[Show abstract][Hide abstract] ABSTRACT: We studied the genetic pattern of 21 Ethiopian populations of Prunus africana by using six nuclear and five plastid microsatellites. In total, 89 alleles were found in the nuclear and 16 haplotypes in the plastid genome. High levels of diversity both in cpSSRs (h
= 0.703) and nSSR (H
= 0.725) were detected. Genetic differentiation among populations at the nuclear and plastid level was moderate (F
ST = 0.122 vs. G
ST = 0.478). While Ethiopian populations harbored the highest plastid haplotype diversity throughout Africa, the level of nuclear diversity was lower than in the remaining part of the species’ range. Ten of the observed 16 plastid haplotypes were unique to Ethiopia, suggesting an isolated plastid evolution. Remarkably, all plastid haplotypes found in Ethiopia belonged to one single lineage, while other populations from East Africa and Madagascar contain haplotypes from up to four more divergent lineages. This suggests that in contrast to previous expectations, the Horn of Africa is a hot spot of plastid diversity but not the ancestral origin for present populations of P. africana. The ratio between pollen to seed flow was estimated to be 7.1, indicating predominant gene flow by pollen. The exhaustive pollen flow also facilitated gene exchange with West African nuclear lineages probably in the early Holocene. The Ethiopian rift formed a genetic barrier resulting in population differentiation east and west of the rift; however, it was less effective in disrupting gene flow than the Eastern Rift in more southern parts of the East African range.
Full-text · Article · Dec 2015 · Tree Genetics & Genomes
[Show abstract][Hide abstract] ABSTRACT: Background and Aims Sorbus domestica (Rosaceae) is one of the rarest deciduous tree species in Europe and is characterized by a scattered distribution. To date, no large-scale geographic studies on population genetics have been carried out. Therefore, the aims of this study were to infer levels of molecular diversity across the major part of the European distribution of S. domestica and to determine its population differentiation and structure. In addition, spatial genetic structure was examined together with the patterns of historic and recent gene flow between two adjacent populations.
Methods Leaf or cambium samples were collected from 17 populations covering major parts of the European native range from north-west France to south-east Bulgaria. Seven nuclear microsatellites and one chloroplast minisatellite were examined and analysed using a variety of methods.
Key Results Allelic richness was unexpectedly high for both markers within populations (mean per locus: 3•868 for nSSR and 1•647 for chloroplast minisatellite). Moreover, there was no evidence of inbreeding (mean Fis = –0•047). The Italian Peninsula was characterized as a geographic region with comparatively high genetic diversity for both genomes. Overall population differentiation was moderate (FST = 0•138) and it was clear that populations formed three groups in Europe, namely France, Mediterranean/Balkan and Austria. Historic gene flow between two local Austrian populations was high and asymmetric, while recent gene flow seemed to be disrupted.
Conclusions It is concluded that molecular mechanisms such as self-incompatibility and high gene flow distances are responsible for the observed level of allelic richness as well as for population differentiation. However, human influence could have contributed to the present genetic pattern, especially in the Mediterranean region. Comparison of historic and recent gene flow may mirror the progress of habitat fragmentation in eastern Austria.
[Show abstract][Hide abstract] ABSTRACT: Serbian spruce, Picea omorika (Panč.) Purk., is a cold-adapted conifer confined to an area of c. 10,000 km2 within the Balkans. This area, which has not been exposed to severe anthropogenic disturbances in the recent past, represents a long-term cryptic refugium of this species. We studied Quaternary dynamics of fragmentary distributed Serbian spruce populations to uncover genetic and demographic processes accounting for high levels of genetic diversities in this endemic species within its long-term cryptic refugium. Based on our data set [499 trees from ten populations, five nuclear microsatellites (EST-SSRs) and a mitochondrial (mtDNA) locus], we found the following: (i) continuous increase of genetic distinctiveness of populations caused by various genetic and/or demographic processes, (ii) decreasing over generations pollen flow, and (iii) almost complete lack of seed flow, are trends applicable not only for post-glacial but also for glacial populations. As a result, populations distant few kilometers or less were poorly connected and highly differentiated (nuclear DNA: average ρ
, Hedrick’s G′
and Jost’s D of 0.165, 0.429 and 0.385, respectively; mtDNA: G
= 0.632). They were characterized as independent gene pools at the nuclear DNA level. Nonetheless, levels of genetic diversity were high at both nuclear (average allelic richness = 16.14; average H
= 0.776) and mtDNA (H
= 0.231) levels. They were maintained not by pronounced gene flow but rather by frequent admixtures of highly differentiated populations, and also by species longevity and overlapping generations in the populations. However, admixtures had been possible only if populations encountered each other over time. Particular genetic and/or demographic changes of populations, such as fragmentations, admixture, size reductions/expansions and extinctions, could not be associated exclusively neither to the post-glacial nor to the last glacial as they were detected during both periods. In accordance with expectations on range alternations in cold-adapted taxa confined to refugia during warm Quaternary periods, our study species was expanding range during the last glacial and contracting range post-glacially. Recommendations for conservation of this IUCN red-listed, endemic and relict species have been provided.
Full-text · Article · Feb 2014 · Conservation Genetics
[Show abstract][Hide abstract] ABSTRACT: The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L.) plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs). Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot θST ranged from 0.025 to 0.124). The proportion of within-population genetic variation due to genetic substructuring (FCluPlot = 0.067) was higher than the differentiation among the 10 plots (FPlotTot = 0.045). Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i) genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii) indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general.
[Show abstract][Hide abstract] ABSTRACT: Conservation priorities for Prunus africana, a tree species found across Afromontane regions, which is of great commercial interest internationally and of local value for rural communities, were defined with the aid of spatial analyses applied to a set of georeferenced molecular marker data (chloroplast and nuclear microsatellites) from 32 populations in 9 African countries. Two approaches for the selection of priority populations for conservation were used, differing in the way they optimize representation of intra-specific diversity of P. africana across a minimum number of populations. The first method (S1) was aimed at maximizing genetic diversity of the conservation units and their distinctiveness with regard to climatic conditions, the second method (S2) at optimizing representativeness of the genetic diversity found throughout the species' range. Populations in East African countries (especially Kenya and Tanzania) were found to be of great conservation value, as suggested by previous findings. These populations are complemented by those in Madagascar and Cameroon. The combination of the two methods for prioritization led to the identification of a set of 6 priority populations. The potential distribution of P. africana was then modeled based on a dataset of 1,500 georeferenced observations. This enabled an assessment of whether the priority populations identified are exposed to threats from agricultural expansion and climate change, and whether they are located within the boundaries of protected areas. The range of the species has been affected by past climate change and the modeled distribution of P. africana indicates that the species is likely to be negatively affected in future, with an expected decrease in distribution by 2050. Based on these insights, further research at the regional and national scale is recommended, in order to strengthen P. africana conservation efforts.
[Show abstract][Hide abstract] ABSTRACT: Background and aims:
Afromontane forest ecosystems share a high similarity of plant and animal biodiversity, although they occur mainly on isolated mountain massifs throughout the continent. This resemblance has long provoked questions on former wider distribution of Afromontane forests. In this study Prunus africana (one of the character trees of Afromontane forests) is used as a model for understanding the biogeography of this vegetation zone.
Thirty natural populations from nine African countries covering a large part of Afromontane regions were analysed using six nuclear microsatellites. Standard population genetic analysis as well as Bayesian and maximum likelihood models were used to infer genetic diversity, population differentiation, barriers to gene flow, and recent and all migration among populations.
Prunus africana exhibits strong divergence among five main Afromontane regions: West Africa, East Africa west of the Eastern Rift Valley (ERV), East Africa east of the ERV, southern Africa and Madagascar. The strongest divergence was evident between Madagascar and continental Africa. Populations from West Africa showed high similarity with East African populations west of the ERV, whereas populations east of the ERV are closely related to populations of southern Africa, respectively.
The observed patterns indicate divergent population history across the continent most likely associated to Pleistocene changes in climatic conditions. The high genetic similarity between populations of West Africa with population of East Africa west of the ERV is in agreement with faunistic and floristic patterns and provides further evidence for a historical migration route. Contrasting estimates of recent and historical gene flow indicate a shift of the main barrier to gene flow from the Lake Victoria basin to the ERV, highlighting the dynamic environmental and evolutionary history of the region.
[Show abstract][Hide abstract] ABSTRACT: European forests are populated with a variety of wind-pollinated tree species. Their pollen productivity and spatio-temporal pattern are largely unknown. Long-term data (17 years) collected at 22 sites across Austria were presented and the pollen production of 12 tree genera was analysed. We ranked the tree genera according to their pollen productivity taking actual tree abundances of the Austrian Forestry Inventory into account. The productivity varied strongly among tree genera with a maximum for Betula. Pollen production in Larix, Abies and Picea amounted to approximately 1/20, while in increasing order Salix, Quercus, Alnus, Populus and Fraxinus produced approximately 1/3 to ¼ of the respective Betula estimate. In general, pollen quantity in broadleaves was higher than in conifers. We analysed the temporal pollen production pattern by means of hierarchical cluster analysis and identified three major groups: [(Fagus, Lanx, Picea, Abies), (Alnus, BetuL Fraxinus)] y [Carpinus], [Populus, Salix, Pinus, Quercus]. Distance matrices based on life-history traits as well as molecular phylogeny were also constructed; they correlated significantly with each other by means of Mantel-tests. However, there was no significant relationship between the distances on temporal pollen production with the other matrices. Intermittent or idiosyncratic pollen production was studied by means of deviation from expected means, skewness and spindle diagrams. We proposed that Fagus, Carpinus, Larix, Picea and Abies belong to 'masting pollen producers', while the remaining genera idiosyncratically produced pollen over the monitored period. Moreover we correlated the distance matrix of pollen production for each tree genus at each sampling site with respective 'ecological distance matrices' based on aerial and altitudinal distance among sites. Significant correlations were detected for tree genera (Fagus, Larix, Picea) which were also prone to pollen masting, thus indicating a Moran effect.
[Show abstract][Hide abstract] ABSTRACT: Junipers are main components of semiarid forests in Central Asia. Conservation of these plant genetic resources should be based on an understanding of factors that have shaped species-level genetic variation. We used Juniperus seravschanica Kom. as a model species to investigate patterns and processes that may be associated with these factors. Novel plastid DNA markers (two minisatellites, one transversion, one indel) were identified and applied to investigate haplotype diversity and population structure in Kyrgyzstan. In total, 540 individuals from 15 populations were analyzed and 11 haplotypes detected. Strong divergence between populations from northern and southern Kyrgyzstan was evident from the haplotype distribution. Gene diversity within populations ranged from 0.083 to 0.765, and was on average higher in southern (0.687) than in northern populations (0.540). A similar pattern was detected in allelic richness. Analysis of molecular variance (AMOVA) revealed that 11.9% of the total genetic variation was due to differences among regions, 1.5% among populations, and 86.6% within populations. NST was not significantly different from GST (0.125), suggesting no evidence of a phylogeographic pattern. A Mantel test detected a weak but significant isolation-by-distance pattern for the whole dataset and southern populations separately. These results suggest that the north of Kyrgyzstan was relatively recently colonized by migrants from southern populations, probably associated with favorable conditions during the early Holocene. The humid Fergana
Valley and Fergana Range are probable ecological barriers to gene flow between northern and southern populations.
No preview · Article · Sep 2012 · Journal of Systematics and Evolution
[Show abstract][Hide abstract] ABSTRACT: Prunus africana - an evergreen tree found in Afromontane forests - is used in traditional medicine to cure benign prostate hyperplasia. Different bioactive constituents derived from bark extracts from 20 tree populations sampled throughout the species' natural range in Africa were studied by means of GC-MSD. The average concentration [mg/kgw/w] in increasing order was: lauric acid (18), myristic acid (22), n-docosanol (25), ferulic acid (49), β-sitostenone (198), β-sitosterol (490), and ursolic acid (743). The concentrations of many bark constituents were significantly correlated and concentration of n-docosanol was highly significantly correlated with all other analytes. Estimates of variance components revealed the highest variation among populations for ursolic acid (66%) and the lowest for β-sitosterol (20%). In general, environmental parameters recorded (temperature, precipitation, altitude) for the samples sites were not correlated with the concentration of most constituents; however, concentration of ferulic acid was significantly correlated with annual precipitation. Because the concentration of compounds in bark extracts may be affected by tree size, the diameter of sampled plants at 1.3m tree height (as proxy of age) was recorded. The only relationship with tree diameter was a negative correlation with ursolic acid. Under the assumption that genetically less variable populations have less variable concentrations of bark compounds, correlations between variation parameters of the concentration and the respective genetic composition based on chloroplast and nuclear DNA markers were assessed. Only variation of β-sitosterol concentration was significantly correlated with haplotypic diversity. The fixation index (F(IS)) was positively correlated with the variation in concentration of ferulic acid. Principal Components Analysis (PCA) indicated a weak geographic pattern. Mantel tests, however, revealed associations between the geographic patterns of bioactive constituents and the phylogenetic relationship among the populations sampled. This suggests an independent evolution of bark metabolism within different phylogeographical lineages, and the molecular phylogeographic pattern is partly reflected in the variation in concentration of bark constituents. The results have important implications for the design of strategies for the sustainable use and conservation of this important African tree species.
[Show abstract][Hide abstract] ABSTRACT: Genetic resources of forest trees are considered as a key factor for the per-sistence of forest ecosystems because the ability of tree species to survive under changing climate depends strongly on their intraspecific variation in climate response. Therefore, utilizing available genetic variation in climate response and planting alternative prove-nances suitable for future climatic conditions is considered as an important adaptation measure for forestry. On the other hand, the distribution of adaptive genetic diversity of many tree species is still unknown and the predicted shift of ecological zones and species' distribution may threaten forest genetic resources that are important for adaptation. Here, we use Norway spruce in Austria as a case study to demonstrate the genetic variation in climate response and to analyse the existing network of genetic conservation units for its effectiveness to safeguard the hotspots of adaptive and neutral genetic diversity of this species. An analysis of the climate response of 480 provenances, clustered into 9 groups of climatically similar provenances, revealed high variation among provenance groups.
Full-text · Article · Jun 2012 · Biodiversity and Conservation
[Show abstract][Hide abstract] ABSTRACT: 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 (~75% of pollen from outside), with the exception of the plot from a highly isolated forest remnant (~50%). 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.
[Show abstract][Hide abstract] ABSTRACT: Sal (Shorea robusta) is a wind-pollinated, hermaphrodite tropical forest tree species in South Asia that has suffered significant habitat loss. Despite its economical and ecological importance in the region, so far, no information about its population genetics is available. Using four highly variable nuclear microsatellites, we compared the genetic diversity between adults and juveniles in a semi-isolated natural population in Nepal, quantified its micro-spatial genetic structure by spatial autocorrelation and assessed its pollen and seed flow. Results showed that genetic diversity (H E = 0.68, N A = 11) was within the range found in other members of the genus. Spatial aggregation of related individuals was weak both in juveniles and adults trees. Selfing rate was 6%, and mean pollen and seed dispersal distances were 194 m and 35 m respectively. The effective neighbourhood size was estimated to be 4,153 trees. The spatial genetic structure and gene flow data presented here can serve as guidelines for conservation and sustainable use of genetic resources of this tropical species.
[Show abstract][Hide abstract] ABSTRACT: Harsh environment at high altitude may affect the mating system of plant species, especially those with wide ecological amplitude.
Smaller effective neighbourhood size, less pollen and seed production, higher rate of inbreeding and a shift towards vegetative
propagation may be involved. These changes can be reflected in spatial genetic structure (SGS). Populations of Norway spruce
[Picea abies (L.) Karst.] were analysed along an altitudinal cline to verify whether SGS increases with altitude. Three putatively autochthonous
populations in Tyrol (Austria) at 800, 1,200 and 1,600m above sea level (asl) were studied. Six highly polymorphic DNA markers
(expressed sequence tag–derived simple sequence repeats, EST-SSRs) were used to genotype a total of 450 contiguous trees (150
trees per population). Loiselle’s kinship coefficient was used to quantify SGS. Against expectation no significant SGS was
found in any of the populations, indicating a random spatial pattern. Significant SGS was observed when all populations were
treated as a single one conforming to an isolation-by-distance pattern. Nearly identical allelic frequencies were found resulting
in very small population differentiation (F
ST=0.002). The fixation index decreased with diameter at breast height (a proxy for age) indicating natural selection against
inbred trees. The results of this study indicate that seed and pollen dispersal mechanisms in Norway spruce are strongly counteracting
spatial aggregation of similar genotypes even at high elevations.
KeywordsAlps–Altitudinal cline–EST-SSRs–Genetic diversity–Norway spruce–Spatial genetic structure
No preview · Article · Apr 2011 · Plant Systematics and Evolution
[Show abstract][Hide abstract] ABSTRACT: The colour morphs of immature female cones in European larch (Larix decidua Mill.) and Norway spruce (Picea abies (L.) Karst.) are green, red, and intermediate in colour. For the first time, these three colour morphs were studied to verify the thermoregulatory hypothesis and to investigate its underlying genetic spatial pattern. The study was based on an extensive systematic sampling, and data were analysed using principal component analysis (PCA), binary logistic regression (BLR), and spatial autocorrelation. Correlations between the nontransformed environmental variables and PC scores revealed two main ecological gradients, (i) altitude–temperate and (ii) annual precipitation. Loadings of the first two principal components exceeded 85% in both species. BLR was used to test the effect of the altitude–temperature gradient on the probability of occurrence of a specific cone colour. In both species, the occurrence of red cones was significantly positively related to high altitude with low temperatures, while green cones were significantly negatively correlated with decreasing temperature and increasing altitude. In both species the spatial pattern based on a putative Mendelian gene was nonrandom as indicated by significantly high Moran’s I values based on altitudinal distance. Spatial genetic structure was probably maintained by limited gene flow and balanced selection that maintained short-distance genetic differentiation.
Full-text · Article · Mar 2011 · Canadian Journal of Botany
[Show abstract][Hide abstract] ABSTRACT: Intra- and among-population variations of Juniperus seravschanica were morphologically examined in eight populations originating from elevations of 1300–2200m a.s.l. in Kyrgyzstan. Eleven traits of needles and cones were studied on 70 vouchers. In addition, height, diameter, stem form, and sex of 172 trees were recorded in the field in order to test whether male trees invest more in vegetative growth than females and if sex ratio is shaped by (limited) environmental resources. Morphological differences among populations were small, but needle length, width and thickness were statistically different. However, differences based on needle traits were independent from geographical, altitudinal and environmental distances. In sharp contrast to studies in other Juniperus species, sex ratio in J. seravschanica was strongly female biased (3.5 females : 1 male). Moreover, no correlation between the habitat conditions and the sex ratio was detected, suggesting that within the altitudinal range of this species, females occur more frequently. This has implications for sustainable use and the conservation of J. seravschanica populations. It is likely, that due to the higher investment of male individuals in vegetative growth males are more exploited than females. An average effective population size of 70% of the respective census suggests that conservation measures and non-selective logging regimes are required to allow reproduction and a natural regeneration of this species.
No preview · Article · Dec 2010 · Flora - Morphology Distribution Functional Ecology of Plants
[Show abstract][Hide abstract] ABSTRACT: Scattered populations of the same tree species in montane forests through Africa have led to speculations on the origins of distributions. Here, we inferred the colonization history of the Afromontane tree Prunus africana using seven chloroplast DNA loci to study 582 individuals from 32 populations sampled in a range-wide survey from across Africa, revealing 22 haplotypes. The predominant haplotype, HT1a, occurred in 13 populations of eastern and southern Africa, while a second common haplotype, HT1m, occurred in populations of western Uganda and western Africa. The high differentiation observed between populations in East Africa was unexpected, with stands in western Uganda belonging with the western African lineage. High genetic differentiation among populations revealed using ordered alleles (N(ST) = 0.840) compared with unordered alleles (G(ST) = 0.735), indicated a clear phylogeographic pattern. Bayesian coalescence modelling suggested that 'east' and 'west' African types likely split early during southward migration of the species, while further more recent splitting events occurred among populations in the East of the continent. The high genetic similarity found between western Uganda and west African populations indicates that a former Afromontane migration corridor may have existed through Equatorial Africa.
Full-text · Article · Nov 2010 · Molecular Ecology
[Show abstract][Hide abstract] ABSTRACT: Sal (Shorea robusta Gaertn., Dipterocarpaceae) is a wind-pollinated tropical tree species found in southern Asia. We investigated the genetic
diversity and structure at four microsatellites of 15 populations comprising continuous-peripheral and disjunct-peripheral
populations in Nepal. Estimates of genetic diversity (N
E=0.69) were similar when compared with those of other tropical tree species. A higher level of genetic diversity was observed
in continuous-peripheral populations (N
E=0.72) as compared to disjunct-peripheral (N
E=0.64). Population differentiation was higher among disjunct-peripheral populations (F
ST=0.043) than among continuous peripherals (F
ST=0.012). There was a significant association between gene flow distances and genetic differentiation (r
2=0.128, P≤0.007). No spatial arrangement of populations according to their geographical locations was found. Based on observed genetic
diversity protection of some populations in continuous-peripheral range are suggested for the sustainable conservation of
genetic resources of the species while protection of some disjunct-peripheral populations are also recommended for conserving
-Microsatellites-Genetic diversity-Peripheral populations-Nepal
No preview · Article · Jun 2010 · Conservation Genetics