An extravariation model for improving confidence intervals of population size estimates from removal data

We propose a new model for estimating the size of a population from successive catches taken during a removal experiment. The data from these experiments often have excessive variation, known as overdispersion, as compared with that predicted by the multinomial model. The new model allows catchability to vary randomly among samplings, which accounts for overdispersion. When the catchability is assumed to have a beta distribution, the likelihood function, which is refered to as beta-multinomial, is derived, and hence the maximum likelihood estimates can be evaluated. Simulations show that in the presence of extravariation in the data, the confidence intervals have been substantially underestimated in previous models (Leslie-DeLury, Moran) and that the new model provides more reliable confidence intervals. The performance of these methods was also demonstrated using two real data sets: one with overdispersion, from smallmouth bass (Micropterus dolomieu), and the other without overdispersion, from rat (Rattus rattus).

Size-dependent melting of nanoparticles: Hundred years of thermodynamic model

Thermodynamic model first published in 1909, is being used extensively to understand the size-dependent melting of nanoparticles. Pawlow deduced an expression for the size-dependent melting temperature of small particles based on the thermodynamic model which was then modified and applied to different nanostructures such as nanowires, prism-shaped nanoparticles, etc. The model has also been modified to understand the melting of supported nanoparticles and superheating of embedded nanoparticles. In this article, we have reviewed the melting behaviour of nanostructures reported in the literature since 1909.

Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei

Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (FST = 0· 09 − 0· 49; P < 0· 05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.

Raw data for "Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson)."

Abstract of Macbeth, G. M., Broderick, D., Buckworth, R. & Ovenden, J. R. (In press, Feb 2013). Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson). G3: Genes, Genomes and Genetics. Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. But, pitfalls are predicted when the effective size is large, as estimates require large numbers of samples from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with sample sizes around 5000. This was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest standard deviation of Ne estimates occurred when low frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or non-breeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were above 24,000.

NEESTIMATOR v2: re-implementation of software for the estimation of contemporary effective population size (N-e) from genetic data

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

Behavioural, population, and genetic processes affecting metapopulation dynamics of the Glanville fritillary butterfly

In my thesis I have been studying the effects of population fragmentation and extinction-recolonization dynamics on genetic and evolutionary processes in the Glanville fritillary butterfly (Melitaea cinxia). By conducting crosses within and among newly-colonized populations and using several fitness measures, I found a strong decrease in fitness following colonization by a few related individuals, and a strong negative relationship between parental relatedness and offspring fitness. Thereafter, I was interested in determining the number and relatedness of individuals colonizing new populations, which I did using a set of microsatellites I had previously developed for this species. Additionally, I am interested in the evolution of key life-history traits. By following the lifetime reproductive success of males emerging at different times in a semi-natural setup, I demonstrated that protandry is adaptive in males, and I was able to rule out, for M. cinxia, alternative incidental hypotheses evoked to explain the evolution of protandry in insects. Finally, in work I did together with Prof. Hanna Kokko, I am proposing bet-hedging as a new mechanism that could explain the evolution of polyandry in M. cinxia.

Size-dependent magnetic properties of iron carbide nanoparticles embedded in a carbon matrix

Here we report on the magnetic properties of iron carbide nanoparticles embedded in a carbon matrix. Granular distributions of nanoparticles in an inert matrix, of potential use in various applications, were prepared by pyrolysis of organic precursors using the thermally assisted chemical vapour deposition method. By varying the precursor concentration and preparation temperature, compositions with varying iron concentration and nanoparticle sizes were made. Powder x-ray diffraction, transmission electron microscopy and Mossbauer spectroscopy studies revealed the nanocrystalline iron carbide (Fe3C) presence in the partially graphitized matrix. The dependence of the magnetic properties on the particle size and temperature (10 K < T < 300 K) were studied using superconducting quantum interference device magnetometry. Based on the affect of surrounding carbon spins, the observed magnetic behaviour of the nanoparticle compositions, such as the temperature dependence of magnetization and coercivity, can be explained.

Size-Dependent Melting of Finite-Length Nanowires

We report on the size-dependent melting of nanowires with finite length based on the thermodynamic as well as liquid drop model. It has been inferred that the length dependency cannot be ignored, unlike the case of infinite length nanowires. To validate the length dependency, we have analyzed a few experimental results reported in the literature.

Size-Dependent Tuning of Mn2+ d Emission in Mn2+-Doped CdS Nanocrystals: Bulk vs Surface

We show that the characteristic Mn2+ d emission color from Mn2+-doped CdS nanocrystals can be tuned over as much as 40 nm, in contrast to what should be expected from such a nearly localized d-d transition. This is achieved surprisingly by a fine-tuning of the host particle diameter from 1.9 to 2.6 nm, thereby changing the overall emission color from red to yellow. Systematic experiments in conjunction with state-of-the-art ab initio calculations with full geometry optimization establish that Mn2+ ions residing at surface/subsurface regions have a distorted tetrahedral coordination resulting in a larger ligand field splitting. Consequently, these near-surface Mn2+ species exhibit a lower Mn2+ d emission energy, compared to those residing at the core of the nanocrystal with an undisturbed tetrahedral coordination. The origin of the tunability of the observed Mn2+ emission is the variation of emission contributions arising from Mn2+ doped at the core, subsurface, and surface of the host. Our findings provide a unique and easy method to identify the location of an emitting Mn2+ ion in the nanocrystal, which would be otherwise very difficult to decipher.

Ions in water: Role of attractive interactions in size dependent diffusivity maximum

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations-with and without dispersion interaction-between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect. (C) 2010 American Institute of Physics. doi:10.1063/1.3481656]

Size-dependent cohesive energy and melting of non-spherical nanoparticles

All most all theoretical models assume spherical nanoparticles. However, thermodynamic properties of non-spherical nanoparticles are the subject of recent interests. In this article, we have discussed the size-dependent cohesive energy and melting of non-spherical nanoparticles based on liquid-drop model. The surface to volume ratio is different for different shapes of nanoparticles and as a consequence, the variation of cohesive energy and melting of non-spherical nanoparticles is different from that of spherical case. By analyzing the reported experimental results, it has been observed that liquid-drop model can be used to understand the size-dependent cohesive energy and melting of non-spherical nanoparticles.

Size dependent microstructure for Ag-Ni nanoparticles

The Ag-Ni system is characterized by large differences in atomic sizes (14%) and a positive heat of mixing (+23 kJ mol(-1)). The binary equilibrium diagram for this system therefore exhibits a large miscibility gap in both solid and liquid state. This paper explores the size-dependent changes in microstructure and the suppression of the miscibility gap which occurs when free alloy particles of nanometer size are synthesized by co-reduction of Ag and Ni metal precursors. The paper reports that complete mixing between Ag and Ni atoms could be achieved for smaller nanoparticles (<7 nm). These particles exhibit a single-phase solid solution with face-centered cubic (fcc) structure. With increase in size, the nanoparticles revealed two distinct regions. One of the regions is composed of pure Ag. This region partially surrounds a region of fcc solid solution at an early stage of decomposition. Experimental observations were compared with the results obtained from the thermodynamic calculations, which compared the free energies corresponding to a physical mixture of pure Ag and Ni phases and a fcc Ag-Ni solid solution for different particle sizes. Results from the theoretical calculations revealed that, for the Ag-Ni system, solid solution was energetically preferred over the physical mixture configuration for particle sizes of 7 nm and below. The experimentally observed two-phase microstructure for larger particles was thus primarily due to the growth of Ag-rich regions epitaxially on initially formed small fcc Ag-Ni nanoparticles. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Size dependent bandgap of molecular beam epitaxy grown InN quantum dots measured by scanning tunneling spectroscopy

InN quantum dots (QDs) were grown on Si (111) by epitaxial Stranski-Krastanow growth mode using plasma-assisted molecular beam epitaxy. Single-crystalline wurtzite structure of InN QDs was verified by the x-ray diffraction and transmission electron microscopy. Scanning tunneling microscopy has been used to probe the structural aspects of QDs. A surface bandgap of InN QDs was estimated from scanning tunneling spectroscopy (STS) I-V curves and found that it is strongly dependent on the size of QDs. The observed size-dependent STS bandgap energy shifts with diameter and height were theoretical explained based on an effective mass approximation with finite-depth square-well potential model.

Efficiency enhancement in DSSC using metal nanoparticles: A size dependent study

The photoelectrode of Eosin-Y sensitised DSSC was modified by incorporating Au-nanoparticles to enhance the power conversion efficiency via scattering from surface plasmon polaritons. Size dependence of Au nanoparticle on conversion efficiency was performed in DSSC for the first time by varying the particle size from 20 to 94 nm. It was found that, the conversion efficiency is highly dependent on the size of the Au nanoparticles. For larger particles (>50 nm), the efficiency was found to be increased due to constructive interference between the transmitted and scattered waves from the Au nanoparticle while for smaller particles, the efficiency decreases due to destructive interference. Also a reduction in the V-oc was observed in general, due to the negative shifting of the TiO2 Fermi level on the adsorption of Au nanoparticle. This shift was negligible for larger particles. When 94 nm size particles were employed the conversion efficiency was doubled from 0.74% to 1.52%. This study points towards the application of the scattering effect of metal nanoparticle to enhance the conversion efficiency in DSSCs. (C) 2011 Elsevier Ltd. All rights reserved.