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PubMed2003

On the accurate counting of tumor cells.

Quantitative analysis of tumor cells is fundamental to pathological studies. Current practices are mostly manual, time-consuming, and tedious, yielding subjective and imprecise results. To understand the behavior of tumor cells, it is critical to have an objective way to count these cells. In addition, these counts must be reproducible and independent of the person performing the count. In this work, we propose a two-stage tumor cell identification strategy. In the first stage, potential tumor cells are segmented automatically using local adaptive thresholding and dynamic water immersion techniques. Unfortunately, due to histological noise in the images, a large number of false identifications are obtained. To improve the accuracy of the identified tumor cells, a second stage of feature rules mining is initiated. Experiment results show that image processing techniques alone are unable to give accurate results for tumor cell counting. However, with the use of features rules, we are able to achieve an identification accuracy of 94.3%.

Algorithms↗
PubMed2006

Implementing online natural gradient learning: problems and solutions.

The online natural gradient learning is an efficient algorithm to resolve the slow learning speed and poor performance of the standard gradient descent method. However, there are several problems to implement this algorithm. In this paper, we proposed a new algorithm to solve these problems and then compared the new algorithm with other known algorithms for online learning, including Almeida-Langlois-Amaral-Plakhov algorithm (ALAP), Vario-eta, local adaptive learning rate and learning with momentum etc., using sample data sets from Proben1 and normalized handwritten digits, automatically scanned from envelopes by the U.S. Postal Services. The strong and weak points of these algorithms were analyzed and tested empirically. We found out that using the online training error as the criterion to determine whether the learning rate should be changed or not is not appropriate and our new algorithm has better performance than other existing online algorithms.

Algorithms↗
PubMed2006

A texture-based method for modeling the background and detecting moving objects.

This paper presents a novel and efficient texture-based method for modeling the background and detecting moving objects from a video sequence. Each pixel is modeled as a group of adaptive local binary pattern histograms that are calculated over a circular region around the pixel. The approach provides us with many advantages compared to the state-of-the-art. Experimental results clearly justify our model.

Algorithms↗
PubMed2000

Outbreeding depression varies among cohorts of Ipomopsis aggregata planted in nature.

Outbreeding depression in progeny fitness may arise from disruption of local adaptation, disruption of allelic coadaptation, or a combination of these "environmental" and "physiological" mechanisms. Thus the minimum spatial scale over which outbreeding depression arises should depend on the spatial scale of gene dispersal and (with an environmental mechanism) of change in selection regimes. We previously reported substantial outbreeding depression in lifetime fitness of progeny resulting from crosses among parents separated by 100 m in natural populations of the herbaceous plant Ipomopsis aggregata. In this paper we explore the effect of crossing distance on fitness in two additional experiments begun in 1987 and 1990. We planted seed progeny derived from partial diallel crossing designs in randomized blocks in maternal environments and scored emergence of seedlings, survival, and eventual flowering of individuals over the subsequent six to eight years. Nested within each diallel design were crossing distances of 1 m, 10 m, and 100 m. Compared to 1-m and 10-m progeny, 100-m progeny of the 1987 diallel suffered a significant reduction in seedling emergence, and both 1-m and 100-m progeny that survived to flower achieved lower lambda-values on average than 10-m progeny. Total outbreeding depression suffered by 100-m relative to 10-m progeny was approximately 10%, compared to approximately 30% in our earlier study of I. aggregata. Progeny of 10-m crosses also outperformed 1-m and 100-m progeny of the 1990 diallel by approximately 5%, but no difference among crossing distance treatments was significant. Thus, the magnitude of outbreeding depression in 100-m crosses varied among experiments. This is not surprising given likely spatial and temporal variation in gene flow and selection regimes, different population histories, and different parental and progeny environments. Characterizing outbreeding depression on the shortest spatial scales over which it is expressed, as well as its variation and causes, is worthwhile because it promises to shed light on the earliest stages of angiosperm speciation.

Breeding↗
PubMed2000

Taxon sampling, correlated evolution, and independent contrasts.

Independent contrasts are widely used to incorporate phylogenetic information into studies of continuous traits, particularly analyses of evolutionary trait correlations, but the effects of taxon sampling on these analyses have received little attention. In this paper, simulations were used to investigate the effects of taxon sampling patterns and alternative branch length assignments on the statistical performance of correlation coefficients and sign tests; "full-tree" analyses based on contrasts at all nodes and "paired-comparisons" based only on contrasts of terminal taxon pairs were also compared. The simulations showed that random samples, with respect to the traits under consideration, provide statistically robust estimates of trait correlations. However, exact significance tests are highly dependent on appropriate branch length information; equal branch lengths maintain lower Type I error than alternative topological approaches, and adjusted critical values of the independent contrast correlation coefficient are provided for use with equal branch lengths. Nonrandom samples, with respect to univariate or bivariate trait distributions, introduce discrepancies between interspecific and phylogenetically structured analyses and bias estimates of underlying evolutionary correlations. Examples of nonrandom sampling processes may include community assembly processes, convergent evolution under local adaptive pressures, selection of a nonrandom sample of species from a habitat or life-history group, or investigator bias. Correlation analyses based on species pairs comparisons, while ignoring deeper relationships, entail significant loss of statistical power and as a result provide a conservative test of trait associations. Paired comparisons in which species differ by a large amount in one trait, a method introduced in comparative plant ecology, have appropriate Type I error rates and high statistical power, but do not correctly estimate the magnitude of trait correlations. Sign tests, based on full-tree or paired-comparison approaches, are highly reliable across a wide range of sampling scenarios, in terms of Type I error rates, but have very low power. These results provide guidance for selecting species and applying comparative methods to optimize the performance of statistical tests of trait associations.

Biological Evolution↗
PubMed2001

The importance of sexual and asexual reproduction in the recent evolution of Allium vineale.

In the weedy plant species Allium vineale (wild garlic), individuals may simultaneously produce sexually and asexually derived offspring, by seed and bulbils, respectively. In this study, genetic and genotypic diversity was determined in samples from 14 European A. vineale populations using nuclear (RAPD) and cytoplasmic (PCR-RFLP of cpDNA) markers to investigate the importance of the different reproductive modes. In the whole sample, 77 nuclear multilocus genotypes and four chloroplast haplotypes (chlorotypes) were found. Populations exhibited a high degree of subdivision for nuclear and cytoplasmic markers as estimated from hierarchical F-statistics; at the same time, identical chlorotypes could be found in populations separated by large distances. Genotypic diversity was significantly lower than expected under free recombination in almost all populations, indicating that recruitment into populations is mostly by asexually produced offspring. Nevertheless, within each chlorotype, the distribution of markers from pairs of nuclear loci was incompatible with a purely clonal structure, suggesting that many multilocus genotypes have originated by sexual recombination rather than by mutation within asexual lineages. It is argued that the weedy habit of A. vineale is likely to have favored bulbil reproduction, whereas sexually generated genotypes may have facilitated local adaptation during the species' expansion across Europe.

Allium↗
PubMed2001

Female choice via indicator traits easily evolves in the face of recombination and migration.

Species that exist in heterogeneous environments experience selection for specialization that is opposed by the homogenizing forces of migration and recombination. Migration tends to reduce associations between alleles and habitats, whereas recombination tends to break down associations among loci. The idea that heterogeneity should favor the evolution of isolating mechanisms has motivated evolutionary studies of reduced migration, habitat preference, and assortative mating. However, costly female choice of high-quality males can also evolve in heterogeneous populations and is not hindered by either recombination or migration. When information on male fitness is available through indicator traits, female choice based on these traits increases associations between female choice alleles and locally adapted alleles. Not only does female choice evolve in a heterogeneous environment, it acts to enhance the level of genetic variation and is thus self-reinforcing. The amount of female choice at equilibrium depends on how well mixed the habitats are, how much information on male genotype is available, and how different the habitats are. Female choice reaches the highest levels for intermediate levels of heterogeneity, because at such levels of heterogeneity there is both a high risk and high cost of mismating.

Alleles↗
PubMed2001

Divergent evolution of dispersal in a heterogeneous landscape.

The evolution of dispersal is investigated in a landscape of many patches with fluctuating carrying capacities and spatial heterogeneity in temporal fluctuations. Although asynchronous temporal fluctuations select for dispersal, spatial heterogeneity in the distribution of fluctuating environmental variables selects against it. We find evolutionary branching in dispersal rate leading to the evolutionarily stable coexistence of a high- and a low-dispersal phenotype. We study how the opposing forces of selection for and against dispersal change with the relative size and the environmental qualities of the source and sink habitats. Our results suggest that the evolution of dispersal dimorphism could be a first step towards speciation and local adaptation.

Animals↗
PubMed2001

The role of introgressive hybridization in the evolution of the Gila robusta complex (Teleostei: Cyprinidae).

The extent and impact of introgressive hybridization was examined in the Gila robusta complex of cyprinid fishes using mitochondrial DNA (mtDNA) sequence variation. Lower Colorado River basin populations of G. robusta, G. elegans, and G. cypha exhibited distinct mtDNAs, with only limited introgression of G. elegans into G. cypha. The impact of hybridization was significant in upper Colorado River basin populations; most upper basin fishes sampled exhibited only G. cypha mtDNA haplotypes, with some individuals exhibiting mtDNA from G. elegans. The complete absence of G. robusta mtDNA, even in populations of morphologically pure G. robusta, indicates extensive introgression that predates human influence. Analysis of the geographic distribution of variation identified two distinctive G. elegans lineages; however, the small number of individuals and localities sampled precluded a comprehensive analysis. Analysis of haplotype and population networks for G. cypha mtDNAs from 15 localities revealed low divergence among haplotypes; however, significant frequency differences among populations within and among drainages were found, largely attributable to samples in the Little Colorado River region. This structure was not associated with G. cypha and G. robusta, as morphotypes from the same location are more similar than conspecific forms in other locations. This indicates that morphological and mtDNA variation are affected by different evolutionary forces in Colorado River Gila and illustrates how both hybridization and local adaptation can play important roles in evolution.

Animals↗
PubMed2002

The importance of the ontogenetic niche in resource-associated divergence: evidence from a generalist grasshopper.

Geographic variation in resource use can produce locally adapted populations that exhibit genetic and phenotypic divergence. In the bird-winged grasshopper (Schistocerca emarginata = [lineata]), we investigate whether genetic data exist in accordance with geographic variation in resource (host) use and coloration. In Texas, juvenile grasshoppers feed almost exclusively on one of two host plants, Rubus trivialis (Rosaceae) or Ptelea trifoliata (Rutaceae), whereas adults of both forms are dietary generalists and consume many plants from unrelated families. Along with differences in juvenile feeding, differences in a density-dependent color polyphenism are concordant with genetic (mitochondrial DNA) variation among eight populations of the bird-winged grasshopper. Forms feeding on R. trivialis and those feeding on P. trifoliata represent monophyletic lineages according to phylogenetic analysis and maximum-likelihood tests of two alternative phylogeographic hypotheses for geographic variation in host use. Character-state optimization of host-plant acceptability on a phylogeny containing S. emarginata and outgroup taxa indicates that populations consuming R. trivialis gave rise to populations consuming P. trifoliata. Juvenile grasshoppers that consume P. trifoliata acquire deterrence against predation, suggesting that enemy-free space facilitated this host shift. In extant populations, adaptations stemming from alternative resource use during ontogeny present possible barriers to gene exchange. This study represents the first demonstration of resource-associated divergence in an otherwise generalist insect that exhibits temporal variation in resource use, characterized as developmental changes in host specialization. Our findings suggest that exploitation of different resources may have unexplored significance for generalist species that compartmentalize specialization to particular life stages.

Amino Acid Sequence↗
PubMed2003

Natural selection on protein polymorphism in the rodent genus Peromyscus: evidence from interlocus contrasts.

The effects of natural selection are generally locus-specific, whereas migration, drift, and inbreeding are expected to have relatively uniform effects across the entire genome. This suggests that multilocus surveys of multiple populations can be used to distinguish selection from demographic effects. The purpose of this study was to test for evidence of selection on protein polymorphism in natural populations of mice in the genus Peromyscus. We analyzed published data from geographic surveys of allozyme variation and used a coalescent-based simulation model to identify specific loci that deviated from neutral expectations. Observed F(ST) values generally exhibited a remarkably close fit to the expected neutral distributions, indicating that the majority of loci are simply tracking stochastic demographic processes. A smaller number of loci exhibited highly significant departures from the expectations of the neutral model and thus appear to be tracking the direct or indirect effects of selection. Most departures from neutrality were characterized by F(ST) values that far exceeded neutral expectations and were therefore attributable to spatially varying selection. Interestingly, the albumin locus was implicated as a candidate gene for local adaptation in four different species of Peromyscus. The results also demonstrate that selection can severely bias marker-based estimates of neutral parameters.

Adaptation, Physiological↗
PubMed2004

Natural selection drives altitudinal divergence at the albumin locus in deer mice, Peromyscus maniculatus.

In populations that are distributed across steep environmental gradients, the potential for local adaptation is largely determined by the spatial scale of fitness variation relative to dispersal distance. Since altitudinal gradients are generally characterized by dramatic ecological transitions over relatively short linear distances, adaptive divergence across such gradients will typically require especially strong selection to counterbalance the homogenizing effect of gene flow. Here we report the results of a study that was designed to test for evidence of adaptive divergence across an altitudinal gradient in a natural population of deer mice, Peromyscus maniculatus. We conducted a multilocus survey of allozyme variation across a steep altitudinal gradient in the southern Rocky Mountains that spanned several distinct biomes, from prairie grassland to alpine tundra. As a control for the effects of altitude, we also surveyed the same loci in mice sampled along a latitudinal transect through the prairie grassland that ran perpendicular to the east-west altitudinal transect. We used a coalescent-based simulation model to identify loci that deviated from neutral expectations, and we then assessed whether locus-specific patterns of variation were nonrandom with respect to altitude. Results indicated that the albumin locus (Alb) reflects a history of diversifying selection across the altitudinal gradient. This conclusion is supported by two main lines of evidence: (1) Alb was characterized by levels of divergence across the altitudinal transect that exceeded neutral expectations in two consecutive years of sampling (in contrast to the spatial pattern of variation across the latitudinal transect), and (2) levels of divergence at the Alb locus exhibited a positive association with altitudinal distance in both years (in contrast to the pattern observed at unlinked loci). We conclude that clinal variation at the Alb locus reflects a balance between gene flow and diversifying selection that results from elevational changes in fitness rankings among alternative genotypes.

Adaptation, Physiological↗
PubMed2005

SINE insertion polymorphism on the X chromosome differentiates Anopheles gambiae molecular forms.

Polymorphic SINE insertions can be useful markers for assessing population structure and differentiation. Maque is a family of SINE elements which, based on bioinformatic analysis, was suggested to have been active recently in Anopheles gambiae, the major vector of malaria. Here, we report the development of polymorphic Maque insertions as population genetic markers in A. gambiae, and the use of these markers to better characterize divergence on the X chromosome between A. gambiae M and S molecular forms in populations from Burkina Faso and Mali. Our data are consistent with the recent activity of Maque. Phylogenetic analysis suggests that at least two recently active lineages may have a role in mediating genome evolution. We found differences in element insertion frequency and sequence between the M and S populations analysed. Significant differentiation was observed between these two groups across a 6 Mb region at the proximal (centromeric) end of the X chromosome. Locus-specific F(ST) values ranged from 0.14 to 1.00 in this region, yet were not significantly different from zero in more distal locations on the X chromosome; the trend was consistent in populations from both geographical locales suggesting that differentiation is not due to local adaptation. Strong differentiation between M and S at the proximal end of the X chromosome, but not outside this region, suggests the action of selection counteracting limited gene flow between these taxa and supports their characterization as incipient species.

Animals↗
PubMed2004

Distribution of genetic variation in the growth hormone 1 gene in Atlantic salmon (Salmo salar) populations from Europe and North America.

The level and hierarchical distribution of genetic variation in complete sequences of the Atlantic salmon (Salmo salar) growth hormone (GH1) gene were investigated in populations from Europe and North America with a view to inferring the major evolutionary forces affecting genetic variation at this locus. Seventeen polymorphic sites were identified in complete sequences from nine populations, with levels of noncoding (intron and untranslated region sequences) nucleotide diversity being similar to those observed in other species. No variation, however, was observed in exonic sequences, indicating that nucleotide diversity in the Atlantic salmon GH1 gene is three and 25 times less than that estimated for human and Drosophila coding sequences, respectively. This suggests that purifying selection is the predominant contemporary force controlling the molecular evolution of GH1 coding sequences. Comparison of haplotype relationships within and between populations indicated that differentiation between populations from Europe and North America was greater than within-continent comparisons. However, several haplotypes observed in the northernmost European populations were more similar to those observed in North American than to any other haplotypes observed in Europe. This is most likely to be a result of historical, rather than contemporary, gene flow. Neutrality test statistics, such as Tajima's D, were significantly positive in the European populations in which North American-like haplotypes were observed. Although a positive Tajima's D is commonly interpreted as the signal of balancing selection, a more likely explanation in this case is that either historical migration or ascertainment bias, rather than within population local adaptation, has given rise to an excess of intermediate frequency alleles.

Amino Acid Sequence↗
PubMed2005

A multilocus population genetic survey of the greater sage-grouse across their range.

The distribution and abundance of the greater sage-grouse (Centrocercus urophasianus) have declined dramatically, and as a result the species has become the focus of conservation efforts. We conducted a range-wide genetic survey of the species which included 46 populations and over 1000 individuals using both mitochondrial sequence data and data from seven nuclear microsatellites. Nested clade and structure analyses revealed that, in general, the greater sage-grouse populations follow an isolation-by-distance model of restricted gene flow. This suggests that movements of the greater sage-grouse are typically among neighbouring populations and not across the species, range. This may have important implications if management is considering translocations as they should involve neighbouring rather than distant populations to preserve any effects of local adaptation. We identified two populations in Washington with low levels of genetic variation that reflect severe habitat loss and dramatic population decline. Managers of these populations may consider augmentation from geographically close populations. One population (Lyon/Mono) on the southwestern edge of the species' range appears to have been isolated from all other greater sage-grouse populations. This population is sufficiently genetically distinct that it warrants protection and management as a separate unit. The genetic data presented here, in conjunction with large-scale demographic and habitat data, will provide an integrated approach to conservation efforts for the greater sage-grouse.

Animals↗
PubMed2005

Comparison of quantitative and molecular variation in agroforestry populations of the shea tree (Vitellaria paradoxa C.F. Gaertn) in Mali.

In this study we investigated the within- and between-population genetic variation using microsatellite markers and quantitative traits of the shea tree, Vitellaria paradoxa, an important agroforestry tree species of the Sudano-Sahelian region in Africa. Eleven populations were sampled across Mali and in northern Côte d'Ivoire. Leaf size and form and growth traits were measured in a progeny test at the nursery stage. Eight microsatellites were used to assess neutral genetic variation. Low levels of heterozygosity were recorded (1.6-3.0 alleles/locus; H(E) = 0.25-0.42) and the fixation index (F(IS) = -0.227-0.186) was not significantly different from zero suggesting that Hardy-Weinberg equilibrium is encountered in all populations sampled. Quantitative traits exhibited a strong genetic variation between populations and between families within populations. The degree of population differentiation of the quantitative traits (Q(ST) = 0.055-0.283, Q(STmean) = 0.189) strongly exceeds that in eight microsatellite loci (F(ST) = -0.011-0.142, F(STmean) = 0.047). Global and pairwise F(ST) values were very low and not significantly different from zero suggesting agroforestry practices are amplifying gene flow (Nm = 5.07). The population means for quantitative traits and the rainfall variable were not correlated, showing variation was not linked with this climatic cline. It is suggested that this marked differentiation for quantitative traits, independent of environmental clines and despite a high gene flow, is a result of local adaptation and human selection of shea trees. This process has induced high linkage disequilibrium between underlying loci of polygenic characters.

Cote d'Ivoire↗
PubMed2005

Variation for neutral markers is correlated with variation for quantitative traits in the plant pathogenic fungus Mycosphaerella graminicola.

We compared genetic variation and population differentiation at RFLP marker loci with seven quantitative characters including fungicide resistance, temperature sensitivity, pycnidial size, pycnidial density, colony size, percentage of leaves covered by pycnidia (PLACP) and percentage of leaves covered by lesions (PLACL) in Mycosphaerella graminicola populations sampled from four regions. Wide variation in population differentiation was found across the quantitative traits assayed. Fungicide resistance, temperature sensitivity, and PLACP displayed a significantly higher Q(ST) than G(ST), consistent with selection for local adaptation, while pycnidial size, pycnidial density and colony size displayed a lower or significantly lower Q(ST) than G(ST), consistent with constraining selection. There was not a statistical difference between Q(ST) and G(ST) in PLACL. We also found a positive and significant correlation between genetic variation in molecular marker loci and quantitative traits at the multitrait scale, suggesting that estimates of overall genetic variation for quantitative traits in M. graminicola could be derived from analysis of the molecular genetic markers.

Ascomycota↗
PubMed2005

Migratory charr schools exhibit population and kin associations beyond juvenile stages.

Few studies have critically investigated the genetic composition of wild fish schools. Yet, such investigations may have profound implications for the understanding of social organization and population differentiation in both fundamental and applied research. Using 20 microsatellite loci, we investigated the composition of 53 schools (total n = 211) of adult and subadult migratory brook charr (Salvelinus fontinalis) sampled from the known feeding areas of two populations inhabiting Mistassini Lake (Québec, Canada). We specifically tested whether (i) school members originated from the same population, (ii) individuals from the same population within schools were kin (half- or full-siblings), and (iii) kin schooling relationships differed between sexes. Randomization tests revealed a tendency for most schools to be population specific, although some schools were population mixtures. Significantly more kin were found within schools than expected at random for both populations (approximately 21-34% of the total number of school members). This result, combined with the observed size range of individuals, indicated that stable associations between kin may occur beyond juvenile stages for up to 4 years. Nevertheless, a high proportion of school members were non-kin (approximately 66-79%). No differences were detected between sexes in the propensity to school with kin. We discuss the hypothesis that the stable kin groups, rather than arising from kin selection, may instead be a by-product of familiarity based on individual selection for the maintenance of local adaptations related to migration (natal and feeding area philopatry). Our results are noteworthy because they suggest that there is some degree of permanence in the composition of wild fish schools. Additionally, they support the hypothesis that schools can be hierarchically structured (from population members down to family groups) and are thus nonrandom genetic entities.

Alleles↗