Spatial Patterns Of Genetic Diversity Research Articles

Isolation and characterization of microsatellite loci in the Norway lobster (Nephrops norvegicus)

AbstractTo assess the level and spatial pattern of genetic diversity of a marine crustacean species, Nephrops norvegicus, hypervariable molecular markers were obtained by screening of a partial genomic library enriched for microsatellite dinucleotide motifs. Following sequencing of the positive clones, 10 pairs of primers were designed and five of them were shown to detect polymorphic loci. These loci were checked for their variability in two natural populations, fished off the Portuguese coast. They showed a high variability for the number of alleles, and for the expected and observed heterozygosities. No significant differentiation between the two localities was observed.

Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe.

Arabidopsis thaliana provides a useful model system for functional, evolutionary and ecological studies in plant biology. We have analysed natural genetic variation in A. thaliana in order to infer its biogeographical and historical distribution across Eurasia. We analysed 79 amplified fragment length polymorphism (AFLP) markers in 142 accessions from the species' native range, and found highly significant genetic isolation by distance among A. thaliana accessions from Eurasia and southern Europe. These spatial patterns of genetic variation suggest that A. thaliana colonized central and northern Europe from Asia and from Mediterranean Pleistocene refugia, a trend which has been identified in other species. Statistically significant levels of multilocus linkage disequilibrium suggest intermediate levels of disequilibrium among subsets of loci, and analysis of genetic relationships among accessions reveal a star or bush-like dendrogram with low bootstrap support. Taken together, it appears that there has been sufficient historical recombination in the A. thaliana genome such that accessions do not conform to a tree-like, bifurcating pattern of evolution - there is no 'ecotype phylogeny.' Nonetheless, significant isolation by distance provides a framework upon which studies of natural variation in A. thaliana may be designed and interpreted.

Conservation Priorities for Chukar Partridge in Israel Based on Genetic Diversity across an Ecological Gradient

Abstract: Recent studies suggest that patterns of genetic diversity significantly influence the viability and persistence of local populations. Revealing and mapping spatial patterns of genetic diversity within species’ ranges may be vital when defining criteria and prioritizing areas for conservation. Chukar Partridges (Alectoris chukar) in Israel occur along a steep ecogeographical gradient extending from mesic Mediterranean zones in the north to steppe and desert regions in the south. To test the hypothesis that the most genetically diverse populations within a species’ range occur within the ecotone, an area of transition between ecosystems where a sharp environmental gradient exists, we examined the allozyme diversity of chukars collected at five locations within the species’ continuous range in each of 2 years. Based on 32 allozyme loci, the genetic diversity of chukars increased significantly along a gradient from populations in Mediterranean regions to those at the ecotone in the northern Negev desert, despite close geographical proximity among populations. Genetic diversity as estimated by percent polymorphic loci, observed and expected heterozygosity, and mean number of alleles was not homogeneous among sampling localities: single and multilocus Hardy‐Weinberg and linkage disequilibria increased along the gradient toward the ecotone. Populations exhibited some isolation by distance effects in the face of substantial gene flow. We therefore recommend that higher conservation priority be assigned to the Mediterranean‐Negev ecotone area. For Chukar Partridges, it supports the highest overall genetic diversity as well as unique alleles. Priorities for other populations, moreover, can also be set based on their genetic diversity across ecological gradients. Rapid urbanization of Israeli landscapes threatens to disrupt unique and perhaps essential genetic connections among chukar populations, and management of chukars in Israel within a metapopulation context is an urgent requirement.

GENETIC FINGERPRINT-INFERRED POPULATION SUBDIVISION AND SPATIAL GENETIC TESTS FOR ISOLATION BY DISTANCE AND ADAPTATION IN THE COASTAL PLANT LIMONIUM CAROLINIANUM.

This paper examines two wild populations of Limonium carolinianum for population genetic subdivision and spatial patterns of genetic variation in an attempt to simultaneously test for both the action of local adaptation to tidal gradients and isolation by distance (IBD). A VNTR (variable number of tandem repeats) genetic "fingerprinting" marker was used to infer relatedness among mapped plants in two populations. Band sharing within and between populations estimated F'ST , an approximate measure of FST . Regression models were used to analyze the relationship between band sharing and spatial separation in tidal elevation and horizontal distance, as well as the relationship of fecundity differences with band sharing and spatial distance. Populations differed in band size frequency distributions and mean number of bands per profile and, therefore, likely differed in effective population size. F'ST was estimated at 0.0678 and was significantly greater than F'ST among randomly constructed subpopulations. Band sharing decreased 0.13% per meter in one population but showed no significant relation to distance in the other. In the population with significant IBD band sharing increased with increasingly different tidal elevation, contrary to an adaptive hypothesis, possibly due to directional gene flow or drift. Deme sizes were approximately 25 meters and greater than 100 meters, spanning larger areas than the entire environmental gradient. Fecundity differences were not associated with spatial parameters or band sharing. Unequal potential maternal fecundity measured as variance in number of seeds per maternal family was a significant source of genetic sampling variance. The VNTR marker employed is capable of detecting adaptation as identity by descent in ecological time and is an appropriate method for estimating the net evolutionary fate of polygenic traits. The results show that the net balance between selection along an environmental gradient and the effects of IBD and unequal maternal fecundity favor genetic differentiation by random processes in populations of Limonium.

The clonal and population structure of a rare endemic plant, Wyethia reticulata (Asteraceae): allozyme and RAPD analysis

Genetic structure arises when limited gene flow between populations favours the development of distinct arrays of genetic characters within each population. Determining the spatial scale at which this differentiation occurs is critical to our understanding of population biology and microevolution of species. The genetic structure and spatial pattern of genetic variation in an endemic, clonal perennial, Wyethia reticulata E. Greene, was investigated using random amplified polymorphic DNA (RAPD) markers and allozyme alleles. Large stands (250–360 m2) were found to contain few genetic individuals. Despite the small population sizes and endemism of the species, W. reticulata was highly diverse genetically, with most of the variation (75–81%) distributed within populations. A population structure in full agreement with spatially defined populations was achieved only by combining RAPD and allozyme markers. Analysis using both types of markers appeared to provide estimates of genetic similarity between individuals that were most consistent with empirical data on plant distributions. We postulated that large, long‐lived clones dominated genetic relationships within populations but also provided opportunities for gene flow between populations on a longer time scale. The two marker types yielded different estimates of between‐individual similarity and revealed disparate patterns of population structure. This result will arise because allozymes and random DNA segments have dissimilar evolutionary dynamics with respect to mutation and selection.

GENE DISPERSAL AND SPATIAL GENETIC STRUCTURE.

Spatial autocorrelation statistics have been studied in theoretical population genetic models and widely used in experimental studies of spatial structure in many plant and animal populations. However, the statistical properties of spatial autocorrelation statistics have remained uncharacterized. Little is known about how values of spatial autocorrelation statistics in population samples depend on the level of dispersal and scheme of sampling. In this paper, we characterize the statistical properties of join-count spatial autocorrelation statistics for population genetic surveys under various conditions of dispersal and sampling. The results indicate generally high statistical power. These results can provide a method to estimate gene dispersal based on standing spatial patterns of genetic variation observed within populations.

Spatial patterns of genetic variation generated by different forms of dispersal during range expansion

We examined the impact of three forms of dispersal, stepping-stone, normal and leptokurtic, on spatial genetic structure of expanding populations using computer simulations. When dispersal beyond neighbouring demes is allowed, rare long-distance migration leads to the establishment of pocket populations in advance of the main invasion front and results in spatial clustering of genotypes which persists for hundreds of generations. Patchiness is more pronounced when dispersal is leptokurtic as is the case in many animal and plant species. These results are of particular interest because population genetic parameters such as gene flow and effective population size are commonly estimated using gene frequency divergence information assuming equilibrium conditions and island models. We show how the three forms of dispersal during colonization bring about contrasting population genetic structures and how this affects estimates of gene flow. The implications for experimental studies of the spatial dimension of population genetic structure are discussed.

Spatial patterns of genetic variation generated by different forms of dispersal during range expansion

We examined the impact of three forms of dispersal, stepping-stone, normal and leptokurtic, on spatial genetic structure of expanding populations using computer simulations. When dispersal beyond neighbouring demes is allowed, rare long-distance migration leads to the establishment of pocket populations in advance of the main invasion front and results in spatial clustering of genotypes which persists for hundreds of generations. Patchiness is more pronounced when dispersal is leptokurtic as is the case in many animal and plant species. These results are of particular interest because population genetic parameters such as gene flow and effective population size are commonly estimated using gene frequency divergence information assuming equilibrium conditions and island models. We show how the three forms of dispersal during colonization bring about contrasting population genetic structures and how this affects estimates of gene flow. The implications for experimental studies of the spatial dimension of population genetic structure are discussed.

Temporal Variation in Genetic Diversity and Structure of a Lotic Population of Burkholderia (Pseudomonas) cepacia

The genetic structure and temporal patterns of genetic diversity in a population of Burkholderia (Pseudomonas) cepacia, isolated from a southeastern blackwater stream, were investigated by multilocus enzyme electrophoresis. Allelic variation in seven structural gene loci was monitored at a single stream location at 0, 6, 12, and 24 h and at 2, 4, 8, 16, and 32 days. Over the length of the study, 217 isolates were collected, from which 65 unique electrophoretic types (ETs) were identified. Most of these ETs were present at only one or two time periods and were considered transients; however, one resident ET was particularly abundant (64 of the 217 isolates [29.4%]) and was found at all time points except day 32. The mean genetic diversity of the entire population was 0.520, and the index of association (a measure of multilocus linkage disequilibrium) was 1.33. These results, taken in conjunction with a previous study focusing on spatial patterns of genetic diversity in lotic B. cepacia, show that these bacterial populations exhibit greater variability among sites than within a site over time, suggesting relative stability over short time periods.

Effect of geographical discontinuity on genetic variation in Quercus ilex L. (holm oak). Evidence from enzyme polymorphism

Allozymes at a maximum of eight loci were used to analyse the spatial patterns of genetic variation in 1942 holm oak trees (Quercus ilex L.) from 57 provenances distributed in the six main disjunct areas of the species distribution area. Polymorphism and genetic diversity were high except in the six marginal populations growing in various locations under unfavourable climatic conditions. Ten per cent of the total genetic diversity (Ht = 0.262) was accounted for by among-population variation. In this long-lived species, the effect of geographical discontinuities on gene flow restriction was shown by the occurrence of: (i) numerous rare alleles limited to a single disjunct region; and (ii) allele frequency variation among the disjunct regions for four alleles. This result was obtained by comparing spatial autocorrelograms from the 57 populations of the entire distribution area and from the 31 populations of the Mediterranean continental region which constitutes the largest continuous area in that distribution. Life history traits (e.g. long life span and high outcrossing rate) and past changes in climate and geographical continuity are assumed to be the main factors responsible for the present genetic variation patterns observed in the species.

Spatial structure of genetic variation within populations of forest trees

The spatial pattern and structure of genetic variation are important aspects of the population genetics of forest stands. Combined with limits to seed and pollen dispersal, spatial structure affects the level of inbreeding and the action of natural selection. The genetic constitution of stand regeneration, following different forestry practices, is also influenced by spatial structure. For example, natural regeneration with seed trees involves sampling seed trees from a stand that may be genetically nonhomogeneous. This paper reviews theoretical and empirical results on spatial patterns of genetic variation, produced under limited gene flow and selection, in terms of recently developed spatial statistics (e.g., spatial autocorrelation). Genetic correlations in samples from spatially structured populations are also described, as well as how spatial samples can be used to characterize the structure of genetic variation, and how inferences can be made about (spatially distributed) components of fitness and yield.

Reply to Sokal and Oden

Previous articleNext article No AccessNotes and CommentsReply to Sokal and OdenMontgomery Slatkin, and Hubert E. ArterMontgomery Slatkin Search for more articles by this author , and Hubert E. Arter Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by The American Naturalist Volume 138, Number 2Aug., 1991 Published for The American Society of Naturalists Article DOIhttps://doi.org/10.1086/285230 Views: 2Total views on this site Citations: 4Citations are reported from Crossref Copyright 1991 The University of ChicagoPDF download Crossref reports the following articles citing this article:T Jombart, S Devillard, A-B Dufour, D Pontier Revealing cryptic spatial patterns in genetic variability by a new multivariate method, Heredity 101, no.11 (Apr 2008): 92–103.https://doi.org/10.1038/hdy.2008.34Stefano Leonardi, Paolo Menozzi Spatial structure of genetic variability in natural stands of Fagus sylvatica L. (beech) in Italy, Heredity 77, no.44 (Oct 1996): 359–368.https://doi.org/10.1038/hdy.1996.154G.N. STONE, P. SUNNUCKS Genetic consequences of an invasion through a patchy environment — the cynipid gallwasp Andricus quercuscalicis (Hymenoptera: Cynipidae), Molecular Ecology 2, no.44 (Aug 1993): 251–268.https://doi.org/10.1111/j.1365-294X.1993.tb00015.xBryan K. Epperson Recent Advances in Correlation Studies of Spatial Patterns of Genetic Variation, (Jan 1993): 95–155.https://doi.org/10.1007/978-1-4615-2878-4_4

Spatial patterns of genetic variability in Italian chestnut (Castanea sativa)

The spatial patterns of genetic variation for 15 loci in 18 Italian populations of chestnut were analyzed. Multivariate analysis and spatial autocorrelation analysis showed two clinal variations, one in a west–east direction, the other in a north–south direction. There was a nonrandom spatial pattern of at least three alleles and a marked heterogeneity among populations of many others. An explanation is proposed in terms of migration flow for the majority of the polymorphisms and of selection for the three autocorrelated alleles. However, anthropic interferences may also be important. Key words: chestnut, electrophoresis, spatial autocorrelation, correspondence analysis, genetic boundaries, discriminant analysis.

Conservation Genetics of a Spring‐dwelling Desert Fish, the Pecos Gambusia (Gambusia nobilis, Poeciliidae)

Abstract:The genetic population structure of the Pecos gambusia was assessed with protein lectrophoresis to determine the best way to preserve the genetic diversity of the species. This small, federally protected live‐bearing fish is endemic to the Chihuahuan Desert region of New Mexico and Texas, where it occupies four isolated spring systems in the Pecos River drainage. Drying of springs due to lowering water tables is the most pervasive threat to the species.Fifty‐two percent of the total gene diversity detected in the species was due to differences between samples at different localities, while 48 percent was due to variability within samples. Most (67%) of the between‐sample diversity was due to differences among populations in the four major areas of occurrence. Populations in the Toyah Creek area of Texas exhibited striking spatial heterogeneity in allele frequencies and, compared with populations in the other three areas, unusually high levels of within‐sample genetic variability.The spatial pattern of genetic variation in the Pecos gambusia closely parallels that of a locally endemic, federally protected pupfish species in each of tux different areas. Also, one or more endemic species of invertebrate occurs in each area occupied by Pecos gambusia Protection of the natural pattern of genetic variability in Pecos gambusia would thus contribute significantly toward conservation of the genetic resources in a diverse assemblage of spring‐adapted species.