Genetic diversity of the green spruce aphid (Elatobium abietinum Walker) in north-west Europe

Abstract 1 The Random Amplified Polymorphic DNA (RAPD) method was used to investigate genetic diversity of anholocyclic populations of the green spruce aphid, Elatobium abietinum Walker, in north‐west Europe. 2 The results showed that the aphid in this region was divided genetically into three major groups. Aphids from the British Isles and north‐west France comprised the first group, the second group consisted of aphids from Denmark and Iceland, and the third group consisted of aphids from Norway. 3 The results indicated a significant level of gene flow within and between sites and geographical regions, especially in the British Isles and north‐west France. Lateral migration of the aphid and/or sexual reproduction is likely to have facilitated the gene flow. 4 The implications of these findings on management of the green spruce aphid are discussed.     

Geographical distribution and host range of entomophthorales infecting the green spruce aphid Elatobium abietinum Walker in Iceland.

Entomophthora planchoniana and Neozygites fresenii caused infection in populations of the green spruce aphid, Elatobium abietinum, in Iceland. On this aphid species En. planchoniana was exclusively found in the western part of Iceland, while N. fresenii was exclusively found in the eastern part of Iceland. This discrete and nearly nonoverlapping geographical distribution correlates with the distribution of two different populations of El. abietinum found in Iceland. On other aphid species N. fresenii, En. planchoniana, Pandora neoaphidis, and Conidiobolus obscurus were documented throughout the country. Transmission experiments showed that Pa. neoaphidis and En. planchoniana could infect the eastern population of El. abietinum, although they have never been found on this population in nature. This strongly indicates that there is little or no interaction among El. abietinum, other aphids, and their respective entomophthoralean fungi in the field. Furthermore, this study is the first to record epizootics caused by N. fresenii and En. planchoniana in the subpolar region.     

Conservation genetics of the threatened horned grebe (<Emphasis Type="Italic">Podiceps auritus</Emphasis> L.) population of the Magdalen Islands,Québec

The horned grebe (Podiceps auritus) population of the Magdalen Islands in the St. Lawrence Gulf (Québec, Canada) has declined sharply over the last decades. It is the only breeding population of this species in eastern North America with nearest breeding populations being >2500 km apart in western North America and Europe, We used three types of genetic markers: mitochondrial (mt) DNA ND2 sequence, α-enolase intron sequence, and 25 amplified fragment length polymorphism loci (AFLPs) to quantify the genetic diversity within the Magdalen Island population and to assess its genetic distinctiveness relative to populations from western Canada (five sites) and Iceland (one site). The Magdalen Island population retained a comparable amount of genetic diversity to the average diversity observed across all populations in all three markers. Horned grebe mtDNA sequences formed a monophyletic group and nearly all haplotypes present in Québec were found elsewhere. In the ND2 fragment, populations partitioned into two groups corresponding to subspecies (Iceland versus North American sites) and more strongly in three groups according to geographic disjunctions (Iceland versus Québec versus western Canada). In contrast, there was no evidence of structure between sites in the α-enolase intron. In the AFLPs, Iceland showed the greatest level of differentiation, followed by the Québec and British Columbia populations. For conservation purposes, we suggest that the Magdalen Islands population should be recognized as a separate unit.     

Patterns of isozyme variation in relation to population size,isolation, and phytogeographic history in royal catchfly (Silene regia; Caryophyllaceae)

The distribution of genetic variation within and among plant populations is influenced by both contemporary and historical factors. I used isozyme analysis of band phenotypes to examine genetic structure in the rare prairie forb Silene regia. Relationships between current-day population size, isolation, and phenotypic variation were assessed for 18 populations in two regions with differing postglacial history. Western populations from unglaciated southern Missouri and Arkansas were more genetically diverse based on the Shannon-Weaver index (H) and a polymorphic index than were more eastern populations. These differences may be due to loss of variation with repeated founding of new populations in previously glaciated sites in Indiana and Ohio. Within the western region, population size was not significantly correlated with genetic variation. In the east, size was correlated with Shannon-Weaver diversity. There was no relationship between variation and isolation in either region, but eastern populations were slightly more differentiated. Greater among-population differentiation and the demonstrated connection between population size and variation in the eastern sites may reflect lower levels of interpopulation gene flow in the fragmented remnant prairies of Indiana and Ohio.     

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.     

Molecular evolution and population genetics of Greater Caribbean green turtles (Chelonia mydas) as inferred from mitochondrial DNA control region sequences

The molecular evolution and population genetics of migratory green turtles (Chelonia mydas) in the Greater Caribbean were examined with mitochondrial DNA (mtDNA) control region I sequences. A total of 488 base positions (bp) per individual were aligned for 44 individuals from four nesting populations in Florida, Costa Rica, Aves Island (Venezuela), and Surinam. Twelve sequence polymorphisms were detected, representing ten transitions, one transversion, and one 10-bp repeat. Sequence analyses of within- and between-population diversity revealed a deep divergence between western and eastern Caribbean nesting colonies and an inverse relationship between reproductive female population size and mtDNA diversity. In small populations, genetic admixture was important to maintaining high diversity, whereas larger populations appear to have experienced historical bottlenecks or resulted from founder effects. Mitochondrial DNA sequences of the control region offer an order of magnitude greater resolution than restriction site data for addressing questions about mtDNA variation, both within and between populations of green turtles.     

East–west genetic differentiation in Musk Ducks (<Emphasis Type="Italic">Biziura lobata</Emphasis>) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (Φ_ST = 0.747), one nuclear intron (Φ_ST = 0.193) and eight microsatellite loci (F_ST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews’ (Austral Avian Record 2:83–107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other.     

Mitochondrial DNA sequence variation and phylogeographic patterns in harbour porpoises (Phocoena phocoena) from the North Atlantic

The harbour porpoise (Phocoena phocoena)experiences high rates of incidental mortalityin commercial fisheries, and in some areasthese rates are sufficiently high to justifyconcern over population sustainability. Giventhe high incidental mortality, the resolutionof population structure will be important toconservation and management, but in the NorthAtlantic the relationships among many of theputative populations remain unclear. Aprevious genetic study demonstrated substantialgenetic differences between eastern and westernNorth Atlantic populations, however thelocation of this break remained unresolved. Inthe present study, we addressed this issue byincluding new samples from Iceland. Toinvestigate population structure, variation inthe mitochondrial DNA of 370 porpoises wascompared among six locations corresponding toseveral of the putative populations (Gulf ofMaine, Gulf of St. Lawrence, Newfoundland, WestGreenland, Iceland, Norway). The first 342base pairs of the control region were sequencedand genetic variation investigated by analysisof molecular variance (F _ST and _ST ) and ² withpermutation. Although some fine scalepopulation structure was detected, porpoisesfrom Iceland were found to be more similar tothe western populations (W. Greenland, Gulf ofSt. Lawrence, Newfoundland, Gulf of Maine) thanto Norway. Furthermore, porpoises from Norwaywere different from all other regions. Thesepatterns suggest the existence of adiscontinuity between Iceland and Norway,possibly the result of isolating events causedby repeated range contractions and expansionsthroughout Quaternary glaciation events withinthe North Atlantic. These results suggest thatharbour porpoise populations within the NorthAtlantic are distinguishable, but patterns mustbe interpreted in light of their historicalbiogeography.     

Morphometric and genetic differentiation among populations of flat‐headed cusimanse (Crossarchus platycephalus) in Nigeria

Geographic barriers can partition genetic diversity among populations and drive evolutionary divergence between populations, promoting the speciation process and affecting conservation goals. We integrated morphological and genomic data to assess the distribution of variation in the flat‐headed cusimanse (Crossarchus platycephalus), a species of least conservation concern, on either side of the River Niger in Nigeria. Ecological disturbances affect the conservation status of many other animals in this region. The two populations were differentiated in the snout and fore limbs, with greater morphological diversity in the western population. We used Restriction site Associated DNA sequencing (RAD‐seq) and identified two genotypic clusters in a STRUCTURE analysis. Individuals from the eastern population are almost entirely assigned to one cluster, whereas genotypes from the western population are a mixture of the two clusters. The population from west of the River Niger also had higher heterozygosity. The morphological and population genetic data are therefore in agreement that the population from west of the River Niger is more diverse than the eastern population, and the eastern population contains a subset of the genetic variation found in the western population. Our results demonstrate that combining morphological and genotypic measures of diversity can provide a congruent picture of the distribution of intraspecific variation. The results also suggest that future work should explore the role of the River Niger as a natural barrier to migration in Nigeria.     

Interactions between green spruce aphid (Elatobium abietinum (Walker)) and Norway and Sitka spruce under high and low nutrient conditions

1 Green spruce aphid (Elatobium abietinum) is a serious pest of spruce (Picea spp.) in north‐west Europe, causing defoliation of one‐year‐old and older needles. 2 Relationships between population development of E. abietinum, needle loss and tree growth were compared for five pure genotypes of Sitka spruce and mixed‐genotype material of Sitka and Norway spruce, grown under high and low nutrient conditions. 3 Despite wide differences in flushing date between spruce genotypes, E. abietinum populations peaked on the same date on each genotype and on the mixed‐genotype material, irrespective of nutrient supply. 4 Larger aphid populations developed on trees grown under high nutrient conditions than under low nutrients. However, more needles were lost per aphid in the low nutrient treatment and overall defoliation rates in the two nutrient treatments were similar. 5 Total aphid numbers differed significantly between Sitka spruce genotypes within nutrient treatments, but not in relation to bud‐burst or needle terpene content. Reductions in height growth caused by infestation were greater (15–44%), and related to mean aphid densities and defoliation, in the low nutrient treatment, but were smaller (11–27%) and not related to aphid density and defoliation in the high nutrient treatment. 6 Development of E. abietinum populations was similar on Norway and Sitka spruce, but Norway spruce lost fewer needles. However, the effects of infestation on tree growth were more closely related to aphid density and were similar for Norway and Sitka spruce. 7 Infestation caused a decrease in total root dry weight of Norway and Sitka spruce in proportion to the reductions observed in above‐ground growth.     

Genetic structure of Hypochaeris uniflora (Asteraceae) suggests vicariance in the Carpathians and rapid post-glacial colonization of the Alps from an eastern Alpine refugium

Aim The range of the subalpine species Hypochaeris uniflora covers the Alps, Carpathians and Sudetes Mountains. Whilst the genetic structure and post‐glacial history of many high‐mountain plant taxa of the Alps is relatively well documented, the Carpathian populations have often been neglected in phylogeographical studies. The aim of the present study is to compare the genetic variation of the species in two major European mountain systems – the Alps and the Carpathians. Location Alps and Carpathians. Methods The genetic variation of 77 populations, each consisting of three plants, was studied using amplified fragment length polymorphism (AFLP). Results Neighbour joining and principal coordinate analyses revealed three well‐supported phylogeographical groups of populations corresponding to three disjunct geographical regions – the Alps and the western and south‐eastern Carpathians. Moreover, two further clusters could be distinguished within the latter mountain range, one consisting of populations from the eastern Carpathians and the second consisting of populations from the southern Carpathians. Populations from the Apuseni Mountains had an intermediate position between the eastern and southern Carpathians. The genetic clustering of populations into four groups was also supported by an analysis of molecular variance, which showed that most genetic variation (almost 46%) was found among these four groups. By far the highest within‐population variation was found in the eastern Carpathians, followed by populations from the southern and western Carpathians. Generally, the populations from the Alps were considerably less variable and displayed substantially fewer region‐diagnostic markers than those from the south‐eastern Carpathians. Although no clear geographical structure was found within the Alps, based on neighbour joining or principal coordinate analyses, some trends were obvious: populations from the easternmost part were genetically more variable and, together with those from the south‐western part, exhibited a higher proportion of rare AFLP fragments than populations in other areas. Moreover, the total number of AFLP fragments per population, the percentage of polymorphic loci and the proportion of rare AFLP fragments significantly decreased from east to west. Main conclusions Deep infraspecific phylogeographical gaps between the populations from the Alps and the western and south‐eastern Carpathians suggest the survival of H. uniflora in three separate refugia during the last glaciation. Our AFLP data provide molecular evidence for a long‐term geographical disjunction between the eastern and western Carpathians, previously suggested from the floristic composition at the end of 19th century. It is likely that Alpine populations survived the Last Glacial in the eastern part of the Alps, from where they rapidly colonized the rest of the Alps after the ice sheet retreated. Multiple founder effects may explain a gradual loss of genetic variation during westward colonization of the Alps.     

Patch size of gall-forming aphids: deme formation revisited

Plants of the genus Pistacia (Anacardiaceae) serve as obligate hosts for a group of specialized gall-forming aphids (Homoptera: Fordinae). The aphids regularly migrate between the Pistacia (primary) host plants and the roots of non-specific grasses and cereals (secondary hosts). Gall density varies considerably between trees and sites. The intimate relationships between the aphids and their primary host, the natural variation of host susceptibility, and the heterogeneous geographical environment may promote local adaptation and deme formation in the aphid populations. Indeed, previous analyses of the genetic structure of the aphid Baizongia pistaciae, which forms large galls on the deciduous P. palaestina trees, suggested deme formation (Martinez et al. 2005). In this study, we analyzed the genetic structure of the B. pistaciae population at eight sites and 78 trees throughout Israel and a single population in Turkey, using two molecular markers (AFLP fingerprints and COI sequencing). The genetic distance between the Israeli populations was found to be low (D = 0.01–0.02), and there was no genetic differentiation found between any population pairs. In five of the Israeli populations, we also compared the genetic identity between aphids forming galls on the same tree and between galls on neighboring trees. The analysis indicated that the genetic identity of different galls within a tree resembles the correspondence between trees within a population. Our results showed no indication of deme formation or any hierarchical genetic substructuring within B. pistaciae populations in Israel. The extensive gene flow between aphid colonies may be explained by their dispersal abilities and the potential bridging role of the secondary hosts.     

GENETIC DIVERSITY AND POPULATION STRUCTURE IN CAMELLIA JAPONICA L. (THEACEAE)

Camellia japonica is a widespread and morphologically diverse tree native to parts of Japan and adjacent islands. Starch gel electrophoresis was used to score allelic variation at 20 loci in seeds collected from 60 populations distributed throughout the species range. In comparison with other plant species, the level of genetic diversity within C. japonica populations is very high: 66.2% of loci were polymorphic on average per population, with a mean number of 2.16 alleles per locus; the mean observed and panmictic heterozygosities were 0.230 and 0.265, respectively. Genotypic proportions at most loci in most populations fit Hardy-Weinberg expectations. However, small heterozygote deficiencies were commonly observed (mean population fixation index = 0.129). It is suggested that the most likely cause of the observed deficiencies is population subdivision into genetically divergent subpopulations. The overall level of population differentiation is greater than is typically observed in out-breeders: The mean genetic distance and identity (Nei's D and I) between pairs of populations were 0.073 and 0.930, respectively, and Wright's Fst was 0.144. Differences among populations appeared to be manifested as variation in gene frequencies at many loci rather than variation in allelic composition per se. However, the patterns of variation were not random. Reciprocal clinal variation of gene frequencies was observed for allele pairs at six loci. In addition, principal components analysis revealed that populations tended to genetically cluster into four regions representing the geographic areas Kyushu, Shikoku, western Honshu, and eastern Honshu. There was a significant relationship between genetic and geographic distance (r = 0.61; P < 0.01). Analysis of variance on allozyme frequencies showed that there was approximately four times as much differentiation among populations within regions, as among regions. It is likely that the observed patterns of population relationships result from the balance between genetic drift in small subpopulations and gene flow between them.     

Genetic variation and population structure of the carpet shell clam <Emphasis Type="Italic">Ruditapes decussatus</Emphasis> along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis

Surveys of allozyme polymorphisms in the carpet shell clam Ruditapes decussatus have revealed sharp genetic differentiation of populations. Analysis of population structure in this species has now been extended to include nuclear and mitochondrial genes. A partial sequence of a mitochondrial COI gene and of the internal transcribed spacer region (ITS-1) were used to study haplotype distribution, the pattern of gene flow, and population genetic structure of R. decussatus. The samples were collected from twelve populations from the eastern and western Mediterranean coasts of Tunisia, one from Concarneau and one from Thau. A total of twenty and twenty-one haplotypes were detected in the examined COI and ITS1 regions respectively. The study revealed higher levels of genetic diversity for ITS1 compared to COI. The analysis of haplotype frequency distribution and molecular variation indicated that the majority of the genetic variation was distributed within populations (93% and 86% for COI and ITS1 respectively). No significant differentiation was found among eastern and western groups on either side of the Siculo-Tunisian strait. However, distinct and significant clinal changes in haplotypes frequencies between eastern and western samples were found at the most frequent COI haplotype and at three out of five major ITS1 haplotypes. These results suggest the relative importance of historical processes and contemporary hydrodynamic features on the observed patterns of genetic structure.     

Population differentiation in the redshank (<Emphasis Type="Italic">Tringa totanus</Emphasis>) as revealed by mitochondrial DNA and amplified fragment length polymorphism markers

The redshank (Tringa totanus) is declining throughout Europe and to implement efficient conservation measures, it is important to obtain information about the population genetic structure. The aim of the present study was two-fold. First, we analysed the genetic variation within and between populations in the Baltic region in southern Scandinavia. Evidence of genetic structure would suggest that different populations might require separate management strategies. Second, in an attempt to study large-scale genetic structure we compared the Baltic populations with redshanks from northern Scandinavia and Iceland. This analysis could reveal insights into phylogeography and long-term population history. DNA samples were collected from six breeding sites in Scandinavia presumed to include two subspecies (totanus and britannica) and a further sample from Iceland (subspecies robusta). Two methods were used to study the population genetic structure. Domain II and III of the mitochondrial control region was analysed by DNA sequencing and nuclear DNA was analysed by screening amplified fragment length polymorphism (AFLP) markers. Mitochondrial DNA showed no variation between individuals in domain II. When analysing an 481 bp fragment of domain III seven haplotypes were found among birds. On the basis of mtDNA sequences, redshanks showed some evidence of a recent expansion from a bottlenecked refugial population. Bayesian analyses of AFLP data revealed a significant genetic differentiation between suggested subspecies but not between populations within the Baltic region. Our results indicate that populations of redshanks in Europe constitute at least three separate management units corresponding to the recognised subspecies.     

Genetic variation in Arabis petraea, a disjunct species in northern Europe

Variation at 7 isoenzyme loci was studied m 15 populations (6 from Iceland, 4 from W Norway, 4 from central Sweden at the Bothnian Gulf, and 1 from Russian Karelia) Heterozygosity within populations was found to be remarkably high compared with taxa with similar reproductive systems and phytogeographical histories Genetic distances calculated from isoenzyme data showed a close connection between the Norwegian and Swedish populations, indicating a western rather than an eastern immigration route for the isolated Swedish population Leaf shape variation displayed a large scale geographical pattern with strong differences between regions and low variation within populations     

Range-wide migration corridors and non-breeding areas of a northward expanding Afro-Palaearctic migrant,the European Bee-eater Merops apiaster

Across their ranges, different populations of migratory species often use separate routes to migrate between breeding and non-breeding grounds. Recent changes in climate and land-use have led to breeding range expansions in many species but it is unclear whether these populations also establish new migratory routes, non-breeding sites and migration phenology. Thus, we compared the migration patterns of European Bee-eaters Merops apiaster from two established western (n = 5) and eastern (n = 6) breeding populations in Europe, with those from a newly founded northern population (n = 19). We aimed to relate the breeding populations to the two known non-breeding clusters in Africa, and to test for similarities of migration routes and timing between the old and new populations. Western Bee-eaters used the western flyway to destinations in West Africa; the eastern birds uniformly headed south to southern African non-breeding sites, confirming a complete separation in time and space between these long-established populations. The recently founded northern population, however, also used a western corridor, but crossed the Mediterranean further east than the western population and overwintered mainly in a new non-breeding area in southern Congo/northern Angola. The migration routes and the new non-breeding range overlapped only slightly with the western, but not with the eastern, population. In contrast, migration phenology appeared to differ between the western and both the northern and the eastern populations, with tracked birds from the western population migrating 2–4 weeks earlier. The northern population thus shares some spatial traits with western Bee-eaters, but similar phenology only with eastern population. This divergence highlights the adjustments in the timing of migration to local environmental conditions in newly founded populations, and a parallel establishment of new breeding and non-breeding sites.     

青杨的遗传分化

分析了10个省市自治区的30个群体的青杨(Populus cathayana Rehd.),共169株,用RAPD方法分析群体间和群体内的DNA多态性。结果显示群体间的DNA多态度远高于群体内的,而且东部群体与西部群体间存在较大的遗传差异,相邻产地之间的遗传差异相对较小。聚类分析结果表明,东、西部群体已出现明显分化。整个聚类图与青杨的地理分布区大致相对应。西部群体内DNA多态性比东部群体高,因此西部群体在研究青杨的起源与演化中将显得更为重要。按照多样性中心与起源中心的关系,青杨可能起源于我国西北部,逐渐向东扩散,形成现代分布格局。     

基于叶绿体DNA非编码序列的蒙古扁桃谱系地理学研究

该研究选取中国西北干旱区第三纪孑遗植物蒙古扁桃（Amygdalus mongolica）,基于叶绿体DNA非编码trnH psbA序列对蒙古扁桃17个居群324个个体进行了谱系地理学研究。结果表明：（1）蒙古扁桃trnH psbA序列长度350 bp,变异位点63个,共有9种单倍型,居群间总遗传多样性为（H_t）为0.758,居群内平均遗传多样性为（H_s）为0.203,贺兰山东麓及阴山南麓边缘的居群具有较高的单倍型多样性及核苷酸多样性并固定较多特有单倍型,推测这2个地区是蒙古扁桃在第四纪冰期时的重要避难所。（2）AMOVA分析表明,居群间的遗传变异为83.84%,居群内的遗传变异为16.16%,居群间遗传分化系数N_st>G_st（N_st=0.733, G_st=0.655, P>0.05）,表明蒙古扁桃不存在明显的谱系地理结构;根据单倍型地理分布及网络关系图,把蒙古扁桃自然地理居群分为东、西两大地理组群,而且东、西地理组群没有共享单倍型;居群遗传结构分析表明,两大地理组群遗传分化较大。（3）蒙古扁桃居群在间冰期或冰期后经历了近期的居群扩张,由于奠基者效应使得多数居群只固定了单一的单倍型。     

The genetic structure of Aphis gossypii populations in Japanese fruit orchards

The genetic structure of Aphis gossypii Glover (Hemiptera: Aphididae) populations was characterized using microsatellite analysis of insects sampled from pear and citrus orchards at three locations in the summer seasons of 2001 and 2003. These data will enable more precise forecasting of infestation and will be of value to the development of better control methods. In total, 89 genotypes were found in 500 aphid samples. The diversity indices in aphid populations on pear trees fluctuated but showed a decrease with time in citrus orchards. Japanese aphid populations have greater variation in their microsatellite loci than African, European, or Southeast Asian populations. Approximately half of the genotypes were found in only one colony, whereas the remainder were identified in two or more colonies. Fifteen genotypes appeared in different years, in samples from different areas, or on different host plants. Our data suggest the existence of aphid populations with pear‐adapted genotypes and with a permanent parthenogenetic life cycle. Some of the genotypes included genes conferring resistance to pirimicarb and pyrethroid insecticides. Japanese A. gossypii populations may maintain their large genetic variation through differences in their life cycles.