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PubMed2006

A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions.

MOTIVATION: The systematic integration of expression profiles and other types of gene information, such as chromosomal localization, ontological annotations and sequence characteristics, still represents a challenge in the gene expression arena. In particular, the analysis of transcriptional data in context of the physical location of genes in a genome appears promising in detecting chromosomal regions with transcriptional imbalances often characterizing cancer. RESULTS: A computational tool named locally adaptive statistical procedure (LAP), which incorporates transcriptional data and structural information for the identification of differentially expressed chromosomal regions, is described. LAP accounts for variations in the distance between genes and in gene density by smoothing standard statistics on gene position before testing the significance of their differential levels of gene expression. The procedure smooths parameters and computes p-values locally to account for the complex structure of the genome and to more precisely estimate the differential expression of chromosomal regions. The application of LAP to three independent sets of raw expression data allowed identifying differentially expressed regions that are directly involved in known chromosomal aberrations characteristic of tumors. AVAILABILITY: Functions in R for implementing the LAP method are available at http://www.dpci.unipd.it/Bioeng/Publications/LAP.htm

Algorithms↗

PubMed2006

Host propagation permits extreme local adaptation in a social parasite of ants.

The Red Data Book hoverfly species Microdon mutabilis is an extreme specialist that parasitises ant societies. The flies are locally adapted to a single host, Formica lemani, more intimately than was thought possible in host-parasite systems. Microdon egg survival plummeted in F. lemani colonies > 3 km away from the natal nest, from c. 96% to 0% to < 50%, depending on the hoverfly population. This is reflected in the life-time dispersal of females, measured at < 2 m, resulting in oviposition back into the same ant nests for generation after generation. To counter destabilizing effects on the host, Microdon manipulates the social dynamics of F. lemani by feeding selectively on ant eggs and small larvae, which causes surviving larvae to switch development into queens. Infested colonies rear double the number of new queens, thus propagating the vulnerable local genotype and compensating for damage to the host colonies. The consequences of such extreme host specificity for insect conservation are discussed.

Adaptation, Physiological↗

PubMed2006

Gene flow's effect on the genetic architecture of a local adaptation and its consequences for QTL analyses.

This paper uses computer simulations to determine how gene flow between populations affects (1) the genetic architecture of a local adaptation and (2) properties of alleles segregating in quantitative trait locus (QTL) mapping populations. Results suggest that the average magnitude of an allele that causes a phenotypic difference between populations declines as the migration rate increases, but with an increase in migration, alleles of larger magnitude cause proportionally more of the phenotypic difference between populations. Gene flow between populations that are used in a QTL study tends to cause the average magnitude and percent variance explained (PVE) of an allele in a mapping population to increase. Thus, although the average magnitude of an allele causing a difference declines with migration the average magnitude or PVE of an allele in a QTL mapping population may increase. The reason is that the probability an allele is sampled for a QTL mapping population is in direct proportion to its frequency and alleles of larger magnitude tend to segregate at relatively higher frequencies than alleles of smaller effect with an increased migration. As the rate of gene flow between populations increases, the proportion of the phenotypic difference explained by alleles that are segregating in a QTL mapping population (and therefore potentially detected) decreases. Lastly, results suggest QTL alleles of large effect (>20% PVE) should be commonly found, provided the divergence time between populations is not too long or optima of populations are not too far apart.

Crosses, Genetic↗

PubMed2025

Genome sequencing and population genomics provide insights into the demographic history, genetic load, and local adaptation of an endangered Tertiary relict.

Endangered Tertiary relict trees represent an exceptional evolutionary heritage with small and isolated populations, yet little is known about how demographic history, local adaptation, and genetic load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Ulmus elongata L. K. Fu & C. S. Ding, an endangered Tertiary relict tree endemic to East Asia. By integrating genomes from U. elongata and seven other endangered trees from public databases, we identified rate-decelerated genes across endangered trees and genes under positive selection of U. elongata associated with tissue development, detoxification, and immune response, and signal transduction and regulation mechanisms potentially leading to endangered status. Demographic analyses revealed continuous population decline from the late Miocene to present, especially during the last glacial maximum (LGM) and last 10 000 years. Spearman correlation indicated a strong negative relationship between effective population size and human population density (rpopulation density = -0.90, P < 0.001) as well as cropland use (rcropland use = -0.89, P < 0.001). Genotype-environment association (GEA) analyses identified a set of candidate genes associated with temperature and precipitation, supporting a polygenic adaptation model in U. elongata. Overall, our findings underscore the severe population bottlenecks that have led to the fixation of strongly deleterious mutations and inbreeding, further compromising the adaptive potential and long-term viability of U. elongata. Furthermore, assessments of genomic vulnerability under future climate scenarios revealed higher genetic offsets in northern region of Fujian and Jiangxi populations, suggesting these regions require prioritized conservation efforts due to reduced adaptive capacity.

Endangered Species↗

PubMed2025

Genomic Insights Into Local Adaptation Across Heterogeneous Understory Habitats and Climate Change Vulnerability.

Understanding adaptive evolution and survival risks in understory herbs is crucial for the effective conservation of biodiversity. How environmental gradients shape species local adaptation patterns is not well understood, nor is how populations of understory herbs respond to a changing climate. In this study, we conducted population genomic analyses of Adenocaulon himalaicum (Asteraceae) with a pan-East Asian distribution, representing a good model for dominant understory herbs to elucidate adaptation mechanisms in heterogeneous forest ecosystems. Based on 34,398 putatively neutral single nucleotide polymorphisms (SNPs) across 27 populations, we identified three genetic lineages accompanied by high levels of genetic differentiation between populations. Our isolation by environment results (IBE) indicated a significant effect of environmental gradients on genomic variation of A. himalaicum (r = 0.18, p = 0.03). To decompose the relative contributions of climate, geography and population structure in explaining genetic variance, our partial RDA found that the prominent contribution of environmental effects (climatic and soil variables) explained 29% and 36% of the neutral and adaptive genetic variation, respectively. Using two genotype-environment association (GEA) methods, we identified 13 SNPs as candidates for core climate-related adaptation loci, with two of these loci further validated by qRT-PCR experiments. Projections of spatiotemporal genomic vulnerability under different future climate scenarios revealed that populations in the southeastern edge of the Himalayas, near the Sichuan Basin, the southernmost region of Northeast China and the northern Korean Peninsula, as well as northern Japan, were identified as the most vulnerable and should be prioritised for conservation. Therefore, our current study provides the genomic foundations for conservation and management strategies to elucidate how these understory herbs cope with future climate changes.

Climate Change↗

PubMed2005

Improvement of the neighborhood based Levenberg-Marquardt algorithm by local adaptation of the learning coefficient.

In this letter, an improvement of the recently developed neighborhood-based Levenberg-Marquardt (NBLM) algorithm is proposed and tested for neural network (NN) training. The algorithm is modified by allowing local adaptation of a different learning coefficient for each neighborhood. This simple add-in to the NBLM training method significantly increases the efficiency of the training episodes carried out with small neighborhood sizes, thus, allowing important savings in memory occupation and computational time while obtaining better performance than the original Levenberg-Marquardt (LM) and NBLM methods.

Algorithms↗

PubMed1973

Phototropism and local adaptation in Phycomyces sporangiophores.

Phototropic responses to unilateral ultraviolet stimuli were studied to determine whether the response of one side of the cell is affected by the previous exposure of the opposite side to ultraviolet. It has been found that the direction of bending is not parallel to the stimulus direction, but is along a straight line rotated 17 degrees clockwise from the stimulus direction. This deviation indicates that the photoreceptors may be in a state of continual clockwise rotation. If before the stimulus the cell is exposed briefly to ultraviolet and rotated through 90 degrees , the response is not along the 17 degrees line, but is deviated a greater or lesser amount, depending on whether the 90 degrees rotation is clockwise or counterclockwise. This difference is evidence that the first ultraviolet exposure leaves a persistent patch of light-adapted receptors and the shaded part of the cell remains dark adapted. The phototropic stimulus straddles the edge between light- and dark-adapted regions, and the differing responses of the two regions affects the direction of phototropic bending. A phototropic mechanism is proposed which combines the features of local adaptation and photoreceptor rotation.

Dark Adaptation↗

PubMed1998

Wheezing Lung Sounds Analysis with adaptive local trigonometric transform.

Wheezes are abnormal sounds which are known to be relevant to Chronic Obstructive Pulmonary Diseases (COPD). The analysis of such signals is especially useful in patient monitoring or pharmacology. Respiratory sounds are dependent on the flow and the volume. Furthermore, they can be the result of a complex mixture of events. The analysis of lung sounds can be greatly improved with time-frequency techniques because these methods highlight the evolution of the spectra of events. In this paper, we present the application of the Adaptive Local Trigonometric Decomposition (ALTD) to lung sound analysis. This analysis provides an optimal representation of the signal in the time-frequency domain with a lattice which is adapted in time. In our work, the parameterization of the ALTD is studied for the detection of wheezing phenomena.

Algorithms↗

PubMed2005

Local adaptation in the rock pocket mouse (Chaetodipus intermedius): natural selection and phylogenetic history of populations.

Elucidating the causes of population divergence is a central goal of evolutionary biology. Rock pocket mice, Chaeotdipus intermedius, are an ideal system in which to study intraspecific phenotypic divergence because of the extensive color variation observed within this species. Here, we investigate whether phenotypic variation in color is correlated with local environmental conditions or with phylogenetic history. First, we quantified variation in pelage color (n=107 mice) and habitat color (n=51 rocks) using a spectrophotometer, and showed that there was a correlation between pelage color and habitat color across 14 sampled populations (R2=0.43). Analyses of mtDNA sequences from these same individuals revealed strong population structure in this species across its range, where most variation (63%) was partitioned between five geographic regions. Using Mantel tests, we show that there is no correlation between color variation and mtDNA phylogeny, suggesting that pelage coloration has evolved rapidly. At a finer geographical scale, high levels of gene flow between neighboring melanic and light populations suggest the selection acting on color must be quite strong to maintain habitat-specific phenotypic distributions. Finally, we raise the possibility that, in some cases, migration between populations of pocket mice inhabiting different lava flows may be responsible for similar melanic phenotypes in different populations. Together, the results suggest that color variation can evolve very rapidly over small geographic scales and that gene flow can both hinder and promote local adaptation.

Adaptation, Physiological↗

PubMed2005

Local adaptation to winter conditions in a passerine spreading north: a common-garden approach.

Sedentary passerine birds living in temperate and boreal regions need a high metabolic capacity for thermogenesis to survive winter conditions. As a consequence of the increased thermogenic capacity, basal energetic demands rise at a time when resources and time to acquire them decrease. In a previous study, great tits (Parus major) from two localities in Fennoscandia with contrasting winter conditions differed in their metabolic response to ambient temperature. To investigate the physiological basis underlying interpopulation differences we performed a common-garden experiment to test whether these differences were genetically based. We found basal metabolic rate to be higher in birds originating from transferred eggs from the southern population compared to the ones from the northern population, contrary to the relationship among birds living in their region of origin. Despite previous evidence suggesting that gene flow prevents local adaptation at the northern range limits of a species expanding northward, we found that great tits differ in their reaction norm to winter conditions according to the population of origin.

Adaptation, Physiological↗

PubMed2005

Generalization of motor learning based on multiple field exposures and local adaptation.

Previous studies have used transfer of learning over workspace locations as a means to determine whether subjects code information about dynamics in extrinsic or intrinsic coordinates. Transfer has been observed when the torque associated with joint displacement is similar between workspace locations-rather than when the mapping between hand displacement and force is preserved-which is consistent with muscle- or joint-based encoding. In the present study, we address the generality of an intrinsic coding of dynamics and examine how generalization occurs when the pattern of torques varies over the workspace. In two initial experiments, we examined transfer of learning when the direction of a force field was fixed relative to an external frame of reference. While there were no beneficial effects of transfer after training at a single location (experiments 1 and 2), excellent performance was observed at the center of the workspace after training at two lateral locations (experiment 2). Experiment 3 and associated simulations assessed the characteristics of this generalization. In these studies, we examined the patterns of transfer observed after adaptation to force fields that were composed of two subfields that acted in opposite directions. The experimental and simulated data are consistent with the idea that information about dynamics is encoded in intrinsic coordinates. The nervous system generalizes dynamics learning by interpolating between sets of control signals, each locally adapted to different patterns of torques.

Adaptation, Physiological↗

PubMed2000

Adaptive local contrast enhancement method for medical images displayed on a video monitor.

It is known that light-box luminance is an important factor in the detection of objects on radiographs. Existing methods for image contrast enhancement do not consider the luminance effect so that the enhancement may be inappropriate for the processed image displayed on a video monitor. Based on the properties of human visual system (HVS), an adaptive local contrast enhancement (ALCE) method was developed to enhance the medical image displayed on the video monitor by investigating the influence on human eyes of display luminance difference between a conventional light-box and a video monitor. The HVS model indicated parts of a radiograph unclear to human eyes at a given display luminance. By calculating the contrast of the image pixel by pixel, we found the parts of an image that are needed to be amplified at low display luminance and provided these parts with adequate enhancement. The processed image displayed on a video monitor was visually equivalent to the raw radiograph displayed on a light-box. A quantitative evaluation method of image quality assessment was used to compare the ALCE-processed image with others.

Biophysical Phenomena↗

PubMed2003

An experimental test of local adaptation in soil bacteria.

We extracted bacterial isolates of similar colony morphology from spatially located soil samples within 1 ha of old-growth forest. The same soil samples were used to prepare growth medium. Each isolate was then cultured in each medium and its growth recorded. There was no overall tendency for isolates to grow more successfully in their home site (i.e., the medium derived from the soil sample from which they had been extracted). Most isolates grew very poorly, however, and when the analysis was restricted to the minority of vigorous isolates there was clear evidence of local adaptation: isolates tended to grow better at their home site than did isolates from elsewhere and grew better at their home site than they did at other sites. The variation of growth within the 1-ha plot made up a complex fitness landscape of peaks, ridges, and valleys. Most of the vigorous isolates were found at or near a local fitness (growth) peak, although seldom at a global peak. In consequence, there was a tendency for growth to diminish away from the home site. The home isolate was about 50% more fit than average at its home site; fitness diminished exponentially away from the home site at a rate of 0.0577 per meter. These figures are similar to those previously reported for plants. This selection gradient has matched the bacterial assemblage to the edaphic structure of the environment, although the fit is far from perfect.

Adaptation, Physiological↗

PubMed2004

Contrasting patterns of quantitative and neutral genetic variation in locally adapted populations of the natterjack toad, Bufo calamita.

The relative importance of natural selection and genetic drift in determining patterns of phenotypic diversity observed in nature is still unclear. The natterjack toad (Bufo calamita) is one of a few amphibian species capable of breeding in saline ponds, even though water salinity represents a considerable stress for them. Results from two common-garden experiments showed a pattern of geographic variation in embryonic salinity tolerance among populations from either fresh or brackish environments, consistent with the hypothesis of local adaptation. Full-sib analysis showed increased variation in survival among sibships within population for all populations as osmotic stress was increased (broad-sense heritability increased as salinity raised). Nevertheless, toads native to the brackish water environment had the highest overall survival under brackish conditions. Levels of population genetic differentiation for salinity tolerance were higher than those of neutral genetic differentiation, the latter obtained through the analysis of eight microsatellite loci. Microsatellite markers also revealed little population differentiation, lack of an isolation-by-distance pattern, and moderate gene flow connecting the populations. Therefore, environmental stress tolerance appears to have evolved in absence of geographic isolation, and consequently we reject the null hypothesis of neutral differentiation.

Adaptation, Physiological↗

PubMed2006

Population differences in host use by a seed-beetle: local adaptation, phenotypic plasticity and maternal effects.

For insects that develop inside discrete hosts, both host size and host quality constrain offspring growth, influencing the evolution of body size and life history traits. Using a two-generation common garden experiment, we quantified the contribution of maternal and rearing hosts to differences in growth and life history traits between populations of the seed-feeding beetle Stator limbatus that use a large-seeded host, Acacia greggii, and a small-seeded host, Pseudosamanea guachapele. Populations differed genetically for all traits when beetles were raised in a common garden. Contrary to expectations from the local adaptation hypothesis, beetles from all populations were larger, developed faster and had higher survivorship when reared on seeds of A. greggii (the larger host), irrespective of their native host. We observed two host plant-mediated maternal effects: offspring matured sooner, regardless of their rearing host, when their mothers were reared on P. guachapele (this was not caused by an effect of rearing host on egg size), and females laid larger eggs on P. guachapele. This is the first study to document plasticity by S. limbatus in response to P. guachapele, suggesting that plasticity is an ancestral trait in S. limbatus that likely plays an important role in diet expansion. Although differences between populations in growth and life history traits are likely adaptations to their host plants, host-associated maternal effects, partly mediated by maternal egg size plasticity, influence growth and life history traits and likely play an important role in the evolution of the breadth of S. limbatus' diet. More generally, phenotypic plasticity mediates the fitness consequences of using novel hosts, likely facilitating colonization of new hosts, but also buffering herbivores from selection post-colonization. Plasticity in response to novel versus normal hosts varied among our study populations such that disentangling the historical role of plasticity in mediating diet evolution requires the consideration of evolutionary history.

Acacia↗

PubMed2004

Evolution of color variation in dragon lizards: quantitative tests of the role of crypsis and local adaptation.

Many animal species display striking color differences with respect to geographic location, sex, and body region. Traditional adaptive explanations for such complex patterns invoke an interaction between selection for conspicuous signals and natural selection for crypsis. Although there is now a substantial body of evidence supporting the role of sexual selection for signaling functions, quantitative studies of crypsis remain comparatively rare. Here, we combine objective measures of coloration with information on predator visual sensitivities to study the role of crypsis in the evolution of color variation in an Australian lizard species complex (Ctenophorus decresii). We apply a model that allows us to quantify crypsis in terms of the visual contrast of the lizards against their natural backgrounds, as perceived by potential avian predators. We then use these quantitative estimates of crypsis to answer the following questions. Are there significant differences in crypsis/conspicuousness among populations? Are there significant differences in crypsis conspicuousness between the sexes? Are body regions "exposed" to visual predators more cryptic than "hidden" body regions? Is there evidence for local adaptation with respect to crypsis against different substrates? In general, our results confirmed that there are real differences in crypsis/conspicuousness both between populations and between sexes; that exposed body regions were significantly more cryptic than hidden ones, particularly in females; and that females, but not males, are more cryptic against their own local background than against the background of other populations [corrected]. Body regions that varied most in contrast between the sexes and between populations were also most conspicuous and are emphasized by males during social and sexual signaling. However, results varied with respect to the aspect of coloration studied. Results based on chromatic contrast ("hue" of color) provided better support for the crypsis hypothesis than did results based on achromatic contrast ("brightness" of color). Taken together, these results support the view that crypsis plays a substantial role in the evolution of color variation and that color patterns represent a balance between the need for conspicuousness for signaling and the need for crypsis to avoid predation.

Adaptation, Physiological↗

PubMed2004

Genetic differentiation and local adaptation in the salt-marsh beetle Pogonus chalceus: a comparison between allozyme and microsatellite loci.

The genetic structure of Pogonus chalceus from 11 Atlantic and seven Mediterranean Western European populations was analysed. Results from seven allozyme loci were compared to five microsatellites to test the hypothesis that some enzymatic loci undergo selection. Both allozyme and microsatellite results showed that Mediterranean beetle populations are genetically distinct from Atlantic populations. The analysis of the genetic structure showed that FST values derived from all microsatellite loci were much smaller than those obtained from allozymes. The enzymatic locus Idh-1 exhibited a high value compared to the other loci, suggesting that it is non-neutral. The same Idh-1 locus was implicated in differentiation between temporary and stable populations, as followed also from a highly significant relationship between the allele two of this Idh-1 locus and dispersal power population estimates. The 'parallel evolution' model may account for the diversification of locally adapted Pogonus chalceus populations between different microhabitats.

Adaptation, Biological↗

PubMed2004

Mitochondrial gene diversity in the common vole Microtus arvalis shaped by historical divergence and local adaptations.

The phylogeography of the common vole (Microtus arvalis) was examined by analysing mitochondrial DNA (mtDNA) sequence variation in 1044 base pairs (bp) of the cytochrome b (cytb) gene and in 322 bp of the control region (ctr) among 106 individuals from 58 locations. The geographical distribution of four previously recognized cytb evolutionary lineages in Europe was refined and a new lineage was found in southern Germany. All lineages were distributed allopatrically, except in one sample that was probably located in a contact zone. The occurrence of several lineages in the Alps is in keeping with their recent recolonization from distinct sources. The translation of 84 cytb DNA sequences produced 33 distinct proteins with relationships that differed from those of the DNA haplotypes, suggesting that the mtDNA lineages did not diverge in response to selection. In comparison with M. agrestis, a neutrality test detected no overall evidence for selection in the cytb gene, but a closer examination of a structural model showed that evolutionarily conserved and functionally important positions were often affected. A new phylogeographical test of random accumulation of nonsynonymous mutations generated significant results in three lineages. We therefore conclude that the molecular diversity of cytb in M. arvalis is overall the result of the demographic history of the populations, but that there have been several episodes of local adaptation to peculiar environments.

Adaptation, Biological↗