Population genetics of Norway spruce ( Picea abies Karst.) at regional scale: sensitivity of different microsatellite motif classes in detecting differentiation (original) (raw)
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Genetic variation between and within populations of Engelmann spruce and subalpine fir
Genome, 1990
SHEA, K. L. 1990. Genetic variation between and within populations of Engelmann spruce and subalpine fir. Genome, 33: 1-8. The genetic structure of Engelmann spruce (Picea engelrnannii) and subalpine fir (Abies lasiocarpa) in two adjacent sites in the Colorado Front Range was examined using allozyme data from 21 loci in spruce and 18 loci in fir. The genetic diversity measures of alleles per locus, percent loci polymorphic, and mean heterozygosity did not differ significantly between or within species. However, the observed heterozygosity (0.126 spruce, 0.081 fir) values suggest that Engelmann spruce is more genetically variable than subalpine fir. Mean inbreeding coefficients were twice as high in fir as in spruce (FIs = 0.154 spruce, 0.341 fir). There were significant differences in allele frequencies in both species between and within sites, and among age-classes, with spatial differences greater than temporal differences. F-statistics showed greater genetic differentiation within (FsT = 2.3-2.6% spruce, 2.0-2.8% fir) than between sites (FsT = 1.7% spruce, 1.3% fir). Both species had higher FsT and genetic distance values, yet lower Fls values, for spatial subdivisions within rather than between sites. This pattern suggests that the size of a spatial subdivision, where maximum gene flow is 54 m, approximates the size of the largest panmictic unit. In contrast with studies on other conifers, these results suggest that factors such as differential selection pressures, seed dispersal patterns, and clumped spatial distribution have resulted in genetic differentiation at the microhabitat level in Engelmann spruce and subalpine fir. between and within populations of Engelmann spruce and subalpine fir. Genome, 33 : 1-8. La structure genetique de l'epinette d'Engelmann (Picea engelrnannii) et celle du sapin concolore subalpin (Abies lasiocarpa) de deux sites adjacents de la region frontalikre du Colorado ont Cte examinees d'apres les donnees relatives aux allozymes de 21 locus chez l'kpinette et de 18 locus chez le sapin. La diversite des mesures genetiques des alleles par locus, les pourcentages de locus polymorphes et les moyennes d'heterogeneite, n'ont pas differe de facon significative entre ou a l'interieur des especes. Toutefois, les valeurs d'heterogeneite observees (0,126 pour les epinettes et 0,081 pour les sapins) suggerent que les epinettes d'Engelmann sont genetiquement plus variables que les sapins concolores subalpins. Les coefficients moyens de l'endogamie ont ete deux fois aussi eleves chez les sapins que chez les epinettes (FlS = 0,154 pour les epinettes et 0,341 pour les sapins). Les differences de frequences d'alleles ont ete significatives chez les deux especes entre et a l'interieur des sites et, parmi les classes d'ilges, les differences ont ete plus grandes sur le plan spatial que temporel. Les tests statistiques F o n t montre une plus grande differenciation genetique a l'interieur des sites (FsT = 2,3-2,6% pour les epinettes et 2,O-2,8% pour les sapins) qu'entre les sites (FsT = 1,7070 pour les epinettes et 1,3% pour les sapins). Les valeurs de distances genetiques et de FsT ont ete plus elevees chez les deux especes, mais les valeurs FIS ont ete inferieures pour les sous-divisions spatiales a l'interieur plutdt qu'entre les sites. Ce schema suggere que la dimension d'une sous-division spatiale, la oh le flux genique maximal est de 54 m, avoisine celle de la plus grande unite panmictique. A l'oppose des etudes portant sur d'autres coniferes, ces resultats suggerent que des facteurs comme des pressions de selection differentielle, des modes de dispersion des graines et des distributions spatiales regroupees ont conduit a des differenciations genetiques au niveau de microhabitats chez les epinettes d'Engelmann et chez les sapins concolores subalpins.
Chloroplast Microsatellite Differentiation in Jack Pine (Pinus Banksiana) Populations in Quebec
2005
In this study we investigated the genetic structure and diversity of jack pine populations in Quebec using chloroplast microsatellite markers. Six cpSSR loci were used to screen 15 Pinus banksiana populations from an economically important region of the boreal zone. The main objective was to quantify the variation within and among populations and to relate this to their geographic pattern. From 3 to 6 size variants were identified at each locus. A total of 29 size variants at the six loci were identified and 5 of the size variants occurred infrequently. The size variants were combined into 87 different haplotypes, of which 49 were unique. The AMOVA analysis revealed that 10.96% of the variation was distributed between populations and 89.04% within populations. Cluster analysis divided the studied populations into two large groups, one from north-western Quebec and the second from eastern Quebec. These results suggest that the genetic structure of the studied jack pine populations is...
Microsatellite DNA as shared genetic markers among conifer species
Canadian Journal of Forest Research, 1999
Polymerase chain reaction (PCR) primer pairs for 21 simple sequence repeat (SSR) loci in Pinus strobus L. and 6 in Pinus radiata D. Don. were evaluated to determine whether SSR marker amplification could be achieved in 10 other conifer species. Eighty percent of SSR primer pairs for (AC) n loci that were polymorphic in P. strobus also amplified SSR loci in two other soft pines of the subgenus Strobus but not in seven hard pines of the subgenus Pinus, nor in Picea glauca (Moench) Voss or Pseudotsuga menziesii (Mirb.) Franco. The six P. strobus SSR primer pairs that did amplify loci from conifers other than soft pines were those that were specific to loci monomorphic within P. strobus. These six loci were also monomorphic within seven other species tested, but four of the loci were polymorphic among species. A comparison of allelic variation among the three soft pine species found only 25 shared alleles among a total of 122 alleles at eight loci. Primer pairs for dinucleotide SSR loci that were polymorphic in Pinus radiata also specifically amplified loci from various other hard pines but not from the soft pines or from the other conifers tested.
Forest tree species of temperate and boreal regions have undergone a long history of demographic changes and evolutionary adaptations. The main objective of this study was to detect signals of selection in Norway spruce (Picea abies [L.] Karst), at different sampling-scales and to investigate, accounting for population structure, the effect of environment on species genetic diversity. A total of 384 single nucleotide polymorphisms (SNPs) representing 290 genes were genotyped at two geographic scales: across 12 populations distributed along two altitudinal-transects in the Alps (micro-geographic scale), and across 27 populations belonging to the range of Norway spruce in central and southeast Europe (macro-geographic scale). At the macrogeographic scale, principal component analysis combined with Bayesian clustering revealed three major clusters, corresponding to the main areas of southern spruce occurrence, i.e. the Alps, Carpathians, and Hercynia. The populations along the altitudinal transects were not differentiated. To assess the role of selection in structuring genetic variation, we applied a Bayesian and coalescent-based F ST-outlier method and tested for correlations between allele frequencies and climatic variables using regression analyses. At the macro-geographic scale, the F ST-outlier methods detected together 11 F ST-outliers. Six outliers were detected when the same analyses were carried out taking into account the genetic structure. Regression analyses with population structure correction resulted in the identification of two (micro-geographic scale) and 38 SNPs (macro-geographic scale) significantly correlated with temperature and/or precipitation. Six of these loci overlapped with F ST-outliers, among them two loci encoding an enzyme involved in riboflavin biosynthesis and a sucrose synthase. The results of this study indicate a strong relationship between genetic and
Genetic diversity in managed subpopulations of Norway spruce [Picea abies (L.) Karst.]
Forest Ecology and Management, 2006
Uniparentally inherited chloroplast simple sequence repeats (cpSSRs), mitochondrial markers (mt), as well as biparentally inherited nuclear simple sequence repeats (SSRs) were used to analyse genetic diversity in different subpopulations of Norway spruce in Austria. For that purpose Norway spruce individuals of different age classes, old (70-100 years) versus young (6-10 years) trees, were fingerprinted to elucidate the genetic effects caused by human management. Three populations from different elevations were selected in a restricted area. Four hundred and fifty individuals, 50 old and 100 young trees from each population, were analysed for this study. Seven paternally inherited cpSSRs revealed no variation within and among populations. In contrast, analysis of three maternal mitochondrial markers showed variation in one locus in individuals originating from the high elevation sample set. Analysis of five polymorphic nuclear SSR loci revealed 135 different alleles. Nuclear SSRs results showed that there is generally more genetic variation and heterozygosity within populations than among populations. Populations from high elevation exhibit more genetic variation than samples from middle and low elevations.
Tree Genetics & Genomes
Wild cherry (Prunus avium L.) is a widespread, partially asexual, noble hardwood European species characterized by a scattered distribution, small population sizes, and human exploitation for its valuable wood. These characteristics, especially at the southern limits of the species natural distribution where additional varying stresses may occur, render P. avium populations prone to potential stochastic, genetic, and demographic events. In this study, we used dominant inter simple sequence repeat (ISSR) and codominant simple sequence repeat (SSR) markers to infer the genetic structure of P. avium. Five populations from northern Greece were evaluated based on 46 ISSR and 11 SSR loci. Populations presented a relatively high level of genetic variation, with a mean genetic diversity of H e = 0.166 and H e = 0.740 regarding ISSR and SSR analysis, respectively. We observed moderate population differentiation for ISSR (G ST = 0.113) and SSR (F ST = 0.097) markers. AMOVA also detected significant differentiation among populations for ISSRs (Φ ST = 0.338) and SRRs (Φ ST = 0.162). According to linkage disequilibrium analysis, estimates of effective population size were generally sufficient for maintaining extant genetic variability and evolutionary potential. A possible bottleneck was detected for only one population. In general, it appears that despite the particular characteristics of the P. avium populations studied, genetic stochasticity events were not apparent. The studied populations, located at the rear edge of the species European distribution, reveal a wealth of genetic variation that is very valuable for the genetic conservation of local adaptive gene complexes, especially under contemporary climatic change scenarios.
Randomly amplified polymorphic DNA linkage relationships in different Norway spruce populations
Canadian Journal of Forest Research, 2001
We tested the constancy of linkage relationships of randomly amplified polymorphic DNA (RAPD) marker loci used to construct a population-based consensus map in material from an Italian stand of Picea abies (L.) Karst. in 29 individuals from three Norwegian populations. Thirteen marker loci linked in the Italian stand did show a consistent locus ordering in the Norwegian population. The remaining 16 unlinked marker loci were spread over different linkage groups and (or) too far apart both in the population map and in this study. The limited validity of RAPD markers as genomic "hallmarks" resilient across populations is discussed. We also investigated the reliability of RAPD markers; only 58% of the RAPD markers previously used to construct the consensus map in the Italian population were repeatable in the same material. Of the repeatable ones 76.3% were amplified and found polymorphic in 29 megagametophyte sibships from three Norwegian populations.
Journal of Mammalogy, 2007
Nucleotide sequences from the mitochondrial control region and genotypes from 5 nuclear microsatellite loci were used to examine genetic structure and infer recent (within approximately the last 3,000 years) evolutionary history of a population (549 individuals) of the southern plains woodrat (Neotoma micropus). Observed heterozygosity values ranged from 0.61 to 0.89 across microsatellite loci and systematically were lower than expected heterozygosity values (0.66-0.95). Probability of unique identity using microsatellite data was high (1 individual in 66,005,424). Fifty-three mitochondrial haplotypes were obtained from 150 individuals. F ST values estimated from sequence and microsatellite data were 0.061 and 0.011, respectively, and the R ST for microsatellite data was 0.007. Within-group genetic variation ranged from 93.90% to 99.99% depending on whether sequence or microsatellite data were examined. Analyses of microsatellite data suggested that all sampled individuals belonged to a single population, albeit genetically diverse. However, combined data analyses suggested the presence of low levels of substructure attributable to maternal lineages within the population. Low nucleotide-diversity values (0.007-0.010) in addition to high haplotype-diversity values (0.915-0.933) indicate a high number of closely related haplotypes, and suggest that this population may have undergone a recent expansion. However, Fu's F S statistic did not fully support this finding, because it did not reveal a significant excess of recent mutations. A phylogenetic approach using the haplotype sequence data and a combined set including both haplotype and genotype data was used to test for evolutionary patterns and history.
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