Spatial distributions of genotypes under isolation by distance

Assessing fine-scale pondscape connectivity with amphibian eyes: An integrative approach using genomic and capture-mark-recapture data

In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behaviour of target species, which can be modelled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1056 individuals of two anuran and three urodele species (1732-3913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework, and combined these genetic data with information obtained in a previous 2-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies, and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results show a significant effect of local population sizes on patterns of genetic differentiation at small spatial scales. In addition, movement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level.

Desert-like badlands and surrounding (semi-)dry grasslands of Central Germany promote small-scale phenotypic and genetic differentiation in Thymus praecox

Environmental heterogeneity among sites can generate phenotypic and genetic variation facilitating differentiation and microevolution of plant populations. Badlands are desert-like, predominantly vegetation-poor habitats often embedded in (semi-)dry grasslands. The desert-like conditions of badlands demand extreme adaptation of plants, that is, phenotypic modifications in short-term and/or natural adaptation in long-term. However, detailed knowledge is missing about both plant phenotypic and genetic differentiation in this unique and widely occurring habitat type. The present study focused on the largest known badlands systems in Central Europe located in the "Drei Gleichen" region, a designated nature conservation area in Central Germany. Locations were suitable for this study in terms of having co-occurring badlands and (semi-)dry grassland habitats (sites) occupied by the pioneer plant Thymus praecox. Here, we studied the environmental preferences, morphological and functional trait variation, and genetic variation using microsatellite markers of T. praecox. Results revealed significant, mainly site-dependent environmental, phenotypic, and genetic differentiation. In general, individuals in badlands are shorter in height and have lower patch sizes (length × width), relative growth rates, and smaller stomata. The PCA additionally unveiled slightly increased leaf robustness, trichome density, decreased stomatal conductance, fewer females, and earlier phenology in badlands. We interpret differentiation patterns as adaptive responses to light, temperature, drought, and nutrient stress conditions supported by reviewed literature. Genetic differentiation was strongest between local badlands and grassland sites, and clearly weaker among locations and between sites (in total) as indicated by G ST, AMOVA, PCoA, and population structure. Our study supports the importance of small-scale microhabitat conditions as a driver of microevolutionary processes, and the population's need for sufficient phenotypic variation and genetic resources to deal with environmental changes. We demonstrated that badlands are an appropriate model system for testing plant response to extreme habitats and that more research is needed on these fascinating landscapes.

The impact of self-incompatibility systems on the prevention of biparental inbreeding

Inbreeding in hermaphroditic plants can occur through two different mechanisms: biparental inbreeding, when a plant mates with a related individual, or self-fertilization, when a plant mates with itself. To avoid inbreeding, many hermaphroditic plants have evolved self-incompatibility (SI) systems which prevent or limit self-fertilization. One particular SI system-homomorphic SI-can also reduce biparental inbreeding. Homomorphic SI is found in many angiosperm species, and it is often assumed that the additional benefit of reduced biparental inbreeding may be a factor in the success of this SI system. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations that displayed three different types of homomorphic SI. We measured the total level of inbreeding avoidance by comparing each population to a self-compatible population (NSI), and we measured biparental inbreeding avoidance by comparing to a population of self-incompatible plants that were free to mate with any other individual (PSI). Because biparental inbreeding is more common when offspring dispersal is limited, we examined the levels of biparental inbreeding over a range of dispersal distances. We also tested whether the introduction of inbreeding depression affected the level of biparental inbreeding avoidance. We found that there was a statistically significant decrease in autozygosity in each of the homomorphic SI populations compared to the PSI population and, as expected, this was more pronounced when seed and pollen dispersal was limited. However, levels of homozygosity and inbreeding depression were not reduced. At low dispersal, homomorphic SI populations also suffered reduced female fecundity and had smaller census population sizes. Overall, our simulations showed that the homomorphic SI systems had little impact on the amount of biparental inbreeding in the population especially when compared to the overall reduction in inbreeding compared to the NSI population. With further study, this observation may have important consequences for research into the origin and evolution of homomorphic self-incompatibility systems.

The effect of the dispersal kernel on isolation-by-distance in a continuous population

Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population which represents a standardized measure of gene flow. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional landscape using seven dispersal kernels: Rayleigh, exponential, half-normal, triangular, gamma, Lomax and Pareto. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform over the neighborhood area which suggests that the common description of neighborhood size as a measure of an effective, local panmictic population is valid for popular families of dispersal distributions. We further show how to draw random variables from the triangular distribution efficiently and argue that it should be utilized in other studies in which computational efficiency is important.

Spatial genetic structure patterns of phenotype-limited and boundary-limited expanding populations: a simulation study

Range expansions may create a unique spatial genetic pattern characterized by alternate genetically homogeneous domains and allele frequency clines. Previous attempts to model range expansions have mainly focused on the loss of genetic diversity during expansions. Using individual-based models, we examined spatial genetic patterns under two expansion scenarios, boundary-limited range expansions (BLRE) and phenotype-limited range expansions (PhLRE). Our simulation revealed that the genetic diversity within populations lost quickly during the range expansion, while the genetic difference accumulated between populations. Consequently, accompanying the expansions, the overall diversity featured a slow decrease. Specifically, during BLREs, high speed of boundary motion facilitated the maintenance of total genetic diversity and sharpened genetic clines. Very slight constraints on boundary motion of BLREs drastically narrowed the homogeneous domains and increased the allele frequency fluctuations from those levels exhibited by PhLREs. Even stronger constraints, however, surprisingly brought the width of homogeneous domains and the allele frequency fluctuations back to the normal levels of PhLREs. Furthermore, high migration rates maintained a higher total genetic diversity than low ones did during PhLREs. Whereas, the total genetic diversities during BLREs showed a contrary pattern: higher when migration was low than those when migration was high. Besides, the increase of migration rates helped maintain a greater number of homogeneous domains during PhLREs, but their effects on the number of homogeneous domains during BLREs were not monotonous. Previous studies have showed that the homogenous domains can merge to form a few broad domains as the expansion went on, leading to fewer homogeneous domains. Our simulations, meanwhile, revealed that the range expansions could also rebuild homogeneous domains from the clines during the range expansion. It is possible that that the number of homogeneous domains was determined by the interaction of merging and newly emerging homogeneous domains.

Geographical patterns of turnover and nestedness-resultant components of allelic diversity among populations

The analysis of geographical patterns in population divergence has always been a powerful way to infer microevolutionary processes involved in population differentiation, and several approaches have been used to investigate such patterns. Most frequently, multivariate spatial patterns of population differentiation are analyzed by computing pairwise genetic distances or F(ST) (or related statistics, such as ϕ(ST) from AMOVA), which are then correlated with geographical distances or landscape features. However, when calculating distances, especially based on presence-absence of alleles in local populations, there would be a confounding effect of allelic richness differences in the population differentiation. Moreover, the relative magnitude of these components and their spatial patterns can help identifying microevolutionary processes driving population differentiation. Here we show how recent methodological advances in ecological community analyses that allows partitioning dissimilarity into turnover (turnover) and richness differences, or nestedness-resultant dissimilarity, can be applied to allelic variation data, using an endemic Cerrado tree (Dipteryx alata) as a case study. Individuals from 15 local populations were genotyped for eight microsatellite loci, and pairwise dissimilarities were computed based on presence-absence of alleles. The turnover of alleles among populations represented 69 % of variation in dissimilarity, but only the richness difference component shows a clear spatial structure, appearing as a westward decrease of allelic richness. We show that decoupling richness difference and turnover components of allelic variation reveals more clearly how similarity among populations reflects geographical patterns in allelic diversity that can be interpreted in respect to historical range expansion in the species.

Panmixia in Zoarces viviparus: implications for environmental monitoring studies

In this study, the genetic population structure of the eelpout Zoarces viviparus was investigated by using microsatellites. Samples were collected at 10 sites in the Baltic Sea, covering a distance of c. 90 km. Ten newly developed microsatellite loci were used to infer the population structure. No global spatial genetic differentiation was found (global F(ST) = 0·0001; D(est) = -0·0003), indicating strong gene flow at this scale, nor any clear pattern of isolation by distance. The results suggest that gene flow among the studied populations of Z. viviparus is stronger than usually thought, which might be caused by environmental homogeneity. This is important for planning and evaluating monitoring activities in this species and for the interpretation of ecotoxicological studies. Strong migration might lead to wrong conclusions concerning the pollution in a given area. Therefore, reference stations should be placed at a larger distance than presently practiced.

Genetic population structure of perch Perca fluviatilis along the Swedish coast of the Baltic Sea

In this study, the genetic variation of perch Perca fluviatilis from 18 different sites along the Swedish coast of the Baltic Sea was assessed. There was a relative strong support for isolation by distance and the results suggest an overall departure from panmixia. The level of genetic divergence was moderate (global F(ST) = 0·04) and indications of differences in the population genetic structure between the two major basins (central Baltic Sea and Gulf of Bothnia) in the Baltic Sea were found. There was a higher level of differentiation in the central Baltic Sea compared to the Gulf of Bothnia, and the results suggest that stretches of deep water might act as barriers to gene flow in the species. On the basis of the estimation of genetic patch size, the results corroborate previous mark--recapture studies and suggest that this is a species suitable for local management. In all, the findings of this study emphasize the importance of considering regional differences even when strong isolation by distance characterize the genetic population structure of species.

Phylogeography of Pinus subsection Australes in the Caribbean Basin

BACKGROUND AND AIMS

Four species of Pinus subsection Australes occur in the Caribbean Basin: P. caribaea, P. cubensis, P. maestrensis and P. occidentalis. This study analyses the phylogeography of these species to assess possible colonization events from Central America to the islands and subsequent population expansions during glacial periods driven by both drier climate and larger emerged land areas.

METHODS

Allele size data were obtained for plastid microsatellites for 314 individuals from 24 populations, covering the distribution range of subsection Australes in the Caribbean Basin.

KEY RESULTS

In total, 113 plastid haplotypes were identified. The highest genetic diversity was found in populations of P. caribaea. Overall, Caribbean Basin populations fit the isolation by distance model. Significant phylogeographical structure was found (R(ST) = 0·671 > permuted R(ST) = 0·101; P < 0·0001). The haplotype network and a Bayesian analysis of population structure (BAPS) indicated different Central American origins for P. caribaea var. bahamensis and P. caribaea var. caribaea plastids, with Central America populations in northern and south-eastern groups. Sudden expansion times for BAPS clusters were close to three glacial maxima.

CONCLUSIONS

Central America contains ancestral plastid haplotypes. Population expansion has played a major role in the distribution of genetic diversity in P. caribaea var. hondurensis. Two colonization events gave rise to the P. caribaea var. bahamensis and P. caribaea var. caribaea lineages. Plastid variation in the eastern species (P. cubensis, P. maestrensis and P. occidentalis) evolved independently from that in P. caribaea var. caribaea. Incomplete lineage sorting between P. cubensis and P. maestrensis is apparent. Inferred expansion times for P. caribaea var. bahamensis and for the eastern lineages correspond to glacial maxima, whereas those for P. caribaea var. hondurensis correspond to the beginning of the temperature decrease that led to Marine Isotope Stage 8.

Statistical methods in spatial genetics

The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls.

Genetic drift on networks: ploidy and the time to fixation

Genetic drift in finite populations ultimately leads to the loss of genetic variation. This paper examines the rate of neutral gene loss for a range of population structures defined by a graph. We show that, where individuals reside at fixed points on an undirected graph with equal degree nodes, the mean time to loss differs from the panmictic value by a positive additive term that depends on the number of individuals (not genes) in the population. The effect of these spatial structures is to slow the time to fixation by an amount that depends on the way individuals are distributed, rather than changing the apparent number of genes available to be sampled. This relationship breaks down, however, for a broad class of spatial structures such as random, small-world and scale-free networks. For the latter structures there is a counter-intuitive acceleration of fixation proportional to the level of ploidy.

Isolation-by-distance and outbreeding depression are sufficient to drive parapatric speciation in the absence of environmental influences

A commonly held view in evolutionary biology is that speciation (the emergence of genetically distinct and reproductively incompatible subpopulations) is driven by external environmental constraints, such as localized barriers to dispersal or habitat-based variation in selection pressures. We have developed a spatially explicit model of a biological population to study the emergence of spatial and temporal patterns of genetic diversity in the absence of predetermined subpopulation boundaries. We propose a 2-D cellular automata model showing that an initially homogeneous population might spontaneously subdivide into reproductively incompatible species through sheer isolation-by-distance when the viability of offspring decreases as the genomes of parental gametes become increasingly different. This simple implementation of the Dobzhansky-Muller model provides the basis for assessing the process and completion of speciation, which is deemed to occur when there is complete postzygotic isolation between two subpopulations. The model shows an inherent tendency toward spatial self-organization, as has been the case with other spatially explicit models of evolution. A well-mixed version of the model exhibits a relatively stable and unimodal distribution of genetic differences as has been shown with previous models. A much more interesting pattern of temporal waves, however, emerges when the dispersal of individuals is limited to short distances. Each wave represents a subset of comparisons between members of emergent subpopulations diverging from one another, and a subset of these divergences proceeds to the point of speciation. The long-term persistence of diverging subpopulations is the essence of speciation in biological populations, so the rhythmic diversity waves that we have observed suggest an inherent disposition for a population experiencing isolation-by-distance to generate new species.

Revealing cryptic spatial patterns in genetic variability by a new multivariate method

Increasing attention is being devoted to taking landscape information into account in genetic studies. Among landscape variables, space is often considered as one of the most important. To reveal spatial patterns, a statistical method should be spatially explicit, that is, it should directly take spatial information into account as a component of the adjusted model or of the optimized criterion. In this paper we propose a new spatially explicit multivariate method, spatial principal component analysis (sPCA), to investigate the spatial pattern of genetic variability using allelic frequency data of individuals or populations. This analysis does not require data to meet Hardy-Weinberg expectations or linkage equilibrium to exist between loci. The sPCA yields scores summarizing both the genetic variability and the spatial structure among individuals (or populations). Global structures (patches, clines and intermediates) are disentangled from local ones (strong genetic differences between neighbors) and from random noise. Two statistical tests are proposed to detect the existence of both types of patterns. As an illustration, the results of principal component analysis (PCA) and sPCA are compared using simulated datasets and real georeferenced microsatellite data of Scandinavian brown bear individuals (Ursus arctos). sPCA performed better than PCA to reveal spatial genetic patterns. The proposed methodology is implemented in the adegenet package of the free software R.

Applying new inter-individual approaches to assess fine-scale population genetic diversity in a neotropical frog, Eleutherodactylus ockendeni

We assess patterns of genetic diversity of a neotropical leaflitter frog, Eleutherodactylus ockendeni, in the upper Amazon of Ecuador without a priori delineation of biological populations and with sufficiently intensive sampling to assess inter-individual patterns. We mapped the location of each collected frog across a 5.4 x 1 km landscape at the Jatun Sacha Biological Station, genotyped 185 individuals using five species-specific DNA microsatellite loci, and sequenced a fragment of mitochondrial cytochrome b for a subset of 51 individuals. The microsatellites were characterized by high allelic diversity and homozygote excess across all loci, suggesting that when pooled the sample is not a panmictic population. We conclude that the lack of panmixia is not attributable to the influence of null alleles or biased sampling of consanguineous family groups. Multiple methods of population cluster analysis, using both Bayesian and maximum likelihood approaches, failed to identify discrete genetic clusters across the sampled area. Using multivariate spatial autocorrelation, kinship coefficients and relatedness coefficients, we identify a continuous isolation by distance population structure, with a first patch size of ca. 260 m and apparently large population sizes. Analysis of mtDNA corroborates the observation of high genetic diversity at fine scales: there are multiple haplotypes, they are non-randomly distributed and a binary haplotype correlogram shows significant spatial genetic autocorrelation. We demonstrate the utility of inter-individual genetic methods and caution against making a priori assumptions about population genetic structure based simply on arbitrary or convenient patterns of sampling.

Pollen Dispersal in Spatially Aggregated Populations

We perform a theoretical study of effective pollen dispersal within plant populations exhibiting intraspecific spatial aggregation. We simulate nonuniform distributions of individuals by means of a Poisson cluster process and use an individual-based spatially explicit model of pollen dispersal to assess the effects of different aggregation patterns on the effective pollen pool size (N(ep)) and the axial variance of pollen dispersal (sigma (p)). Results show clear interactions between clumping and both N(ep) and sigma (p), whose precise form and intensity depend on the relative spatial scale of aggregation to pollen dispersal range. If clump size is small relative to dispersal range, clumping results in lower N(ep) and sigma (p) than in randomly distributed populations. Interestingly, by contrast, aggregation may actually enlarge N(ep) and has minimum impact on sigma (p) if clump size is near or above the scale of dispersal. High intraclump to global density ratios enhance the sensitivity of both N(ep) and sigma (p) to clumping, while leptokurtic pollen dispersal generates sharper reductions of both N(ep) and sigma (p) for small clump sizes and stronger increments of N(ep) for larger clump sizes. Overall, our results indicate that isolation-by-distance models in plants should not ignore the effects of intraspecific spatial aggregation on effective dispersal.

Genetic evaluation of in situ conserved and reintroduced populations of wild rice (Oryza rufipogon: Poaceae) in China

We evaluated the genetic consequences and efficiency of conservation practices in Oryza rufipogon using microsatellite DNA markers. Spatial autocorrelation analysis from 12 microsatellite loci revealed that microsatellite alleles were exclusively distributed in patches within the population, indicating that large populations were unlikely to be homogeneous. An in situ conserved stand of O. rufipogon, which has been protected by a concrete wall from a large population, captured only 67.9% of the total genetic variation of the previous large population. The concrete wall was built to protect the wild rice, but it acted more as a physical barrier to gene exchanges between the two sides. An assignment test revealed only 11.1% putative seed exchanges across the wall. A reintroduced population was found to be genetically very diverse. About 76.3% of the total genetic variation detected in other populations was captured in this reintroduced population, and 24.8% of the total genetic variation in this population was not found in other populations. These results display two important findings for conservation of O. rufipogon. First, conserving one part of a large population of O. rufipogon will not preserve an adequate sample of the genetic variability, since populations are not homogeneous, and genotype distribution varies among localities. Second, a reintroduced population is not genetically depauperate, but it is too early to assess its long-term survival.

Genetic (RAPD) Diversity Across Species Range: Core vs. Peripheral Populations of Wild Barley in Israel and Turkmenistan

Populations of wild barley,Hordeum spontaneum, were collected in two countries, Israel and Turkmenistan, in environments representing two similar sharp clines of aridity. This allowed us to use the same criteria to define species core and periphery in the two regions. Plants from 21 Israeli and 11 Turkmenian populations were analyzed for 59 putative loci by randomly amplified polymorphic DNA. Extent of variation was similar in populations at species border (periphery) and in populations inhabiting favorable environments away from the border (core). In contrast, the two regions (Israel and Turkmenistan) differed in extent of genetic diversity as estimated by mean number of alleles per locus, the proportion of polymorphic loci, and the percent of expected heterozygosity, with Israel harboring more variation than Turkmenistan. The genetic population structure revealed by RAPDs did not differ between species core and periphery in each region and between the two regions. The pattern of RAPD variation corresponded to inter-population mosaic structure characterized by genetic differentiation over short geographic distances.

The major conclusion of this study is that there is no simple relationship between neutral genetic variability and population location with respect to the species range (core vs. periphery).

Microsatellite analyses reveal fine-scale genetic structure in grey mouse lemurs (Microcebus murinus)

Information on genetic structure can be used to complement direct inferences on social systems and behaviour. We studied the genetic structure of the solitary grey mouse lemur (Microcebus murinus), a small, nocturnal primate endemic to western Madagascar, with the aim of getting further insight on its breeding structure. Tissue samples from 167 grey mouse lemurs in an area covering 12.3 km2 in Kirindy Forest were obtained from trapping. The capture data indicated a noncontinuous distribution of individuals in the study area. Using 10 microsatellite markers, significant genetic differentiation in the study area was demonstrated and dispersal was found to be significantly male biased. Furthermore, we observed an overall excess of homozygotes in the total population (F(IT) = 0.131), which we interpret as caused by fine-scale structure with breeding occurring in small units. Evidence for a clumped distribution of identical homozygotes was found, supporting the notion that dispersal distance for breeding was shorter than that for foraging, i.e. the breeding neighbourhood size is smaller than the foraging neighbourhood size. In conclusion, we found a more complex population structure than what has been previously reported in studies performed on smaller spatial scales. The noncontinuous distribution of individuals and the effects of social variables on the genetic structure have implications for the interpretation of social organization and the planning of conservation activities that may apply to other solitary and endangered mammals as well.

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.

Streams over mountains: influence of riparian connectivity on gene flow in the Pacific jumping mouse (Zapus trinotatus)

In species affiliated with heterogeneous habitat, we expect gene flow to be restricted due to constraints placed on individual movement by habitat boundaries. This is likely to impact both individual dispersal and connectivity between populations. In this study, a GIS-based landscape genetics approach was used, in combination with fine-scale spatial autocorrelation analysis and the estimation of recent intersubpopulation migration rates, to infer patterns of dispersal and migration in the riparian-affiliated Pacific jumping mouse (Zapus trinotatus). A total of 228 individuals were sampled from nine subpopulations across a system of three rivers and genotyped at eight microsatellite loci. Significant spatial autocorrelation among individuals revealed a pattern of fine-scale spatial genetic structure indicative of limited dispersal. Geographical distances between pairwise subpopulations were defined following four criteria: (i) Euclidean distance, and three landscape-specific distances, (ii) river distance (distance travelled along the river only), (iii) overland distance (similar to Euclidean, but includes elevation), and (iv) habitat-path distance (a least-cost path distance that models movement along habitat pathways). Pairwise Mantel tests were used to test for a correlation between genetic distance and each of the geographical distances. Significant correlations were found between genetic distance and both the overland and habitat-path distances; however, the correlation with habitat-path distance was stronger. Lastly, estimates of recent migration rates revealed that migration occurs not only within drainages but also across large topographic barriers. These results suggest that patterns of dispersal and migration in Pacific jumping mice are largely determined by habitat connectivity.

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.

Phenotypic and allozyme variation in Mediterranean and desert populations of wild barley, Hordeum spontaneum Koch

Populations of wild barley, Hordeum spontaneum Koch, were collected in two distinct climatic regions, desert and Mediterranean. Plants from five desert and five Mediterranean populations were compared and contrasted for extent and structure of phenotypic variation. These same 10 and one other population from each region were analyzed for allozyme variation. In a field trial of phenotypic diversity, two phenological and 14 morphological traits were examined. Study of allozyme variation was performed using eight enzyme systems encoding for 13 loci. Plants from the desert and Mediterranean regions were significantly different in seven of 16 phenotypic traits, exhibited a high (30%) interregional component of phenotypic variation, and showed a high degree of segregation on a principal component scattergram indicating ecotypic differentiation. Mediterranean populations were twice as variable as desert populations in reproductive growth parameters (stem and spike length) and grain filling (spikelet weight), but half as variable for onset of reproduction. The extent and structure of phenotypic and allozyme variation did not match. The Mediterranean and desert populations did not differ in amount of allozyme variation as estimated by mean number of alleles per locus, effective number of alleles, polymorphism, and gene diversity (n(a), n(e), P, and H(e)), did not segregate on the basis of population genetic distances, and exhibited a low proportion of interregion allozyme diversity (2%). No effect of selection on allozyme distribution was detected. Our results suggest that the adaptation of plants originating from desert and Mediterranean environments is reflected in phenotypic but not in allozyme variation.

Spatial autocorrelation and linkage of Mendelian RAPD markers in a population of Picea abies Karst

The spatial clustering of single- and di-locus genotypes in a natural, continuous population of Norway spruce was investigated using 69 Mendelian Random Amplified Polymorphic DNA (RAPD) markers that covered about 15 of the species genome, and whose linkage relationships were known. Spatial autocorrelation techniques and randomization tests, applied to both single- and di-locus genotypes, revealed a weak, though significant, spatial structure at the scale 0-200 m (5 of single-locus and 7 of di-locus genotypes). To assess the relative importance of isolation by distance and linkage between markers on their spatial genetic structuring, we grouped joins between sampled trees into equivalence categories expected to show similar, specific patterns of spatial distribution under isolation by distance. Results from both single- and di-locus analyses were consistent with the existence of patches of like homozygotes (about 8 and 11 of loci at the single- and di-locus level, respectively) surrounded by a mix of like heterozygotes. Similar structuring has been predicted by simulation models under isolation by distance and selective neutrality. Overall, linkage between markers accounted for an increase of spatial clumping of di-locus genotypes involving tightly linked loci with recombination fractions up to 0.1, a consequence of limited, stochastic spread of single-locus genotypes in space. Our results support the hypothesis that isolation by distance and linkage have a small, though significant, effect even within continuous forest tree populations. In general, the spatial distribution of multilocus genotypes within populations should be interpreted with caution when linkage relationships among the markers used are unknown.

Pollen pool heterogeneity in shortleaf pine,Pinus echinataMill

Pollen is the dominant vector of gamete exchange for most temperate tree species. Because pollen movement influences the creation, maintenance and erosion of genetic structure in adult populations, it is important to understand what factors influence the process of pollen movement. Isolation by distance in pollen donor populations can create highly structured pollen polls by increased sampling of local fathers. Extrinsic factors, such as the intervening vegetative structure and local pollen donor densities, can also influence the genetic composition of local pollen pools. Using paternally inherited chloroplast microsatellite markers, we examined the structure and diversity of pollen pools in Pinus echinata Mill. in southern Missouri, USA. Our analysis is based on a multivariate AMOVA analysis of stands ( approximately 1 ha; six per region) nested within regions (approximately 800 ha; four each). Significant multilocus structure of the pollen pool within regions (phiSR = 0.095), but not among regions (phiRT = 0.010), indicates that pollen movement is relatively restricted. Furthermore, the significant correlation between pairwise genetic and physical distances (Mantel correlation; rho = 0.32) provided support for the isolation by distance hypothesis. Our results indicated that availability of pollen donors did not affect diversity of the pollen pool, measured by the number of unique multilocus genotypes at each stand. However, pollen pool diversity was negatively associated with vegetative structure, measured as total forest tree density. Our findings indicated that on-going pollen movement within continuous forest is relatively restricted as a result of both isolation by distance and vegetative structure.

Variability in phenotypic traits in core and peripheral populations of wild barley Hordeum spontaneum Koch

Populations of wild barley, H. spontaneum Koch., were collected in two countries, Israel and Turkmenistan, in environments representing two similar sharp clines of aridity. This allowed us to use the same criteria to define species core and periphery in two regions. Plants from 10 Israeli and 19 Turkmenian populations were grown in a field trial with three water treatments and compared for amount and structure of variation in phenological and morphological traits. Extent of variation was similar in populations at species border (periphery by aridity criterion) or at species border and near it (by habitat), and in populations inhabiting favorable environments away from the border (core). In contrast, two regions (Israel and Turkmenistan) exhibited different amount of variation in phenotypic traits. Israeli populations were more diverse than Turkmenian populations in all except one phenotypic traits and the variation was differently structured among regionally specific core and periphery. While Turkmenian core and periphery defined by either criterion did not differ for all except one trait, corresponding Israeli populations exhibited opposite patterns of variation for trait complexes. Israeli core (Mediterranean) populations were twice as variable than peripheral (desert) populations in parameters of reproductive growth (stem, spike and awn length) and grain filling (spikelet weight) and half as variable in the length of flag and penultimate leaves and onset of reproduction. Possible modes of regionally specific natural selection as a cause of regional/local variation in phenotypic triats are discussed.

Spatial analysis of allozyme and microsatellite DNA polymorphisms in the land snail Helix aspersa (Gastropoda: Helicidae)

The genetic structure of the land snail Helix aspersa was investigated for 21 populations collected along a road located in the polders of the Bay of Mont-Saint-Michel (Brittany, France), following a sampling scheme the area of which did not exceed 900 m in length. A total of 369 individuals were genotyped for five enzymatic markers and seven microsatellite loci. We used sequential hierarchical F-statistics at different spatial scales and spatial autocorrelation statistics to explore recent historical patterns involved in the observed genetic distribution. Whatever the statistics used, congruent levels of spatial genetic substructuring across loci were demonstrated, excepted for one allozyme locus. Overall spatial genetic arrangement matched in a substantial fashion theoretical predictions based on the limited dispersal power of land snails. Positive autocorrelation over short-distance classes may result from the development of genetically distinct patches of individuals organized in family-structured colonies. Therefore, spatial signatures of average I correlograms can be viewed as the expression of a stepping-stone model of population structure, sometimes involving external migrational events. Overall, the revealed pattern of population subdivision on a microgeographical scale was suggestive of a neighbourhood structure. Finally, microsatellite loci are especially suitable for the detection of small genetic clustering, and combining different classes of markers offers the potential to gain further insight into the description of spatial genetic variability over short temporal and geographical scales.

Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.