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High-Density SNP Genotyping Reveals High Population Connectivity and Limited Spatial Genetic Structure in Apodemus flavicollis and Apodemus sylvaticus.

High-density SNP arrays are increasingly used in ecological and evolutionary studies, yet their application in wild species remains challenging. In this study, we evaluated the performance of the Affymetrix Axiom Mouse HD array, originally developed for Mus musculus, in two wild small mammals, Apodemus flavicollis and Apodemus sylvaticus, with particular focus on genetic diversity and population connectivity across seven sampling sites within a fragmented landscape. A total of 96 individuals (43 A. flavicollis and 53 A. sylvaticus) were genotyped using a 616K SNP array. After quality control filtering for missingness and minor allele frequency, more than 160,000 high-quality autosomal SNPs were retained for each species. Despite being designed for a different species, the array effectively discriminated between A. flavicollis and A. sylvaticus, with principal component analysis clearly separating the two species. Levels of genetic diversity were comparable across sites, with mean observed heterozygosity around 0.33 and consistently negative F IS values, indicating a slight excess of heterozygotes. Population structure analyses revealed extremely weak spatial genetic differentiation. ADMIXTURE supported a single genetic cluster (K = 1) within each species, while analysis of molecular variance attributed more than 99% of genetic variation to within-individual components. Pairwise relationship analyses showed that related individuals were not confined to single sites but occurred across sampling locations, supporting ongoing gene flow even across the fragmented landscape. No significant isolation-by-distance pattern was detected. Overall, our results indicate high population connectivity and limited spatial genetic structuring in both species across the study area, consistent with the documented dispersal capacity of these species at the spatial scale investigated. Moreover, this study demonstrates that high-density SNP arrays can provide powerful genomic tools for investigating dispersal dynamics and population structure in closely related wildlife species under habitat fragmentation, where subtle genetic patterns may otherwise remain undetected.

Apodemus species↗

Quantifying gene flow from spatial genetic structure data in a metapopulation of Chamaecrista fasciculata (Leguminosae).

An extensive allozyme survey was conducted within a natural "meta" population of the native North American annual legume, Chamaecrista fasciculata (Leguminosae) to quantify genetic structure at different spatial scales. Gene flow was then estimated by a recently developed indirect method based on a continuous population model, using pairwise kinship coefficients between individuals. The indirect estimates of gene flow, quantified in terms of neighborhood size, with an average value on the order of 150 individuals, were concordant among different spatial scales (subpopulation, population, metapopulation). This gene-flow value lies within the range of direct estimates previously documented from observations of pollen and seed dispersal for the same metapopulation. Monte Carlo simulations using the direct measures of gene flow as parameters further demonstrated that the observed spatial pattern of allozyme variation was congruent with a model of isolation by distance. Combining previously published estimates of pollen dispersal distances with kinship coefficients from this study, we quantified biparental inbreeding relative to either a single subpopulation or the whole metapopulation. At the level of a neighborhood, little biparental inbreeding was observed and most departure from Hardy-Weinberg genotypic proportions was explained by self-fertilization, whereas both selfing and biparental inbreeding contributed to nonrandom mating at the metapopulation level. Gene flow was also estimated from indirect methods based on a discontinuous population structure model. We discuss these results with respect to the effect of a patchy population structure on estimation of gene flow.

Chamaecrista↗

Optimal sampling strategy for estimation of spatial genetic structure in tree populations.

Fine-scale spatial genetic structure (SGS) in natural tree populations is largely a result of restricted pollen and seed dispersal. Understanding the link between limitations to dispersal in gene vectors and SGS is of key interest to biologists and the availability of highly variable molecular markers has facilitated fine-scale analysis of populations. However, estimation of SGS may depend strongly on the type of genetic marker and sampling strategy (of both loci and individuals). To explore sampling limits, we created a model population with simulated distributions of dominant and codominant alleles, resulting from natural regeneration with restricted gene flow. SGS estimates from subsamples (simulating collection and analysis with amplified fragment length polymorphism (AFLP) and microsatellite markers) were correlated with the 'real' estimate (from the full model population). For both marker types, sampling ranges were evident, with lower limits below which estimation was poorly correlated and upper limits above which sampling became inefficient. Lower limits (correlation of 0.9) were 100 individuals, 10 loci for microsatellites and 150 individuals, 100 loci for AFLPs. Upper limits were 200 individuals, five loci for microsatellites and 200 individuals, 100 loci for AFLPs. The limits indicated by simulation were compared with data sets from real species. Instances where sampling effort had been either insufficient or inefficient were identified. The model results should form practical boundaries for studies aiming to detect SGS. However, greater sample sizes will be required in cases where SGS is weaker than for our simulated population, for example, in species with effective pollen/seed dispersal mechanisms.

Computer Simulation↗

Evaluating kriging as a tool to improve moderate resolution maps of forest biomass.

The USDA Forest Service, Forest Inventory and Analysis program (FIA) recently produced a nationwide map of forest biomass by modeling biomass collected on forest inventory plots as nonparametric functions of moderate resolution satellite data and other environmental variables using Cubist software. Efforts are underway to develop methods to enhance this initial map. We explored the possibility of modeling spatial structure to make such improvements. Spatial structure in the field biomass data as well as in residuals from the map was investigated across 18 ecological zones in the Interior Western U.S. Exploratory tools included directional graphs of summary statistics, three dimensional maps, Moran's I correlograms, and variograms. Where spatial pattern was present, field and residual biomass were kriged, and predictions made for an independent test set were evaluated for improvement over predictions in the initial biomass map. While kriging has some potential benefit when analyzing the field data and exploring spatial structure, kriging residuals resulted in little or no improvement in the initial biomass map developed using Cubist software. Stationarity assumptions, variogram behavior, and appropriate model fitting strategies are discussed.

Biomass↗

Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea.

The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Aland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran's I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100-150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.

Animals↗

Strong spatial genetic structure in peripheral but not core populations of Sitka spruce [Picea sitchensis (Bong.) Carr.].

We examined spatial genetic structure within eight populations of Sitka spruce classified as core or peripheral based on ecological niche, and continuous or disjunct based on species distribution. In each population, 200 trees were spatially mapped and genotyped for eight cDNA-based sequence tagged site (STS) codominant markers. Spatial autocorrelation was assessed by estimating p(ij), the average co-ancestry coefficient, between individuals within distance intervals. The distribution of alleles and genotypes within core populations was almost random, with nonsignificant co-ancestry values among trees as close as 50 m in core populations. In contrast, the distribution of alleles and genotypes within peripheral populations revealed an aggregation of similar multilocus genotypes, with co-ancestry values greater than 0.20 among trees up to 50 m apart and significant, positive values between trees up to 500 m. The relatively high density of reproductive adults in core populations may lead to highly overlapping seed shadows that limit development of spatial genetic structure. However, in peripheral populations with a lower density of adults, the distribution of alleles and genotypes was highly structured, likely due to offspring establishment near maternal trees and subsequent biparental inbreeding, as well as more recent population establishment at the leading edge of post-Pleistocene range expansion. Conserving genetic diversity in peripheral populations may require larger reserves for in situ conservation than required in core populations. These data on spatial genetic structure can be used to provide guidance for sampling strategies for both ex situ conservation and research collections.

British Columbia↗

Inferring colonization history from analyses of spatial genetic structure within populations of Pinus strobus and Quercus rubra.

Many factors interact to determine genetic structure within populations including adult density, the mating system, colonization history, natural selection, and the mechanism and spatial patterns of gene dispersal. We examined spatial genetic structure within colonizing populations of Quercus rubra seedlings and Pinus strobus juveniles and adults in an aspen-white pine forest in northern Michigan, USA. A 20-year spatially explicit demographic study of the forest enables us to interpret the results in light of recent colonization of the site for both species. We assayed 217 Q. rubra seedlings and 171 P. strobus individuals at 11 polymorphic loci using nine allozyme systems. Plant genotypes and locations were used in an analysis of spatial genetic structure. Q. rubra and P. strobus showed similar observed levels of heterozygosity, but Q. rubra seedlings have less heterozygosity than expected. Q. rubra seedlings show spatial genetic clumping of individuals on a scale to 25 m and levels of genetic relatedness expected from the clumped dispersion of half-siblings. In contrast, P. strobus has low levels of genetic relatedness at the smallest distance class and positive spatial genetic structure at scales < 10 m within the plot. The low density of adult Q. rubra outside the study plot and limited, spatially clumped rodent dispersal of acorns is likely responsible for the observed pattern of spatial genetic structure and the observed heterozygote deficit (i.e. a Wahlund effect). We attribute weaker patterns observed in P. strobus to the longer dispersal distance of seeds and the historical overlap of seed shadows from adults outside of the plot coupled with the overlap of seed shadows from younger, more recently established reproductive adults. The study demonstrates the utility of long-term demographic data in interpreting mechanisms responsible for generating contemporary patterns of genetic structure within populations.

Genetic Variation↗

Rotations in a vertebrate setting: evaluation of the symmetry group of the disynaptic canal-neck projection.

Organizational structures intrinsic to nervous systems can be more precisely analyzed and compared with other logical structures once they are expressed in mathematical languages. A standard mathematical language for expressing organizational structure is that of groups. Groups are especially well suited to organizational structures involving multiple symmetries such as spatial structures. The vestibular system is widely believed to mediate many neural functions involving spatial structure. The vestibular nuclei receive direct projections from the vestibular endorgans, the semicircular canals and the otolith organs. The near-orthogonal directions of the semicircular canals are embedded in the bone. However, those canal directions are external to the nervous system. This study addresses the way the three-dimensional space of rotations is also embedded in the group structure of neural connectivity. Although we know a great deal about physical rotation, it is not clear that nervous systems organize rotations in the same way as physicists do. It would make sense for nervous systems to organize rotations in such a way as to provide physiologically relevant information about performing or compensating for rotations. The vestibular nuclei, which might be expected to display an organization that binds rotations into a rotation space, do not give a clear organization. This may be because of the multiplicity of spatial functions performed by the vestibular nuclei; rather than one spatial organization, the vestibular nuclei are likely to accommodate multiple, related spatial organizations. This study evaluates one particular data set from the literature that specifies the organization of the disynaptic canal-neck projection; other projections and neuronal populations may have other intrinsic organizations. The data are evaluated directly for their symmetry group. In the symmetry group, the vertebrate requirement that physiology have a right and left is found to be satisfied in two ways: (i) by a hexagonal symmetry arising from the right-left doubling of front and back, (ii) along with separate organizations on the two sides that may be required to operate independently to some extent. The eight observed muscle innervation patterns from the data are the complete set of possible combinations of inhibitory/excitatory polarities from three canal pairs. These eight innervation patterns are organized as the vertices of a cube. The two types of side muscles provide the vertical direction. As the head rotates in physical space, the cube rotates in sensorimotor space. Like the canal-neck projection, otolith projections and proprioceptive afferents contact both the vestibular nuclei and neck motoneurons. They may have a similar organization, perhaps with extensions of the same pattern. Otherwise, like a checkerboard superimposed over a paisley, they will form an overlapping organization with the disynaptic canal-neck projection. Further research is required to determine whether the sensorimotor spatial structure of the canal-neck projection is widespread in nervous systems or whether there are several complete structures that are fragmented and reintegrated.

Animals↗

Spatial and structural segregation of the transcribed and nontranscribed alleles of c-myc in Namalva-S cells.

By using various approaches we received evidence that, in Namalva-S cells carrying a t(8;14) translocation and highly expressing c-myc, the two alleles of the gene are spatially and structurally segregated. Spatial segregation of the alleles was observed in all nuclei analyzed by in situ hybridization technique. Their structural segregation, i.e., association with different intranuclear structures, was confirmed in a number of experiments. When high-salt extracted nuclei were digested with EcoRI, which is known to produce fragments containing the entire c-myc locus, the sequences of the gene were found separated between the pellet, containing sequences firmly associated with the heavier matrix structures, and the supernatant, containing sequences from the free length of the DNA loops. Southern hybridization performed with a probe representative for the constant region of the human IgH locus revealed that this fractionation in fact segregates the reorganized from the normal allele of c-myc. Run-on experiments carried out with two fractions, topologically equivalent to the above P and S but isolated as intact chromatin structures, indicated that the allele associated with nuclear matrix is actively transcribed, while that located in the free length of the chromatin loops is practically nontranscribed. Studies on the chromatin organization of transcribed and nontranscribed alleles revealed the existence in them of two alternative chromatin structures. Control experiments with beta-globin gene, performed with cells constitutively nontranscribing or actively transcribing this gene, confirmed our conclusions about the spatial segregation of the two alleles and clarified that their structural segregation occurs when the gene is activated for transcription.

Alleles↗

A computer algorithm for representing spatial-temporal structure of human motion and a motion generalization method.

Inspired by the generalized motor program (GMP) theory, this study presents a symbolic motion structure representation (SMSR) algorithm that identifies a basic spatial-temporal structure of a human motion. The algorithm resolves each joint angle-time trajectory of a multi-joint motion into a sequence of elemental motion segments and labels each motion segment with a symbol representing its shape ("U": monotonically increasing; "D": monotonically decreasing; "S": stationary). By concatenating symbols according to their order in time, the spatial-temporal structure of a joint angle-time trajectory is represented as a symbolic string. The structure of a multi-joint motion is then represented as a set of symbolic strings. A sample motion, whose structure is identified by the SMSR algorithm, can be generalized to produce an infinite number of similar motion variants. To generate a variant of a sample motion, segment boundary points of the sample motion are first relocated to new locations in the angle-time space, and then individual motion segments of the original joint angle trajectories are shifted and proportionally rescaled to fit the new segment boundary points. This motion generalization method provides a basis for developing GMP-based motion simulation models, and exploring ideas and hypotheses related to the GMP theory through simulation. As an application of the motion generalization method, a motion modification (MoM) algorithm is presented, which adapts existing reach motions for new target locations. Some examples generated by the MoM algorithm are illustrated.

Algorithms↗

Effects of seed dispersal on spatial genetic structure in populations of Rutidosis leptorrhychoides with different levels of correlated paternity.

Rutidosis leptorrynchoides is a perennial forb endemic to grasslands and grassy woodlands in southeastern Australia. Studies of seed dispersal, spatial genetic structure and clonality were carried out in four populations around the Canberra region that varied in levels of correlated paternity to examine: (1) whether R. leptorrhynchoides populations exhibit fine-scale spatial genetic structure and whether this varies between populations as a function of correlated paternity; (2) whether there is a correlation between seed dispersal distance and genetic relatedness within populations; and (3) whether clonal reproduction occurs in this species and to what degree this could account for the observed spatial genetic structure. The results show that there is variation in the magnitude and extent of spatial genetic structure between R. leptorrhynchoides populations. The three larger populations, with low to moderate full-sib proportions, showed significant patterns of coancestry between plants over scales of up to one metre, whereas the smallest population, with a high full-sib proportion, had erratically high but non-significant coancestry values. The observed patterns of genetic clumping could be explained by a combination of limited seed dispersal and correlated mating owing to limited mate availability resulting from the species' sporophytic self-incompatibility system. Clonality does not appear to be an important factor contributing to genetic structure in this species.

Australia↗

Modelling non-stationary spatial covariance structure from space-time monitoring data.

Accurate interpolation of soil and climate variables at fine spatial scales is necessary for precise field management. Interpolation is needed to produce the input variables necessary for crop modelling. It is also important when deciding on regulations to limit environmental impacts from processes such as nitrate leaching. Non-stationarity may arise due to many factors, including differences in soil type, or heterogeneity in chemical concentrations. Many geostatistical methods make stationarity assumptions. Substantial improvements in interpolation or in the estimation of standard errors may be obtained by using non-stationary models of spatial covariances. This paper presents recent methodological developments for an approach to modelling non-stationary spatial covariance structure through deformations of the geographic coordinate system. This approach was first introduced by Sampson & Guttorp, although the estimation approach is updated in more recent papers. They compute a deformation of the geographic plane so that the spatial covariance structure can be considered stationary in terms of a new spatial coordinate system. This provides a non-stationary model for the spatial covariances between sampled locations and prediction locations. In this paper, we present a cross-validation procedure to avoid over-fitting of the sample dispersions. Results concerning the variability of the spatial covariance estimates are also presented. An example of the modelling of the spatial correlation field of rainfall at small regional scale is presented. Other directions in methodological development, including modelling temporally varying spatial correlation, and approaches to model temporal and spatial correlation are mentioned. Future directions for methodological development are indicated, including the modelling of multivariate processes and the use of external spatially dense covariables. Such covariates are frequently available in precision agriculture.

Agriculture↗

New insights from fine-scale spatial genetic structure analyses in plant populations.

Many empirical studies have assessed fine-scale spatial genetic structure (SGS), i.e. the nonrandom spatial distribution of genotypes, within plant populations using genetic markers and spatial autocorrelation techniques. These studies mostly provided qualitative descriptions of SGS, rendering quantitative comparisons among studies difficult. The theory of isolation by distance can predict the pattern of SGS under limited gene dispersal, suggesting new approaches, based on the relationship between pairwise relatedness coefficients and the spatial distance between individuals, to quantify SGS and infer gene dispersal parameters. Here we review the theory underlying such methods and discuss issues about their application to plant populations, such as the choice of the relatedness statistics, the sampling scheme to adopt, the procedure to test SGS, and the interpretation of spatial autocorrelograms. We propose to quantify SGS by an 'Sp' statistic primarily dependent upon the rate of decrease of pairwise kinship coefficients between individuals with the logarithm of the distance in two dimensions. Under certain conditions, this statistic estimates the reciprocal of the neighbourhood size. Reanalysing data from, mostly, published studies, the Sp statistic was assessed for 47 plant species. It was found to be significantly related to the mating system (higher in selfing species) and to the life form (higher in herbs than trees), as well as to the population density (higher under low density). We discuss the necessity for comparing SGS with direct estimates of gene dispersal distances, and show how the approach presented can be extended to assess (i) the level of biparental inbreeding, and (ii) the kurtosis of the gene dispersal distribution.

Demography↗

Spatial genetic structure of delphinium nuttallianum populations: inferences about gene flow

The spatial genetic structure of a plant population provides a potential record of past gene flow and mating. We used hierarchical F-statistics and spatial autocorrelation to characterize spatial genetic differentiation of allozymes in adult Delphinium nuttallianum plants within and among six natural populations separated from one another by up to 3 km. Previous direct estimates suggested that gene flow is highly localized, averaging << 10 m. Earlier studies of seed-set, pollen-tube growth and progeny fitness suggested that partial reproductive isolation exists between plants growing too close together (<3 m) and too far apart (>100 m). Thus we anticipated substantial genetic differentiation on scales of a few to hundreds of metres. However, we detected little differentiation among the six populations, among replicate study plots within populations, or among subsections of study plots, except at the smallest scale of cm to m. These results suggest that relatively rare long-distance pollen movement has gone undetected and that postpollination selection may further modify genetic structure during the life cycle. Lack of differentiation is not at odds with the observation of partial reproductive isolation, because some loci may respond to spatial variation in selection without this response being evident at marker loci.

Journal Article↗

Cytoplasmic and nuclear markers reveal contrasting patterns of spatial genetic structure in a natural Ipomopsis hybrid zone.

Spatial variation in natural selection may play an important role in determining the genetic structure of hybridizing populations. Previous studies have found that F1 hybrids between naturally hybridizing Ipomopsis aggregata and Ipomopsis tenuituba in central Colorado differ in fitness depending on both genotype and environment: hybrids had higher survival when I. aggregata was the maternal parent, except in the centre of the hybrid zone where both hybrid types had high survival. Here, we developed both maternally (cpDNA PCR-RFLP) and biparentally inherited (nuclear AFLP) species-diagnostic markers to characterize the spatial genetic structure of the natural Ipomopsis hybrid zone, and tested the prediction that the majority of natural hybrids have I. aggregata cytoplasm, except in areas near the centre of the hybrid zone. Analyses of 352 individuals from across the hybrid zone indicate that cytoplasmic gene flow is bidirectional, but contrary to expectation, most plants in the hybrid zone have I. tenuituba cytoplasm. This cytotype distribution is consistent with a hybrid zone in historical transition, with I. aggregata nuclear genes advancing into the contact zone. Further, nuclear data show a much more gradual cline than cpDNA markers that is consistent with morphological patterns across the hybrid populations. A mixture of environment- and pollinator-mediated selection may contribute to the current genetic structure of this hybrid system.

Base Sequence↗

Spatial genetic structure in two congeneric epiphytes with different dispersal strategies analysed by three different methods.

Three different approaches were used to assess the kinship structure of two epiphytic bryophytes, Orthotrichum speciosum and O. obtusifolium, that have different dispersal strategies. The two species were sampled in a 200 ha landscape where species occurrence and host trees had been mapped previously. Local environmental conditions at sampled trees were recorded and kinship between individuals was calculated based on amplified fragment length polymorphism (AFLP)-marker data. We did not detect any association between AFLP-markers and investigated environmental conditions. In both species, significant kinship coefficients were found between individuals up to 300-350 m apart which shows that both species have a restricted dispersal range. The spatial kinship structure was detected with both autocorrelation analysis and generalized additive models (GAMs), but linear regression failed to detect any structure in O. speciosum. Although the dioecious O. obtusifolium is currently the more common species it may, none the less, due to its restricted dispersal range and reproduction mode, become threatened in the future by current silvicultural practices which enhance the distance between host trees and decrease their life span. Finally, GAMs seem most appropriate for analysing spatial genetic structure because the effects of local environmental conditions and spatial structure can be analysed simultaneously, no assumption of a parametric form between kinship coefficient and distance is required, and spatial data resolution is not lost in the arbitrary choice of distance classes characterizing autocorrelation analysis.

Bryopsida↗

Spatial genetic structure of allozyme polymorphisms within populations of Pinus Strobus (Pinaceae).

The population structure of genetic variation for four allozyme loci was investigated for two populations (one old growth, OG, and the other logged, SS) of eastern white pine (Pinus strobus). Both seedlings and reproductive adults were studied for both study populations. Spatial autocorrelation statistics were used to examine the distribution of allozyme polymorphisms. The spatial genetic structure in adults of population OG indicated that individual genotypes were distributed in a structured, isolation-by-distance manner, consistent with observed levels of pollen and seed dispersal. In contrast, adult genotypes in population SS were nearly randomly distributed, probably as a result of logging. Nonetheless, spatial structuring of genotypes of seedlings occurred at both sites, indicating the power of limited seed flow, as well as temporal Wahlund effects, to create structure. None of four loci in both seedling populations showed a significant departure from Hardy-Weinberg proportions, whereas one and two significant deviations were found for loci in the two respective adult populations. These departures may be attributed to episodic reproductive events.

Journal Article↗

Velocity invariance of receptive field structure in somatosensory cortical area 3b of the alert monkey.

This is the second in a series of studies of the neural representation of tactile spatial form in cortical area 3b of the alert monkey. We previously studied the spatial structure of 330 area 3b neuronal receptive fields (RFs) on the fingerpad with random dot patterns scanned at one velocity (40 mm/sec; ). Here, we analyze the temporal structure of 84 neuronal RFs by studying their spatial structure at three scanning velocities (20, 40, and 80 mm/sec). As in the previous study, most RFs contained a single, central, excitatory region and one or more surrounding or flanking inhibitory regions. The mean time delay between skin stimulation and its excitatory effect was 15.5 msec. Except for differences in mean rate, each neuron's response and the spatial structure of its RF were essentially unaffected by scanning velocity. This is the expected outcome when excitatory and inhibitory effects are brief and synchronous. However, that interpretation is consistent neither with the reported timing of excitation and inhibition in somatosensory cortex nor with the third study in this series, which investigates the effect of scanning direction and shows that one component of inhibition lags behind excitation. We reconcile these observations by showing that overlapping (in-field) inhibition delayed relative to excitation can produce RF spatial structure that is unaffected by changes in scanning velocity. Regardless of the mechanisms, the velocity invariance of area 3b RF structure is consistent with the velocity invariance of tactile spatial perception (e.g., roughness estimation and form recognition).

Adaptation, Physiological↗