Isolation-by-distance within naturally established populations of European beech (Fagus sylvatica)

Botany ◽  
2009 ◽  
Vol 87 (8) ◽  
pp. 791-798 ◽  
Author(s):  
Igor J. Chybicki ◽  
Magdalena Trojankiewicz ◽  
Andrzej Oleksa ◽  
Artur Dzialuk ◽  
Jaroslaw Burczyk
Keyword(s):  
Genetic Structure ◽  
Fagus Sylvatica ◽  
Spatial Clustering ◽  
Scale Effects ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Pollen Dispersal ◽  
Distance Effect ◽  
European Beech ◽  
Biparental Inbreeding

In plants, the magnitude of seed and pollen dispersal plays a pivotal role in shaping genetic structure of populations. Restricted dispersal of genes can stimulate the increase of inbreeding as well as spatial clustering of relatives. These phenomena are explained by the theory of isolation-by-distance. Because of its biology, European beech ( Fagus sylvatica L.) seems to be susceptible to isolation-by-distance. However, to date fine-scale effects, including biparental inbreeding and a spatial genetic structure are not fully recognized for this species. In this study, two populations of European beech were investigated, both representing a dense beech forest, typical for Central Europe. Using nine microsatellite markers and a recently developed method, we found a significant level of biparental inbreeding in both populations. Spatial autocorrelation analysis revealed that both populations exhibit clustering of related individuals up to 40 m. The observed spatial genetic structure fit well to the log-linear regression model. Thus, results confirmed our hypothesis of the presence of the isolation-by-distance effect. Furthermore, based on these results we inferred a dispersal mode, both for seeds and pollen; in particular, seed dispersal was 10–100 times more restricted than pollen flow, although a significant portion of short-distance pollinations responsible for biparental inbreeding cannot be excluded.

scholarly journals Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability

Heredity ◽  
2012 ◽  
Vol 108 (6) ◽  
pp. 633-639 ◽  
Author(s):  
A S Jump ◽  
L Rico ◽  
M Coll ◽  
J Peñuelas
Keyword(s):  
Genetic Structure ◽  
Fagus Sylvatica ◽  
Spatial Genetic Structure ◽  
Natural Populations ◽  
European Beech

scholarly journals Fine-Scale Spatial Genetic Structure with Nonuniform Distribution of Individuals

Genetics ◽  
1998 ◽  
Vol 148 (2) ◽  
pp. 905-919
Author(s):  
Agnès Doligez ◽  
Claire Baril ◽  
Hélène I Joly
Keyword(s):  
Genetic Structure ◽  
Local Density ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Pollen Dispersal ◽  
Continuous Distribution ◽  
Fine Scale ◽  
Independent Locus ◽  
Continuous Plant ◽  
Input Variables

Abstract This paper presents the first theoretical study of spatial genetic structure within nonuniformly distributed continuous plant populations. A novel individual-based model of isolation by distance was constructed to simulate genetic evolution within such populations. We found larger values of spatial genetic autocorrelations in highly clumped populations than in uniformly distributed populations. Most of this difference was caused by differences in mean dispersal distances, but aggregation probably also produced a slight increase in spatial genetic structure. Using an appropriate level of approximation of the continuous distribution of individuals in space, we assessed the potential effects of density, seed and pollen dispersal, generation overlapping, and overdominance selection at an independent locus, on fine-scale genetic structure, by varying them separately in a few particular cases with extreme clumping. When selfing was allowed, all these input variables influenced both aggregation and spatial genetic structure. Most variations in spatial genetic structure were closely linked to variations in clumping and/or local density. When selfing was not allowed, spatial genetic structure was lower in most cases.

scholarly journals A Circular Chloroplast Genome of Fagus sylvatica Reveals High Conservation between Two Individuals from Germany and One Individual from Poland and an Alternate Direction of the Small Single-Copy Region

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 180
Author(s):  
Bagdevi Mishra ◽  
Bartosz Ulaszewski ◽  
Sebastian Ploch ◽  
Jaroslaw Burczyk ◽  
Marco Thines
Keyword(s):  
Chloroplast Genome ◽  
Fagus Sylvatica ◽  
Pollen Dispersal ◽  
European Beech ◽  
Single Copy ◽  
Migration History ◽  
Chloroplast Genomes ◽  
Long Read ◽  
The Individual ◽  
Small Single Copy

Chloroplasts are difficult to assemble because of the presence of large inverted repeats. At the same time, correct assemblies are important, as chloroplast loci are frequently used for biogeography and population genetics studies. In an attempt to elucidate the orientation of the single-copy regions and to find suitable loci for chloroplast single nucleotide polymorphism (SNP)-based studies, circular chloroplast sequences for the ultra-centenary reference individual of European Beech (Fagus sylvatica), Bhaga, and an additional Polish individual (named Jamy) was obtained based on hybrid assemblies. The chloroplast genome of Bhaga was 158,458 bp, and that of Jamy was 158,462 bp long. Using long-read mapping on the configuration inferred in this study and the one suggested in a previous study, we found an inverted orientation of the small single-copy region. The chloroplast genome of Bhaga and of the individual from Poland both have only two mismatches as well as three and two indels as compared to the previously published genome, respectively. The low divergence suggests low seed dispersal but high pollen dispersal. However, once chloroplast genomes become available from Pleistocene refugia, where a high degree of variation has been reported, they might prove useful for tracing the migration history of Fagus sylvatica in the Holocene.

scholarly journals Spatial genetic structure of the sea sandwort (<i>Honckenya peploides</i>) on Surtsey: an immigrant's journey

2014 ◽  
Vol 11 (22) ◽  
pp. 6495-6507 ◽  
Author(s):  
S. H. Árnason ◽  
Ǽ. Th. Thórsson ◽  
B. Magnússon ◽  
M. Philipp ◽  
H. Adsersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Early Stage ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Rapid Expansion ◽  
Aflp Markers ◽  
Plant Colonization ◽  
Southern Coast ◽  
Binary Matrix

Abstract. Sea sandwort (Honckenya peploides) was one of the first plants to successfully colonize and reproduce on the volcanic island Surtsey, formed in 1963 off the southern coast of Iceland. Using amplified fragment length polymorphic (AFLP) markers, we examined levels of genetic variation and differentiation among populations of H. peploides on Surtsey in relation to populations on the nearby island Heimaey and from the southern coast of Iceland. Selected populations from Denmark and Greenland were used for comparison. In addition, we tested whether the effects of isolation by distance could be seen in the Surtsey populations. Using two primer combinations, we obtained 173 AFLP markers from a total of 347 plant samples. The resulting binary matrix was then analysed statistically. The main results include the following: (i) Surtsey had the highest proportion of polymorphic markers as well as a comparatively high genetic diversity (55.5% proportion of polymorphic loci, PLP; 0.1974 HE) and Denmark the lowest (31.8% PLP; 0.132 HE), indicating rapid expansion during an early stage of population establishment on Surtsey and/or multiple origins of immigrants; (ii) the total genetic differentiation (FST) among Surtsey (0.0714) and Heimaey (0.055) populations was less than half of that found among the mainland populations in Iceland (0.1747), indicating substantial gene flow on the islands; (iii) most of the genetic variation (79%, p < 0.001) was found within localities, possibly due to the outcrossing and subdioecious nature of the species; (iv) a significant genetic distance was found within Surtsey, among sites, and this appeared to correlate with the age of plant colonization; and (v) the genetic structure analysis indicated multiple colonization episodes on Surtsey, whereby H. peploides most likely immigrated from the nearby island of Heimaey and directly from the southern coast of Iceland.

scholarly journals Can We Compare Effect Size of Spatial Genetic Structure Between Studies and Species Using Moran Eigenvector Maps?

2021 ◽  
Vol 9 ◽  
Author(s):  
Celia Hein ◽  
Hossam E. Abdel Moniem ◽  
Helene H. Wagner
Keyword(s):  
Genetic Structure ◽  
Effect Size ◽  
Stationary Process ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Sampling Locations ◽  
Number Of Individuals ◽  
Moran Eigenvector Maps

As the field of landscape genetics is progressing toward comparative empirical studies and meta-analysis, it is important to know how best to compare the strength of spatial genetic structure between studies and species. Moran’s Eigenvector Maps are a promising method that does not make an assumption of isolation-by-distance in a homogeneous environment but can discern cryptic structure that may result from multiple processes operating in heterogeneous landscapes. MEMgene uses spatial filters from Moran’s Eigenvector Maps as predictor variables to explain variation in a genetic distance matrix, and it returns adjusted R2 as a measure of the amount of genetic variation that is spatially structured. However, it is unclear whether, and under which conditions, this value can be used to compare the degree of spatial genetic structure (effect size) between studies. This study addresses the fundamental question of comparability at two levels: between independent studies (meta-analysis mode) and between species sampled at the same locations (comparative mode). We used published datasets containing 9,900 haploid, biallelic, neutral loci simulated on a quasi-continuous, square landscape under four demographic scenarios (island model, isolation-by-distance, expansion from one or two refugia). We varied the genetic resolution (number of individuals and loci) and the number of random sampling locations. We considered two measures of effect size, the MEMgene adjusted R2 and multivariate Moran’s I, which is related to Moran’s Eigenvector Maps. Both metrics were highly sensitive to the number of locations, even when using standardized effect sizes, SES, and the number of individuals sampled per location, but not to the number of loci. In comparative mode, using the same Moran Eigenvector Maps for all species, even those with missing values at some sampling locations, reduced bias due to the number of locations under isolation-by-distance (stationary process) but increased it under expansion from one or two refugia (non-stationary process). More robust measures of effect size need to be developed before the strength of spatial genetic structure can be accurately compared, either in a meta-analysis of independent empirical studies or within a comparative, multispecies landscape genetic study.

Staying close: short local dispersal distances on a managed forest of two Patagonian Nothofagus species

2020 ◽  
Vol 93 (5) ◽  
pp. 652-661 ◽  
Author(s):  
Georgina Sola ◽  
Verónica El Mujtar ◽  
Leonardo Gallo ◽  
Giovanni G Vendramin ◽  
Paula Marchelli
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Pollen Dispersal ◽  
Dispersal Distance ◽  
Restricted Gene Flow ◽  
Fine Scale ◽  
Gene Dispersal ◽  
Mature Trees ◽  
The Impact

Abstract Understanding the impact of management on the dispersal potential of forest tree species is pivotal in the context of global change, given the implications of gene flow on species evolution. We aimed to determine the effect of logging on gene flow distances in two Nothofagus species from temperate Patagonian forests having high ecological relevance and wood quality. Therefore, a total of 778 individuals (mature trees and saplings) of Nothofagus alpina and N. obliqua, from a single plot managed 20 years ago (2.85 hectares), were mapped and genotyped at polymorphic nuclear microsatellite loci. Historical estimates of gene dispersal distance (based on fine-scale spatial genetic structure) and contemporary estimates of seed and pollen dispersal (based on spatially explicit mating models) were obtained. The results indicated restricted gene flow (gene distance ≤ 45 m, both pollen and seed), no selfing and significant seed and pollen immigration from trees located outside the studied plot but in the close surrounding area. The size of trees (diameter at breast height and height) was significantly associated with female and/or male fertility. The significant fine-scale spatial genetic structure was consistent with the restricted seed and pollen dispersal. Moreover, both estimates of gene dispersal (historical and contemporary) gave congruent results. This suggests that the recent history of logging within the study area has not significantly influenced on patterns of gene flow, which can be explained by the silviculture applied to the stand. The residual tree density maintained species composition, and the homogeneous spatial distribution of trees allowed the maintenance of gene dispersal. The short dispersal distance estimated for these two species has several implications both for understanding the evolution of the species and for defining management, conservation and restoration actions. Future replication of this study in other Nothofagus Patagonian forests would be helpful to validate our conclusions.

Population genetic structure of the Gulf of St. Lawrence aster, Symphyotrichum laurentianum (Asteraceae), a threatened coastal endemic

Botany ◽  
2009 ◽  
Vol 87 (11) ◽  
pp. 1089-1095 ◽  
Author(s):  
Stephen B. Heard ◽  
Linley K. Jesson ◽  
Kirby Tulk
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Threatened Species ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Population Decline ◽  
Allelic Diversity ◽  
Magdalen Islands

The Gulf of St. Lawrence aster ( Symphyotrichum laurentianum (Fernald) G.L. Nesom) is an endemic annual of saline habitats in the southern Gulf of St. Lawrence. It is listed as a threatened species, and has recently experienced population declines in much of its range. We used 11 allozyme markers to assay population genetic variation in six wild populations of S. laurentianum from the Magdalen Islands, Quebec (QC), the only remaining wild population from Prince Edward Island National Park (PEI), and a greenhouse population founded in 1999 with seed collected from PEI. Symphyotrichum laurentianum harbours moderate genetic diversity (Ps = 0.36, As = 1.54), with only modest spatial genetic structure (pairwise FST < 0.15) and no significant isolation by distance. The PEI population had greatly reduced allelic diversity compared with the populations from the Magdalen Islands, which likely act as a reservoir of genetic variation in S. laurentianum. Recent loss of alleles during population decline in PEI is suggested by the retention of greater allelic diversity in the greenhouse population. Estimates of breeding structure suggest small but nonzero rates of outcross pollination (FIS = 0.73, 95% CI = 0.48–0.97; outcrossing rate ∼16%). Population genetic structure in S. laurentianum can inform those forming and carrying out conservation and recovery plans for this threatened species.

scholarly journals Temporal patterns of spatial genetic structure and effective population size in European plaice (Pleuronectes platessa) along the west coast of Scotland and in the Irish Sea

2009 ◽  
Vol 67 (4) ◽  
pp. 607-616 ◽  
Author(s):  
Phillip C. Watts ◽  
Suzanne M. Kay ◽  
Drew Wolfenden ◽  
Clive J. Fox ◽  
Audrey J. Geffen ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
West Coast ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Irish Sea ◽  
Effective Population ◽  
The West ◽  
Pleuronectes Platessa

Abstract Watts, P. C., Kay, S. M., Wolfenden, D., Fox, C. J., Geffen, A. J., Kemp, S. J., and Nash, R. D. M. 2010. Temporal patterns of spatial genetic structure and effective population size in European plaice (Pleuronectes platessa) along the west coast of Scotland and in the Irish Sea. – ICES Journal of Marine Science, 67: 607–616. The European plaice (Pleuronectes platessa) is a relatively mobile flatfish species, and previous studies have reported broad-scale genetic homogeneity among samples distributed throughout much of its northern European range, with no evidence for isolation-by-distance (IBD) population structure. Using microsatellite loci, the pattern of spatial genetic structure and effective population size is characterized for >800 plaice collected from locations off the west coast of Great Britain over a 3-year period (2001–2003). The plaice populations are characterized by weak spatial genetic structure, consistent with tagging data, and relatively low effective population sizes. In contrast to previous work, a pattern of isolation by distance is present among pairs of plaice from within each sampling period. However, IBD spatial structure was not observed for comparisons of plaice from different sampling years or using the entire dataset, indicating a patchy temporal genetic structure. Therefore, pooling the data from several years can mask subtle patterns of population structure and potentially confound estimation of other important demographic parameters, such as effective population size.

scholarly journals Spatial genetic structure in the very rare and species-rich Picea chihuahuana tree community (Mexico)

2014 ◽  
Vol 63 (1-6) ◽  
pp. 149-158 ◽  
Author(s):  
C. Z. Quiñones-Pérez ◽  
S. L. Simental-Rodríguez ◽  
C. Sáenz-Romero ◽  
J. P. Jaramillo-Correa ◽  
C. Wehenkel
Keyword(s):  
Genetic Structure ◽  
Populus Tremuloides ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Strong Support ◽  
Forest Tree ◽  
Conservation Strategies ◽  
Fine Scale ◽  
Ecological Features ◽  
Tree Community

Abstract In natural plant populations, the spatial genetic structure (SGS) is occasionally associated with evolutionary and ecological features such as the mating system, individual fitness, inbreeding depression and natural selection of the species of interest. The very rare Mexican P. chihuahuana tree community covers an area no more than 300 ha and has been the subject of several studies concerning its ecology and population genetics. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. However, analysis of the fine-scale SGS in this special forest tree community has not yet been conducted, which might help enrich the above mentioned conservation programs. In this study, we examined the SGS of this community, mostly formed by P. chihuahuana Martínez, Pinus strobiformis Ehrenberg ex Schlechtendah, Pseudotsuga menziesii (Mirb.) Franco, and Populus tremuloides Michx, in 14 localities at both the fine and large scales, with the aim of obtaining a better understanding of evolutionary processes. We observed a non-significant autocorrelation in fine-scale SGS, suggesting that the genetic variants of all four tree species are randomly distributed in space within each sampled plot of 50 x 50 m. At the larger scale, the autocorrelation was highly significant for P. chihuahuana and P. menziesii, probably as a result of insufficient gene flow due to the extreme population isolation and small sizes. For these two species our results provided strong support for the theory of isolation by distance.

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