Intraspecific flavonoid variation

This review is concerned with variation of flavonoid patterns within species. Many examples of species with invariant flavonoid patterns are known; there are at least as many examples where complex arrays of pigments are known. Eight categories of variation are discussed: 1) qualitatively invariant pigment profiles, 2) quantitative variation, 3) flavonoid races that do not correspond to recognized taxonomic groups, 4) flavonoid races that do correspond to recognized taxonomic groups, 5) flavonoid profile differences between different ploidy levels, 6) differences between organs or between tissues, 7) differences between developmental stages, and 8) environmentally influenced flavonoid profiles. These types of variation seem to occur randomly in the plant kingdom. Members of the same family, or in some cases, the same genus, can display different types of variation. Careful attention to these sources of variation is necessary before flavonoid characters can be used in taxonomic studies.     

Echinococcus: biology and strain variation

Biology and strain variation in the causative agent of hydatid disease is reviewed with emphasis on developmental and genetic aspects. In vitro cultivation experiments have made a significant contribution to current knowledge of the developmental plasticity of Echinococcus. However, the mechanisms which regulate and determine developmental strategies in the parasite, as well as the characteristics, source and cytodifferentiation of germinal cells, are not understood. The nature, significance and origin of strain variation in Echinococcus are examined. Before we can fully appreciate the phenotypic consequences of genetic differentiation between populations, we need to know something about the genetic and environmental components of variation in traits such as development rate, host preference, host specificity, virulence and drug resistance. There is an urgent need for research on the developmental pathways by which genetic differences within and between strains of E. granulosus are translated to phenotypic differences in these traits.     

Intraspecific variation in limblessness in vertebrates: a unique example of microevolution

Many species of arboreal marine snails in the genus Littoraria are polymorphic for shell colour, with morphs that correspond in both colour and frequency to those predominant in the habitat. Although the combined effects of selection for crypsis and apostasy have been suggested as the most likely reasons for this, they have not been demonstrated directly in the field. We investigated whether two parasitoid flies, Sarcophaga megafilosia and Sarcophaga meiofilosia, select for crypsis in Littoraria filosa . It was possible to compare the proportions that matched and did not match the background between samples of live and dead snails because the shells of individuals killed by these parasitoids, within which the larva and pupa develop, remain attached to the substratum. This comparison was necessary because these snails frequently move among different coloured microhabitats, which will tend to obscure any effect of selection for crypsis if only live individuals are censused. The method appeared reliable since there was no change in background colour and very little loss of shells between larviposition and emergence of flies. S. megafilosia killed a significantly greater than expected proportion of snails that did not match their background. In contrast, there was no evidence of selective attack by S. meiofilosia. These results are discussed in relation to previous work on polymorphisms in Littoraria species. We also suggest that the role of parasitoid insects as selective agents contributing to the maintenance of colour polymorphisms in terrestrial molluscs may have been overlooked.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77, 367−377.     

Intraspecific variation in a predator drives cascading variation in primary producer community composition

Predation has important cascading impacts on primary producer biomass and community composition in many ecosystems. While most studies have focused on the consequences of interspecific or density differences in predators, it is recognized that phenotypic variation within species can have strong and cascading community and ecosystem consequences at lower trophic levels. In coastal New England lakes, both the presence and life history form of the zooplanktivorous fish alewife, Alosa pseudoharengus, have strong influence on the biomass, size structure and community composition of crustacean zooplankton communities. Here we test the hypothesis that alewife presence and life history will have cascading impacts on phytoplankton biomass and community composition in a mesocosm experiment that previously reported strong biomass and compositional differences of crustacean zooplankton communities among alewife treatments. We show that alewife life history led to small but statistically significant differences in phytoplankton community composition among treatments. This compositional difference was driven primarily by an increase in the density of two edible phytoplankton genera associated with lower zooplankton biomass in the anadromous alewife treatment. Our results show that intraspecific variation in a predator can have cascading effects on primary producer communities. However we did not observe significant differences in total algal biomass.     

Echinococcus granulosus tegumental enzymes as in vitro markers of pharmacological damage: A biochemical and molecular approach

Cystic echinococcosis is a chronic, complex, and neglected disease. Novel therapeutical tools are needed to optimize human treatment. A number of compounds have been investigated, either using in vitro cultured parasites and/or applying in vivo rodent models. Although some of these compounds showed promising activities in vitro, and to some extent also in the rodent models, they have not been translated into clinical applications. Membrane enzyme activities in culture supernatants of treated protoscoleces with calcium modulator drugs and anthelmintic drugs were measured and provided an indication of compound efficacy. This work describes for the first time the detection of alkaline phosphatase, gamma-glutamyl-transpeptidase and acetylcholinesterase activities in supernatants of in vitro treated Echinococcus granulosus protoscoleces. Marked differences on the enzymatic activities in supernatants from drug treated cultures were detected. We demonstrated that those genes that show the highest degree of conservation when compared to orthologs, are constitutively and highly expressed in protoscoleces and metacestodes. Due to high sensibility and the lack of activity in supernatants of intact protoscoleces, gamma-glutamyl-transpeptidase is proposed as the ideal viability marker during in vitro pharmacological studies against E. granulosus protoscoleces.     

Intraspecific nuclear DNA variation in Drosophila

We have summarized and analyzed all available nuclear DNA sequence polymorphism studies for three species of Drosophila, D. melanogaster (24 loci), D. simulans (12 loci), and D. pseudoobscura (5 loci). Our major findings are: (1) The average nucleotide heterozygosity ranges from about 0.4% to 2% depending upon species and function of the region, i.e., coding or noncoding. (2) Compared to D. simulans and D. pseudoobscura (which are about equally variable), D. melanogaster displays a low degree of DNA polymorphism. (3) Noncoding introns and 3' and 5' flanking DNA shows less polymorphism than silent sites within coding DNA. (4) X-linked genes are less variable than autosomal genes. (5) Transition (Ts) and transversion (Tv) polymorphisms are about equally frequent in non-coding DNA and at fourfold degenerate sites in coding DNA while Ts polymorphisms outnumber Tv polymorphisms by about 2:1 in total coding DNA. The increased Ts polymorphism in coding regions is likely due to the structure of the genetic code: silent changes are more often Ts's than are replacement substitutions. (6) The proportion of replacement polymorphisms is significantly higher in D. melanogaster than in D. simulans. (7) The level of variation in coding DNA and the adjacent noncoding DNA is significantly correlated indicating regional effects, most notably recombination. (8) Surprisingly, the level of polymorphism at silent coding sites in D. melanogaster is positively correlated with degree of codon usage bias. (9) Three proposed tests of the neutral theory of DNA polymorphisms have been performed on the data: Tajima's test, the HKA test, and the McDonald-Kreitman test. About half of the loci fail to conform to the expectations of neutral theory by one of the tests. We conclude that many variables are affecting levels of DNA polymorphism in Drosophila, from properties of nucleotides to population history and, perhaps, mating structure. No simple, all encompassing explanation satisfactorily accounts for the data.      

Intraspecific variation in the lens proteins

A review of the literature indicates that intraspecific variation among the lens proteins (crystallins) is almost invariably quantitative rather than qualitative. Lens extracts were examined from inbred strains of the laboratory mouse, rat, and guinea pig and from domestic breeds of sheep. Differences in the mobilities of protein bands after electrophoresis in polyacrylamide gels were never found to be greater than the variation observed when a sample was repeatedly subjected to electrophoresis. Differences, however, were observed between widely separated populations of the bank vole (Clethrionomys glareolus). In bank voles and mice, there were variations in the intensities of bands. Electrophoresis of extracts in the presence of 6 m urea indicated that there were no major differences between six mouse strains in the subunits constituting their - and -crystallins. More detailed examination of -crystallins from two mouse strains by isoelectric focusing and amino acid analysis supported this conclusion.This work was carried out while one of the authors (T.H.D.) was supported by a Medical Research Council Research Studentship and a European Molecular Biology Organisation Fellowship. A grant from the Edinburgh University Weir Memorial Fund allowed the collection of some of the Yugoslavian bank voles.     

Intraspecific variation and species coexistence

We use a two-species model of plant competition to explore the effect of intraspecific variation on community dynamics. The competitive ability ("performance") of each individual is assigned by an independent random draw from a species-specific probability distribution. If the density of individuals competing for open space is high (e.g., because fecundity is high), species with high maximum (or large variance in) performance are favored, while if density is low, species with high typical (e.g., mean) performance are favored. If there is an interspecific mean-variance performance trade-off, stable coexistence can occur across a limited range of intermediate densities, but the stabilizing effect of this trade-off appears to be weak. In the absence of this trade-off, one species is superior. In this case, intraspecific variation can blur interspecific differences (i.e., shift the dynamics toward what would be expected in the neutral case), but the strength of this effect diminishes as competitor density increases. If density is sufficiently high, the inferior species is driven to extinction just as rapidly as in the case where there is no overlap in performance between species. Intraspecific variation can facilitate coexistence, but this may be relatively unimportant in maintaining diversity in most real communities.     

I. Pathogenic variation in fungi and bacteria and mycorrhizal compatibility: Intraspecific variation in a mycorrhizal association

Laboratory studies with combinations of the fly agaric, Amanita muscaria (L. ex Fries) Hooker and birch (Betula pendula (Roth.)) suggest that the genetical control of mycorrhizal formation has features in common with the legume/Rhizobium symbiosis. There are at least four factors that can be genetically controlled by either the host or the fungus: (a) mycorrhizal formation; (b) the extent of mycorrhizal development; (c) the pattern of mycorrhizal branching, and (d) the shape and size of the host root system.     

Intraspecific variation for resource use in Drosophila

Individuals within natural populations of Drosophila tripunctata and D. falleni varied significantly in their responses to alternative types of food baits; no such variation was detected in D. putrida. The food type at which laboratory-reared D. melanogaster tended to settle in the field was influenced by the type of food on which they had been kept prior to release. Although flies apparently forgot their previous experience within hours, its effect on their behaviour can be manifested for at least 1 day in the field. Mark -recapture experiments on wild flies are shown to be very inefficient at detecting individual variation in behaviour.     

Intraspecific variation of recombination rate in maize

Background

In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation.

Results

Here, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotype 23 doubled-haploid populations derived from crosses between these lines with a 50 k-SNP array and construct high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtain the recombination rates along chromosomes specific to each population. We identify significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework reveals a negative association between recombination rate and interference strength.

Conclusions

To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms.     

Intraspecific variation in movement patterns: modeling individual behaviour in a large marine predator

In large marine predators, foraging entails movement. Quantitative models reveal how behaviours can mediate individual movement, such that deviations from a random pattern may reveal specific search tactics or behaviour. Using locations for 52 grey seals fitted with satellite-linked recorders on Sable Island; we modeled movement as a correlated random walk (CRW) for individual animals, at two temporal scales. Mean move length, turning angle, and net squared displacement (R²_n: the rate of change in area over time) at successive moves over 3 to 10 months were calculated. The distribution of move lengths of individual animals was compared to a Lévy distribution to determine if grey seals use a Lévy flight search tactic. Grey seals exhibited three types of movement as determined by CRW model fit: directed movers – animals displaying directed long distance travel that were significantly underpredicted by the CRW (23% of animals); residents – animals remaining in the area surrounding Sable Island that were overpredicted by the model (29% of animals); and correlated random walkers – those (48% of animals) in which movement was predicted by the CRW model. Kernel home range size differed significantly among all three movement types, as did travel speed, mean move length, mean R²_n and total distance traveled. Sex and season of deployment were significant predictors of movement type, with directed movers more likely to be male and residents more likely to be female. Only 30% of grey seals fit a Lévy distribution, which suggests that food patches used by the majority of seals are not randomly distributed. Intraspecific variation in movement behaviour is an important characteristic in grey seal foraging ecology, underscoring the need to account for such variability in developing models of habitat use and predation.     

Intraspecific and interspecific genetic variation in Drosophila

Utilizing the technique of DNA-DNA hybridization, we have characterized the degree of genetic variability in single-copy DNA both within and between several species of Drosophila. The results of intraspecific variation studies indicate considerable variation both for levels of nucleotide heterozygosity (estimated to be over 2%) as well as for insertions-deletions. Interspecific studies confirm this great deal of variability and further establish an extreme heterogeneity within Drosophila genomes for rates of divergence. This heterogeneity is much more extreme than that seen between exons and introns. The degree of single-copy DNA divergence generally supports phylogenetic affinities deduced from more traditional methods. However, exceptions occur where single-copy DNA divergence is not correlated with other properties such as degree of chromosomal differentiation, morphology, or ability to form interspecific hybrids. We argue that single-copy DNA divergence as measured by DNA-DNA hybridization is an accurate indicator of phylogenetic relationships and therefore sheds light on the evolution of other biological properties. Many, if not most, evolutionary tests require an accurate phylogeny of the group being studied and DNA, because of the high information content inherent within the molecule, offers the best hope of deriving true phylogenies.     

Modeling biochemical networks: a cellular-automata approach

The potential of the cellular-automata (CA) method for modeling biological networks is demonstrated for the mitogen-activated protein kinase (MAPK) signaling cascade. The models derived reproduced the high signal amplification through the cascade and the deviation of the cascade enzymes from the Michaelis-Menten kinetics, evidencing cooperativity effects. The patterns of pathway change upon varying substrate concentrations and enzyme efficiencies were identified and used to show the ways for controlling pathway processes. Guidance in the selection of enzyme inhibition targets with minimum side effects is one outcome of the study.     

Intraspecific variation in genome size in angiosperms: identifying its existence

BACKGROUND: The 6 years since the last Angiosperm Genome Size Discussion Meeting in 1997 have experienced the decline of the then widely held idea of the 'plastic' genome. Several published cases of intra-specific variation in cultivated plants have been questioned on re-investigation with an improved technical approach. At the same time, technical problems caused by staining inhibitors present in the plant material have been recognized. In the accumulation of genome size data more critical methods and rules for best practice are urgently needed. INFRA-SPECIFIC VARIATION RE-VISITED: This review is about (a) the basic requirement for repeatability of results and the need for self-criticism on the part of the investigator and (b) the critical points in the technical procedure, particularly the quantitative Feulgen reaction. Case studies are presented on Dasypyrum villosum (refuting a previously reported 'plastic genome' phenomenon), on Glycine max (refuting previously claimed intraspecific variation) and on Arachis hypogaea and A. duranensis, in which reported C-values are too high by roughly two-fold. In A. hypogaea the reported intraspecific genome size variation could not be confirmed. Furthermore, a claimed negative correlation between altitude and genome size in A. duranensis was shown to be based on an arbitrary omission of data points that did not fit the correlation (although a correlation was found). BEST PRACTICE METHODOLOGY: The finding of previously published questionable studies was the incentive for a re-consideration of the quantitative Feulgen procedure with regard to best practice in genome size studies. Clarification here of the critical steps of the method should help to improve the data in the literature. It must be stressed that the most important requirement is the need for a self-critical attitude of researchers to their data.     

Intraspecific variation in tolerance of warming in fishes

Intraspecific variation in key traits such as tolerance of warming can have profound effects on ecological and evolutionary processes, notably responses to climate change. The empirical evidence for three primary elements of intraspecific variation in tolerance of warming in fishes is reviewed. The first is purely mechanistic that tolerance varies across life stages and as fishes become mature. The limited evidence indicates strongly that this is the case, possibly because of universal physiological principles. The second is intraspecific variation that is because of phenotypic plasticity, also a mechanistic phenomenon that buffers individuals’ sensitivity to negative impacts of global warming in their lifetime, or to some extent through epigenetic effects over successive generations. Although the evidence for plasticity in tolerance to warming is extensive, more work is required to understand underlying mechanisms and to reveal whether there are general patterns. The third element is intraspecific variation based on heritable genetic differences in tolerance, which underlies local adaptation and may define long-term adaptability of a species in the face of ongoing global change. There is clear evidence of local adaptation and some evidence of heritability of tolerance to warming, but the knowledge base is limited with detailed information for only a few model or emblematic species. There is also strong evidence of structured variation in tolerance of warming within species, which may have ecological and evolutionary significance irrespective of whether it reflects plasticity or adaptation. Although the overwhelming consensus is that having broader intraspecific variation in tolerance should reduce species vulnerability to impacts of global warming, there are no sufficient data on fishes to provide insights into particular mechanisms by which this may occur.     

Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association

Buchnera are maternally transmitted bacterial endosymbionts that synthesize amino acids that are limiting in the diet of their aphid hosts. Previous studies demonstrated accelerated sequence evolution in Buchnera compared to free-living bacteria, especially for nonsynonymous substitutions. Two mechanisms may explain this acceleration: relaxed purifying selection and increased fixation of slightly deleterious alleles under drift. Here, we test the divergent predictions of these hypotheses for intraspecific polymorphism using Buchnera associated with natural populations of the ragweed aphid, Uroleucon ambrosiae. Contrary to expectations under relaxed selection, U. ambrosiae from across the United States yielded strikingly low sequence diversity at three Buchnera loci (dnaN, trpBC, trpEG), revealing polymorphism three orders of magnitude lower than in enteric bacteria. An excess of nonsynonymous polymorphism and of rare alleles was also observed. Local sampling of additional dnaN sequences revealed similar patterns of polymorphism and no evidence of food plant-associated genetic structure. Aphid mitochondrial sequences further suggested that host bottlenecks and large-scale dispersal may contribute to genetic homogenization of aphids and symbionts. Together, our results support reduced N(e) as a primary cause of accelerated sequence evolution in Buchnera. However, our study cannot rule out the possibility that mechanisms other than bottlenecks also contribute to reduced N(e) at aphid and endosymbiont loci.     

Intraspecific variation in Triassic Ophthalmidiid Foraminifera from Timor

Four ophthalmidiid species are described as free specimens extracted from mudstones and wackestones of Triassic age: Atsabella bandeiraensis nov. gen. nov. sp., Karaburunia atsabensis nov. sp., Ophthalmidium sp. cf. O. primitivum Ho and Spirophthalmidium grunaui nov. sp. Analysis of morphological variation found in large suites of specimens suggests that, as in modern miliolids, apertural characteristics, chamber shape and adult test size are features that vary within narrow limits and may be used to define species. In genera with milioline coiling in the post-embryonic stage, chamber arrangement may be highly variable. Post-embryonic coiling in K. atsabensis varies from quinqueloculine to almost spiroloculine and encompasses morphotypes that, in thin-section studies, have been attributed to a number of other genera. In Timor Leste, A. bandeiraensis, K. atsabensis and S. grunaui have been found with conodonts indicative of the Carnian, but the full local stratigraphic range of these species is uncertain. K. atsabensis occurs at another locality with conodonts suggestive of the Middle Triassic or less likely Carnian. Ophthalmidium sp. cf. O. primitivum has been found at one locality associated with A. bandeiraensis and K. atsabensis in a stratigraphic succession that suggests a correlation to the Carnian or Norian. The ophthalmidiids are found commonly associated with organic-cemented agglutinated and hyaline foraminifera and at some localities common to abundant ostracods and mollusc debris. They were most common in organic-rich carbonate mud of shallow-marine environments.