dropout: a program to identify problem loci and samples for noninvasive genetic samples in a capture‐mark‐recapture framework

Abstract Genotyping error, often associated with low‐quantity/quality DNA samples, is an important issue when using genetic tags to estimate abundance using capture‐mark‐recapture (CMR). dropout , an MS‐Windows program, identifies both loci and samples that likely contain errors affecting CMR estimates. dropout uses a ‘bimodal test’, that enumerates the number of loci different between each pair of samples, and a ‘difference in capture history test’ (DCH) to determine those loci producing the most errors. Importantly, the DCH test allows one to determine that a data set is error‐free. dropout has been evaluated in McKelvey & Schwartz (2004) and is now available online.     

genecap: a program for analysis of multilocus genotype data for non‐invasive sampling and capture‐recapture population estimation

We created genecap to facilitate analysis of multilocus genotype data for use in non‐invasive DNA sampling and genetic capture‐recapture studies. genecap is a Microsoft excel macro that uses multilocus genetic data to match samples with identical genotypes, calculate frequency of alleles, identify sample genotypes that differ by one and two alleles, calculate probabilities of identity, and match probabilities for matching samples. genecap allows the user to include background data and samples with missing genotypes for multiple loci. Capture histories for each user‐defined sampling period are output in formats consistent with commonly employed population estimation programs.     

Assessment of individual and conspecific reproductive success as determinants of breeding dispersal of female tree swallows: A capture–recapture approach

Breeding dispersal is a key process of population structure and dynamics and is often triggered by an individual's breeding failure. In both colonial and territorial birds, reproductive success of conspecifics (RSc) can also lead individuals to change breeding sites after a failure on a site. Yet, few studies have simultaneously investigated the independent contribution of individual reproductive success (RSi) and of RSc on dispersal decision. Here, we develop a modeling framework to disentangle the effects of RSi and RSc on demographic parameters, while accounting for imperfect individual detection and other confounding factors such as age or dispersal behavior in the previous year. Using a 10‐year capture–recapture dataset composed of 1,595 banded tree swallows, we assessed the effects of nonmanipulated RSi and RSc on female breeding dispersal in this semicolonial passerine. Dispersal was strongly driven by RSi, but not by RSc. Unsuccessful females were 9.5–2.5 times more likely to disperse than successful ones, depending if they had dispersed or not in the previous year, respectively. Unsuccessful females were also three times less likely to be detected than successful ones. Contrary to theoretical and empirical studies, RSc did not drive the decision to disperse but influenced the selection of the following breeding site once dispersal had been initiated. Because detection of individuals was driven by RSi, which was positively correlated to RSc, assuming a perfect detection as in previous studies may have lead us to conclude that RSc affected dispersal patterns, yet our approach corrected for this bias. Overall, our results suggest that the value and use of RSc as public information to guide dispersal decisions are likely dictated by multiple ecological determinants, such as landscape structure and extent, if this cue is indeed used.     

Long‐term mark‐and‐recapture study of a freshwater mussel reveals patterns of habitat use and an association between survival and river discharge

相似文献   

Nest‐site fidelity in parental male bluegill Lepomis macrochirus: spatial patterns and the influence of prior mating success

A 4 year mark–recapture study examined the pattern of nesting site fidelity of parental‐type male bluegill Lepomis macrochirus. The study results indicated that iteroparous male L. macrochirus choose new nest sites near their own previously used sites. The scale of site fidelity varied, but generally males choose to renest within shoreline areas rather than specific or exact nest locations (94% within‐year, 86% among‐years). Iteroparous males also displayed no preference to nest in proximity to neighbouring males from previous colonies to suggest social fidelity. Contrary to expectation, manipulating males' reproductive success had no significant effect on the pattern or scale of male reproductive site fidelity.     

Linking hydrological,geomorphological and biological properties in hyper‐arid conditions: Distribution processes of a dominant clonal cactus by run‐off

The objective was to analyse the asexual spread of Tephrocactus aoracanthus (Cactaceae) related to run‐off triggered by torrential summer rains in a hyper‐arid desert. Through a manipulative essay, 30 joints (asexual dispersing stems) were placed in the mainstream of an alluvial fan and 30 joints out of the alluvial fan, without run‐off influence (control). All joints were labelled, and their weight and diameter were measured. After each rain event with run‐off, joints were surveyed identifying their spatial coordinates and environmental context. For this, two factors with two levels each one was selected: position respect to both microrelief (channels with concentrated run‐off, or inter‐channels as flat areas between channels, without run‐off) and vegetation (entangled or not entangled in shrubs). Through a geographic information system, changes in slope angle and rugosity of terrain were analysed. Linear regressions were performed between the partial displacement of joints and their weight and diameter, grouped according to environmental context before each rainfall. None of the joints of the control treatment were moved, but all joints located in the mainstream were relocated. Three rainfall events triggered a mean displacement of 480.4 ± 210.0 m (SD); 103.0 ± 138.9 m (SD) and 33.2 ± 52.3 m (SD), respectively. The mean accumulated displacement of all joints during the experience was 577.12 ± 220.0 m (SD). As they moved, the joints passed through several different environmental contexts, increasing the proportion of joints entangled in vegetation and in inter‐channel position. Until rooted, joints could be displaced by run‐off in an anisotropic process, with an evident effect of slope angle and rugosity of terrain. On the other hand, no direct relationship was found between the displacement and the magnitude of the event, or both the size and the weight of joints. We assess the strategies related to the dispersal mechanism of clonal plants, related to conditions and enabling its agamic dispersal over long distances.     

Seed dispersal by lizards on a continental‐shelf island: predicting interspecific variation in seed rain based on plant distribution and lizard movement patterns

Aim We estimated the patterns of seed deposition provided by the eyed lizard, Timon lepidus, and evaluated whether these patterns can be generalized across plant species with different traits (fruit and seed size) and spatial distributions. Location Monteagudo Island, Atlantic Islands National Park (north‐western Spain). Methods We radio‐tracked seven lizards for 14 days and estimated their home ranges using fixed kernels. We also geo‐referenced all fruit‐bearing individuals of four plant species dispersed by eyed lizards in the study area (Corema album, Osyris alba, Rubus ulmifolius and Tamus communis), measured the passage time of their seeds through the lizard gut, and estimated seed predation in four habitats (bare sand, grassland, shrub and gorse). Seed dispersal kernels were estimated using a combination of these data and were combined with seed predation probability maps to incorporate post‐dispersal seed fate (‘seed survival kernels’). Results Median seed gut‐passage times were around 52–98 h, with maximum values up to 250 h. Lizards achieved maximum displacement in their home ranges within 24–48 h. Seed predation was high (80–100% of seeds in 2 months), particularly under Corema shrub and gorse. Seed dispersal kernels showed a common pattern, with two areas of preferential seed deposition, but the importance of these varied among plant species. Interspecific differences among dispersal kernels were strongly reduced by post‐dispersal seed predation; hence, seed survival kernels of the different plant species showed high auto‐ and pairwise‐correlations at small distances (< 50 m). As a result, survival to post‐dispersal seed predation increased with dispersal distance for O. alba and T. communis, but not for C. album. Main conclusions Seed dispersal by lizards was determined primarily by the interaction between the dispersers’ home ranges and the position of the fruit‐bearing plants. As a result, seed rain shared a common template, but showed considerable variation among species, determined by their specific spatial context. Seed predation increased the spatial coherence of the seed rain of the different species, but also resulted in contrasting relationships between seed survival and dispersal distance, which may be of importance for the demographic and evolutionary processes of the plants.     

Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait‐based phylogeographic approach

Hypotheses to explain phylogeographic structure traditionally invoke geographic features, but often fail to provide a general explanation for spatial patterns of genetic variation. Organisms' intrinsic characteristics might play more important roles than landscape features in determining phylogeographic structure. We developed a novel comparative approach to explore the role of ecological and life‐history variables in determining spatial genetic variation and tested it on frog communities in Panama. We quantified spatial genetic variation within 31 anuran species based on mitochondrial DNA sequences, for which hierarchical approximate Bayesian computation analyses rejected simultaneous divergence over a common landscape. Regressing ecological variables, on genetic divergence allowed us to test the importance of individual variables revealing that body size, current landscape resistance, geographic range, biogeographic origin and reproductive mode were significant predictors of spatial genetic variation. Our results support the idea that phylogeographic structure represents the outcome of an interaction between organisms and their environment, and suggest a conceptual integration we refer to as trait‐based phylogeography.     

Recognition of silver nanoparticles surface‐adsorbed citrate anions by macrocyclic polyammonium cations: a spectrophotometric approach to study aggregation kinetics and evaluation of association constant

In this report, we have studied the recognition of citrate anions adsorbed on the surface of silver nanoparticles (cit‐Ag‐NPs), by macrocyclic polyammonium cations (MCPACs): Me₆[14]ane‐N₄H₈⁴⁺ (Tet‐A/Tet‐B cations) and [32]ane‐N₈H₁₆⁸⁺, which are well reputed anion recognizers and are treated as to mimic of biological polyamines. The study was monitored on ultraviolet–visible spectroscopy by performing a titration of the aqueous dispersion of the cit‐Ag‐NPs by the aqueous solution of MCPACs. The ultraviolet–visible time‐scan plots over the reduction of the absorption band of surface plasmon resonance of cit‐Ag‐NPs at 390 nm are well fitted with fourth‐order polynomial equation and are employed to determine the initial aggregation rate constants. It has been stated that the aggregation is the result in electrostatic attraction followed by H‐bond formation between the surface‐adsorbed citrate anions and added MCPACs. The atomic force microscopy results have evidenced aggregation of cit‐Ag‐NPs in presence of MCPACs. The evaluated H‐bonded association constant (K_asso) using Benesi–Hildebrand method reveals that [32]ane‐N₈H₁₆⁸⁺ cations form stronger association complex, as expected, with the citrate anions than the Me₆[14]ane‐N₄H₈⁴⁺ cations. The study would thus provide the insight of molecular interactions involved in nanoparticle surface‐adsorbed anions with biological polyamines. Copyright © 2016 John Wiley & Sons, Ltd.     

Synthesis of ZnSe and ZnSe:Cu quantum dots by a room temperature photochemical (UV‐assisted) approach using Na2SeO3 as Se source and investigating optical properties

In this study, ZnSe and ZnSe:Cu quantum dots (QDs) were synthesized using Na₂SeO₃ as the Se source by a rapid and room temperature photochemical (UV‐assisted) approach. Thioglycolic acid (TGA) was employed as the capping agent and UV illumination activated the chemical reactions. Synthesized QDs were successfully characterized using X‐ray diffraction (XRD), transmission electron microscopy (TEM), photoluminescence (PL) and UV–visible (UV–vis) spectroscopy, Fourier transform‐infrared (FT‐IR), and energy dispersive X‐ray spectroscopy (EDX). XRD analysis demonstrated the cubic zinc blend phase QDs. TEM images indicated that round‐shaped particles were formed, most of which had a diameter of about 4 nm. The band gap of the ZnSe QDs was higher than that for ZnSe in bulk. PL spectra indicated an emission with three peaks related to the excitonic, surface trap states and deep level (DL) states. The band gap and QD emission were tunable only by UV illumination time during synthesis. ZnSe:Cu showed green emission due to transition of electrons from the Conduction band (CB) or surface trap states to the ²T₂ acceptor levels of Cu²⁺. The emission was increased by increasing the Cu²⁺ ion concentration, such that the optimal value of PL intensity was obtained for the nominal mole ratio of Cu:Zn 1.5%.