A diagnostic test for autocorrelation in increment-averaged data with application to soil sampling

Motivated by the problem of detecting spatial autocorrelation in increment- averaged data from soil core samples, we use the Cholesky decomposition of the inverse of an autocovariance matrix to derive a parametric linear regression model for autocovariances. In the absence of autocorrelation, the off-diagonal terms in the lower triangular matrix from the Cholesky decomposition should be identically zero, and so the regression coefficients should be identically zero. The standard F-test of this hypothesis and two bootstrapped versions of the test are evaluated as autocorrelation diagnostics via simulation. Size is assessed for a variety of heteroskedastic null hypotheses. Power is evaluated against autocorrelated alternatives, including increment-averaged Ornstein-Uhlenbeck and Matérn processes. The bootstrapped tests maintain approximately the correct size and have good power against moderately autocorrelated alternatives. The methods are applied to data from a study of carbon sequestration in agricultural soils.     

Estimation of rare and clustered population mean using stratified adaptive cluster sampling

For many clustered populations, the prior information on an initial stratification exists but the exact pattern of the population concentration may not be predicted. Under this situation, the stratified adaptive cluster sampling (SACS) may provide more efficient estimates than the other conventional sampling designs for the estimation of rare and clustered population parameters. For practical interest, we propose a generalized ratio estimator with the single auxiliary variable under the SACS design. The expressions of approximate bias and mean squared error (MSE) for the proposed estimator are derived. Numerical studies are carried out to compare the performances of the proposed generalized estimator over the usual mean and combined ratio estimators under the conventional stratified random sampling (StRS) using a real population of redwood trees in California and generating an artificial population by the Poisson cluster process. Simulation results show that the proposed class of estimators may provide more efficient results than the other estimators considered in this article for the estimation of highly clumped population.

     

Comparison of distribution function estimators for forestry applications following variable probability sampling

Practical considerations often motivate employing variable probability sampling designs when estimating characteristics of forest populations. Three distribution function estimators, the Horvitz-Thompson estimator, a difference estimator, and a ratio estimator, are compared following variable probability sampling in which the inclusion probabilities are proportional to an auxiliary variable, X. Relative performance of the estimators is affected by several factors, including the distribution of the inclusion probabilities, the correlation () between X and the response Y, and the position along the distribution function being estimated. Both the ratio and difference estimators are superior to the Horvitz-Thompson estimator. The difference estimator gains better precision than the ratio estimator toward the upper portion of the distribution function, but the ratio estimator is superior toward the lower end of the distribution function. The point along the distribution function at which the difference estimator becomes more precise than the ratio estimator depends on the sampling design, as well as the coefficient of variation of X and . A simple confidence interval procedure provides close to nominal coverage for intervals constructed from both the difference and ratio estimators, with the exception that coverage may be poor for the lower tail of the distribution function when using the ratio estimator.     

Geochemistry of soil around a fluoride contaminated area in Nayagarh District,Orissa, India: Factor analytical appraisal

Fluoride contamination in soil was studied in the vicinity of a hot spring in Nayagarh district of Orissa. Both bulk soil from 0 to 30 cm depth and profile soils from 0 to 90 cm depth were analyzed for total fluoride (F_t) and 0.01 M CaCl₂ extractable fluoride (F_ca), major elements, pH, EC and Organic Carbon (OC). High concentrations of both F_t and F_ca were observed in the area surrounding the hot spring and the village of Singhpur. Principal factor analysis (PFA) on the parameters of the bulk soils suggests that two major chemical processes due to three factors, control the soil geochemistry of the area. Factor-1 contributes 37.11% of the total variance and is strongly loaded with Al, Si, Fe, F_tand F_ca, and explains the fluoride enrichment of the soil, whereas the second and the third factors contribute 16.6 and 12.2%, respectively and explain the controlling process of carbonate precipitation and soil alkalinity. Multiple regression analysis of the scores of the factors was performed to derive a fluoride contamination index in soil. The magnitude of the factor effect on the contamination index follows the order of Factor-1 > Factor-2 > Factor-3. The spatial distribution of the contamination index is used to classify the area into highly contaminated, moderately contaminated and uncontaminated zones.     

Small-scale genetic structure in the sea palm Postelsia palmaeformis Ruprecht (Phaeophyceae)

Documenting the scale of movement among populations is an important challenge for marine ecology. Using nine microsatellite markers, evidence of genetic structure in a marine kelp, the sea palm Postelsia palmaeformis Ruprecht, was examined in the vicinity of Cape Flattery, Washington state, USA (48° 24′ N, 124°44′ W). Genetic clustering analysis implemented without reference to geographic structure strongly suggested that a number of distinct genetic clusters existed among the 245 plants sampled in August in the years 1997–2001. Subsequent analysis showed that clustering was associated with geographically defined populations both among (km scale) and within (m scale) sampling sites. F _st analysis of geographically defined populations revealed significant genetic differentiation among populations of plants as little as 5 m apart, evidence of genetic structuring at even smaller scales, and a sharp increase in F _st across populations separated by up to 23 m. F _st values were also high and approximately unchanging (F _st=0.470) for populations separated by greater distances (up to 11 km), consistent with a scenario of rare dispersal by detached, floating plants carried by variable currents. The results corroborate natural history observations suggesting that P. palmaeformis has extremely short (1–3 m) spore dispersal distances, and indicate that the dynamics of sea palm populations are more affected by local processes than recruitment from distant populations.     

Estimating animal densities and home range in regions with irregular boundaries and holes: A lattice-based alternative to the kernel density estimator

Density estimates based on point processes are often restrained to regions with irregular boundaries or holes. We propose a density estimator, the lattice-based density estimator, which produces reasonable density estimates under these circumstances. The estimation process starts with overlaying the region with nodes, linking these together in a lattice and then computing the density of random walks of length k on the lattice. We use an approximation to the unbiased crossvalidation criterion to find the optimal walk length k. The technique is illustrated using walleye (Sander vitreus) radiotelemetry relocations in Lake Monroe, Indiana. We also use simulation to compare the technique to the traditional kernel density estimate in the situation where there are no significant boundary effects.     

Comparison between Hansen-Hurwitz and Horvitz-Thompson estimators for adaptive cluster sampling

Thompson (1990) introduced the adaptive cluster sampling design. This sampling design has been shown to be a useful sampling method for parameter estimation of a clustered and scattered population (Roesch, 1993; Smith et al., 1995; Thompson and Seber, 1996). Two estimators, the modified Hansen-Hurwitz (HH) and Horvitz-Thompson (HT) estimators, are available to estimate the mean or total of a population. Empirical results from previous researches indicate that the modified HT estimator has smaller variance than the modified HH estimator. We analytically compare the properties of these two estimators. Some results are obtained in favor of the modified HT estimator so that practitioners are strongly recommended to use the HT estimator despite easiness of computations for the HH estimator.     

Population genetics of the Antarctic heteronemertean Parbolasia corrugatus from the South Orkney Islands

An allozyme survey, using starch-gel electrophoresis, was carried out on eight populations of the Antarctic nemertean worm Parborlasia corrugatus (McIntosh, 1876) collected from locations around the South Orkney Islands, Antarctica. These populations were separated by distances in the order of tens of kilometres. Genetic variation was estimated over 22 enzyme loci for all populations examined, giving an observed heterozygosity of 0.142. This was much lower than the expected heterozygosity (H _e  = 0.201), and it was found that there was a significant deficiency of het‐erozygotes across four enzyme loci ( p ≤ 0.01). A more detailed examination of this deficiency of heterozygotes was undertaken for the six populations and six variable enzyme loci for which the most complete data sets existed. A significant deficiency of heterozygotes was found at the enzyme locus Odh-1 for four of the six populations examined ( p ≤ 0.01). Mean F _is (0.240) indicated a significant ( p ≤ 0.01) within-population component of the heterozygote deficiency estimated for the six populations sampled, and this was mainly due to the␣Ap-1, Odh-1 and Pgm-1 loci. The mean F _st value (0.036) was also significant ( p ≤ 0.01), indicating a degree of genetic differentiation between populations. The observed levels of genetic differentiation between populations of P. corrugatus and the significant heterozygote deficiencies were unexpected, because this species has been reported to have a long-lived planktotrophic larva. It is hypothesised that recruitment of P. corrugatus in the South Orkney Islands originates from genetically distinct populations located in the Weddell Sea and to the west of the Antarctic Peninsula. Shifts in the relative position of the Weddell Sea Front, Weddell–Scotia Confluence and Scotia Front, relative to the South Orkney Islands, provide a mechanism for variation in the origin of recruits over time. Received: 24 July 1997 / Accepted: 31 October 1997     

Allozyme and mitochondrial DNA evidence of population subdivision in the purple sea urchin Strongylocentrotus purpuratus

Despite high potential for dispersal, the purple sea urchin Strongylocentrotus purpuratus was found to have significant genetic subdivision among locations. Ten geographic locations along the coast of California and Baja California were sampled between 1994 and 1995. Samples from some locations included both adult and recruit urchins. Allozyme analyses revealed a genetic mosaic, where differentiation over short geographic distances could exceed differentiation over much larger distances. Significant allozyme differentiation was found among subpopulations of adults (standardized variance, F _ST =0.033), among subpopulations of recruits (F _ST =0.037), and between adults and recruits from the same location. DNA-sequence data for the mitochondrial cytochrome oxidase I gene also showed significant heterogeneity among locations, with a mild break in haplotype frequencies observed 300 km south of Point Conception. California. Repeated sampling over time is necessary to determine whether these patterns of differentiation are stable and to begin to understand what forces produce them.     

Estimation of abundance from presence–absence maps using cluster models

A presence–absence map consists of indicators of the occurrence or nonoccurrence of a given species in each cell over a grid, without counting the number of individuals in a cell once it is known it is occupied. They are commonly used to estimate the distribution of a species, but our interest is in using these data to estimate the abundance of the species. In practice, certain types of species (in particular flora types) may be spatially clustered. For example, some plant communities will naturally group together according to similar environmental characteristics within a given area. To estimate abundance, we develop an approach based on clustered negative binomial models with unknown cluster sizes. Our approach uses working clusters of cells to construct an estimator which we show is consistent. We also introduce a new concept called super-clustering used to estimate components of the standard errors and interval estimators. A simulation study is conducted to examine the performance of the estimators and they are applied to real data.     

Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals

Severely fragmented habitats increase the risk of extirpation of native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically altered landscapes can inform conservation. We used metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the wheat belt of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system. We investigated whether the localization of the iDNA signal reflected the predicted distribution of 4 native species—echidna (Tachyglossus aculeatus), numbat (Myrmecobius fasciatus), woylie (Bettongia penicillata), and chuditch (Dasyurus geoffroii)—and 2 non-native, invasive mammal species—fox (Vulpes vulpes) and feral cat (Felis catus). We collected bulk iDNA samples (n = 150 samples from 3428 carrion flies) at 3 time points from 3 conservation reserves and 35 road edges between them. We detected 14 of the 40 mammal species known from the region, including our target species. Most detections of target taxa were in conservation reserves. There were a few detections from road edges. We detected foxes and feral cats throughout the study area, including all conservation reserves. There was a significant difference between the diversity (F_3, 98 = 5.91, p < 0.001) and composition (F_3, 43 = 1.72, p < 0.01) of taxa detections on road edges and conservation reserves. Conservation reserves hosted more native biodiversity than road edges. Our results suggest that the signals from iDNA reflect the known distribution of target mammals in this region. The development of iDNA methods shows promise for future noninvasive monitoring of mammals. With further development, iDNA metabarcoding could inform decision-making related to conservation of endangered taxa, invasive species management, and impacts of habitat fragmentation.     

Intertype mark correlation function: A new tool for the analysis of species interactions

The spatial pattern of the different species in complex ecosystems reflects the underlying ecological processes. In this paper a second order moment function is proposed and tested to analyse the spatial distribution of a mark, which could be a tree characteristic such as diameter or height, between two different types of points, which could be two different tree species. The proposed function was a conditional density function based on the intertype K_rs(d) function, incorporating as test function the correlation of the marks between pairs composed of points of different types. The results obtained in simulated and real plots prove that the function is capable of revealing the scale at which spatial correlation of the mark between two types of points exists. The proposed function allows the spatial association between individuals of different species at different life stages to be identified. This analysis may reveal information on species ecology and interspecific interactions in forest ecosystems.     

Estimation of the CDF of a finite population in the presence of acalibration sample

We compare the performance of a number of estimators of the cumulative distribution function (CDF) for the following scenario: imperfect measurements are taken on an initial sample from afinite population and perfect measurements are obtained on a small calibration subset of the initial sample. The estimators we considered include two naive estimators using perfect and imperfect measurements; the ratio, difference and regression estimators for a two-phasesample; a minimum MSE estimator; Stefanski and Bay's SIMEX estimator (1996); and two proposed estimators. The proposed estimators take the form of a weighted average of perfect and imperfect measurements. They are constructed by minimizing variance among the class of weighted averages subject to an unbiasedness constraint. They differ in the manner of estimating the weight parameters. The first one uses direct sample estimates. The second one tunes the unknown parameters to an underlying normal distribution. We compare the root mean square error (RMSE) of the proposed estimator against other potential competitors through computer simulations. Our simulations show that our second estimator has the smallest RMSE among thenine compared and that the reduction in RMSE is substantial when the calibration sample is small and the error is medium or large.     

Semi-parametric Bayesian density estimation using ranked set sample in the presence of ranking error

In this paper, we propose a Bayesian method to estimate the underlying density function of a study variable Y using a ranked set sample in which an auxiliary variable X is used to rank the sampling units. The amount of association between X and Y is not known, resulting in an unknown degree of ranking error. We assume that (X, Y) follows a Morgenstern family of distributions. The study variable Y is assumed to have a parametric distribution, with the distribution of the parameters having a Dirichlet process prior. A Markov chain Monte Carlo procedure is developed to obtain a Bayesian estimator of the desired density function as well as of the ranking error. A simulation study is used to evaluate the performance of the proposed method. An example from forestry is used to illustrate a real-life application of the proposed methodology.     

Allozyme electrophoresis indicates high gene flow between populations of Holothuria (Microthele) nobilis (Holothuroidea: Aspidochirotida) on the Great Barrier Reef

 Genetic variation in 15 Holothuria (Microthele) nobilis (Selenka, 1867) populations on the Great Barrier Reef was studied at seven polymorphic allozyme loci. Although populations were separated by distances up to 1300 km, there were no apparent restrictions to gene flow (F _ST values were not significantly different from 0) and the maximum Nei's unbiased genetic distance was 0.003. Populations were in Hardy–Weinberg equilibrium at all loci. The estimated maximum sexual input [this is the ratio of the number of sexually produced individuals (N*) to the sample size (N _i )] and the minimum sexual input [this is the ratio of the number of genotypes (N _go ) over the sample size (N _i )] were used as estimators for the amount of asexual reproduction. Both parameters suggested that H. nobilis reproduces solely by sexual means (N*:N _i : = 1; N _go :N _i  = 0.74 to 1). The allozyme data indicated high gene flow between populations, but the possibility that allozyme frequencies may not be at equilibrium means that it was not possible to distinguish whether the patterns reflect present-day dispersal or dispersal that occurred in the past. Received: 27 March 2000 / Accepted: 29 June 2000     

The influence of contrasting life history traits and oceanic processes on genetic structuring of rabbitfish populations Siganus argenteus and Siganus fuscescens along the eastern Philippine coasts

Genetic variability and structuring of rabbitfish populations with contrasting life histories, Siganus argenteus and Siganus fuscescens were determined using allozyme analysis. A total of 13–14 polymorphic loci were examined from samples collected in 2002 and 2003 from eight reefs representing 25 populations north (Kuroshio Current) and south (Mindanao Current) of the bifurcation of the North Equatorial Current along the eastern Philippine coast. S. fuscescens populations (H _OBS = 0.085) showed higher heterozygosity than S. argenteus (H _OBS = 0.053), consistent with predictions of the neutral theory for demersal egg spawners compared to pelagic egg spawners. The generally lower genetic variability of Kuroshio populations may be due to greater environmental disturbance affecting larval mortality and recruitment success. There was no significant overall population genetic structuring for S. argenteus (F _ST = 0.01485, P > 0.05) compared to S. fuscescens (F _ST = 0.03275, P < 0.05). The latter species showed highly significant genetic structuring among Kuroshio and Mindanao Current populations in both 2002 and 2003 (F _CT = 0.08120, P < 0.05; F _CT = 0.07500, P < 0.05, respectively), as well as among populations within regions. This conforms to expectations of correlations between observed population genetic structure and life history features related to dispersal potential and gene flow. However, there were significant temporal (i.e., 2002 vs. 2003 samples) genetic variations for both S. fuscescens (F _CT = 0.08542, P < 0.05) and S. argenteus (F _CT = 0.06330, P < 0.05), which may reflect interannual variability in recruitment success. Differences in population spatial genetic patterns between the two reef fish species suggest that broad scale physical factors (e.g. NEC bifurcation) and regional environmental perturbations (e.g. incidence of typhoons) affect population genetic structure of sympatric congeneric species with different life histories differently. Finer scale ecological processes, which affect larval dispersal and recruitment (e.g., local hydrographic features, distribution of habitats), particularly in the Mindanao Current region, exert more influence on structuring populations of S. fuscescens.     

Regression models for some solute distribution equilibria in the terrestrial environment

Sorption coefficients (K_p) of several organochlorine insecticides (OCs) in volcanic ash silt from Central Java are presented.

Selected experimental and estimated octanol‐water partition coefficient (P) values are used to study log‐log regressions with K_p data collected from the literature (PAHs, chlorophenols, phenylureas, chloro‐s‐triazines, carbamates and organophosphorus insecticides) and those of the OCs determined in the present study. Leaching distances and bioactivities in soil are correlated with the K_p values of the pesticides, and with the organic matter and the water content of the soil.     

Diurnal measurements of F v/F m used to improve productivity estimates in macroalgae

The ratio of variable fluorescence to maximal fluorescence (F _v/F _m) was measured during a night and day cycle in five different macroalgae growing in the littoral zone at the Swedish west coast; the green algae Ulva lactuca, Cladophora sp. and Enteromorpha flexousa, the red alga Ceramium nodulosum and the brown alga Fucus vesiculosus. All the green algae and C. nodulosum showed both diurnal fluctuations in F _v/F _m during days of high light intensities and a significant negative correlation between F _v/F _m and photon irradiance (PI). An attempt has been made to improve calculations of macroalgal net growth based on carbon fixation (α_net) considering this diurnal change in F _v/F _m. By assuming that the negative linear correlation between F _v/F _m and the maximum quantum yield for photosynthesis (Φ) is proportional to that between F _v/F _m and α_net, it was possible to include the daily variation of α_net due to photoinhibition. To compensate for the variation of F _v/F _m, a representative value for each day was obtained by weighting all values of F _v/F _m over the diurnal period in relation to total PI. For all algal species there was a fairly good agreement between this representative value and the F _v/F _m value measured around noon. As the daily representative F _v/F _m value showed a negative linear correlation with the daily mean PI, it was possible to correct α_net for differences of daily mean PI. Received: 10 March 1997 / Accepted: 25 August 1997     

Genetic structure of a scleractinian coral, Mycedium elephantotus, in Taiwan

The genetic structure of Mycedium elephantotus (Pallas, 1766) populations from three regions around Taiwan was examined using allozyme electrophoresis. Eight loci were scored from seven enzyme systems. Seven loci were polymorphic under the 95% criterion. The high ratio of observed to expected genotypic diversities at the collection sites (G _O:G _E=0.8 to 1.0) indicate that M. elephantotus propagates predominantly by sexual reproduction. Allele frequencies of M. elephantotus differed significantly among regions (D=0.024 to 0.256, F _ST=0.032 to 0.218, p < 0.001), while populations among collection sites within each region were homogeneous (D=0.000 to 0.015, F _ST=0.010 to 0.022, p > 0.05). Genetic differentiation between populations from southern Taiwan and the Penghu Islands is greater than that between southern and northern Taiwan populations, although the former two regions are much closer geographically. The UPGMA dendrogram based on Nei's unbiased genetic distance showed a clear subdivision of populations into two groupings, northern Taiwan/Penghu Islands and southern Taiwan. A higher level of gene flow was found between M. elephantotus populations in northern Taiwan and the Penghu Islands (N _m=7.56) than that between populations in southern Taiwan and other regions (N _m=0.90 to 1.72). The pattern of genetic subdivision among regions is consistent with the pattern of ocean currents, indicating that genetic differentiation is likely driven by surface circulation vicariance. Received: 2 December 1997 / Accepted: 15 September 1998     

Late Pleistocene dispersal of Indian-Pacific sardine populations in an ancient lineage of the genusSardinops

Temperate sardines fall into two related monotypic genera,Sardina andSardinops. Sardina exists as a cluster of subpopulations in the northeastern Atlantic and Mediterranean, andSardinops encompasses five geographically-isolated regional populations: (1) South Africa-Namibia, (2) Australia-New Zealand, (3) Chile-Peru, (4) Mexico-California and (5) Japan-Russia. We surveyed electrophoretic variability in the products of 34 protein encoding loci inSardina (N=26) and the five Indian-Pacific populations ofSardinops (N=222), collected from 1983 to 1991. Nei's genetic distances () between samples ofSardina andSardinops averaged 1.04 and are typical of distances between species of related genera.s between the regional forms ofSardinops were <-0.011, indicating thatSardinops consists of a single species with widely-scattered subpopulations. Assuming a molecular clock calibrated by the rise of the Panama Isthmus and the opening of the Bering Strait, these genetic distances correspond to times since divergence of <200 000 yr. AlthoughSardinops populations showed a significant degree of allele-frequency heterogeneity (F _ST, a measure of population differentiation, averaged 0.085 over 8 polymorphic loci), the distribution of genetic distances and tests of allele-frequency heterogeneity could not distinguished between hypotheses of north-south antitropical or east-west oceanic dispersal. Low levels of gene diversity inSardinops and mutation-drift disequilibria are consistent with a strong reduction in population size before the Late Pleistocene dispersal to the corners of the Indian-Pacific Oceans of an ancestralSardinops population.