Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Oddou‐Muratorio, Sylvie; Vendramin, Giovanni G.; Buiteveld, J.; Fady, Bruno

doi:10.1007/s10592-008-9648-4

Cited by 68 publications

(56 citation statements)

References 14 publications

(25 reference statements)

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“…Nevertheless, positive F IS values were only revealed for single SSR markers and not constantly across all loci, suggesting that they were not due to inbreeding, but rather due to null alleles that indeed were detected for a few SSR markers. However, null alleles were at very low frequency and were not expected to largely bias the population genetic parameters [65]. In general, no statistically significant differences of the genetic diversity indices were detected between adult stands and seedlings.…”

Section: Neutral Genetic Variationmentioning

confidence: 77%

Genetic Variation of European Beech Populations and Their Progeny from Northeast Germany to Southwest Switzerland

Müller

Cuervo-Alarcon

Gailing

et al. 2018

Forests

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Climate change can adversely affect the growth of European beech (Fagus sylvatica L.) across its entire distribution range. Therefore, knowledge of the adaptive potential of this species to changing climatic conditions is of foremost importance. Genetic diversity is the basis for adaptation to environmental stress, and the regeneration phase of forests is a key stage affecting genetic diversity. Nevertheless, little is known about the effect of climate change on the genetic diversity of adult trees compared to their progeny. Here, we present genetic diversity data for 24 beech populations ranging from northeast Germany to southwest Switzerland. Potentially adaptive genetic variation was studied using single nucleotide polymorphism (SNP) markers in candidate genes that are possibly involved in adaptive trait variation. In addition, more than 2000 adult trees and 3000 of their seedlings were genotyped with simple sequence repeat (SSR) markers to determine selectively neutral genetic diversity and differentiation among populations. All populations showed high SSR and SNP variation, and no differences in genetic diversity were found between adult trees and their offspring. The genetic differentiation between adults and seedlings within the same stands was also insignificant or very low. Therefore, we can conclude tentatively that the transfer of genetic variation among tree generations, currently, is not much affected by climate change, at least in the studied beech populations.

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Section: Neutral Genetic Variationmentioning

confidence: 77%

Genetic Variation of European Beech Populations and Their Progeny from Northeast Germany to Southwest Switzerland

Müller

Cuervo-Alarcon

Gailing

et al. 2018

Forests

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“…In addition, the frequencies of null alleles were directly estimated by using the program INEst, running the individual inbreeding model (IIM) with a Gibbs sampler of 10 5 iterations (Chybicki and Burczyk, 2009a). An estimate of null allele frequencies in the data sets from French stands based on different approaches was also conducted by Oddou-Muratorio et al (2009). To take into account possible genotyping errors during microsatellite scoring, we accommodated loci for which the presence of null alleles was suspected, and performed parentage analysis following different approaches, as suggested in recent literature (Bacles and Ennos, 2008;Oddou-Muratorio et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

“…PCR amplifications were performed following the conditions reported in Pastorelli et al (2003) and fragment size detection was conducted as described by Buiteveld et al (2007). To rule out amplification failure due to laboratory errors or poor DNA quality, PCR was performed at least twice on samples without any amplification product, and DNA was re-isolated when amplification failure was systematic across loci (Oddou-Muratorio et al, 2009). …”

Section: Study Sites Sample Collection and Microsatellite Analysismentioning

confidence: 99%

Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

et al. 2011

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The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of factors such as isolation and tree density on gene movements. We used two paternity analysis approaches and different strategies to handle the possible presence of genotyping errors to obtain robust estimates of pollen flow in four European beech (Fagus sylvatica L.) populations from Austria and France. In each country one of the two plots is located in an unmanaged forest; the other plots are managed with a shelterwood system and inside a colonization area (in Austria and France, respectively). The two paternity analysis approaches provided almost identical estimates of gene flow. In general, we found high pollen immigration (B75% of pollen from outside), with the exception of the plot from a highly isolated forest remnant (B50%). In the two unmanaged plots, the average within-population pollen dispersal distances (from 80 to 184 m) were higher than previously estimated for beech. From the comparison between the Austrian managed and unmanaged plots, that are only 500 m apart, we found no evidence that either gene flow or reproductive success distributions were significantly altered by forest management. The investigated phenotypic traits (crown area, height, diameter and flowering phenology) were not significantly related with male reproductive success. Shelterwood seems to have an effect on the distribution of within-population pollen dispersal distances. In the managed plot, pollen dispersal distances were shorter, possibly because adult tree density is three-fold (163 versus 57 trees per hectare) with respect to the unmanaged one.

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“…This methodology was implemented in the software GENEPOP 4.0 (Rousset 2008). This statistical approach gives similar results to direct comparison between the maternal alleles and offspring as shown in Oddou-Muratorio et al (2008). The established procedure allowed detection of the percentage of null allele frequencies at each plot.…”

Section: Discarding Markers With Null Allelesmentioning

confidence: 99%

Genetic differentiation of European larch along an altitudinal gradient in the French Alps

Nardin

Musch

Rousselle

et al. 2015

Annals of Forest Science

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& Key message Despite variable dynamics of genetic diversification at the different altitudinal levels, strong gene flow tends to standardize larch genetic diversity: the larch forest distributed along the altitudinal gradient can be regarded as a single population. & Context While in forest tree species many studies focus on the structure of the genetic diversity at the natural range and at the forest stand levels, few studies have worked at intermediate levels like the landscape level. & Aims We tried to determine to what degree altitude variation can affect the genetic diversity and the local structure of the genetic diversity of European larch (Larix decidua Miller) at the landscape level. & Methods Using microsatellite markers, we determined the between-and within-plot genetic structure and the spatial genetic structure (SGS) of four altitudinal plots distributed between 1,350 and 2,300 m a.s.l. in a European larch forest located in the French Alps. & Results A homogenous neutral genetic structure was detected along this gradient. The intensity of the SGS was found to be stronger at 2,300 m and decreased at the 2,000-m plot. It was low or non-existent at the 1,700-and 1,350-m altitudinal levels. & Conclusion Our results suggest that the genetic structure observed at the landscape level in this European larch forest was only slightly affected by climatic variation, human activities, or historical events. However, the variation of intensity of the SGS within the altitudinal plots indicates the existence Contribution of the co-authors Maxime Nardin is the PhD student in charge of the study. Dr. Brigitte Musch supervised the writing of the article, then reviewed and commented on successive drafts of the paper. Dr. Yves Rousselle reviewed and commented on successive drafts of the paper. Vanina Guerin participated in cambium sampling and development of the genetic markers, supervised and organized the genotyping, and commented on successive drafts of the paper. Dr. Leopoldo Sanchez participated in the project and trial design and establishment, cambium sampling, and project coordination. Dr. Jean-Pierre Rossi participated in cambium sampling, designed and helped in performing the spatial genetic analysis (SGS), and reviewed and commented on successive drafts of the paper. Dr. Sophie Gerber supervised the development of the genetic markers and participated in cambium sampling, trial design and establishment, and project coordination. Sara Marin participated in the trial design and establishment, increment core and cambium sampling, and microdensity preparation and analysis process. Dr. Luc E. Pâques participated in the trial design and establishment and coordination of the research project, reviewed and commented on successive drafts of the paper, and co-supervised Maxime Nardin. Dr. Philippe Rozenberg led the project and trial design and establishment, participated in cambium sampling, reviewed and commented on successive drafts of the paper, coordinated the research project, and co-supervised Maxime Nar...

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Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Cited by 68 publications

References 14 publications

Genetic Variation of European Beech Populations and Their Progeny from Northeast Germany to Southwest Switzerland

Genetic Variation of European Beech Populations and Their Progeny from Northeast Germany to Southwest Switzerland

Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

Genetic differentiation of European larch along an altitudinal gradient in the French Alps

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