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PubMed2000

An analysis of genetic variation in natural populations of Sticherus flabellatus [R. Br. (St John)] using amplified fragment length polymorphism (AFLP) markers.

Amplified fragment length polymorphisms (AFLPs) were used to characterize the genetic diversity within and among natural populations of Sticherus flabellatus. Eight populations within the Sydney region of New South Wales, Australia were surveyed using 11 primer combinations. A total of 1108 reproducible bands were detected of which 469 (42%) were polymorphic. FST estimates averaged over all polymorphic loci indicated that significant genomic differentiation occurs among populations (average = 0.783). Genetic diversity within populations was assessed according to average heterozygosity (H) and percentage polymorphic loci (P) per population. Within-population diversity ranged from H = 0.12 and P = 33.69 to H = 0.04 and P = 15.99. Analysis of genetic similarity among populations suggested that the eight populations studied fall into two groups of four populations, based on population size and the condition of the habitat. Phenetic analysis (AMOVA) indicated that genetic variation is greater among populations (74.34%) than within populations (25.66%). These findings suggest that the breeding system of S. flabellatus is predominantly inbreeding, with genetic diversity maintained by occasional outcrossing in larger populations. The results presented in this study could provide evidence to support the proposal to protect natural stands of S. flabellatus, which has implications for the Australian horticulture industry.

Crosses, Genetic↗
PubMed2000

Genetic variation in natural populations of maté (Ilex paraguariensis A. st.-hil., aquifoliaceae) using RAPD markers.

This study characterized the genetic diversity of four populations of Ilex paraguariensis, a plant species native to South America, using random amplified polymorphic DNA (RAPD) markers. A total of 341 different RAPD bands were generated by the 15 primers analysed. High genetic variability was detected within each population, with an average diversity of 0.163. The within-population variation was large, probably as a result of the life history characteristics of I. paraguariensis. The average distance between individuals from each population was 0.392 and that between populations was 0.433, indicating a low between-population divergence. Most bands were common to all populations and the population-specific bands occurred at low frequencies. Partitioning of the genetic diversity indicated that 85% of the variation occurred within populations and only 15% between populations. Although most of the variability is within populations, clusterings of plants in each population were observed in the dendrogram.

Base Sequence↗
PubMed1998

Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum.

Molecular phylogenetic surveys have recently revealed an ecologically widespread crenarchaeal group that inhabits cold and temperate terrestrial and marine environments. To date these organisms have resisted isolation in pure culture, and so their phenotypic and genotypic characteristics remain largely unknown. To characterize these archaea, and to extend methodological approaches for characterizing uncultivated microorganisms, we initiated genomic analyses of the nonthermophilic crenarchaeote Cenarchaeum symbiosum found living in association with a marine sponge, Axinella mexicana. Complex DNA libraries derived from the host-symbiont population yielded several large clones containing the ribosomal operon from C. symbiosum. Unexpectedly, cloning and sequence analysis revealed the presence of two closely related variants that were consistently found in the majority of host individuals analyzed. Homologous regions from the two variants were sequenced and compared in detail. The variants exhibit >99.2% sequence identity in both small- and large-subunit rRNA genes and they contain homologous protein-encoding genes in identical order and orientation over a 28-kbp overlapping region. Our study not only indicates the potential for characterizing uncultivated prokaryotes by genome sequencing but also identifies the primary complication inherent in the approach: the widespread genomic microheterogeneity in naturally occurring prokaryotic populations.

Animals↗
PubMed1986

Internal thermodynamics of position 51 mutants and natural variants of tyrosyl-tRNA synthetase.

Natural variation and evolution impose structural changes on an enzyme that can affect the energetics of catalysis. The energy profile of reaction could, in theory, be altered in three distinct ways: uniform binding changes, differential binding changes, and catalysis of elementary steps. Residue threonine-51 of tyrosyl-tRNA synthetase from Bacillus stearothermophilus is subject to natural variation, being replaced by alanine and proline in the enzymes from Bacillus caldotenax and Escherichia coli, respectively. The consequences of this variation on the energetics of formation of tyrosyl adenylate have been investigated by constructing free energy profiles for wild-type and mutant enzymes constructed by introducing these amino acids into the B. stearothermophilus enzyme. Mutation of Thr-51 to alanine, proline, and cysteine by site-directed mutagenesis improves the stabilization of the transition state in the formation of tyrosyl adenylate. Most marked is the mutation Thr-51----Pro-51 which stabilizes the transition state by 2.2 kcal/mol and accelerates the forward rate 20-fold to a level near that of the enzyme from E. coli. However, the improved transition-state binding is accompanied by an even greater stabilization of tyrosyl adenylate. This reduces the rate of pyrophosphorolysis of tyrosyl adenylate and/or weakens the binding of pyrophosphate in the reverse reaction, shifting the equilibrium between enzyme-bound reactants greatly in favor of the enzyme-intermediate complex. The more stable mutant enzyme-tyrosyl adenylate complexes have lower rates of aminoacylation, suggesting that mutations which stabilize the intermediate slow down the subsequent transfer of tyrosine from tyrosyl adenylate to tRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Effects of natural sequence variation on recognition by monoclonal antibodies neutralize simian immunodeficiency virus infectivity.

The determinants of immune recognition by five monoclonal antibodies (KK5, KK9, KK17, Senv7.1, and Senv101.1) that neutralize simian immunodeficiency virus infectivity were analyzed. These five neutralizing monoclonal antibodies were generated to native SIVmac251 envelope glycoprotein expressed by a vaccinia virus recombinant vector. All five recognize conformational or discontinuous epitopes and require native antigen for optimal recognition. These monoclonal antibodies also recognize SIVmac239 gp120, but they do not recognize gp120 of two natural variants of SIVmac239, 1-12 and 8-22, which evolved during the course of persistent infection in vivo (D.P.W. Burns and R.C. Desrosiers, J. Virol. 65:1843-1854, 1991). Recombinant viruses which were constructed by exchanging variable regions between SIVmac239 and variant 1-12 were used to define domains important for recognition. Radioimmunoprecipitation analysis demonstrated that sequence changes in variable regions 4 and 5 (V4/V5) were primarily responsible for the loss of recognition of the 1-12 variant. Site-specific mutants were used to define precise changes that eliminate recognition by these neutralizing antibodies. Changing N-409 to D, deletion of KPKE, and deletion of KEQH in V4 each resulted in loss of recognition by all five monoclonal antibodies. SIVs with these natural sequence changes are still replication competent and viable. Changing A-417 to T or A/N-417/418 to TK in V4 or Q-477 to K in V5 did not alter recognition detectably. These results define specific, naturally occurring sequence changes in V4 of SIVmac that result in loss of recognition by one class of SIVmac neutralizing antibodies.

Amino Acid Sequence↗
PubMed2006

The nature of variations of ammonia proton affinity in an argon environment.

The presence of solvent molecules, even inert, may significantly influence processes taking place in the gas phase. The reason for the solvent activity may be found in studies of complexes originating from microsolvation. The structure, thermodynamics, and vibrational properties of NH(4)(+)Ar(n) (n = 0-5) and NH(3)Ar(n) (n = 0-4) complexes are presented in this work with the aim to elucidate the effect of microsolvation on protonation/deprotonation processes. The relation between the nature of interactions in cationic and neutral clusters and the proton affinity is studied as a function of the number of ligands in complexes.

Journal Article↗
PubMed1992

A comprehensive study of genic variation in natural populations of Drosophila melanogaster. VI. Patterns and processes of genic divergence between D. melanogaster and its sibling species, Drosophila simulans.

We present here an extensive set of data on allelic differences between homologous proteins of Drosophila melanogaster and its sibling species, Drosophila simulans, obtained by nondenaturing one-dimensional, and denaturing two-dimensional gel electrophoresis. The data suggest that, for these two species, (1) approximately 10% of protein-coding loci have no alleles in common in our sample, (2) the extent of genic variation at a locus (mean heterozygosity) within a species is not correlated with the extent of divergence (Nei's genetic distance) at that locus between species, and (3) significant heterogeneity of divergence rates exists for different structural/functional classes of loci. These results are discussed in the context of the dynamics of genetic variation within and between species.

Alleles↗
PubMed2002

Genes, culture, and aging flies--what the lab can and cannot tell us about natural genetic variation for senescence.

Model organisms cultured in the lab provide a powerful way to explore basic biological processes. However, lab culture can select for high early fecundity and dramatically shorten the life-span of lab organisms. Studies that use these short-lived organisms to identify aging-related genes might identify genes that simply restore the organism's original life-span. These results might not be fully relevant to wild populations. Experiments that reduce selection for shorter life-span or seek genes in naturally long-lived cohorts should lead to a more accurate understanding of aging.

Aging↗
PubMed2002

Timing of current reproduction directly affects future reproductive output in European coots.

Life-history theory suggests that the variation in the seasonal timing of reproduction within populations may be explained on the basis of individual optimization. Optimal breeding times would vary between individuals as a result of trade-offs between fitness components. The existence of such trade-offs has seldom been tested empirically. We experimentally investigated the consequences of altered timing of current reproduction for future reproductive output in the European coot (Fulica atra). First clutches of different laying date were cross-fostered between nests, and parents thereby experienced a delay or an advance in the hatching date. The probability and success of a second brood, adult survival until and reproduction in the next season were then compared to the natural variation among control pairs. Among control pairs the probability of a second brood declined with the progress of season. Delayed pairs were less likely and advanced pairs were more likely to produce a second brood. These changes were quantitatively as predicted from the natural seasonal decline. The number of eggs in the second clutch was positively related to egg number in the first clutch and negatively related to laying date. Compared to the natural variation, delayed females had more and advanced females had fewer eggs in their second clutch. The size of the second brood declined with season, but there was no significant effect of delay or advance. Local adult survival was higher following a delay and reduced following an advance. The effect of the experiment on adult survival was independent of sex. Laying date and clutch size of females breeding in the next year were not affected by treatment. The study demonstrates the existence of a trade-off between increased probability of a second brood and decreased parental survival for early breeding. Timing-dependent effects of current reproduction on future reproductive output may thus play an important role in the evolution of the seasonal timing of reproduction.

Analysis of Variance↗
PubMed1992

Dynamics of cytoplasmic incompatibility and mtDNA variation in natural Drosophila simulans populations.

In Drosophila simulans a cytoplasmically transmitted microorganism causes reduced egg hatch when infected males mate with uninfected females. The infection is rapidly spreading northward in California. Data on a specific mtDNA restriction site length polymorphism show that changes in the frequency of mtDNA variants are associated with this spread. All infected flies possess the same mtDNA allele, whereas the uninfected flies are polymorphic. Given that both paternal inheritance of the infection and imperfect maternal transmission have been demonstrated, one might expect instead that both infected and uninfected flies would possess both mtDNA variants. Our data suggest that imperfect female transmission of the infection (and/or the loss of the infection among progeny) is more common in nature than paternal transmission. A simple model of intrapopulation dynamics, with empirically supported parameter values, adequately describes the joint frequencies of the mtDNA variants and incompatibility types.

Animals↗
PubMed1997

Ultraviolet plumage colors predict mate preferences in starlings.

Avian plumage has long been used to test theories of sexual selection, with humans assessing the colors. However, many birds see in the ultraviolet (<400 nm), to which humans are blind. Consequently, it is important to know whether natural variation in UV reflectance from plumage functions in sexual signaling. We show that female starlings rank males differently when UV wavelengths are present or absent. Principal component analysis of approximately 1300 reflectance spectra (300-700 nm) taken from sexually dimorphic plumage regions of males predicted preference under the UV+ treatment. Under UV- conditions, females ranked males in a different and nonrandom order, but plumage reflectance in the human visible spectrum did not predict choice. Natural variation in UV reflectance is thus important in avian mate assessment, and the prevailing light environment can have profound effects on observed mating preferences.

Animals↗
PubMed2006

Heat sensitivity of photosynthetic electron transport varies during the day due to changes in sugars and osmotic potential.

In water-stressed leaves, accumulation of neutral osmotica enhances the heat tolerance of photosynthetic electron transport. There are large diurnal and day-to-day changes in leaf sugar content because of variations in net photosynthetic production, respiration and retranslocation. To test the hypothesis that diurnal and day-to-day variations in leaf sugar content and osmotic potential significantly modify the responses to temperature of photosynthetic electron transport rate, we studied chlorophyll fluorescence rise temperatures (i.e. critical temperatures at break-points in fluorescence versus temperature response curves, corresponding to enhanced damage of PSII centers and detachment of pigment-binding complexes) in the dark at a background of weak far-red light (T(FR)) and under actinic light (T(L)), and responses of foliar photosynthetic electron transport rate to temperature using gas-exchange and chlorophyll fluorescence techniques in the temperate tree Populus tremula L. Sucrose and sorbitol feeding experiments demonstrated strong increases of fluorescence rise temperatures T(FR) and T(L) with decreasing leaf osmotic potential and increasing internal sugar concentration. Similar T(FR) and T(L) changes were observed in response to natural variation in leaf sugar concentration throughout the day. Increases in leaf sugar concentration led to an overall down-regulation of the rate of photosynthetic electron transport (J), but increases in the optimum temperature (Topt) of J. For the entire dataset, Topt varied from 33.8 degrees C to 43 degrees C due to natural variation in sugars and from 33.8 degrees C to 52.6 degrees C in the sugar feeding experiments, underscoring the importance of sugars in modifying the response of J to temperature. However, the correlations between the sugar concentration and fluorescence rise temperature varied between the days. This variation in fluorescence rise temperature was best explained by the average temperature of the preceding 5 or 6 days. In addition, there was a significant year-to-year variation in heat sensitivity of photosynthetic electron transport that was associated with year-to-year differences in endogenous sugar content. Our data demonstrate a diurnal variation in leaf heat tolerance due to changes in sugar concentration, but they also show that this short-term modification in heat tolerance is super-imposed by long-term changes in heat resistance driven by average temperature of preceding days.

Carbohydrate Metabolism↗
PubMedDate not supplied

Genetic variation among natural and laboratory colony populations of Lutzomyia longipalpis (Lutz & Neiva, 1912)(Diptera: Psychodidae) from Colombia.

Genetic diversity among three field populations of Lutzomyia longipalpis in Colombia was studied using isozyme analysis. Study sites were as much as 598 km apart and included populations separated by the eastern Cordillera of the Andes. Genetic variability among populations, estimated by heterozygosity, was within values typical for insects in general (8.1%). Heterozygosity for field populations were compared with a laboratory colony from Colombia (Melgar colony) and were only slightly lower. These results suggest that establishment and long term maintenance of the Melgar colony has had little effect on the level of isozyme variability it carries. Genetic divergences between populations was evaluated using estimates of genetic distance. Genetic divergence among the three field populations was low (D = 0.021), suggesting they represent local populations within a single species. Genetic distance between field populations and the Melgar colony was also low (D = 0.016), suggesting that this colony population does not depart significantly from natural populations. Finally, comparisons were made between Colombian populations and colonies from Brazil and Costa Rica. Genetic distance values were high between Colombian and both Brazil and Costa Rica colony populations (D = 0.199 and 0.098 respectively) providing additional support for our earlier report that populations from the three countries represent distinct species.

Animals↗
PubMed2004

Analysis of natural allelic variation of Arabidopsis seed germination and seed longevity traits between the accessions Landsberg erecta and Shakdara, using a new recombinant inbred line population.

Quantitative trait loci (QTL) mapping was used to identify loci controlling various aspects of seed longevity during storage and germination. Similar locations for QTLs controlling different traits might be an indication for a common genetic control of such traits. For this analysis we used a new recombinant inbred line population derived from a cross between the accessions Landsberg erecta (Ler) and Shakdara (Sha). A set of 114 F9 recombinant inbred lines was genotyped with 65 polymerase chain reaction-based markers and the phenotypic marker erecta. The traits analyzed were dormancy, speed of germination, seed sugar content, seed germination after a controlled deterioration test, hydrogen peroxide (H2O2) treatment, and on abscisic acid. Furthermore, the effects of heat stress, salt (NaCl) stress, osmotic (mannitol) stress, and natural aging were analyzed. For all traits one or more QTLs were identified, with some QTLs for different traits colocating. The relevance of colocation for mechanisms underlying the various traits is discussed.

Abscisic Acid↗
PubMed1992

A comprehensive study of genic variation in natural populations of Drosophila melanogaster. VII. Varying rates of genic divergence as revealed by two-dimensional electrophoresis.

Four sibling species from the melanogaster subgroup (Drosophila melanogaster, D. simulans, D. sechellia, and D. mauritiana) were studied for genetic divergence, by high-resolution two-dimensional protein electrophoresis (2DE) coupled with ultrasensitive silver staining. A total of eight tissues from larval and adult developmental stages representing both gonadal (germ-line) and nongonadal (somatic) tissues were analyzed for protein divergence between species. Close to 400 polypeptides (protein spots) were scored from each tissue and species, and protein divergence was measured on the basis of qualitative differences (presence/absence) of protein spots in pairwise species comparisons. The observed levels of genic divergence varied among tissues and among species. When larval hemolymph proteins (which are known to be highly polymorphic) were excluded, there was no evidence to suggest that either the larval or adult-stage proteins, as a whole, are more diverged than the other; variation between different tissues rather than between developmental stages appears to be the most significant factor affecting genetic divergence between species. The reproductive tissue (testis and accessory gland) showed more divergence than did the nonreproductive tissue; D. melanogaster testis (from both larvae and adult males) showed the highest level of divergence. In view of the previous observation that D. simulans, D. mauritiana, and D. sechellia show similar but significantly less reproductive isolation from each other than from D. melanogaster, the present results suggest a correlation between the levels of reproductive-tract-protein divergence and the degree of reproductive isolation in these species.

Animals↗
PubMed1976

Unimodality, symmetry and the step-state hypothesis of electrophoretic variation in natural populations.

The population frequency distributions of electromorphs of polymorphic loci, when ordered by electrophoretic mobility, tend strongly and significantly to be both unimodal and symmetrical. Such distributions are predicted by all step-change models and their generality in published data can be construed as supportive of the step-change hypothesis. On the other hand, unimodality and symmetry might also be due to artifactual "unit perception" biases that affect the interpretation and reporting of electrophoretic data. In any case, it appears that perceived electromorphs are highly heterogeneous.

Alleles↗
PubMed1973

Allozyme genotype-environment relationships. I. Variation in natural populations of Drosophila pachea.

Remarkable geographic and seasonal uniformities in gene and genotype frequencies were found for four enzyme loci. Principal component analysis revealed two patterns of allele frequency changes in three of the allozyme loci (Est-b, Est-c and Acph) and one pattern in the Mdh-d locus. These patterns accounted for 90% to 100% of the variability at these loci. Significant positive correlations were obtained between several of the components and the variability in the non-saponifiable and alkaloid fractions of the senita cactus host plant. The genetic variance within a single locality (Guaymas, Mexico) was as great as the variance between all localities sampled. This is interpreted as a local founder effect. The temporary nature of the rotting cactus breeding site, the delayed maturation and the differential maturation rate of females and males are three factors proposed to cause forced outbreeding and counter the local founder effect. A combination of selection resulting from a direct interaction of the genotype and the environment, in addition to migration, is proposed to maintain the uniform gene frequencies.

Acid Phosphatase↗
PubMed1987

Variations of natural 15N abundances in the tissues and digesta of domestic animals.

The natural abundance of 15N (expressed as delta 15N per mil relative to air N2) in the tissues and the change of 15N abundance during the digestion processess in cattle, pig, and goat were investigated. The 15N abundances of cattle tissues differed by about 3.5% with high values in heart, urinary bladder and diaphragm. The ages of cattle did not affect on the 15N abundances of liver and kidney in cattle. The 15N abundances of urine were lower, and those of feces were a little higher than the values of diets in cattle and pigs. The delta 15N values of milk and blood were higher than the value of diets. Two peaks of 15N abundances at forestomach and caecum were observed during the digestion processes of diet in goats. The mechanisms of the variation of 15N abundances in animal bodies were briefly discussed.

Age Factors↗