Within-population genetic structure in beech (Fagus sylvatica L.) stands characterized by different disturbance histories: does forest management simplify population substructure?
Piotti, A. ; Leonardi, S. ; Heuertz, M. ; Buiteveld, J. ; Geburek, T. ; Gerber, S. ; Kramer, K. ; Vettori, C. ; Vendramin, G.G. - \ 2013
PLoS ONE 8 (2013)9. - ISSN 1932-6203 - 9 p.
european beech - populus-trichocarpa - natural-populations - plant-populations - pollen dispersal - estimating seed - f-statistics - null alleles - douglas-fir - white-pine
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 hST 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.
Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis
Lombaert, E. ; Guillemaud, T. ; Thomas, C.E. ; Handley, L.J.L. ; Li, J. ; Wang, S. ; Pang, H. ; Goryacheva, I. ; Zakharov, I.A. ; Jousselin, E. ; Poland, R.L. ; Migeon, A. ; Lenteren, J.C. van; Clercq, P. de; Berkvens, N. ; Jones, W. ; Estoup, A. - \ 2011
Molecular Ecology 20 (2011)22. - ISSN 0962-1083 - p. 4654 - 4670.
multiple transatlantic introductions - western corn-rootworm - microsatellite loci - harlequin ladybird - biological invasion - pallas coleoptera - united-states - f-statistics - gene flow - coccinellidae
Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that native area of H. axyridis most probably consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete and (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.
Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation
Muya, S.M. ; Bruford, M.W. ; Muigai, A.W.T. ; Osiemo, Z.B. ; Mwachiro, E. ; Ouma, B.O. ; Goossens, B. - \ 2011
Conservation Genetics 12 (2011)6. - ISSN 1566-0621 - p. 1575 - 1588.
mitochondrial control region - multilocus genotype data - diceros-bicornis - population-structure - microsatellite loci - dna variation - f-statistics - diversity - software - cheetah
Kenya’s black rhinoceros population declined by more than 98% from 20,000 individuals in the 1970s to around 400 individuals in 1990 due to the effects of poaching, at which time the surviving individuals were isolated in a series of demographically inviable subpopulations. An initial management exercise translocated the survivors into four high security sanctuaries to control poaching and enhance breeding, and this measure successfully arrested the decline. Subsequently, new sanctuaries were established and the metapopulation size reached 650 animals by 2008. However, translocations and the current management strategy that partitions the metapopulation into ‘montane’ and ‘lowland’ rhinoceros may have substantial consequences at the population level and their impact on population genetic diversity has not been investigated. In this study, 12 of the 16 extant subpopulations were analysed using 408 bp of mitochondrial control region sequence (n = 170) and nine microsatellite loci (n = 145). Both markers detected moderate to high genetic diversity (h = 0.78 ± 0.027, n = 170; HO = 0.70 ± 0.087, n = 145) consistent with previous studies on Diceros bicornis michaeli. However, mtDNA and nDNA diversity varied substantially between subpopulations. The results suggest that the Masai Mara is more differentiated, inbred and isolated than other subpopulations. It also suggests that there are neither distinct montane and lowland groups nor other detectable historical barriers to gene flow. Instead the large majority of genetic diversity was partitioned at the level of individuals; highlighting the need to conserve as many individuals as possible. Future translocations should consider the genetic profile of individuals and the demographic history of both the donor and recipient subpopulations.
Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?
Odong, T.L. ; Heerwaarden, J. van; Jansen, J. ; Hintum, T.J.L. van; Eeuwijk, F.A. van - \ 2011
Theoretical and Applied Genetics 123 (2011)2. - ISSN 0040-5752 - p. 195 - 205.
multilocus genotype data - genome-wide association - forming core subsets - population-structure - data set - linkage disequilibrium - f-statistics - number - inference - diversity
Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.
Effects of landscape structure on genetic diversity of Geum urbanum L. populations in agricultural landscapes
Schmidt, T. ; Arens, P.F.P. ; Smulders, M.J.M. ; Billeter, R. ; Liira, J. ; Augenstein, I. ; Durka, W. - \ 2009
Flora 204 (2009)7. - ISSN 0367-2530 - p. 549 - 559.
habitat fragmentation - f-statistics - land-use - flow - distance - biodiversity - asteraceae - ecology - systems - europe
Plant species in fragmented populations are affected by landscape structure because persistence within and migration among inhabited patches may be influenced by the identity and configuration of surrounding habitat elements. This may also be true for species of the semi-natural vegetation in agricultural landscapes. To determine the effect of landscape elements we analyzed Wood Avens (Geum urbanum L.) populations within three 4×4 km2 agricultural landscapes in Germany, Switzerland and Estonia, which differ in levels of land use intensity and habitat fragmentation. Genetic variation was determined in 15 randomly selected populations in each landscape using 10 microsatellite loci. The landscape structure was assessed at two circles around each population, with radii defined by the range limits of spatial genetic autocorrelation. Multiple regression analysis was used to determine the influence of landscape structure variables for inter- and intrapopulation genetic diversity. Gene diversity was equally high in Germany (He=0.27) and Switzerland (He=0.26) but lower in Estonia (He=0.16). A high overall inbreeding coefficient (FIS=0.89) was found, as expected for a selfing breeding system in G. urbanum. Genetic differentiation among populations was high (overall FST=0.43, 0.48, and 0.45 in Estonia, Switzerland and Germany, respectively), and did not differ among the three landscapes. Only a moderate influence of individual land use types on genetic diversity within and among populations was found with some idiosyncratic relationships. Genetic variation within populations was correlated to the amount of hedgerows positively in Estonia but negatively in Switzerland. The study demonstrates that the distribution of individual land use types affects the genetic pattern of a common plant species. However, different variables were identified to influence the genetic structure in three different landscapes. This indicates a major influence of landscape-specific land use history and stochastic processes determining gene flow and plant population structure
Dispersal in Mastomys natalensis mice: use of fine-scale genetic analyses for pest management
Hooft, W.F. van; Cosson, J.F. ; Vibe-Petersen, S. ; Leirs, H. - \ 2008
Hereditas 145 (2008)6. - ISSN 0018-0661 - p. 262 - 273.
sex-biased dispersal - african rodent - differentiation measure - population-structure - paternity inference - peromyscus-leucopus - microsatellite loci - f-statistics - tanzania - density
Mastomys natalensis is the major pest rodent in sub-Saharan Africa. In this study, population genetic techniques were used to gain new insights into its dispersal behaviour, a critical parameter in pest management. Using 11 microsatellites, 272 individuals from a 300 ha area in Tanzania were genotyped. Genetic diversity was high, with no isolation by distance and little differentiation between field plots far apart, indicating a large effective population size and high dispersal rates in agreement with ecological observations. On the other hand, genetic differentiation between nearby field plots, isolation by distance within a single field plot and kin clustering were also observed. This apparent contradiction may be explained by yearly founder effects of a small number of breeding individuals per square area, which is consistent with the presence of linkage disequilibrium. An alternative, not mutually exclusive explanation is that there are both dispersing and sedentary animals in the population. The low-density field plots were characterized by low relatedness and small genetic distances to other field plots, indicating a high turnover rate and negative density-dependent dispersal. In one field plot female-biased dispersal was observed, which may be related to inbreeding avoidance or female competition for resources. Most juveniles appeared to be local recruits, but they did not seem to stay in their native area for more than two months. Finally, possible implications for pest management are discussed
Genetic diversity and differentiation in European beech (Fagus sylvatica L.) stands varying in management history
Buiteveld, J. ; Vendramin, G.G. ; Leonardi, S. ; Kramer, K. ; Geburek, T. - \ 2007
Forest Ecology and Management 247 (2007)1-3. - ISSN 0378-1127 - p. 98 - 106.
microsatellite markers - natural-populations - spatial differentiation - f-statistics - douglas-fir - regeneration - crenata - consequences - silviculture - variability
The impact of forest management on genetic diversity and mating was examined in European beech (Fagus sylvatica L.). Ten beech stands located in Europe were studied in pair-wise plots, differing in management intensity. The stands were genotyped with four highly polymorphic microsatellite loci. Comparison for genetic diversity measures between the stands with limited management and the high management-intensity stands (mostly shelter wood system) revealed no significant differences for allelic richness (A), effective number of alleles (Ae), number of rare alleles (Arare), neither for observed (Ho) nor expected heterozygosity (He). In all stands a significant excess of homozygotes was found, which is in agreement with previous isozyme publications. However, the increase in the inbreeding coefficient (Fis) in the stands with limited management was significantly higher than in the highly managed stands. Expectedly a low, but significant, differentiation among all stands was found (Fst = 0.058) which still reveals a clear geographic structure. The results indicate that the shelter wood system has no or minimum impact on the genetic diversity in European beech.
Mating-type genes and the genetic structure of a world-wide collection of the tomato pathogen Cladosporium fulvum
Stergiopoulos, I. ; Groenewald, M. ; Staats, M. ; Lindhout, P. ; Crous, P.W. ; Wit, P.J.G.M. de - \ 2007
Fungal Genetics and Biology 44 (2007)5. - ISSN 1087-1845 - p. 415 - 429.
fungus mycosphaerella-graminicola - population-genetics - plant-pathogen - cryptococcus-neoformans - spliceosomal introns - magnaporthe-grisea - f-statistics - evolution - recombination - dna
Two mating-type genes, designated MAT1-1-1 and MAT1-2-1, were cloned and sequenced from the presumed asexual ascomycete Cladosporium fulvum (syn. Passalora fulva). The encoded products are highly homologous to mating-type proteins from members of the Mycosphaerellaceae, such as Mycosphaerella graminicola and Cercospora beticola. In addition, the two MAT idiomorphs of C. fulvum showed regions of homology and each contained one additional putative ORF without significant similarity to known sequences. The distribution of the two mating-type genes in a world-wide collection of 86 C. fulvum strains showed a departure from a 1:1 ratio (chi(2)=4.81, df=1). AFLP analysis revealed a high level of genotypic diversity, while strains of the fungus were identified with similar virulence spectra but distinct AFLP patterns and opposite mating-types. These features could suggest the occurrence of recombination in C. fulvum.
Microsatellites reveal extensive geographical, ecological and genetic contacts between invasive and indigenous whitefly biotypes in an insular environment
Delatte, H. ; David, P. ; Granier, M. ; Lett, J.M. ; Goldbach, R.W. ; Peterschmitt, M. ; Reynaud, B. - \ 2006
Genetical Research 87 (2006)2. - ISSN 0016-6723 - p. 109 - 124.
bemisia-tabaci hemiptera - species complex - competitive displacement - population-structure - dna-polymerase - f-statistics - sweet-potato - b-biotype - aleyrodidae - resistance
Human-mediated bioinvasions provide the opportunity to study the early stages of contact between formerly allopatric, divergent populations of a species. However, when invasive and resident populations are morphologically similar, it may be very difficult to assess their distribution in the field, as well as the extent of ecological overlap and genetic exchanges between invasive and resident populations. We here illustrate the use of data obtained from a set of eight microsatellite markers together with Bayesian clustering methods to document invasions in a group of major tropical pests, Bemisia tabaci, which comprises several morphologically indistinguishable biotypes with different agronomic impacts. We focus on the island of La Réunion, where an invasive biotype (B) has recently been introduced and now interacts with the resident biotype (Ms). The temporal and spatial distribution, host-plant range and genetic structure of both biotypes are investigated. We showed (i) that, without prior information, clustering methods separate two groups of individuals that can safely be identified as the B and Ms biotypes; (ii) that the B biotype has invaded all regions of the island, and showed no signs of genetic founder effect relative to the Ms biotype; (iii) that the B and Ms biotypes coexist in sympatry throughout most of their geographical ranges, although they tend to segregate into different host plants; and finally (iv) that asymmetrical and locus-specific introgression occurs between the two biotypes when they are in syntopy.
Phylogeography and population structure of thornback rays (Raja clavata L., Rajidae)
Chevolot, M. ; Hoarau, G. ; Rijnsdorp, A.D. ; Stam, W.T. - \ 2006
Molecular Ecology 15 (2006)12. - ISSN 0962-1083 - p. 3693 - 3705.
pleuronectes-platessa l. - genetic-structure - north-sea - english-channel - geographical-distribution - secondary contact - fucus-serratus - f-statistics - ice-age - dna
The phylogeography of thornback rays (Raja clavata) was assessed from European waters, using five nuclear microsatellite loci and mitochondrial cytochome b sequences. Strong regional differentiation was found between the Mediterranean basin, the Azores and the European continental shelf. Allelic and haplotype diversities were high in Portuguese populations, consistent with the existence of a refugium along the Iberian Peninsula. Unexpectedly, high diversity was also found in the English Channel/North Sea area. The lowest genetic diversity was found in the Black Sea. Populations sampled from the Mediterranean, Adriatic and Black Seas were characterized by a single mitochondrial haplotype. This haplotype was also the most ancestral and widespread outside of the Mediterranean basin except for the Azores. Populations from the Azores were dominated by a second ancestral haplotype which was shared with British populations. Results from multidimensional scaling, amova and nested clade analysis indicate that British waters are a secondary contact zone recolonized from at least two refugia ¿ one around the Iberian Peninsula and one possibly in the Azores. Links to a potential refugium known as the Hurd Deep, between Cornwall and Brittany, are discussed. Finally, a historical demographic analysis indicates that thornback ray populations started to expand between 580 000 and 362 000 years ago, which suggests that the Last Glacial Maximum (20 000 years ago) had mainly affected the distribution of populations rather than population size
Pollinating fig wasps: genetic consequences of island recolonization
Zavodna, M. ; Arens, P.F.P. ; Dijk, P.J. ; Partomihardjo, T. ; Vosman, B.J. ; Damme, J.M.M. van - \ 2005
Journal of Evolutionary Biology 18 (2005)5. - ISSN 1010-061X - p. 1234 - 1243.
keystone plant resource - population-structure - krakatau islands - breeding structure - f-statistics - sex-ratios - colonization - dispersal - differentiation - dynamics
The levels of genetic diversity and gene flow may influence the long-term persistence of populations. Using microsatellite markers, we investigated genetic diversity and genetic differentiation in island (Krakatau archipelago, Indonesia) and mainland (Java and Sumatra, Indonesia) populations of Liporrhopalum tentacularis and Ceratosolen bisulcatus, the fig wasp pollinators of two dioecious Ficus (fig tree) species. Genetic diversity in Krakatau archipelago populations was similar to that found on the mainland. Population differentiation between mainland coastal sites and the Krakatau islands was weak in both wasp species, indicating that the intervening 40 km across open sea may not be a barrier for wasp gene flow (dispersal) and colonization of the islands. Surprisingly, mainland populations of the fig waSPS may be more genetically isolated than the islands, as gene flow between populations on the Javan mainland differed between the two wasp species. Contrasting growth forms and relative 'immunity' to the effects of deforestation in their host fig trees may account for these differences
Population structure of plaice (Pleuronectes platessa L.) in northern Europe: a comparison of resolving power between microsatellites and mitochondrial DNA data
Hoarau, G. ; Piquet, A.M.T. ; Veer, H.W. van der; Rijnsdorp, A.D. ; Stam, W.T. ; Olsen, J.L. - \ 2004
Journal of Sea Research 51 (2004). - ISSN 1385-1101 - p. 183 - 190.
sex-biased dispersal - genetic-structure - inbreeding avoidance - fucus-serratus - f-statistics - fish - diversity - flatfish - differentiation - phaeophyceae
We used Single Strand Conformation Polymorphism (SSCP) of mtDNA control region to assess the population structure of the flatfish Pleuronectes platessa (plaice), to compare these data with a previous study based on microsatellite loci, and to test for possible sex-biased dispersal. From 461 individuals, 163 haplotypes were identified across 11 locations. Diversity was higher with mtDNA (h =0.776 to 0.981; = 0.0178 to 0.0298) as compared to microsatellite loci using the same samples (He = 0.721 to 0.77). Genetic diversity was lower in samples from Iceland and Faroe, as compared to the continental shelf samples. Although both classes of markers revealed a relatively strong differentiation between shelf and off-shelf populations ( = 0.1015 and = 0.0351, respectively), only the mtDNA data were able to detect differentiation within the continental shelf, i.e., a North Sea-Irish Sea group which was weakly distinguishable from Norway ( = 0.0046), the Baltic ( = 0.0136) and the Bay of Biscay ( = 0.0162). No evidence was obtained for isolation by distance, nor for sex-biased dispersal. This study demonstrates the importance of using more than one class of markers, especially for species such as plaice, with large populations, high dispersal and recent colonisation histories