Molecular Ecology Notes

Published by Blackwell Publishing
Online ISSN: 1471-8286
Publications
Article
Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes presents a problem for statistical analysis. Similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. Here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish. The approach is implemented in the program structure version 2.2, which is available from http://pritch.bsd.uchicago.edu/structure.html.
 
Article
There has been a great increase in both the number of population genetic analysis programs and the size of data sets being studied with them. Since the file formats required by the most popular and useful programs are variable, automated reformatting or conversion between them is desirable. formatomatic is an easy to use program that can read allelic data files in genepop, raw (csv) or convert formats and create data files in nine formats: raw (csv), arlequin, genepop, immanc/bayesass +, migrate, newhybrids, msvar, baps and structure. Use of formatomatic should greatly reduce time spent reformatting data sets and avoid unnecessary errors.
 
Article
DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap support of 98%. In the remaining 6%, barcode clusters correspond to small sets of closely related species, most of which hybridize regularly. Fifteen (2%) currently recognized species are comprised of two distinct barcode clusters, many of which may represent cryptic species. Intraspecific variation is weakly related to census population size and species age. This study confirms that DNA barcoding can be effectively applied across the geographical and taxonomic expanse of North American birds. The consistent finding of constrained intraspecific mitochondrial variation in this large assemblage of species supports the emerging view that selective sweeps limit mitochondrial diversity.
 
Article
DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences - of various lengths - and we have monitored the effect of reducing sequence length on the utility of the data for both species identification and phylogenetic reconstruction. Our results demonstrate that reducing sequence length has a profound effect on the accuracy of resulting phylogenetic trees, but surprisingly short sequences still yield accurate species identifications. We conclude that the standard short barcode sequences ( approximately 600 bp) are not suitable for inferring accurate phylogenetic relationships, but they are sufficient for species identification among the fungi.
 
Article
We describe 11 microsatellite loci isolated from the Banded Wren (Thryothorus pleurostictus), a Neotropical species for which understanding the genetic mating system is important for testing questions about the species' unusual vocal behavior. Screening of these loci revealed extremely low allelic variation in a Costa Rican population. Allelic variation at these and other previously developed loci is substantially higher in two other wren species, the southern house wren (Troglodytes aedon bonariae) and rufous-and-white wren (Thryothorus rufalbus), suggesting that the low allelic diversity in the banded wren results from demographic bottlenecks rather than locus-sampling artifacts.
 
Article
The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.
 
Article
Trypanosoma brucei, unicellular parasites causing human sleeping sickness and animal nagana, have a great impact on the socio-economic environment of sub-Saharan Africa. The dynamics of the parasite are still poorly understood. We have characterized 14 polymorphic di-, tri-, and tetranucleotide microsatellite loci with perfect repeats (only one motif) exhibiting between 5 and 16 alleles in T. brucei isolates from all over Africa and from all described subspecies. The microsatellites will be useful in addressing population genetic questions in T. brucei to better understand the population structure and spread of this important parasite.
 
Genetic variability in Glossina taxa estimated by using primers derived from G. pallidipes Locus Taxa N No. of alleles Size (bp) H O H E F IS H-W (P-value) 
Article
Glossina pallidipes is a vector of African trypanosomiasis. Here we characterize eight new polymorphic microsatellite loci in 288 G. pallidipes sampled from 12 Kenya populations. The number of alleles per locus ranged from four to 36 with a mean of 20.5 +/- 10.1. Expected single locus heterozygosities varied from 0.044 to 0.829. Heterozygosity averaged 0.616 +/- 0.246. No linkage disequilibrium was found. We also report results in eight other tsetse species estimated by using the primers developed in G. pallidipes. The primers worked best in G. swynnertoni and G. austeni and worst in G. m. morsitans and G. m. submorsitans.
 
Article
Genomic libraries enriched for simple sequence repeats were constructed for Glossina morsitans morsitans, G. m. submorsitans, and G. m. centralis. Sixteen microsatellite markers were isolated from the libraries and evaluated on flies from natural G. m. morsitans populations and other Glossina species in the Morsitans and Palpalis species groups. The primers amplified appropriate sized DNA fragments in the Morsitans and Palpalis groups. In G. morsitans s.l., eight of 12 dinucleotide repeats and four of 12 trinucleotide repeats were polymorphic. The polymorphic loci showed a mean 7.5 +/- 4.8 alleles per locus and their mean heterozygosity was 55.8 +/- 7.7%.
 
Article
For eukaryotic pathogens that are depauperate in genetic variation, multilocus microsatellite typing (MLMT) offers an accurate and reproducible method of characterizing genetic diversity; herein we describe the development of an MLMT system for the emerging pathogenic fungus Penicillium marneffei based on 23 microsatellite loci. Screening isolates held within the Centraalbureau voor Schimmelcultures culture collection demonstrate high levels of genetic diversity and 100% reproducibility. This MLMT system provides a powerful epidemiological tool to analyse the underlying parameters that are responsible for the emergence of P. marneffei in human HIV-positive populations.
 
Article
Estimating effective population size is an important issue in population and conservation genetics. Recently, we proposed a new method to infer effective size and migration rate from one- and two-locus identity probability measures. We now announce the release of a user-friendly Microsoft® Windows program that uses this method to provide joint estimates of local effective population size and immigration rate for each subpopulation in a population genetics data set.
 
Article
trees sifter 1.0 implements an approximate method to estimate the time to the most recent common ancestor (TMRCA) of a set of DNA sequences, using population evolution modelling. In essence, the program simulates genealogies with a user-defined model of coalescence of lineages, and then compares each simulated genealogy to the genealogy inferred from the real data, through two summary statistics: (i) the number of mutations on the genealogy (Mn), and (ii) the number of different sequence types (alleles) observed (Kn). The simulated genealogies are then submitted to a rejection algorithm that keeps only those that are the most likely to have generated the observed sequence data. At the end of the process, the accepted genealogies can be used to estimate the posterior probability distribution of the TMRCA.
 
Article
We present the program spip for simulating multilocus genetic data on individuals in age-structured populations. In addition to genetic data on sampled individuals, the pedigree connecting all individuals in the population is recorded. This allows investigation of the relationship between family structure and population parameters. We foresee that spip will be useful for evaluating multilocus estimators of pairwise relatedness and population structure, and for simulating the distribution of relatedness in populations with varying demographies. It also provides a method for simulating genetic drift in complex populations.
 
Article
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.
 
Article
metasim provides a flexible environment in which to perform individual-based population genetic simulations. A wide range of landscape-level dynamics, population structures, and within-population demographies can be represented using the framework implemented in this software. In addition, temporal variation in all demographic characteristics can be simulated, both deterministically and stochastically. Such simulations can be used to produce null distributions of genotypes under realistic conditions. These genotypic data can then be used by a variety of analytical programs to develop null expectations of any population genetic statistic estimated from genotypic data.
 
Article
champuru is an interactive, user-friendly web software that facilitates the deconvolution of mixed chromatograms obtained when sequencing directly mixtures of two DNA templates of unequal lengths. The program takes as input two strings of characters describing the forward and reverse chromatograms as obtained by direct sequencing and returns, most often after several iterations aimed at correcting basecalling errors, the sequences of the two templates present in the mixture. champuru was written in perl, with a web interface accessible online at http://134.157.186.185/champuru/champuru.htm.
 
Article
The number of alleles in a sample (allelic richness) is a fundamental measure of genetic diversity. However, this diversity measure has been difficult to use because large samples are expected to contain more alleles than small samples. The statistical technique of rarefaction compensates for this sampling disparity. Here I introduce a computer program that performs rarefaction on private alleles and hierarchical sampling designs.
 
Article
We have isolated 102 polymorphic microsatellite loci from an enriched Murray cod DNA library and also assessed their amplification success in 13 native and six introduced freshwater fish species. The loci will serve the dual purpose of assessing wild population genetic structure for future conservation efforts, and for identifying markers for key quantitative trait loci important for aquaculture.
 
Article
Amplification of 105 Lolium perenne SSR markers was studied in 23 grass species representing seven tribes from three subfamilies of Poaceae. Twelve of the SSR markers are published for the first time. Between 2% and 96% of the SSR markers could be amplified within a given species. A subset of eight SSR markers was evaluated for polymorphism across nine of the 23 grass species. Four to seven of the markers were polymorphic within each species, with an average detection of 2.4 alleles per species.
 
Article
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.
 
Article
Eleven microsatellite loci derived from the genomic sequence data of Capitella capitata were characterized using 30 samples. The observed number of alleles per locus ranged from four to 36. The levels of observed and expected heterozygosities for polymorphic loci were from 0.10 to 0.87 and from 0.37 to 0.98, averaging 0.52 and 0.77, respectively. Analyses of Hardy–Weinberg equilibrium and genotypic linkage disequilibrium suggest the possible presence of both null alleles and Wahlund effect. One of the 11 loci was difficult to amplify for genotyping. Therefore, the rest 10 loci are good molecular markers for population genetic analysis.
 
Article
Because of its long-lived planktonic stage, the marine gastropod Concholepas concholepas is expected to exchange larvae over large distances. However, discrepancies between expected and realized dispersal have been documented in marine invertebrates. To investigate relationships between potential and effective (i.e. gene flow) dispersal, we developed 11 microsatellite markers and investigate their usefulness by analysing two populations distant by c. 4000 km. The 11 loci were found to be highly polymorphic in both populations, with 12–51 alleles according to the locus. This polymorphism is strong enough to allow fine-scale population analyses including larval studies and paternity analyses.
 
Article
Eleven polymorphic tetranucleotide microsatellite loci have been developed for forensic use in the protection of California elk. Based on a reference sample of elk taken from three races throughout California, the loci consist of 4–9 alleles (average 6.125). Probabilities of identity (Paetkau et al. 1995) range from 0.079 to 0.288, with an overall probability of identity of 1.3 × 10−9 (one in 7.8 × 108).
 
Article
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.
 
Article
Eleven microsatellite loci were developed in the swordfish, Xiphias gladius, to examine population structure. Loci were amplified in samples from two geographically distant populations (Ecuador and Mediterranean Sea). Observed heterozygosity ranged from 0.150 to 0.960. Most loci conformed to Hardy–Weinberg expectations with the exception of locus Xg-59, which had a heterozygote deficit caused probably by null alleles. Locus Xg-402 did not show significant divergence between the populations. The remaining nine loci showed statistically significant spatial heterogeneity (genic differentiation) between the two populations, making them useful for future studies of population structure in swordfish.
 
Article
Microsatellite loci were developed for the giant white-tailed rat (Uromys caudimaculatus) to aid in assigning paternity and to subsequently investigate their mating system and sex-biased dispersal characteristics. Twenty-two primer sets were originally developed and of these, 11 were polymorphic with between five and 10 alleles per locus. In addition, two primer sets designed for Hydromys chyrsogaster also amplified in this species despite an evolutionary divergence of 15 million years (Myr).
 
Article
Eleven dinucleotide microsatellites were developed in Geoffroea spinosa (Leguminosae), a widespread tree of the seasonally dry Neotropical forests, and characterized on six populations from Peru, Argentina and Paraguay. Four of them amplified on the Peruvian populations only, probably because of mutations in the microsatellite flanking regions in the other populations. Ten microsatellites were found polymorphic, with within population gene diversities ranging from 0.17 to 0.95, and a number of alleles varying from seven to 19. A significant overall genetic differentiation was also found (θ = 0.212; P < 0.01).
 
Article
We identified 11 polymorphic microsatellite loci in collared lizards (Crotaphytus collaris). Polymorphism assessment in 512 individuals from 52 populations sampled across much of the species distribution revealed a fairly high degree of genetic diversity (six to 20 alleles per locus) and a wide range of average expected heterozygosity values (0.143–0.530). We found no evidence for linkage, very few deviations from HW expectation (two of 572 possible population/locus analyses) and thus no evidence for null alleles. There was a tendency for reduced polymorphism towards the northern periphery.
 
Article
In birds, feathers and faeces can be used as a source of DNA for genetic analyses. If the materials are derived from an absentee bird(s), however, the species must first be identified. Here, we developed four pairs of primers for amplification of mitochondrial 12S ribosomal RNA fragments in the black woodpecker Dryocopus martius, a vulnerable species in Japan, and three other sympatric woodpeckers including Dendrocopos leucotos, D. major and Picus awokera. Because each primer pair gave a PCR product in only one of the examined species, these primer sets will be useful in identifying the species of woodpeckers.
 
Article
We report the characterization of 13 single nucleotide polymorphism (SNP) genotyping assays for chum salmon (Oncorhynchus keta). These assays are based on the 5′-nuclease reaction and thus facilitate high-throughput genotyping with minimal optimization time. Because data generated using these markers may be transported and combined across laboratories, SNPs offer the potential to reduce the amount of redundant work being done in mixture and migratory studies of chum salmon.
 
Article
We developed 13 microsatellite markers from a genomic library enriched for dinucleotide (CT) repeats in a dioecious evergreen tree, Myrica rubra. We screened loci from 32 adult trees. The number of alleles ranged from two to 14, and the expected heterozygosity ranged from 0.324 to 0.884. The total paternity exclusionary power where the mother was known equalled 0.99965. These loci are of clear value in studying mating system and parentage analysis of this species.
 
Article
Here we describe 13 polymorphic, dinucleotide microsatellite loci for Trachinotus carolinus (Florida pompano), isolated by using PIMA, a polymerase chain reaction-based technique. The number of alleles at each locus ranged from 3 to 29 (mean = 11.4) in 45 specimens collected from bay and nearshore waters around St Petersburg, Florida. Levels of expected and observed heterozygosities ranged from 0.15 to 0.94 (mean = 0.69) and from 0.16 to 0.98 (mean = 0.70), respectively. No significant departures from Hardy–Weinberg equilibrium expectations were observed. In exact tests for genotypic disequilibrium, there was no evidence of linkage for any pair of loci. The ability of these markers to cross-amplify in two congeneric Trachinotus species —T. falcatus (permit) and T. goodei (palometa) — was also assessed. The loci were well-resolved, highly polymorphic, and independently segregating in these taxa, also suggesting a general utility for intraspecific studies, species identification, and investigation of interspecific hybridization.
 
Article
Thirteen polymorphic microsatellite loci were isolated and characterized from the clam shrimp Eulimnadia texana. In analyses of 20–50 individuals from two populations the number of alleles ranged from two to seven with observed heterozygosity ranging between 0.00 and 0.37. The low values for heterozygosity were not unexpected for a group characterized by its unusual androdioecious mating system, in which males compete with self-compatible hermaphrodites for offspring production. These microsatellites are likely to be useful for further evolutionary investigations of this rare mating system in these crustaceans.
 
Article
In order to complement ecological information with genetic data we isolated and characterized 14 polymorphic microsatellite markers from raccoons (Procyon lotor). Three multiplexed panels comprising the loci were developed and 29 individuals from a contiguous habitat patch in northern Indiana, USA were genotyped. The number of alleles per locus ranged from four to 18, and overall heterozygosities ranged from 0.31 to 1.00. One locus was identified as possibly being X-linked, since males appeared to be hemizygous. Data generated using these markers will be used to further our understanding of small-scale raccoon population dynamics in a highly fragmented landscape.
 
Article
Zostera marina, the dominant seagrass on the Northern Hemisphere, forms the basis of important but threatened marine ecosystems. Here, we report 14 microsatellite DNA markers derived from an expressed sequence tag library corresponding to a wide range of genes. All loci were moderately to highly polymorphic, with allele numbers ranging from three to eight in a single Wadden Sea population of 48 individuals. Observed heterozygosities ranged from 0.082 to 0.837. Reaction conditions for five pooled polymerase chain reactions are given. The markers will advance the population genetics of seagrasses because they allow indirect tests of selection on closely linked genes.
 
Article
Fourteen nuclear microsatellite loci were isolated from a genomic DNA library derived from a free-ranging bamboo lemur (Hapalemur griseus griseus) from Ranomafana National Park, Madagascar. Expected and observed heterozygosity levels were determined for populations of bamboo lemurs from Ranomafana National Park and a nonprotected area near Tsinjoarivo, Madagascar. Although genotype frequencies for all but one marker were within Hardy–Weinberg expectations for the Tsinjoarivo population, this was not the case for the Ranomafana samples. It is probable that the deviation of genotype frequencies from Hardy–Weinberg expectations in Ranomafana was precipitated by the presence of two taxa within the sample population.
 
Article
We report the development of 14 polymorphic microsatellite markers for the black-tailed prairie dog, Cynomys ludovicianus. The number of alleles per locus ranges from three to 11, and the observed heterozygosity ranges from 0.37500 to 1.0000. These markers will benefit studies of landscape effects on prairie dog migration, disease dynamics, and conservation efforts.
 
Representative cumulative allele length distributions. (a) Pattern obtained from a standard locus (d7s798) showing a clear, discrete allele size distribution; (b) one of the worst cases found (locus d7s2465), showing indistinct allele size classes where even manual binning would struggle to identify allele class boundaries. Alternate allele classes as inferred are shown in contrasting colours.
Frequency distribution of effective repeat sizes obtained for 276 human autosomal dinucleotide markers.
Relationship between mean allele length (bp) and standard deviation summarized over 276 autosomal markers showing that the majority of alleles have a low standard deviation (< 0.4) making misclassification unlikely.
Article
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.
 
Article
Spawning aggregations of Pacific herring (Clupea pallasi) often exhibit significant interannual variation in allele frequencies of neutral gene markers. We isolated 14 tetranucleotide microsatellites to examine hypothetical processes that may produce this unique genetic signal. We developed and tested primer pairs for each locus and then estimated locus variability in samples (n = 60) from two populations. The number of alleles per locus ranged from five to 49. The expected heterozygosity across loci and populations ranged from 0.20 to 0.96. These microsatellites will be useful for estimating genetic variation in herring on a fine geographical scale.
 
Article
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.
 
Article
Discrete and commercially important patches of weathervane scallops (Patinopecten caurinus) are found in the northeastern Pacific Ocean. Little is known about weathervane scallop life history and population structure, but the species is vulnerable to overexploitation because of their large size and long lifespan. Here we describe 16 polymorphic microsatellite loci developed to study the relatedness of these discrete patches. All loci were polymorphic in the 32 individuals tested; the number of alleles range from four to 26 and heterozygosities ranged from 0.437 to 1.000.
 
Article
Sixteen polymorphic microsatellite markers with an average allele size of k = 4.3 are identified from a genomic plasmid library constructed for giraffe (Giraffa camelopardalis ssp.). Primer sequences and marker data are reported in tabular form. The markers were screened in a population of 25 Maasai giraffe (G. c. tippelskirchi) collected near the Athi River, Kenya. The average observed heterozygosity for each marker was 0.36 with an average expected heterozygosity of 0.535. Hardy–Weinberg deviations are reported from this population, which is suspected to be inbred. The markers will be used to screen the captive giraffe population for subspecific or hybrid classification.
 
Article
We developed 16 pairs of primers for microsatellite loci of the fierce shrimpgoby, Ctenogobiops feroculus. Analysis of 35–40 gobies per locus from five islands in French Polynesia indicated that allele frequency varied from two to 30 per locus, while observed heterozygosity ranged between 0.05 and 0.98. These microsatellites should provide insight into patterns of dispersal and connectivity among populations of this common coral reef fish.
 
Article
We describe the isolation and development of 16 polymorphic tetranucleotide microsatellite loci for the endangered Oregon chub (Oregonichthys crameri). Two loci appear to be duplicated. For the remaining 14 loci, we observed between three and 19 alleles per locus in a sample of 42 fish. Thirteen of these loci were also polymorphic in the closely related Umpqua chub (O. kalawatseti). These loci will aid in our understanding of the molecular ecology and conservation of these two species.
 
Article
A total of 15 polymorphic tetranucleotide microsatellite loci in the red panda, Ailurus fulgens, were characterized in this study. Based on evaluations of 33 red pandas, the number of observed alleles for each locus ranged from seven to 17 and the expected and observed heterozygosities were 0.412–0.897 and 0.121–0.909, respectively. The mean polymorphic information content was 0.721. These markers would greatly strengthen the utilization of microsatellite tools in genetic variation studies in red panda populations.
 
Article
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.
 
Article
Through multiple alignment analysis of 16S rDNA sequences from all known genera of Cytophaga–Flavobacteria (CF) cluster, a new primer pair specifically targeting this cluster was developed, greatly facilitating their diversity and function's exploration in marine ecosystems. Compared with previously reported primers, the new primer pair could theoretically retrieve broader CF diversity without decreasing specificity. The effectiveness for field samples was further evaluated by testing the community DNA samples from various marine environments using the optimal polymerase chain reaction (PCR) conditions established in this work. The results showed its robustness and high specificity for amplifying CF cluster's 16S rDNA fragments from complex marine environments.
 
Article
Molecular environmental sampling of the phototrophic complexity in a given environment may be important in a number of research disciplines. Because of the broad evolutionary diversity of photosynthetic organisms, however, primers that can recover sequences from all phototrophs also target other organisms, often preferentially. Therefore, PCR primers that selectively amplify genes of phototrophs over those of other prokaryotic and eukaryotic organisms could prove extremely useful. Here we report two such primers that target 16S rDNA from Cyanobacteria and eukaryotic plastids, but do not amplify genes from abundant Bacteria in a mixed sample.
 
Article
Fifteen polymorphic dinucleotide and two trinucleotide microsatellite loci were identified in the Anise swallowtail, Papilio zelicaon, from DNA genomic libraries enriched for simple sequence repeats. Allele numbers varied from eight to 29, with an excess of homozygotes observed for nine loci. This homozygosity is a feature of other lepidopteran microsatellites and is probably due to null alleles. Sixteen markers were amplified successfully in other representatives of Papilio with 11 loci retaining polymorphism in at least one species. These results suggest that the microsatellites reported here may be appropriate for measuring population genetic structure in a number of Papilio species.
 
Article
We describe the isolation and characterization of 17 polymorphic microsatellite loci for the ember parrotfish Scarus rubrioviolaceus. In a Hawaiian sample of 69 fish, we found between three and 20 alleles per locus, and observed heterozygosity ranging from 0.283 to 0.896. Four of these loci consistently cross-amplified in the stareye parrotfish Calotomus carolinus, the spectacled parrotfish Chlorurus perspicillatus, the palenose parrotfish Scarus psittacus, and the bullethead parrotfish Chlorurus sordidus, but others gave mixed results. These loci will be useful for describing mating systems and population structure in marine species with broad dispersal potential that play key ecological roles in tropical environments.
 
Top-cited authors
Rod Peakall
  • Australian National University
Paul D N Hebert
  • University of Guelph
Keith A. Crandall
  • George Washington University
David Posada
  • University of Vigo
Mark Clement
  • Brigham Young University - Provo Main Campus