicrobial defense in both invertebrates and vertebrates. Three main groups of animal defensins are known: insect defensins; mammalian alpha-defensins and vertebrate beta-defensins. It has been difficult to determine whether these molecules are homologous or have independently evolved similar features, but overall the evidence favors a distant relationship. The best evidence of this relationship is structural, particularly from their overall three-dimensional structure and from the spacing of half-cystine residues involved in intra-chain disulfide bonds. Some evidence favors a closer relationship between vertebrate beta-defensins and insect defensins than between the two groups of vertebrate defensins. Examination of nucleotide substitutions between recently duplicated mammalian defensin genes shows that the rate of nonsynonymous (amino-acid-altering) substitution exceeds that of synonymous substitution in the region of the gene encoding the mature defensin. This highly unusual pattern of nucleotide substitution is evidence that natural selection has acted to diversify defensins at the amino acid level. The resulting rapid evolution explains why it is difficult to reconstruct the evolutionary history of these molecules.

Amino Acid Sequence↗
PubMed1991

A model of onshore-offshore change in faunal diversity.

Onshore-offshore patterns of faunal change occurred at many taxonomic scales during the Paleozoic Era, ranging from replacement of the Cambrian evolutionary fauna by the Paleozoic fauna to the environmental expansion of many orders and classes. A simple mathematical model is constructed to investigate such change. The environmental gradient across the marine shelf-slope is treated as a linear array of discrete habitats, each of which holds a set number of species, as observed in the fossil record. During any interval of time, some portion of the species in each habitat becomes extinct by background processes, with rates of extinction varying among both clades and habitats, as also observed in the record. After extinction, species are replaced from within the habitat and from immediately adjacent habitats, with proportions dependent on surviving species. This model leads to the prediction that extinction-resistant clades will always diversify at the expense of extinction-prone clades. But if extinction intensity is highest in nearshore habitats, extinction-resistant clades will expand preferentially in the onshore direction, build up diversity there, and then diversify outward toward the offshore. Thus, onshore-offshore patterns of diversification may be the expectation for faunal change quite independently of whether or not clades originate onshore. When the model is parameterized for Paleozoic trilobites and brachiopods, numerical solutions exhibit both a pattern of faunal change and a time span for diversification similar to that seen in the fossil record. They also generate structure similar to that seen in global diversification, including logistic patterns of growth, declining origination but constant extinction within clades through time, and declining overall extinction across clades through time.

Algorithms↗
PubMed1996

Microsatellite and chromosome evolution of parthenogenetic sitobion aphids in Australia.

Single-locus microsatellite variation correlated perfectly with chromosome number in Sitobion miscanthi aphids. The microsatellites were highly heterozygous, with up to 10 alleles per locus in this species. Despite this considerable allelic variation, only seven different S. miscanthi genotypes were discovered in 555 individuals collected from a wide range of locations, hosts and sampling periods. Relatedness between genotypes suggests only two successful colonizations of Australia. There was no evidence for genetic recombination in 555 S. miscanthi so the occurrence of recent sexual reproduction must be near zero. Thus diversification is by mutation and chromosomal rearrangement alone. Since the aphids showed no sexual recombination, microsatellites can mutate without meiosis. Five of seven microsatellite differences were a single repeat unit, and one larger jump is likely. The minimum numbers of changes between karyotypes corresponded roughly one-to-one with microsatellite allele changes, which suggests very rapid chromosomal evolution. A chromosomal fission occurred in a cultured line, and a previously unknown chromosomal race was detected. All 121 diverse S. near fragariae were heterozygous but revealed only one genotype. This species too must have a low rate of sexual reproduction and few colonizations of Australia.

Animals↗
PubMed1993

An outbreak of pellagra related to changes in dietary niacin among Mozambican refugees in Malawi.

Between February and October 1990, 18,276 cases of pellagra dermatitis (due to niacin deficiency) were reported among 285,942 Mozambican refugees in Malawi. Overall, 6.3% of the refugee population developed pellagra and the attack rate was 7.8 times higher among women than men. This outbreak followed a 5-month cessation of groundnut distribution (the major source of niacin) to refugees. A matched-pair case-control study confirmed the protective role of the daily consumption of groundnuts (Odds Ratio [OR] = 0.08), as well as the independent role of garden ownership (OR = 0.34), and home maize milling (OR = 0.3). Recommended corrective action included early case finding and treatment, distribution of niacin tablets, prompt identification of groundnut supply on the world market, fortification with niacin of the food ration and diversification of the food basket through access to local markets.

Adolescent↗
PubMed2002

Mass extinctions, biodiversity explosions and ecological niches.

The logistic model proposed by Courtillot and Gaudemer to describe the growth of biodiversity during geological ages is more explored here and further developed. A new parameterisation is first proposed. Another expression of this model is obtained by introducing a new variable representing the number of ecological niches. It appears that the rates of increase of biodiversity during Jurassic and Cretaceous periods is quite different from other ones. The classical literature essentially focuses on possible extinction mechanisms, but explosions in biodiversity must be more precisely explored. For this purpose, on the basis of data analysis through different expressions of the logistic model, different ecological mechanisms can be assumed (e.g., qualitative and quantitative niches changes, possible appearance of new kinds of ecological relationships, such as 'niche-sharing', which involves coexistence or cooperation), even if genetic processes must also be involved. Finally, we emphasise the astonishing speed of biological diversification following a 'catastrophic' mass extinction. We could refer to this feature as 'catastrophic biological diversification'.

Animals↗
PubMed2000

Reproductive mode and speciation: the viviparity-driven conflict hypothesis.

In birds and frogs, species pairs retain the capacity to produce viable hybrids for tens of millions of years, an order of magnitude longer than mammals. What accounts for these differences in relative rates of pre- and postzygotic isolation? We propose that reproductive mode is a critically important but previously overlooked factor in the speciation process. Viviparity creates a post-fertilization arena for genomic conflicts absent in egg-laying species. With viviparity, conflict can arise between: mothers and embryos; sibling embryos in the womb, and maternal and paternal genomes within individual embryos. Such intra- and intergenomic conflicts result in perpetual antagonistic coevolution, thereby accelerating interpopulation postzygotic isolation. In addition, by generating intrapopulation genetic incompatibility, viviparity-driven conflict favors polyandry and limits the potential for precopulatory divergence. Mammalian diversification is characterized by rapid evolution of incompatible feto-maternal interactions, asymmetrical postzygotic isolation, disproportionate effects of genomically-imprinted genes, and "F(2) hybrid enhancement. " The viviparity-driven conflict hypothesis provides a parsimonious explanation for these patterns in mammalian evolution.

Animals↗
PubMed2001

Patterns of carpal development among anuran amphibians.

The unity and diversity of developmental processes in the vertebrate limb have singular importance in the interpretation of evolutionary hypotheses of tetrapod diversification. In anurans, the intraordinal diversity of forelimbs seems to be related to the fusion of distal carpals, whereas proximal carpals are invariable. However, there are different ontogenetic pathways involved in the differentiation of proximal carpals. This study presents a comparative analysis of early developmental features in one archeobatrachian and 23 neobatrachian species representing five families and explores the variability in the differentiation of carpal cartilages. We found new evidence supporting the presence of an embryonic intermedium that incorporates with the ulnare. Difference between the pipid Xenopus and the neobatrachians is interpreted as a change in the rate of differentiation of Distal Carpal 5 that does not affect the developmental pattern of digits. The developmental variability exhibited by the intermedium, radiale, and Element Y is combined in patterns that converge on the same adult carpal morphology among neobatrachians; these patterns appear to contain potentially useful phylogenetic information.

Animals↗
PubMed2005

Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection.

HIV type 1 (HIV-1) can rapidly escape from neutralizing antibody responses. The genetic basis of this escape in vivo is poorly understood. We compared the pattern of evolution of the HIV-1 env gene between individuals with recent HIV infection whose virus exhibited either a low or a high rate of escape from neutralizing antibody responses. We demonstrate that the rate of viral escape at a phenotypic level is highly variable among individuals, and is strongly correlated with the rate of amino acid substitutions. We show that dramatic escape from neutralizing antibodies can occur in the relative absence of changes in glycosylation or insertions and deletions ("indels") in the envelope; conversely, changes in glycosylation and indels occur even in the absence of neutralizing antibody responses. Comparison of our data with the predictions of a mathematical model support a mechanism in which escape from neutralizing antibodies occurs via many amino acid substitutions, with low cross-neutralization between closely related viral strains. Our results suggest that autologous neutralizing antibody responses may play a pivotal role in the diversification of HIV-1 envelope during the early stages of infection.

Adult↗
PubMed1998

New approaches for the analysis of molecular recognition using the IAsys evanescent wave biosensor.

Trends in the analysis of molecular recognition using the IAsys evanescent wave biosensor are outlined. Diversification of sensor surface chemistry, an open cuvette format and the advent of robotics controlled by intelligent software are widening the range and throughput of applications. Analyses of binding and dissociation are now carried out across a wide spectrum of biomolecules, including protein, nucleic acid, carbohydrate and lipid. Determinations are obtained from a range of experimental formats. These include qualitative 'yes/no' screening assays, through semi quantitative ranking of kinetic association, dissociation and equilibrium constants for a family of binding partners, to deriving constants comparable with those which would be obtained in free solution. A dependence of the initial rate of biomolecular association on concentration allows analyte concentration to be measured--an increasingly common application class. This is often employed in situations where a rapid determination is required The ability to recover bound analyte from the sensor surface in sufficient amounts for subsequent characterization is opening up new routes to the parallel analysis of structure and function.

Animals↗
PubMed2001

Venomous cone snails: molecular phylogeny and the generation of toxin diversity.

In order to investigate the generation of conotoxin diversity, delta-conotoxin sequences from nine Conus species were analyzed in the context of their phylogeny. Using a standard molecular marker, mitochondrial 16S RNA, we determined that the delta-conotoxins were derived from three distinct species clades based on the phylogenetic reconstruction of a large set (>80) of Conus species and other toxoglossate molluscs. Four different mechanisms appear to have contributed to the diversity of the delta-conotoxins analyzed: (1) Speciation: Delta-conotoxins in different species diverge from each other (the prepro regions of orthologous genes somewhat more slowly than the reference rRNA rate, the mature toxin regions significantly faster). (2) Duplication: Intraspecific delta-conotoxin divergence is initiated by gene duplication events, some of which may have predated the species itself. (3) Recombination: A novel delta-conotoxin may arise through recombination of two parental delta-contoxin genes. (4) 'Focal hypermutation': This sudden, almost saltatory change in sequence is always restricted to the mature toxin region. The first three have been recognized previously as mechanisms important for the evolution of gene families in other phylogenetic systems; the last is a remarkable, mechanistically unexplained and specialized feature of Conus peptide diversification.

Animals↗
PubMed2005

Archaeobatrachian paraphyly and pangaean diversification of crown-group frogs.

Current models for the early diversification of living frogs inferred from morphological, ontogenetic, or DNA sequence data invoke very different scenarios of character evolution and biogeography. To explore central controversies on the phylogeny of Anura, we analyzed nearly 4000 base pairs of mitochondrial and nuclear DNA for the major frog lineages. Likelihood-based analyses of this data set are congruent with morphological evidence in supporting a paraphyletic arrangement of archaeobatrachian frogs, with an (Ascaphus + Leiopelma) clade as the sister-group of all other living anurans. The stability of this outcome is reinforced by screening for phylogenetic bias resulting from site-specific rate variation, homoplasy, or the obligatory use of distantly related outgroups. Twenty-one alternative branching and rooting hypotheses were evaluated using a nonparametric multicomparison test and parametric bootstrapping. Relaxed molecular clock estimates situate the emergence of crown-group anurans in the Triassic, approximately 55 million years prior to their first appearance in the fossil record. The existence of at least four extant frog lineages on the supercontinent Pangaea before its breakup gains support from the estimation that three early splits between Laurasia- and Gondwana-associated families coincide with the initial rifting of these landmasses. This observation outlines the potential significance of this breakup event in the formation of separate Mesozoic faunal assemblages in both hemispheres.

Animals↗
PubMed2006

Ion-mediated flow changes suppressed by minimal calcium presence in xylem sap in Chrysanthemum and Prunus laurocerasus.

After the discovery of ion-mediated changes in xylem hydraulic resistance a few years ago, a number of research papers were published that related ion-mediated flow changes in the xylem to various aspects of whole plant functioning and evolutionary diversification of vascular cells. Ion-mediated changes in xylem hydraulic resistance are commonly quantified as the percentile change in hydraulic resistance, relative to the hydraulic resistance measured using a reference fluid, usually (ultra) pure deionized water. In this research the impact was investigated of the complete absence of all ions in deionized water compared with reference fluids containing a minimal amount of free calcium on the quantification of ion-mediated flow changes in stem segments of Chrysanthemum (Dendranthemaxgrandiflorum Tzvelev) and Prunus L. (Prunus laurocerasus L.). The addition of 10 mM KCl to deionized water significantly increased flow rate in Chrysanthemum (17-24%) and Prunus L. (16%). The addition of 1 mM CaCl(2) to the reference fluid reduced this KCl-mediated increase in flow rate to 1-2% in both species. 1 mM Ca(2+) is within the lower range of Ca(2+)-concentrations normally measured in xylem sap of many plant species, and three times lower than the original Ca(2+)-concentration measured in the xylem sap of Chrysanthemum plants used for the present measurements. The present results indicate that the complete removal of cations from the xylem fluid with deionized water causes the major part of the ion-mediated flow change previously reported in the xylem of plants. It is concluded that the use of deionized water as a reference fluid should be avoided. Earlier proposed relationships between ion-mediated changes and water flow in xylem of plants should be re-evaluated if they were based on deionized water as the reference fluid.

Botany↗
PubMed2004

Simian cytomegalovirus encodes five rapidly evolving chemokine receptor homologues.

Many herpesviruses, poxviruses and retroviruses encode proteins related to chemokines and chemokine receptors. The first one discovered, US28 of human cytomegalovirus (HCMV), is a 7-transmembrane domain G protein-coupled chemokine receptor able to activate diverse cellular responses, including cell migration and gene expression. A related ORF named US27 is adjacent to US28, but no functions have been defined yet. Recently ORFs 3-7, a cluster of five concatenated ORFs with highest homology to US28 and mammalian chemokine receptors, were sequenced from a prototype "stealth virus", an African green monkey simian CMV (SCMV)-related entity with unusual fungal, bacterial and mammalian gene homologues. Stealth viruses have not yet been independently replicated in tissue culture, and therefore their biological significance remains unclear. ORF3, ORF4, ORF5 and ORF6 are complete ORFs whereas the sequence of ORF7 is incomplete. In the present study, we identified five corresponding ORFs in the genome of a clinical isolate of bonafide simian CMV (SCMV), strain 9610. We found substantial differences between the SCMV and "stealth virus" ORFs, especially for ORF5 where there are 31% non-identities at the amino acid level. Four conserved genes unrelated to chemokines (64K/CAP, DNBI, UL32, and IE2) in SCMV and HCMV had on average 52% identity at the deduced amino acid level, whereas the corresponding values for the SCMV ORFs versus US28 ranged from 21% to 30%, suggesting rapid gene diversification in this cluster. Consistent with this, the amino acid identity for any pairwise comparison among the SCMV ORFs is only 21-52%. The chemokine receptor homologues are estimated to comprise approximately 2-3% of the SCMV genome. HCMV US27 and US28 homologues have also been identified in the chimpanzee CMV genome, whereas mouse and rat CMV lack chemokine receptor homologues. This genomic analysis indicates that SCMV has an unusually high concentration of US28-related chemokine receptor homologues that have arisen by gene duplication and have diverged extensively from their closest relatives in mammals and other beta herpesviruses. The rate of divergence appears to be very rapid compared to other known SCMV genes, suggesting strong positive selection.

Amino Acid Sequence↗
PubMed2025

Large-scale Genome Analyses Provide Insights into Hymenoptera Evolution.

The order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution of this diverse order, we performed large-scale comparative genomics on 131 species from 13 superfamilies, covering most representative groups. We used these genomes to reveal an overall pattern of genomic change in terms of gene content and evolutionary rate throughout hymenopteran history. We identified genes that possibly contributed to the evolution of several key innovations, such as parasitoidism, wasp-waist, stinger, and secondary phytophagy. We also discovered the distinct genomic trajectories between the clade containing major parasitoid wasps (Parasitoida) and stinging species (Aculeata) since their divergence, which are involved in many aspects of genomic change, such as rapidly evolving gene families, gene gain and loss, and metabolic pathway evolution. In addition, we explored the genomic features accompanying the three independent evolution of secondary phytophagy. Our work provides insights for understanding genome evolution and the genomic basis of diversification in Hymenoptera.

Animals↗
PubMedDate not supplied

Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family.

Trichomonads, together with diplomonads and microsporidia, emerge at the base of the eukaryotic tree, on the basis of the small subunit rRNA phylogeny. However, phylogenies based on protein sequences such as tubulin are markedly different with these protists emerging much later. We have investigated 70 kDa heat-shock protein (HSP70), which could be a reliable phylogenetic marker. In eukaryotes, HSP70s are found in cytosol, endoplasmic reticulum, and organelles (mitochondria and chloroplasts). In Trichomonas vaginalis we identified nine different HSP70-encoding genes and sequenced three nearly complete cDNAs corresponding to cytosolic, endoplasmic reticulum, and mitochondrial-type HSP70. Phylogenies of eukaryotes were reconstructed using the classical methods while varying the number of species and characters considered. Almost all the undoubtedly monophyletic groups, defined by ultrastructural characters, were recovered. However, due to the long branch attraction phenomenon, the evolutionary rates were the main factor determining the position of species, even with the use of a close outgroup, which is an important advantage of HSP70 with respect to many other markers. Numerous variable sites are peculiar to Trichomonas and probably generated the artefactual placement of this species at the base of the eukaryotes or as the sister group of fast-evolving species. The inter-phyla relationships were not well supported and were sensitive to the reconstruction method, the number of species; and the quantity of information used. This lack of resolution could be explained by the very rapid diversification of eukaryotes, likely after the mitochondrial endosymbiosis.

Animals↗
PubMed1987

Diversification of health care services: the effects of ownership, environment, and strategy.

The present findings suggest that the trend toward greater diversification of hospital services is likely to be most strongly influenced by state Medicaid policies and certain hospital characteristics. Increasing Medicaid eligibility and payment levels is likely to have a positive effect on services diversification. Growth in the number of inpatient services provided and a more severe case mix are also likely to be involved with greater service diversification. Affiliation with a not-for-profit hospital system is likely to be associated with more diversified hospital services but not affiliation with an investor-owned system. There is also some indication that the overall portfolio of services which a hospital offers in regard to market share and market growth characteristics influences diversification. Specifically, a low market share portfolio is likely to be associated with less diversification. Competition is likely to be associated with more diversification; particularly for hospitals belonging to systems. The effect of competition on hospital strategy and services diversification is a particularly important area for further investigation. Increasing Medicaid payment and eligibility levels are also likely to have a positive effect on the provision of services which are usually unprofitable. Raising such levels is likely to be particularly beneficial to inner-city hospitals who are already providing a greater number of such services. However, the present data suggest that investor-owned hospitals are least likely to provide such services. Increasing Medicaid eligibility levels is also likely to be associated with fewer services for which charity care has to be provided. State regulation in the form of rate review and certificate of need is likely to be associated with more services for which hospitals provide some charity care. But such policies alone do not deal with the larger issue of how to finance care for the medically indigent. Present data suggest the charity care issue may be particularly salient in markets characterized by a relatively high degree of competition. Finally, investor-owned hospitals provide as many services involving charity care as not-for-profit system hospitals, although investor-owned system hospitals provide fewer such services than not-for-profit freestanding hospitals. Throughout, the findings indicate the importance of distinguishing between ownership and system affiliation. Previous research has failed to make a distinction between ownership form and system affiliation, thus attributing to ownership form differences which, as present findings suggest, appear to be more associated with system affiliation.(ABSTRACT TRUNCATED AT 400 WORDS)

Factor Analysis, Statistical↗
PubMed2005

Host-associated genetic differentiation in phytophagous insects: general phenomenon or isolated exceptions? Evidence from a goldenrod-insect community.

There is growing awareness of the importance of natural selection in driving genetic divergence and speciation, and several of the most apparent cases of this ecological speciation are provided by the existence of genetically distinct host forms in phytophagous insects. Such examples of host-associated differentiation (HAD) have become increasingly documented, and the implications of this phenomenon for the diversification of insects are becoming widely appreciated. However, instances of HAD remain rare relative to insect diversity and are sparsely distributed both ecologically and taxonomically. We sought to assess the frequency of HAD in a model herbivore community by examining genetic divergence in a variety of herbivores that feed on two closely related and broadly sympatric species of goldenrod (Solidago altissima and S. gigantea). Using mitochondrial DNA and allozyme data, in conjunction with previously published studies, we found that four of nine herbivores exhibited evidence of HAD, including possible host races or cryptic species. Using a range of reasonable substitution rate estimates for cytochrome oxidase I mitochondrial DNA, we found that HAD appears to have proceeded asynchronously across taxa. This pattern, along with the broadly sympatric distribution of host plants and the specialized life histories of the phytophagous insects, is consistent with sympatric divergence in some or all of these taxa. Although further behavioral and ecological study is needed, our survey of HAD in a community of herbivores indicates that ecological (perhaps sympatric) speciation may have been responsible for generating a significant fraction of the extant diversity of phytophagous insects.

Animals↗
PubMed2006

[Clinical analysis of 170 cases head and neck lymphoma].

OBJECTIVE: To study the characteristics of head and neck lymphoma in order to improve its diagnose rate. METHODS: Review and analysis 170 patients with head and neck lymphoma in department of otolaryngology of Xiangya hospital from 1997 to 2005. RESULTS: Nasal cavity and nasal sinuses, neck, tonsil were the common place of the origin of head and neck lymphoma. There are 9 cases Hodgkin disease and 161 cases non-Hodgkin lymphoma (NHL). T cellularity, B cellularity lymphoma, the mixed pattern and nullityping accounted for 60.9%, 36.0% and 3.1% of these patients with NHL, respectively. CHOP and radiotherapy were the main treatment method. CONCLUSION: The clinical and imageology manifestation of head and neck lymphoma were of diversification and no specificity, whose final diagnosis depended on immunohistochemistry.

Adolescent↗