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Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data.

ABSTRACT: A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation.

SUBMITTER: Wagner HH

PROVIDER: S-EPMC1449570 | biostudies-other | 2005 Mar

REPOSITORIES: biostudies-other

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Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data.

Wagner Helene H HH Holderegger Rolf R Werth Silke S Gugerli Felix F Hoebee Susan E SE Scheidegger Christoph C

Genetics 20050116 3

A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of ...[more]

PMID: 15654102

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Project description:BackgroundThe dynamic re-emergence of visceral leishmaniasis (VL) in south Europe and the northward shift to Leishmania-free European countries are well-documented. However, the epidemiology of VL due to Leishmania infantum in southeastern (SE) Europe and the Balkans is inadequately examined. Herein, we aim to re-evaluate and compare the population structure of L. infantum in SE and southwestern (SW) Europe.MethodsLeishmania strains collected from humans and canines in Turkey, Cyprus, Bulgaria, Greece, Albania and Croatia, were characterized by the K26-PCR assay and multilocus enzyme electrophoresis (MLEE). Genetic diversity was assessed by multilocus microsatellite typing (MLMT) and MLM Types were analyzed by model- and distance- based algorithms to infer the population structure of 128 L. infantum strains.ResultsL. infantum MON-1 was found predominant in SE Europe, whilst 16.8% of strains were MON-98. Distinct genetic populations revealed clear differentiation between SE and SW European strains. Interestingly, Cypriot canine isolates were genetically isolated and formed a monophyletic group, suggesting the constitution of a clonal MON-1 population circulating among dogs. In contrast, two highly heterogeneous populations enclosed all MON-1 and MON-98 strains from the other SE European countries. Structure sub-clustering, phylogenetic and Splitstree analysis also revealed two distinct Croatian subpopulations. A mosaic of evolutionary effects resulted in consecutive sub-structuring, which indicated substantial differentiation and gene flow among strains of both zymodemes.ConclusionsThis is the first population genetic study of L. infantum in SE Europe and the Balkans. Our findings demonstrate the differentiation between SE and SW European strains; revealing the partition of Croatian strains between these populations and the genetic isolation of Cypriot strains. This mirrors the geographic position of Croatia located in central Europe and the natural isolation of the island of Cyprus. We have analysed the largest number of MON-98 strains so far. Our results indicate extensive gene flow, recombination and no differentiation between MON-1 and MON-98 zymodemes. No correlation either to host specificity or place and year of strain isolation was identified. Our findings may be associated with intensive host migration and common eco-epidemiological characteristics in these countries and give valuable insight into the dynamics of VL.

Project description:Summer flounder Paralichthys dentatus supports one of the most valuable commercial and recreational fisheries along the Atlantic Coast of the U.S. However, in recent decades the management of this species has proven to be one of the most contentious for any exploited marine resource in the region. A coastwide catch quota is imposed annually for summer flounder of which 60% is allocated to the commercial fishery and 40% to the recreational fishery. The allocation is further divided among the individual coastal states from North Carolina to Massachusetts based on their landings in the 1980s. This process, based on political jurisdictions, does not consider the species' biological stock structure. Previous genetic studies (allozyme, mtDNA, and SNPs) provided contradictory results regarding the possible population structure of summer. To address this issue, we used DNA microsatellite analysis at 9 loci to define the coastwide population structure of summer flounder. In total, 1,182 specimens were analyzed from 18 collection sites. Most collections were from the continental shelf during the fall-winter spawning season. These were supplemented with additional samples from inshore waters from North Carolina to Florida, and inshore sites which support significant recreational fisheries at Nantucket Shoals, Massachusetts and Fire Island, New York. The overall level of genetic differentiation in pairwise comparison between collections was very low, mean F ST = 0.001. There was no evidence of genetic differentiation between collections from north and south of Cape Hatteras. Our microsatellite results are consistent with an earlier SNP study which failed to find significant allelic heterogeneity among coastwide collections of summer flounder. However, a subset of pairwise F ST comparisons between some collections proved statistically significant. Furthermore, in STRUCTURE analysis we found evidence of two genetic clusters within the species' northern landings area, however, this finding was not supported by DPAC analysis. We conclude that summer flounder most likely constitute a single population along their entire Atlantic Coast distribution.

Dataset Information

Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data.

Publications

Variogram analysis of the spatial genetic structure of continuous populations using multilocus microsatellite data.

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