Development of polymorphic microsatellite loci in the hermaphroditic freshwater snails Drepanotrema surinamense and Drepanotrema depressissimum

We characterized new variable microsatellites in two congeneric species of hermaphroditic freshwater snails (Drepanotrema depressissimum and D. surinamense), as well as conditions for multiplexing and simultaneously genotyping sets of loci. D. depressissimum had high mean gene diversity (> 0.8) and large number of alleles (= 10.9) per population. Most loci and populations were at Hardy–Weinberg equilibrium. The F_ST estimates were low among lesser Antilles populations and larger with a Venezuelan population. Far less diversity was found in D. surinamense with mean number of alleles and gene diversity per population of 2.8 and 0.34, respectively. Very few heterozygous individuals were observed. The most likely explanation is a high selfing rate (> 0.825) in this species. Unsurprisingly, the F_ST estimates among populations were much higher than in D. depressissimum. Cross‐species amplification in three congeneric species was on the whole unsuccessful.     

Ecological genetics of Italian peach‐potato aphid (Myzus persicae) populations in relation to geography,dispersal and insecticide resistance as studied using microsatellite and resistance markers

相似文献   

Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites

Genotype data from 30 microsatellites were used to assess genetic diversity and relationships among 10 native Portuguese cattle breeds, American Charolais and the Brazilian Caracú. Hardy–Weinberg equilibrium was observed for all loci/population combinations except for five loci in Brava de Lide and one locus in Alentejana that exhibited heterozygote deficiency. Estimates of average observed and expected heterozygosities, total number of alleles (TNA) per breed and mean number of alleles (MNA) per locus/population were obtained. A total of 390 alleles were detected. TNA among Iberian cattle ranged from 170 to 237 and MNA ranged from 5.67 to 8.07. The highest observed heterozygosities were found in the Caracú, Maronesa, Garvonesa and Arouquesa and the lowest in Brava de Lide and Mirandesa. Estimation of population subdivision using Wright's F_ST index showed that the average proportion of genetic variation explained by breed differences was 9%. Neighbour‐joining phylogenetic trees based on D_A distances showed that the genetic relationships of present‐day Portuguese native breeds are consistent with historical origins in the Brown Concave (Arouquesa, Mirandesa, Marinhoa) and Red Convex (Mertolenga, Alentejana, Garvonesa, Minhota) evolutionary groups. The Iberian Black Orthoide group, represented by Brava de Lide and Maronesa, and the Barrosã breed appeared to be more closely related to the Brown Concave group but may represent a separate lineage. The Caracú breed was not found to be closely associated with any of the native Portuguese breeds.     

Generalization of the QST framework in hierarchically structured populations: Impacts of inbreeding and dominance

Q_ST is a differentiation parameter based on the decomposition of the genetic variance of a trait. In the case of additive inheritance and absence of selection, it is analogous to the genic differentiation measured on individual loci, F_ST. Thus, Q_ST?F_ST comparison is used to infer selection: selective divergence when Q_ST > F_ST, or convergence when Q_ST < F_ST. The definition of Q‐statistics was extended to two‐level hierarchical population structures with Hardy–Weinberg equilibrium. Here, we generalize the Q‐statistics framework to any hierarchical population structure. First, we developed the analytical definition of hierarchical Q‐statistics for populations not at Hardy–Weinberg equilibrium. We show that the Q‐statistics values obtained with the Hardy–Weinberg definition are lower than their corresponding F‐statistics when F_IS > 0 (higher when F_IS < 0). Then, we used an island model simulation approach to investigate the impact of inbreeding and dominance on the Q_ST?F_ST framework in a hierarchical population structure. We show that, while differentiation at the lower hierarchical level (Q_SR) is a monotonic function of migration, differentiation at the upper level (Q_RT) is not. In the case of additive inheritance, we show that inbreeding inflates the variance of Q_RT, which can increase the frequency of Q_RT > F_RT cases. We also show that dominance drastically reduces Q‐statistics below F‐statistics for any level of the hierarchy. Therefore, high values of Q‐statistics are good indicators of selection, but low values are not in the case of dominance.     

Genetic variability and individual assignment of Chinese indigenous sheep populations (Ovis aries) using microsatellites

The purpose of this study was to assess the genetic characteristics of six breeds of Chinese local sheep using 19 microsatellite loci and to effectively validate statistical methods for individual assignment based on informative microsatellites. All the six breeds deviated from Hardy–Weinberg equilibrium expectations, while the majority of markers complied. The polymorphism information content (PIC) of overall loci for the six populations ranged from 0.283 (SRCRSP5) to 0.852 (OarVH72). Tibetan sheep were the most diverse population with the highest mean allelic richness (6.895), while Ujmuqin (UQ) harboured the lowest allelic richness (6.000). The F‐statistics for the six populations were F_IS = ?0.172, F_IT = ?0.082 and F_ST = 0.077, respectively. Furthermore, the pair‐wise F_IS revealed a moderate genetic differentiation among populations (P < 0.01), indicating that all breeds can be considered genetically independent entities. The lowest genetic differentiation was between Tengchong (TC) and UQ (F_ST = 0.041), and the highest one was between TC and Fat‐tailed Han (F_ST = 0.111). In comparing the three statistical models, we note that the seven microsatellite loci (MAF65, OarJMP58, SRCRSP9, MCM140, OarAE129, BM8125 and SRCRSP5) commonly used for individual assignment will ensure a powerful detection of individual origin, with accuracy up to 91.87%, when the likelihood‐based method is used. Overall, these findings shed light onto the genetic characteristics of Chinese indigenous sheep and offer a set of microsatellite loci that is simple, economic and highly informative for individual assignment of Chinese sheep.     

Characterization of microsatellite markers for Couch's spadefoot toad (Scaphiopus couchii) and cross‐amplification in other species of the family Scaphiopodidae

I developed 12 di‐ and tetranucleotide microsatellite loci for Couch's spadefoot toad (Scaphiopus couchii). These loci have 3–37 alleles per locus and observed heterozygosities ranging from 0.157 to 0.941 among 85 individuals from four populations. Global and within‐population exact tests do not reveal departure from Hardy–Weinberg expectations and all loci pairs are in linkage equilibrium. These independent markers will be useful for studies of population structure and kinship in this commonly studied amphibian. Additionally, several of these loci may be applicable for studies of other North American toads of the family Scaphiopodidae.     

Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

Fine‐scale genetic structure of large mammals is rarely analysed. Yet it is potentially important in estimating gene flow between the now fragmented wildlife habitats and in predicting re‐colonization following local extinction events. In this study, we examined the extent to which warthog populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection practices and the other (Luwero), not a protected area, is characterized by a great deal of hunting. In the total sample, significant genetic differentiation was observed at both the mtDNA locus (F_ST = 0.68; P < 0.001) and the microsatellite loci (F_ST = 0.14; P < 0.001). Despite the relatively short geographical distances between populations, significant genetic differentiation was observed in all pair‐wise population comparisons at the two marker sets (mtDNA F_ST = 0.21–0.79, P < 0.001; microsatellite F_ST = 0.074–0.191, P < 0.001). Significant heterozygote deficiency was observed at most loci within protected areas while no significant deviation from Hardy–Weinberg expectation was observed in the unprotected Luwero population. We explain these results in terms of: (i) a strong philopatry among warthogs, (ii) a Wahlund effect resulting from the sampling regime and (iii) break down of social structure in the disturbed Luwero population.     

Breeding system and population genetics of the vulnerable plant Dillwynia tenuifolia (Fabaceae)

Dillwynia tenuifolia Sieber ex DC. is a vulnerable species endemic to the Sydney region in Australia. This investigation focused on the breeding system and genetic structuring of the species in locations encompassing its entire geographical range. A field pollination experiment showed that D. tenuifolia produced fruit from both self‐ and cross‐pollination events, and thus has a facultative breeding system. Fruiting success from self‐ pollination was approximately half that observed from cross‐pollination. The genetic structure of D. tenuifolia populations was investigated by using allozyme electrophoresis. A survey of 16 loci revealed a high level of genetic variation with approximately two‐thirds of the loci being polymorphic and a mean of 1.84 alleles per loci. The genotype frequencies deviated from the Hardy–Weinberg equilibrium, with the observed level of heterozygosity significantly less than expected. The inbreeding coefficient was 0.31. There was very little divergence between populations (F_ST = 0.04) but the fixation indices were high within populations. Spatial autocorrelation, using Moran’s I, showed that neighbouring plants were closely related (I > 0.4). The genetic neighbourhood and effective population size in the species were estimated at one location as 1.1 ha and 10⁴ plants, respectively.     

Polymorphic microsatellite loci for population studies of the Japanese scallop,Patinopecten yessoensis

Fifteen microsatellite loci were developed to examine the population structure of Japanese scallop, Patinopecten yessoensis. These markers were tested in samples from two geographically distant populations: the Sakhalin Island (Russia) and Dalian City (China). The mean numbers of alleles, observed and expected heterozygosities between the two populations were summarized by locus, but none of them show significant divergence between the two populations. Most loci conformed to Hardy–Weinberg expectation with the exception of loci HLJX‐06, HLJX‐12, HLJX‐13 and HLJX‐28, which had heterozygote deficits.     

Development and characterization of 12 microsatellite markers from the deep-sea hydrothermal vent siboglinid Riftia pachyptila

Ecological processes at deep‐sea hydrothermal vents on fast‐spreading mid‐ocean ridges are punctuated by frequent physical disturbance, often accompanied by a high occurrence of population turnover. To persist through local extinction events, sessile invertebrate species living in these geologically and chemically dynamic habitats depend on larval dispersal. We characterized 12 polymorphic microsatellite loci from one such species, the siboglinid tubeworm Riftia pachyptila. All loci conformed to Hardy–Weinberg expectations without linkage (mean H_E = 0.9405, mean N_A = 20.25). These microsatellites are being employed in the investigation of spatial and temporal population genetic structure in the eastern Pacific Ocean.     

Isolation and characterization of microsatellite loci in the Bang's leaf‐nosed bat Hipposideros turpis

The Bang's leaf‐nose bat, Hipposideros turpis, is an endangered cave‐dwelling species inhabiting the southwesternmost islands of Japan. We isolated six dinucleotide microsatellite markers from the partial genomic library of the bat, and examined their allelic variation using a sample (N = 33) from the largest colony in Japan. All the loci showed a moderate allelic variation ranging from two to eight alleles, with the observed heterozygosities from 0.33 to 0.73, and conformed to Hardy–Weinberg expectations. The present microsatellite markers will be useful in assessing population genetic structure and gene flow among populations of this species.     

Microsatellite loci for behavioural studies of rainbow bee‐eaters (Merops ornatus: Aves)

A set of polymorphic microsatellite loci was identified for population and behavioural studies of the rainbow bee‐eater (Merops ornatus). Eight loci were newly isolated from a rainbow bee‐eater genomic library enriched for GA‐containing repeats, and six loci from those previously reported for the European bee‐eater (Merops apiaster). From these two sources, the seven most variable loci that amplified reliably were unlinked and in Hardy–Weinberg equilibrium, had five to 13 alleles (mean 7.7) and an expected heterozygosity of 0.60–0.86 (mean 0.73).     

Characterization of 35 microsatellite loci in the Pacific lion‐paw scallop (Nodipecten subnodosus) and their cross‐species amplification in four other scallops of the Pectinidae family

Four microsatellite‐enriched DNA libraries yielded 35 microsatellite loci from 100 primer pairs designed for Pacific lion‐paw scallop, Nodipecten subnodosus. The number of alleles ranged from four to 28. Three of the 35 loci were not in Hardy–Weinberg equilibrium and linkage disequilibrium was found for one pair of loci. These microsatellites will be used to analyse the population structure of the species in Mexico's Baja Peninsula to propose management strategies for scallop aquaculture development. Twenty‐six primer pairs cross‐amplified in Nodipecten nodosus, whereas none (Argopecten ventricosus) or few cross‐amplified in the Argopecten species.     

Patterns of genetic variation in isolated Danish populations of the endangered butterfly Euphydryas aurinia

In the present study, we report an investigation on molecular variation in the endangered univoltine butterfly Euphydryas aurinia (Rottemburg, 1775), a species heavily affected by habitat degradation and fragmentation in Denmark. Levels of genetic variation in extant populations were estimated using six variable number tandem repeat loci and were found to be low compared to other butterfly species with low migration rates. An analysis of genetic structure, based on both allele frequencies and genotype distributions, divided the entire sample into four distinct clusters. This was partially concordant with the a priori subdivision based on collection areas. An overall F_ST value of 0.16 (pairwise values ranging from 0.087–0.276) indicated restrictions of gene flow. Especially two populations had higher F_ST values than the others, suggesting their isolation, and showed signs of bottlenecks/founder events. One population deviated significantly from Hardy–Weinberg equilibrium, suggesting a possible Wahlund effect or the presence of null alleles. The results suggest habitat fragmentation, resulting in genetic drift and possibly inbreeding. Future management is therefore recommended to increase gene flow between the remaining populations while habitats are restored in order to increase carrying capacity. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 677–687.     

Isolation and characterization of microsatellite markers in Pterocarpus officinalis Jacq.

The leguminous Pterocarpus officinalis Jacq. is one of the dominant freshwater wetland tree species in the Caribbean basin. Anthromorphic factors threaten to reduce its population. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. One hundred ninety‐one individuals were analysed within nine Caribbean and continental populations. These loci were polymorphic in all the populations, with four to 20 alleles per locus. Significant Hardy–Weinberg deviation was detected and was interpreted as a result of Wahlund effect. These loci constitute a powerful tool to investigate the genetic patterns within populations of the swamp species P. officinalis.     

Microsatellite DNA markers for Lysiphlebus testaceipes

Microsatellite loci were isolated from the aphid parasitoid Lysiphlebus testaceipes (Hymenoptera: Braconidae). Ten loci were obtained from an enriched partial genomic library. Genetic diversity was analysed at seven of these loci and two natural populations, one on oleander and one on citrus. The observed number of alleles ranged from one to 17, and the observed heterozygosity ranged from 0.37 to 0.82. In both populations, no departure from Hardy–Weinberg equilibrium was detected except for one locus. The differentiation between the two populations was characterized by an F_ST of 0.09.     

Genetic signatures in an invasive parasite of Anguilla anguilla correlate with differential stock management

In this article, it is shown that available genetic tools for the omnipresent parasite Anguillicoloides crassus in European eels Anguilla anguilla are sensitive to different immigration rates into local A. anguilla stocks for two separated river systems. Relying on four highly polymorphic microsatellite markers, it was inferred that under natural recruitment, nematode samples meet Hardy–Weinberg expectations for a single panmictic population, while genetic signals show signs for a strong Wahlund effect most likely due to very recent population mixing under frequent restocking of young A. anguilla. This was indicated by a low but significant F_ST value among within‐host populations (infrapopulations) along with high inbreeding indices F_IS consistent over all loci. The latter signal is shown to stem from high levels of admixture and the presence of first‐generation migrants, and alternative explanations such as marker‐ and sex‐specific biases in the nematode populations could be dismissed. Moreover, the slightly increased degree of relatedness within infrapopulations in the stocked river system cannot explain the excessive inbreeding values found and are most likely a direct consequence of recent influx of already infected fish harbouring parasites with different genetic signatures. Applying a simulation approach using known variables from the nematode's invasion history, only the artificial introduction of a Wahlund effect leads to a close match between simulated and real data, which is a strong argument for using the parasite as a biological tag for detecting and characterizing fish translocation.     

Isolation and characterization of microsatellite markers for Viola mirabilis (Violaceae) using a next‐generation sequencing platform

We isolated and characterized microsatellite loci in Viola mirabilis (Violaceae), an endangered species from South Korea. Twenty‐three polymorphic microsatellite loci were developed and tested in Korean, Chinese and Japanese populations. The number of alleles per locus varied from two to eight. The observed and expected heterozygosities within the three populations were 0.000–0.625 and 0.469–0.695, respectively. A total of six loci in the Korean population, one locus in the Chinese population and seven loci in the Japanese population deviated from Hardy–Weinberg equilibrium. We expect that these newly developed microsatellite markers will contribute to understanding the phylogeography and population genetics of V. mirabilis, which will aid in developing conservation strategies for this species.     

Isolation and characterization of 11 polymorphic trinucleotide microsatellite markers in the stonefly Arcynopteryx compacta (Plecoptera: Perlodidae)

We describe the isolation of 11 polymorphic trinucleotide microsatellite loci from the stonefly Arcynopteryx compacta. Loci were highly variable with 3 to 14 alleles (mean = 6.45). Observed heterozygosity ranged from 0 to 0.867. Seven loci showed significant deviation from Hardy–Weinberg equilibrium across both populations. There was no evidence for null alleles, and thus, Hardy–Weinberg departures could have resulted from genetic structure between populations or subpopulations. No linkage between loci was found. The 11 loci should prove highly informative for population genetic studies.     

Comparison of quantitative and molecular variation in agroforestry populations of the shea tree (Vitellaria paradoxa C.F. Gaertn) in Mali

In this study we investigated the within- and between-population genetic variation using microsatellite markers and quantitative traits of the shea tree, Vitellaria paradoxa, an important agroforestry tree species of the Sudano–Sahelian region in Africa. Eleven populations were sampled across Mali and in northern Côte d’Ivoire. Leaf size and form and growth traits were measured in a progeny test at the nursery stage. Eight microsatellites were used to assess neutral genetic variation. Low levels of heterozygosity were recorded (1.6–3.0 alleles/locus; H_E = 0.25–0.42) and the fixation index (F_IS = −0.227–0.186) was not significantly different from zero suggesting that Hardy–Weinberg equilibrium is encountered in all populations sampled. Quantitative traits exhibited a strong genetic variation between populations and between families within populations. The degree of population differentiation of the quantitative traits (Q_ST = 0.055–0.283, Q_STmean = 0.189) strongly exceeds that in eight microsatellite loci (F_ST = −0.011–0.142, F_STmean = 0.047). Global and pairwise F_ST values were very low and not significantly different from zero suggesting agroforestry practices are amplifying gene flow (Nm = 5.07). The population means for quantitative traits and the rainfall variable were not correlated, showing variation was not linked with this climatic cline. It is suggested that this marked differentiation for quantitative traits, independent of environmental clines and despite a high gene flow, is a result of local adaptation and human selection of shea trees. This process has induced high linkage disequilibrium between underlying loci of polygenic characters.