Estimating and Correcting for Bias in Population Assessments of Sooty Shearwaters

Abstract: We investigated the precision and accuracy of an infrared burrowscope for detecting sooty shearwater (Pufffinus griseus) chicks at 13 plots from 3 islands in southern New Zealand in 2003. We partially excavated burrows systems to reveal the entire burrow contents after 2 teams of observers had prospected all burrow entrances. Accuracy was similar between islands and observer teams at approximately 85%. The majority of the inaccuracy stemmed from failure to detect some chicks. Logistic regression modeling identified 4 burrow characteristics occurring between the entrance and the nest-site that influenced detection of burrow occupants. Detection was lower at nest-sites further from burrow entrances, in burrows with a high rate of burrow division, and in burrows with a high level of curvature. There was a positive relationship between the interaction of rate of division and curvature and detection of chicks. Distance from the burrow entrance was the only parameter that could be reliably used as a predictor of detection rate, so a reduced model containing only this variable was constructed to correct for burrowscope bias. The correction factor performed well on The Snares and Bench Island where predicted bias was very similar to observed levels (within 5%), but bias was overestimated on Putauhinu by up to 19.1%. Consistent bias, lack of damage to burrows from excavation, and the successful application of a correction factor all indicate the value of further testing burrowscope accuracy on other burrow-nesting seabird species.     

Impact of mate availability, population size, and spatial aggregation of morphs on sexual reproduction in a distylous, aquatic plant

In distylous, self-incompatible plants, clonal propagation, unbalanced floral morph frequencies, and reduced population size can interfere with the functioning of distyly by compromising legitimate intermorph pollinations, resulting in reduced reproductive output. Here, we examined the mating system and the impact of mate availability, population size, and spatial aggregation of morphs on reproductive output in the distylous, clonal, aquatic plant Hottonia palustris. Controlled pollinations under greenhouse conditions detected no spontaneous selfing without the action of a pollen vector (autonomous autogamy) and demonstrated very low fruit and seed development after self-pollination. Intermorph (legitimate) crossings resulted in high reproductive output in both floral morphs (long- and short-styled individuals), whereas intramorph (illegitimate) crossings decreased fruit and seed development by more than 50%, indicating that the species has partial intramorph-incompatibility. In natural populations, small population size and increasing deviation of floral morph frequencies negatively affected reproductive outcome. Individuals of the majority morph type developed significantly fewer fruit and seeds than individuals of the minority morph type. This rapid decline in fecundity was symmetrical, indicating that regardless of which morph was in the majority, the same patterns of negative frequency-dependent mating occurred. Increasing spatial isolation between compatible morphs significantly reduced fruit and seed set in both morphs similarly. This study provides clear indications of frequency- and context-dependent mating in natural populations of a distylous plant species.     

Assessment of non-response bias in a survey of residential magnetic field exposure in Taiwan

We assessed potential non-response bias in obtaining information on residential extremely low-frequency power frequency magnetic field (MF) in Taiwan. All households occupied by children aged less than 7 years in two study districts, one in an urban town and the other in a rural town, were visited and solicited for on-site measurements in late 2003. The initial response rate was only 32% (33/104, urban) and 60% (61/101, rural). In the same season 1 year later, we performed a second survey of those who declined to be measured at the initial survey and successfully measured another 77 residences (50 and 27 for urban and rural districts, respectively). The two districts were selected mainly because the local public health officers were quite willing to assist the initial survey and to inform residents of the second survey. Except for meteorological conditions, the two surveys came up with very similar findings regarding residential characteristics and power facilities surrounding the houses. The mean residential MF for the urban residences was .121 and .140 micro-Tesla (microT) (P = .620) for the two surveys. The corresponding figures for the rural residences were .119 and .115 microT (P = .802). Although limited in its scope, this study tends to indicate that measurement studies of residential MF are less likely to suffer from serious selection bias if sampling is confined within a small district where people have similar socioeconomic characteristics.     

Photosynthetic efficiency as a function of thermal stratification and phytoplankton size structure in an oligotrophic alpine lake

Allometric relationships of phytoplankton communities were studied on the basis of a five-year data-set in a deep oligotrophic alpine lake in Austria. The seasonal phytoplankton succession in Mondsee is characterised by diatoms during winter mixing and a distinct metalimnetic population of Planktothrix rubescens during stratification in summer. The variation of phytoplankton photosynthetic efficiency between seasons was assessed using in situ carbon-uptake rates (5 years data) and Fast Repetition Rate Fluorometry (FRRF) (2 years data). The light-saturated, chlorophyll-specific rate of photosynthesis (P*_max), irradiance at the onset of saturation (E _k) and maximum light-utilisation efficiency (α*) were determined for winter mixing and summer stratification. Fluorescence-based parameters as the functional absorption cross section of Photosystem II (σ _PSII) and the photochemical quantum yield (F _v/F _m) were additionally analysed in 2003 and 2004 to study the underlying physiological mechanisms for the variability in photosynthetic performance. Beyond their sensitivity to changing environmental conditions like thermal stratification, phytoplankton populations differ in their photosynthetic behaviour according to their size structure. Therefore Photosynthesis vs. Irradiance (P/E)-relationships were analysed in detail within a 1-year period from size fractionated cell counts, chlorophyll-a and carbon-uptake.     

尖吻蝮毒液类凝血酶的克隆及序列分析

以类凝血酶的RT—PCR产物为模板,PCR扩增出其cDNA片断克隆尖吻蝮的毒液类凝血酶cDNA,分析其密码子运用的特点。用软件进行多序列比对并分析。克隆出多个尖吻蝮毒液类凝血酶的cDNA,得到其基因密码子运用的有关数据。结果表明尖吻蝮毒液类凝血酶同时存在着保守性与多样性,有着较明显的密码子偏好性,在进化中承受了碱基组成和自然选择的压力。     

Determining minimum ultimate size, setting size limits, and developing trophy standards and indices of comparable size for maintaining quality muskellunge (Esox masquinongy) populations and sports fisheries

Growth and ultimate size can provide important population insights and a sound biological basis for setting length limits, which can be the best single regulation for preventing overexploitation of muskellunge (Esox masquinongy) populations. A system was developed, using cleithral age and total length at age confidence limits (CL) data, to determine reproductive and growth potential (ultimate size) for calculating and setting increased size limits based on minimum reproductive size (upper 99% CL at age at first maturity + 2 year) and minimum ultimate size (MUS) calculated from the lower 99% CL—minimum ultimate size limit (MUSL). MUS also provides a trophy standard and an index of relative size for comparing trophy potential of individuals within and among populations. Guidelines are provided for determining minimum sample size (mean ± 95% confidence interval = 12 ± 4) and minimum age (8–10 ± 2.0 year) required to produce valid von Bertalanffy growth trajectories. MUS, MUSL, and trophy standards for both length and estimated weight are provided for female and male muskellunge from 14 Ontario sources. Mean MUS, or trophy standard, for females was 115 ± 10.3 cm (MUSL range 75–135) and 11.1 ± 2.6 kg (2.5–17.5) and for males was 95 ± 7.5 cm (66–110) and 6.1 ± 1.3 kg (1.9–9.2). These indices can precisely define growth and growth potential for muskellunge populations and individuals and can be used to better manage and maintain or improve the quality of muskellunge populations and fisheries. Dedicated to the late Dr. E.J. Crossman.     

Consequences of fission in the coral <Emphasis Type="Italic">Siderastrea siderea</Emphasis>: growth rates of small colonies and clonal input to population structure

Colony age and size can be poorly related in scleractinian corals if colonies undergo fission to form smaller independent patches of living tissue (i.e., ramets), but the implications of this life-history characteristic are unclear. This study explored the ecological consequences of the potential discrepancy between size and age for a massive scleractinian, first by testing the effect of colony origin on the growth of small colonies, and second by quantifying the contribution of ramets to population structure. Using Siderastrea siderea in St. John (US Virgin Islands) as an experimental system, the analyses demonstrated that the growth of small colonies derived from sexual reproduction was 2.5-fold greater than that of small ramets which were estimated to be ≈100 years older based on the age of the parent colonies from which they split. Although fission can generate discrete colonies, which in the case of the study reef accounted for 42% of all colonies, it may depress colony success and reef accretion through lowered colony growth rates.     

Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals

In mammals there is a bias in amino acid usage near splice sites that is explained, in large part, by the high density of exonic splicing enhancers (ESEs) in these regions. Is there a similar bias for the relative use of synonymous codons, and can any such bias be predicted by their abundance in ESEs? Prior reports suggested that such trends may exist. From analysis of human exons, we find that 47 of the 59 codons with at least one synonym show differential usage in the proximity of exon ends, of which 42 remain significant after correction for multiple testing. Within sets of synonymous codons those more preferred near splice sites are generally those that are relatively more abundant within the ESEs. However, the examples given previously appear exceptionally good fits and there exist many exceptions, the usage of lysine's codons being a case in point. Similar results are observed in mouse exons. We conclude that splice regulation impacts on the choice of synonymous codons in mammals, but the magnitude of this effect is less than might at first have been supposed.     

Disease mapping and spatial regression with count data

In this paper, we provide critical reviews of methods suggested for the analysis of aggregate count data in the context of disease mapping and spatial regression. We introduce a new method for picking prior distributions, and propose a number of refinements of previously used models. We also consider ecological bias, mutual standardization, and choice of both spatial model and prior specification. We analyze male lip cancer incidence data collected in Scotland over the period 1975-1980, and outline a number of problems with previous analyses of these data. In disease mapping studies, hierarchical models can provide robust estimation of area-level risk parameters, though care is required in the choice of covariate model, and it is important to assess the sensitivity of estimates to the spatial model chosen, and to the prior specifications on the variance parameters. Spatial ecological regression is a far more hazardous enterprise for two reasons. First, there is always the possibility of ecological bias, and this can only be alleviated by the inclusion of individual-level data. For the Scottish data, we show that the previously used mean model has limited interpretation from an individual perspective. Second, when residual spatial dependence is modeled, and if the exposure has spatial structure, then estimates of exposure association parameters will change when compared with those obtained from the independence across space model, and the data alone cannot choose the form and extent of spatial correlation that is appropriate.     

A comparison of survey and focal follow methods for estimating individual activity budgets of cetaceans

Activity budget data are essential for determining behavioral responses to physiological and ecological variables. Yet, few studies are available to investigate the robustness, accuracy, and biases of the methods used to estimate activity budgets for cetaceans. In this study, we compare activity budgets of 55 adult female bottlenose dolphins in Shark Bay, Australia derived from two methods: surveys (n = 6,903) and focal follows (n = 1,185, totaling 2,721 h of observation). Activity budgets estimated from survey data differed in all behavioral states compared to focal follow data. However, when controlling for temporal autocorrelation, only time spent socializing and time spent traveling remained disparate between the methods. To control for biases associated with assigning group‐level behavior to individuals, we also compared survey and focal follow activity budgets for lone females. Here we found differences between methods in time spent foraging and traveling regardless of whether we controlled for temporal autocorrelation, which suggests detection biases likely play a role in explaining differences in activity budget estimates between the two methodologies. Our results suggest that surveys are less representative of individual‐level activity budgets, and thus, when individual‐level knowledge about behavior is needed, focal follows are preferred.