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 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.     

Intraspecific variation in survival and mitochondrial oxidative phosphorylation in wild-caught Drosophila simulans

Lifespans of organisms vary greatly even among individuals of the same species. Under the framework of the free oxygen radical theory of aging, it is predicted that variation in individual lifespan within a species will correlate with variation in the accumulation of oxidative damage to cell components from reactive oxygen species. In this study we test the hypothesis that variation in survival of three wild-caught Drosophila simulans fly lines (HW09, NC48 and MD106) correlates with three key aspects of mitochondrial bioenergetics. The rank order of median survival was HW09 > MD106 > NC48. Young HW09 flies (11-18 days) had (i) highest ADP:O (quantity of oxygen consumed by mitochondria when provided with a quantity of ADP) when metabolizing both electron transport chain complex I and complex III substrates; (ii) lowest rate of mitochondrial hydrogen peroxide production from complex III; and (iii) highest cytochrome c oxidase activity from complex IV. Rate of hydrogen peroxide production increased and cytochrome c oxidase activity decreased in all lines in the age range 11-25 days. This is the first study to correlate natural variation in organism survival with natural variation in mitochondrial bioenergetics.     

Intraspecific variation of chloroplast DNA in Dioscorea bulbifera L.

Summary Restriction fragment length polymorphism (RFLP) analysis of chloroplast (ct) DNAs from 15 accessions of Dioscorea bulbifera collected from Africa and Asia was carried out using the Southern hybridization technique. Eight cloned ctDNA fragments of D. bulbifera and D. opposita, which cover 80% of the total chloroplast genome, were used as the probes to detect variation in ctDNA digested with nine restriction endonucleases. Ten variable sites, located in the large and small single-copy regions, were disclosed among the 15 accessions, of which six showed base substitution and four carried length mutation. Positions of the latter mutations were determined on the physical map of ctDNA. Based on these results, chloroplast genomes of the 15 accessions could be classified into nine types. Their phylogenetic relationships are assumed to be as follows: (1) African and Asian chloroplast genomes diverged from each other at the earliest point in time; (2) E-type chloroplast genome, occurring in the south-east edge of the Asian continent, appears to be the most ancient among all the Asian chloroplast genomes; and (3) four chloroplast genomes, found in Asian insular regions, are probably derived independently from the E-type genome. The discrepancy between the taxonomic relationship and the proposed chloroplast genome phylogeny of the present materials is noted.     

Intraspecific variation in nuclear DNA content among world populations of a mosquito,Aedes albopictus (Skuse)

Summary Aedes albopictus is commonly distributed in most parts of the Oriental region and on many islands in the Indian and the Pacific Oceans. The species was recently introduced into the United States and Brazil. Feulgen cytophotometric quantitation of haploid nuclear DNA content was carried out for 37 populations of Ae. albopictus to determine the extent of intraspecific variation in nuclear DNA content and whether the range expansion of the species has coincided with an increase in DNA content. The haploid nuclear DNA content varied nearly three-fold. The minimum DNA content was 0.62 pg in Koh Samui from Thailand, and the maximum DNA content was 1.66 pg in Houston-61 from the United States. Statistical comparisons of populations revealed significant differences in DNA contents. No geographic clustering of populations was noted with respect to DNA content. In general, populations from the United States and Brazil had higher DNA contents, but there was no indication that the range expansion had occurred hand in hand with an increase in DNA content. Each population had a specific amount of DNA that is probably imposed by the microenvironment.     

Sexual isolation in Drosophila. II. Intraspecific variation in mate recognition systems

A simple behavioral model is used to investigate whether differences in the specific-mate-recognition system (SMRS), occur within species of the Drosophila genus. This model takes into account, and overcomes, the distorting effect of vigor differences on experimental results. Analysis shows significant deviations from the expected values under the assumption of identical SMRSs in around one fifth of the multiple-choice experiments performed with natural strains of twelve different Drosophila species. Different selection procedures raise the number of significant assortative mating results between strains of D. melanogaster and D. pseudoobscura from 3.0% to 32.8%. Finally, sub- or semispecific taxa show variations in their SMRS even more frequently (74.5%). Differences in male vigor and female receptivity are also found. These results show that a classification of Drosophila species based on SMRS stability, as proposed by the “Recognition concept of species”, is virtually impossible.     

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.     

Intraspecific sexual isolation in Drosophila.

Intraspecific sexual isolation was examined among wild strains of Drosophila malerkotliana, D. parabipectinata and D. pseudoananassae by multiple-choice method in Elens-Wattiaux mating chamber. In D. pseudoananassae, mating between two strains tested was random and isolation estimate was close to one. In one out of 6 crosses, involving geographic strains of D. malerkotliana, there was significant deviation from randomness and isolation estimate remained low which shows non-random (preferential or positive assortative) mating. In D. parabipectinata, the deviation from randomness was statistically significant due to higher number of homogamic matings in three crosses involving wild strains derived from geographically distant places and isolation estimate remained low in these crosses. The results provide evidence for incipient sexual isolation within D. malerkotliana and D. parabipectinata as a result of genetic divergence.     

Intraspecific DNA divergence in Drosophila: a study on parthenogenetic D. mercatorum

Drosophila mercatorum is a species that can give rise to totally homozygous parthenogenetic strains. Using the technique of DNA-DNA hybridization, we have assessed the overall single-copy DNA differences among three independently derived strains that represent three independent genomes. Among strains, the average difference between homoduplex and heteroduplex median melting temperatures is 1.3 degrees C. This represents greater than or equal to 1.3% base-pair mismatch. Normalized percent of reassociation indicates further genetic differences, probably reflecting insertion/deletion differences and/or regions of the genome that are highly variable. This overall intraspecific genetic variation is higher than generally is thought to exist but is consistent with growing evidence of extensive DNA diversity within species of invertebrates. High intraspecific DNA variation may be correlated with rapid phyletic rates of evolution. Because of this high level of variation, the technique of DNA-DNA hybridization may be used to study intraspecific variation in invertebrates but is limited in its usefulness for higher systematic studies.      

X chromosome DNA variation in Drosophila virilis.

Comparisons of polymorphism patterns between distantly related species are essential in order to determine their generality. However, most work on the genus Drosophila has been done only with species of the subgenus Sophophora. In the present work, we have sequenced one intron and surrounding coding sequences of 6 X-linked genes (chorion protein s36, elav, fused, runt, suppressor of sable and zeste) from 21 strains of wild-type Drosophila virilis (subgenus Drosophila). From these data, we have estimated the average level of DNA polymorphism, inferred the effective population size and population structure of this species, and compared the results with those obtained for other Drosophila species. There is no reduction in variation at two loci close to the centromeric heterochromatin, in contrast to Drosophila melanogaster.     

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.     

Intraspecific genetic variation in host vigour,viral load and disease tolerance during Drosophila C virus infection

Genetic variation for resistance and disease tolerance has been described in a range of species. In Drosophila melanogaster, genetic variation in mortality following systemic Drosophila C virus (DCV) infection is driven by large-effect polymorphisms in the restriction factor pastrel (pst). However, it is unclear if pst contributes to disease tolerance. We investigated systemic DCV challenges spanning nine orders of magnitude, in males and females of 10 Drosophila Genetic Reference Panel lines carrying either a susceptible (S) or resistant (R) pst allele. We find among-line variation in fly survival, viral load and disease tolerance measured both as the ability to maintain survival (mortality tolerance) and reproduction (fecundity tolerance). We further uncover novel effects of pst on host vigour, as flies carrying the R allele exhibited higher survival and fecundity even in the absence of infection. Finally, we found significant genetic variation in the expression of the JAK-STAT ligand upd3 and the epigenetic regulator of JAK-STAT G9a. However, while G9a has been previously shown to mediate tolerance of DCV infection, we found no correlation between the expression of either upd3 or G9a on fly tolerance or resistance. Our work highlights the importance of both resistance and tolerance in viral defence.     

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 and phylogeographic patterns of Fagus crenata (Fagaceae) mitochondrial DNA

Mitochondrial (mt) DNA variation in Japanese beech, Fagus crenata (Fagaceae), was studied in 17 populations distributed throughout the species' range. Total genomic DNA of samples from single trees representing each of 12 populations were digested with 18 restriction enzymes and hybridized with three probes containing coxI, coxIII, and atpA gene sequences. Thirty-four of the 54 enzyme/probe combinations showed polymorphisms and all the individuals were subsequently analyzed with six combinations of three probes and two enzymes. Restriction fragment length polymorphisms were evident around all three genes, allowing the identification of eight distinct haplotypes. Haplotype diversity within the populations was found to be very low (HS = 0.031), but population differentiation to be much higher (GST = 0.963). The mtDNA variation was strikingly different from allozyme variation (HS = 0.209; GST = 0.039). Gene flow for maternally inherited mtDNA should be restricted to seed dispersal while nuclear gene flow occurs by both seed and pollen dispersal. Therefore, the difference in the variation between mtDNA and allozymes may be largely a result of the much higher rate of gene flow associated with pollen dispersal than with seed dispersal. The mtDNA variation displayed strong geographic structure, which may reflect the species' distribution in the last glacial maximum and subsequent colonization, and probably also reflects intraspecific phylogeography of the species.     

Intraspecific nuclear ribosomal DNA divergence and reticulation in sexual diploid Erigeron strigosus (Asteraceae)

Apomictic complexes in flowering plants often harbor multiple sexual taxa, which must be studied to interpret accurately the origin and diversity of apomictic derivatives. The daisy fleabane group in North America (Erigeron sect. Phalacroloma) includes the widespread polyploid apomictic taxa E. annuus, E. strigosus, and E. tenuis, as well as recently discovered sexual diploid populations in the southeastern United States (E. strigosus var. calcicola, E. strigosus var. dolomiticola, sexual E. strigosus var. strigosus). Phylogenetic analysis for 35 sexual populations was conducted using sequences from the internal and external transcribed spacers (ITS and ETS) of ribosomal DNA. Results indicate that the three groups of sexual plants form separate monophyletic clades and that edaphic specialization is ancestral in the group. Sequence analysis for sexual E. strigosus var. strigosus was confounded by the fact that 13 of 31 samples (42%) possessed nucleotide polymorphisms at 1.0-1.8% of sites. However, analysis of the genomic sequence for plants with low polymorphism levels in conjunction with analysis of cloned PCR products for plants with high levels of intra-individual polymorphism indicated that three combinations of haplotypes (N I + N II, two plants; N I + N III, five plants; N II + N III, six plants) accounted for the majority of sequence polymorphisms encountered. These data are consistent with historical diversification and subsequent reticulate evolution at the diploid level in sexual E. strigosus var. strigosus.     

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 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.