The consequences of the variance-mean rescaling effect on effective population size

The effective population size (N_e), and the ratio between N_e and census population size (N) are often used as measures of population viability. We show that using the harmonic mean of population sizes over time – a common proxy for N_e– has some important evolutionary consequences and implications for conservation management. This stems from the fact that there is no unambiguous relationship between the arithmetic and harmonic means for populations fluctuating in size. As long as the variance of population size increases moderately with increasing arithmetic mean population size, the harmonic mean also increases. However, if the variance of population size increases more rapidly, which existing data often suggest, then the harmonic mean may actually decrease with increasing arithmetic mean. Thus maximizing N may not maximize N_e, but could instead lower the adaptive potential and hence limit the evolutionary response to environmental change. Large census size has the clear advantage of lowering demographic stochasticity, and hence extinction risk, and under certain conditions large census size also minimizes the loss of genetic variation. Consequently, maximising census size has served as a useful dogma in ecology, genetics and conservation. Nonetheless, due to the intricate relationships among N_e, population viability and the properties of population fluctuations, we suggest that this dogma should be taken only as a rule of thumb.     

Competition between anoxygenic phototrophic bacteria and colorless sulfur bacteria in a microbial mat

Abstract The populations of chemolithoautotrophic (colorless) sulfur bacteria and anoxygenic phototrophic bacteria were enumerated in a marine microbial mat. The highest population densities were found in the 0–5 mm layer of the mat: 2.0 × 10⁹ cells cm⁻³ sediment, and 4.0 × 10⁷ cells cm⁻³ sediment for the colorless sulfur bacteria and phototrophs, respectively. Kinetic parameters for thiosulfate-limited growth were assessed for Thiobacillus thioparus T5 and Thiocapsa roseopersicina M1, both isolated from microbial mats. For Thiobacillus T5, growing at a constant oxygen concentration of 43 μmol l⁻¹, μ_max was 0.336 h⁻¹ and K _s 0.8 μmol l⁻¹. Phototrophically grown Thiocapsa strain M1 displayed a μ_max of 0.080 h⁻¹ and a K _s of 8 μmol l⁻¹ when anoxically grown under thiosulfate limitation. In a competition experiment with thiosulfate as electron donor, Thiocapsa became dominant during a 10-h oxic/14-h anoxic regimen at continuous illumination, despite the higher affinity for thiosulfate of Thiobacillus .     

The genetic effective size of a metapopulation

The structure of a population over time, space and categories of social and sexual role governs its ability to retain genetic variation in the face of drift. A metapopulation is an extreme form of spatial structure in which loosely coupled local populations 'turnover', that is, suffer extinction followed by recolonization from elsewhere within the metapopulation. These local populations turn over with a characteristic half-life. Based on a simulation model that incorporates both realistic features of population ecology and population genetics, the ability of such a metapopulation to retain genetic variation, which may be defined as proportional to its so-called effective population size, denoted N_e(^meta), can be one to two orders of magnitude lower than the maximum total number of individuals in the system. N_e(meta) depends on the persistence time associated with longevity of local populations (the turnover half-life), the average number of local populations extant in the metapopulation and the gene flow between local populations. Habitat fragmentation, which can create a metapopulation from a formerly continuously distributed species, may have unappreciated large genetic consequences for species impacted by human development.     

A TEST AND REVIEW OF THE ROLE OF EFFECTIVE POPULATION SIZE ON EXPERIMENTAL SEXUAL SELECTION PATTERNS

Experimental evolution, particularly experimental sexual selection in which sexual selection strength is manipulated by altering the mating system, is an increasingly popular method for testing evolutionary theory. Concerns have arisen regarding genetic diversity variation across experimental treatments: differences in the number and sex ratio of breeders (effective population size; N_e ) and the potential for genetic hitchhiking, both of which may cause different levels of genetic variation between treatments. Such differences may affect the selection response and confound interpretation of results. Here we use both census-based estimators and molecular marker-based estimates to empirically test how experimental evolution of sexual selection in Drosophila pseudoobscura impacts N_e and autosomal genetic diversity. We also consider effects of treatment on X-linked N_e s, which have previously been ignored. Molecular autosomal marker-based estimators indicate that neither N_e nor genetic diversity differs between treatments experiencing different sexual selection intensities; thus observed evolutionary responses reflect selection rather than any confounding effects of experimental design. Given the increasing number of studies on experimental sexual selection, we also review the census N_e s of other experimental systems, calculate X-linked N_e , and compare how different studies have dealt with the issues of inbreeding, genetic drift, and genetic hitchhiking to help inform future designs.     

Apparent phytotoxicity of mononuclear hydroxy-aluminum to four dicotyledonous species

It has long been assumed that Al³⁺ is an important rhizotoxic ion in acid soils around the world, but the toxicity of Al³⁺ relative to mononuclear hydroxy-Al [AlOH²⁺ and Al(OH)⁺₂] has been examined in detail only for an Al-sensitive wheat variety ( Triticum aestivum L. cv. Tyler). That plant appears to be sensitive to Al³⁺ but not to AlOH²⁺ and Al(OH)⁺₂. New experiments, and reanalyses of previously published experiments, provide evidence that dicotyledonous species may be sensitive to mononuclear hydroxy-Al and that Al³⁺ may be nontoxic, or less toxic, to those plants. Despite these consistently measured differences between wheat and the dicotyledons, the determination of relative toxicities (Al³⁺ vs mononuclear hydroxy-Al) may be an intractable problem. Because of hydrolysis equilibria, (AlOH²⁺) and (Al(OH)⁺₂) are equivalent to (Al³⁺)k₁(H⁺)⁻¹ and (l³⁺)k₂(H⁺)⁻², respectively, in which k₁ and k₂ are the first and second hydrolysis constants (braces denote activities). Thus, any expression of root elongation as a function of mononuclear hydroxy-Al can be alternatively expressed as a function of (Al³⁺) and (H⁺). Toxicity attributed to mononuclear hydroxy-Al may actually be Al³⁺ toxicity that increases as pH rises (i.e. Al³⁺ toxicity ameliorated by H⁺).     

Most probable number enumeration of H2-utilizing acetogenic bacteria from the digestive tract of animals and man

Abstract A method is proposed that allows the enrichment and most probable number estimation of H₂/CO₂-utilizing acetogenic bacteria. It is based on the difference in acetate production for serial dilutions incubated under either a test H₂/CO₂ (4:1), or a control N₂/CO₂ (4:1) headspace atmosphere. A nutritionally non-selective medium was used, containing bromoethane-sulfonic acid as inhibitor of methanogenic archaea and 10% pre-incubated clarified rumen fluid. Acetogenic bacteria were enumerated in rumen and hindgut contents of animals and in human feces. They ranged from below 10² to above 10⁸ per gram wet weight gut content and their population levels were the highest in the absence of methanogenesis. The method described therein should prove useful to better understand the diversity and ecological importance of dominant gut acetogens.     

Extra-pair fertilization and effective population size in the song sparrow Melospiza melodia

The concept of effective population size (N_e) is used widely by conservation and evolutionary biologists as an indicator of the genetic state of populations, but its precision and relation to the census population size is often uncertain. Extra-pair fertilizations have the potential to bias estimates of N_e when they affect the number of breeders or their estimated reproductive success tallied from social pedigrees. We tested if the occurrence of extra-pair fertilizations influenced estimates of N_e in a resident population of song sparrows Melospiza melodia using four years of detailed behavioural and genetic data. Estimates of N_e based on social and genetic data were nearly identical and averaged c. 65% of the census population size over four years, despite that 28% of 471 independent young were sired outside of social pairs. Variance in male reproductive success also did not differ between estimates based on social and genetic data, indicating that extra-pair mating had little effect on the distribution of reproductive success in our study population. Our results show that the genetic assignment will not always be necessary to estimate N_e precisely.     

Stress-related hormones and genetic diversity in sea otters (Enhydra lutris)

Sea otters ( Enhydra lutris ) once ranged throughout the coastal regions of the north Pacific, but were extirpated throughout their range during the fur trade of the 18th and 19th centuries, leaving only small, widely scattered, remnant populations. All extant sea otter populations are believed to have experienced a population bottleneck and thus have lost genetic variation. Populations that undergo severe population reduction and associated inbreeding may suffer from a general reduction in fitness termed inbreeding depression. Inbreeding depression may result in decreased testosterone levels in males, and reduced ability to respond to stressful stimuli associated with an increase in the stress-related adrenal glucocorticoid hormones, cortisol and corticosterone. We investigated correlations of testosterone, cortisol, and corticosterone with genetic diversity in sea otters from five populations. We found a significant negative correlation between genetic diversity and both mean population-level ( r ²= 0.27, P < 0.001) and individual-level ( r ²= 0.54, P < 0.001) corticosterone values, as well as a negative correlation between genetic diversity and cortisol at the individual level ( r ²= 0.17, P = 0.04). No relationship was found between genetic diversity and testosterone ( P = 0.57). The strength of the correlations, especially with corticosterone, suggests potential negative consequences for overall population health, particularly for populations with the lowest genetic diversity.     

Pharmacological and Regional Characterization of [3H]LY278584 Binding Sites in Human Brain

Abstract: Binding of [³H]LY278584, which has been previously shown to label 5-hydroxytryptamine₃ (5-HT₃) receptors in rat cortex, was studied in human brain. Saturation experiments revealed a homogeneous population of saturable binding sites in amygdala ( K _D= 3.08 ± 0.67 n M, B _max= 11.86 ± 1.87 fmol/mg of protein) as well as in hippocampus, caudate, and putamen. Specific binding was also high in nucleus accumbens and entorhinal cortex. Specific binding was negligible in neocortical areas. Kinetic studies conducted in human hippocampus revealed a K _on of 0.025 ± 0.009 n M ⁻¹ min⁻¹ and a K _off of 0.010 ± 0.002 min⁻¹. The kinetics of [³H]LY278584 binding were similar in the caudate. Pharmacological characterization of [³H]LY278584 specific binding in caudate and amygdala indicated the compound was binding to 5-HT₃ receptors. We conclude that 5-HT₃ receptors labeled by [³H]LY278584 are present in both limbic and striatal areas in human brain, suggesting that 5-HT₃ receptor antagonists may be able to influence the dopamine system in humans, similarly to their effects in rodent studies.     

Influence of woodlot floor topography on microbial decomposer distribution

The distribution of microbial populations that decomposed sugar, cellulose and lignin-related substrates was examined in a beech Fagus grandifolia Ehrh. and maple Acer saccharum Marsh. dominated woodlot developed on glacial till. The topography of the woodlot, characterized by rises, depressions and more extensive level areas about 1 m in diameter with a 0.5 m vertical maximum, produced a mosaic of decomposer habitats designated as high, level and low sites.
In general, populations of sugar, cellulose and lignin decomposing organisms (based on ten estimates made from April to October) were two to four times higher in litter and soil samples from low sites than those from high sites. Sugar decomposing bacteria in litter were most abundant at all topographic sites. 135 × 10⁶ g⁻¹ dry litter at high sites, 396 × 10⁶ g⁻¹ at level sites and 456 × 10⁶ g⁻¹ at low sites; lignolytic fungi were least abundant, 391 × 10² g⁻¹ dry litter at high sites. 700 × 10⁶ g⁻¹ at level sites and 954 × 10² g⁻¹ at low sites. Numbers of microbial decomposers in the topographic sites were correlated with organic matter content. Distribution of fungal genera did not appear to be related to topographic site. Most populations examined showed two numerical peaks, one in late May or June and one in late September or October. It is suspected that these peaks were influenced by the coincident timing of favourable physical conditions and priming by soluble nutrients leached from litter.     

A new method for estimating effective population sizes from a single sample of multilocus genotypes

Equations for the effective size ( N_e ) of a population were derived in terms of the frequencies of a pair of offspring taken at random from the population being sibs sharing the same one or two parents. Based on these equations, a novel method (called sibship assignment method) was proposed to infer N_e from the sibship frequencies estimated from a sibship assignment analysis, using the multilocus genotypes of a sample of offspring taken at random from a single cohort in a population. Comparative analyses of extensive simulated data and some empirical data clearly demonstrated that the sibship assignment method is much more accurate [measured by the root mean squared error, RMSE, of 1/(2 N_e )] than other methods such as the heterozygote excess method, the linkage disequilibrium method, and the temporal method. The RMSE of 1/(2 N_e ) from the sibship assignment method is typically a small fraction of that from other methods. The new method is also more general and flexible than other methods. It can be applied to populations with nonoverlapping generations of both diploid and haplodiploid species under random or nonrandom mating, using either codominant or dominant markers. It can also be applied to the estimation of N_e for a subpopulation with immigration. With some modification, it could be applied to monoecious diploid populations with self-fertilization, and to populations with overlapping generations.     

Behaviour of Staphylococcus aureus strains, producers of enterotoxins C1 or C2, during the manufacture and storage of Burgos cheese

Burgos cheese was manufactured from pasteurized ewes milk inoculated with Staphylococcus aureus strains FRI 137 and FRI 361, at levels of ca 10³ and 10⁵ cfu/ml and stored at 4°, 10° and 15°C and at room temperature (10°-15°C). Populations of Staph. aureus and mesophilic aerobes, pH, and production of thermonuclease and enterotoxins C₁ and C₂ were investigated. Aerobic counts increased during cheese-making and storage. With both test strains, important growth was observed only during the storage period, the larger levels corresponding to the higher temperatures. Although Staph. aureus strains attained populations of over 10⁸ cfu/g, no enterotoxin was detected. Strain FRI 361 reached 10⁷ cfu/g without production of a detectable amount of thermonuclease. With strain FRI 137, the minimal population associated with enzyme activity was influenced by the inoculum size. Staphylococcus aureus counts are better indicators of staphylococcal growth in Burgos cheese than the thermonuclease test.     

Seasonal patterns of viruses, bacteria and dissolved organic carbon in a riverine wetland

SUMMARY 1. Viral and bacterial abundances were studied in relation to environmental attributes over an annual period, for both planktonic and attached (sediment, aquatic macrophyte and submerged wood) habitats, in a riverine wetland.
2. Annual mean abundance of planktonic viruses ranged from 2.3 × 10⁵−3.8 × 10⁵ particles mL⁻¹ and varied according to sampling site. Significant seasonal patterns in viral abundance were evident and appeared to be linked to variations in bacterial abundance, dissolved organic carbon and inorganic nutrients.
3. Annual mean abundance of viruses associated with surfaces ranged from 1.3 × 10⁶ particles cm⁻² on aquatic macrophytes to 1.1 × 10⁷ particles cm⁻² on wood and also showed seasonal patterns. The difference in viral dynamics among the different sites emphasizes the importance of considering habitat diversity within wetlands when examining microbial communities.     

Microbial activity associated with seston in headwater streams: effects of nitrogen, phosphorus and temperature

SUMMARY 1. The influences of temperature and dissolved nitrates and phosphates on microbial activity associated with suspended fine particulate organic matter (seston) were evaluated in four headwater streams in the southern Appalachian Mountains.
2. Temperature manipulations of ± 5°C always induced significant changes in [¹⁴C] glucose mineralization (ANOVA; P <0.05) and [³H]thymidine incorporation (ANOVA; P <0.05).
3. Nutrient amendments of 1.0 mg NO₃ I⁻¹ and 0.05 mg PO₄I⁻¹ induced no significant alterations in bacterial mineralization of [¹⁴C]glucose (ANOVA; P >0.05) or incorporation of [³H]thymidine (ANOVA; P >0.05) in short-term (i.e. 3 h) experiments.
4. Microorganisms attached to refractory particulate organic matter do not appear to be limited by nitrogen or phosphorus even in streams with ambient nutrient concentrations as low as 0.06 mg NO₃ I⁻¹ and <0.03 mg PO₄ I⁻¹.
5. Our results indicate that variations in water temperature resulting from diurnal and seasonal temperature fluctuations, forest clear-cutting, and catchment elevation and aspect can have marked effects upon microbial activity and production, while short-term alterations in nutrient regime appear to have no significant effect on microbial activity associated with seston.     

Allozymes and the genetics of antler development in red deer (Cervus elsphus)

In order to examine a previously hypothesized influence of selective hunting on allele frequency changes at some regularly polymorphic allozyme loci in red deer ( Cervus eluphus ), antler characters, serving as criteria for culling, were examined in relation to electrophoretic variation in two free-ranging populations of the Vosges, Eastern France, and an enclosure in Central France. When homozygous for the allele Idh-2 ¹²⁵, stags ≥ 2 years old had a significantly higher number of antler points (NAP). When homozygous for the allele Acp-2 ¹⁰⁰, stags older than 5 years had antlers that were significantly larger for a number of traits (NAP, main beam length and circumference, coronet circumference, brow tine length). Among younger stags, all antler traits in Acp-2 ¹⁰⁰ homozygotes were significantly smaller than in carriers of the alternative allele, Acp-2 ⁸⁵. Our data suggest the presence of at least two independent genetic components (one associated with early development of a high NAP, the other with generally large antler size in adults), affecting antler expression in red deer. Those genetic components, possibly major genes which are chromosomally linked with the allozyme loci studied, compensate or reinforce each other in their phenotypic effects. By playing a role in balancing benefits and costs of male reproductive success, they may be part of a genetic mechanism enabling the rapid adaptation of a population to various environmental and demographic conditions. The three populations studied originate from one another, and, based on an assessment of effective population sizes, it could be demonstrated that selective hunting for antler shape has changed allelic frequencies at the associated marker loci within a few generations.     

Diel rhythmicity in amino acid uptake by Prochlorococcus

The marine cyanobacterium Prochlorococcus , the most abundant phototrophic organism on Earth, numerically dominates the phytoplankton in nitrogen (N)-depleted oceanic gyres. Alongside inorganic N sources such as nitrite and ammonium, natural populations of this genus also acquire organic N, specifically amino acids. Here, we investigated using isotopic tracer and flow cytometric cell sorting techniques whether amino acid uptake by Prochlorococcus is subject to a diel rhythmicity, and if so, whether this was linked to a specific cell cycle stage. We observed, in contrast to diurnally similar methionine uptake rates by Synechococcus cells, obvious diurnal rhythms in methionine uptake by Prochlorococcus cells in the tropical Atlantic. These rhythms were confirmed using reproducible cyclostat experiments with a light-synchronized axenic Prochlorococcus (PCC9511 strain) culture and ³⁵S-methionine and ³H-leucine tracers. Cells acquired the tracers at lower rates around dawn and higher rates around dusk despite >10⁴ times higher concentration of ammonium in the medium, presumably because amino acids can be directly incorporated into protein. Leucine uptake rates by cells in the S+G₂ cell cycle stage were consistently 2.2 times higher than those of cells at the G₁ stage. Furthermore, S+G₂ cells upregulated amino acid uptake 3.5 times from dawn to dusk to boost protein synthesis prior to cell division. Because Prochlorococcus populations can account from 13% at midday to 42% at dusk of total microbial uptake of methionine and probably of other amino acids in N-depleted oceanic waters, this genus exerts diurnally variable, strong competitive pressure on other bacterioplankton populations.     

Methanogenesis in the hypersaline Solar Lake (Sinai)

Abstract Enrichment studies on microbial mat sediments (potential stromatolites) from the hypersaline Solar Lake (Sinai) indicated high numbers of methanogenic bacteria (up to 10⁵ ml⁻¹ sediment) in spite of the high sulfate reduction rate, sulfate concentration and salinity. Among H₂/CO₂, acetate and monomethylamine, the methylated amine was the preferred substrate. The predominant species enriched was a Methanosarcina sp. The findings indicate that methanogenic bacteria play an important role in hypersaline sulfate-enriched anoxic sediments and stromatolithic microbial mats.     

Transmembrane 36CI− Flux Measurements and Desensitization of the γ-Aminobutyric AcidA Receptor

Abstract: Some data on the concentration range of response and the concentration for half-response (EC₅₀) of γ-aminobutyric acid (GABA) for the GABA_A receptor are reviewed and compared. An analysis of the ³⁶CI⁻ flux assay demonstrates that both the EC₅₀ and the slope of a Hill plot depend on the ion influx or efflux assay time. The effects of depletion of the ³⁶CI⁻ concentration gradient during the assay and of receptor desensitization on the result for a range of assay times are considered. The EC₅₀ can be decreased by orders of magnitude by increasing the assay time. The EC₅₀ measured in a finite time is less than the half-response concentration for the response(s) of the receptor. The extent of this difference depends on the receptor concentration per internal volume. The maximal decrease of EC₅₀ depends on the rate of receptor desensitization. The computer simulations showed that a GABA_A receptor with a half-response concentration of 100 μ M GABA can give ³⁶CI⁻ flux measurements with an EC₅₀ value 100-fold lower.     

The rapid estimation of microbial contamination of raw meat by measurement of adenosine triphosphate (ATP)

Bacteria were separated from raw meat homogenate by a simple three-stage process. Centrifugation (10 s at 2000 g) removed coarse particles; stirring with the cation exchange resin Bio-Rex 70 removed smaller particles and filtration through 0.22 μm membranes removed soluble materials. By this process 70—80% of the microbial populations of meat homogenates were consistently isolated on the filters. A linear relationship was found between log₁₀ microbial ATP and log₁₀ colony count of meat over the range 10⁵—10⁹ cfu/g. The value of ATP/cfu for meat samples was within the range previously reported for pure cultures. These data indicated that ATP extracted from the filters originated from bacteria in the meat samples. Several samples can be analysed simultaneously in an elapsed time of 20—25 min. The variability associated with estimates of both colony counts and ATP levels has been determined.     

A Note on the Enumeration of Epiphytic Bacteria by Microscopic Methods with Particular Reference to Two Freshwater Plants

Bacteria on plant surfaces were examined using epifluorescence, bright-field microscopy and an impression technique. Staining bacteria directly on the plant surface with phenolic aniline blue was found to be the best method to use for the determination of bacterial density. The effect on the estimation of population density of pretreatment of the plant with agents such as methanol and eosin yellowish was investigated. The average sizes of the bacterial populations on two freshwater plants, Rorippa and Lemna , estimated after staining by this method, were 5 times 10⁶ and 9 times 10⁶ bacteria cm-^z respectively.