Abdominal pigmentation variation in drosophila polymorpha: geographic variation in the trait, and underlying phylogeography

Drosophila polymorpha is a widespread species that exhibits abdominal pigmentation variation throughout its range. To gain insight into this variation we combined phenotypic and genotypic data to test a series of nested hypotheses. First, we tested the null hypothesis that geographic variation in pigmentation is due to neutral factors. We used nested clade analysis to examine the distribution of haplotypes from a nuclear and a mitochrondrial locus. Restricted gene flow via isolation by distance, the primary inference of this phylogeographic analysis, was then used to generate and test the hypothesis of increasing average abdominal pigmentation difference with increasing geographic distance. We found no correlation between geographic distance and phenotypic distance. We then tested the hypothesis that pigmentation is affected by environmental differences among localities. We found a significant effect of habitat type on the average abdominal pigmentation phenotype of different localities. Finally, we tested the hypothesis that pigmentation in D. polymorpha is associated with desiccation resistance. We found that dark individuals of both sexes survived significantly longer in a desiccating environment than light individuals. These patterns combined lead us to hypothesize that abdominal pigmentation variation in D. polymorpha is important in mediating the organism's interactions with local ecological factors.     

Endotherms,ectotherms, and mitochondrial genome-size variation

The patterns of mitochondrial genomesize variation were investigated in endothermic and ectothermic species to examine the role that thermal habit might play in the evolution of animal mitochondrial DNA (mtDNA). Data on mtDNA size (the modal, largest, and smallest mtDNA reported within a species), the percent variation in mtDNA size (the difference in size between the largest and smallest mtDNAs divided by the model genome size for a given species), and the frequency of heteroplasmic individuals (those carrying more than one mtDNA length variant) were tabulated from the literature. Endotherms showed significantly less variation in mtDNA size and tended to have smaller mtDNAs than ectotherms. Further comparisons between endothermic and ectothermic vertebrates revealed that the largest genome and the percent variation in genome size were significantly smaller in the former than the latter. There was no difference between endothermic and ectotherms in the frequency of heteroplasmy. These data are discussed in light of two hypotheses: (1) more intense directional and purifying selection for small genome size in the cytoplasms of species with higher metabolic rates and (2) reduced mutation pressures generating mtDNA size variants in endotherms relative to those in ectotherms. The general trends are consistent with the selection hypothesis but in certain species mtDNA size variation appears to be governed by mutational pressures. To test these competing hypotheses further, comparative studies are proposed where mitochondrial genome size is quantified in sister taxa and tissue types with very different metabolic rates.     

Associations between dermatoglyphic variation, topography, and climate in Kenya

Correlations between a number of dermatoglyphic finger and palmar taxonomic traits relating to 57 male and 53 female Kenyan populations, and altitude and mean annual rainfall are significant, not only in terms of the full range of samples, but also when samples are divided into independent smaller groups. These results are discussed and contrasted with those of other studies which have found no relationships between dermatoglyphic variation and climate in sub-Saharan Africa.     

Species coexistence, intransitivity, and topological variation in competitive tournaments

Competitive intransitivity occurs when species’ competitive abilities cannot be listed in a strict hierarchy, but rather form competitive loops, as in the game ‘Rock-Paper-Scissors’. Indices are useful for summarizing intransitivity in communities; however, as with most indices, a great deal of information is compressed into single number. So while recent ecological theory, experiments, and natural history observations demonstrate that competitive intransitivity can promote species coexistence, the consequence of variation in the ‘topology’ of competitive interactions that is not accounted for by intransitivity indices is much less well understood. We use a continuous analytical model and two complementary discrete lattice models (one spatially explicit, the other aspatial) to demonstrate that such variation does indeed greatly affect species coexistence. Specifically, we show that although intransitivity indices are good at capturing broad patterns of coexistence, communities with different levels of intransitivity can have equal coexistence, and communities with equal intransitivity can have different coexistence, due to underlying variation in competitive network topology.     

Cranial ontogeny, diet, and ecogeographic variation in African lorises

A series of 22 craniodental measurements were obtained for the three subspecies of potto (Perodicticus) and angwantibos (Arctocebus). To describe patterns of variation in Perodicticus, a discriminant function analysis (DFA) was performed with adult data. To investigate the ecogeographic correlates of size variation in Perodicticus, adult cranial dimensions were compared with field data on latitudinal and longitudinal coordinates for available specimens as well as altitudinal data for a more limited sample. Ontogenetic series for larger-bodied Perodicticus and smaller-bodied Arctocebus were compared to test the hypothesis that inter- and intrageneric variation in skull form results from the differential extension/truncation of shared patterns of relative growth, and to assess morphological variation in the masticatory complex of sister taxa with differing dietary habits. Analyses of relative growth indicate that skull proportions in Perodicticus subspecies are largely ontogenetically scaled. In comparisons between Perodicticus and Arctocebus, most facial dimensions also are ontogenetically scaled, with all but one of the seven divergent comparisons (interorbital breadth) representing a feature of the masticatory apparatus. The DFA provided independent support for prior classifications of Perodicticus into three taxa. Size differentiation in African lorises appears to be correlated with altitudinal variation (Bergmann's Rule) as well as character displacement. The smallest pottos, P. p. potto, occupy low-lying coastal habitats in western Africa, whereas the larger, eastern forms inhabit higher, presumably colder elevations. The largest potto, P. p. edwardsi, is sympatric throughout most of its range with the smallest and most insectivorous African lorises (Arctocebus). A basis for intrageneric taxonomic variation in Perodicticus is supported by such nonclinal size variation, as well as divergences in the ontogeny of masticatory proportions corresponding to interspecific variation in dietary proclivities.     

Genetic variation in endocannabinoid metabolism, gastrointestinal motility, and sensation

Cannabinoid agonist inhibits gastrointestinal motility. The endocannabinoid, anandamide, is inactivated by fatty acid amide hydrolase (FAAH). A single nucleotide polymorphism in the human FAAH gene (C385A) reduces FAAH expression. Our aim was to evaluate associations between FAAH genotype variation and symptom phenotype, gastric emptying and volume, colonic transit, and rectal sensation in patients with functional gastrointestinal disorders (FGID). 482 FGID patients [Rome II positive, 159 constipation disorders, 184 diarrhea disorders (D-IBS), 86 mixed bowel function (M-IBS), 20 chronic abdominal pain (CAP), 33 functional dyspepsia], and 252 healthy volunteers (HV) underwent questionnaires and studies of phenotype and genotype from 2000 to 2007: 250 gastric emptying, 210 fasting and postprandial gastric volume, 152 colonic transit, and 123 rectal sensation. All had FAAH genotype [CC vs. polymorphic (CA/AA)] determined by TaqMan. FAAH genotype distribution of FGID patients and HV did not deviate from Hardy-Weinberg equilibrium. There was a significant association of FAAH genotype with FGID phenotype (overall chi(2), P = 0.011) and with specific individual phenotypes (P = 0.048). Thus FAAH CA/AA increases the odds (relative to HV) for D-IBS (P = 0.008), M-IBS (P = 0.012), and, possibly, CAP (P = 0.055). There was a significant association of FAAH CA/AA genotype with accelerated colonic transit in D-IBS (P = 0.037). There was no association of FAAH genotype with rectal sensation thresholds or ratings. The association of genetic variation in metabolism of endocannabinoids with symptom phenotype in D-IBS and M-IBS and with faster colonic transit in D-IBS supports the hypothesis that cannabinoid mechanisms may play a role in the control of colonic motility in humans and deserve further study.     

Mitochondria,sex and variation in routine metabolic rate

Variation in the metabolic costs associated with organismal maintenance may play a key role in determining fitness, and thus these differences among individuals are likely to be subject to natural selection. Although the evolvability of maintenance metabolism depends on its underlying genetic architecture, relatively little is known about the nature of genetic variation that underlies this trait. To address this, we measured variation in routine metabolic rate (?O_2routine), an index of maintenance metabolism, within and among three populations of Atlantic killifish, Fundulus heteroclitus, including a population from a region of genetic admixture between two subspecies. Polygenic association tests among individuals from the admixed population identified 54 single nucleotide polymorphisms (SNPs) that were associated with ?O_2routine, and these SNPs accounted for 43% of interindividual variation in this trait. However, genetic associations with ?O_2routine involved different SNPs if females and males were analysed separately, and there was a sex‐dependent effect of mitochondrial genotype on variation in routine metabolism. These results imply that there are sex‐specific genetic mechanisms, and potential mitonuclear interactions, that underlie variation in ?O_2routine. Additionally, there was evidence for epistatic interactions between 17% of the possible pairs of trait‐associated SNPs, suggesting that epistatic effects on ?O_2routine are common. These data demonstrate not only that phenotypic variation in this ecologically important trait has a polygenic basis with considerable epistasis among loci, but also that these underlying genetic mechanisms, and particularly the role of mitochondrial genotype, may be sex‐specific.     

Nucleotide variation at the myrosinase-encoding locus, TGG1, and quantitative myrosinase enzyme activity variation in Arabidopsis thaliana

The Arabidopsis thaliana TGG1 gene encodes thioglucoside glucohydrolase (myrosinase), an enzyme catalysing the hydrolysis of glucosinolate compounds. The enzyme is involved in plant defence against some insect herbivores, and is present in species of the order Capparales (Brassicales). Nucleotide variation was surveyed by sequencing c. 2.4 kb of the TGG1 locus in a sample of 28 worldwide A. thaliana accessions, and one Arabidopsis lyrata ssp. lyrata individual. Myrosinase activity was quantified for 27 of these same A. thaliana accessions, plus five additional others. Overall, estimated nucleotide diversity in A. thaliana was low compared to other published A. thaliana surveys, and the frequency distribution was skewed toward an excess of low-frequency variants. Furthermore, comparison to the outgroup species A. lyrata demonstrated that A. thaliana exhibited an excess of high-frequency derived variants relative to a neutral equilibrium model, suggesting a selective sweep. A. thaliana accessions differed significantly in total myrosinase activity, but analysis of variance detected no statistical evidence for an association between quantitative enzyme activity and alleles at the TGG1 myrosinase-encoding locus. We thus conclude that other, unsurveyed factors primarily affect the observed myrosinase activity levels in this species. The pattern of nucleotide variation was consistent with a model of positive selection but might also be compatible with a completely neutral model that takes into account the metapopulation behaviour of this highly inbreeding species which experienced a relatively recent worldwide expansion.     

Riverscape genetic variation,migration patterns,and morphological variation of the threatened Round Rocksnail,Leptoxis ampla

Within riverine systems, headwater populations are hypothesized to harbour higher amounts of genetic distinctiveness than populations in the main stem of a river and display increased genetic diversity in large, downstream habitats. However, these hypotheses were mostly developed with insects and fish, and they have not been tested on many invertebrate lineages. Pleuroceridae gastropods are of particular ecological importance to rivers of eastern North America, sometimes comprising over 90% of macroinvertebrate biomass. Yet, virtually nothing is known of pleurocerid landscape genetics, including whether genetic diversity follows predictions made by hypotheses developed on more mobile species. Moreover, the commonly repeated hypothesis that intraspecific morphological variation in gastropods results from ecophenotypic plasticity has not been well tested on pleurocerids. Using 2bRAD‐seq to discover single nucleotide polymorphisms, we show that the threatened, Cahaba River endemic pleurocerid, Leptoxis ampla, has limited gene flow among populations and that migration is downstream‐biased, conflicting with previous hypotheses. Both tributary and main stem populations harbour unique genomic profiles, and genetic diversity was highest in downstream populations. Furthermore, L. ampla shell morphology was more correlated with genetic differences among individuals and populations than habitat characteristics. We anticipate similar genetic and demographic patterns to be seen in other pleurocerids, and hypotheses about gene flow and population demographics that were based on more mobile taxa often, but not always, apply to freshwater gastropods. From a conservation standpoint, genetic structure of L. ampla populations suggests distinctive genetic diversity is lost with localized extirpation, a phenomenon common across the range of Pleuroceridae.     

Genetic,ontogenetic, and tissue-specific variation of dipeptidases in Drosophila melanogaster

Three dipeptidases in Drosophila melanogaster are under independent genetic control and their structural genes have been localized, Dip-A to 2R and Dip-B and Dip-C to 3R (Voelker and Langley, 1978; Ohnishi and Voelker, 1981). These enzymes were characterized with respect to their substrate specificities, genetic variability (electrophoretic mobility and quantitative activity level), ontogeny (activity and isozyme pattern), and tissue localization. The dipeptide substrate specificities of DIP-A and DIP-B overlap each other considerably, but do not overlap with DIP-C. In natural populations, DIP-B and DIP-C are essentially monomorphic electrophoretically whereas DIP-A is polymorphic for three allozymes. Both DIP-A and DIP-B show quantitative genetic variation of activity level within an allozyme class. All three enzymes are expressed at all stages in the life cycle, but DIP-A and DIP-B activities vary considerably according to developmental stage and sex of adult. The tissue localizations of DIP-A and DIP-B activities show similar patterns and a nearly ubiquitous occurrence of both enzymes, but with particularly high values in larval and adult midguts and in the adult female reproductive system. These results suggest a general metabolic role for the enzymes, such as regulation of the concentrated pools of amino acids and oligopeptides found in Drosophila tissues.This work was supported by Public Health Service Grant GM 11546.Paper No. 7066 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh.