61 research outputs found
Statistical inference in population genetics using microsatellites
Statistical inference from molecular population genetic data is currently a very active
area of research for two main reasons. First, in the past two decades an enormous
amount of molecular genetic data have been produced and the amount of data is
expected to grow even more in the future. Second, drawing inferences about complex
population genetics problems, for example understanding the demographic and genetic
factors that shaped modern populations, poses a serious statistical challenge.
Amongst the many different kinds of genetic data that have appeared in the past
two decades, the highly polymorphic microsatellites have played an important role.
Microsatellites revolutionized the population genetics of natural populations, and were
the initial tool for linkage mapping in humans and other model organisms. Despite
their important role, and extensive use, the evolutionary dynamics of microsatellites
are still not fully understood, and their statistical methods are often underdeveloped
and do not adequately model microsatellite evolution. In this thesis, I address some
aspects of this problem by assessing the performance of existing statistical tools, and
developing some new ones. My work encompasses a range of statistical methods from
simple hypothesis testing to more recent, complex computational statistical tools. This
thesis consists of four main topics.
First, I review the statistical methods that have been developed for microsatellites
in population genetics applications. I review the different models of the microsatellite
mutation process, and ask which models are the most supported by data, and how
models were incorporated into statistical methods. I also present estimates of mutation
parameters for several species based on published data.
Second, I evaluate the performance of estimators of genetic relatedness using real
data from five vertebrate populations. I demonstrate that the overall performance
of marker-based pairwise relatedness estimators mainly depends on the population
relatedness composition and may only be improved by the marker data quality within
the limits of the population relatedness composition.
Third, I investigate the different null hypotheses that may be used to test for
independence between loci. Using simulations I show that testing for statistical
independence (i.e. zero linkage disequilibrium, LD) is difficult to interpret in
most cases, and instead a null hypothesis should be tested, which accounts for the
âbackground LDâ due to finite population size. I investigate the utility of a novel
approximate testing procedure to circumvent this problem, and illustrate its use on a
real data set from red deer.
Fourth, I explore the utility of Approximate Bayesian Computation, inference
based on summary statistics, to estimate demographic parameters from admixed
populations. Assuming a simple demographic model, I show that the choice of
summary statistics greatly influences the quality of the estimation, and that different
parameters are better estimated with different summary statistics. Most importantly, I
show how the estimation of most admixture parameters can be considerably improved
via the use of linkage disequilibrium statistics from microsatellite data
abc: an R package for Approximate Bayesian Computation (ABC)
Many recent statistical applications involve inference under complex models,
where it is computationally prohibitive to calculate likelihoods but possible
to simulate data. Approximate Bayesian Computation (ABC) is devoted to these
complex models because it bypasses evaluations of the likelihood function using
comparisons between observed and simulated summary statistics. We introduce the
R abc package that implements several ABC algorithms for performing parameter
estimation and model selection. In particular, the recently developed
non-linear heteroscedastic regression methods for ABC are implemented. The abc
package also includes a cross-validation tool for measuring the accuracy of ABC
estimates, and to calculate the misclassification probabilities when performing
model selection. The main functions are accompanied by appropriate summary and
plotting tools. Considering an example of demographic inference with population
genetics data, we show the potential of the R package.
R is already widely used in bioinformatics and several fields of biology. The
R abc package will make the ABC algorithms available to the large number of R
users. abc is a freely available R package under the GPL license, and it can be
downloaded at http://cran.r-project.org/web/packages/abc/index.html
Discerning Oriental from European beech by leaf spectroscopy: Operational and physiological implications
European beech (Fagus sylvatica L.) forests have recently experienced severe diebacks that are expected to increase in future. Oriental beech (Fagus sylvatica spp. orientalis (Lipsky) Greut. & Burd) is a potential candidate for
assisted migration (AM) in European forests due to its greater genetic diversity and potentially higher drought
resistance. Yet AM entails not only benefits, but also risks, and it is therefore important to monitor the progression
of introduced (sub)species. Here, we demonstrate the potential of leaf spectroscopy to replace resourceintensive
genetic analysis and field phenotyping for the discrimination and characterization of these two beech subspecies.
We studied two European beech forests, one in France and one in Switzerland, where Oriental beech from the Greater Caucasus was introduced over 100 years ago. During two summers (2021, 2022), we measured leaf spectral reflectance, leaf morphological and biochemical traits from genotyped adult trees. Subspecies prediction models were developed separately for top-of-canopy leaves (amenable to remote sensing) and bottom-of-canopy leaves (easier to harvest) using partial least squares discriminant analysis (PLS-DA) and different sets of spectral predictors.
Morphological, biochemical and spectra-derived leaf traits indicated that Oriental beech trees at the sites studied were characterized by higher lignin and nitrogen per unit leaf area than European beech, suggesting more protein-rich leaves on a per-area basis. The model based on top-of-canopy leaf reflectance spectra in the short-wave-infrared region (SWIR I: 1450â1750 nm) most accurately distinguished Oriental from European beech (BA = 0.86 ± 0.08, k = 0.72 ± 0.15), closely followed by models based on SWIR II, and on spectra-derived traits (BA â„ 0.84, k â„ 0.67).
This study provides a proof-of-principle for the development of spectroscopy-based approaches when monitoring
introduced species, subspecies or provenances. Our findings hold promise for upscaling to large forest areas using airborne remote sensing
Phylogenetic analysis of Tomato spotted wilt virus (TSWV) NSs protein demonstrates the isolated emergence of resistance-breaking strains in pepper
Resurgence of
Tomato spotted wilt virus
(TSWV) worldwide as well as in Hungary causing heavy
economic losses directed the attention to the factors con-
tributing to the outbreak of this serious epidemics. The
introgression of
Tsw
resistance gene into various pepper
cultivars seemed to solve TSWV control, but widely used
resistant pepper cultivars bearing the same, unique resis-
tance locus evoked the rapid emergence of resistance-
breaking (RB) TSWV strains. In Hungary, the sporadic
appearance of RB strains in pepper-producing region was
first observed in 2010â2011, but in 2012 it was detected
frequently. Previously, the non-structural protein (NSs)
encoded by small RNA (S RNA) of TSWV was verified as
the avirulence factor for
Tsw
resistance, therefore we
analyzed the S RNA of the Hungarian RB and wild type
(WT) isolates and compared to previously analyzed TSWV
strains with RB properties from different geographical
origins. Phylogenetic analysis demonstrated that the dif-
ferent RB strains had the closest relationship with the local
WT isolates and there is no conserved mutation present in
all the NSs genes of RB isolates from different geograph-
ical origins. According to these results, we concluded that
the RB isolates evolved separately in geographic point of
view, and also according to the RB mechanism
VirolĂłgia vizsgĂĄlatok Ă©tkezĂ©si Ă©s fƱszerpaprikĂĄn elĆfordulĂł uborka mozaik vĂrussal
Az idei Ă©vben jelentĆs vĂrusfertĆzöttsĂ©get tapasztaltunk szĂĄmos papri
katermesztĆ körzetben. A
hajtatĂĄsbĂłl Ă©s a szabadföldrĆl szĂĄrmazĂł mintĂĄk uborka mozaik vĂr
us fertĆzĂ©st mutattak. A
korĂĄbbi tapasztalattĂłl (a CMV II csoportba tartozĂł izolĂĄtum
ok dominĂĄltak) eltĂ©rĆen c. egyforma
arĂĄnyban fordultak elĆ a CMV I. Ă©s II. csoportjĂĄba tartozĂł
izolĂĄtumok. VizsgĂĄlatunk sorĂĄn
megĂĄllapĂtottuk, hogy egy Ășjabban termesztĂ©sbe kerĂŒlĆ CMV rez
isztens fajta Ă©s az ismert, de
rezisztenciĂĄval nem rendelkezĆ Ă©tkezĂ©si fajta között nem talĂĄlt
unk lĂ©nyegi kĂŒlönbsĂ©get a CMV
tolerancia tekintetĂ©ben sem a tĂŒnetek megjelenĂ©sĂ©ben, sem a vĂr
uskoncentrĂĄciĂłban. Azt
tapasztaltuk, hogy a CMV rezisztens fajtĂĄt idĆsebb korban fertĆz
ve a növĂ©nyben a vĂrus
lassabban szisztemizĂĄlĂłdik. Ărdekes tapasztalat volt, hogy a to
bamovĂrus rezisztencia gĂ©nt
tartalmazó fƱszerpaprika fajtåk érzékenyebbek voltak az ubor
ka mozaik vĂrus fertĆzĂ©sĂ©vel
szemben, mint a rezisztencia gént nem tartalmazó fajtåk
A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia
Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (Fagus sylvatica L.) is a dominant European forest tree species that increasingly suffers from climate change-related die-back. Here, we conducted a systematic literature review of neutral genetic diversity in European beech and created a meta-data set of expected heterozygosity (He) from all past studies providing nuclear microsatellite data. We propose a novel approach, based on population genetic theory and a minâmax scaling to make past studies comparable. Using a new microsatellite data set with unprecedented geographic coverage and various re-sampling schemes to mimic common sampling biases, we show the potential and limitations of the scaling approach. The scaled meta-dataset reveals the expected trend of decreasing genetic diversity from glacial refugia across the species range and also supports the hypothesis that different lineages met and admixed north of the European mountain ranges. As a result, we present a map of genetic diversity across the range of European beech which could help to identify seed source populations harboring greater diversity and guide sampling strategies for future genome-wide and functional investigations of genetic variation. Our approach illustrates how to combine information from several nuclear microsatellite data sets to describe patterns of genetic diversity extending beyond the geographic scale or mean number of loci used in each individual study, and thus is a proof-of-concept for synthesizing knowledge from existing studies also in other species
Discerning Oriental from European beech by leaf spectroscopy : operational and physiological implications
European beech (Fagus sylvatica L.) forests have recently experienced severe diebacks that are expected to increase in future. Oriental beech (Fagus sylvatica spp. orientalis (Lipsky) Greut. & Burd) is a potential candidate for assisted migration (AM) in European forests due to its greater genetic diversity and potentially higher drought resistance. Yet AM entails not only benefits, but also risks, and it is therefore important to monitor the progression of introduced (sub)species. Here, we demonstrate the potential of leaf spectroscopy to replace resource-intensive genetic analysis and field phenotyping for the discrimination and characterization of these two beech subspecies.
We studied two European beech forests, one in France and one in Switzerland, where Oriental beech from the Greater Caucasus was introduced over 100 years ago. During two summers (2021, 2022), we measured leaf spectral reflectance, leaf morphological and biochemical traits from genotyped adult trees. Subspecies prediction models were developed separately for top-of-canopy leaves (amenable to remote sensing) and bottom-of-canopy leaves (easier to harvest) using partial least squares discriminant analysis (PLS-DA) and different sets of spectral predictors.
Morphological, biochemical and spectra-derived leaf traits indicated that Oriental beech trees at the sites studied were characterized by higher lignin and nitrogen per unit leaf area than European beech, suggesting more protein-rich leaves on a per-area basis. The model based on top-of-canopy leaf reflectance spectra in the short-wave-infrared region (SWIR I: 1450â1750 nm) most accurately distinguished Oriental from European beech (BA = 0.86 ± 0.08, k = 0.72 ± 0.15), closely followed by models based on SWIR II, and on spectra-derived traits (BA â„ 0.84, k â„ 0.67).
This study provides a proof-of-principle for the development of spectroscopy-based approaches when monitoring introduced species, subspecies or provenances. Our findings hold promise for upscaling to large forest areas using airborne remote sensing
Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations
Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multi-locus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene-level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes Factors over many possible phase reconstructions. Epistatic selection offers a realistic multi-locus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Over all populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a non-synonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low-elevations and northern or southern populations. Several haplotypes contained non-synonymous mutations situated in genes with known functional importance for adaptation to climatic factor
Risks, benefits, and knowledge gaps of non-native tree species in Europe
Changing ecosystem conditions and diverse socio-economical events have contributed to an ingrained presence of non-native tree species (NNTs) in the natural and cultural European landscapes. Recent research endeavors have focused on different aspects of NNTs such as legislation, benefits, and risks for forestry, emphasizing that large knowledge gaps remain. As an attempt to fulfill part of these gaps, within the PEN-CAFoRR COST Action (CA19128) network, we established an open-access questionnaire that allows both academic experts and practitioners to provide information regarding NNTs from 20 European countries. Then, we integrated the data originating from the questionnaire, related to the country-based assessment of both peer-reviewed and grey literature, with information from available datasets (EUFORGEN and EU-Forest), which gave the main structure to the study and led to a mixed approach review. Finally, our study provided important insights into the current state of knowledge regarding NNTs. In particular, we highlighted NNTs that have shown to be less commonly addressed in research, raising caution about those characterized by an invasive behavior and used for specific purposes (e.g., wood production, soil recultivation, afforestation, and reforestation). NNTs were especially explored in the context of resilient and adaptive forest management. Moreover, we emphasized the assisted and natural northward migration of NNTs as another underscored pressing issue, which needs to be addressed by joint efforts, especially in the context of the hybridization potential. This study represents an additional effort toward the knowledge enhancement of the NNTs situation in Europe, aiming for a continuously active common source deriving from interprofessional collaboration.info:eu-repo/semantics/publishedVersio
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