Showing papers in "Molecular Ecology Notes in 2003"
TL;DR: Distortion as discussed by the authors provides a general method for visualizing membership coefficients in multilocus genotypes from structured populations, and can be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.
Abstract: In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as STRUCTURE . DISTRUCT provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. DISTRUCT , available at www.cmb.usc.edu/∼ noahr/distruct.html, can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.
4,668 citations
TL;DR: A new software tool, specifically designed to facilitate the analysis of large microsatellite data sets, and an improved method to deal with inbred samples (such as Drosophila isofemale lines).
Abstract: In molecular ecology the analysis of large microsatellite data sets is becoming increasingly popular. Here we introduce a new software tool, which is specifically designed to facilitate the analysis of large microsatellite data sets. All common microsatellite summary statistics and distances can be calculated. Furthermore, the microsatellite analyser (msa) software offers an improved method to deal with inbred samples (such as Drosophila isofemale lines). Executables are available for Windows and Macintosh computers.
1,609 citations
TL;DR: Highly variable tetranucleotide microsatellites are isolated and developed for the specific goal of increasing discriminatory power among closely related populations, providing a new power towards the reliable differentiation of nonwinter runs.
Abstract: The unambiguous identification of Central Valley spring-run chinook salmon has become imperative since their proposed listing in 1998. The accuracy of methods used to assign individuals to their stock of origin is critical for understanding juvenile migration patterns and determining the success of protection measures. Existing microsatellites discriminate between the endangered winter-run and other chinook but are insufficient to characterize phylogenetically less distinct runs. Here, we isolated and developed highly variable tetranucleotide microsatellites for the specific goal of increasing discriminatory power among closely related populations, providing a new power towards the reliable differentiation of nonwinter runs
320 citations
TL;DR: The procedure allows the preparation of genomic DNA of a quality suitable for polymerase chain reaction-based studies of large populations at around one-tenth of the cost of commercially available kits.
Abstract: We describe here a procedure for the purification of high molecular weight genomic DNA that combines the economies of 'do-it-yourself', single-tube protocols with the sample throughput and DNA quality of microplate-based DNA extraction and purification kits from commercial suppliers. The procedure allows the preparation of genomic DNA of a quality suitable for polymerase chain reaction-based studies of large populations at around one-tenth of the cost of commercially available kits. Furthermore, 96 samples can be purified from crude tissue digests in around 30 min and are produced in microtitre plate format to allow efficient downstream processing of samples.
307 citations
TL;DR: FAMOZ (an acronym for father/mother) is a software useful in reconstructing parentage for dominant, codominant and uniparentally inherited markers.
Abstract: FAMOZ (an acronym for father/mother) is a software useful in reconstructing parentage for dominant, codominant and uniparentally inherited markers. It is written in C and TclTk languages and is available for Unix, Linux and Windows systems at http://www.pierroton.inra.fr/ genetics/labo/Software/Famoz/index.html. Parameters and assumptions used in the calculations are few and simple. Exclusion and identity probabilities, log-likelihoods of any genetic relationship, potential father and parent or parent pair, half- and full-sibship are calculated based on real or simulated data. Error rates for genotypic mistyping can be introduced. Simulations can be done to build statistical tests for parentage assignment.
242 citations
TL;DR: The availability of these primers to the insect research community should facilitate the use of internal transcribed spacer regions in intraspecific studies as well as phylogenetic analysis of closely related taxa.
Abstract: The evolutionary conservation and versatility of a new set of nuclear primers for the amplification of the ribosomal internal transcribed spacer regions in insects and other invertebrates have been studied. These primers, conserved across Insecta and other invertebrates, are based on a comprehensive taxonomic survey of the current DNA sequence databases. Their versatility was demonstrated by extensive polymerase chain reaction assays in 16 species from two arachnid orders, eight insect orders, three invertebrate and vertebrate chordate orders and by direct sequencing of the amplified products. The availability of these primers to the insect research community should facilitate the use of internal transcribed spacer regions in intraspecific studies as well as phylogenetic analysis of closely related taxa.
205 citations
TL;DR: The structure of the core sequence of 552 microsatellites, together with the sequences of the primers and the length of the sequenced allele are presented, which are currently considered the most useful genetic markers with wide applications in genomics, quantitative and population genetics.
Abstract: SummaryMicrosatellites are currently considered the most useful genetic markers with wide appli-cations in genomics, quantitative and population genetics. We present here the structure ofthe core sequence of 552 microsatellites, together with the sequences of the primers and thelength of the sequenced allele. These microsatellites were isolated from several librariesconstructed from either fractions of total genomic DNA or from clones of a bacterial artifi-cial chromosome (BAC) library. All 552 loci are polymorphic in the honeybee. Many ofthem were also successfully amplified in three other species of Apis : A. cerana (58%), A.dorsata (59%) and A. florea (38%). A summary of the variability of 36 loci in the three mainevolutionary lineages of A. mellifera is given. Keywords : Apis mellifera , cross-priming, linkage map, population genetics Received 9 January 2003; revision accepted 27 February 2003 Because microsatellite markers have been developedmainly for population genetics studies, the number of lociisolated in most species is usually small. Large numbers ofloci are available only in a few vertebrate species, such ashuman, mouse, rat and an increasing number of farmanimals and fishes, as well as model and cultivated plants(Gentles & Karlin 2001; Katti
200 citations
TL;DR: The evolution of Otiorynchid weevils, mainly Otiorhynchus scaber and sulcatus is examined in an attempt to trace the evolutionary history and find out what causes the variation in success of different parthenogens.
Abstract: Asexual reproduction and polyploidy are relatively rare in animals with chromosomal sex determination and always represent a derived condition. To accomplish asexual reproduction several changes in gene expression are required in the mechanism of oogenesis. Polyploidy increases the cell volume and also gives rise to alterations in general physiology. Nevertheless, there are asexual animals that not only survive but seem to be doing better than their sexual progenitors. This is expressed in the distribution pattern called geographical parthenogenesis. Using molecular phylogeny, I here examine the evolution of Otiorynchid weevils, mainly Otiorhynchus scaber and sulcatus in an attempt to trace the evolutionary history and find out what causes the variation in success of different parthenogens. I also evaluate the contribution of asexuality, hybridity and polyploidy as explanations behind geographical parthenogenesis in insects. I conclude that what is called O. scaber is, in fact, a set of geographical polyploids as polyploidy and not asexuality explains the difference in clonal success. I also argue that O. sulcatus is a recently formed clonal species of non-hybrid origin that may well be a good example of a true general purpose genotype. I find little support for asexuality or a hybrid origin as explanations behind geographical parthenogenesis in insects. Finally, I argue that polyploidy in all eukaryotes should be seen as an opportunity for the species evolution, not as a limitation that ensures the demise of the taxa.
185 citations
TL;DR: 79 microsatellite DNA markers, which were obtained from genomic libraries enriched for CA, GA, ATG and TAGA motif repeats, in the Pacific oyster Crassostrea gigas were characterized and showed a precipitous decline with distance from the focal species C. gigas.
Abstract: We characterized 79 microsatellite DNA markers, which were obtained from genomic libraries enriched for CA, GA, ATG and TAGA motif repeats, in the Pacific oyster Crassostrea gigas. For eight F1 grandparents or great-grandparents of mapping families, the average heterozygosity, 0.705, and average number of alleles per locus, 5.7, did not vary among motif-repeat or motif-complexity categories. Non-amplifying polymerase chain reaction null alleles, which were confirmed by segregation in the mapping families, were detected at 41 (51.9%) of the 79 loci. Cross-species amplifications from C. angulata, C. sikamea, C. ariakensis and C. virginica showed a precipitous decline with distance from the focal species C. gigas.
156 citations
TL;DR: PCR primers developed yielded a high number of alleles (8–14) and high observed heterozygosities (0.57–1.0) in the Diamondback terrapin isolates.
Abstract: We describe polymerase chain recation (PCR) primers and conditions to amplify one dinucleotide and five tetranucleotide microsatellite DNA loci isolated from the Diamondback terrapin (Malaclemys terrapin). The PCR primers were tested on 21 terrapins from Cape Romain, SC, USA. The microsatellite primers developed yielded a high number of alleles (8–14) and high observed heterozygosities (0.57–1.0).
128 citations
TL;DR: bottlesim is a program for simulating bottlenecks to estimate the impact on genetic diversity; the novelties include an overlapping-generation model, a wide range of reproductive systems, and flexible population size settings.
Abstract: Population bottlenecks reduce genetic diversity and thus cause great concern in conservation biology. Previous theoretical studies often assume discrete generations in projecting declines in genetic diversity caused by bottlenecks. This assumption creates complexities when applying the models to long-lived species with overlapping generations. bottlesim is a program for simulating bottlenecks to estimate the impact on genetic diversity; the novelties include an overlapping-generation model, a wide range of reproductive systems, and flexible population size settings. With these features, bottlesim will be a useful tool for estimating the genetic consequences of bottlenecks, evaluating conservation plans, and performing power analysis.
TL;DR: Six polymorphic loci were characterized which produced 3-21 alleles in 70 individuals from one Italian population, with an observed heterozygosity between 0.58 and 0.85 and should be very useful in gene flow studies of these species.
Abstract: Using an enrichment procedure, we cloned microsatellite repeats from European beech (Fagus sylvatica L.) and developed primers for the amplification of microsatellite markers. Six polymorphic loci were characterized which produced 3-21 alleles in 70 individuals from one Italian population, with an observed heterozygosity between 0.58 and 0.85. All six loci amplified fragments which were polymorphic in the closely related species, Fagus orientalis, also. Owing to their very high degree of variation, these markers should be very useful in gene flow studies of these species
TL;DR: Twelve primer pairs reliably amplified products in three peach cultivars of which seven revealed polymorphisms, and revealed segregation in an interspecific progeny and polymorphism in P. dulcis.
Abstract: Primers were developed for 21 microsatellite loci isolated by enrichment from Prunus avium‘Napoleon’. Twelve loci contained uninterrupted dinucleotide repeats and nine were more complex. Nineteen primer pairs (EMPA001–019) showed single locus polymorphisms in a cultivar survey of 14 sweet cherries, with two to seven alleles per locus. Three primer pairs in combination (EMPA014, 015 and 018) discriminated all cultivars. Two primer pairs for loci monomorphic in P. avium were included: EMPA020 revealed segregation in an interspecific progeny and EMPA021 revealed polymorphism in P. dulcis. Twelve primer pairs reliably amplified products in three peach cultivars of which seven revealed polymorphisms.
TL;DR: Five polymorphic tri- and tetranucleotide microsatellite loci suitable for population genetic analysis were identified in the cotton bollworm Helicoverpa armigera from two partial phagemid genomic libraries enriched for micros satellite inserts, supporting the notion of a relative low frequency of micros Satellite sequences in lepidopteran genomes.
Abstract: Five polymorphic tri- and tetranucleotide microsatellite loci suitable for population genetic analysis were identified in the cotton bollworm Helicoverpa armigera from two partial phagemid genomic libraries enriched for microsatellite inserts. The overall microsatellitecloning efficiency in H. armigera is 2.5% , which is approximately eightfold lower than that for the gadoid fishes (20%) employing the same enrichment protocol, supporting the notion of a relative low frequency of microsatellite sequences in lepidopteran genomes. In addition, a large proportion of cloned microsatellite sequences turned out to be repetitive DNA, thus further increasing the difficulty of developing such markers in butterflies and moths.
TL;DR: Thirteen polymorphic microsatellite loci were isolated from Castanea sativa (Mill.) and the number of alleles revealed varied from two to 14 (mean = 5.15) per loci.
Abstract: Thirteen polymorphic microsatellite loci were isolated from Castanea sativa (Mill.). Six contained dinucleotide repeats, six contained trinucleotide repeats, and one contained a compound microsatellite of a trinucleotide and a tetranucleotide repeat. The loci were characterized using C. sativa trees from three populations in the UK and the parents and six seedlings from a Turkish mapping population. The number of alleles revealed varied from two to 14 (mean = 5.15) per loci. Eight loci were found to be useful in the mapping family.
TL;DR: These markers provide a system to study paternity, genetic diversity in natural populations, gene flow, dispersal and inbreeding in the great tit Parus major.
Abstract: Six dinucleotide, three trinucleotide and seven tetranucleotide microsatellite loci developed for the great tit Parus major are presented. Thirty individual birds were screened at each locus. Loci were polymorphic (four to 19 alleles per locus). These markers provide a system to study paternity, genetic diversity in natural populations, gene flow, dispersal and inbreeding.
TL;DR: Nine polymorphic microsatellite markers for the fucoid seaweeds Fucus vesiculosus, F. serratus and Ascophyllum nodosum were developed using a combined, enriched library and showed polymorphic in at least two species.
Abstract: The Fucaceae is a family of brown seaweeds that dominate and frequently co-occur on North Atlantic rocky shores. We developed nine polymorphic microsatellite markers for the fucoid seaweeds Fucus vesiculosus, F. serratus and Ascophyllum nodosum using a combined, enriched library. Six of these loci were polymorphic in at least two species, showing from two to eight alleles with heterozygosities ranging from 0.41 to 0.85. Loci were also tested on F. spiralis, revealing five polymorphic microsatellite loci in this species.
TL;DR: Amplification of the markers in different species comprising the subfamilies Anatinae and Anserinae indicates their potential value for population genetic applications in a wide range of waterfowl species.
Abstract: We have isolated and characterized 18 microsatellite loci in the Peking duck (Anas platyrhynchos) The average number of alleles per locus was 35, ranging from one to six in domestic Peking ducks (n = 40) All of the markers were polymorphic in a sample of five mallards (A platyrhynchos; two to eight alleles) Seventeen of the 18 markers amplified in Muscovy ducks (Cairina moschata) with 11 being polymorphic in our sample (n = 14) Amplification of the markers in different species comprising the subfamilies Anatinae and Anserinae indicates their potential value for population genetic applications in a wide range of waterfowl species
TL;DR: This work has identified 17 potential cpSSRs motifs from available oak sequences and tested their variability among French oak populations, finding six loci were polymorphic at the intraspecific level in Quercus petraea and Q. robur.
Abstract: The increase in demand for the certification of oak seed lots, as well as control of the geographical origin of oak wood, has led us to develop powerful genetic markers permitting us to discriminate among provenance regions. With the aim of detecting new chloroplast variants, we have identified 17 potential cpSSRs motifs from available oak sequences and tested their variability among French oak populations. Six loci were polymorphic at the intraspecific level in Quercus petraea and Q. robur . Moreover, conservation of the primer pairs was checked on a set of 21 forest tree species and they were all shown to work well on several Quercus species, and even within Fagacaea.
TL;DR: 22 new SSR markers developed from the diploid species F. viridis, including amplified polymorphic alleles in the parents of a F. vesca mapping population, are presented.
Abstract: To date, the development of microsatellite (SSR) markers in the genus Fragaria has focused on F. vesca. However, further species are thought to have contributed to the complex allo-octoploid genome of the cultivated strawberry, F.×ananassa. Here, we present 22 new SSR markers developed from the diploid species F. viridis. Twenty-one of the primer pairs amplified polymorphisms in six F. viridis accessions, with an average of 4.95 alleles per primer pair and an average expected heterozygosity of 0.68. Fourteen of these primer pairs, and a locus monomorphic in F. viridis, amplified polymorphic alleles in the parents of a F. vesca mapping population.
TL;DR: The isolation and characterization of eight microsatellite loci that amplify successfully from strains representative of the phylogenetic diversity in the B .
Abstract: Beauveria bassiana, an entomogenous fungus used for the biological control of pest insects, comprises a globally-distributed species complex of regionally endemic lineages. In order to study the population genetics of B. bassiana, detail species boundaries, conduct ecological studies of natural populations and track fates of experimentally-released strains, sensitive genetic markers are required. We describe the isolation and characterization of eight microsatellite loci that amplify successfully from strains representative of the phylogenetic diversity in the B. bassiana complex.
TL;DR: Testing amplification success rates over a one-year storage period for DNA extracted from brown bear hair samples preserved using silica desiccation and −20 °C freezing found that minimizing delays between collection and DNA extraction will maximize success rates for hair-based noninvasive genetic sampling projects.
Abstract: Hair samples are an increasingly important DNA source for wildlife studies, yet optimal storage methods and DNA degradation rates have not been rigorously evaluated. We tested amplification success rates over a one-year storage period for DNA extracted from brown bear (Ursus arctos) hair samples preserved using silica desiccation and −20 °C freezing. For three nuclear DNA microsatellites, success rates decreased significantly after a six-month time point, regardless of storage method. For a 1000 bp mitochondrial fragment, a similar decrease occurred after a two-week time point. Minimizing delays between collection and DNA extraction will maximize success rates for hair-based noninvasive genetic sampling projects.
TL;DR: The development of nine new microsatellite markers from partial genomic library of an elite variety of Coffea arabica reveal robust cross-species amplifications in 17 related species of coffee and suggest their potential use as genetic markers for assessment of germplasm diversity and linkage analysis of coffee.
Abstract: Genetic improvement of coffee ( Coffea arabica L.) is constrained by low genetic diversity and lack of genetic markers, suitable screening tools, information on the genetic makeup of available gene pool and long generation time. In this context, use of DNA markers such as microsatellites that provide high genetic-resolution becomes highly desirable. Here, we report the development of nine new microsatellite markers from partial genomic library of an elite variety of Coffea arabica . The developed microsatellites revealed robust cross-species amplifications in 17 related species of coffee, and their Polymorphic Information Content varied from 0 to 0.6, 0 to 0.78 and 0.67 to 0.90 for the arabica, robusta genotypes and species representatives, respectively. The data thus suggest their potential use as genetic markers for assessment of germplasm diversity and linkage analysis of coffee.
TL;DR: Eleven tetranucleotide microsatellite loci were characterized in the African elephant, all of which were polymorphic in 32 faecal samples and two tissue samples from 33 individual African savannah elephants.
Abstract: Most African elephant (Loxodonta africana africana) populations are isolated and thus threatened by a loss of genetic diversity. As a consequence, genetic analysis of African elephant populations will play an increasing role in their conservation, and microsatellite loci will be an important tool in these analyses. Previously published sets of polymorphic microsatellites developed for African elephants are all dinucleotide repeats, which are prone to typing error. Here, we characterize 11 tetranucleotide microsatellite loci in the African elephant. All loci were polymorphic in 32 faecal samples and two tissue samples from 33 individual African savannah elephants.
TL;DR: 16 microsatellite loci from the blacktip shark, Carcharhinus limbatus, were isolated and characterized, and cross-species amplification in 11 CarchARhinus species and five additional shark genera were tested.
Abstract: We isolated and characterized 16 microsatellite loci from the blacktip shark, Carcharhinus limbatus, and tested cross-species amplification in 11 Carcharhinus species and five additional shark genera. Thirty-six (1.6%) and 180 (48%) colonies were positive for dinucleotide repeat motifs from unenriched and enriched libraries, respectively. Heterozygosities of polymorphic loci ranged from 0.04 to 0.96 with two to 22 alleles per locus. Amplification products were observed at nine to 13 loci (five to 11 of which where polymorphic) in 10 Carcharhinus species. Several loci were also polymorphic in each of the additional genera examined.
TL;DR: The isolation and characterization of the first microsatellite loci specifically developed for the Common Eider duck, Somateria mollissima are described, which show Mendelian inheritance and no linkage disequilibrium between any pair of loci.
Abstract: We describe the isolation and characterization of the first microsatellite loci specifically developed for the Common Eider duck, Somateria mollissima. Our 10 loci show Mendelian inheritance and no linkage disequilibrium between any pair of loci. In the Eider duck, we observed between two and 16 alleles per locus, an expected heterozygosity between 0.31 and 0.97, and an observed heterozygosity between 0.14 and 1.00. Most primers also yield reproducible results in several other anatid species. These loci comprise a set of autosomal molecular markers for various applications, from moderately polymorphic loci suitable for population studies to highly polymorphic loci for pedigree analysis in waterfowl.
TL;DR: The characterization of 12 polymorphic microsatellite markers in the biotrophic fungus Puccinia triticina, the causal agent of leaf rust on wheat, is reported.
Abstract: We report the characterization of 12 polymorphic microsatellite markers in the biotrophic fungus Puccinia triticina , the causal agent of leaf rust on wheat. An enrichment protocol was used to isolate microsatellite loci and polymorphism was explored with 15 European isolates. Significant level of cross-amplification (44% of the loci) was found in P. striiformis .
TL;DR: Results indicate that the mitochondrial control region in shrimps provides more informative sites and reveals more haplotypes, making it most useful for evaluating genetic variations within and between populations of Penaeus species.
Abstract: This study reports a primer set for amplifying a partial fragment of about 610 bp in the fast mutating mitochondrial control region in shrimps of the genus Penaeus (Decapoda: Penaeidae). The utility of this amplified fragment for studying population differentiation and structuring, compared with more conservative mitochondrial genes (16S rRNA and COI), was explored in P. merguiensis populations over a vast geographical range based on sequence and RFLP analyses. The results indicate that the mitochondrial control region provides more informative sites and reveals more haplotypes, making it most useful for evaluating genetic variations within and between populations of Penaeus species.
TL;DR: Microsatellites were isolated and characterized in the northern house mosquito, Culex pipiens, a widespread pest species and important vector of diseases such as West Nile virus, and will be useful for studies of population structure and intraspecific variation in epidemiological characteristics.
Abstract: Microsatellites were isolated and characterized in the northern house mosquito, Culex pipiens , a widespread pest species and important vector of diseases such as West Nile virus. An enrichment protocol yielded 150 positive clones. We designed primers to amplify 17 unique (GT) n microsatellites, eight of which amplified cleanly and were polymorphic. A survey of 29 individuals showed that these loci are highly variable with the number of alleles ranging from seven to 19 and expected heterozygosity ranging from 0.66 to 0.93. These markers will be useful for studies of population structure and intraspecific variation in epidemiological characteristics of Cx. pipiens .
TL;DR: Microsatellite-enriched genomic libraries were obtained from the whitefly Bemisia tabaci using a magnetic/biotin capture of repetitive sequences to assess variation and identify dinucleotide markers.
Abstract: Microsatellite-enriched genomic libraries were obtained from the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) using a magnetic/biotin capture of repetitive sequences. Ten dinucleotide markers were successfully isolated and characterized from these libraries. Variability was assessed in six populations of B. tabaci collected from different localities of the island of Crete, Greece. The number of alleles per locus in approximately 105 individuals screened across populations ranged from two to 13. Averaged observed heterozygosity over the six populations ranged from 0.001 to 0.58.