The influence of sea currents, past disruption of gene flow and species biology on the phylogeographical structure of coastal flowering plants

Aim We investigate the geographical genetic structure of two coastal plant species, Cakile maritima Scop. (Brassicaceae) and Eryngium maritimum L. (Apiaceae), through three sea straits and along one continuous stretch of coast using amplified fragment length polymorphisms (AFLPs). The two species have a similar ecology in that they grow in sandy habitats, but differ in life‐form (annual vs. perennial) and dispersability of seeds by sea water as inferred from floating experiments. The sea straits differ in their geological history and their modern current systems. The primary goal of our study was to test the hypothesis that sea straits have an influence on the geographical patterns of genetic variation at the population level. Location The areas around the Strait of Gibraltar, the Dardanelles, the Bosporus and the Atlantic coast of western France. Methods For both species we investigated AFLP variation in several populations from each area. Bayesian clustering and diversity and differentiation measures were used to analyse the genetic data. Results In most areas the spatial genetic structure was similar between the two species. They share the presence of distinct genetic gaps along the coast through the Strait of Gibraltar and the Bosporus, and these genetic gaps coincide with the straits. Both species show genetic continuity along the coast of western France. A distinct genetic gap was found through the Dardanelles for C. maritima but not for E. maritimum. Main conclusions The study shows that sea straits have an influence on the geographical patterns of genetic variation. Sea currents are inferred to cause the genetic gap through the Strait of Gibraltar. In the Bosporus and, for C. maritima, through the Dardanelles, the genetic gaps found are explained by the past closure of these two straits as well as by present‐day factors. Simulations indicate that the lower differentiation of C. maritima through the Dardanelles than through the Bosporus cannot be explained by the difference in geological history of these two straits. The difference in seed dispersability between the two species is argued to be responsible for the observation that differentiation among genetic clusters is higher in E. maritimum than in C. maritima where a direct comparison is possible.     

Phylogenetic relationships, evolutionary origin, taxonomic status, and genetic structure of the endangered local Lower Elbe river (Germany) endemic Oenanthe conioides (Nolte ex Rchb.f.) Lange (Apiaceae): ITS and AFLP evidence

Oenanthe conioides is an endangered local endemic of the Lower Elbe river region in Germany where it is found in areas with freshwater tides. Internal transcribed spacer (ITS) and amplified fragment length polymorphism (AFLP) markers were used to investigate its phylogenetic relationships, evolutionary origin, taxonomic status, and genetic structure.Oe. conioides is most closely related to Oe. aquatica and Oe. fluviatilis, and cannot be distinguished from Oe. aquatica by ITS sequence variation. Oe. aquatica is found mainly in standing or slow-flowing freshwater habitats. The AFLP analysis indicated that Oe. conioides may constitute a monophyletic lineage nested within Oe. aquatica. Considering this result on the background of the sympatric distribution of the two species and their ecological differentiation, it is hypothesized that Oe. conioides arose sympatrically from Oe. aquatica through ecological divergence. It is concluded that Oe. conioides is best considered a subspecies of Oe. aquatica.AFLP analysis of Oe. conioides revealed low levels of genetic differentiation among populations reflecting the small geographical distance, the recent decline in population number and size, the connection of populations through the river, and their presumably high population dynamics.Considering this pattern of genetic variation, it is concluded that no individual population can be singled out as being particularly important from a genetic point of view. Also, all populations could be used as source material should the establishment of new populations or the enlargement of small populations be considered as a measure to consolidate the persistence of the species.     

Amplified fragment length polymorphism (AFLP) analysis of the genetic structure of the zebra mussel, Dreissena polymorpha, in the Mississippi River

1. We predicted that zebra mussel, Dreissena polymorpha (Pallas), genetic structure in the Mississippi River would follow a model of invasive species genetics, which predicts low genetic structure among populations of recently established species. This prediction was upheld in our previous genetic study using allozymes, however, one locus yielded anomalous results. 2. We employed amplified fragment length polymorphism (AFLP) analysis as a neutral marker to assess the amount of genetic structure within and among populations, and as a test of expected population structure from both invasion genetic theory, and the results from our previous study. 3. There was greater spatial differentiation, as measured by F_st, observed using AFLP's than for allozymes (P < 0.001). There was no evidence that AFLP variation conformed to an isolation by distance model, and genetic relationships of populations, as measured by AFLP markers, were not similar to those detected in our allozyme survey. 4. The lack of concordance between these two genetic marker systems probably reflects their differential responses to drift, migration, and selection occurring during this rapid invasion. Strong population structure is counter to predictions that populations of invasive species will not be differentiated, as with observations based on allozyme markers. Therefore, newly established species may require genetic surveys using multiple marker systems to evaluate population structure.     

‘Good-genes’ and ‘compatible-genes’ effects in an Alpine whitefish and the information content of breeding tubercles over the course of the spawning season

Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Φst (AFLP) = 0.550 and Φst (SSR) = 0.289) and among regions (Φct (AFLP) = 0.139 and Φct (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.     

Genetic diversity,population structure and sex‐biased dispersal in three co‐evolving species

Genetic diversity and spatial structure of populations are important for antagonistic coevolution. We investigated genetic variation and population structure of three closely related European ant species: the social parasite Harpagoxenus sublaevis and its two host species Leptothorax acervorum and Leptothorax muscorum. We sampled populations in 12 countries and analysed eight microsatellite loci and an mtDNA sequence. We found high levels of genetic variation in all three species, only slightly less variation in the host L. muscorum. Using a newly introduced measure of differentiation (Jost’s D_est ), we detected strong population structuring in all species and less male‐biased dispersal than previously thought. We found no phylogeographic patterns that could give information on post‐glacial colonization routes – northern populations are as variable as more southern populations. We conclude that conditions for Thompson’s geographic mosaic of coevolution are ideal in this system: all three species show ample genetic variation and strong population structure.     

Evaluation of biodiversity and conservation strategies in <Emphasis Type="Italic">Pancratium maritimum</Emphasis> L. for the NorthernTyrrhenian Sea

Pancratium maritimum L. is an Amaryllidaceous species whose presence is severely endangered in its original range, the sandy coasts of the Mediterranean sea. A molecular analysis has been performed to evaluate the genetic distance among populations coming from different locations, in order to define the best repopulating strategy. The plant genome, analysed by AFLP markers, was found to be extremely homogeneous and conserved, evoking vegetative or autogamous reproductive habits. Seeds from two different locations showed a good germination capability in greenhouse tests, indicating the potential presence of an efficient sexual reproduction. The combination of molecular data and germination tests would support the hypothesis of an autogamous reproduction for this species.     

Genetic variation relevant for the conservation of the narrow endemic Senecio carbonensis (Asteraceae) from the southern Andes

We studied morphological variation, reproductive biology and genetic structure of Senecio carbonensis, a narrow endemic from high elevations of the southern Andes, and compared it to Senecio peteroanus, a closely related widespread congeneric species. Using ANOVAs and discriminant analysis we showed that populations of S. carbonensis were more similar to each other in their morphology, had comparatively limited reproductive capacity and presented lower plant density and more reduced plant cover than populations of S. peteroanus. Similar high genetic variation was found at the population and species level in both species, based on isozyme variation at 14 and 11 putative gene loci that were resolved in S. carbonensis and S. peteroanus, respectively. The two species were genetically distinct. However, the small genetic distance between populations of each species suggests that either they were recently founded and that genetic drift did not have time to promote divergence, or that its effects are masked by significant current gene flow. These results show that ecological and reproductive characteristics of S. carbonensis may limit its extension and abundance. In contrast, high genetic variation at the population level is probably favored by self‐incompatibility. Despite the restricted geographical distribution and low plant density of S. carbonensis populations, genetic characteristics do not seem to be limiting their long‐term persistence. This information suggests that populations of S. carbonensis are not at risk of extinction as a result of genetic factors, although it is important to study and monitor population dynamics to further assess the degree of recruitment through time.     

Polymorphism of RAPD,ISSR and AFLP markers of the <Emphasis Type="Italic">Panax ginseng</Emphasis> C. A. Meyer (Araliaceae) genome

The genus Panax (Araliaceae) is world-famous because many its members have important medicinal properties. Panax ginseng C. A. Meyer is more popular than other species of the genus because remedies prepared from this plant stimulate immunity, help to prevent diseases, and have antistress effects. In addition, the ginseng root extract is traditionally used as a means against aging. At present, this species is found in the wild only in Primorsky krai, Russia, but its populations are extremely exhausted and need to be restored. In this study, effectiveness of molecular DNA markers in detecting genetic variation and differentiation of the ginseng populations was tested. Genetic variation of ginseng, identified using RAPD (P = 4%; H _pop = 0.0130) and ISSR (P = 9.3%; H _pop = 0.0139) markers was low. The AFLP* approach, according to which amplicons are separated in polyacrylamide gel and visualized by means of silver staining, showed somewhat higher variability (P = 21.8%; H _pop = 0.0509), while its effectiveness in population differentiation was as low as that of RAPD and ISSR. The AFLP** technique, which included analysis of the fragments using genetic analyzer, revealed high genetic diversity of ginseng (P = 94.4%; H _pop = 0.3246). All populations examined using the AFLP** markers were statistically significantly differentiated based on the AMOVA results. Our result suggest effectiveness of AFLP** markers for characterization of the genetic structure and genetic relationships of the ginseng populations. These markers are recommended for use in large-scale population genetic studies of this species to develop measures of its conservation.     

Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

Habitat fragmentation can have severe genetic consequences for trees, such as increased inbreeding and decreased effective population size. In effect, local populations suffer from reduction of genetic variation, and thus loss of adaptive capacity, which consequently increases their risk of extinction. In Europe, Taxus baccata is among a number of tree species experiencing strong habitat fragmentation. However, there is little empirical data on the population genetic consequences of fragmentation for this species. This study aimed to characterize local genetic structure in two natural remnants of English yew in Poland based on both amplified fragment length polymorphism (AFLP) and microsatellite (SSR) markers. We introduced a Bayesian approach that estimates the average inbreeding coefficient using AFLP (dominant) markers. Results showed that, in spite of high dispersal potential (bird-mediated seed dispersal and wind-mediated pollen dispersal), English yew populations show strong kinship structure, with a spatial extent of 50–100 m, depending on the population. The estimated inbreeding levels ranged from 0.016 to 0.063, depending on the population and marker used. Several patterns were evident: (1) AFLP markers showed stronger kinship structure than SSRs; (2) AFLP markers provided higher inbreeding estimates than SSRs; and (3) kinship structure and inbreeding were more pronounced in denser populations regardless of the marker used. Our results suggest that, because both kinship structure and (bi-parental) inbreeding exist in populations of English yew, gene dispersal can be fairly limited in this species. Furthermore, at a local scale, gene dispersal intensity can be more limited in a dense population.     

Conservation genetics of endangeredBrasenia schreberi based on RAPD and AFLP markers

Brasenia schreberi J.F. Gmelin is a declared endangered species found in the lakes and ponds of South Korea. For planning its conservation strategy, we examined the genetic diversity within and among six populations, using randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). Polymorphisms were more frequently detected per loci with AFLP (69.3%) than RAPD (36.8%). High genetic diversity was recognized within populations: polymorphic loci (PPL) values ranged from 36.3% in the CJM population to 74.5% in the GGT population, with a mean value of 47.8% based on AFLP markers. Great genetic differentiation (θ^B) was detected among the six populations (0.670 on RAPD and 0.196 on AFLP), and we calculated a low rate of gene flow (N_em), i.e., 0.116 on RAPD and 0.977 on AFLP. Furthermore, a Mantel test revealed that no correlation existed between genetic distances and geographical distances among the six local populations, based on RAPD or AFLP markers. These results are attributed to a number of factors, including an insufficient length of time for genetic diversity to be reduced following a natural decline in population size and isolation, adaptation of the genetic system to small population conditions, and a restricted gene flow rate. Based on both its genetic diversity and population structure, we suggest that a strategy for conserving and restoringB. schreberi must focus on maintaining historical processes, such as high levels of outbreeding, while monitoring increased gene flow among populations. This is because a reduction in genetic diversity as a result of genetic drift is undesirable.     

Consequences of multiple mating‐system shifts for population and range‐wide genetic structure in a coastal dune plant

Evolutionary transitions from outcrossing to selfing can strongly affect the genetic diversity and structure of species at multiple spatial scales. We investigated the genetic consequences of mating‐system shifts in the North American, Pacific coast dune endemic plant Camissoniopsis cheiranthifolia (Onagraceae) by assaying variation at 13 nuclear (n) and six chloroplast (cp) microsatellite (SSR) loci for 38 populations across the species range. As predicted from the expected reduction in effective population size (N_e) caused by selfing, small‐flowered, predominantly selfing (SF) populations had much lower nSSR diversity (but not cpSSR) than large‐flowered, predominantly outcrossing (LF) populations. The reduction in nSSR diversity was greater than expected from the effects of selfing on N_e alone, but could not be accounted for by indirect effects of selfing on population density. Although selfing should reduce gene flow, SF populations were not more genetically differentiated than LF populations. We detected five clusters of nSSR genotypes and three groups of cpSSR haplotypes across the species range consisting of parapatric groups of populations that usually (but not always) differed in mating system, suggesting that selfing may often initiate ecogeographic isolation. However, lineage‐wide genetic variation was not lower for selfing clusters, failing to support the hypothesis that selection for reproductive assurance spurred the evolution of selfing in this species. Within three populations where LF and SF plants coexist, we detected genetic differentiation among diverged floral phenotypes suggesting that reproductive isolation (probably postzygotic) may help maintain the striking mating‐system differentiation observed across the range of this species.     

Conservation Genetics of the Endemic Mexican Heliconia uxpanapensis in the Los Tuxtlas Tropical Rain Forest

Heliconia uxpanapensis (Heliconiaceae) is an outcrossing endemic herb that grows within continuous and fragmented areas of the tropical rain forest of southeast Veracrúz (México). The genetic diversity, population differentiation, and genetic structure of seven populations of the studied species were assessed using inter‐simple sequence repeat) markers. Population differentiation was moderately high (F_ST range: 0.18–0.22) and indirect estimates of gene flow were rather low (Nm=0.65–0.83). Analysis of molecular variance indicated that the populations explained 22.2 percent of the variation, while individuals within the populations accounted for 77.8 percent. The similar and high level of genetic diversity found within populations of the continuous and fragmented forest suggests that H. uxpanapensis has not suffered yet the expected negative effect of fragmentation. Genetic structure analyses indicated the presence of fewer genetic clusters (K=4) than populations (N=7). Three of the four fragmented forest populations were assigned each to one of the clusters found within the continuous forest, suggesting the absence of a negative fragmentation effect on the amount and distribution of genetic variation. Given the significant genetic structure combined with high genetic diversity and low levels of gene flow, theoretical simulations indicated that H. uxpanapensis might be highly susceptible to changes in the mating system, which promotes inbreeding within fragmented populations. Thus, future conservation efforts in this species should be directed to ensure that levels of gene flow among populations are sufficient to prevent an increment in the magnitude of inbreeding within fragments.     

High levels of genetic structuring as a result of population fragmentation in the tropical tree species <Emphasis Type="Italic">Caesalpinia echinata</Emphasis> Lam.

We have investigated levels of genetic diversity within and among seven remnant populations of Caesalpinia echinata Lam., an endangered species found as fragmented populations in three major areas around the coastal regions of Brazil. Using amplified fragment length polymorphism (AFLP) genetic markers, we detected levels of within-population genetic diversity ranging from 0.092 to 0.163, with the lowest values generally being found in the smallest populations. Estimates of between-population genetic differentiation were strongly correlated with geographical distance (r = 0.884, p < 0.001), which,along with a neighbour-joining phylogenetic analysis, strongly suggested high levels of genetic isolation by distance. Over half (62%) of the total genetic diversity was partitioned between populations, further highlighting the genetic distinctness of individual populations. Taken together, these results suggest that fragmentation has led to an increase in population differentiation between fragments of C. echinata. These formations will be of great value in the development of conservation plans for species exhibiting high levels of genetic differentiation due to fragmentation, such as indication of conservation unit size, which populations should be chosen as priority in conservation plans and which samples should be introduced in areas with a low number of individuals of brazilwood.     

GENETIC VARIATION IN ASTERIONELLA FORMOSA (BACILLARIOPHYCEAE): IS IT LINKED TO FREQUENT EPIDEMICS OF HOST‐SPECIFIC PARASITIC FUNGI?1

Understanding of the genetic basis for susceptibility and resistance is still lacking for most aquatic host–parasite systems, for instance, for phytoplankton and their fungal parasites. Fungal parasites can have significant effects on phytoplankton populations, mainly through their ability to decimate algal host populations during epidemics. We used random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) analysis to study levels of genetic variation within a population of the freshwater diatom Asterionella formosa Hassall in relation to parasitism by the obligate, host‐specific, fungal parasite Zygorhizidium planktonicum Canter. The level of genetic variation within the A. formosa population in Lake Maarsseveen, The Netherlands was found to be high despite the presumed absence or very low frequency of sexual reproduction in this species, the limited gene flow, and the severity of parasite attack that would purge the population from susceptible genotypes. RAPD analysis revealed four distinct banding patterns, with 3 of 21 markers (14%) being polymorphic. In AFLP analysis, every single isolate of A. formosa showed a unique banding pattern, and 120 of the 210 AFLP markers (57%) were found to be polymorphic. Furthermore, character compatibility analysis revealed that sexual reproduction may be one of the mechanisms that generates and maintains genetic variation in the A. formosa population in Lake Maarsseveen. The presence of genetic variation in A. formosa was reflected in infection experiments, which showed that genetically different A. formosa strains differed in their susceptibility to various Z. planktonicum strains and that parasite strains differed in their ability to infect particular host strains.     

DNA fingerprinting of Leonurus cardiaca L. germplasm in Iran using amplified fragment length polymorphism and inter-retrotransposon amplified polymorphism

In the present study, the extent of inter and intra-population genetic variation was evaluated in Leonurus cardiaca accessions naturally growing in Iran by AFLP and IRAP markers. The fingerprints corresponding to AFLP and IRAP markers revealed high levels of heterozygosity, indicating that L. cardiaca is predominantly an out-crossing species. The average percentage polymorphism was detected as 58% and 90.8% on utilizing AFLP and IRAP data, respectively. Gene diversity values within populations varied 0.14 to 0.20 for AFLP and 0.12 to 0.21 for IRAP. The overall levels of genetic variation present in the L. cardiaca germplasm in Iran were finally determined by combining the AFLP and IRAP datasets to ensure wide genome coverage. The phenogram depicted that the accessions of Dargaz population were genetically distinct from other populations. Based on AFLP and IRAP analysis, it is concluded that L. cardiaca maintains high levels of genetic variation at inter and intra-population level.     

Patterns of genetic diversity in natural populations of Paspalum agamic complexes

Paspalum has many multiploid species displaying a wide range of ploidy levels and reproductive systems including apomixis. However, not much is known about the genetic structure of natural populations of the apomictic species of Paspalum. The aim of this work was to evaluate the genetic diversity of several natural populations belonging to five species of Paspalum. A total of 13 populations were analyzed using amplified fragment length polymorphism (AFLP). The AFLP data revealed maximal genotypic diversity and significant levels of genetic diversity in diploid and mixed diploid–tetraploid populations of P. denticulatum and P. rufum, where all individuals represent different genotypes. This may be mainly due to the reproductive system of diploid members and the gene flow from diploids to polyploids. The pure populations of tetraploids consist of either multiple genotypes (P. nicorae) or of one dominant genotype with a few deviated genotypes (P. denticulatum and P. lividum). Here, the main source of variability may be the residual sexuality, which continues generating new genotypic combinations. The hexaploid populations of P. buckleyanum consist of a single AFLP genotype and each population represents a particular genotype suggesting that populations arose from independent polyploidization events. This study represents one of the first reports of genetic diversity in natural populations of several Paspalum agamic complexes. Apomixis in these five species may be acting as a successful method for the dispersion of better adapted genotypes.     

The significance of genetic erosion in the process of extinction

Summary The amount of genetic variation within a population is, among other things, related to population size. In small populations loss of genetic variation due to high levels of genetic drift and inbreeding may result in decline of individual fitness and increase the chance of population extinction. This chain of processes is known as genetic erosion. In this study we tested the genetic erosion hypothesis by investigating the relation between morphological variation and population size in two perennial, outbreeding plant species, Salvia pratensis and Scabiosa columbaria. To relate phenotypic variation to genetic variation the experiments were performed under common environmental conditions. For both species a positive correlation was observed between the amount of phenotypic variation and population size (Salvia r=0.915; Scabiosa r=0.703). Part of this variation is likely to have a genetic base, although maternal effects were present in the seedling and juvenile life stages. Differences between populations could in both species be attributed to parameters related to fitness, i.e. growth rate in Salvia and reproductive effort in Scabiosa. Discriminant functions reflecting these parameters did not however discriminate between large and small populations.Results are discussed in relation to the common environment approach and to electrophoretic results obtained earlier (Van Treuren et al. 1991).     

Reproductive ecology and genetic variability in natural populations of the wild potato,Solanum kurtzianum

The cultivated potato (Solanum tuberosum ssp. tuberosum) has more than 200 related wild species distributed along the Andes, adapted to a wide range of geographical and ecological areas. Since the last century, several collection expeditions were carried out to incorporate genetic variability into the potato germplasm around the world. However, little is known about the reproductive ecology and genetic population structure of natural potato population from field studies. The aim of this work is to study, in the field, the genetic variability and reproductive strategies of populations of one of the most widely distributed potato species in Argentina, Solanum kurtzianum, growing in Mendoza province. AFLP markers showed that the genetic variability is mainly present among plants within populations, indicating that in the sampled populations, sexual reproduction is more relevant than clonal multiplication (by tubers). Additional evidence was obtained evaluating the genetic diversity in populations with a distribution in patches, where several genotypes were always detected. From a field study performed in the Villavicencio Natural Reserve, we found that the average number of plump seeds per fruit was 94.3, identified and calculated the foraging distance of four insect pollinators, and demonstrated the seed dispersal by storm water channels. We argue that the breeding system, the two modes of reproduction and the ecological interaction described here may have a prominent role in determining the genetic structure of S. kurtzianum populations, and discuss the importance of field studies on population genetics, reproductive biology and ecology to design collections and conservation strategies.     

AFLP and breeding system studies indicate vicariance origin for scattered populations and enigmatic low fecundity in the Moroccan endemic Hypochaeris angustifolia (Asteraceae), sister taxon to all of the South American Hypochaeris species

We used Amplified Fragment Length Polymorphism markers (AFLP) and breeding system studies to investigate the population structure and reproductive biology of Hypochaeris angustifolia (Asteraceae: Cichorieae). This species is endemic to altiplanos of the Atlas Mountains (Morocco) where it occurs in scattered populations, and it is the sister species to c. 40 species of this genus in South America. PCoA, NJ, and Bayesian clustering, revealed that the populations are very isolated whilst AFLP parameters show that almost all populations have marked genetic divergence. We contend that these features are more in accord with a vicariance origin for the scattered populations of H. angustifolia, rather than establishment by long-distance dispersal. The breeding system studies revealed that H. angustifolia is a self-incompatible species, with low fecundity in natural and in experimental crosses, probably due to a low frequency of compatible phenotypes within and between the populations.     

Population structure and genetic diversity distribution in wild and cultivated populations of the traditional Chinese medicinal plant Magnolia officinalis subsp. biloba (Magnoliaceae)

Magnolia officinalis subsp. biloba, a traditional Chinese medicinal plant, experienced severe declines in the number of populations and the number of individuals in the late 20th century due to the widespread harvest of the subspecies. A large-scale cultivation program was initiated and cultivated populations rapidly recovered the loss in individual plant numbers, but wild populations remained small as a consequence of cutting. In this study, the levels of genetic variation and genetic structure of seven wild populations and five domestic populations of M. officinalis subsp. biloba were estimated employing an AFLP methodology. The plant exhibited a relatively high level of intra-population genetic diversity (h = 0.208 and H _j = 0.268). The cultivated populations maintained approximately 95% of the variation exhibited in wild populations, indicating a slight genetic bottleneck in the cultivated populations. The analysis of genetic differentiation revealed that most of the AFLP diversity resided within populations both for the wild group (78.22%) and the cultivated group (85.92%). Genetic differentiation among populations in the wild group was significant (F _ST = 0.1092, P < 0.005), suggesting wild population level genetic structure. Principal coordinates analysis (PCO) did not discern among wild and cultivated populations, indicating that alleles from the wild population were maintained in the cultivated gene pool. Results from the present study provide important baseline data for effectively conserving the genetic resources of this medicinal subspecies.