A range wide geographic pattern of genetic diversity and population structure of Castanea mollissima populations inferred from nuclear and chloroplast microsatellites

Understanding geographical pattern of genetic diversity and population structure is of great importance for formulating conservation and utilization strategies. In this study, we investigated the genetic diversity and population structure of 28 natural populations of Castanea mollissima in China using eight nuclear and six chloroplast microsatellite makers (nSSRs and cpSSRs). Populations from central China harbored the highest genetic diversity at both nSSR and cpSSR markers (nSSR: H _E?=?0.705; cpSSR: H?=?0.461). The standardized measure of genetic differentiation estimated as G′ _ST was 0.447 for nSSR and 0.803 for cpSSR, respectively. The G′_ST-based pollen to seed flow ratio is 3.043, indicating that pollen flow is not extensive among C. mollissima populations. No obvious population genetic structure by geographical locations was found by STRUCTURE analysis based on nSSR data, and similarly, no signal of phylogeographic structure was detected for cpSSR analysis. Five boundaries defining zones of maximum genetic differences within the network of the C. mollissima populations were found, and the locations of those barriers were consistent with those of four mountains, i.e., Daloushan Mountain, Dabashan Mountain, Wushan Mountain, and Qingliangfeng Mountain, indicating that those mountains might act as genetic barriers obstructing the genetic exchange among natural C. mollissima populations. These results provide valuable baseline data for conservation and utilization of this species.     

Spatial and temporal population genetic variation and structure of Nothotsuga longibracteata (Pinaceae), a relic conifer species endemic to subtropical China

Nothotsuga longibracteata, a relic and endangered conifer species endemic to subtropical China, was studied for examining the spatial-temporal population genetic variation and structure to understand the historical biogeographical processes underlying the present geographical distribution. Ten populations were sampled over the entire natural range of the species for spatial analysis, while three key populations with large population sizes and varied age structure were selected for temporal analyses using both nuclear microsatellites (nSSR) and chloroplast microsatellites (cpSSR). A recent bottleneck was detected in the natural populations of N. longibracteata. The spatial genetic analysis showed significant population genetic differentiation across its total geographical range. Notwithstanding, the temporal genetic analysis revealed that the level of genetic diversity between different age class subpopulations remained constant over time. Eleven refugia of the Last Glacial Maximum were identified, which deserve particular attention for conservation management.     

Characterization of chloroplast microsatellite loci from whole chloroplast genome of Camellia taliensis and their utilization for evaluating genetic diversity of Camellia reticulata (Theaceae)

This study characterized chloroplast microsatellite markers for Camellia reticulata, a famous ornamental and edible economic tree species only distributed in Southwestern China. Thirty-two chloroplast microsatellite markers were originally annotated in the whole chloroplast genome of Camellia taliensis, ten polymorphic microsatellite markers were tested in 96 individuals from four natural populations of C. reticulata. Alleles numbered from two to four, and average value of Shannon's Information index, Nei's gene diversity, total genetic diversity, genetic diversity within populations, gene differentiation coefficient and gene flow index were 0.408, 0.225, 0.217, 0.102, 0.530 and 0.443, respectively. Our results showed high genetic differentiation and limited gene flow among the studied populations, which may be explained by recent fragmentation of the remnant populations due to human destruction and disturbance of natural habitats of the species. The identified cpSSR markers will be useful for the future studies on population genetics, conservation biology and phylogeography of C. reticulata.     

Low genetic diversity and limited gene flow in a dominant mangrove tree species (Rhizophora stylosa) at its northern biogeographical limit across the chain of three Sakishima islands of the Japanese archipelago as revealed by chloroplast and nuclear SSR analysis

We examined the genetic diversity, population structure and gene flow in a dominant mangrove tree (Rhizophora stylosa) at its northern biogeographical limit in Sakishima islands of the Japanese archipelago. Simple sequence repeat (SSR) markers from chloroplast (cpSSR) and nuclear DNA were used to analyze 16 populations recovered from various river basins across the chain of three Sakishima islands—Iriomote, Ishigaki and Miyako. The average number of alleles (1.7–2.7) and observed heterozygosities (0.031–0.216) at nuclear SSR and haploid diversity (0.000–0.489) at cpSSR across the populations suggested low genetic diversity in R. stylosa in Sakishima islands. cpSSR analysis identified two haplotypes, and Bayesian clustering analysis (nuclear SSR) revealed two genetic clusters. Analysis of molecular variance (nuclear SSR) showed significant population differentiations. Pairwise tests consistently revealed significant differentiation between most of the population pairs; however, the degrees of differentiations are generally correspondent to the relative geographical distances as suggested from pairwise F _ST and cpSSR genetic distances. Moreover, Mantel tests showed some signals of correlations between genetic distances (nuclear and chloroplast) and geographical distances. These results suggest that combined contribution of gene flow via pollen and propagule dispersal in R. stylosa mostly occurred between neighboring river basins. The appearances of two cpSSR haplotypes (maternal lineages) as well as two nuclear genetic clusters (putative ancestral lineages) at various river basins support the hypothesis that present-day R. stylosa populations across the Sakishima islands were established from few identical founders; however, significant differentiations among various river basins most likely resulted from the limited gene flow and high inbreeding.     

Habitat fragmentation,genetic diversity,and inbreeding depression in a threatened grassland legume: is genetic rescue necessary?

Kincaid’s lupine (Lupinus oreganus), a threatened perennial legume of western Oregon grasslands, is composed of small, fragmented populations that have consistently low natural seed set, suggesting they may have accumulated high enough levels of genetic load to be candidates for genetic rescue. We used simple sequence repeat (SSR) loci, both nuclear DNA and chloroplast DNA, to screen populations throughout the species’ range for evidence of severe inbreeding and recent genetic bottlenecks due to habitat fragmentation. After genotyping about 40% of the known populations, only one of 24 populations had strong statistical evidence for a recent genetic bottleneck (H _e > H _eq). Both mean nSSR fixation coefficients and genetic diversity did not statistically differ between very small, small, medium, and large lupine population size classes. Within population chloroplast DNA haplotype number was high for an animal pollinated species, ≈4.2 haplotypes/population, and within population haplotype diversity was also relatively evenly distributed. Within population patterns of nSSR and cpSSR genetic diversity suggest that genetic diversity has not been lost over the last century of habitat fragmentation. With genet lifespan thought to exceed 100 years, overlap of several to many generations, and substantial reductions in seed set from inbreeding depression that shifts cohort composition towards those generated by outcrossing events, Kincaid’s lupine is likely maintain the currently high levels of within population genetic diversity. The case of Kincaid’s lupine provides an example of how the assumptions of severe inbreeding depression with small population size and habitat fragmentation can be inaccurate.     

Chloroplast microsatellite diversity of Clintonia udensis (Liliaceae) populations in East Asia

Nineteen populations of Clintonia udensis Trautv. & Mey. were examined to quantify genetic diversity and genetic structure by chloroplast DNA microsatellites (cpSSR). Significant cpSSR genetic diversity (PPB = 63.64%) was detected in this species. Tetraploid populations demonstrated approximately the same level of genetic diversity as the diploid ones. A significant differentiation, however, was found between tetraploids and diploids. Most of the sixteen chloroplast haplotypes were limited to a single population. The level of haplotype diversity was high (Hd = 0.915). AMOVA, PCA and Bayesian clustering analysis revealed that there were significant genetic differences among populations. Inter-population genetic distances among population sites correlated significantly with geographic distances. These results indicate that the mixed-mating – breeding system, limited gene flow, environmental stress, and historical factors may be the main factors causing geographical differentiation in the genetic structure of C. udensis.     

Genetic diversity and differentiation of the endangered Japanese endemic tree Magnolia stellata using nuclear and chloroplast microsatellite markers

Genetic diversity and differentiation were analyzed in 11 populations of Magnolia stellata (Sieb. and Zucc.) Maxim. (Magnoliaceae) in the Tokai district, Japan. Variation at four nuclear microsatellite (nSSR) loci was examined, three chloroplast microsatellite (cpSSR) markers were developed and 13 haplotypes identified. The 11 populations were divided into three groups (A, B and C). Each population within the group was separated less than 40 km. Group B harbored the highest gene diversity (H) and allelic richness (Ar) for nSSR (H=0.74 and Ar=8.02). Group C had the highest diversity of chloroplast haplotypes (H=0.79 and Ar=6.8): 2.5 times more haplotypes than the other groups. Each population contributed differently to the total diversity, with respect to nSSR and cpSSR. AMOVA revealed that 58% of haplotypic and 15% of nSSR variation was partitioned among populations within groups. A Mantel test revealed significant correlations between population pairwise geographic ln(distance) and F_ST/(1−F_ST) for both nSSR (r=0.479; P=0.001) and cpSSR (r=0.230; P=0.040). Dendrograms of populations for nSSR, based on Nei’s genetic distance, were constructed using UPGMA and the neighbor-joining method. These results suggest that populations in group C have diverged from the other populations, while those in group B are similar to each other. For group B, fragmentation between populations should be avoided in order to maintain gene flow. For group C, the uniqueness of each population should be given the highest priority when planning genetic conservation measures for the species.     

Genetic structure of gall oak (<Emphasis Type="Italic">Quercus infectoria</Emphasis>) characterized by nuclear and chloroplast SSR markers

Quercus infectoria, commonly known as gall oak, is a small shrub found in Iran. Unfortunately, it is subjected to genetic erosion, and so, its conservation and evaluation are desirable. Thus, in the current research, 16 microsatellite primer pairs (seven nuclear simple sequence repeats (nSSRs) and nine chloroplast simple sequence repeats (cpSSRs)) were used in an attempt to assess the genetic diversity of 121 individuals of Q. infectoria belonging to 11 populations from three provinces in northern Zagros forests of Iran. In total, 69 alleles of nSSR and 18 alleles of cpSSR were detected among the individuals. The results of the overall analysis of molecular variance based on nSSRs indicated that 89.00% of the variation was due to differences within populations and 11.00% occurred among populations, while according to cpSSRs, 94.00% of the variation resided among populations, and only 6.00% could be attributed to variation within populations. A higher genetic differentiation of Q. infectoria populations was found according to cpSSR data in comparison to nSSR data. Cophenetic correlation coefficient values were statistically insignificant between nSSR and cpSSR data. The unweighted pair group method with arithmetic mean and Bayesian cluster analyses grouped the studied individuals into two main clusters based on both nSSR and cpSSR data. nSSR data could not completely clustered individuals next each other according to their geographical collection area. Information detailed by nSSR loci revealed that north-Zagros gall oak preserves average levels of genetic diversity at the species level, high level of within-population genetic diversity, and moderate level of genetic variation among populations. The present results provide valuable data for in situ or ex situ conservation and utilization of the studied germplasm.     

Chloroplast microsatellites reveal that metallicolous populations of the Mediterranean shrub Cistus ladanifer L have multiple origins

Cistus ladanifer L. (Cistaceae) is a Mediterranean shrub covering different kinds of soils in the Western Mediterranean area. This species has colonised several metalliferous areas (serpentine outcrops as well as human-polluted sites) throughout its distribution range, and is therefore an interesting species to study the possible effects on genetic diversity and differentiation produced by the colonisation of areas polluted with heavy metals. The genetic structure of 33 natural populations distributed across its entire natural distribution range (Morocco, Portugal and Spain) and growing on either metalliferous or non-metalliferous soils was investigated using chloroplast microsatellites. Population genetic parameters were estimated and genetic groups were identified using Bayesian inference. In addition, we compared the genetic diversity and differentiation among metallicolous and non-metallicolous populations within each Bayesian-defined group. The cpSSR data suggested that metallicolous populations of Cistus ladanifer have arisen through multiple independent evolutionary origins within two different chloroplast lineages. Evidence that the soil type provoked genetic bottlenecks in metallicolous populations or genetic differentiation among metallicolous and non-metallicolous populations was not observed. Historical factors are the main cause of the present genetic structure of C. ladanifer. The nature of tolerance to heavy metals as a species-wide trait in this shrub is discussed.     

An extreme cytoplasmic bottleneck in the modern European cultivated potato (Solanum tuberosum) is not reflected in decreased levels of nuclear diversity

We have used the polymorphic chloroplast (cp) and nuclear simple sequence repeats (SSRs) to analyse levels of cytoplasmic and nuclear diversity in the gene pool of the European cultivated potato (Solanum tuberosum ssp. tuberosum). Primers designed from the complete chloroplast sequence of tobacco (Nicotiana tabacum) were used to amplify polymorphic products in a range of potato cultivars. Combining the data from seven polymorphic cpSSR loci gave 26 haplotypes, one of which (haplotype A) accounted for 151 out of the 178 individuals studied and corresponded to the T-type cytoplasm previously identified in cultivated potatoes using chloroplast restriction fragment length polymorphism analysis. Phylogenetic and diversity analyses of the relationships between cpSSR haplotypes confirmed much higher levels of cytoplasmic diversity outwith the T-type group. Diversity levels at eight nuclear SSR loci, however, were not significantly different between cytoplasmic groups, suggesting a severe maternal bottleneck in the evolution of the modern cultivated potato. These results highlight the importance in quantifying levels of cytoplasmic as well as nuclear diversity and confirm the need for a change in breeding practices to increase levels of non-T-type cytoplasm in the cultivated gene pool, thus helping reduce problems associated with pollen sterility. This may be facilitated by germplasm analysis using cpSSRs, which will allow efficient selection of diverse cytoplasm donors.     

Geographic structure of genetic and phenotypic variation in the hybrid zone between Quercus affinis and Q. laurina in Mexico

Analyzing the structure of hybrid zones is important for inferring their origin, dynamics and evolutionary significance. We examined the geographic structure of phenotypic and genetic variation in the contact zone between two Mexican red oaks, Quercus affinis and Q. laurina. A total of 105 individuals from seven populations were sampled along a 600‐km latitudinal gradient representing the distribution area of the two species and their contact zone. Individuals were genotyped for nine nuclear and four chloroplast DNA microsatellite loci (ncSSR and cpSSR, respectively), and characterized for several leaf and acorn traits. The cpSSR data revealed extensive haplotype sharing among populations of the two species, while a Bayesian assignment analysis based on ncSSRs identified two main genetic groups, each corresponding to one of the species, and two populations in the contact zone showing evidence of admixture. The proportion of genetic ancestry in the populations was strongly associated with latitude and showed a pattern of variation with the shape of a narrow sigmoidal cline. The variation in three of the seven phenotypic traits was partially congruent with molecular variation, while the other traits did not conform to a geographic cline but instead were correlated with environmental variables. In conclusion, the hybrid zone between the two oak species has some of the characteristics of a tension zone, but heterogeneous variation across traits suggests differential introgression and the action of extrinsic selection.     

A unifying study of phenotypic and molecular genetic variability in natural populations of Anadenanthera colubrina var. cebil from Yungas and Paranaense biogeographic provinces in Argentina

Anadenanthera colubrina var. cebil is a discontinuously distributed native tree species in South American subtropical forests. Thirteen quantitative traits and eight nuclear microsatellite loci were examined in individuals from two biogeographic provinces of Argentina to determine the number and composition of genetically distinguishable groups of individuals and explore possible spatial patterns of the phenotypic and genetic variability. Means of reproductive traits were higher in the Yungas than in the Paranaense biogeographic province, whereas five out of eight nonreproductive quantitative traits showed higher mean values in the latter. Variance coefficients were moderate, and there were significant differences between and within provinces. Three clusters were defined based on spatial model for cluster membership for quantitative traits. One cluster grouped the individuals from the Paranaense biogeographic province whereas the individuals from the Yungas biogeographic province grouped regarding its population of origin. Parameters of molecular genetic variability showed higher values in the Yungas than in the Paranaense biogeographic province. Observed heterozygosity was lower than expected heterozygosity in both biogeographic provinces, indicating an excess of homozygosity. The homozygosity test by Watterson and the exact test by Slatkin suggested diversifying selection for locus Ac41.1. Bayesian clustering spatial model for microsatellites loci data were performed for both all loci and for all loci excluding locus Ac41.1. In both analyses two clusters were inferred. Analysis of molecular variance revealed similar results for all genotypes and for all genotypes defined excluding locus Ac41.1. Most of the total variance is attributable to genetic variation within clusters. The presence of homogeneous clusters was detected for both the phenotypic and molecular genetic variability. Two Bayesian clustering analyses were performed according to molecular genetic data, and two clusters were inferred. Individuals were assigned to their provinces of origin. Genetic molecular variation was higher in the populations of the Yungas biogeographic province which translates into highly qualified populations for conservation. Populations from the Paranaense biogeographic province showed the highest mean value of number of seeds per fruit making them valuable as well with regard to the exploitation of management strategies as a means to recover the impacted areas where these populations are located.     

Dissimilar patterns of Pinus heldreichii Christ. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis

In the present study we investigated the genetic structure and genetic diversity of Pinus heldreichii populations in Bulgaria using chloroplast microsatellite markers and terpene analysis. We were interested in addressing the following questions: (1) can population structuring in Bosnian pine be detected via chloroplast microsatellite markers; (2) are there differences in population differentiation as determined by terpenes and microsatellites; and (3) how are the patterns of size variant frequencies and geographical distances related. Four provenances were chosen throughout the species' range in Bulgaria. Following DNA extraction, chloroplast microsatellite (cpSSR) loci were surveyed using 6 primer pairs. Between 2 and 5 size variants were identified at each locus. A total of 16 size variants at the 6 loci were identified, 4 occurring at low frequencies. They were combined in 21 different haplotypes including 11 that were unique. AMOVA analysis revealed that 18.25% of the variation was found among populations, while 81.75% was expressed within populations. The cpSSR analysis divided Bosnian pine populations into two groups, the first represented by populations B, C and D located in the south and north-western part of the Pirin and Slavianka mountains, while the second group, represented by population A, is located in the north-eastern Pirin mountain. Terpene analysis revealed that on average, 59% of the monoterpene pool in P. heldreichii is accounted for by limonene (range 36–48%) followed by α-pinene (range 16–17%). The presence of two distinct groups (Pop-A, Pop-D and Pop-B, Pop-C) is more consistent with physical distances between populations. No significant correlation between genetic distance determined by chloroplast microsatellites analysis and chemotype distance determined by terpenes was observed. Our results suggest that the structural pattern of genetic diversity of cpDNA in Bosnian pine populations is the consequence of historical and biogeographical processes.     

Structure of Pinus nigra Arn. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: Provenance tests

Pinus nigra is a forest and low elevation mountain species found around the Mediterranean Sea that has had its distribution reduced and fragmented by anthropogenic disturbance. Due to commercial interest it is currently being replanted, however, the genetic structure of populations is little known and current planting strategies could threaten its genetic diversity. In the present study we investigated the genetic structure and genetic diversity of P. nigra populations in Bulgaria using chloroplast microsatellite markers and terpene analysis. Nine provenances were chosen throughout the species' range in Bulgaria. Following DNA extraction, chloroplast microsatellite (cpSSR) loci were surveyed using three primer pairs. Between 5 and 9 size variants were identified at each locus. A total of 22 size variants at the 3 loci were identified, that were combined in 68 different haplotypes, of which 7 represent 39.81% of the genetic structure. AMOVA analysis revealed that 6.06% of the variation was found among populations, while 93.94% was expressed within populations. The cpSSR analysis divided European Black pine populations into four groups, the first represented by populations located the eastern Rhodopes, Sr. Gora and St. Planina mountains, while the second group is primarily located in the Phodopes and Slavianca mountains. The populations from Pirin and Osogovo mountains show different genetic patterns. Terpene analysis revealed that most of the monoterpene pool in P. nigra was accounted for by α-pinene followed by β-pinene. The presence of four distinct terpene groups is not consistent with physical distances between populations, and a similar non-significant correlation between genetic distance determined by chloroplast microsatellites analysis and chemotype distance (determined by terpenes) was observed. Our results suggest that the structural pattern of genetic diversity of cpDNA in European Black pine populations is the consequence of historical biogeographic processes.     

Geographic patterns of genetic variation in native pecans

A structured collection of 80 seedling pecan trees [Carya illinoinensis (Wangenh.) K. Koch], representing 19 putatively native pecan populations across the species range, was evaluated at three plastid and 14 nuclear microsatellite (simple sequence repeat, SSR) loci. Data were analyzed using a priori population designations and also within a Bayesian framework, in which individuals were assigned to clusters regardless of population of origin. Population genetic analyses using a priori populations, clusters based on chloroplast microsatellite data (cpSSR), and clusters based on nuclear microsatellite data (nSSR) yielded consistent results. For all groupings, cpSSR variation exhibited more geographic structure than the nSSR data. Furthermore, cpSSR microsatellite diversity decreased with increasing latitude, but this pattern was not observed with the nuclear data. Contrasting patterns in plastid and nuclear genetic diversity demonstrate unique aspects of postglacial recolonization reflected in the movement of seeds versus pollen. These data suggest that plastid SSRs are useful tools for identifying population structure in pecan and hold promise for ongoing efforts to identify and conserve representative germplasm in ex situ collections.     

Genetic Diversity and Structure in Fragmented Populations of the Tropical Orchid Myrmecophila christinae var christinae1

In recent years the coastal dune vegetation of the state of Yucatan, Mexico has become highly fragmented due to clearing for development. We evaluated patterns of genetic differentiation and genetic variability among orchid populations (Myrmecophila christinae var christinae) in eight habitat fragments along a west‐to‐east disturbance gradient in which sites located on the western end began experiencing fragmentation earlier than those in the east. Leaf samples from adult individuals and juvenile plants were collected from all eight populations, and analyzed using starch‐gel electrophoresis in a lithium buffer system. Per population estimates of genetic diversity, proportion of polymorphic loci at 95 percent, mean number of alleles per locus, allelic richness, and population structure were calculated, as well as estimate comparisons between generations. Genetic diversity at the loci analyzed did not show significant differences among the eight populations. Based on the results, the model of isolation by distance does not fit the M. christinae populations under study; in some cases, populations close to one another apparently experienced very little genetic exchange. Thus, we propose that so far, fragmentation has not led to significant genetic differences between populations subject to different historical backgrounds of disturbance (i.e., time since onset of disturbance), as well as between generations within each of the M. christinae study populations. Nevertheless, the genetic characteristics of some remnant populations might change over time due to a future decrease in the opportunities for genetic exchange with other populations.     

Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci.

Genetic variation was compared between uniparentally-inherited (chloroplast simple sequence repeats, cpSSRs) vs. biparentally-inherited (isozyme and random amplified polymorphic DNA, RAPD) genetic markers in Douglas-fir (Pseudotsuga mensiezii) from British Columbia. Three-hundred twenty-three individuals from 11 populations were assayed. In Douglas-fir, the cpSSR primer sites were well-conserved relative to Pinus thunbergii (11 of 17 loci clearly amplified), but only 3 loci were appreciably polymorphic. At these cpSSR loci, we found an unexpectedly low level of polymorphism within populations, and no genetic differentiation among populations. By contrast, the nuclear markers showed variation typical of conifers, with significant among-population differentiation. This difference is likely the outcome of both historical factors and high pollen dispersal.     

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.     

Genetic Diversity and Population Structure of Acacia senegal (L) Willd. in Kenya

The level of genetic diversity and population structure of Acacia senegal variety kerensis in Kenya was examined using seven polymorphic nuclear microsatellite loci and two chloroplast microsatellite loci. In both chloroplast and nuclear datasets, high levels of genetic diversity were found within all populations and genetic differentiation among populations was low, indicating extensive gene flow. Analysis of population structure provided support for the presence of two groups of populations, although all individuals had mixed ancestry. Groups reflected the influence of geography on gene flow, with one representing Rift Valley populations whilst the other represented populations from Eastern Kenya. The similarities between estimates derived from nuclear and chloroplast data suggest highly effective gene dispersal by both pollen and seed in this species, although population structure appears to have been influenced by distributional changes in the past. The few contrasts between the spatial patterns for nuclear and chloroplast data provided additional support for the idea that, having fragmented in the past, groups are now thoroughly mixed as a result of extensive gene flow. For the purposes of conservation and in situ management of genetic resources, sampling could target a few, large populations ideally distributed among the spatial groups identified. This should ensure the majority of extant variation is preserved, and facilitate the investigation of variation in important phenotypic traits and development of breeding populations.