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PubMed1990

The nature and extent of hospital competition in a government-funded health system.

A national study of Canadian hospitals assessed the perceived level and types of competition and the strategies pursued by these hospitals. Questionnaire data were obtained from chief executive officers in 715 hospitals, yielding a national response rate of 68%. Respondents indicated the perceived level of competition in the environment, the content of competition, and stated hospital strategies. Additional data were obtained on market share and hospital type. Close to half of the respondents indicated little or no competition in their environment, while 30% indicated substantial levels of competition. This represents a significant deviation from conventional wisdom about the Canadian health services environment. Respondents in hospitals with more than 75% of the market share were less likely to perceive competition than those with a smaller market share. CEOs in teaching hospitals and in hospitals located in larger communities reported higher levels of competition. Hospitals competed mostly for capital, programs, and staff; about a third of hospitals competed for patients and no differences were found by type of institution. Those hospitals in more competitive environments were more likely to indicate the use of diversification and horizontal integration as organizational strategies.

Canada↗
PubMed2003

Red palm oil as a source of vitamin A for mothers and children: impact of a pilot project in Burkina Faso.

OBJECTIVE: To demonstrate the effectiveness of the commercial introduction of red palm oil (RPO) as a source of vitamin A (VA) for mothers and children in a non-consuming area, as a dietary diversification strategy. DESIGN: A pre-post intervention design (no control area) was used to assess changes in VA intake and status over a 24-month pilot project. SETTING AND SUBJECTS: The pilot project involved RPO promotion in 10 villages and an urban area in east-central Burkina Faso, targeting approximately 10 000 women and children aged <5 years. A random sample of 210 mother-child (12-36-months-old) pairs was selected in seven out of the 11 pilot sites for the evaluation. RESULTS: After 24 months, RPO was reportedly consumed by nearly 45% of mothers and children in the previous week. VA intake increased from 235+/-23 microg retinol activity equivalents (RAE) to 655+/-144 microg RAE in mothers (41 to 120% of safe intake level), and from 164+/-14 microg RAE to 514+/-77 microg RAE in children (36 to 97%). Rates of serum retinol <0.70 micromol l(-1) decreased from 61.8+/-8.0% to 28.2+/-11.0% in mothers, and from 84.5+/-6.4% to 66.9+/-11.2% in children. Those with a lower initial concentration of serum retinol showed a higher serum retinol response adjusted for VA intake. CONCLUSIONS: Commercial distribution of RPO was effective in reducing VA deficiency in the pilot sites. While it is promising as part of a national strategy, additional public health and food-based measures are needed to control VA malnutrition, which remained high in the RPO project area.

Breast Feeding↗
PubMedDate not supplied

Evolution in microcosm: the rapid somatic diversification of lymphocytes.

The characteristic task of the immune system is learning to respond specificially to entirely novel antigens. How it may do this is discussed under 6 headings. 1. -- Vertebrate and invertebrate immune strategies are contrasted. Whereas among invertebrates whole individuals appear to be selected for their immunological fitness, vertebrates have developed an internal population of lymphocytes among which variants arise and are selectively stimulated by antigen to give a response which protects the "host". 2. -- The genetic mechanism underlying this variation of lymphocytes is of great interest, but its discovery will not, given present ignorance of eukarote DNA, answer those questions about variation at the phenotypic level which are vital to the rest of immunology: e.g. when, how fast, and under what conditions do variantes arise? 3. -- A great deal of indirect evidence suggests that the production of entirely new variant lymphocytes occurs throughout life, particularly after antigenic stimulation. 4. -- Experimental approaches are discussed which might provide direct evidence for or against the idea of rapid variation among stimulated lymphocytes. The method used was based on detecting the cross-reactive specificity of antibody produced by single cells. 5. -- Evidence obtained with this technique is briefly described. There were two main kinds of experiment. In the first, rapid variation (at the rate of about one variation event per 30 divisions) was demonstrated within single clones of proliferating antibody-forming cells. In the second group of experiments, it was shown that certain uncommon antibody-forming cell specificities present at the peak of a primary response were entirely absent at earlier stages. 6. -- A new immunological paradigm may emerge from work on the generation of diversity and on active control of response. There may be relatively few types of lymphocytes with germ-line-coded receptors. These are stimulated by environmental antigens and mitogens, and perhaps by self stimulated by environmental antigens and mitogens, and perhaps by self antigens. Extensive proliferation and variation occurs, which in turn elicits suppressor reactions directed against antigen or against idiotypes of responding clones. The immune repertoire of the adult vertebrate is a product of the evolution of its lymphocytes under the competing pressures of antigenic stimulation and active suppression.

Aging↗
PubMed2002

Postgenomic chemical ecology: from genetic code to ecological interactions.

Environmental response genes are defined as those encoding proteins involved in interactions external to the organism, including interactions among organisms and between the organism and its abiotic environment. The general characteristics of environmental response genes include high diversity, proliferation by duplication events, rapid rates of evolution, and tissue- or temporal-specific expression. Thus, environmental response genes include those that encode proteins involved in the manufacture, binding, transport, and breakdown of semiochemicals. Postgenomic elucidation of the function of such genes requires an understanding of the chemical ecology of the organism and, in particular, of the "small molecules" that act as selective agents either by promoting survival or causing selective mortality. In this overview, the significance of several groups of environmental response genes is examined in the context of chemical ecology. Cytochrome P-450 monooxygenases provide a case in point; these enzymes are involved in the biosynthesis of furanocoumarins (furocoumarins), toxic allelochemicals, in plants, as well as in their detoxification by lepidopterans. Biochemical innovations in insects and plants have historically been broadly defined in a coevolutionary context. Considerable insight can be gained by defining with greater precision components of those broad traits that contribute to diversification. Molecular approaches now allow chemical ecologists to characterize specifically those biochemical innovations postulated to lead to adaptation and diversification in plant/insect interactions.

Animals↗
PubMed2004

Evolutionary diversification of pigment pattern in Danio fishes: differential fms dependence and stripe loss in D. albolineatus.

The developmental bases for species differences in adult phenotypes remain largely unknown. An emerging system for studying such variation is the adult pigment pattern expressed by Danio fishes. These patterns result from several classes of pigment cells including black melanophores and yellow xanthophores, which differentiate during metamorphosis from latent stem cells of presumptive neural crest origin. In the zebrafish D. rerio, alternating light and dark horizontal stripes develop, in part, owing to interactions between melanophores and cells of the xanthophore lineage that depend on the fms receptor tyrosine kinase; zebrafish fms mutants lack xanthophores and have disrupted melanophore stripes. By contrast, the closely related species D. albolineatus exhibits a uniform pattern of melanophores, and previous interspecific complementation tests identified fms as a potential contributor to this difference between species. Here, we survey additional species and demonstrate marked variation in the fms-dependence of hybrid pigment patterns, suggesting interspecific variation in the fms pathway or fms requirements during pigment pattern formation. We next examine the cellular bases for the evolutionary loss of stripes in D. albolineatus and test the simplest model to explain this transformation, a loss of fms activity in D. albolineatus relative to D. rerio. Within D. albolineatus, we demonstrate increased rates of melanophore death and decreased melanophore migration, different from wild-type D. rerio but similar to fms mutant D. rerio. Yet, we also find persistent fms expression in D. albolineatus and enhanced xanthophore development compared with wild-type D. rerio, and in stark contrast to fms mutant D. rerio. These findings exclude the simplest model in which stripe loss in D. albolineatus results from a loss of fms-dependent xanthophores and their interactions with melanophores. Rather, our results suggest an alternative model in which evolutionary changes in pigment cell interactions themselves have contributed to stripe loss, and we test this model by manipulating melanophore numbers in interspecific hybrids. Together, these data suggest evolutionary changes in the fms pathway or fms requirements, and identify changes in cellular interactions as a likely mechanism of evolutionary change in Danio pigment patterns.

Alleles↗
PubMed2003

Diversity in the structure of electrocommunication signals within a genus of electric fish, Apteronotus.

Some gymnotiform electric fish modulate their electric organ discharge for intraspecific communication. In Apteronotus leptorhynchus, chirps are usually rapid (10-30 ms) modulations that are activated through non- N-methyl- d-aspartate (non-NMDA) glutamate receptors in the hindbrain pacemaker nucleus. Males produce longer chirp types than females and chirp at higher rates. In Apteronotus albifrons, chirp rate is sexually monomorphic, but chirp structure (change in frequency and amplitude during a chirp) was unknown. To better understand the neural regulation and evolution of chirping behavior, we compared chirp structure in these two species under identical stimulus regimes. A. albifrons, like A. leptorhynchus, produced distinct types of chirps that varied, in part, by frequency excursion. However, unlike in A. leptorhynchus, chirp types in A. albifrons varied little in duration, and chirps were all longer (70-200 ms) than those of A. leptorhynchus. Chirp type production was not sexually dimorphic in A. albifrons, but within two chirp types males produced longer chirps than females. We suggest that species differences in chirp duration might be attributable to differences in the relative proportions of fast-acting (non-NMDA) and slow-acting (NMDA) glutamate receptors in the pacemaker. Additionally, we map species difference onto a phylogeny and hypothesize an evolutionary sequence for the diversification of chirp structure.

Acoustics↗
PubMed1999

Age-related alterations of somatic hypermutation and CDR3 lengths in human Vkappa4-expressing B lymphocytes.

The lower avidity and/or affinity of antibodies generated by an aged immune system could be attributed to two major changes in the antibody repertoire: a shift in germline gene usage and a decrease in the rate of immunoglobulin hypermutation. In an attempt to identify the mechanisms involved in the observed humoral immune deficiency in the elderly, we studied whether differences in the somatic diversity of a particular Vkappa region occurred with ageing. By using the polymerase chain reaction and sequencing, we analysed and compared Vkappa4-Jkappa rearrangements isolated from young (mean age 21 years) and aged (mean age 83 years) healthy adults. Mutations in the Vkappa4 gene compared with the germline sequence were determined as well as the length and structure of the CDR3 sequence. We analysed in detail various mechanisms contributing to CDR3 and Vkappa variability in rearrangements involving the Vkappa4 gene. Our data revealed that, despite strong individual variations, significantly lower levels of somatic mutation were found in the aged group, both for complementarity-determining regions (CDRs) and framework regions (FRs) encoding Vkappa4 sequences. This decrease mostly affected mutations responsible for replacements and thus resulted in a lowered somatic diversification of the encoded Vkappa4 proteins in aged individuals. Moreover, comparison of the CDR3 regions of the Vkappa4-Ckappa cDNA revealed changes in light-chain junctional diversity that correlated with age. Altogether these data suggest an impaired light-chain somatic diversity in connection with human senescence.

Adult↗
PubMed2004

Error in estimation of rate and time inferred from the early amniote fossil record and avian molecular clocks.

The best reconstructions of the history of life will use both molecular time estimates and fossil data. Errors in molecular rate estimation typically are unaccounted for and no attempts have been made to quantify this uncertainty comprehensively. Here, focus is primarily on fossil calibration error because this error is least well understood and nearly universally disregarded. Our quantification of errors in the synapsid-diapsid calibration illustrates that although some error can derive from geological dating of sedimentary rocks, the absence of good stem fossils makes phylogenetic error the most critical. We therefore propose the use of calibration ages that are based on the first undisputed synapsid and diapsid. This approach yields minimum age estimates and standard errors of 306.1 +/- 8.5 MYR for the divergence leading to birds and mammals. Because this upper bound overlaps with the recent use of 310 MYR, we do not support the notion that several metazoan divergence times are significantly overestimated because of serious miscalibration (sensuLee 1999). However, the propagation of relevant errors reduces the statistical significance of the pre-K-T boundary diversification of many bird lineages despite retaining similar point time estimates. Our results demand renewed investigation into suitable loci and fossil calibrations for constructing evolutionary timescales.

Animals↗
PubMed2004

Early duplication and functional diversification of the opsin gene family in insects.

Recent analysis of the complete mosquito Anopheles gambiae genome has revealed a far higher number of opsin genes than for either the Drosophila melanogaster genome or any other known insect. In particular, the analysis revealed an extraordinary opsin gene content expansion, whereby half are long wavelength-sensitive (LW) opsin gene duplicates. We analyzed this genomic data in relationship to other known insect opsins to estimate the relative timing of the LW opsin gene duplications and to identify "missing" paralogs in extant species. The inferred branching patterns of the LW opsin gene family phylogeny indicate at least one early gene duplication within insects before the emergence of the orders Orthoptera, Mantodea, Hymenoptera, Lepidoptera, and Diptera. These data predict the existence of one more LW opsin gene than is currently known from most insects. We tested this prediction by using a degenerate PCR strategy to screen the hymenopteran genome for novel LW opsin genes. We isolated two LW opsin gene sequences from each of five bee species, Bombus impatiens, B. terrestris, Diadasia afflicta, D. rinconis, and Osmia rufa, including 1.1 to 1.2 kb from a known (LW Rh1) and 1 kb from a new opsin gene (LW Rh2). Phylogenetic analysis suggests that the novel hymenopteran gene is orthologous to A. gambiae GPRop7, a gene that is apparently missing from D. melanogaster. Relative rate tests show that LW Rh2 is evolving at a slower rate than LW Rh1 and, therefore, may be a useful marker for higher-level hymenopteran systematics. Site-specific rate tests indicate the presence of several amino acid sites between LW Rh1 and LW Rh2 that have undergone shifts in selective constraints after duplication. These sites and others are discussed in relationship to putative structural and functional differences between the two genes.

Amino Acid Sequence↗
PubMed2006

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.

Eukaryotic Cells↗
PubMed1995

The molecular evolution of the small heat-shock proteins in plants.

The small heat-shock proteins have undergone a tremendous diversification in plants; whereas only a single small heat-shock protein is found in fungi and many animals, over 20 different small heat-shock proteins are found in higher plants. The small heat-shock proteins in plants have diversified in both sequence and cellular localization and are encoded by at least five gene families. In the study, 44 small heat-shock protein DNA and amino acid sequences were examined, using both phylogenetic analysis and analysis of nucleotide substitution patterns to elucidate the evolutionary history of the small heat-shock proteins. The phylogenetic relationships of the small heat-shock proteins, estimated using parsimony and distance methods, reveal the gene duplication, sequence divergence and gene conversion have all played a role in the evolution of the small heat-shock proteins. Analysis of nonsynonymous substitutions and conservative and radical replacement substitutions )in relation to hydrophobicity) indicates that the small heat-shock protein gene families are evolving at different rates. This suggests that the small heat-shock proteins may have diversified in function as well as in sequence and cellular localization.

Amino Acid Sequence↗
PubMed2005

Patterns of hybridization and population genetic structure in the terrestrial orchids Liparis kumokiri and Liparis makinoana (Orchidaceae) in sympatric populations.

We investigated the potential for gene flow and genetic assimilation via hybridization between common and rare species of the terrestrial orchid genus Liparis, focusing specifically on sympatric and allopatric populations of the common Liparis kumokiri and the rare Liparis makinoana. We utilized analyses of genetic diversity, morphology, and the spatial distributions of individuals and genotypes to quantify the dynamics of interspecific gene flow at within- and among-population scales. High levels of allozyme genetic diversity (HE) were found in populations of the rare L. makinoana (0.317), whereas the common L. kumokiri (N = 1744 from 14 populations) revealed a complete lack of variation. This contrast may reflect different breeding systems and associated rates of genetic drift (L. makinoana is self-incompatible, whereas L. kumokiri is self-compatible). At the two known sympatric sites, individuals were found that recombined parental phenotypes, possessing floral characteristics of L. kumokiri and vegetative characteristics of L. makinoana. These putative hybrids were the only individuals found segregating alleles diagnostic of both parental species. Analysis of these individuals indicated that hybrid genotypes were skewed towards L. kumokiri and later generation recombinants of L. kumokiri at both sympatric sites. Furthermore, Ripley's bivariate L(r) statistics revealed that at one site these hybrids are strongly spatially clustered with L. kumokiri. Nonetheless, the relatively low frequency of hybrids, absence of ongoing hybridization (no F1s or first generation backcrossess), and strong genetic differentiation between morphologically 'pure' parental populations at sympatric sites (FST = 0.708-0.816) indicates that hybridization was not an important bridge for gene flow. The results from these two species suggest that natural hybridization has not played an important role in the diversification of Liparis, but instead support the view that genetic drift and limited gene flow are primarily responsible for speciation in Liparis. Based on genetic data and current status of the species, implications of the research for conservation are considered to provide guidelines for appropriate conservation and management strategies.

Conservation of Natural Resources↗
PubMed2005

Evolutionary conservation and diversification of Rh family genes and proteins.

Rhesus (Rh) proteins were first identified in human erythroid cells and recently in other tissues. Like ammonia transporter (Amt) proteins, their only homologues, Rh proteins have the 12 transmembrane-spanning segments characteristic of transporters. Many think Rh and Amt proteins transport the same substrate, NH(3)/NH(4)(+), whereas others think that Rh proteins transport CO(2) and Amt proteins NH(3). In the latter view, Rh and Amt are different biological gas channels. To reconstruct the phylogeny of the Rh family and study its coexistence with and relationship to Amt in depth, we analyzed 111 Rh genes and 260 Amt genes. Although Rh and Amt are found together in organisms as diverse as unicellular eukaryotes and sea squirts, Rh genes apparently arose later, because they are rare in prokaryotes. However, Rh genes are prominent in vertebrates, in which Amt genes disappear. In organisms with both types of genes, Rh had apparently diverged away from Amt rapidly and then evolved slowly over a long period. Functionally divergent amino acid sites are clustered in transmembrane segments and around the gas-conducting lumen recently identified in Escherichia coli AmtB, in agreement with Rh proteins having new substrate specificity. Despite gene duplications and mutations, the Rh paralogous groups all have apparently been subject to strong purifying selection indicating functional conservation. Genes encoding the classical Rh proteins in mammalian red cells show higher nucleotide substitution rates at nonsynonymous codon positions than other Rh genes, a finding that suggests a possible role for these proteins in red cell morphogenetic evolution.

Amino Acid Sequence↗
PubMed2006

Chromosome localization of microsatellite markers in the shrews of the Sorex araneus group.

The extremely high rate of karyotypic evolution that characterizes the shrews of the Sorex araneus group makes this group an exceptionally interesting model for population genetics and evolutionary studies. Here, we attempted to map 46 microsatellite markers at the chromosome arm level using flow-sorted chromosomes from three karyotypically different taxa of the Sorex araneus group (S. granarius and the chromosome races Cordon and Novosibirsk of S. araneus). The most likely localizations were provided for 35 markers, among which 25 were each unambiguously mapped to a single locus on the corresponding chromosomes in the three taxa, covering the three sexual chromosomes (XY1Y2) and nine of the 18 autosomal arms of the S. araneus group. The results provide further evidence for a high degree of conservation in genome organization in the S. araneus group despite the presence of numerous Robertsonian rearrangements. These markers can therefore be used to compare the genetic structure among taxa of the S. araneus group at the chromosome level and to study the role of chromosomal rearrangements in the genetic diversification and speciation process of this group.

Animals↗
PubMed2005

The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories.

The RNase A superfamily has been important in biochemical, structural, and evolutionary studies and is believed to be the sole vertebrate-specific enzyme family. To understand the origin and diversification of the superfamily, we here determine its entire repertoire in the sequenced genomes of human, mouse, rat, and chicken. We report a previously unnoticed gene cluster in mouse chromosome 10 and a number of new genes, including mammalian RNases 11-13, which are close relatives of the recently identified RNases 9 and 10. Gene expression data imply male-reproductive functions for RNases 9-13, although their sequences suggest the lack of ribonucleolytic activities. In contrast to the presence of 13-20 functional genes in mammals, chicken has only 3 RNase genes, which are evolutionarily close to mammalian RNase 5, like other nonmammalian RNases. This and other evidence suggests that the RNase A superfamily originated from an RNase 5-like gene and expanded in mammals. Together with the fact that multiple lineages of the superfamily, including RNases 2, 3, 5, and 7, have antipathogenic activities, we suggest that the superfamily started off as a host-defense mechanism in vertebrates. Consistent with this hypothesis, all members of the superfamily exhibit high rates of amino acid substitution as is commonly observed in immunity genes.

Amino Acid Sequence↗
PubMed2006

Evolutionary mechanisms of persistence and diversification of a calicivirus within endemically infected natural host populations.

In order to understand the evolutionary mechanisms of persistence and diversification within the Caliciviridae, we have been exploiting endemic infection of feline calicivirus within five geographically distinct household groups of cats. By sequencing immunodominant and variable regions of the capsid gene, we identified the relative contribution of the different evolutionary processes employed by the virus to ensure its long-term survival in the host population. Such strategies included progressive evolution of a given variant of a strain through mutation accumulation within an individual, sequential reinfection with either a variant of the same strain or with a different strain, and mixed infection. Recombination between different strains in this study has been reported in detail elsewhere (K. P. Coyne et al., J. Gen. Virol. 87:921-926, 2006). Here, we provide evidence to suggest that true long-term persistent infection in individuals is relatively rare, with the majority of apparent viral carriers undergoing a combination of progressive evolution and cyclical reinfection. Progressive evolution at the individual level and variant reinfection at both the individual and population levels were associated with positive selection. Two measures of evolution rate were determined; for a virus progressively evolving within an individual (1.32 x 10(-2) to 2.64 x 10(-2) substitutions per nucleotide per year, i.e., no transmission) and for a strain circulating within a population (3.84 x 10(-2) to 4.56 x 10(-2) substitutions per nucleotide per year, i.e., including transmission). Reiteration of both progressive evolution and variant reinfection appeared to lead to a gradual increase in the diversity of a given strain of virus, both in the individual and in the population, until eventually new strains emerged.

Animals↗
PubMed2000

Incipient speciation in sympatric Nicaraguan crater lake cichlid fishes: sexual selection versus ecological diversification.

The growing body of empirical evidence for sympatric speciation has been complemented by recent theoretical treatments that have identified evolutionary conditions conducive to speciation in sympatry. The Neotropical Midas cichlid (Amphilophus citrinellum) fits both of the key characteristics of these models, with strong assortative mating on the basis of a colour polymorphism coupled with trophic and ecological differentiation derived from a polymorphism in their pharyngeal jaws. We used microsatellite markers and a 480 bp fragment of the mitochondrial DNA control region to study four polymorphic populations of the Midas cichlid from three crater lakes and one large lake in Nicaragua in an investigation of incipient sympatric speciation. All populations were strongly genetically differentiated on the basis of geography. We identified strong genetic separation based on colour polymorphism for populations from Lake Nicaragua and one crater lake (Lake Apoyo), but failed to find significant genetic structuring based on trophic differences and ecological niche separation in any of the four populations studied. These data support the idea that sexual selection through assortative mating contributes more strongly or earlier during speciation in sympatry than ecological separation in these cichlids. The long-term persistence of divergent cichlid ecotypes (as measured by the percentage sequence divergence between populations) in Central American crater lakes, despite a lack of fixed genetic differentiation, differs strikingly from the patterns of extremely rapid speciation in the cichlids in Africa, including its crater lakes. It is unclear whether extrinsic environmental factors or intrinsic biological differences, e.g. in the degree of phenotypic plasticity, promote different mechanisms and thereby rates of speciation of cichlid fishes from the Old and New Worlds.

Animals↗
PubMed1997

Genetic diversity of feline immunodeficiency virus: dual infection, recombination, and distinct evolutionary rates among envelope sequence clades.

For the rapid genetic analysis of feline immunodeficiency virus (FIV), we developed a heteroduplex mobility assay (HMA) that utilizes a PCR-amplified fragment of the FIV envelope gene spanning the third and fourth variable regions of the envelope surface protein coding sequence. Viral sequences were successfully amplified from blood specimens from 98 naturally infected cats from Australia, Canada, Germany, Italy, South Africa, and the United States. Eighty were clearly assignable to the A or B envelope sequence subtypes. Three belonged to subtype C, one was dually infected with viruses harboring the A and B env subtypes, and several were categorized as outliers to any of the established subtypes or as probable intersubtype recombinants. Some geographic clustering was evident, with subtypes A and B found in greater frequency in the western and eastern regions of the United States, respectively. Subtypes A, B, and C were found on more than one continent, and countries with more than two samples analyzed contained at least two subtypes. The broadest representation of subtypes was found in Munich, Germany, where three subtypes and one virus that was not classifiable by HMA were found. Thirteen samples were selected for DNA sequence determination over the same region of env used for HMA. Analysis of all available FIV env sequences from this and previous studies revealed the existence of recombinant viruses generated from subtype A/B, B/D, and A/C envelope gene sequences. Subtype A env sequences were less diverse than subtype B sequences, although both groups had well-supported clusters. Furthermore, the mutational pattern giving rise to diversification in the two subtypes differed, with the subtype A viruses showing half as many synonymous site mutations compared to subtype B yet showing similar levels of nonsynonymous site changes. These results are consistent with the hypothesis that FIV-B is an older virus group and is possibly more host adapted than FIV-A.

Amino Acid Sequence↗