Nineteen new microsatellite DNA polymorphisms in pigtailed macaques (Macaca nemestrina)

Microsatellite loci known to be polymorphic in baboons (Papio hamadryas) and/or humans were tested in pigtailed macaques (Macaca nemestrina) from the Washington Regional Primate Research Center. Nineteen polymorphisms were identified in the macaques, with an average of 9.2 alleles per locus and an average heterozygosity of 0.76. Seven loci were analyzed using radiolabelled PCR primers and standard gel electrophoresis. Twelve loci were studied using fluorescently labelled primers and the Perkin-Elmer ABI 377 genotyping system. Of these 19 pigtailed macaque polymorphisms, 12 were used to perform paternity testing among captive animals. In a set of 15 infants, this panel of 12 genetic polymorphisms was sufficient to establish paternity in all cases. The number of alleles per locus in pigtailed macaques was compared with the number of alleles in a sample of baboons, and no significant correlation was observed. This indicates that population genetic processes such as genetic drift and recurrent mutation act rapidly enough on these loci to eliminate any relationship in levels of polymorphism across those two species. These 19 loci will be valuable for a range of genetic studies in pigtailed macaques, including paternity testing, analysis of population structure and differentiation among wild populations, and genetic linkage mapping.     

Isolation and characterization of polymorphic microsatellites in Iris ensata (Iridaceae)

• Premise of the study: Microsatellite primers were developed in Iris ensata (Iridaceae) to provide polymorphic markers for further studies into population genetics. • Methods and Results: Thirteen polymorphic microsatellite loci were isolated from I. ensata. These loci were successfully amplified in two natural populations of I. ensata from eastern China (Longwangshan, Zhejiang Province) and northeastern China (Jinchuan, Jilin Province). There was no significant linkage disequilibrium found for any pair of loci. These loci contained between two and 12 alleles per locus across all 48 individuals of I. ensata. The number of alleles per locus varied from two to 10 at the population level and the observed and expected heterozygosities ranged from 0.167 to 0.958 and from 0.284 to 0.853, respectively. • Conclusions: These loci showed high levels of polymorphism and could be used to study the population genetic structure, genetic relationships, and phylogeography of I. ensata.     

Demographic history of the trace metal hyperaccumulator Noccaea caerulescens (J. Presl and C. Presl) F. K. Mey. in Western Europe

Noccaea caerulescens (Brassicaceae) is a major pseudometallophyte model for the investigation of the genetics and evolution of metal hyperaccumulation in plants. We studied the population genetics and demographic history of this species to advance the understanding of among‐population differences in metal hyperaccumulation and tolerance abilities. Sampling of seven to 30 plants was carried out in 62 sites in Western Europe. Genotyping was carried out using a combination of new chloroplast and nuclear neutral markers. A strong genetic structure was detected, allowing the definition of three genetic subunits. Subunits showed a good geographic coherence. Accordingly, distant metallicolous populations generally belonged to distinct subunits. Approximate Bayesian computation analysis of demographic scenarios among subunits further supported a primary isolation of populations from the southern Massif Central prior to last glacial maximum, whereas northern populations may have derived during postglacial recolonization events. Estimated divergence times among subunits were rather recent in comparison with the species history, but certainly before the establishment of anthropogenic metalliferous sites. Our results suggest that the large‐scale genetic structure of N. caerulescens populations pre‐existed to the local adaptation to metalliferous sites. The population structure of quantitative variation for metal‐related adaptive traits must have established independently in isolated gene pools. However, features of the most divergent genetic unit (e.g. extreme levels of Cd accumulation observed in previous studies) question the putative relationships between adaptive evolution of metal‐related traits and subunits isolation. Finally, admixture signals among distant metallicolous populations suggest a putative role of human activities in facilitating long‐distance genetic exchanges.     

Isolation and characterization of the first microsatellite loci from the order Psocoptera in the economically important pest insect Liposcelis decolor (Pearman) and cross‐species amplification

A total of 11 microsatellite loci from the invasive insect pest Liposcelis decolor were isolated and characterized of which six loci were polymorphic. A population survey involving a total of 30–192 individuals per locus from five populations revealed a range of four to seven alleles per locus and moderate observed heterozygosities (0.183–0.565), highlighting the utility of these loci in further population genetic studies. Cross‐species amplifications were successful for two to 11 loci in five other Liposcelis species also of international economic importance.     

Cadmium hyperaccumulation and genetic differentiation of Thlaspi caerulescens populations

Although the knowledge on heavy metal hyperaccumulation mechanisms is increasing, the genetic basis of cadmium (Cd) hyperaccumulation remains to be elucidated. Thlaspi caerulescens is an attractive model since Cd accumulation polymorphism observed in this species suggests genetic differences between populations with low versus high Cd hyperaccumulation capacities. In our study, a methodology is proposed to analyse at a regional scale the genetic differentiation of T. caerulescens natural populations in relation to Cd hyperaccumulation capacity while controlling for different environmental, soil, plant parameters and geographic origins of populations. Twenty-two populations were characterised with AFLP markers and cpDNA polymorphism. Over all loci, a partial Mantel test showed no significant genetic structure with regard to the Cd hyperaccumulation capacity. Nevertheless, when comparing the marker variation to a neutral model, seven AFLP fragments (9% of markers) were identified as presenting particularly high genetic differentiation between populations with low and high Cd hyperaccumulation capacity. Using simulations, the number of outlier loci was showed to be significantly higher than expected at random. These loci presented a genetic structure linked to Cd hyperaccumulation capacity independently of the geography, environment, soil parameters and Zn, Pb, Fe and Cu concentrations in plants. Using a canonical correspondence analysis, we identified three of them as particularly related to the Cd hyperaccumulation capacity. This study demonstrates that populations with low and high hyperaccumulation capacities can be significantly distinguished based on molecular data. Further investigations with candidate genes and mapped markers may allow identification and characterization of genomic regions linked to factors involved in Cd hyperaccumulation.     

Isolation and characterization of microsatellite DNA loci from the golden cuttlefish,Sepia esculenta Hoyle (Cephalopoda)

The first microsatellite markers were isolated from the golden cuttlefish, Sepia esculenta Hoyle. Eleven primer sets were designed to amplify the marker sequences via polymerase chain reaction. The 45–50 individuals from one wild population in the coastal waters of Ehime Prefecture, Japan were used to screen polymorphism in the 11 microsatellite loci. All the microsatellite loci were polymorphic, with the range of alleles from seven to 27 per locus. The observed and expected heterozygosities ranged from 0.380 to 0.980 and from 0.654 to 0.940, respectively. These marker loci except for one locus showing significant deviation from Hardy–Weinberg equilibrium will be useful for the assessment of genetic variation and population structure of this species.     

Isolation and characterization of polymorphic microsatellite loci in the gudgeon,Gobio gobio (Cyprinidae)

A total of seven polymorphic microsatellite loci from Gobio gobio were isolated and characterized. A preliminary population survey of 82 specimens from four populations, located in a downstream pollution gradient of cadmium and zinc, demonstrated the usefulness of these primers both in population genetic studies in general, as well as in evaluating the effects of anthropogenic pollution on genetic structure. Overall locus polymorphism ranged from two to 13 alleles. Observed heterozygosity per locus ranged from 0.39 to 0.73.     

Isolation of tetranucleotide microsatellite loci in the burrowing parrot (Cyanoliseus patagonus)

We isolated seven novel polymorphic microsatellite DNA loci from the burrowing parrot (Cyanoliseus patagonus) and optimised them for future studies of population differentiation and genetic variation. The loci were screened for polymorphism using 38 samples from wild individuals from three neighbouring colonies in Argentina. The primers amplified highly variable loci characterised by 3–10 alleles per locus and their observed and expected heterozygosities ranged from 0.15 to 0.78 and 0.15 to 0.81, respectively. When we analysed 52 samples across Argentina and Chile, we found strong genetic differentiation between the Chilean and the Argentinean subspecies as well as significant differentiation between two geographically separated subspecies within Argentina. Our results indicate the suitability of these microsatellites for investigating further questions regarding the population genetics in this species.     

红色原鸡群体遗传多样性

为了阐明红色原鸡的群体遗传结构,以对其有效保护提供遗传学依据,采用33个微卫星标记对其群体中56个个体进行了PCR-聚丙烯酰胺多态性电泳检测。33个微卫星座位共检测到140个等位基因,所有座位都呈现出多态性,每个座位的等位基因数在2～8个之间,平均每个座位等位基因数4.24个,有效等位基因数3.30个。根据等位基因频率,计算出的群体表观杂合度、期望杂合度及多态信息含量分别为0.7980、0.6506和0.5948。结果表明,红色原鸡群体遗传多样性较丰富。     

Development of microsatellite markers for the critically endangered Limonium dufourii (Girard) Kuntze (Plumbaginaceae)

Limonium dufourii is an endemic plant from the eastern Mediterranean coast of Spain with a triploid chromosome number and apomictic reproduction. We have isolated and characterized 13 polymorphic microsatellite loci from an enriched library in order to investigate its population genetic structure. Simple sequence repeat (SSR) loci were screened in 120 individuals from the six extant populations of this species. They show an average of 5.76 alleles per locus, ranging from 2 to 18, with seven loci exhibiting heterozygosities larger than 0.60. Three loci present one single allele in each individual, whereas one locus presents three alleles in every individual analysed.     

Microsatellite loci in eelgrass Zostera marina reveal marked polymorphism within and among populations

Using an enriched genomic library, we developed seven (CT)n/(GA)n microsatellite loci for eelgrass Zostera marina L. Enrichment is described and highly recommended for genomes in which microsatellites are rare, such as in many plants. A test for polymorphism was performed on individuals from three geographically separated populations (N = 15/population) and revealed considerable genetic variation. The number of alleles per locus varied between five and 11 and the observed heterozygosities for single loci ranged from 0.16 to 0.81 within populations. Mean allele lengths were markedly different among populations, indicating that the identified loci will be useful in studying population structure in Z. marina. As the frequency of the most abundant multilocus genotype within populations was always < 1%, these loci have sufficient resolving power to address clone size in predominantly vegetatively reproducing populations.     

Isolation and characterization of new microsatellite markers in the surfclam Mactromeris polynyma

We describe primers and amplification conditions for seven microsatellite loci that were developed and characterized in the commercially harvested surfclam Mactromeris polynyma. Five of these loci were polymorphic: we found 6 to 23 alleles per locus among 100 individuals from one population in Nova Scotia, with some large heterozygote deficits that may reflect unrecognized temporal genetic variation. We are using these markers to investigate temporal and spatial genetic structure in this species.     

Development of microsatellite markers in black locust (Robinia pseudoacacia) using a dual‐supression‐PCR technique

Black locust (Robinia pseudoacacia) is an economically and ecologically important tree species in the world. We isolated seven polymorphic microsatellite loci from R. pseudoacacia using a dual‐suppression‐PCR technique. These loci provided microsatellite markers with high polymorphism ranging from three to 12 alleles per locus and expected heterozygosity between 0.538 and 0.944. The markers are now available for more detailed investigation of population genetic structure and pollen and seed dispersal.     

Polymorphic microsatellite loci in the bush‐cricket Metrioptera roeseli

Metrioptera roeseli is a common bush‐cricket in Europe which prefers grassland as habitat. We developed microsatellite loci in order to study the population genetic structure and the effects of different habitat types on the genetic structure of the bush‐cricket in a rural landscape. In this paper, we report on six polymorphic microsatellite loci with seven to 16 alleles per locus in 20 individuals from the Lahn‐Dill‐Bergland in Hesse, Germany.     

Characterization of polymorphic microsatellite markers in the Indian meal moth,Plodia interpunctella (Hübner)

The Indian meal moth, Plodia interpunctella (Hübner), is a serious and widespread pest of stored food commodities worldwide. Studies on the population genetics and breeding structure of P. interpunctella are lacking. Understanding the breeding structure of this pest has implications for its management. Fifteen microsatellite loci were isolated, cloned and characterized using an enrichment method. Forty individuals from six subpopulations were tested for polymorphism. Nine loci were found to be polymorphic. The number of alleles varied from three to six per locus.     

Isolation of highly polymorphic microsatellite markers from the intertidal barnacle Chthamalus montagui Southward

This study reports the isolation and characterization of seven highly polymorphic microsatellite loci in Chthamalus montagui (Crustacea, Cirripedia). The loci were isolated from a library constructed from genomic DNA enriched for CA repeats. The markers yielded three to 43 alleles per locus (mean 16.7) in samples averaging 49 individuals. Observed heterozygosity ranged from 0.08 to 0.58 (mean 0.39). These microsatellite loci will be valuable tools for population genetic studies of this species.     

Polymorphic microsatellite loci and PCR multiplexing in the common vole,Microtus arvalis

We isolated and characterized 14 dinucleotide microsatellite loci in the common vole Microtus arvalis (Palas). Two multiplex panels both comprising seven loci were developed. Application to a set of 21 individuals allowed clear and easy characterization of allele sizes except for two loci which were then withdrawn from further analyses. The number of alleles ranged from four to 19 per locus with the observed heterozygosity ranging from 0.55 to 0.95. These sets of microsatellite loci provide high throughput capacity for population genetic studies at a minimum cost.     

Isolation and characterization of 11 polymorphic microsatellite loci in collared lizards (Crotaphytus collaris)

We identified 11 polymorphic microsatellite loci in collared lizards (Crotaphytus collaris). Polymorphism assessment in 512 individuals from 52 populations sampled across much of the species distribution revealed a fairly high degree of genetic diversity (six to 20 alleles per locus) and a wide range of average expected heterozygosity values (0.143–0.530). We found no evidence for linkage, very few deviations from HW expectation (two of 572 possible population/locus analyses) and thus no evidence for null alleles. There was a tendency for reduced polymorphism towards the northern periphery.     

Characterization of nine microsatellite loci in Cynoglossum officinale (Boraginaceae)

Cynoglossum officinale is a biennial plant pollinated by bumblebees. We developed microsatelllite loci in order to study the population genetic structure and effects of inbreeding in this species. In this paper, we describe nine polymorphic microsatellites for C. officinale. Between two and four alleles per locus were observed in a sample of 20 individuals from one population. Multiplexing allowed the seven most useful loci to be genotyped using three polymerase chain reaction (PCR) reactions.