Low levels of quantitative and molecular genetic differentiation among natural populations of Medicago ciliaris Kroch. (Fabaceae) of different Tunisian eco-geographical origin

In this paper, we analyze the genetic variability in four Tunisian natural populations of Medicago ciliaris using 19 quantitative traits and six polymorphic microsatellite loci. We investigated the amplification transferability of 30 microsatellites developed in the model legume M. truncatula to M. ciliaris. Results revealed that about 56.66% of analyzed markers are valuable genetic markers for M. ciliaris. The most genetic diversity at quantitative traits and microsatellite loci was found to occur within populations (>80%). Low differentiations among populations at quantitative traits Q _ST  = 0.146 and molecular markers F _ST  = 0.18 were found. The majority of measured traits exhibited no significant difference in the level of Q _ST and F _ST . Furthermore, significant correlations established between these traits and eco-geographical factors suggested that natural selection should be invoked to explain the level of phenotypic divergence among populations rather than drift. There was no significant correlation between population differentiation at quantitative traits and molecular markers. Significant spatial genetic structure consistent with models of isolation by distance was detected within all studied populations. The site-of-origin environmental factors explain about 9.07% of total phenotypic genetic variation among populations. The eco-geographical factors that influence more the variation of measured traits among populations are the soil texture and altitude. Nevertheless, there were no consistent pattern of associations between gene diversity (He) and environmental factors.     

Dissimilar patterns of genetic variation in two insular endemic plants sharing species characteristics,distribution, habitat,and ecological history

Camssonia guadalupensis ssp. clementina (Onagraceae) and Cryptantha traskiae (Boraginaceae) share many species characteristics that affect levels and pattern of genetic variation. In addition, they have a similar distribution, are found in the same habitat, and share ecological history by virtue of co-occurring at nearly all of the locations at which they are found. All populations of the two taxa on San Clemente Island were surveyed for genotypes at 16 allozyme loci, revealing generally low levels of genetic variation. However, Cam. g. clementina has more genetic variation than Cryp. traskiae at the taxon level (P = 37.5 versus 18.8, A = 1.69 versus 1.31, and H_E = 0.088 versus 0.003) and significantly more alleles and higher heterozygosity within populations (A = 1.09 versus 1.03, A_E = 1.02 versus 1.00; H_O = 0.013 versus 0.001 and H_E = 0.017 versus 0.003). Some populations of each taxon are monomorphic at all loci. Much greater differentiation among populations occurs in Cam. g. clementina (G_ST = 0.810) than in Cryp. traskiae (G_ST = 0.042). Locations of the more variable populations of each taxon do not coincide, and the pattern of genetic similarity of localities differs in the two taxa. Striking population genetic differences exist between these taxa despite shared species characteristics, distribution, habitat, and recent history.     

Population Genetic Structure of Two Columnar Cacti with a Patchy Distribution in Eastern Brazil

The genetic variability and population genetic structure of six populations of Praecereus euchlorus and Pilosocereus machrisii were investigated. The genetic variability in single populations of Pilosocereus vilaboensis, Pilosocereus aureispinus, and Facheiroa squamosa was also examined. All of these cacti species have a patchy geographic distribution in which they are restricted to small areas of xeric habitats in eastern Brazil. An analysis of genetic structure was used to gain insights into the historical mechanisms responsible for the patchy distribution of P. euchlorus and P. machrisii. High genetic variability was found at the populational level in all species (P=58.9–92.8%, A_p=2.34–3.33, H_e=0.266–0.401), and did not support our expectations of low variability based on the small population size. Substantial inbreeding was detected within populations (F_IS=0.370–0.623). In agreement with their insular distribution patterns, P. euchlorus and P. machrisii had a high genetic differentiation (F_ST=0.484 and F_ST=0.281, respectively), with no evidence of isolation by distance. Accordingly, estimates of gene flow (N_m) calculated from F_ST and private alleles were below the level of N_m=1 in P. machrisii and P. euchlorus. These results favored historical fragmentation as the mechanism responsible for the patchy distribution of these two species. The genetic distance between P. machrisii and P. vilaboensis was not compatible with their taxonomic distinction, indicating a possible local speciation event in this genus, or the occurrence of introgression events.     

Biogeographic history of the threatened species <Emphasis Type="Italic">Araucaria araucana</Emphasis> (Molina) K. Koch and implications for conservation: a case study with organelle DNA markers

Fragmentation of the habitat due to glaciations, fires and human activities affected the distribution range of Araucaria araucana in southern South America. On the borders of the Argentinean Patagonian steppe, the species is restricted to isolated patches without natural regeneration. Our objective is to test the hypothesis that these populations are relicts of pre-Pleistocene origin. A total of 224 individuals from 16 populations were sampled. Twenty chloroplast microsatellites, 19 non-coding chloroplast DNA regions and eight mitochondrial DNA fragments were screened for polymorphisms. A low transferability rate of universal primers from Pinaceae and also a low variation were detected for this ancient species. Only one non-coding region of the chloroplast DNA showed polymorphism allowing the identification of five haplotypes. A low genetic differentiation (G _ST  = 0.11; G′ _ST  = 0.267) and lack of geographic structure was found. Allelic richness was lower and genetic differentiation higher among the eastern isolated populations, suggesting a long lasting persistence. Conservation guidelines are given for these relictual populations, which are located outside the limits of the National Parks.     

Genetic diversity of insular natural populations of <Emphasis Type="Italic">Festuca pratensis</Emphasis> Huds.: RAPD analysis

In natural populations of Festuca pratensis Huds. from the islands of Onega Lake, the level of genetic diversity was evaluated. In three populations variability of 64 RAPD loci was tested. The level of genetic diversity (P _95% = 30.2; H _exp = 0.093) was low for a cross-pollinating plant species. Furthermore, genetic similarity between the plants from insular populations was found to be high (I _N = 0.887). It was demonstrated that genetic variation among the population accounted for at most 5.3% of total genetic diversity, which, however, was higher than the F _ST values for continental populations (F _ST = 0.022). It was suggested that specific features of the genetic structure of insular population, i.e., low gene diversity within the populations along with high differentiation among the populations, were caused by the gene flow attenuation, as a result of isolation, and intensification of inbreeding. These features had negative effect on total population adaptation.     

Patterns of allozyme variation in western Eurasian Fagus

Fagus sylvatica L. is one of the most widespread broad‐leaved trees in the temperate forests of the northern hemisphere. In addition to two subspecies, F. sylvatica ssp. sylvatica in Europe and F. sylvatica ssp. orientalis in south‐western Asia, two further taxa were described: F. moesiaca (Maly) Czeczott in the south‐western Balkans and F. taurica Popl. in Crimea. The opinions about the number and ranks of taxa within this complex are highly controversial. To assess the degree of genetic differentiation among them, and to reveal geographical patterns of genetic diversity and their relationships to history and biogeography of beech populations, genetic variation at 12 allozyme loci was studied in 279 populations in western Eurasia. A Bayesian analysis of population structure revealed the existence of two clusters, which fairly well coincided with F. sylvatica ssp. sylvatica and F. sylvatica ssp. orientalis, whereby the populations from the south‐western Balkans and Crimea contained a mixture of these two gene pools. On the other hand, a neighbour‐joining tree based on pairwise F_ST failed to separate the subspecies into well‐defined distinct clades. Populations of F. sylvatica ssp. orientalis proved to be incomparably more differentiated than ssp. sylvatica (F_ST = 0.157 and 0.032, respectively). Asian populations also showed higher levels of allelic richness both on population and taxon levels than the European ones (the number of alleles after rarefaction was 3.40 and 4.27 in F. sylvatica ssp. sylvatica and ssp. orientalis, respectively). This indicates that the gene pool of F. sylvatica ssp. orientalis has not been depleted by reduced population sizes during the Pleistocene glaciations, as is the case of F. sylvatica ssp. sylvatica. Genetic similarities between isolated regional populations are explained by shared ancestral polymorphisms and/or range overlaps with subsequent hybridization in the past. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 165–174.     

A cline of allozyme variation inAbies mariesii

Genetic variation at 22 allozyme loci was examined for 1,003 trees from 11 isolated natural populations ofAbies mariesii covering all except the southernmost region of its geographic range. Genetic diversity within species (H _es=0.063) was low compared to many other long-lived woody species. Most of the genetic variation is found within populations (G _ST=0.144) despite their isolated distribution. Genetic distance between populations was positively correlated with geographic distance. Genetic diversity within populations was generally low (meanH _ep=0.054), but varied across populations in a clinal fashion such that genetic variation decreased with increasing latitude. These genetic characteristics may reflect the distribution history of this species.     

Allozyme variation in the diploid (A genome) populations ofScilla scilloides (Hyacinthaceae)

Allozyme variation at eleven loci encoding seven enzyme systems were examined in 20 populations of diploid (genome AA, 2n = 16)Scilla scilloides in China. In comparison with the average species of seed plants studied, populations of this species display a high amount of genetic variation (A = 2.0, P = 58.6%, H_o = 0.172, and H_e = 0.185). Allozyme variation pattern revealed predominant outcrossing within populations and considerable differentiation (F_ST = 0.314) among populations as well as between the subtropic and temperate regions. The wide distribution, long existence and outcrossing are presumably the main factors responsible for the high genetic diversity within populations. But the gravity dispersal of seeds and pollination by small insects set limits to the increase of genetic variation within populations and promote differentiation between populations and regions. In addition, allozyme variation does not distinguishS. scilloides var.albo-viridis and suggests that subtropic populations may be considered as a genetic entity.     

Pleistocene glaciations and contemporary genetic diversity in a Beringian fish,the broad whitefish,Coregonus nasus (Pallas): inferences from microsatellite DNA variation

The contemporary distribution of genetic variation within and among high latitude populations cannot be fully understood without taking into consideration how species responded to the impacts of Pleistocene glaciations. Broad whitefish, Coregonus nasus, a species endemic to northwest North America and the Arctic coast of Russia, was undoubtedly impacted by such events because its geographic distribution suggests that it survived solely within the Beringian refuge from where it dispersed post‐glacially to achieve its current range. We used microsatellite DNA to investigate the role of glaciations in promoting intraspecific genetic variation in broad whitefish (N = 14 localities, 664 fish) throughout their North American range and in one Russian sample. Broad whitefish exhibited relatively high intrapopulation variation (average of 11.7 alleles per locus, average H_E = 0.61) and moderate levels of interpopulation divergence (overall F_ST = 0.10). The main regions assayed in our study (Russia, Alaska, Mackenzie River and Travaillant Lake systems) were genetically differentiated from each other and there were declines in genetic diversity with distance from putative refugia. Additionally, Mackenzie River system populations showed less developed and more variable patterns of isolation‐by‐distance than populations occupying former Alaskan portions of Beringia. Finally, our data suggest that broad whitefish dispersed from Beringia using coastal environments and opportunistically via headwater stream connections that once existed between Yukon and Mackenzie River drainages. Our results illustrate the importance of history (e.g. glaciation) and contemporary dispersal ecology in shaping the current genetic population structure of Arctic faunas.     

The effects of Quaternary glaciations in Patagonia as evidenced by chloroplast DNA phylogeography of Southern beech Nothofagus obliqua

Climatic oscillations during the Quaternary strongly affected the distribution of warm-temperate tree species, which experienced local restrictions into ice-free areas and posterior expansions. To evaluate the impact of these range movements on the genetic structure of populations, we performed a phylogeographical analysis of the species Nothofagus obliqua with chloroplast DNA markers. A total of 27 populations covering the whole natural distribution range were analyzed using polymerase chain reaction-restriction fragment length polymorphism. Diversity (h _T, h _S), allelic richness (r _g), and differentiation among populations for unordered (G _ST) and ordered alleles (N _ST) were calculated. The relationships among haplotypes were evaluated by the construction of a minimum spanning network. The spatial distribution of the genetic variation was analyzed through a Mantel test and with a nested analysis of molecular variance to differentiate between geographic regions. The screening of 11 non-coding regions allowed the identification of 14 haplotypes. A high genetic differentiation was detected (N _ST = 0.875 and G _ST = 0.824) with the existence of phylogeographic structure (p < 0.05). The distribution of the genetic variation was partially explained by the topography of the region when the populations were divided longitudinally into Coastal Mountains, Central Valley, and Andes Mountains (ϕ _RT = 0.093, p = 0.001). In agreement with pollen records, our results support the hypothesis of Coastal refuges since the region harbors high diversity together with older and private haplotypes. Long-lasting persistence of some Coastal populations without contribution to re-colonization is proposed. Additional refuges are also postulated along the Andes and Longitudinal Valley. Survival in multiple glacial refuges is discussed together with the possible migratory routes.     

Genetic diversity among wild and cultivated barley as revealed by RFLP

Genetic variability of cultivated and wild barley, Hordeum vulgare ssp. vulgare and spontaneum, respectively, was assessed by RFLP analysis. The material consisted of 13 European varietes, single-plant offspring lines of eight land races from Ethiopia and Nepal, and five accessions of ssp. spontaneum from Israel, Iran and Turkey. Seventeen out of twenty-one studied cDNA and gDNA probes distributed across all seven barley chromosomes revealed polymorphism when DNA was digested with one of four restriction enzymes. A tree based on genetic distances using frequencies of RFLP banding patterns was estimated and the barley lines clustered into five groups reflecting geographical origin. The geographical groups of land-race lines showed less intragroup variation than the geographical groups of spontaneum lines. The group of European varieties, representing large variation in agronomic traits, showed an intermediate level. The proportion of gene diversity residing among geographical groups (F_ST) varied from 0.19 to 0.94 (average 0.54) per RFLP pattern, indicating large diversification between geographical groups.     

Genetic Diversity and Geographic Differentiation in the Threatened Species Dysosma pleiantha in China as Revealed by ISSR Analysis

Dysosma pleiantha, an important threatened medicinal plant species, is restricted in distribution to southeastern China. The species is capable of reproducing both sexually and asexually. In this study, inter-simple sequence repeat marker data were obtained and analyzed with respect to genetic variation and genetic structure. The extent of clonality, together with the clonal and sexual reproductive strategies, varied among sites, and the populations under harsh ecological conditions tended to have large clones with relatively low clonal diversity caused by vegetative reproduction. The ramets sharing the same genotype show a clumped distribution. Across all populations surveyed, average within-population diversity was remarkably low (e.g., 0.111 for Nei’s gene diversity), with populations from the nature reserves maintaining relatively high amounts of genetic diversity. Among all populations, high genetic differentiation (AMOVA: Φ_ST = 0.500; Nei’s genetic diversity: G _ST = 0.465, Bayesian analysis: Φ_B = 0.436) was detected, together with an isolation-by-distance pattern. Low seedling recruitment due to inbreeding, restricted gene flow, and genetic drift are proposed as determinant factors responsible for the low genetic diversity and high genetic differentiation observed.     

Impact of altitude and topography on the genetic diversity of Quercus serrata populations in the Chichibu Mountains, central Japan

In order to elucidate the factors affecting the genetic diversity of Quercus serrata in secondary forests in mountainous regions, we evaluated the level and distribution of genetic variation within and between 15 populations using seven microsatellite markers. The populations were at altitudes ranging from 140 to 1200 m in and around the Chichibu Mountains, central Japan.The expected heterozygosity (H_E) ranged from 0.766 to 0.837. The two populations that exhibited the highest and the second highest values of H_E are located beside a river and a lake, respectively. The two populations exhibiting the lowest and the second lowest values of H_E are, in contrast, located on a summit and a ridge. The observed heterozygosity (H_O) varied between 0.638 and 0.844, and the value of this variable was also higher for the populations beside water than those on summits or ridges. The soils at the waterside are wet, in contrast to those on ridges and summits, which tend to be shallow and subject to rapid desiccation. These results suggest that a lack of soil moisture is likely to inhibit the development and regeneration of Q. serrata, and that genetic diversity is reduced in arid areas. The genetic differentiation was low (F_ST=0.013) among the investigated populations, although all five populations in Yamanashi prefecture clustered together in an UPGMA tree. According to a multiple regression analysis, there was no significant isolation by distance among the populations along either the horizontal or vertical axes. Therefore, genetic variation within populations is affected by topography, but variation between populations is hardly affected by geographical factors. Furthermore, the results of this study suggest two conclusions. First, that altitude is not always a useful variable when estimating the genetic diversity of plant populations in mountainous regions. Second, that genetic diversity can vary even among the undifferentiated plant populations in small areas like the Chichibu Mountains.     

Morphological and microsatellite diversity associated with ecological factors in natural populations of Medicago laciniata Mill. (Fabaceae)

Genetic variability in 10 natural Tunisian populations of Medicago laciniata were analysed using 19 quantitative traits and 12 polymorphic microsatellite loci. A large degree of genetic variability within-populations and among-populations was detected for both quantitative characters and molecular markers. High genetic differentiation among populations for quantitative traits was seen, with Q _ST = 0.47, and F _ST = 0.47 for microsatellite markers. Several quantitative traits displayed no statistical difference in the levels of Q _ST and F _ST . Further, significant correlations between quantitative traits and eco-geographical factors suggest that divergence in the traits among populations may track environmental differences. There was no significant correlation between genetic variability at quantitative traits and microsatellite markers within populations. The site-of-origin of eco-geographical factors explain between 18.13% and 23.40% of genetic variance among populations at quantitative traits and microsatellite markers, respectively. The environmental factors that most influence variation in measured traits among populations are assimilated phosphorus (P₂0₅) and mean annual rainfall, followed by climate and soil texture, altitude and organic matter. Significant associations between eco-geographical factors and gene diversity, H _e , were established in five-microsatellite loci suggesting that these simple sequence repeats (SSRs) are not necessarily biologically neutral.     

Microsatellite DNA Polymorphism in Intensely Enhanced Populations of Sea Trout (Salmo trutta) in the Southern Baltic

Sea trout (Salmo trutta) is an anadromous form of brown trout, a commercially important salmonid species in Europe. Stocking has been used to compensate for the decrease of natural populations and maintenance of fishery and angling catches. Over 1.5 million smolts and 4.5 million alevins are released to Polish coastal rivers each year. Variation at 7 microsatellite loci (Ssa197, Ssa171, Ssa85, Str15, Str73, Str591, and Str543) was used to study genetic polymorphism of spawners returning to 6 rivers. Application of distance method for comparison of pairs of populations based on number of different alleles (F _ST) revealed significant differences between Vistula and Wieprza, and Parseta as well as between Drweca and Wieprza, and Slupia. The level of heterozygosity was similar between most of the studied sea trout populations; considerable differences were found only for Str591. Differences in frequencies of a few alleles between populations were observed. An exact test of sample differentiation based on allele frequencies confirmed lack of significance of differentiation between the 6 pairs of populations (F _ST and R _ST). No admixture was observed in the studied populations. Possible effects of stocking on the genetic polymorphism of the sea trout populations in wild with implications for biotechnology are discussed.     

Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine (Perisoreus canadensis)

An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, Φ_ST, SAMOVA, F_ST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.     

GENETIC STRUCTURE OF NATURAL POPULATIONS IN THE RED ALGAE GELIDIUM CANARIENSE (GELIDIALES,RHODOPHYTA) INVESTIGATED BY RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS1

Random amplified polymorphic DNA (RAPD) marker variation was analyzed in female gametophytes in natural populations of Gelidium canariense (Grunow) Seoane‐Camba ex Haroun, Gil‐Rodríguez, Diaz de Castro et Prud'Homme van Reine from the Canary Islands to estimate the degree and distribution of genetic variability and differentiation. A total of 190 haploid individuals were analyzed with 60 polymorphic RAPDs bands which produced 190 distinct multilocus genotypes. A high level of polymorphism was detected in all populations analyzed. Within‐population gene diversity ranged from 0.156 to 0.264. The populations on the island of Gran Canaria showed higher genetic variation than the other populations analyzed. The partitioning of molecular variance by analysis of molecular variance showed that most genetic variation resides within populations (68.85%). These results suggest that sexual reproduction is the predominant mode of reproduction for G. canariense gametophytic populations, and the main determinant in reaching high levels of genetic diversity. The Neighbor‐Joining tree and FCA analysis displayed two subclusters that correspond to the populations from the western islands (Tenerife, La Palma, Gomera) and the eastern island (Gran Canaria). In addition, we have detected a significant relationship between F_ST/(1?F_ST) and geographical distance consistent with data on water circulation and age of islands. The results obtained agree with an isolation by distance model, with gene flow from eastern to the western islands, and a high level of genetic differentiation between populations (F_ST=0.311, P<0.001).     

The effects of selection,drift and genetic variation on life‐history trait divergence among insular populations of natterjack toad,Bufo calamita

Although loss of genetic variation is frequently assumed to be associated with loss of adaptive potential, only few studies have examined adaptation in populations with little genetic variation. On the Swedish west coast, the northern fringe populations of the natterjack toad Bufo calamita inhabit an atypical habitat consisting of offshore rock islands. There are strong among‐population differences in the amount of neutral genetic variation, making this system suitable for studies on mechanisms of trait divergence along a gradient of within‐population genetic variation. In this study, we examined the mechanisms of population divergence using Q_ST–F_ST comparisons and correlations between quantitative and neutral genetic variation. Our results suggest drift or weak stabilizing selection across the six populations included in this study, as indicated by low Q_ST–F_ST values, lack of significant population × temperature interactions and lack of significant differences among the islands in breeding pond size. The six populations included in this study differed in both neutral and quantitative genetic variation. Also, the correlations between neutral and quantitative genetic variation tended to be positive, however, the relatively small number of populations prevents any strong conclusions based on these correlations. Contrary to the majority of Q_ST–F_ST comparisons, our results suggest drift or weak stabilizing selection across the examined populations. Furthermore, the low heritability of fitness‐related traits may limit evolutionary responses in some of the populations.     

Genetic Variation in Remnant Populations of the Woolly Spider Monkey (Brachyteles arachnoides)

The muriqui or woolly spider monkey (Brachyteles arachnoids) is an endangered primate endemic to the Atlantic Forest of Brazil, <5% of which remains. The known muriqui population consists of <700 individuals separated into approximately 15 geographically isolated forest fragments. I present data on the distribution of genetic variation within and between two such remnant populations (FE and FBR) and summarize the implications of these results for long-range management of species genetic diversity. Eleven of 32 allozyme loci were polymorphic, representing an overall level of polymorphism of 34.4% and a mean heterozygosity per locus of 11%. Both values are among the highest reported for New World monkeys. Genetic differentiation between the two localities is highly significant (F_ST = 0.413, p < 0.001). Genetic distance between them is an order of magnitude greater than that between other populations of platyrrhine subspecies, but this could be an artifact of the small sample size from FBR. High levels of genetic diversity apparently characteristic of this species persist because (1) fragmentation and size reduction of muriqui populations has occurred very rapidly relative to the muriqui life span—although both polymorphism and heterozygosity were lost between generations in the largest population, the high genetic diversity present in the parent population was still in evidence; and (2) genetic diversity before population fragmentation by human activity was not distributed uniformly throughout the species' historic distribution. Thus, remnant muriqui populations are important genetic reservoirs of alleles that are unique or rare in the species gene pool as a whole. These results emphasize the need for the integration of conservation management efforts throughout the species range.     

Comparative population structure of Chinese sumac aphid <Emphasis Type="Italic">Schlechtendalia chinensis</Emphasis> and its primary host-plant <Emphasis Type="Italic">Rhus chinensis</Emphasis>

Most of our current understanding of comparative population structure has been come from studies of parasite–host systems, whereas the genetic comparison of gallnut-aphids and their host-plants remain poorly documented. Here, we examined the population genetic structure of the Chinese sumac aphid Schlechtendalia chinensis and its unique primary host-plant Rhus chinensis in a mountainous province in western China using inter-simple sequence repeat (ISSR) markers. Despite being sampled from a mountainous geographic range, analysis of molecular variance (AMOVA) showed that the majority of genetic variation occurred among individuals within populations of both the aphid and its host. The aphid populations were found to be structured similarly to their primary host populations (F _ST values were 0.239 for the aphid and 0.209 for its host), suggesting that there are similar patterns of gene flow between the populations of the aphid and between populations of its host-plant. The genetic distances (F _ST/1 − F _ST) between the aphid populations and between its host-plant populations were uncorrelated, indicating that sites with genetically similar host-plant populations may not always have genetically similar aphid populations. The lack of relationships between genetic and geographical distance matrices suggested that isolation by distance (IBD) played a negligible role at this level. This may be mainly attributed to the founder effect, genetic drift and the relative small spatial scale between populations. Zhumei Ren and Bin Zhu contributed equally to this work.