Study on a Brazilian isolate. I. Population structure and random genetic drift

A number of parameters were evaluated in order to determine the level of isolation of a small Brazilian community existing in partial geographic isolation and thereby evaluate the random genetic drift potential in the population. On a theoretical basis, it is concluded that the probability of genetic drift is low but cannot be excluded. The relatively small proportion of migrants (26%), the limited individual mobility, as given by marital distance (29 +/- 7 km), the mean migrational distance (46 +/- 11 km), the small effective size (122), and the value of the product Neme (26) agree with the possibility of genetic drift in this population. The observed coefficient of inbreeding (0.00239) is lower than that expected (0.0066) for random mating, suggesting some pressures against consanguineous marriage.     

Linkage Modification with Mixed Random Mating and Selfing: A Numerical Study

Although recombination cannot increase under conditions of random mating or complete selfing in regimes of constant selection, with mixed random mating and selfing, selection for increased recombination can occur. For some fitness regimes there may be selection for reduced recombination with both low and high degrees of selfing but selection for increased recombination with moderate degrees of selfing. With some fitness regimes there is a historical effect: depending on which equilibrium a population starts from, there may be selection for either increased or decreased recombination. In other cases the direction of selection may be determined by the present state of individuals within the population. If recombination is already fairly limited, there may be selection for further reduction. If recombination is already fairly frequent, there may be selection for increased recombination. For certain symmetric viability systems there may be an intermediate value of the recombination fraction between 0 and 0.5 toward which the population will evolve. Although it is not yet possible to classify precisely those fitness matrices that can exhibit selection for increased recombination, it does appear that selection for increased recombination can occur only if at least two of the double homozygotes are less fit than would be expected on the basis of a comparison of the fitnesses of the single and double heterozygotes on an additive scale.     

Screening of a Small Set of Random Peptides: A New Strategy to Identify Synthetic Peptides that Mimic Epitopes

Small diversity libraries, composed of 4550 synthetic dodecapeptides and 8000 synthetic tripeptides, have been used to identify sequences homologous to small linear and non-linear parts of epitopes. Here we report that synthetic peptides identified through alignment of dodecapeptides and tripeptides derived from these small libraries have, in direct ELISA and/or competitive ELISA, activities similar to that of peptides covering the native epitope and similar to that of peptides derived from large expression libraries composed of 10⁶–10⁷ random peptides. This result was obtained with the monoclonal antibodies 6A.A6 and M2. Mab 6A.A6 binds the transmissible gastroenteritis virus (TGEV) and mAb M2 binds the FLAG^®-peptide, an affinity tag. It was also found that the antibody binding activity of peptides, derived from small or large libraries, can strongly depend on the way in which the peptide is presented to the antibody, i.e. high antibody titers were obtained when these peptides were synthesized on pins or coated onto microtiter plates, whereas low IC₅₀s were obtained with these peptides in solution. We postulate that small peptide libraries may be a powerful tool to quickly identify new peptides that can be used as sensitive markers for mAbs of interest. © 1997 John Wiley & Sons, Ltd.     

The assimilation of tri- and tetrapeptides by human erythrocytes

Evidence is presented that tripeptides enter human erythrocytes via saturable transport system(s) at rates similar to those previously described for dipeptides (King, G.F. and Kuchel, P.W. (1985) Biochem. J. 227, 833-842) but that the transmembrane flux rates for tetrapeptides are considerably less. 1H spin-echo NMR spectroscopy was used to monitor the coupled uptake and hydrolysis of peptides by red cells, since it enabled the simultaneous measurement of the levels of substrates and products of peptidase-catalysed reactions in suspensions with haematocrits similar to those found in vivo. Weighted non-linear least-squares regression of the integrated Michaelis-Menten equation onto progress curves obtained from the hydrolysis of Tyr-Gly-Gly and Gly-Gly-Gly in RBC lysates gave Km = 2.11 +/- 0.08 and 23.4 +/- 0.9 mmol/l and Vmax = 307 +/- 3 and 905 +/- 22 mmol/h per 1 packed cells, respectively. In whole cell suspensions, the rate of hydrolysis was considerably less and was dominated by the transmembrane flux of tripeptide. Progress curve analysis thus yielded the steady-state kinetic parameters for peptide transport; the values were Km = 11.6 +/- 1.1 and 56 +/- 18 mmol/l and Vmax = 12.9 +/- 3.0 and 36.4 +/- 3.2 mmol/h per 1 packed cells, respectively, for the previously mentioned peptides. The rate of transport of the tetrapeptide Gly-Gly-Gly-Gly was considerably less than either of the tripeptides. The above mentioned steady-state kinetic parameters were used in computer simulations of the coupled uptake and hydrolysis of tripeptides by human erythrocytes under physiological conditions; these simulations revealed certain similarities between the rates of peptide uptake by erythrocytes and the intestine in vivo.     

Collagen type IV-specific tripeptides for selective adhesion of endothelial and smooth muscle cells

Controlling the balance of endothelial cells (ECs) and smooth muscle cells (SMCs) in blood vessels is critically important to minimize the risk associated with vascular implants. Extracellular matrix (ECM) plays a key role in controlling the cellular balance, suggesting a promising source of cell-selective peptides. To obtain EC- or SMC-selective peptides, we start by highlighting sequence differences found among ECM molecules as enriched targets for cell-selective peptides. We explored the EC- or SMC-selective performance of tripeptides that are specifically enriched only in collagen type IV, but not in types I, II, III, and V. Collagen type IV was chosen since it is the major ECM in the basement membrane of blood vessels, which separates ECs and SMCs. Among 114 collagen type IV-derived tripeptides pre-screened from in silico analysis, 22 peptides (19%) were found to promote cell-selective adhesion, as determined by peptide array. One of the best performing EC-selective peptides (Cys-Ala-Gly (CAG)) was mixed into an electrospun fine-fiber, a vascular graft material, for practical application. Compared to unmodified fiber, the CAG containing fiber surface was found to enhance adhesion of ECs (+190%) while limiting SMCs (-20%). These results are not only consistent with the hypothesis of ECM as a source of cell selective peptides, but also suggest a new genre of EC- or SMC-selective peptides for tissue engineering applications. Collectively, these findings favorably support the screening approach used to discover new peptides for these purposes.     

Allozyme variation in bumble bees (Hymenoptera: Apidae)

Allozyme variation at an average of 37.3 loci was assessed in queens of 16 Bombus and 2 Psithyrus bumble bee species from North America. The mean expected heterozygosity (H) for the Bombus species was 0.008 +/- 0.006 (95% confidence limits) and that for the Psithyrus was 0.007 +/- 0.007. These levels are significantly lower than found in other Hymenoptera but are comparable to those found in previous studies of bumble bees based on far fewer loci. Neutral mutation and random genetic drift can account for the observed variation, but this implies a very small effective population size for species of bumble bees.     

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins

A statistical analysis of a representative data set of 169 known protein structures was used to analyze the specificity of residue interactions between spatial neighboring strands in beta-sheets. Pairwise potentials were derived from the frequency of residue pairs in nearest contact, second nearest and third nearest contacts across neighboring beta-strands compared to the expected frequency of residue pairs in a random model. A pseudo-energy function based on these statistical pairwise potentials recognized native beta-sheets among possible alternative pairings. The native pairing was found within the three lowest energies in 73% of the cases in the training data set and in 63% of beta-sheets in a test data set of 67 proteins, which were not part of the training set. The energy function was also used to detect tripeptides, which occur frequently in beta-sheets of native proteins. The majority of native partners of tripeptides were distributed in a low energy range. Self-correcting distance geometry (SECODG) calculations using distance constraints sets derived from possible low energy pairing of beta-strands uniquely identified the native pairing of the beta-sheet in pancreatic trypsin inhibitor (BPTI). These results will be useful for predicting the structure of proteins from their amino acid sequence as well as for the design of proteins containing beta-sheets.     

Fluorescence and 13C NMR determination of side-chain and backbone dynamics of synthetic melittin and melittin analogues in isotropic solvents

The dynamics in isotopic solvents of selectively 13C labeled synthetic melittin and three analogues have been investigated by using NMR and fluorescence techniques both separately and in combination. In conjunction with the "model-free" approach to interpretation of NMR relaxation data [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4570], the availability of steady-state fluorescence anisotropy and lifetime data augment T1, T2, and NOE data to provide quantitative information about fluorophore dynamics in these peptides. A method is presented for using combined fluorescence and NMR data to obtain technique- and model-independent values for parameters describing local motion of 13C-labeled fluorophores in peptides and proteins. The dynamics of melittin and melittin analogues are found to be consistent with structural characteristics inferred from CD, fluorescence, and NMR spectral information presented in the preceding paper (Weaver et al., 1989). In particular, the mobility of the random coil peptide monomers is shown to be quite similar, while side-chain as well as peptide backbone motion in the aggregated or oligomeric species differs markedly among the analogues. For melittin itself, experimentally determined overall rotational correlation times for the monomer and tetramer agree very well with values predicted on the basis of solvent-accessible protein surface area. The local dynamics of selectively 13C-labeled Trp-19 and Gly-12 residues of melittin are also found to be consistent with peptide structure. In random coil melittin monomer, a specific model for the motion indicates that the Trp side chain moves through an approximate angle of +/- 71 degrees about the beta-gamma bond with a correlation time of 159 +/- 24 ps. In melittin tetramer, the indole moiety is spatially more confined with a flip angle of +/- 37 degrees, yet demonstrates an increased rate of motion with a correlation time of 56 +/- 8 ps. The constrained mobility of the Trp-19 side chain is consistent with motional constraints inferred from the X-ray structure of melittin tetramer. These results show that protein side-chain motion, even of moieties as large as indole, can occur on the picosecond time scale and that these motions are reasonably similar to those inferred from molecular dynamics simulations.     

Evidence for two different broad-specificity oligopeptide transporters in intestinal cell line Caco-2 and colonic cell line CCD841

Recently the existence of two different Na(+)-coupled oligopeptide transport systems has been described in mammalian cells. These transport systems are distinct from the previously known H(+)/peptide cotransporters PEPT1 and PEPT2, which transport only dipeptides and tripeptides. To date, the only peptide transport system known to exist in the intestine is PEPT1. Here we investigated the expression of the Na(+)-coupled oligopeptide transporters in intestinal cell lines, using the hydrolysis-resistant synthetic oligopeptides deltorphin II and [d-Ala(2),d-Leu(5)]enkephalin (DADLE) as model substrates. Caco-2 cells and CCD841 cells, both representing epithelial cells from human intestinal tract, were able to take up these oligopeptides. Uptake of deltorphin II was mostly Na(+) dependent, with more than 2 Na(+) involved in the uptake process. In contrast, DADLE uptake was only partially Na(+) dependent. The uptake of both peptides was also influenced by H(+) and Cl(-), although to a varying degree. The processes responsible for the uptake of deltorphin II and DADLE could be differentiated not only by their Na(+) dependence but also by their modulation by small peptides. Several dipeptides and tripeptides stimulated deltorphin II uptake but inhibited DADLE uptake. These modulating small peptides were, however, not transportable substrates for the transport systems that mediate deltorphin II or DADLE uptake. These two oligopeptide transport systems were also able to take up several nonopioid oligopeptides, consisting of 9-17 amino acids. This represents the first report on the existence of transport systems in intestinal cells that are distinct from PEPT1 and capable of transporting oligopeptides consisting of five or more amino acids.     

Big plants—do they limit species coexistence?

Aims According to conventional theory, larger plant species are likely to inflict more intense competition on other (smaller) species. We tested a deducible prediction from this: that a larger species should generally be expected to impose greater limits on the number of species that can coexist with it.Methods Species richness was sampled under plant canopies for a selection of woody species ('host' species) that display a wide range of adult sizes (from small shrubs to large trees), growing within natural vegetation of the Interior Douglas-fir zone of southern British Columbia, Canada. These data were compared with species richness levels sampled within randomly placed plots within the host species habitat.Important findings A prominent host species size effect on species richness was detected but only narrowly at the small end of the species size range. Across most (90%) of the increasing size range of host species, the number of species residing under the host canopy showed no significant decrease relative to the number expected by random assembly, based on species richness within randomly defined equivalent areas within the habitat of the host species. This apparent 'null effect', we suggest, is explained not because these larger species have no effect on community assembly. We postulate that larger species are indeed likely to be more effective in causing competitive exclusion of some smaller species (as expected from conventional theory), but that any potential limitation effect of this on resident species richness is offset for two reasons: (i) larger species also generate niche spaces that they cannot exploit under their own canopies and so have minimal impact (as competitors) on smaller species that can occupy these niches and (ii) certain other small species—despite small size—have effective competitive abilities under the severe competition that occurs within host neighbourhoods of larger species. These and other recent studies call for re-evaluation of traditional views on the role of plant size in affecting competitive ability and community assembly.     

Evaluating the effect of stage-specific survivorship on the N(e)/N ratio

Evaluating effective population size (Ne) and the effective size to census size ratio (Ne/N) in species with Type III survivorship curves is complicated when key demographic parameters [mean (k macro) and variance (V(k)) of family size] are measured during early life stages. The method of Crow & Morton (1955) for scaling demographic data collected at a juvenile stage to expected values at adulthood is extended to consider sequential episodes of random and family correlated survival. Results show the following: (i) The order in which the episodes of random and family-correlated survival occur does not affect N(e) or N(e)/N; (ii) If a population experiences an episode of family-correlated survival, N(e)/N scaled to its expected value in a population of constant size (k macro= 2) is simply the survival rate during the family-correlated stage. If multiple such stages occur, scaled N(e)/N is the product of the survivals during all family-correlated life stages; (iii) Under the assumption of random post-enumeration survival, adjusting the variance effective size to its expected value at k macro= 2 is equivalent to computing the inbreeding effective size at the earlier life stage. Application to experimental data for hatchery populations of Pacific salmon (Oncorhynchus spp.) indicates that nonrandom survival during the marine phase led to estimated reductions in effective size of 0-62 (mean 19) in 12 different cohorts. This approach can provide insights into N(e)/N in highly fecund species, including some marine species in which N(e) has been estimated to be several orders of magnitude less than N.     

Fine-scale spatio-temporal patterns in a mountain grassland: do species replace each other in a regular fashion?

Abstract. Long-term ‘high spatial resolution’ permanent plot data were used to determine whether fine-scale species replacements in space occur more often than expected on the basis of random processes, and to test whether these replacements are species-specific. Monte Carlo tests were used. There was no indication of significance in associated positive change (species A increased when B increased); the overall number of significant results was not higher than expected on a random basis. For associated negative change, or replacements (species A increased when B decreased) the overall number of significant results was significantly higher than expected. Significant reciprocal replacements between Deschampsia flexuosa, Festuca rubra and Nardus stricta were frequent; changes in Anthoxanthum alpinum and Polygonum bistorta were uncorrelated with changes of the former three. The first three species thus use the ‘same’ space. Both the latter species often reproduce by seeds and their turnover is much higher. The prevalence of negative correlations of changes (i.e. correlation of increase with decrease) supports the concept of an internal structuring within the grassland community.     

Inheritance of song and stridulatory peg number divergence between Chorthippus brunneus and C. jacobsi, two naturally hybridizing grasshopper species (Orthoptera: Acrididae)

Knowledge of the genetic basis of divergence in mating signal characters that contribute to reproductive isolation is critical to understanding speciation. Here, we describe a semi-automated system for characterizing grasshopper acoustic signals. We used this system to study the genetic basis of divergence in three male calling song components [echeme (EL), syllable (SL) and phrase (PL) lengths] between Chorthippus brunneus and C. jacobsi, two species of grasshoppers that hybridize in northern Spain. We also studied the number of pegs in the stridulatory file. For all characters, additive effects accounted for most of the genetic differentiation between species. However, the three song components also showed small but significant epistatic effects. No sex linkage was detected. Wright-Castle-Lande estimates of the minimum numbers of genetic factors underlying song and peg number divergence were low: peg number (n(e)=5.87+/-5.84), SL (n(e)=2.37+/-4.79) and PL (n(e)=0.87+/-0.86). On the other hand, EL appeared to be controlled by many genes. These results suggest that divergence in SL and PL might be driven by sexual selection whereas EL might not be under selection. This is consistent with experimental results on female song preference in related species. However, the fact that few factors appear to underlie the differences in peg number is surprising. Peg number is not closely related to song characteristics. It often varies between closely related grasshopper species and it has been assumed to be a neutral character. The biometrical approaches used here tend to underestimate the number of factors influencing a trait but provide valuable background for subsequent quantitative trait loci analyses.     

Predominant torsional forms adopted by oligopeptide conformers in solution: parameters for molecular recognition.

In this paper, we describe the predominant conformational forms adopted by tripeptides and higher oligopeptides in aqueous solution. About 50 tripeptides and almost 20 higher oligopeptides (4-6 residues) were subjected to conformational analysis using SYBYL Random Search. As with dipeptides (Grail BM, Payne JW. J. Peptide Sci. 2000; 6: 186-199), both tripeptides and higher oligopeptides were found to occupy relatively few combinations of psi-phi space that were distinct from those associated with predominant protein secondary structures (e.g. helices and beta-sheets). Again, the preferred psi (psi) values for the first residue (i - 1) were in sectors encompassed by the ranges from +150 degrees to +/-180 degrees, +60 degrees to +90 degrees and -60 degrees to -90 degrees, which were combined with preferred phi (phi) values for the second residue (i) in sectors with ranges from -150 degrees to +/-180 degrees, -60 degrees to -90 degrees and +30 degrees to +60 degrees. It was notable that tripeptides and, to a greater extent, higher oligopeptides adopted an initial psi (psi) (Tor2) from +150 degrees to +/-180 degrees. For tripeptides, their N-C distances (distance between N-terminal nitrogen and C-terminal carbon atoms) distribute about 6.5 A to give shorter, 'folded' conformers that are similar in length to dipeptides, and longer, 'extended' conformers that are distinct. Furthermore, for higher oligopeptides, their N-C distances did not increment in relation to their increasing number of residues and short, 'folded' conformers were still present. These findings have a bearing upon the recognition of these molecules as substrates for widely distributed peptidases and peptide transporters.     

Niches within a niche: ecological differentiation of subterranean amphipods across Europe's interstitial waters

Species that successfully colonized subterranean environments are subject to two opposing selection processes. Stringent abiotic factors select for convergent adaptations, such as loss of eyes and pigments, while interspecific competition drives between‐species divergence. Subterranean species can resolve opposing selection by adaptation to physically different microhabitats. Yet, species frequently co‐occur in physically homogeneous subterranean habitats, like interstitial. These co‐occurrences in such a narrow ecological context can be explained either by equalizing mechanisms, in which neither of the co‐occurring species has a competitive advantage, or by more complex niche models that include species’ differentiation along a trophic niche axis. We tested these hypotheses using the amphipod genus Niphargus. We analysed Europe‐wide co‐occurrence records of Niphargus species from interstitial habitats, split into six independent large‐scale regions. Firstly, we addressed whether species’ pairwise co‐occurrences are random using a probabilistic model. Secondly, we tested whether species cluster into distinct functional–morphological groups and whether ecologically or phylogenetically distinct species are more likely to co‐occur. We found that 68% of species co‐occurrences were not different from random expectation, indicating that most species had access to most sites within each region. The remaining 32% co‐occurred either significantly more or less often than expected by chance. Cluster analysis of functional morphological characters showed that interstitial species belong to two feeding types, micro‐ and macrofeeders, likely representing two peaks of the interstitial adaptive landscape, and hinting that niche divergence, as a mechanism allowing coexistence, is favoured. Finally, we found that the number of co‐occurrences increases with increasing differentiation of functional morphology, but not phylogenetic differences. We conclude that ecological differentiation may be important in shaping such interstitial communities.     

Isolation of a peptide transport-deficient mutant of yeast.

A peptide transport mutant of a leucine-lysine auxotroph of Saccharomyces cerevisiae (strain Z1-2D) was isolated on the basis of its resistance to L-ethionyl-L-alanine. The mutant, designated Z1-2D Etar, did not utilize di- and tripeptides containing leucine or lysine although it contained peptidases which released the required amino acids from these substrates. S. cerevisiae Z1-2D Etar did not accumulate radioactivity from [14C]glycyl-L-leucine under conditions identical to those in which the parent took up the label from this dipeptide. These results indicate that the mutant lacks the cellular mechanism to transport peptides to the site of the peptidase activity and that di- and tripeptides share a common mode of entry into yeast.     

Lack of nonadditive genetic effects on early fecundity in Drosophila melanogaster

Fecundity is usually considered as a trait closely connected to fitness and is expected to exhibit substantial nonadditive genetic variation and inbreeding depression. However, two independent experiments, using populations of different geographical origin, indicate that early fecundity in Drosophila melanogaster behaves as a typical additive trait of low heritability. The first experiment involved artificial selection in inbred and non-inbred lines, all of them started from a common base population previously maintained in the laboratory for about 35 generations. The realized heritability estimate was 0.151 +/- 0.075 and the inbreeding depression was very small and nonsignificant (0.09 +/- 0.09% of the non-inbred mean per 1% increase in inbreeding coefficient). With inbreeding, the observed decrease in the within-line additive genetic variance and the corresponding increase of the between-line variance were very close to their expected values for pure additive gene action. This result is at odds with previous studies showing inbreeding depression and, therefore, directional dominance for the same trait and species. All experiments, however, used laboratory populations, and it is possible that the original genetic architecture of the trait in nature was subsequently altered by the joint action of random drift and adaptation to captivity. Thus, we carried out a second experiment, involving inbreeding without artificial selection in a population recently collected from the wild. In this case we obtained, again, a maximum-likelihood heritability estimate of 0.210 +/- 0.027 and very little nonsignificant inbreeding depression (0.06 +/- 0.12%). The results suggest that, for fitness-component traits, low levels of additive genetic variance are not necessarily associated with large inbreeding depression or high levels of nonadditive genetic variance.     

Evolution in metacommunities

A metacommunity can be defined as a set of communities that are linked by migration, and extinction and recolonization. In metacommunities, evolution can occur not only by processes that occur within communities such as drift and individual selection, but also by among-community processes, such as divergent selection owing to random differences among communities in species composition, and group and community-level selection. The effect of these among-community-level processes depends on the pattern of migration among communities. Migrating units may be individuals (migrant pool model), groups of individuals (single-species propagule pool model) or multi-species associations (multi-species propagule pool model). The most interesting case is the multi-species propagule pool model. Although this pattern of migration may a priori seem rare, it becomes more plausible in small well-defined 'communities' such as symbiotic associations between two or a few species. Theoretical models and experimental studies show that community selection is potentially an effective evolutionary force. Such evolution can occur either through genetic changes within species or through changes in the species composition of the communities. Although laboratory studies show that community selection can be important, little is known about how important it is in natural populations.     

Species selection and random drift in macroevolution

Species selection resulting from trait‐dependent speciation and extinction is increasingly recognized as an important mechanism of phenotypic macroevolution. However, the recent bloom in statistical methods quantifying this process faces a scarcity of dynamical theory for their interpretation, notably regarding the relative contributions of deterministic versus stochastic evolutionary forces. I use simple diffusion approximations of birth‐death processes to investigate how the expected and random components of macroevolutionary change depend on phenotype‐dependent speciation and extinction rates, as can be estimated empirically. I show that the species selection coefficient for a binary trait, and selection differential for a quantitative trait, depend not only on differences in net diversification rates (speciation minus extinction), but also on differences in species turnover rates (speciation plus extinction), especially in small clades. The randomness in speciation and extinction events also produces a species‐level equivalent to random genetic drift, which is stronger for higher turnover rates. I then show how microevolutionary processes including mutation, organismic selection, and random genetic drift cause state transitions at the species level, allowing comparison of evolutionary forces across levels. A key parameter that would be needed to apply this theory is the distribution and rate of origination of new optimum phenotypes along a phylogeny.     

Peptide Utilization by Amino Acid Auxotrophs of Neurospora crassa

The ability of auxotrophs of Neurospora crassa to grow on certain tripeptides, despite the presence of excess competing amino acids, suggests it has an oligopeptide transport system. In general, dipeptides did not support growth except in those instances where extracellular hydrolysis occurred, or where the dipeptide appeared to be accumulated by an uptake system which is sensitive to inhibition by free amino acids. Considerable intracellular peptidase activity toward a large number of peptides was demonstrated, including a number of peptides which could not be utilized for growth. The intracellular peptidase activity was shown to be selective for amino acid composition and sequence (N-terminal or C-terminal) within the peptide; glycine-containing peptides were particularly poor substrates for peptidase activity. Only a small amount of extracellular peptidase activity could be detected.