Showing papers in "Molecular Ecology Notes in 2001"
TL;DR: This paper presents a modification of IA that removes this dependency on sample size and has been implemented in a software package.
Abstract: Linkage disequilibrium is an ubiquitous biological phenomenon. However a common metric for disequilibrium – the index of association or IA– is dependent on sample size. In this paper we present a modification of IA that removes this dependency. This method has been implemented in a software package.
1,028 citations
TL;DR: The authors describe the isolation, the polymerase chain reaction conditions, and characterize the cross-species amplification of 17 microsatellite loci in six species of salmonids, finding 14 of these loci are polymorphic in fall-run chinook from the San Joaquin River drainage.
Abstract: Previous studies of population genetic structure of fall-run chinook salmon ( Oncorhynchus tshawytscha ) in California’s Central Valley have either not focused on or have been unable to resolve intertributary differences within the San Joaquin River basin The authors describe the isolation, the polymerase chain reaction conditions, and characterize the cross-species amplification of 17 microsatellite loci in six species of salmonids Fourteen of these loci are polymorphic in fall-run chinook from the San Joaquin River drainage These results indicate the potential utility of microsatellite markers developed for one species, for both congenerics and species within a closely related genus
163 citations
TL;DR: 20 conserved cpDNA primer pairs that, in combination with 18 previously described ones, amplify overlapping fragments spanning the large single copy (LSC) region from Eudicots are designed.
Abstract: Conserved chloroplast (cp) DNA primer pairs are useful in plant molecular genetics, evolution and ecology. We have designed 20 conserved cpDNA primer pairs that, in combination with 18 previously described ones, amplify overlapping fragments (mean size of 2.5 kb) spanning the large single copy (LSC) region from Eudicots. These 38 primer pairs as well as eight primer pairs flanking cpDNA microsatellites were tested on 20 plant species belonging to 13 families. At least 79% and up to 100% of the LSC (> 86 kb) can be amplified. Many primer pairs are robust and work with all species.
157 citations
TL;DR: Using an enrichment procedure, cloned microsatellites from black poplar (Populus nigra L.) and developed primers for microsatellite marker analysis and produced primer pairs, mostly for trinucleotide repeats, produced polymorphic fragments in P. nigra.
Abstract: Using an enrichment procedure, we have cloned microsatellite repeats from black poplar (Populus nigra L.) and developed primers for microsatellite marker analysis. Ten primer pairs, mostly for trinucleotide repeats, produced polymorphic fragments in P. nigra. Some of them also showed amplification in other poplar species. (P. deltoides, P. tricocarpa, P. tremula, P. tremuloides, P. candicans, P. lasiocarpa). The best six loci were tested on 23 P. nigra genotypes collected across Europe. The microsatellites produced up to 12 alleles per locus in this set, with observed heterozygosity between 0.32 and 0.91.
145 citations
TL;DR: Thirteen polymorphic microsatellite loci were developed in the Japanese pear by using an enriched genomic library and showed a high degree of polymorphism with 3–6 alleles per locus.
Abstract: Thirteen polymorphic microsatellite loci were developed in the Japanese pear (Pyrus pyrifolia Nakai) by using an enriched genomic library. The obtained microsatellite loci showed a high degree of polymorphism in the Japanese pear with 3–6 alleles per locus. The average values of observed and expected heterozygosities among these 13 loci were 0.69 and 0.71, respectively. Ten microsatellites could successfully amplify loci in the European pear (Pyrus communis L.), which were highly polymorphic as well.
139 citations
TL;DR: The potential difficulties caused by a polymorphism such as that identified in auklets are discussed and the merits of alternative CHD -based sexing protocols and primers are discussed.
Abstract: The sexes of non-ratite birds can be determined routinely by PCR amplification of the CHD-Z and CHD-W genes.
CHD -based molecular sexing of four species of auklets revealed the presence of a polymorphism in the Z chromosome. No deviation from a 1:1 sex ratio was observed among the chicks, though the analyses were of limited power. Polymorphism in the CHD-Z
gene has not been reported previously in any bird, but if undetected it could lead to the incorrect assignment of sex. We discuss the potential difficulties caused by a
polymorphism such as that identified in auklets and the merits of alternative CHD -based sexing protocols and primers.
120 citations
TL;DR: The cloning and characterization of five highly polymorphic microsatellite loci cloned from aduncus dolphins from Western Australia are described, and it is found that these markers are likely to be useful in a number of cetacean population studies.
Abstract: We describe the cloning and characterization of five highly polymorphic microsatellite loci cloned from aduncus dolphins (Tursiops aduncus) from Western Australia. Five polymorphic microsatellite loci were isolated and tested on up to 350 animals, showing 7–23 alleles and expected heterozygosity values from 0.68 to 0.89. We also tested the loci on striped dolphins and franciscana dolphins, where we also found high levels of polymorphism (9–16 alleles in 102 striped, and 4–5 alleles in 13 franciscana dolphins). Considering that the cetacean genome is highly conserved, the characterized markers are likely to be useful in a number of cetacean population studies.
113 citations
TL;DR: A computer program is presented that uses the multilocus genotypes of parents and offspring to reconstruct the genotype of unknown parents contributing gametes to a progeny array for which one parent is known a priori.
Abstract: We have no standard computer algorithm for the reconstruction of parental genotypes from the data generated by molecular studies of progeny arrays. Here I present a computer program that uses the multilocus genotypes of parents and offspring to reconstruct the genotypes of unknown parents contributing gametes to a progeny array for which one parent is known a priori . A second program performs simulations to assess the reliability of the algorithm under various scenarios. These programs will aid scientists engaged in parentage analyses, particularly in species with large clutches.
112 citations
TL;DR: The resolving power of agarose gels is poor relative to that provided by sequencing gels and double priming ISSR is an easy and informative genetic marker system in cotton for revealing both inter- and intraspecific variations.
Abstract: We studied the applicability of intersimple sequence repeat (ISSR) polymorphism in cotton. We found that: (i) the resolving power of agarose gels is poor relative to that provided by sequencing gels; (ii) fluorescent labelling of ISSR amplification primers produced numerous scorable bands; (iii) primer mixing (double priming) generated more bands than the sum of fragments resulting from two single primers, although an unexplained disappearance of several larger fragments also reproducibly occurred; (iv) ISSR fingerprinting patterns are highly heritable; and (v) double priming ISSR is an easy and informative genetic marker system in cotton for revealing both inter- and intraspecific variations.
107 citations
TL;DR: Twenty-five primers produced unambiguous amplification products of 23 microsatellite-containing loci and two micros Satellite-like polymorphic loci, with 2–10 alleles at each locus in the plant pathogenic fungus, Sclerotinia sclerotiorum, facilitating epidemiological monitoring worldwide.
Abstract: Twenty-five primers produced unambiguous amplification products of 23 microsatellite-containing loci and two microsatellite-like polymorphic loci, with 2–10 alleles at each locus in the plant pathogenic fungus, Sclerotinia sclerotiorum. Haplotypes are polymorphic among individuals sharing the same DNA fingerprint and DNA sequence haplotype, facilitating epidemiological monitoring worldwide. Fourteen of these primers also successfully amplified the closely related S. trifoliorum and S. minor.
100 citations
TL;DR: Six microsatellite loci in the song sparrow, Melospiza melodia, their amplification in related species and problems encountered in genotyping from high quality DNA are described.
Abstract: We describe the isolation, development and application of six microsatellite loci in the song sparrow, Melospiza melodia, their amplification in related species and problems encountered in genotyping from high quality DNA. Heterozygosity in an island song sparrow population was high (> 70%) for five out of six loci. Small scale cross-species amplification showed up to three alleles per locus for other Emberizidae. Relatively high levels of allelic dropout were observed with two loci when using standard template DNA. These problems could be partially alleviated by diluting template DNA, and could always be eliminated by repeated genotyping.
TL;DR: Ten GATA microsatellite DNA markers were isolated and characterized from black grouse (Tetrao tetrix) using an enrichment cloning procedure, indicating these markers will be useful for examining parentage, inbreeding and population structure inblack grouse.
Abstract: Ten GATA microsatellite DNA markers were isolated and characterized from black grouse (Tetrao tetrix) using an enrichment cloning procedure. High levels of heterozygosity (mean HO = 0.74 ± 0.026), and a large number of alleles (range = 5–16) were resolved in 70 individuals, indicating these markers will be useful for examining parentage, inbreeding and population structure in black grouse. No evidence for linkage disequilibrium or the presence of null alleles was found.
TL;DR: The sequences of 21 primer pairs of microsatellite loci screened from a genomic library of apricot (Prunus armeniaca L.) are reported and showed to be more informative than isozymes and restriction fragment length polymorphisms (RFLPs) reported in the literature.
Abstract: The sequences of 21 primer pairs of microsatellite loci screened from a genomic library of apricot (Prunus armeniaca L.) are reported in this study. All the identified microsatellite loci were characterized in a set of 25 apricot cultivars and revealed to be polymorphic with 3–12 alleles per locus. These markers showed to be more informative than isozymes and restriction fragment length polymorphisms (RFLPs) reported in the literature.
TL;DR: Except for one microsatellite locus, the observed heterozygosity was higher than the expected value and gave amplification products in 17 other Ficus species in 86% of the cases.
Abstract: We developed microsatellites in fig ( Ficus carica L.) . A TC and TG-enriched genomic library was screened, and after sequencing, primers were designed for 20 microsatellites. Eight primer pairs produced amplification products that were both interpretable and polymorphic in 14 fig cultivars and two French wild-growing populations of F. carica ( n 1 = 9 and n 2 = 10). Number of alleles per locus ranged from three to six. Except for one microsatellite locus, the observed heterozygosity was higher than the expected value. The F. carica microsatellites gave amplification products in 17 other Ficus species in 86% of the cases.
TL;DR: A set of 10 simple sequence repeat markers have been developed, which exhibit polymorphism across a range of pigeonpea varieties, which offers an efficient system for the assessment of genetic diversity within populations of pigeon pea.
Abstract: Pigeonpea (Cajanus cajan) is an important subsistence crop in India where traditional landraces and improved hybrids are grown alongside each other. Gene flow may result in genetic erosion of these landraces and their wild relatives, whilst transgene escape from future genetically engineered varieties is another potential hazard. To assess the impact of these factors gene flow needs to be measured. A set of 10 simple sequence repeat markers have been developed, which exhibit polymorphism across a range of pigeonpea varieties. Use of these markers also offers an efficient system for the assessment of genetic diversity within populations of pigeonpea.
TL;DR: Twelve primer pairs, which amplify noncoding regions of chloroplast DNA, were designed for grass species and the majority showed intraspecific variation.
Abstract: Twelve primer pairs, which amplify noncoding regions of chloroplast DNA, were designed for grass species. Their universality was tested on the six major grass subfamilies, and several were sequenced to examine their variability in Phragmites australis. The primers amplified well for most species tested and the majority showed intraspecific variation.
TL;DR: A rapid and simple method is proposed to discriminate the three species in processing field-collected biopsies as well as ethanol-preserved museum samples.
Abstract: The woodmouse (Apodemus sylvaticus) and yellow-necked fieldmouse (Apodemus flavicollis) are sympatric and even syntopic in many regions throughout their European range. Their field discrimination on the basis of external characters is a real challenge for many fields of research. The problem is even more complicated in the Alpine chain where they live sympatrically with a third similar species: A. alpicola. A rapid and simple method is proposed to discriminate the three species in processing field-collected biopsies as well as ethanol-preserved museum samples.
TL;DR: A simple approach is described, using ‘double peaks’ in the chromatogram upon direct sequencing of PCR products from males, to identify Y-specific restriction sites, and its utility is demonstrated by application to a range of taxa.
Abstract: Mammals can be molecular sexed by polymerase chain reaction (PCR) amplification of Y chromosome fragments or coamplification of homologous fragments from both sex chromosomes, which are discriminated by size polymorphism or Y-specific restriction digestion. Although coamplification of X and Y fragments is more reliable, size polymorphism in homologous fragments is uncommon and Y-specific restriction site identification requires screening with a battery of enzymes or cloning. Here we describe a simple approach, using ‘double peaks’ in the chromatogram upon direct sequencing of PCR products from males, to identify Y-specific restriction sites, and demonstrate its utility by application to a range of taxa.
TL;DR: This pilot study demonstrates the use of dolphin faeces in multilocus microsatellite genotyping studies of free-ranging mammals, with positive results for both captive and wild bottlenose dolphins.
Abstract: Noninvasive samples have proved useful in genotyping studies of free-ranging mammals. However, potential genotyping errors associated with such samples dictate the need for validation studies. This pilot study demonstrates the use of dolphin faeces in multilocus microsatellite genotyping studies. An empirical approach to calculating the rate of genotyping error was applied to data from matched pairs of blood or tissue and faecal samples from both captive and wild bottlenose dolphins. Microsatellite genotypes were assigned to dolphin faecal extracts with greater than 95% confidence by using a multiple tube approach, and at least two independent replicate genotypings.
TL;DR: Cross-specific amplifications suggests that some of these microsatellites may be used in other tetraonids and, to a lesser extent, in some other phylogenetically more distant galliforms.
Abstract: We isolated eight microsatellite loci in the black grouse (Tetraonidae). Polymorphism ranged from 2 to 15 alleles (48 individuals from the same locality examined). Cross-specific amplifications suggests that some of these microsatellites may be used in other tetraonids and, to a lesser extent, in some other phylogenetically more distant galliforms.
TL;DR: High polymorphism makes these new markers interesting for use in genotyping studies and completing the set of microsatellite markers already available for V. vinifera.
Abstract: We present here characterization data for seven new microsatellite markers designed from new microsatellite loci isolated from a microsatellite-enriched DNA library from Vitis vinifera. The observed heterozygosity varied from 0.73 up to 0.93 and the number of alleles per locus ranged from 12 to 26. This high polymorphism makes these new markers interesting for use in genotyping studies and completing the set of microsatellite markers already available for V. vinifera. Additionally these seven new markers appear to be conserved in four other Vitis species and 15 Vitis hybrids used as rootstocks for V. vinifera cultivation.
TL;DR: A battery of 18 highly polymorphic microsatellite markers was developed from an enriched genomic library that allow extremely precise paternity testing, estimation of gene flow and of parentage coefficients among trees in the wild.
Abstract: Euterpe edulis is the species of palm found in the Atlantic Forest and Cerrado gallery forest that yields the best heart of palm. A battery of 18 highly polymorphic microsatellite markers was developed from an enriched genomic library. Using fluorescence automated detection an average of 10.6 alleles per locus were found on a sample of 66 individuals sampled from a natural population. These loci allow extremely precise paternity testing, estimation of gene flow and of parentage coefficients among trees in the wild.
TL;DR: Nine of 10 microsatellite loci were found to be polymorphic amongst 20 unrelated T. carbonaria workers, with observed heterozygosity estimates ranging from 0.168 to 0.800.
Abstract: Microsatellite loci were isolated from Trigona carbonaria (family Apidae; tribe Meliponini), a stingless bee endemic to Australia, following the screening of a partial genomic library with several simple-repeat oligonucleotide probes. Polymerase chain reaction (PCR) primers were designed to DNA sequence flanking a selection of trinucleotide and dinucleotide repeat sequences within positive clones. Nine of 10 microsatellite loci were found to be polymorphic amongst 20 unrelated T. carbonaria workers, with observed heterozygosity estimates ranging from 0.168 to 0.800. For many of the primers, distinct polymorphic products were also amplified when used in reactions with DNA from a selection of other bee species.
TL;DR: Eight microsatellite loci of the invasive weed Rubus alceifolius were characterized and proved to be highly polymorphic in Asian natural populations, and could be used to compare the reproductive biology of this weed between its native range and its areas of introduction.
Abstract: This study characterized eight microsatellite loci of the invasive weed Rubus alceifolius , and represents the first microsatellite markers published for any Rubus species. They proved to be highly polymorphic in Asian natural populations, and could be used to compare the reproductive biology of this weed between its native range and its areas of introduction. A screening of a Vietnamese half-sib progeny showed that sexuality occurs in this geographical range of R. alceifolius . Moreover, four of them could be potentially transferable to 14 other tropical Rubus species from the subgenera Idaeobatus and Malachobatus .
TL;DR: 21 novel, polymorphic microsatellite markers for S. vulgaris are developed to enable analysis of population genetic structure in this species, allowing a comparison of population structure of both the introduced and native squirrel species.
Abstract: The geographical range of the red squirrel (Sciurus vulgaris) in Britain has decreased substantially since the introduction of the American grey squirrel (S. carolinensis). We have developed 21 novel, polymorphic microsatellite markers for S. vulgaris to enable analysis of population genetic structure in this species. All 21 markers amplify well, and are generally polymorphic in S. carolinensis, allowing a comparison of population structure of both the introduced and native squirrel species.
TL;DR: A user-friendly Microsoft® Windows program is released that uses a new method to infer effective size and migration rate from one- and two-locus identity probability measures to provide joint estimates of local effective population size and immigration rate for each subpopulation in a population genetics data set.
Abstract: 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.
TL;DR: The characterization of five polymorphic microsatellite loci from the human blood fluke Schistosoma mansoni are described, which can now be applied in assessments of schistosome genetic diversity.
Abstract: Blood flukes in the genus Schistosoma are important human parasites in tropical regions. Genetic heterogeneity of the parasite contributes to the observed phenotypic variation in this host—parasite interaction and may play a role in disease epidemiology. In this paper, we describe the characterization of five polymorphic microsatellite loci from the human blood fluke Schistosoma mansoni , which can now be applied in assessments of schistosome genetic diversity. The five loci revealed extensive polymorphism, as 5—8 alleles per locus were detected among five isolates (from both human patients and snail intermediate hosts) from two Brazilian villages.
TL;DR: Genomic libraries enriched for simple sequence repeats were constructed for Glossina morsitans moritans, G. m.
Abstract: Tsetse flies (Diptera: Glossinidae) are exclusively haematophagous and confined to sub-Saharan Africa. Their medical and veterinary importance is great because they are the only vectors of African trypanosomiasis, ‘sleeping sickness’ in humans and nagana in cattle. In east and southern Africa, Glossina morsitans sensu lato and G. pallidipes are the most important vectors of trypanosomiasis. These species are assigned to the subgenus Glossina, the morsitans group (Leak 1998). Three allopatric subspecies of G. morsitans are recognized, G. m. morsitans (Gmm), G. m. centralis (Gmc), and G. m. submorsitans (Gms).
Some genetic markers have been developed in Glossina. Allozyme polymorphism were detected and mapped in G. morsitans and G. palpalis by Gooding (1992). Krafsur & Griffiths (1997) examined isozyme variation at 31–45 loci in G. pallidipes, G. morsitans sensu lato, and G. swynnertoni. They found 23% of the loci were polymorphic, and heterozygosity was a statistically homogeneous 6.2% averaged over taxa. Isozyme loci in tsetse are inconvenient because it is difficult to obtain liquid nitrogen in Africa. DNA techniques, in contrast, allow use of alcohol preserved or dried material and provides more genetic variation.
Solano et al. (1997) isolated an autosomal and two X-chromosome linked microsatellite loci in G. palpalis gambiense. Luna et al. (2001) recovered 13 polymorphic microsatellite loci from G. palpalis palpalis. G. palpalis primers did not amplify G. morsitans DNA. We therefore developed G. morsitans s.l. genomic libraries enriched for microsatellites and proceeded to identify and characterize them.
DNA was extracted as outlined (Wohlford et al. 1999). G. m. morsitans, G. morsitans, and G. m. centralis DNA was digested with RsaI and electrophoresed on an agarose gel. Fragments between 300 and 1500 bp were excised and purified. Gel purified fragments were ligated to BglII adapter (21-mer: 5′-CTCTTGCTTAGATCTGGACTA-3′; 24-mer: 5′-pTAGTCCAGATCTAAGCAAGAGCACA-3′), using T4 DNA ligase (Promega). Ligated DNA was PCR amplified in 50 μL reactions containing 3 μm 21-mer adapter primer for 35 cycles of 94 °C for 1 min, 55 °C for 1 min, and 72 °C for 2 min.
Amplification products were enriched for simple sequence repeat (SSR) loci by either hybridizing to probes bound to nylon membranes (MBP) after Edwards et al. (1996) or to biotinylated probes bound to magnetic beads (BP) following Kijas et al. (1994). Enriched fragments were amplified to and cloned in pGEM7 plasmids (Promega) and plated. Colonies were picked and their DNA amplified by using polymerase chain reaction (PCR). Amplified products of appropriate size were sequenced and primers designed for those loci containing repeats.
G. m. morsitans DNA was used for the initial evaluations of presumptive loci for polymorphisms. Primers were also tested against DNA from G. m. centralis, G. m. submorsitans, G. pallidipes, G. swynnertoni, G. austeni, G. fuscipes, G. palpalis, G. tachinoides, G. brevipalpis, G. longipennis, and G. fuscipleuris. Genomic DNA was amplified in 10 μL reactions for 35 cycles of 94 °C for 40 s, 50 °C for 40 s, and 72 °C for 30 s. Samples were electrophoresed on 5% acrylamide gels and genotypes scored after silver staining.
The MBP method afforded 14 positive clones that were sequenced. Seven of the 14 possessed SSRs. Six were polymorphic (Table 1). No AT repeats were found.
Table 1
Characteristics of microsatellite loci in Glossina morsitans morsitans
Sixty-eight clones constructed by the BP method were sequenced. Primers were made for 16 of the cloned loci, 10 pairs of which produced appropriately sized amplification products, only four of which were polymorphic. Heterozygotes were found only in females at Gmm127, Gmm14, and GmcCA16C.
Allele numbers varied from three to 19. The mean was 7.5 alleles. Heterozygosities varied from eight to 92%. The mean diversity was 55.8 ± 7.7%. The frequency of polymorphic loci was greater among dinucleotide (eight of 12) than trinucleotide (four of 12) loci (Fisher’s exact test P = 0.11). Dinucleotide repeats were more diverse (60.7%) than trinucleotide repeats (13.8%).
All primers derived from G. morsitans s.l. amplified template DNA from other members of the species complex (Table 2). Five G. m. morsitans loci amplified DNA in G. swynnertoni and G. austeni and the Palpalis group. Only GmcCAG6 amplified DNA in Fusca group flies. The dinucleotide repeats in G. morsitans were more polymorphic than the trinucleotide repeats and variances were greater. Diversities at five dinucleotide (HE = 0.80) and five trinucleotide loci (HE = 0.81) in Drosophila did not differ but variances were much greater among the dinucleotide loci (Goldstein & Clark 1995).
Table 2
Application of G. morsitans morsitans s.l. microsatellite primers against other Glossina species
Both the MBP and the BP methods were successful in isolating microsatellites. The BP library was 100% enriched for SSRs, whereas the MBP library was about 50% enriched. Moreover, the MBP method took 2–3 times longer to complete.
Our microsatellites are used to analyse the breeding structure of G. morsitans s.l. populations. We have successfully automated scoring genotypes on an ABI 377 Prism™ automated DNA sequencer by using genescan™ software and fluorescent labelled primers.
TL;DR: These primers will be valuable for genetic analyses of the brood parasitic indigobirds and whydahs (genus Vidua) as well as other Old World finches.
Abstract: We characterized 11 microsatellite primer pairs for the village indigobird Vidua chalybeata. The loci were highly polymorphic, with 7–13 alleles per locus. Gene diversity, estimated as expected heterozygosity, ranged from 0.52 to 0.86, and was generally matched by levels of observed heterozygosity (0.49–0.91). Many of these primer pairs amplified polymorphic loci in cross-species amplification trials with a variety of estrildid and ploceid finches and a sparrow, Passer griseus. These primers will be valuable for genetic analyses of the brood parasitic indigobirds and whydahs (genus Vidua) as well as other Old World finches.
TL;DR: Nine tetranucleotide microsatellite loci developed for Atlantic herring exhibited high levels of observed heterozygosity and were suitable for population studies and the analysis of mating systems.
Abstract: Nine tetranucleotide microsatellite loci developed for Atlantic herring are presented. Loci were isolated using a magnetic bead hybridization selection protocol that yielded an 80% enrichment for tetranucleotide microsatellites. Fifty Atlantic herring from each of a North-west and North-east Atlantic spawning group were screened at each locus. Loci were polymorphic (12–56 alleles per locus) and exhibited high levels of observed heterozygosity (0.66–0.98). These loci are therefore suitable for population studies and the analysis of mating systems.