Mitochondrial mismatch analysis is insensitive to the mutational process

Mismatch distributions are histograms showing the pattern of nucleotide (or restriction) site differences between pairs of individuals in a sample. They can be used to test hypotheses about the history of population size and subdivision (if selective neutrality is assumed) or about selection (if a constant population size is assumed). Previous work has assumed that mutations never strike the same site twice, an assumption that is called the model of infinite sites. Fortunately, the results are surprisingly robust even when this assumption is violated. We show here that (1) confidence regions inferred using the infinite- sites model differ little from those inferred using a model of finite sites with uniform site-specific mutation rates, and (2) even when site- specific mutation rates follow a gamma distribution, confidence regions are little changed until the gamma shape parameter falls well below its plausible range, to roughly 0.01. In addition, we evaluate and reject the proposition that mismatch waves are produced by pooling data from several subdivisions of a structured population.      

Dynamics of Cytoplasmic Incompatibility and Mtdna Variation in Natural Drosophila Simulans Populations

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

Micro-spatial population differentiation in activity of glycerol-3-phosphate oxidase (GPO) from mitochondria of Drosophila melanogaster

Replicate mass-bred laboratory populations of D. melanogaster were derived from females collected in the Tahbilk winery cellar and from females collected outside but from within two kilometres of the cellar. When mitochondrial extracts from larvae were assayed for specific activity of glycerol-3-phosphate oxidase the cellar populations had levels only 50% of those from the outside area, confirming an earlier report of such a difference among isofemale lines derived from these same areas. This micro-spatial differentiation occurred when larvae were raised on a medium supplemented with both sucrose (5% w/v) and ethanol (4% v/v), known to effect high GPO activity, but was not detected when the larvae were raised on unsupplemented medium.A heritable basis for larval GPO activity variation was confirmed in a set of 32 isogenic second chromosome substitution lines and measured in a subset of 4 of these lines about 25 generations later. A reciprocal cross using two isogenic substitution lines with the highest and lowest activities suggested the difference was attributable to genes acting additively and that there were no maternal or paternal effects. The detection of a collection site difference in GPO enzyme activity in the isogenic lines suggests that polymorphic variation on the second chromosome is responsible for the differentiation at the winery.Variation in adult GPO activity did not show a dependence on the winery location from where the isogenic lines were derived nor was there an effect of line. Adult GPO activity was significantly higher than that detected in larval tissues and did not show a dependence on the sugar/ethanol level in the growth medium.     

Vacuolar reticulum in oomycete hyphal tips: An additional component of the Ca2+Regulatory system?

Cultures of Achlya sp., Phytophthora cinnamomi, Saprolegnia diclina, S. ferax, and S. parasitica, treated with 6-carboxyfluorescein diacetate solution, accumulate 6-carboxyfluorescein in a reticulate system of fine tubules. The network shows longitudinal polarity within the hyphae, tubules being finest toward the hyphal tips. In more mature subapical regions the network is connected with large vacuoles that also accumulate 6-carboxyfluorescein. A morphologically similar system has also been identified in freeze-substituted hyphae of S. ferax. The network is considered to be vacuolar, but differs from the tubular vacuole system of true fungi in that tubules are less motile, more frequently branched, and do not alternate with clusters of spherical vacuoles. The appearance of the network resembles patterns of calcium-sensitive dye staining and it is suggested that the vacuolar reticulum in the tip region of oomycete hyphae may act as a Ca2+ sink. The tubular reticulum in oomycetes is very fragile and can be shown with 6-carboxyfluorescein in only those hyphal tips with a motility and organelle distribution characteristic of growing hyphae with normal morphology. Diverse abnormal hyphae show a range of other fluorochrome localizations. These include large irregular compartments filled with fluorochrome, and fluorescent cytoplasm with organelles and vacuoles standing out in negative contrast. These localizations in abnormal hyphae are correlated with other structural changes indicative of damage. Special care is required in experiments with oomycetes to avoid such artefacts of localization. Copyright 1997 Academic Press. Copyright 1997 Academic Press     

A reassessment of decreased amino acid accumulation by ehrlich ascites tumor cells in the presence of metabolic inhibitors

This study was undertaken to examine the mechanism by which metabolic inhibition reduces amino acid active transport in ehrlich ascites tumor cells. At 37 degrees C the metabolic inhibitor combination 0.1 mM 2,4-dinitrophenol (DNP) + 10 mM 2- deoxy-D-glucose (DOG) reduced the cell ATP concentration to 0.10- 0.15 mM in less than 5 min. This inhibition was associated with a 20.6 percent +/- 6.4 percent (SD) decrease in the initial influx of α-aminoisobutyric acid (AIB), and a two- to fourfold increase in the unidirectional efflux. These effects could be dissociated from changes in cell Na(+) or K(+) concentrations. Cells incubated to the steady state in 1.0-1.5 mM AIB showed an increased steady-state flux in the presence of DNP + DOG. Steady- state fluxes were consistent with trans-inhibition of AIB influx and trans-stimulation of efflux in control cells, but trans- stimulation of both fluxes in inhibited cells. In spite of the reduction of the cell ATP concentration to less than 0.15 mM and greatly reduced transmembrane concentration gradients of Na(+) and K(+), cells incubated to the steady state in the presence of the inhibitors still established an AIB distribution ration 13.8 +/- 2.6. The results are interpreted to indicate that a component of the reduction of AIB transport produced by metabolic inhibition is attributable to other actions in addition to the reduction of cation concentration gradients. Reduction of cell ATP alone is not responsible for the effects of metabolic inhibition, and both the transmembrane voltage and direct coupling to substrate oxidation via plasma-membrane-bound enzymes must be considered as possible energy sources for amino acid active transport.     

Phylogenetic analysis of the allometric scaling of therapeutic regimes for birds

The use of allometric scaling to estimate drug doses, regimes, and clearance rates (metabolic dosing) is based on the principle that the amount of drug to be administered is more closely related to daily energy use than to body mass (kg). Thus, by using the allometric estimations of minimal energy consumption (MEC) in kcal day⁻¹ based on the formula MEC= kM _b ^b , where b =3, it is thought to be possible to extrapolate appropriate drug dosage regimens to species for which direct MEC data are unavailable. However, the allometric equations for respiratory variables in birds were developed 30 years ago, and were based on a very small sample size, while the appropriate scaling exponent for the allometry of energy use is a matter of considerable debate. Hence, we revisit the issue of the scaling of therapeutic regimes in birds using the most current expanded database available (resting metabolic rate data for 296 species across 17 bird orders), taking account of the non-independence of species in this process using a phylogenetically independent approach. We show that the use of caloric values to estimate daily energy consumption introduces significant error into the formula, as there are a number of assumptions that are made when converting rate of oxygen consumption to a caloric value. We also show that there are significant differences in the proportionality or Hainsworth coefficients k across taxa when the data are examined in a phylogenetic context, although the allometric scaling exponent does not vary. We therefore recommend the use of only data based on oxygen consumption values, and not caloric values, and a multi-order phylogenetic model when calculating the appropriate drug dosage regime.     

Environment, migratory tendency, phylogeny and basal metabolic rate in birds

Basal metabolic rate (BMR) represents the minimum maintenance energy requirement of an endotherm and has far-reaching consequences for interactions between animals and their environments. Avian BMR exhibits considerable variation that is independent of body mass. Some long-distance migrants have been found to exhibit particularly high BMR, traditionally interpreted as being related to the energetic demands of long-distance migration. Here we use a global dataset to evaluate differences in BMR between migrants and non-migrants, and to examine the effects of environmental variables. The BMR of migrant species is significantly higher than that of non-migrants. Intriguingly, while the elevated BMR of migrants on their breeding grounds may reflect the metabolic machinery required for long-distance movements, an alternative (and statistically stronger) explanation is their occupation of predominantly cold high-latitude breeding areas. Among several environmental predictors, average annual temperature has the strongest effect on BMR, with a 50% reduction associated with a 20 degrees C gradient. The negative effects of temperature variables on BMR hold separately for migrants and non-migrants and are not due their different climatic associations. BMR in migrants shows a much lower degree of phylogenetic inertia. Our findings indicate that migratory tendency need not necessarily be invoked to explain the higher BMR of migrants. A weaker phylogenetic signal observed in migrants supports the notion of strong phenotypic flexibility in this group which facilitates migration-related BMR adjustments that occur above and beyond environmental conditions. In contrast to the findings of previous analyses of mammalian BMR, primary productivity, aridity or precipitation variability do not appear to be important environmental correlates of avian BMR. The strong effects of temperature-related variables and varying phylogenetic effects reiterate the importance of addressing both broad-scale and individual-scale variation for understanding the determinants of BMR.     

Immunocontraception for population control: will resistance evolve?

The prospect for successful biocontrol using immunocontraception is threatened if there is adaptation to the vaccine through natural selection of individuals that are genetically resistant to the contraceptive agent. To assess this possibility we examined the literature and found that little relevant data are available for any species on the appropriate trait, fertility variation among immunized individuals, or about appropriate population and genetic parameters influencing the likelihood of a selection response. Some data are available on variation in antibody response to immunocontraceptives, but the relationship between antibody response and fertility levels is poorly documented. The antibody response data indicate low heritability for this trait suggesting that fertility levels of contraceptive-resistant individuals will also have a low heritability. Slow evolution of contraception resistance might therefore be anticipated. The absence of information about relevant parameters makes the construction of quantitative models premature. We discuss factors in particular need of investigation if predictions about resistance evolution are to be made. These include: 1. the genetic basis of fertility retention, 2. the proportion of the population resistant to the contraceptive agent and how this is affected by gene flow from refuge populations, 3. the genetically-based fitness tradeoffs of resistant individuals that often accompany selection, 4. cross-generation effects that can thwart the effects of selection, and 5. the efficiency of delivery of the contraceptive agent. An understanding of the above for particular species, and the development of appropriate divergently acting multiple vaccines that can be used in temporal rotation or in mixtures, should facilitate the development of management options to minimize resistance evolution.     

Estimating regional population size and annual harvest intensity of the sooty shearwater in New Zealand

Abstract

Recent comprehensive survey data from multiple New Zealand offshore islands were combined with demographic population models to produce the first formal estimate of the total population of sooty shearwaters within New Zealand territory. We estimated the total population over 1994–2005 to be 21.3 (19.0–23.6) million individual birds in the New Zealand region. This population consisted of 12.8 (12.0–13.6) million adults, 2.8 (2.5–3.1) million chicks, and 4.4 (4.2–4.7) million breeding pairs. Breeding sooty shearwaters were concentrated primarily around the southern islands of New Zealand, with 53% breeding in the Titi Islands surrounding Rakiura (Stewart Island). Rakiura Maori muttonbirders were estimated to harvest 360 000 (320 000–400 000) sooty shearwaters per year, equivalent to 18% of the chicks produced in the harvested areas and 13% of chicks in the New Zealand region. Overall, 11% of the chicks within the Titi Islands live on unharvested ground. Systematic and widespread surveys of breeding colonies in South America are needed before a reliable global sooty shearwater population estimate can be calculated.     

Effects of geolocation archival tags on reproduction and adult body mass of sooty shearwaters (Puffinus griseus)

Abstract

We attached 11 g (1.4% body‐mass equivalent) global location sensing (GLS) archival tag packages to tarsi of 25 breeding sooty shearwaters (Puffinus griseus, titi) on Whenua Hou (Codfish Island), New Zealand during the chick‐rearing period in 2005. Compared with chicks reared by non‐handled adults that did not carry tags, deployment of tags on one or both adult parents ultimately resulted in 35% reduction in chick body mass and significantly reduced chick skeletal size preceding fledging (19 April). However, body mass between chick groups was not significantly different after controlling for skeletal size. Effects on chicks were more pronounced in six pairs where both parents carried tags. Chick mass was negatively related to the duration that adults carried tags. In this study, none of the chicks reared by pairs where both parents were tagged, 54% of chicks reared by pairs where one parent was tagged, and 83% of chicks reared by non‐handled and non‐tagged parents achieved a previously determined pre‐fiedging mass threshold (564 g; Sagar & Horning 1998). Body mass of adults carrying tags and returning from trans‐equatorial migration the following year were 4% lighter on average than non‐tagged birds, but this difference was not statistically significant. Reduced mass among chicks reared by adults carrying tags during the chick‐provisioning period indicated that adults altered “normal” provisioning behaviours to maintain their own body condition at the expense of their chicks. Population‐level information derived from telemetry studies can reveal important habitat‐linked behaviours, unique aspects of sea‐bird foraging behaviours, and migration ecology. Information for some species (e.g., overlap with fisheries) can aid conservation and marine ecosystem management. We advise caution, however, when interpreting certain data related to adult provisioning behaviours (e.g., time spent foraging, provisioning rates, etc.). If effects on individuals are of concern, we suggest shorter‐term deployments, smaller and lighter tags, and alternative attachment techniques, especially when investigating threatened or endangered species.