Showing papers in "Molecular Ecology Notes in 2006"
TL;DR: Genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data.
Abstract: genalex is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include amova, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/
15,786 citations
TL;DR: This study presents a silica-based method that is sensitive, inexpensive and compliant with automation that has now been tested on more than 5000 animal specimens with highly positive results.
Abstract: Although commercial kits are available for automated DNA extraction, ‘artisanal’ protocols are not. In this study, we present a silica-based method that is sensitive, inexpensive and compliant with automation. The effectiveness of this protocol has now been tested on more than 5000 animal specimens with highly positive results.
1,233 citations
TL;DR: A computer program, ml - relate, that calculates maximum likelihood estimates of relatedness and relationship and uses simulation to determine which relationships are consistent with genotype data and to compare putative relationships with alternatives.
Abstract: Genetic data are useful for estimating the genealogical relationship or relatedness between individuals of unknown ancestry. We present a computer program, ml - relate that calculates maximum likelihood estimates of relatedness and relationship. ml - relate is designed for microsatellite data and can accommodate null alleles. It uses simulation to determine which relationships are consistent with genotype data and to compare putative relationships with alternatives. ml - relate runs on the Microsoft Windows operating system and is available from www.montana.edu/kalinowski.
894 citations
TL;DR: GENCLONE 1.0 is designed for studying clonality and its spatial components using genotype data with molecular markers from haploid or diploid organisms with adapted spatial autocorrelation methods and clonal subrange estimates.
Abstract: GENCLONE 1.0 is designed for studying clonality and its spatial components using genotype data with molecular markers from haploid or diploid organisms. GENCLONE 1.0 performs the following tasks. (i) discriminates distinct multilocus genotypes (MLGs), and uses permutation and resampling approaches to test for the reliability of sets of loci and sampling units for estimating genotypic and genetic diversity (a procedure also useful for nonclonal organisms); (ii) computes statistics to test for clonal propagation or clonal identity of replicates; (iii) computes various indices describing genotypic diversity; and (iv) summarizes the spatial organization of MLGs with adapted spatial autocorrelation methods and clonal subrange estimates.
725 citations
TL;DR: Powsim as mentioned in this paper is a 32-bit Windows/DOS simulation-based computer program that estimates power (and α error) for chi-square and Fisher's exact tests when evaluating the hypothesis of genetic homogeneity.
Abstract: Knowledge of statistical power is essential for sampling design and data evaluation when testing for genetic differentiation. Yet, such information is typically missing in studies of conservation and evolutionary genetics, most likely because of complex interactions between the many factors that affect power. powsim is a 32-bit Windows/DOS simulation-based computer program that estimates power (and α error) for chi-square and Fisher's exact tests when evaluating the hypothesis of genetic homogeneity. Optional combinations include the number of samples, sample sizes, number of loci and alleles, allele frequencies, and degree of differentiation (quantified as FST). powsim is available at http://www.zoologi.su.se/~ryman.
548 citations
TL;DR: This work introduces a method that allows repeat units to be fractionally shorter or longer than their theoretical value, and performs well over a wide range of dinucleotide repeat loci.
Abstract: As genotyping methods move ever closer to full automation, care must be taken to ensure that there is no equivalent rise in allele-calling error rates. One clear source of error lies with how raw allele lengths are converted into allele classes, a process referred to as binning. Standard automated approaches usually assume collinearity between expected and measured fragment length. Unfortunately, such collinearity is often only approximate, with the consequence that alleles do not conform to a perfect 2-, 3- or 4-base-pair periodicity. To account for these problems, we introduce a method that allows repeat units to be fractionally shorter or longer than their theoretical value. Tested on a large human data set, our algorithm performs well over a wide range of dinucleotide repeat loci. The size of the problem caused by sticking to whole numbers of bases is indicated by the fact that the effective repeat length was within 5% of the assumed length only 68.3% of the time.
524 citations
TL;DR: Short barcodes were effective in identifying specimens, confirming their utility in circumstances where full barcodes are too expensive to obtain and the identification comparisons are within a confined taxonomic group.
Abstract: A DNA barcode based on 650 bp of mitochondrial gene cytochrome c oxidase I is proving to be highly functional in species identification for various animal groups. However, DNA degradation complicates the recovery of a full-length barcode from many museum specimens. Here we explore the use of shorter barcode sequences for identification of such specimens. We recovered short sequences — i.e. ∼ 100 bp — with a single PCR pass from more than 90% of the specimens in assemblages of moth and wasp museum specimens from which full barcode recovery was only 50%, and the latter were usually less than 8 years old. Short barcodes were effective in identifying specimens, confirming their utility in circumstances where full barcodes are too expensive to obtain and the identification comparisons are within a confined taxonomic group.
511 citations
TL;DR: A collection of R functions that facilitates the handling of dominant genotypic data that calculates the proportion of polymorphic markers in each population, and estimates gene diversity as the average proportion of pairwise differences between individuals with confidence intervals based on bootstrapping across markers.
Abstract: aflpdat is a collection of R functions that facilitates the handling of dominant genotypic data It converts data from a standard tab-separated table to the input formats of the following programs: arlequin, structure, treecon, paup and hickory In addition, it calculates the proportion of polymorphic markers in each population, and estimates gene diversity as the average proportion of pairwise differences between individuals with confidence intervals based on bootstrapping across markers It also produces summary tables of marker frequencies and the presence or absence of markers in each population aflpdat can be downloaded from http://wwwnhmuiono/ncb/
457 citations
TL;DR: The computer program HYBRIDLAB 1.0 for simulating intraspecific hybrids from population samples of nuclear genetic markers such as microsatellites, allozymes or SNPs, has a wide range of applications for studying natural and artificial hybridization.
Abstract: We present the computer program HYBRIDLAB 1.0 for simulating intraspecific hybrids from population samples of nuclear genetic markers such as microsatellites, allozymes or SNPs ( single nucleotide polymorphisms). The program generates a user-specified number of multilocus F1 hybrid genotypes between any pair of potentially hybridizing populations included in a standard input-file of multilocus genotypes for population genetic analysis. This simple, user-friendly program has a wide range of applications for studying natural and artificial hybridization; in particular, for evaluating the statistical power for individual assignment of parental and hybrid individuals. An example of application for Atlantic cod populations is given.
428 citations
TL;DR: This work presents a method that uses random assignments of band presence-absence to the missing data, implemented by the computer program [smallcapital famd] (available from http://homepage.univie.ac.at/philipp.schlueter/famd), for analyses based on pairwise similarity and Shannon's index.
Abstract: Missing data are commonly encountered using multilocus, fragment-based (dominant) fingerprinting methods, such as random amplified polymorphic DNA (RAPD) or amplified fragment length polymorphism (AFLP). Data sets containing missing data have been analysed by eliminating those bands or samples with missing data, assigning values to missing data or ignoring the problem. Here, we present a method that uses random assignments of band presence-absence to the missing data, implemented by the computer program [smallcapital famd] (available from http://homepage.univie.ac.at/philipp.maria.schlueter/famd.html), for analyses based on pairwise similarity and Shannon's index. When missing values group in a data set, sample or band elimination is likely to be the most appropriate action. However, when missing values are scattered across the data set, minimum, maximum and average similarity coefficients are a simple means of visualizing the effects of missing data on tree structure. Our approach indicates the range of values that a data set containing missing data points might generate, and forces the investigator to consider the effects of missing values on data interpretation.
407 citations
TL;DR: A novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, F IS or F ST are available is proposed.
Abstract: Nonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy–Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients ( F ) or fixation indices ( F IS or F ST ). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F , F IS or F ST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker. hull.ac.uk/ and will be incorporated into the software MICRO - CHECKER .
TL;DR: This paper considers three typical sources of scoring errors capable of biasing biological conclusions: stuttering, large-allele dropout and null alleles.
Abstract: Microsatellite data are widely used to test ecological and evolutionary hypotheses in wild populations. In this paper, we consider three typical sources of scoring errors capable of biasing biological conclusions: stuttering, large-allele dropout and null alleles. We describe methods to detect errors and propose conventions to mitigate scoring errors and report error rates in studies of wild populations. Finally, we discuss potential bias in ecological or evolutionary conclusions based on data sets containing these scoring errors.
TL;DR: In this article, the authors present inexpensive techniques for simultaneously machine grinding large numbers of plant samples for DNA extraction using a commercially available reciprocating saw; and DNA recovery using silica column-based extractions similar to that used in some commercially available kits.
Abstract: The time needed for hand grinding and the cost of commercially available extraction kits remain to be the major limitations in plant DNA extraction for many researchers We present inexpensive techniques for (i) simultaneously machine grinding large numbers of plant samples for DNA extraction using a commercially available reciprocating saw; and (ii) DNA recovery using silica column-based extractions similar to that used in some commercially available kits Used together, these allow for the rapid recovery of plant DNA at relatively low cost Furthermore, these methods appear to be widely applicable within plants with good yields recovered in test extractions across major plant groups (ferns, gymnosperms, monocots and eudicots)
TL;DR: It is found that phase could be reconstructed from direct sequencing of mixed PCR products by combining for each individual the complementary information contained in its forward and reverse chromatograms, provided these products had different lengths.
Abstract: For diploid organisms, haplotype determination usually requires sequencing cloned polymerase chain reaction (PCR) products or comparing the genotypes of several individuals. We found out that phase could be reconstructed from direct sequencing of mixed PCR products by combining for each individual the complementary information contained in its forward and reverse chromatograms, provided these products had different lengths. When applied to the internal transcribed spacer 2 (ITS2) from corals of the genus Pocillopora, this new method allowed us to identify two dominant sequence types in some specimens; however, sequencing cloned PCR products from the same specimens yielded more variants, including possible PCR-generated recombination artifacts.
TL;DR: Using stochastic simulations, the possibility to allow for mismatches at one or more allele as a way to recover assignment power was very efficient provided the set of loci used had a high assignment power and the error rate was not too high.
Abstract: In parentage assignment by exclusion, using multiple and very polymorphic loci, genotyping errors are a major cause of non-assignment. Using stochastic simulations, we tested the possibility to allow for mismatches at one or more allele as a way to recover assignment power. This was very efficient provided the set of loci used had a high assignment power (> 99%) and the error rate was not too high (below 3–4%). In these cases, most of the theoretical assignment power could be recovered. We also showed the efficiency of the method in a practical experiment with rainbow trout.
TL;DR: The complete mitochondrial genome sequences from Anthozoa and recently from Porifera allow us to compare the resolution power of the 5′′ partition, which has also been proposed as the standard marker for DNA barcoding, with a less frequently used partition further downstream, and report on the finding of significantly different substitution patterns of the downstream partition opposed to the 5″′ partition.
Abstract: Partitions of the cytochrome oxidase subunit 1 (CO1) gene, especially the 5′′′ ′ end, are frequently recruited to infer lower level phylogenies in animals. In diploblasts, mitochondrial genes were found to evolve in a slower rate than their bilaterian counterparts. Therefore, diploblast CO1 gene trees repeatedly remained unresolved, which also raises doubts on the suitability of CO1 for DNA barcoding in these animals. The complete mitochondrial genome sequences from Anthozoa and recently from Porifera allow us to compare the resolution power of the 5′′ partition, which has also been proposed as the standard marker for DNA barcoding, with a less frequently used partition further downstream. We report on the finding of significantly different substitution patterns of the downstream partition opposed to the 5′′ partition. We discuss the consequences and potential in the light of diploblast phylogenetic reconstruction and DNA barcoding.
TL;DR: A standardized method for testing the reliability of the genotyping procedure when using the multiple-tube approach is proposed and the quality indexes generated will allow reliable comparisons among samples, loci, studies, and field and/or laboratory protocols.
Abstract: In noninvasive studies, the intersample variance in DNA quality and quantity is large, and produces multilocus genotypes of highly variable quality. Here we propose a standardized method for testing the reliability of the genotyping procedure when using the multiple-tube approach. The quality indexes generated will allow reliable comparisons among samples, loci, studies, and field and/or laboratory protocols. These indexes represent a powerful tool for the quality management of noninvasive studies.
TL;DR: Fap as mentioned in this paper is a DOS-based computer program that calculates exclusion-based family assignment probabilities within family mixtures where all parental genotypes are known, and provides useful aids to identify problematic loci/misscoring during actual assignment.
Abstract: In molecular-based parentage analyses, the accurate prediction of resolving power for a panel of loci is important for the critical assessment of results. A DOS-based computer program, fap (Family Analysis Program), is described that calculates exclusion-based family assignment probabilities within family mixtures where all parental genotypes are known. Three levels of hierarchy can be explored (sample, groups of families, individual families). The package also provides useful aids to identify problematic loci/misscoring during actual assignment. fap is available for free download from http://www.aqua.stir.ac.uk/rep-general/downloads.html.
TL;DR: To increase the effectiveness of microsatellite genotyping of otter faeces, it is recommended collecting samples in cold months and early in the morning, preferably in a frozen state, and the collection of anal jelly samples, or the jelly part from faece, whenever possible.
Abstract: We investigated the effect of multiple variables on the amplification success rate of microsatellite DNA extracted from faeces of wild Eurasian otters. The success rate was affected by (i) type of sample, with higher success rates in anal jelly samples than faeces, and (ii) temperature, with a negative effect of increased temperature at time of collection. To increase the effectiveness of microsatellite genotyping of otter faeces, we recommend collecting samples in cold months and early in the morning, preferably in a frozen state, and the collection of anal jelly samples, or the jelly part from faeces, whenever possible.
TL;DR: A set of 14 polymorphic microsatellite markers for the human malaria parasite Plasmodium vivax, all of them consisting of either tri- or tetranucleotide repeats, are optimized and used to screen 25 parasite isolates from malaria-endemic areas in Sri Lanka.
Abstract: We have optimized a set of 14 polymorphic microsatellite markers for the human malaria parasite Plasmodium vivax, all of them consisting of either tri- or tetranucleotide repeats These markers, whose polymerase chain reaction amplification conditions are identical, were used to screen 25 parasite isolates from malaria-endemic areas in Sri Lanka The total number of alleles per locus ranged between 6 and 13 (average, 78), and expected heterozygosity ranged from 0627 to 0913 (average, 0790) These markers are now being used to characterize the population structure of P vivax in other endemic areas
TL;DR: The genetic variation at 17 microsatellite loci identified in the A. aegypti genome is evaluated in an effort to develop useful markers for the study of the genetics and the population structure of this medically important species.
Abstract: A significant challenge to population genetic studies of the dengue vector, Aedes aegypti, has been the lack of polymorphic microsatellite loci. In an effort to develop useful markers, we evaluated the genetic variation at 17 microsatellite loci identified in the A. aegypti genome. Nine loci with at least five alleles were identified in field-collected specimens from Thailand. An additional two loci carried five alleles if samples from an A. aegypti laboratory colony were included. Our results greatly increase the number of highly variable markers available for the study of the genetics and the population structure of this medically important species.
TL;DR: The exact equations implemented in the program GEODIS for the calculation of the NCA statistics are described, showing how the nested clade analysis methodology works.
Abstract: Nested clade analysis (NCA) is a flexible and powerful method to study the phylogeography of species and populations, implemented in the software GEODIS . Despite the popularity of this method, an explicit description of the exact equations used to compute the NCA statistics has never been published. Given the importance of the methodology and increased interest in exactly how it works, here we describe the exact equations implemented in the program GEODIS for the calculation of these statistics.
TL;DR: The development and characterization of 19 microsatellite primer pairs developed from genomic DNA of European pear (Pyrus communis) and their transferability to other Pyrus and Malus material are reported and transferability of nine primer pairs to Malus was demonstrated.
Abstract: This study reports the development and characterization of 19 microsatellite primer pairs developed from genomic DNA of European pear (Pyrus communis) and their transferability to other Pyrus and Malus material. The primers were designed from two different genomic libraries enriched for di- and trinucleotide repeats. When tested in six P. communis cultivars and 15 other Pyrus species, 13 primers revealed single-locus polymorphism and six showed more complex patterns that suggest multiple loci. Two to 18 alleles were detected per locus and two primer pairs were sufficient to discriminate all accessions. Transferability of nine primer pairs to Malus was demonstrated through amplification of discrete products in two accessions.
TL;DR: Results suggest that stored DNA samples extracted from whole predatory specimens could be an alternative to dissected gut contents as starting source for DNA-based dietary studies.
Abstract: Here, I show that prey sequences can be detected from DNA of tiger beetles of the genus Rivacindela using whole specimens, nondestructive methods, and universal cytochrome b primers for arthropods. BLAST searches of the obtained sequences against public databases revealed that the diet of Rivacindela is mostly composed of flies but also termites and other beetles. Accurate determination of order, family and even genus was achieved in most cases but rarely to species level. Results suggest that stored DNA samples extracted from whole predatory specimens could be an alternative to dissected gut contents as starting source for DNA-based dietary studies.
TL;DR: Most of the novel microsatelllite loci reported are highly polymorphic in Bombus terrestris, and a high degree of polymorphism is also found where these primers have been tested in 10 other bumblebee species.
Abstract: We report the details and characteristics of a total of 44 novel microsatelllite loci for Bombus spp. Most of them are highly polymorphic in Bombus terrestris, and a high degree of polymorphism is also found where these primers have been tested in 10 other bumblebee species. These markers will therefore be useful for the genetic study of this group.
TL;DR: A genomic library enriched for AG/TC repeat sequences was constructed for Phaseolus vulgaris and the results indicate that the new markers can be readily used in genetically analysis of common bean.
Abstract: Efforts to develop molecular tools for genetic analysis and breeding of common bean in the tropics are still limited. The number of microsatellite markers available for the crop is small compared to other crops of similar social and economic importance. As part of a project to broaden the use of molecular tools in bean breeding, a genomic library enriched for AG/TC repeat sequences was constructed for Phaseolus vulgaris. Twenty microsatellite markers were initially developed and 10 were characterized using a panel of 85 representative accessions of the bean gene bank. The number of alleles per marker ranged from three to 10. The polymorphism information content (PIC) varied from 0.23 to 0.80. The results indicate that the new markers can be readily used in genetically analysis of common bean.
TL;DR: Of 93 designed primer pairs, seven were found to amplify polymorphic microsatellite loci, which were then characterized using 34 mung bean accessions and showed significant departure from linkage disequilibrium.
Abstract: The present work reports the isolation and characterization of new polymorphic microsatellites in mung bean (Vigna radiata L.). Of 93 designed primer pairs, seven were found to amplify polymorphic microsatellite loci, which were then characterized using 34 mung bean accessions. The number of alleles ranged from two to five alleles per locus with an average of three alleles. Observed and expected heterozygosity values ranged from 0 to 0.088 and from 0.275 to 0.683, respectively. All seven loci showed significant deviations from Hardy-Weinberg equilibrium, whereas only one pairwise combination (GBssr-MB77 and GBssr-MB91) exhibited significant departure from linkage disequilibrium. These newly developed markers are currently being utilized for diversity assessment within the mung bean germplasm collection of the Korean Gene Bank.
TL;DR: Cross-species tests revealed that all but one of the polymorphic markers are applicable to more than one species, which allows intra- and interspecific genetic studies on, i.e. population structure, hybridization events and introgression.
Abstract: We present 32 polymorphic microsatellite markers for species of the European Daphnia longispina group: D. galeata , D. hyalina , D. rosea , D. cucullata and D. curvirostris . Microsatellite markers were either isolated from genomic libraries or optimized based on previously published sequence information of sister taxa. Cross-species tests revealed that all but one of the polymorphic markers are applicable to more than one species, which allows intra- and interspecific genetic studies on, i.e. population structure, hybridization events and introgression.
TL;DR: Chifish is a 32-bit Windows/DOS program evaluating divergence at multiple gene loci both by means of Pearson's traditional chi-square and by using Fisher's method of combining P values obtained by Fisher's exact test.
Abstract: chifish is a 32-bit Windows/DOS program evaluating divergence at multiple gene loci It tests the hypothesis of no difference at any locus both by means of Pearson's traditional chi-square and by using Fisher's method of combining P values obtained by Fisher's exact test Input data are read from a file formatted for genepop Commonly used population genetics software do not perform chi-square tests, and the simultaneous application of both techniques aids in situations where poor power of the ‘exact approach’ may prevent detection of true differentiation (eg few populations and few alleles per locus)
TL;DR: This methodology, using for the first time these materials as a fish DNA source, combines speed of sampling and processing, with a twofold to a threefold time and costs saving.
Abstract: A rapid, nondestructive, reproducible and cheap DNA extraction method from body mucus and buccal cells of northern pike and brown trout is described. Buccal cells and body mucus were sampled on FTA Cards; the captured DNA was used directly for microsatellite and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analyses. A complete concordance with control DNA was found. The genotyping error rate for microsatellite ranged from 1.9% to 3.3% for the northern pike and brown trout, respectively. This methodology, using for the first time these materials as a fish DNA source, combines speed of sampling and processing, with a twofold to a threefold time and costs saving.