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Parentage Analysis (parentage + analysis)
Selected AbstractsParentage analysis in Gabonese colonies of soil-feeding termites belonging to the Cubitermes sp. affinis subarquatus complex of species (Termitidae: Termitinae)INSECT SCIENCE, Issue 2 2010Virginie Roy Abstract,Cubitermes spp. are widely distributed soil-feeding termite species in sub-Saharan Africa which play a fundamental role in soil structure and fertility. A complex of at least four cryptic species (i.e., Cubitermes sp. affinis subarquatus complex of species) has been recently described using molecular markers. In order to investigate the breeding system of these species, five microsatellite markers were used to carry out parentage and relatedness analyses in 15 Gabonese colonies. Monogamy was confirmed as the predominant reproductive organization in Cubitermes spp. (76% of the colonies). Within 30% of these monogamous colonies, a high relatedness between reproductives was shown, suggesting that mating between related individuals occurs. However, Cubitermes colonies can deviate from monogamy. Indeed, parental contributions by at least two related reproductives of the same sex were revealed in four colonies and polyandry was demonstrated in two of them. Infiltration of reproductives in the colony is the most plausible explanation for such cases of polygamy in Cubitermes spp. [source] Patterns and levels of gene flow in Rhododendron metternichii var. hondoense revealed by microsatellite analysisMOLECULAR ECOLOGY, Issue 1 2001Yoshiaki Kameyama Abstract Parentage analysis was conducted to elucidate the patterns and levels of gene flow in Rhododendron metternichii Sieb. et Zucc. var. hondoense Nakai in a 150 × 70 m quadrat in Hiroshima Prefecture, western Japan. The population of R. metternichii occurred as three subpopulations at the study site. Seventy seedlings were randomly collected from each of three 10 × 10 m plots (S1, S2, and S3) on the forest floor of each subpopulation (A1, A2, and A3). Almost all parents (93.8%) of the 70 seedlings were unambiguously identified by using 12 pairs of microsatellite markers. Within the quadrat, adult trees less than 5 m from the centre of the seedling bank (plots S1, S2, and S3) produced large numbers of seedlings. The effects of tree height and distance from the seedling bank on the relative fertilities of adult trees were highly variable among subpopulations because of the differences in population structure near the seedling bank: neither distance nor tree height had any significant effect in subpopulation A1; distance from the seedling bank had a significant effect in subpopulation A2; and tree height had a significant effect in subpopulation A3. Although gene flow within each subpopulation was highly restricted to less than 25 m and gene flow among the three subpopulations was extremely small (0,2%), long-distance gene flow from outside the quadrat reached 50%. This long-distance gene flow may be caused by a combination of topographical and vegetational heterogeneity, differences in flowering phenology, and genetic substructuring within subpopulations. [source] Multigenerational analysis of spatial structure in the terrestrial, food-deceptive orchid Orchis masculaJOURNAL OF ECOLOGY, Issue 2 2009Hans Jacquemyn Summary 1In long-lived, terrestrial orchids, strong aggregation of adults and recruits within populations and pronounced spatial association between recruits and adults can be expected when seed dispersal is limited, probabilities of seed germination decrease with increasing distance from mother plants and/or not all mother plants contribute to future generations. When individuals are distributed evenly across life-history stages, these processes can also be expected to result in a significant fine-scale spatial genetic structure in recruits that will persist into the adult-stage class. 2We combined detailed spatial genetic and point pattern analyses across different generations with parentage analyses to elucidate the role of the diverse processes that might determine spatial structure in Orchis mascula. 3Analyses of spatial point patterns showed a significant association between adults and recruits and similar clustering patterns for both. Weak, but highly significant spatial genetic structure was observed in adults and recruits, but no significant differences were observed across life stages, indicating that the spatial genetic structure present in recruits persists into the adult stage. 4Parentage analyses highlighted relatively short seed dispersal distances (median offspring-recruitment distance: 1.55 and 1.70 m) and differential contribution of mother plants to future generations. 5Persistence of fine-scale spatial genetic structure from seedlings into the adult stage class is consistent with the life history of O. mascula, whereas relatively large dispersal distances of both pollen and seeds compared to the fine-scale clustering of adults and seedlings suggest overlapping seed shadows and mixing of genotypes within populations as the major factors explaining the observed weak spatial genetic structure. 6Nonetheless, comparison of the spatial association between recruits and adults with the genetic analysis of offspring-parent distances suggests that the tight clustering of recruits around adults was probably caused by decreasing probabilities of seed germination with increasing distance from mother plants. 7Synthesis. This study shows that the approach presented here, which combines spatial genetic and spatial pattern analyses with parentage analyses, may be broadly applied to other plant species to elucidate the processes that determine spatial structure within their populations. [source] Do marker-based paternity assignments favour heterozygous and unrelated males?MOLECULAR ECOLOGY, Issue 9 2010JINLIANG WANG Abstract Genetic marker-based parentage analyses are widely applied to studies of natural populations in the fields of evolutionary biology, conservation biology and ecology. When the same markers used in a parentage analysis are used together with the inferred parentage in a downstream analysis, such as the analysis of mate choice in terms of heterozygosity or relatedness, a bias may be incurred because a subset of the genotypes are favoured in parentage assignments or non-exclusions. A previous simulation study shows that exclusion-based paternity analyses are biased in favour of heterozygous males, and males less related to the mothers than expected under random mating. In this study, I investigated the biases of genetic paternity analyses achieved by both exclusion- and likelihood-based methods, using both analytical and simulation approaches. It is concluded that while both exclusion- and likelihood-based methods can lead to biased paternity assignments or non-exclusions in favour of a subset of genotypes, the bias is not consistently towards heterozygous males or males apparently less related to mothers. Both the direction and extent of the bias depend heavily on the allele frequency distribution and the number of markers, the methods used for paternity assignments, and the estimators of relatedness. There exist important differences in the patterns of the biases between exclusion- and likelihood-based paternity analysis methods. It is concluded that the markers, except when they are highly informative to yield accurate paternity assignments or exclusions, should be split into two subsets which are used separately in the paternity and downstream analyses. [source] Parentage versus two-generation analyses for estimating pollen-mediated gene flow in plant populationsMOLECULAR ECOLOGY, Issue 8 2005JAROSLAW BURCZYK Abstract Assessment of contemporary pollen-mediated gene flow in plants is important for various aspects of plant population biology, genetic conservation and breeding. Here, through simulations we compare the two alternative approaches for measuring pollen-mediated gene flow: (i) the neighborhood model , a representative of parentage analyses, and (ii) the recently developed twogener analysis of pollen pool structure. We investigate their properties in estimating the effective number of pollen parents (Nep) and the mean pollen dispersal distance (,). We demonstrate that both methods provide very congruent estimates of Nep and ,, when the methods' assumptions considering the shape of pollen dispersal curve and the mating system follow those used in data simulations, although the neighborhood model exhibits generally lower variances of the estimates. The violations of the assumptions, especially increased selfing or long-distance pollen dispersal, affect the two methods to a different degree; however, they are still capable to provide comparable estimates of Nep. The neighborhood model inherently allows to estimate both self-fertilization and outcrossing due to the long-distance pollen dispersal; however, the twogener method is particularly sensitive to inflated selfing levels, which in turn may confound and suppress the effects of distant pollen movement. As a solution we demonstrate that in case of twogener it is possible to extract the fraction of intraclass correlation that results from outcrossing only, which seems to be very relevant for measuring pollen-mediated gene flow. The two approaches differ in estimation precision and experimental efforts but they seem to be complementary depending on the main research focus and type of a population studied. [source] How to use molecular marker data to measure evolutionary parameters in wild populationsMOLECULAR ECOLOGY, Issue 7 2005DANY GARANT Abstract Estimating the genetic basis of phenotypic traits and the selection pressures acting on them are central to our understanding of the evolution and conservation of wild populations. However, obtaining such evolutionary-related parameters is not an easy task as it requires accurate information on both relatedness among individuals and their breeding success. Polymorphic molecular markers are very useful in estimating relatedness between individuals and parentage analyses are now extensively used in most taxa. The next step in the application of molecular data to wild populations is to use them to derive estimates of evolutionary-related parameters for quantitative traits, such as quantitative genetic parameters (e.g. heritability, genetic correlations) and measures of selection (e.g. selection gradients). Despite their great appeal and potential, the optimal use of molecular tools is still debated and it remains unclear how they should best be used to obtain reliable estimates of evolutionary parameters in the wild. Here, we review the methods available for estimating quantitative genetic and selection parameters and discuss their merits and shortcomings, to provide a tool that summarizes the potential uses of molecular data to obtain such parameters in wild populations. [source] Genetic parentage assessment in the crayfish Orconectes placidus, a high-fecundity invertebrate with extended maternal brood careMOLECULAR ECOLOGY, Issue 10 2002D. Walker Abstract Microsatellite data have recently been introduced in the context of genetic maternity and paternity assignments in high-fecundity fish species with single-parent-tended broods. Here we extend such analyses to an aquatic invertebrate, the crayfish Orconectes placidus, in which gravid females carry large numbers of offspring. Genetic parentage analyses of more than 900 progeny from 15 wild crayfish broods revealed that gravid females were invariably the exclusive dams of the offspring they tended (i.e. there was no allomaternal care), and that most of the females had mated with multiple (usually two) males who contributed sometimes highly skewed numbers of offspring to a brood. Within any multiply sired brood, the unhatched eggs (or the hatched juveniles) from different fathers were randomly distributed across the mother's brood space. All of these genetic findings are discussed in the light of observations on the mating behaviours and reproductive biology of crayfishes. [source] Isolation and characterization of microsatellite loci in a cooperatively breeding corvid, the American crow (Corvus brachyrhynchos)MOLECULAR ECOLOGY RESOURCES, Issue 1 2007L. A. SCHOENLE Abstract We describe 11 microsatellite loci isolated from the American crow (Corvus brachyrhynchos), the most wide-spread cooperatively breeding bird in North America. Polymorphism at these loci ranged from four to 43 alleles, and observed heterozygosities from 0.53 to 0.92. Genetic parentage analyses using these markers will allow us to describe the mating system of this common but socially complex species, and to interpret their behavioural interactions in light of relatedness. [source] Parentage assignment in Haliotis midae L.: a precursor to future genetic enhancement programmes for South African abaloneAQUACULTURE RESEARCH, Issue 9 2010Nicol-Candice Van Den Bergb Abstract The establishment and evaluation of family lines using pedigree information provides an advanced understanding of the variability that exists for complex, economically valuable traits and is a necessary step in the execution of an effective breeding programme. The aim of this study was to assign parentage to mass-spawned Haliotis midae juveniles using species-specific microsatellite markers. Screening of wild abalone individuals revealed that the nine loci selected complied with the minimum requirements for parentage analyses: a null allele frequency <5% as well as a high number and frequency of alleles per locus. A total of 598 individuals were genotyped (198 breeding individuals and 400 F1 progeny) from two farms, with parentage results yielding 91% and 90% successful assignment for Farms A and B respectively. This study, therefore, provided the necessary pedigree information required for controlled breeding of individual adult abalone and indicated the usefulness of the panel of microsatellite markers selected for parentage assignment. [source] The consequences of differential family survival rates and equalizing maternal contributions on the effective population size (Ne) of cultured silver-lipped pearl oysters, Pinctada maximaAQUACULTURE RESEARCH, Issue 8 2010Curtis E Lind Abstract The effective population size (Ne) is a critical gauge of how efficiently an aquaculture operation is capturing or maintaining genetic diversity and can govern the long-term success of genetic selection programmes. In communally reared pearl oysters (Pinctada maxima), high variance in family sizes is a significant contributor towards low Ne and its severity may be compounded by differential survival rates of individual families. To determine the effect of variable survival on Ne in cultured P. maxima, families from two commercial populations were analysed using DNA parentage analyses to monitor survival and changes in relative contributions. Significant shifts in relative contributions were observed between 72 days and 18 months of age in both commercial cohorts (P<0.001). Survival rates were found to be highly variable among families (ranging from 2.5% to 49.5%) when reared in a common environment. Additionally, we investigated whether equalizing maternal family sizes before communal rearing will reduce family size variance, and increase Ne, compared with stocking at naturally produced proportions. Family equalization (E) significantly improved Ne (P=0.013) compared with rearing at natural (N) proportions (E: Ne=7.18±0.34; N: Ne=5.60±0.15); however, this practice may unintentionally magnify negative influences of poor performing families if survival is correlated with other commercially important traits. It is concluded that highly variable family survival will affect Ne in communally reared P. maxima, and the practice of equalizing family sizes in order to maximize Ne may only become consistently beneficial once further progress is made towards understanding, and then reducing variation in family survival rates. [source] Evaluation of relative growth performance and genotype by environment effects for cross-bred yellow perch families reared in communal ponds using DNA parentage analysesAQUACULTURE RESEARCH, Issue 12 2009Han-Ping Wang Abstract From 24 mating sets, 6300 fingerling of yellow perch (Perca flavescens) were stocked into one pond and equal numbers of progeny from six representative sets out of the 24 were stocked into each of two other ponds. After communal rearing for 21 months, total length and body weight were assessed for n=300 fish in each of the three ponds and molecular pedigrees were performed for each sampled individual to assign the progeny back to the original parents. The overall average number of alleles per locus was A=16.4 and observed and expected heterozygosities were Ho=0.88 and He=0.77 respectively. The mean weight of random samples and the top 10% fast-growing fish from the pond with all the sets was significantly greater than those from either of the two replicate ponds with six crosses. For the two replicate ponds, no significant differences were found in family rankings and assignment of the top 10% fast-growing fish, indicating that families with superior growth performance in one pond also exhibited the same superior growth performance in the replicate pond. However, there were no significant correlations detected in family mean weights of the top 10% fish between any two of the three ponds. [source] Does male extra-territory foray effort affect fertilization success in hooded warblers Wilsonia citrina?JOURNAL OF AVIAN BIOLOGY, Issue 6 2005Bridget J. M. Stutchbury Hooded warbler Wilsonia citrina males vary greatly in the frequency and duration of their off-territory forays in search of extra-pair copulations. We used radiotracking and microsatellite parentage analysis in high and low density populations to determine if (1) high foray rate or time off-territory reduces within-pair fertilization success, and (2) if a high foray rate onto the territory of a fertile female increases the likelihood of obtaining EPFs with that female. Males who left their territory often, or for longer periods, did not have lower within-pair fertilization success. Some males repeatedly visited a neighboring fertile female, but in only 3 of 19 cases where radiotagged males visited a fertile female did the male actually sire offspring with that female. Male foray rate onto a fertile female's territory was not a good predictor of whether or not he sired extra-pair offspring with that female. We suggest that mate choice and extra-pair behavior by females may explain why male foray behavior does not correspond closely with actual fertilization success. [source] Do marker-based paternity assignments favour heterozygous and unrelated males?MOLECULAR ECOLOGY, Issue 9 2010JINLIANG WANG Abstract Genetic marker-based parentage analyses are widely applied to studies of natural populations in the fields of evolutionary biology, conservation biology and ecology. When the same markers used in a parentage analysis are used together with the inferred parentage in a downstream analysis, such as the analysis of mate choice in terms of heterozygosity or relatedness, a bias may be incurred because a subset of the genotypes are favoured in parentage assignments or non-exclusions. A previous simulation study shows that exclusion-based paternity analyses are biased in favour of heterozygous males, and males less related to the mothers than expected under random mating. In this study, I investigated the biases of genetic paternity analyses achieved by both exclusion- and likelihood-based methods, using both analytical and simulation approaches. It is concluded that while both exclusion- and likelihood-based methods can lead to biased paternity assignments or non-exclusions in favour of a subset of genotypes, the bias is not consistently towards heterozygous males or males apparently less related to mothers. Both the direction and extent of the bias depend heavily on the allele frequency distribution and the number of markers, the methods used for paternity assignments, and the estimators of relatedness. There exist important differences in the patterns of the biases between exclusion- and likelihood-based paternity analysis methods. It is concluded that the markers, except when they are highly informative to yield accurate paternity assignments or exclusions, should be split into two subsets which are used separately in the paternity and downstream analyses. [source] Sex-biased natal dispersal and inbreeding avoidance in American black bears as revealed by spatial genetic analysesMOLECULAR ECOLOGY, Issue 21 2008CECILY M. COSTELLO Abstract We tested the hypothesis that sex-biased natal dispersal reduces close inbreeding in American black bears, a solitary species that exhibits nearly complete male dispersal and female philopatry. Using microsatellite DNA and spatial data from reproductively mature bears (, 4 years old), we examined the spatial genetic structure of two distinct populations in New Mexico from 1993 to 2000. As predicted, relatedness (r) and the frequency of close relationships (parent,offspring or full siblings) decreased with distance among female dyads, but little change was observed among male or opposite-sex dyads. Neighbouring females were more closely related than neighbouring males. The potential for inbreeding was low. Most opposite-sex pairs that lived sufficiently close to facilitate mating were unrelated, and few were close relatives. We found no evidence that bears actively avoided inbreeding in their selection of mates from this nearby pool, as mean r and relationship frequencies did not differ between potential and actual mating pairs (determined by parentage analysis). These basic patterns were apparent in both study areas despite a nearly two-fold difference in density. However, the sex bias in dispersal was less pronounced in the lower-density area, based on proportions of bears with male and female relatives residing nearby. This result suggests that male bears may respond to reduced competition by decreasing their rate or distance of dispersal. Evidence supports the hypothesis that inbreeding avoidance is achieved by means of male-biased dispersal but also indicates that competition (for mates or resources) modifies dispersal patterns. [source] Estimation of the seed dispersal kernel from exact identification of source plantsMOLECULAR ECOLOGY, Issue 23 2007JUAN J. ROBLEDO-ARNUNCIO Abstract The exact identification of individual seed sources through genetic analysis of seed tissue of maternal origin has recently brought the full analytical potential of parentage analysis to the study of seed dispersal. No specific statistical methodology has been described so far, however, for estimation of the dispersal kernel function from categorical maternity assignment. In this study, we introduce a maximum-likelihood procedure to estimate the seed dispersal kernel from exact identification of seed sources. Using numerical simulations, we show that the proposed method, unlike other approaches, is independent of seed fecundity variation, yielding accurate estimates of the shape and range of the seed dispersal kernel under varied sampling and dispersal conditions. We also demonstrate how an obvious estimator of the dispersal kernel, the maximum-likelihood fit of the observed distribution of dispersal distances to seed traps, can be strongly biased due to the spatial arrangement of seed traps relative to source plants. Finally, we illustrate the use of the proposed method with a previously published empirical example for the animal-dispersed tree species Prunus mahaleb. [source] Mix and match , hybridization reveals hidden complexity in seal breeding behaviourMOLECULAR ECOLOGY, Issue 15 2007WILLIAM AMOS Not so long ago, mammalian breeding systems were seen as dominated by males fighting each other for the right to mate with passive females. Genetic parentage analysis has been instrumental in changing this view and exposing the key role of female choice. Some of the most interesting discoveries have emerged from work on seals, where extreme polygyny is common but females often seem to have a bigger say than was previously thought. A remarkable case in question involves Macquarie Island, where three species of fur seal recently formed a mixed breeding colony (Goldsworthy et al. 1999). Here, the true colours of both sexes lie unusually exposed, because classical models predict that males of the biggest species will dominate the beach and force females of smaller species to conceive mainly hybrid pups. In a fascinating paper in this issue of Molecular Ecology, Lancaster and colleagues (Lancaster et al. 2007) show that females are not this naïve. Although happy to gain protection for most of the season by sitting in the territory of one of the largest males, regardless of whether he is the same species, females almost always conceive to one of their own kind. The females do this, not because any hybrid male offspring they conceive will be sickly and fail to hold good territories, but because females who pup in their hybrid son's territories will be disproportionately likely to mate elsewhere. Hybrid males seem physically fit but sexually unattractive! [source] Fat-tailed gene flow in the dioecious canopy tree species Fraxinus mandshurica var. japonica revealed by microsatellitesMOLECULAR ECOLOGY, Issue 10 2006S. GOTO Abstract Pollen flow, seed dispersal and individual reproductive success can be simultaneously estimated from the genotypes of adults and offspring using stochastic models. Using four polymorphic microsatellite loci, gene flow of the wind-pollinated and wind-seed-dispersed dioecious tree species, Fraxinus mandshurica var. japonica, was quantified in a riparian forest, in northern Japan. In a 10.5-ha plot, 74 female adults, 76 male adults and 292 current-year seedlings were mapped and genotyped, together with 200 seeds. To estimate dispersal kernels of pollen and seeds, we applied normal, exponential power, Weibull, bivariate t -distribution kernels, and two-component models consisting of two normal distribution functions, one with a small and one with a large variance. A two-component pollen flow model with a small contribution (26.1%) from short-distance dispersal (, = 7.2 m), and the rest from long-distance flow (, = 209.9 m), was chosen for the best-fitting model. The average distance that integrated pollen flows inside and outside the study plot was estimated to be 196.8 m. Tree size and flowering intensity affected reproduction, and there appeared to be critical values that distinguished reproductively successful and unsuccessful adults. In contrast, the gene flow model that estimated both pollen and seed dispersal from established seedlings resulted in extensive seed dispersal, and the expected spatial genetic structures did not satisfactorily fit with the observations, even for the selected model. Our results advanced small-scale individual-based parentage analysis for quantifying fat-tailed gene flow in wind-mediated species, but also clarified its limitations and suggested future possibilities for gene flow studies. [source] Patterns of vegetative growth and gene flow in Rhizopogon vinicolor and R. vesiculosus (Boletales, Basidiomycota)MOLECULAR ECOLOGY, Issue 8 2005ANNETTE M. KRETZER Abstract We have collected sporocarps and tuberculate ectomycorrhizae of both Rhizopogon vinicolor and Rhizopogon vesiculosus from three 50 × 100 m plots located at Mary's Peak in the Oregon Coast Range (USA); linear map distances between plots ranged from c. 1 km to c. 5.5 km. Six and seven previously developed microsatellite markers were used to map the approximate size and distribution of R. vinicolor and R. vesiculosus genets, respectively. Genetic structure within plots was analysed using spatial autocorrelation analyses. No significant clustering of similar genotypes was detected in either species when redundant samples from the same genets were culled from the data sets. In contrast, strong clustering was detected in R. vesiculosus when all samples were analysed, but not in R. vinicolor. These results demonstrate that isolation by distance does not occur in either species at the intraplot sampling scale and that clonal propagation (vegetative growth) is significantly more prevalent in R. vesiculosus than in R. vinicolor. Significant genetic differentiation was detected between some of the plots and appeared greater in the more clonal species R. vesiculosus with ,ST values ranging from 0.010 to 0.078*** than in R. vinicolor with ,ST values ranging from ,0.002 to 0.022** (*P < 0.05, **P < 0.01, ***P < 0.001). When tested against the null hypothesis of no relationship between individuals, parentage analysis detected seven likely parent/offspring pairs in R. vinicolor and four in R. vesiculosus (, = 0.001). Of these 11 possible parent/offspring pairs, only two R. vinicolor pairs were still supported as parent/offspring when tested against the alternative hypothesis of being full siblings (, = 0.05). In the latter two cases, parent and offspring were located at approximately 45 m and 28 m from each other. Challenges to parentage analysis in ectomycorrhizal fungi are discussed. [source] Male reproductive competition in spawning aggregations of cod (Gadus morhua, L.)MOLECULAR ECOLOGY, Issue 1 2002D Bekkevold Abstract Reproductive competition may lead to a large skew in reproductive success among individuals. Very few studies have analysed the paternity contribution of individual males in spawning aggregations of fish species with huge census population sizes. We quantified the variance in male reproductive success in spawning aggregations of cod under experimental conditions over an entire spawning season. Male reproductive success was estimated by microsatellite-based parentage analysis of offspring produced in six separate groups of spawning cod. In total, 1340 offspring and 102 spawnings distributed across a spawning season were analysed. Our results show that multiple males contributed sperm to most spawnings but that paternity frequencies were highly skewed among males, with larger males on average siring higher proportions of offspring. It was further indicated that male reproductive success was dependent on the magnitude of the size difference between a female and a male. We discuss our results in relation to the cod mating system. Finally, we suggest that the highly skewed distribution of paternity success observed in cod may be a factor contributing to the low effective population size/census population size ratios observed in many marine organisms. [source] Statistical confidence in parentage analysis with incomplete sampling: how many loci and offspring are needed?MOLECULAR ECOLOGY, Issue 5 2000B. D. Neff Abstract We have recently presented models to estimate parentage in breeding systems with multiple mating and incomplete sampling of the candidate parents. Here we provide formulas to calculate the statistical confidence and the optimal trade-off between the number of loci and offspring. These calculations allow an understanding of the statistical significance of the parentage estimates as well as the appropriate sampling regime required to obtain a desired level of confidence. We show that the trade-off generally depends on the parentage of the putative parents. When parentage is low, sampling effort should concentrate on increasing the number of loci. Otherwise, there are similar benefits from increasing the number of loci or offspring. We demonstrate these methods using genetic data from a nest of the bluegill sunfish (Lepomis macrochirus). [source] A practical guide to methods of parentage analysisMOLECULAR ECOLOGY RESOURCES, Issue 1 2010ADAM G. JONES Abstract The use of molecular techniques for parentage analysis has been a booming science for over a decade. The most important technological breakthrough was the introduction of microsatellite markers to molecular ecology, an advance that was accompanied by a proliferation and refinement of statistical techniques for the analysis of parentage data. Over the last several years, we have seen steady progress in a number of areas related to parentage analysis, and the prospects for successful studies continue to improve. Here, we provide an updated guide for scientists interested in embarking on parentage analysis in natural or artificial populations of organisms, with a particular focus on computer software packages that implement various methods of analysis. Our survey of the literature shows that there are a few established methods that perform extremely well in the analysis of most types of parentage studies. However, particular experimental designs or study systems can benefit from some of the less well-known computer packages available. Overall, we find that parentage analysis is feasible and satisfying in most systems, and we try to provide a simple roadmap to help other scientists navigate the confusing topography of statistical techniques. [source] Identification and characterization of 18 novel polymorphic microsatellite makers derived from expressed sequence tags in the Pacific oyster Crassostrea gigasMOLECULAR ECOLOGY RESOURCES, Issue 3 2009C. SAUVAGE Abstract We report the development of 18 new polymorphic microsatellite DNA markers derived from Crassostrea gigas expressed sequences tags. Genotyping of 48 wild adult oysters sampled from Marennes-Oléron bay (France) revealed 12 to 48 alleles per locus. Observed and expected heterozygosity levels ranged from 0.64 to 1 and from 0.77 to 0.97, respectively. The development of these new markers creates a useful complementary tool for population genetics studies, parentage analysis and mapping in Pacific oyster, a species of major aquacultural and ecological importance. [source] Isolation and characterization of 19 microsatellite markers in a tropical and warm subtropical birch, Betula alnoides Buch.,Ham. ex D. DonMOLECULAR ECOLOGY RESOURCES, Issue 4 2008J. J. GUO Abstract Betula alnoides is an ecologically and economically important species in the tropics and warm subtropics. Nineteen polymorphic microsatellite markers were isolated from this species, which displayed three to 12 alleles per locus. The observed heterozygosities ranged from 0.100 to 0.905, and the expected heterozygosities from 0.510 to 0.893. These markers would be useful tools in genetic resource assessment, molecular marker-assistant breeding, parentage analysis and genetic diversity studies for this species. [source] PRIMER NOTE: A set of polymorphic microsatellite loci for the bay scallop, Argopecten irradiansMOLECULAR ECOLOGY RESOURCES, Issue 3 2007HONGJUN LI Abstract The method of creating enriched microsatellite libraries can supply an abundant source of microsatellite sequences at a considerably reduced cost. Here we report the development of 15 polymorphic microsatellite loci from the bay scallop, Argopecten irradians, using enrichment protocol. Polymorphism was assessed in a sample of hatchery population (n = 38) revealing three to seven alleles per locus. The expected and observed heterozygosities ranged from 0.198 to 0.813 and from 0.083 to 0.833, respectively. These markers will be useful for genetic variation monitoring and parentage analysis. [source] PRIMER NOTE: Isolation and characterization of microsatellite loci in the flat-headed bat (Tylonycteris pachypus)MOLECULAR ECOLOGY RESOURCES, Issue 3 2007P. Y. HUA Abstract Microsatellite loci were developed in the flat-headed bat (Tylonycteris pachypus) from genomic DNA using an enriched library method. Nine loci were tested on 48 individuals sampled from Guangxi Province, China. The mean number of observed alleles per locus was 6.4 (range 4,12). Observed and expected heterozygosity values ranged from 0.24 to 0.83 and from 0.30 to 0.89, respectively. One locus revealed significant departure from Hardy,Weinberg equilibrium and no significant linkage disequilibrium was detected between loci pairs. These markers will be used to examine genetic structure and parentage analysis in this species. [source] Isolation, characterization and evaluation of 11 autosomal STRs suitable for population studies in black and gold howler monkeys Alouatta carayaMOLECULAR ECOLOGY RESOURCES, Issue 1 2007LUCIANA I. OKLANDER Abstract We identified 11 polymorphic microsatellite markers for Alouatta caraya. Three markers were isolated from an enriched genomic library of A. caraya (AC14, AC17, AC45), five were previously described in Homo sapiens (TGMS1, TGMS2, D5S117, D8S165, D17S804), and three were identified for Lagothix lagotricha (1110, 1118, 157). Forty-eight individuals from one Argentinean population were genotyped, yielding heterozygosity values between 0.146 and 0.792. These markers provide an exclusion power of 0.922 when neither parent is known (0.992 when one parent is known) and are suitable for parentage analysis, population genetics and phylogeographical studies of A. caraya, the southernmost primate in the New World. [source] Development and characterization of 11 microsatellite markers in the rock sparrow, Petronia petroniaMOLECULAR ECOLOGY RESOURCES, Issue 4 2006ALESSANDRO GRAPPUTO Abstract Eleven polymorphic microsatellite loci were isolated in the passeriform Petronia petronia using the enrichment protocol FIASCO (fast isolation by AFLP of sequences containing repeats). We detected three to 13 alleles per locus in 25 specimens collected from an Italian population. The level of expected heterozygosity ranged from 0.439 to 0.856. One locus is sex linked to the Z chromosome. The total exclusionary probabilities using these loci for the first and the second parent were 0.978 and 0.999, respectively. These are the first microsatellite loci characterized from the rock sparrow that can be used for estimating population structure and for large-scale parentage analysis. [source] Development and characterization of novel tetra-, tri-, and dinucleotide microsatellite markers in rainbow trout (Oncorhynchus mykiss)MOLECULAR ECOLOGY RESOURCES, Issue 2 2005I. B. SPIES Abstract We discuss the development and characterization of 40 polymorphic rainbow trout (Oncorhynchus mykiss) microsatellite loci. We used enriched libraries to isolate 14 dinucleotide, seven trinucleodide, eight compound di/tetranucleotide, and 11 tetranucleotide loci. These markers will be useful for selective breeding via marker-assisted selection, population genetics studies, parentage analysis, and have already been used for genome mapping. [source] Isolation and characterization of microsatellite markers from the Hypoptychus dybowskii (Pisces, Gasterosteiformes)MOLECULAR ECOLOGY RESOURCES, Issue 1 2002Hiroyuki Munehara Abstract Hypoptychus dybowskii (Gasterosteiformes) exhibits allopaternal care frequently caused by various types of male reproductive tactics (sneaking, egg desertion and taking over). In order to understand this interesting reproductive system, we isolated microsatellites loci from H. dybowskii. Five microsatellites showed 2,10 alleles and expected heterozygosities ranged from 0.15 to 0.84. These were not significant deviations from Hardy,Weinberg expectations. These results suggest that these novel polymorphic loci should be useful for parentage analysis of H. dybowskii. [source] Genetic diversity among parental lines of Indica hybrid rice (Oryza sativa L.) in China based on coefficient of parentagePLANT BREEDING, Issue 6 2006S. Wang Abstract Genetic diversity constitutes the raw material for plant improvement, and provides protection against genetic vulnerability to biotic and abiotic stresses. Diversity of parental lines of indica hybrid rice in China is not well-characterized. The major objective of this study was to quantify genetic diversity of Chinese parental lines of hybrid rice via coefficient of parentage (COP). All 100 parental lines of hybrid rice widely used in hybrid breeding and commercial production during 1976,2003 were studied by COP analysis. The mean COP for the 100 parental lines was low (0.056), indicating a potentially high degree of diversity in Chinese hybrid rice breeding. Forty-nine percent of all pairs of parental lines were completely unrelated by pedigree data. The low mean COP for the parental lines was attributed to a continual incorporation of exotic germplasm (wild rice, japonica and javanica etc.) into the genetic base over time, to the introduction of foreign germplasm from the Philippines (International Rice Research Institute), Korea, the United States, Thailand, and Guyana as breeding stock. The mean COP from 1976 to 1990 was twice as much as that from 1990 to 2003. Cluster analysis was an effective method to discriminate diversity, ten clusters were identified, and maintainer lines, restorer lines and other parental lines with special genetic background were clearly grouped. In addition, restorer lines were further divided into 11 sub-clusters, which basically was in agreement with hybrid rice breeding. Among ten provinces, Hunan, Sichuan and Fujian were outstanding for breeding 54 of 100 parental lines in hybrid rice production, and the genetic diversity of parental lines in Fujian, Sichuan,Guangxi, Hunan and Jiangsu were all narrower than that in Hubei, Guangdong, Zhejiang and Jiangxi. The result of coefficient of parentage analysis for 100 parental lines may promote the management of parental diversity and hybrid rice breeding in China. [source] | ||||||||||