Optimal feature subset selection for neuron spike sorting using the genetic algorithm

It is crucial for a neuron spike sorting algorithm to cluster data from different neurons efficiently. In this study, the search capability of the Genetic Algorithm (GA) is exploited for identifying the optimal feature subset for neuron spike sorting with a clustering algorithm. Two important objectives of the optimization process are considered: to reduce the number of features and increase the clustering performance. Specifically, we employ a binary GA with the silhouette evaluation criterion as the fitness function for neuron spike sorting using the Super-Paramagnetic Clustering (SPC) algorithm. The clustering results of SPC with and without the GA-based feature selector are evaluated using benchmark synthetic neuron spike data sets. The outcome indicates the usefulness of the GA in identifying a smaller feature set with improved clustering performance.

Applying both positive and negative selection to supervised learning for anomaly detection

This paper presents a novel approach of applying both positive selection and negative selection to supervised learning for anomaly detection. It first learns the patterns of the normal class via co-evolutionary genetic algorithm, which is inspired from the positive selection, and then generates synthetic samples of the anomaly class, which is based on the negative selection in the immune system. Two algorithms about synthetic generation of the anomaly class are proposed. One deals with data sets containing a few anomalous samples; while the other deals with data sets containing no anomalous samples at all. The experimental results on some benchmark data sets from UCI data set repertory show that the detection rate is improved evidently, accompanied by a slight increase in false alarm rate via introducing novel synthetic samples of the anomaly class. The advantages of our method are the increased ability of classifiers in identifying both previously known and innovative anomalies, and the maximal degradation of overfitting phenomenon.

Variation of mohair staple length across Angora goat fleeces : implications for animal selection and fleece evaluation

The present study aimed to determine how the average mohair staple length (SL) differences between nine sampling sites vary between sex and flock, to identify differences in SL variability between sampling sites as a result of between-animal and between-sire variability and to determine SL correlations between sampling sites in between-animal and between-sire variability. Australian Angora goats (n=301) from two farms in southern Australia were sampled at 12 and 18 months of age at nine sites (mid side, belly, brisket, hind flank, hip, hock, mid back, neck and shoulder). Staples were taken prior to shearing at skin level and stretched SL determined. For each shearing, differences in SL between sampling sites, how these differences were affected by farm, sex and sire, and the covariance between sites for sire and individual animal effects were investigated by restricted maximum likelihood (REML) analyses. The median mid-side SL at 12 and 18 months of age was 110 and 130 mm, respectively, but the actual range in mid-side SL was 65–165 mm. There was an anterior–posterior decline in SL with the hock being particularly short. There was no evidence that the between-site correlation of the sire effects differed from 1, indicating that genetic selection for SL at one site will be reflected in SL over the whole fleece. However, low heritabilities of SL at the hock, belly and brisket or at any site at 12 months of age were obtained. There was more variability between sites than between sires, but the between-animal variation was greater. The hip and mid-back sites can be recommended for within-flock (culling) and genetic selection for SL due to their low sampling variability, moderate heritability and ease of location.

An embedded two-layer feature selection approach for microarray data analysis

Feature selection is an important technique in dealing with application problems with large number of variables and limited training samples, such as image processing, combinatorial chemistry, and microarray analysis. Commonly employed feature selection strategies can be divided into filter and wrapper. In this study, we propose an embedded two-layer feature selection approach to combining the advantages of filter and wrapper algorithms while avoiding their drawbacks. The hybrid algorithm, called GAEF (Genetic Algorithm with embedded filter), divides the feature selection process into two stages. In the first stage, Genetic Algorithm (GA) is employed to pre-select features while in the second stage a filter selector is used to further identify a small feature subset for accurate sample classification. Three benchmark microarray datasets are used to evaluate the proposed algorithm. The experimental results suggest that this embedded two-layer feature selection strategy is able to improve the stability of the selection results as well as the sample classification accuracy.

Multilocus phylogeography of Australian teals (Anas spp.) : a case study of the relationship between vagility and genetic structure

Biogeographic barriers potentially restrict gene flow but variation in dispersal or vagility can influence the effectiveness of these barriers among different species and produce characteristic patterns of population genetic structure. The objective of this study was to investigate interspecific and intraspecific genetic structure in two closely related species that differ in several life-history characteristics. The grey teal Anas gracilis is geographically widespread throughout Australia with a distribution that crosses several recognized biogeographic barriers. This species has high vagility as its extensive movements track broad-scale patterns in rainfall. In contrast, the closely related chestnut teal A. castanea is endemic to the mesic southeastern and southwestern regions of Australia and is more sedentary. We hypothesized that these differences in life-history characteristics would result in more pronounced population structuring in the chestnut teal. We sequenced five nuclear loci (nuDNA) for 49 grey teal and 23 chestnut teal and compared results to published mitochondrial DNA (mtDNA) sequences. We used analysis of molecular variance to examine population structure, and applied coalescent based approaches to estimate demographic parameters. As predicted, chestnut teal were more strongly structured at both mtDNA and nuDNA (ΦST= 0.163 and 0.054, respectively) than were grey teal (ΦST < 0.0001 for both sets of loci). Surprisingly, a greater proportion of the total genetic variation was partitioned among populations within species (ΦSC= 0.014 and 0.047 for nuDNA and mtDNA, respectively) than between the two species (ΦCT < 0.0001 for both loci). The ‘Isolation with Migration’ coalescent model suggested a late Pleistocene divergence between the taxa, but remarkably, a deeper divergence between the southeastern and southwestern populations of chestnut teal. We conclude that dispersal potential played a prominent role in the structuring of populations within these species and that divergent selection associated with ecology and life history traits likely contributed to rapid and recent speciation in this pair.

A genetic fuzzy system to model pedestrian walking path in a built environment

A study on the pedestrian's steering behaviour through a built environment in normal circumstances is presented in this paper. The study focuses on the relationship between the environment and the pedestrian's walking trajectory. Owing to the ambiguity and vagueness of the relationship between the pedestrians and the surrounding environment, a genetic fuzzy system is proposed for modelling and simulation of the pedestrian's walking trajectory confronting the environmental stimuli. We apply the genetic algorithm to search for the optimum membership function parameters of the fuzzy model. The proposed system receives the pedestrian's perceived stimuli from the environment as the inputs, and provides the angular change of direction in each step as the output. The environmental stimuli are quantified using the Helbing social force model. Attractive and repulsive forces within the environment represent various environmental stimuli that influence the pedestrian's walking trajectory at each point of the space. To evaluate the effectiveness of the proposed model, three experiments are conducted. The first experimental results are validated against real walking trajectories of participants within a corridor. The second and third experimental results are validated against simulated walking trajectories collected from the AnyLogic® software. Analysis and statistical measurement of the results indicate that the genetic fuzzy system with optimised membership functions produces more accurate and stable prediction of heterogeneous pedestrians' walking trajectories than those from the original fuzzy model. © 2014 Elsevier B.V. All rights reserved.

Building fuzzy inference systems with similarity reasoning : NSGAII-based fuzzy rule selection and evidential functions

In our previous investigations, two Similarity Reasoning (SR)-based frameworks for tackling real-world problems have been proposed. In both frameworks, SR is used to deduce unknown fuzzy rules based on similarity of the given and unknown fuzzy rules for building a Fuzzy Inference System (FIS). In this paper, we further extend our previous findings by developing (1) a multi-objective evolutionary model for fuzzy rule selection; and (2) an evidential function to facilitate the use of both frameworks. The Non-Dominated Sorting Genetic Algorithms-p (NSGA-p) is adopted for fuzzy rule selection, in accordance with the Pareto optimal criterion. Besides that, two new evidential functions are developed, whereby given fuzzy rules are considered as evidence. Simulated and benchmark examples are included to demonstrate the applicability of these suggestions. Positive results were obtained.

Is there evidence of selection in the dopamine receptor D4 gene in Australian invasive starling populations?

 Although population genetic theory is largely based on the premise that loci under study are selectively neutral, it has been acknowledged that the study of DNA sequence data under the influence of selection can be useful. In some circumstances, these loci show increased population differentiation and gene diversity. Highly polymorphic loci may be especially useful when studying populations having low levels of diversity overall, such as is often the case with threatened or newly established invasive populations. Using common starlings Sturnus vulgaris sampled from invasive Australian populations, we investigated sequence data of the dopamine receptor D4 gene (DRD4), a locus suspected to be under selection for novelty-seeking behaviour in a range of taxa including humans and passerine birds. We hypothesised that such behaviour may be advantageous when species encounter novel environments, such as during invasion. In addition to analyses to detect the presence of selection, we also estimated population differentiation and gene diversity using DRD4 data and compared these estimates to those from microsatellite and mitochondrial DNA sequence data, using the same individuals. We found little evidence for selection on DRD4 in starlings. However, we did find elevated levels of within-population gene diversity when compared to microsatellites and mitochondrial DNA sequence, as well as a greater degree of population differentiation. We suggest that sequence data from putatively nonneutral loci are a useful addition to studies of invasive populations, where low genetic variability is expected.

Variation at the DRD4 locus is associated with wariness and local site selection in urban black swans

 BACKGROUND: Interactions between wildlife and humans are increasing. Urban animals are often less wary of humans than their non-urban counterparts, which could be explained by habituation, adaptation or local site selection. Under local site selection, individuals that are less tolerant of humans are less likely to settle in urban areas. However, there is little evidence for such temperament-based site selection, and even less is known about its underlying genetic basis. We tested whether site selection in urban and non-urban habitats by black swans (Cygnus atratus) was associated with polymorphisms in two genes linked to fear in animals, the dopamine receptor D4 (DRD4) and serotonin transporter (SERT) genes.

RESULTS: Wariness in swans was highly repeatable between disturbance events (repeatability = 0.61) and non-urban swans initiated escape from humans earlier than urban swans. We found no inter-individual variation in the SERT gene, but identified five DRD4 genotypes and an association between DRD4 genotype and wariness. Individuals possessing the most common DRD4 genotype were less wary than individuals possessing rarer genotypes. As predicted by the local site selection hypothesis, genotypes associated with wary behaviour were over three times more frequent at the non-urban site. This resulted in moderate population differentiation at DRD4 (FST = 0.080), despite the sites being separated by only 30 km, a short distance for this highly-mobile species. Low population differentiation at neutrally-selected microsatellite loci and the likely occasional migration of swans between the populations reduces the likelihood of local site adaptations.

CONCLUSION: Our results suggest that wariness in swans is partly genetically-determined and that wary swans settle in less-disturbed areas. More generally, our findings suggest that site-specific management strategies may be necessary that consider the temperament of local animals.

The relative importance of spatial proximity, kin selection and potential ‘greenbeard’ signals on provisioning behaviour among helpers in a cooperative bird

© 2015 Springer-Verlag Berlin Heidelberg Many hypotheses have been proposed to account for cooperative behaviour, with those favouring kin selection receiving the greatest support to date. However, the importance of relatedness becomes less clear in complex societies where interactions can involve both kin and non-kin. To help clarify this, we examined the relative effect of indirect versus key direct benefit hypotheses in shaping cooperative decisions. We assessed the relative importance of likely reciprocal aid (as measured by spatial proximity between participants), kin selection (using molecular-based relatedness indices) and putative signals of relatedness (vocal similarity) on helper/helper cooperative provisioning dynamics in bell miners (Manorina melanophrys), a species living in large, complex societies. Using network analysis, we quantified the extent of shared provisioning (helping at the same nests) among individual helpers (excluding breeding pairs) over three seasons and 4290 provisioning visits, and compared these with the location of individuals within a colony and networks built using either genetic molecular relatedness or call similarity indices. Significant levels of clustering were observed in networks; individuals within a cluster were more closely related to each other than other colony members, and cluster membership was stable across years. The probability of a miner helping at another’s nest was not simply a product of spatial proximity and thus the potential for reciprocal aid. Networks constructed using helping data were significantly correlated to those built using molecular data in 5 of 10 comparisons, compared to 8 of 10 comparisons for networks constructed using call similarity. This suggests an important role of kinship in shaping helping dynamics in a complex cooperative society, apparently determined via an acoustic ‘greenbeard’ signal in this system.

Optimal ground control points for geometric correction using genetic algorithm with glboal accuracy

Establishing the ground control point (GCP) network is a pre-requisite for georeferencing raw image data. Given current typical digital spatial database quality, much interest among users is about the accuracy of the geometric correction model that yields the final product. This paper reports an approach to optimizing GCP assembly using a genetic/evolution algorithm. The paper also suggests an optimal criterion for accuracy assessment through appraisal of global accuracy of the transformation, which is computed at each point of the image space. Experimental results demonstrate that the proposed approach has a great potential for selection of the best GCPs, and considerable improvement to the accuracy of geometric correction models can be expected when it is implemented.

Selection on mitochondrial variants occurs between and within individuals in an expanding invasion

Mitochondria are critical for life, yet their underlying evolutionary biology is poorly understood. In particular, little is known about interaction between two levels of evolution: between individuals and within individuals (competition between cells, mitochondria or mitochondrial DNA molecules). Rapid evolution is suspected to occur frequently in mitochondrial DNA, whose maternal inheritance predisposes advantageous mutations to sweep rapidly though populations. Rapid evolution is also predicted in response to changed selection regimes after species invasion or removal of pathogens or competitors. Here, using empirical and simulated data from a model invasive bird species, we provide the first demonstration of rapid selection on the mitochondrial genome within individuals in the wild. Further, we show differences in mitochondrial DNA copy number associated with competing genetic variants, which may provide a mechanism for selection. We provide evidence for three rarely documented phenomena: selection associated with mitochondrial DNA abundance, selection on the mitochondrial control region, and contemporary selection during invasion.

Population genetic structuring in Acanthopagrus butcheri (Pisces: Sparidae): does low gene flow among estuaries apply to both sexes?

Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic divergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results; allozyme variation exhibited minimal spatial structuring (θ = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (θ = 0.263) and genetic divergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 individuals). Overall structuring of microsatellite variation was weaker (θ = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.

The colour of paternity: extra-pair paternity in the wild Gouldian finch does not appear to be driven by genetic incompatibility between morphs

In socially monogamous species, individuals can use extra-pair paternity and offspring sex allocation as adaptive strategies to ameliorate costs of genetic incompatibility with their partner. Previous studies on domesticated Gouldian finches (Erythrura gouldiae) demonstrated a genetic incompatibility between head colour morphs, the effects of which are more severe in female offspring. Domesticated females use differential sex allocation, and extra-pair paternity with males of compatible head colour, to reduce fitness costs associated with incompatibility in mixed-morph pairings. However, laboratory studies are an oversimplification of the complex ecological factors experienced in the wild, and may only reflect the biology of a domesticated species. This study aimed to examine the patterns of parentage and sex-ratio bias with respect to colour pairing combinations in a wild population of the Gouldian finch. We utilized a novel PCR assay that allowed us to genotype the morph of offspring before the morph phenotype develops, and to explore bias in morph paternity and selection at the nest. Contrary to previous findings in the laboratory, we found no effect of pairing combinations on patterns of extra-pair paternity, offspring sex ratio, or selection on morphs in nestlings. In the wild, the effect of morph incompatibility is likely much smaller, or absent, than was observed in the domesticated birds. Furthermore, the previously studied domesticated population is genetically differentiated from the wild population, consistent with the effects of domestication. It is possible that the domestication process fostered the emergence (or enhancement) of incompatibility between colour morphs previously demonstrated in the laboratory.

Colour polymorphism is likely to be disadvantageous to some populations and species due to genetic architecture and morph interactions

Polymorphism describes two or more distinct, genetically determined, phenotypes that co-occur in the same population, where the rarest morph is maintained at a frequency above the mutation rate (Ford 1945; Huxley 1955). In a recent opinion piece, we explored a new idea regarding the role of genetic architectures and morph interactions in colour polymorphisms and how this can negatively affect population performance (Bolton et al. 2015). In this issue of Molecular Ecology, Forsman (2016) thoroughly discusses the current evidence for polymorphisms enhancing population performance and critiques the validity of the definitions of polymorphism we use in our original paper. We respond by clarifying that the negative consequences of polymorphisms that we discussed are likely to be most pertinent in species that have a particular set of characteristics, such as strong sexual or social interactions between morphs and discrete genetic architectures. Although it was not our intention to redefine polymorphism, we do believe that there should be further discussion about refining or characterizing balanced polymorphisms with respect to the degree of morph sympatry, discreteness of traits and their underlying genetic architecture, and the types of selection that drive and maintain the variation. The latter describes whether polymorphism is primarily maintained by external factors such as predation pressure or internal factors such as interactions with members of the same species. The contribution of Forsman (2016) is useful to this discussion, and we hope that our exchange of opinions will inspire new empirical and theoretical ideas on the origin and maintenance of colour polymorphisms.